10-Q

UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington D.C. 20549

FORM 10-Q

(Mark One)

x QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934

For the quarterly period ended June 30, 2014

OR

o TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934

For the Transition Period from              to             

Commission File Number: 001-34885

AMYRIS, INC.

(Exact name of registrant as specified in its charter)

Delaware	55-0856151
(State or other jurisdiction of incorporation or organization)	(I.R.S. Employer Identification No.)

Amyris, Inc.

5885 Hollis Street, Suite 100

Emeryville, CA 94608

(510) 450-0761

(Address and telephone number of principal executive offices)

Indicate by check mark whether the registrant (1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during the preceding 12 months (or for such shorter period that the registrant was required to file such reports), and (2) has been subject to such filing requirements for the past 90 days.    Yes  x    No  o

Indicate by check mark whether the registrant has submitted electronically and posted on its corporate Web site, if any, every Interactive Data File required to be submitted and posted pursuance to Rule 405 of Regulation S-T (§232.405 of this chapter) during the preceding 12 months (or for such shorter period that the registrant was required to submit and post such files).    Yes  x    No  o

Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, or a non-accelerated filer.

Large accelerated filer	o	Accelerated filer	x
Non-accelerated filer	o	Smaller reporting company	o

Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b-2 of the Exchange Act).    Yes  o    No  x

Indicate the number of shares outstanding of each of the issuer’s classes of common stock, as of the latest practicable date.

Class	Outstanding at July 31, 2014
Common Stock, $0.0001 par value per share	78,942,580

AMYRIS, INC.

QUARTERLY REPORT ON FORM 10-Q

For the Quarterly Period Ended June 30, 2014

INDEX

		Page
	PART I - FINANCIAL INFORMATION
Item 1.	Financial Statements (unaudited)	3
Item 2.	Management’s Discussion and Analysis of Financial Condition and Results of Operations	42
Item 3.	Quantitative and Qualitative Disclosures About Market Risk	56
Item 4.	Controls and Procedures	58
	PART II - OTHER INFORMATION
Item 1.	Legal Proceedings	58
Item 1A.	Risk Factors	59
Item 2.	Unregistered Sales of Equity Securities and Use of Proceeds	84
Item 3.	Defaults Upon Senior Securities	84
Item 4.	Mine Safety Disclosures	84
Item 5.	Other Information	84
Item 6.	Exhibits
	Signatures
	Exhibit Index

PART I

ITEM 1. FINANCIAL STATEMENTS

Amyris, Inc.

Condensed Consolidated Balance Sheets

(In Thousands, Except Share and Unaudited Per Share Amounts)

	June 30, 2014			December 31, 2013
Assets
Current assets:
Cash and cash equivalents	$	88,828		$	6,868
Short-term investments	1,379			1,428
Accounts receivable, net of allowance of $479 and $479, respectively	4,675			7,734
Related party accounts receivable	51			484
Inventories, net	14,753			10,888
Prepaid expenses and other current assets	7,138			9,518
Total current assets	116,824			36,920
Property, plant and equipment, net	140,656			140,591
Restricted cash	1,721			1,648
Other assets	15,826			10,585
Goodwill and intangible assets	9,120			9,120
Total assets	$	284,147		$	198,864
Liabilities and Deficit
Current liabilities:
Accounts payable	$	8,503		$	6,512
Deferred revenue	10,372			2,222
Accrued and other current liabilities	12,761			21,221
Capital lease obligation, current portion	882			956
Debt, current portion	9,923			6,391
Total current liabilities	42,441			37,302
Capital lease obligation, net of current portion	228			287
Long-term debt, net of current portion	111,952			56,172
Related party debt	100,480			89,499
Deferred rent, net of current portion	10,223			10,191
Deferred revenue, net of current portion	4,100			5,000
Derivative liability	147,840			134,717
Other liabilities	6,560			1,544
Total liabilities	423,824			334,712
Commitments and contingencies (Note 6)
Stockholders’ deficit:
Preferred stock - $0.0001 par value, 5,000,000 shares authorized, none issued and outstanding	—			—
Common stock - $0.0001 par value, 300,000,000 and 200,000,000 shares authorized as of June 30, 2014 and December 31, 2013; 78,914,451 and 76,662,812 shares issued and outstanding as of June 30, 2014 and December 31, 2013, respectively	8			8
Additional paid-in capital	717,167			706,253
Accumulated other comprehensive loss	(15,634		)	(20,087		)
Accumulated deficit	(840,532		)	(821,438		)
Total Amyris, Inc. stockholders’ deficit	(138,991		)	(135,264		)
Noncontrolling interest	(686		)	(584		)
Total stockholders' deficit	(139,677		)	(135,848		)
Total liabilities and stockholders' deficit	$	284,147		$	198,864

See the accompanying notes to the unaudited condensedconsolidated financial statements.

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Amyris, Inc.

Condensed Consolidated Statements of Operations

(In Thousands, Except Share and Per Share Amounts)

(Unaudited)

	Three Months Ended June 30,						Six Months Ended June 30,
	2014			2013			2014			2013
Revenues
Renewable product sales	$	4,379		$	4,011		$	7,221		$	6,991
Related party renewable product sales	31			174			34			177
Total product sales	4,410			4,185			7,255			7,168
Grants and collaborations revenue	4,897			6,555			8,093			8,903
Related party grants and collaborations revenue	—			109			—			2,647
Total grants and collaborations revenue	4,897			6,664			8,093			11,550
Total revenues	9,307			10,849			15,348			18,718
Cost and operating expenses
Cost of products sold	7,511			8,853			13,747			17,813
Loss on purchase commitments and write-off of production assets	52			8,423			159			8,423
Research and development	12,175			13,992			25,161			29,746
Sales, general and administrative	13,971			14,718			27,370			29,545
Total cost and operating expenses	33,709			45,986			66,437			85,527
Loss from operations	(24,402		)	(35,137		)	(51,089		)	(66,809		)
Other income (expense):
Interest income	148			57			204			93
Interest expense	(6,802		)	(1,558		)	(11,552		)	(3,120		)
Gain (loss) from change in fair value of derivative instruments	(3,252		)	(254		)	54,148			785
Loss from extinguishment of debt	(1,082		)	—			(10,512		)	—
Other income (expense), net	5			(1,776		)	(117		)	(1,696		)
Total other income (expense)	(10,983		)	(3,531		)	32,171			(3,938		)
Loss before income taxes	(35,385		)	(38,668		)	(18,918		)	(70,747		)
Provision for income taxes	(125		)	(246		)	(236		)	(482		)
Net loss	(35,510		)	(38,914		)	(19,154		)	(71,229		)
Net income (loss) attributable to noncontrolling interest	31			38			60			(261		)
Net loss attributable to Amyris, Inc. common stockholders	$	(35,479	)	$	(38,876	)	$	(19,094	)	$	(71,490	)
Net income (loss) per share attributable to common stockholders:
Basic	$	(0.45	)	$	(0.51	)	$	(0.25	)	$	(0.96	)
Diluted	$	(0.45	)	$	(0.51	)	$	(0.66	)	$	(0.96	)
Weighted-average shares of common stock outstanding used in computing net loss per share of common stock:
Basic	78,604,692			75,959,228			77,722,437			74,640,314
Diluted	78,604,692			75,959,228			110,632,078			74,640,314

See the accompanying notes to the unaudited condensedconsolidated financial statements.

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Amyris, Inc.

Condensed Consolidated Statements of Comprehensive Income (Loss)

(In Thousands)

(Unaudited)

	Three Months Ended June 30,						Six Months Ended June 30,
	2014			2013			2014			2013
Comprehensive income (loss):
Net loss	$	(35,510	)	$	(38,914	)	$	(19,154	)	$	(71,229	)
Foreign currency translation adjustment, net of tax	1,578			(4,742		)	4,411			(4,031		)
Total comprehensive loss	(33,932		)	(43,656		)	(14,743		)	(75,260		)
Income (loss) attributable to noncontrolling interest	31			38			60			(261		)
Foreign currency translation adjustment attributable to noncontrolling interest	19			(62		)	42			(54		)
Comprehensive loss attributable to Amyris, Inc.	$	(33,882	)	$	(43,680	)	$	(14,641	)	$	(75,575	)

See the accompanying notes to the unaudited condensed consolidated financial statements.

5

Amyris, Inc.

Condensed Consolidated Statements of Stockholders' Deficit

(In Thousands, Except Share Amounts)

(Unaudited)

	Common Stock
	Shares	Amount		Additional Paid-in Capital			Accumulated Deficit			Accumulated Other Comprehensive Income (Loss)			Noncontrolling Interest			Total Deficit
December 31, 2013	76,662,812	$	8	$	706,253		$	(821,438	)	$	(20,087	)	$	(584	)	$	(135,848	)
Issuance of common stock upon exercise of stock options	551,707	—		1,507			—			—			—			1,507
Shares issued under restricted stock unit settlement	756,536	—		(1,790		)	—			—			—			(1,790		)
Issuance of common stock in a private placement	943,396	—		4,000			—			—			—			4,000
Stock-based compensation	—	—		7,197			—			—			—			7,197
Foreign currency translation adjustment, net of tax	—	—		—			—			4,453			(42		)	4,411
Net loss	—	—		—			(19,094		)	—			(60		)	(19,154		)
June 30, 2014	78,914,451	$	8	$	717,167		$	(840,532	)	$	(15,634	)	$	(686	)	$	(139,677	)

See the accompanying notes to the unaudited condensed consolidated financial statements.

6

Amyris, Inc.

Condensed Consolidated Statements of Cash Flows

(In Thousands)

(Unaudited)

	Six Months Ended June 30,
	2014			2013
Operating activities
Net loss	$	(19,154	)	$	(71,229	)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation and amortization	7,539			8,491
Loss (gain) on disposal of property, plant and equipment	57			(38		)
Stock-based compensation	7,197			9,178
Amortization of debt discount	3,763			1,061
Loss on extinguishment of debt	10,512			—
Loss on purchase commitments and write-off of production assets	159			8,423
Change in fair value of derivative instruments	(54,148		)	(719		)
Other non-cash expenses	(113		)	213
Changes in assets and liabilities:
Accounts receivable	3,423			(3,812		)
Related party accounts receivable	147			345
Inventories, net	(3,570		)	1,150
Prepaid expenses and other assets	(323		)	1,098
Accounts payable	1,879			(1,912		)
Accrued and other liabilities	(608		)	(5,619		)
Deferred revenue	7,380			8,549
Deferred rent	33			(447		)
Net cash used in operating activities	(35,827		)	(45,268		)
Investing activities
Purchase of investments	(883		)	(1,763		)
Maturities of investments	1,032			334
Change in restricted cash	—			(1		)
Investment in joint venture	(2,075		)	—
Purchases of property and equipment, net of disposals	(2,064		)	(3,711		)
Net cash used in investing activities	(3,990		)	(5,141		)
Financing activities
Proceeds from issuance of common stock, net of repurchases	71			167
Proceeds from issuance of common stock in private placements, net of issuance costs	4,000			19,980
Principal payments on capital leases	(515		)	(867		)
Proceeds from debt issued, net of issuance costs	83,171			2,645
Proceeds from debt issued to related party	39,012			10,000
Principal payments on debt	(3,596		)	(1,902		)
Net cash provided by financing activities	122,143			30,023
Effect of exchange rate changes on cash and cash equivalents	(366		)	1,297
Net increase (decrease) in cash and cash equivalents	81,960			(19,089		)
Cash and cash equivalents at beginning of period	6,868			30,592
Cash and cash equivalents at end of period	$	88,828		$	11,503

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Amyris, Inc.

Condensed Consolidated Statements of Cash Flows—(Continued)

(In Thousands)

	Six Months Ended June 30,
	2014			2013
Supplemental disclosures of cash flow information:
Cash paid for interest	$	1,847		$	1,004
Cash paid for income taxes, net of refunds	$	—		$	—
Supplemental disclosures of non-cash investing and financing activities:
Acquisitions of property, plant and equipment under accounts payable, accrued liabilities and notes payable	$	(226	)	$	307
Financing of insurance premium under notes payable	$	(318	)	$	147
Receivable of proceeds for options exercised	$	(355	)	$	—
Accrued offering cost of common stock in private placement	$	—		$	(19	)
Capitalized interest	$	2,812		$	—
Non-cash investment in joint venture	$	(237	)	$	—

See the accompanying notes to the unaudited condensed consolidated financial statements.

8

Amyris, Inc.

Notes to Unaudited Condensed Consolidated Financial Statements

1. The Company

Amyris, Inc. (the “Company”) was incorporated in California on July 17, 2003 and reincorporated in Delaware on June 10, 2010 for the purpose of leveraging breakthroughs in industrial bioscience technology to develop and provide renewable compounds for a variety of markets. The Company is currently applying its industrial bioscience technology platform to provide alternatives to select petroleum-sourced products used in consumer care, specialty chemical and transportation fuel markets worldwide. The Company's first commercialization efforts have been focused on a renewable hydrocarbon molecule called farnesene (Biofene®), which forms the basis for a wide range of products including emollients, fragrance oils and diesel fuel. While the Company's platform is able to use a wide variety of feedstocks, the Company is initially focused on Brazilian sugarcane. In addition, the Company has entered into various contract manufacturing agreements to support commercial production. The Company has established two principal operating subsidiaries, Amyris Brasil Ltda. (formerly Amyris Brasil S.A., or "Amyris Brasil") for production in Brazil, and Amyris Fuels, LLC (or "Amyris Fuels").

The Company's renewable products business strategy is to focus on direct commercialization of specialty products while moving established commodity products into joint venture arrangements with leading industry partners. To commercialize its products, the Company must be successful in using its technology to manufacture its products at commercial scale and on an economically viable basis (i.e., low per unit production costs). The Company is building its experience producing renewable products at commercial scale. The Company's prospects are subject to risks, expenses and uncertainties frequently encountered by companies in this stage of development.

The Company expects to fund its operations for the foreseeable future with cash and cash equivalents and investments currently on hand, with cash inflows from collaboration and grant funding, cash contributions from product sales, and with new debt and equity financings. The Company's planned 2014 and 2015 working capital needs and its planned operating and capital expenditures are dependent on significant inflows of cash from new and existing collaboration partners and from cash contributions from growth in renewable product sales, as well as additional funding from new joint ventures or other collaborations, and may also require additional funding from debt or equity financings. The Company will continue to need to fund its research and development and related activities and to provide working capital to fund production, storage, distribution and other aspects of its business. The Company's operating plan contemplates capital expenditures of approximately $9.0 million in 2014 and the Company expects to continue to incur costs in connection with its existing contract manufacturing arrangements.

Liquidity

The Company has incurred significant losses since its inception and believes that it will continue to incur losses and negative cash flow from operations through 2014. As of June 30, 2014, the Company had an accumulated deficit of $840.5 million and had cash, cash equivalents and short term investments of $90.2 million. The Company has significant outstanding debt and contractual obligations related to purchase commitments, as well as capital and operating leases. As of June 30, 2014, the Company's debt, net of discount of $83.9 million, totaled $222.4 million, of which $9.9 million matures within the next twelve months. In addition, the Company's debt agreements contain various covenants, including restrictions on the Company's business that could cause the Company to be at risk of defaults. Please refer to Note 5, “Debt” and Note 6, “Commitments and Contingencies” for further details regarding the Company's debt obligations and commitments.

The Company’s operating plan for 2014 contemplates significant reduction in the Company’s net cash outflows, resulting from (i) revenue growth from sales of existing and new products, (ii) reduced production costs compared to prior periods as a result of manufacturing and technical developments in 2013, (iii) cash inflows from collaborations consistent with levels achieved in 2013 and (iv) operating expenses maintained at reduced levels. Achieving a reduction in net cash outflows from these factors is subject to risks and uncertainties, including those set forth in Part II, Item 1A of this Quarterly Report on Form 10-Q, “Risk Factors.”

In addition to cash contributions from product sales and debt and equity financings, the Company also depends on collaboration funding to support its operating expenses. While part of this funding is committed based on existing collaboration agreements, the Company will need to identify and obtain funding under additional collaborations that are not yet subject to any definitive agreement or are not yet identified. In addition, some of the Company’s existing collaboration funding is subject to achievement by the Company of milestones or other funding conditions.

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If the Company is unable to increase positive gross margin product sales or generate sufficient additional payments from existing and new collaboration partners, it may need to obtain additional funding from equity financings, credit facilities, loans or issue additional preferred and/or discounted equity, agree to burdensome covenants, grant further security interest in its assets, enter into collaboration and licensing arrangements that require it to relinquish commercial rights, or grant licenses on terms that are not favorable. If the Company fails to generate positive gross margins product sales or secure such funding, the Company could be forced to curtail its operations, which would have a material adverse effect on the Company's ability to continue with its business plans.

2. Summary of Significant Accounting Policies

Basis of Presentation

The accompanying interim condensed consolidated financial statements have been prepared in accordance with the accounting principles generally accepted in the United States of America (“GAAP”) and with the instructions for Form 10-Q and Regulation S-X. Accordingly, they do not include all of the information and notes required for complete financial statements. These interim condensed consolidated financial statements should be read in conjunction with the consolidated financial statements and notes thereto contained in the Company’s Form 10-K filed with the Securities and Exchange Commission (“SEC”) on April 2, 2014. The unaudited condensed consolidated financial statements include the accounts of the Company and its consolidated subsidiaries. All intercompany accounts and transactions have been eliminated in consolidation.

Principles of Consolidation

The Company has interests in joint venture entities that are variable interest entities (“VIEs”). Determining whether to consolidate a variable interest entity requires judgment in assessing (i) whether an entity is a VIE and (ii) if the Company is the entity’s primary beneficiary and thus required to consolidate the entity. To determine if the Company is the primary beneficiary of a VIE, the Company evaluates whether it has (i) the power to direct the activities that most significantly impact the VIE’s economic performance and (ii) the obligation to absorb losses or the right to receive benefits of the VIE that could potentially be significant to the VIE. The Company’s evaluation includes identification of significant activities and an assessment of its ability to direct those activities based on governance provisions and arrangements to provide or receive product and process technology, product supply, operations services, equity funding and financing and other applicable agreements and circumstances. The Company’s assessment of whether it is the primary beneficiary of its VIEs requires significant assumptions and judgment.

The condensed consolidated financial statements of the Company include the accounts of Amyris, Inc., its subsidiaries and two consolidated VIEs with respect to which the Company is considered the primary beneficiary, after elimination of intercompany accounts and transactions. Disclosure regarding the Company’s participation in the VIEs is included in Note 7, "Joint Ventures and Noncontrolling Interest."

Use of Estimates

In preparing the unaudited condensed consolidated financial statements, management must make estimates and assumptions that affect the reported amounts of assets and liabilities and disclosure of contingent assets and liabilities as of the date of the unaudited condensed consolidated financial statements and the reported amounts of revenue and expenses during the reporting period. Actual results could differ from those estimates.

Unaudited Interim Financial Information

The accompanying interim condensed consolidated financial statements and related disclosures are unaudited, have been prepared on the same basis as the annual consolidated financial statements and, in the opinion of management, reflect all adjustments, which include only normal recurring adjustments, necessary for a fair statement of the results of operations for the periods presented.

The year-end condensed consolidated balance sheet data was derived from audited financial statements, but does not include all disclosures required by GAAP. The condensed consolidated results of operations for any interim period are not necessarily indicative of the results to be expected for the full year or for any other future year or interim period.

Recent Accounting Pronouncements

In July 2013, the Financial Accounting Standards Board ("FASB") issued an amended accounting standard update on the financial statement presentation of unrecognized tax benefits. The amended guidance provides that a liability related to an

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unrecognized tax benefit would be presented as a reduction of a deferred tax asset for a net operating loss carryforward, a similar tax loss or a tax credit carryforward if such settlement is required or expected in the event the uncertain tax position is disallowed. The new guidance became effective for the Company on January 1, 2014 and will be applied prospectively to unrecognized tax benefits that exist at the effective date with retrospective applications permitted. The Company's current presentation of unrecognized tax benefits conforms with the amended guidance. Accordingly, there was no significant impact to the Company resulting from the guidance.

In May 2014, the FASB issued a new guidance related to revenue recognition. This new standard will replace all current GAAP guidance on this topic and eliminate all industry-specific guidance. The new revenue recognition standard provides a unified model to determine how revenue is recognized. The core principle of the guidance is that an entity should recognize revenue to depict the transfer of promised goods or services to customers in an amount that reflects the consideration to which the entity expects to be entitled in exchange for those goods or services. This guidance will be effective for the Company beginning January 1, 2017 and can be applied either retrospectively to each period presented or as a cumulative-effect adjustment as of the date of adoption. The Company is currently assessing the impact of adopting this new accounting standard on its financial statements.

3. Fair Value of Financial Instruments

The inputs to the valuation techniques used to measure fair value are classified into the following categories:

Level 1: Quoted market prices in active markets for identical assets or liabilities.

Level 2: Observable market-based inputs or unobservable inputs that are corroborated by market data.

Level 3: Unobservable inputs that are not corroborated by market data.

As of June 30, 2014, the Company’s financial assets and financial liabilities are presented below at fair value and were classified within the fair value hierarchy as follows (in thousands):

	Level 1		Level 2		Level 3		Balance as of June 30, 2014
Financial Assets
Money market funds	$	74,765	$	—	$	—	$	74,765
Certificates of deposit	1,453		—		—		1,453
Total financial assets	$	76,218	$	—	$	—	$	76,218
Financial Liabilities
Loans payable (1)	$	—	$	20,360	$	—	$	20,360
Credit facilities  (1)	—		39,864		—		39,864
Convertible notes (1)	—		—		227,638		227,638
Compound embedded derivative liability	—		—		145,032		145,032
Currency interest rate swap derivative liability	—		2,808		—		2,808
Total financial liabilities	$	—	$	63,032	$	372,670	$	435,702

________

⁽¹⁾ These liabilities are carried on the condensed consolidated balance sheet on a historical basis.

The Company’s assessment of the significance of a particular input to the fair value measurement in its entirety requires management to make judgments and consider factors specific to the asset or liability. The fair values of money market funds are based on fair values of identical assets. The fair values of the loans payable, convertible notes, credit facilities and currency interest rate swaps are based on the present value of expected future cash flows and assumptions about current interest rates and the creditworthiness of the Company. Market risk associated with the fixed and variable rate long-term debt relates to the potential reduction in fair value and negative impact to future earnings, respectively, from an increase in interest rates.

The carrying amounts of certain financial instruments, such as cash equivalents, short term investments, accounts receivable, accounts payable and accrued liabilities, approximate fair value due to their relatively short maturities and low market interest rates, if applicable. The fair values of the loans payable, convertible notes and credit facilities are based on the present value of expected future cash flows and assumptions about current interest rates and the creditworthiness of the Company.

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The following table provides a reconciliation of the beginning and ending balances for the convertible notes measured at fair value using significant unobservable inputs (Level 3) (in thousands):

	2014
Balance at January 1	$	131,952
Additions to convertible notes	93,295
Change in fair value of convertible notes	2,391
Balance at June 30	$	227,638

The Company’s financial assets and financial liabilities as of December 31, 2013 are presented below at fair value and were classified within the fair value hierarchy as follows (in thousands):

	Level 1		Level 2		Level 3		Balance as of December 31, 2013
Financial Assets
Money market funds	$	398	$	—	$	—	$	398
Certificates of deposit	1,428		—		—		1,428
Total financial assets	$	1,826	$	—	$	—	$	1,826
Financial Liabilities
Loans payable	$	—	$	18,491	$	—	$	18,491
Credit facilities	—		7,571		—		7,571
Convertible notes	—		—		131,952		131,952
Compound embedded derivative liability	—		—		131,117		131,117
Currency interest rate swap derivative liability	—		3,600		—		3,600
Total financial liabilities	$	—	$	29,662	$	263,069	$	292,731

Derivative Instruments

The following table provides a reconciliation of the beginning and ending balances for the compound embedded derivative liability measured at fair value using significant unobservable inputs (Level 3) (in thousands):

	2014
Balance at January 1	$	131,117
Transfers in to Level 3 net of cancellation (1)	86,551
Total (income) loss from change in fair value of derivative liability	(72,636		)
Balance at June 30	$	145,032

________

⁽¹⁾ Includes $1.1 million removal of derivative liability related to debt extinguishment.

The compound embedded derivative liability represents the fair value of the bifurcated conversion options that contain "make-whole" provisions or down round conversion price adjustment provisions of outstanding convertible promissory notes issued to Total Energies Nouvelles Activités USA (formerly known as Total Gas & Power USA, SAS, or “Total”), as well as Tranche I Notes, Tranche II Notes and notes issued under the Rule 144A Convertible Note Offering (see Note 5, "Debt"). There is no current observable market for this type of derivative and, as such, the Company determined the fair value of the embedded derivative using a Monte Carlo simulation valuation model for the Total Notes and the binomial lattice model for the Tranche I Notes, Tranche II Notes and the Rule 144A Convertible Note Offering. A Monte Carlo simulation valuation model combines expected cash outflows with market-based assumptions regarding risk-adjusted yields, stock price volatility, probability of a change of control and the trading information of the Company's common stock into which the notes are convertible. A binomial lattice model generates two probable outcomes - one up and another down - arising at each point in time, starting from the date of valuation until the maturity date. A lattice model was initially used to determine if the convertible notes would be converted,

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called or held at each decision point. Within the lattice model, the following assumptions are made: (i) the convertible notes will be converted early if the conversion value is greater than the holding value or (ii) the convertible notes will be called if the holding value is greater than both (a) redemption price and (b) the conversion value at the time. If the convertible notes are called, then the holder will maximize their value by finding the optimal decision between (1) redeeming at the redemption price and (2) converting the convertible notes. Using this lattice method, the Company valued the embedded derivative using the "with-and-without method", where the fair value of the convertible notes including the embedded derivative is defined as the "with", and the fair value of the convertible notes excluding the embedded derivative is defined as the "without". This method estimates the fair value of the embedded derivative by looking at the difference in the values between the convertible notes with the embedded derivative and the fair value of the convertible notes without the embedded derivative. The lattice model uses the stock price, conversion price, maturity date, risk-free interest rate, estimated stock volatility and estimated credit spread. The Company marks the compound embedded derivative to market due to the conversion price not being indexed to the Company's own stock. Except for the "make-whole interest" provision included in the conversion option, which is only required to be settled in cash upon a change of control at the noteholder's option, the compound embedded derivative will be settled in either cash or shares. As of June 30, 2014, the Company has sufficient common stock available to settle the conversion option in shares. As of June 30, 2014 and December 31, 2013, included in "Derivative Liability" on the condensed consolidated balance sheet is the Company's compound embedded derivative liability of $145.0 million and $131.1 million, respectively, which represents the fair value of the equity conversion option or a "make-whole" provision relating to the outstanding senior secured convertible promissory notes issued to Total, Tranche I Notes, Tranche II Notes and notes issued under the Rule 144A Convertible Note Offering as described above.

In June 2012, the Company entered into a loan agreement with Banco Pine S.A. (or "Banco Pine") under which Banco Pine provided the Company with a short term loan (referred to as the "Banco Pine Bridge Loan") (see Note 5, "Debt"). At the time of the Banco Pine Bridge Loan, the Company also entered into a currency interest rate swap arrangement with Banco Pine with respect to the repayment of R$22.0 million (approximately US$10.0 million based on the exchange rate as of June 30, 2014). The swap arrangement exchanges the principal and interest payments under the Banco Pine Bridge Loan of R$22.0 million entered into in July 2012 for alternative principal and interest payments that are subject to adjustment based on fluctuations in the foreign exchange rate between the U.S. dollar and Brazilian real. The swap has a fixed interest rate of 3.94%. Changes in the fair value of the swap are recognized in “Gain (loss) from change in fair value of derivative instruments" in the condensed consolidated statements of operations.

Derivative instruments measured at fair value as of June 30, 2014 and December 31, 2013, and their classification on the condensed consolidated balance sheets and condensed consolidated statements of operations, are presented in the following tables (in thousands except contract amounts):

	Liability as of
	June 30, 2014			December 31, 2013
Type of Derivative Contract	Quantity of Short Contracts	Fair Value		Quantity of Short Contracts	Fair Value
Currency interest rate swap, included as net liability in derivative liability	1	$	2,808	1	$	3,600

	Income Statement Classification	Three Months Ended June 30,					Six Months Ended June 30,
Type of Derivative Contract		2014		2013			2014	2013
		Gain (Loss) Recognized					Gain (Loss) Recognized
Currency interest rate swap (1)	Gain (loss) from change in fair value of derivative instruments	$	722	$	(1,639	)	$1,056	$	(1,651	)

___________ 

⁽¹⁾  Certain classifications of prior period amounts have been made to conform to the current period presentation. Such reclassifications did not materially change previously reported consolidated financial statements.

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4. Balance Sheet Components

Inventories, net

Inventories are stated at the lower of cost or market and consist of the following (in thousands):

	June 30, 2014		December 31, 2013
Raw materials	$	2,468	$	1,796
Work-in-process	6,536		7,292
Finished goods	5,749		1,800
Inventories, net	$	14,753	$	10,888

Prepaid Expenses and Other Current Assets

Prepaid expenses and other current assets is comprised of the following (in thousands):

	June 30, 2014		December 31, 2013
Maintenance (1)	$	393	$	258
Prepaid insurance(1)	603		894
Manufacturing catalysts	1,715		1,536
Recoverable VAT and other taxes	2,776		5,125
Other (1)	1,651		1,705
Prepaid expenses and other current assets	$	7,138	$	9,518

______________ 

⁽¹⁾  Certain classifications of prior period amounts have been made to conform to the current period presentation. Such reclassifications did not materially change previously reported consolidated financial statements.

Property, Plant and Equipment, net

Property, plant and equipment, net is comprised of the following (in thousands):

	June 30, 2014			December 31, 2013
Leasehold improvements	$	39,208		$	39,034
Machinery and equipment	101,383			96,585
Computers and software	8,946			8,509
Furniture and office equipment	2,584			2,535
Buildings	7,606			7,148
Vehicles	436			488
Construction in progress	44,635			41,387
	204,798			195,686
Less: accumulated depreciation and amortization	(64,142		)	(55,095		)
Property, plant and equipment, net	$	140,656		$	140,591

The Company's first, purpose-built, large-scale Biofene production plant in southeastern Brazil commenced operations in December 2012. This plant is located at Brotas in the state of São Paulo, Brazil and is adjacent to an existing sugar and ethanol mill, Paraíso Bioenergia. The Company's construction in progress consists primarily of the upfront plant design and the initial construction of a second large-scale production plant in Brazil, located at the Sao Martinho S.A. (or "SMSA") (formerly Usina São Martinho S.A.) sugar and ethanol mill (also in the state of São Paulo, Brazil).

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Property, plant and equipment, net includes $3.8 million and $3.4 million of machinery and equipment under capital leases as of June 30, 2014 and December 31, 2013, respectively. Accumulated amortization of assets under capital leases totaled $1.8 million and $1.5 million as of June 30, 2014 and December 31, 2013, respectively.

Depreciation and amortization expense, including amortization of assets under capital leases was $3.7 million and $4.1 million for the three months ended June 30, 2014 and 2013, respectively, and was $7.5 million and $8.5 million for the six months ended June 30, 2014 and 2013, respectively.

The Company capitalizes interest costs incurred to construct plant and equipment. The capitalized interest is recorded as part of the depreciable cost of the asset to which it relates to and is amortized over the asset's estimated useful life. Interest cost capitalized as of June 30, 2014 and December 31, 2013 was $0.5 million and $0.5 million, respectively.

Other Assets

Other assets are comprised of the following (in thousands):

	June 30, 2014		December 31, 2013
Deposits on property and equipment, including taxes	$	2,095	$	1,970
Recoverable taxes from Brazilian government entities	9,064		6,599
Debt issuance cost (2)	978		454
Investments in joint venture (1)	2,170		68
Other (2)	1,519		1,494
Total other assets	$	15,826	$	10,585

______________ 

⁽¹⁾  The investments in joint venture represents the Company's investments in the joint venture with Novvi LLC and Total Amyris Biosolutions B.V. of $2.1 million and $0.1 million as of June 30, 2014, respectively, and zero and $0.1 million as of December 31, 2013, respectively.

⁽²⁾  Certain classifications of prior period amounts have been made to conform to the current period presentation. Such reclassifications did not materially change previously reported consolidated financial statements.

Accrued and Other Current Liabilities

Accrued and other current liabilities are comprised of the following (in thousands):

	June 30, 2014		December 31, 2013
Professional services	$	2,093	$	2,279
Accrued vacation	2,516		2,274
Payroll and related expenses	3,939		5,066
Tax-related liabilities	157		825
Deferred rent, current portion	1,111		1,111
Accrued interest	1,246		3,176
Contractual obligations to contract manufacturers	853		4,241
Other	846		2,249
Total accrued and other current liabilities	$	12,761	$	21,221

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Derivative Liability

Derivative liability is comprised of the following (in thousands):

	June 30, 2014		December 31, 2013
Fair market value of swap obligation	$	2,808	$	3,600
Fair value of compound embedded derivative liability(1)	145,032		131,117
Total derivative liability	$	147,840	$	134,717

______________ 

⁽¹⁾  The compound embedded derivative liability represents the fair value of the bifurcated conversion options that contain "make-whole" provisions or down round conversion price adjustment provisions included in the outstanding Total Notes, Tranche I Notes, Tranche II Notes and the Rule 144A Convertible Note Offering (see Note 3, "Fair value of financial instruments" and Note 5, "Debt").

5. Debt

Debt is comprised of the following (in thousands):

	June 30, 2014			December 31, 2013
Credit facilities	$	37,972		$	8,767
Convertible notes	57,904			28,537
Related party convertible notes	100,480			89,499
Loans payable	25,999			25,259
Total debt	222,355			152,062
Less: current portion	(9,923		)	(6,391		)
Long-term debt	$	212,432		$	145,671

FINEP Credit Facility

In November 2010, the Company entered into a credit facility with Financiadora de Estudos e Projetos (referred to as the “FINEP Credit Facility”). The FINEP Credit Facility was extended to partially fund expenses related to the Company’s research and development project on sugarcane-based biodiesel (“FINEP Project”) and provided for loans of up to an aggregate principal amount of R$6.4 million (approximately US$2.9 million based on the exchange rate as of June 30, 2014), which is secured by a chattel mortgage on certain equipment of the Company as well as by bank letters of guarantee. All available credit under this facility is fully drawn.

Interest on loans drawn under the FINEP Credit Facility is fixed at 5% per annum. In case of default under or non-compliance with the terms of the agreement, the interest on loans will be dependent on the long-term interest rate as published by the Central Bank of Brazil (such rate, the “TJLP”). If the TJLP at the time of default is greater than 6%, then the interest will be 5% plus a TJLP adjustment factor, otherwise the interest will be at 11% per annum. In addition, a fine of up to 10% shall apply to the amount of any obligation in default. Interest on late balances will be 1% interest per month, levied on the overdue amount. Payment of the outstanding loan balance is being made in 81 monthly installments, which commenced in July 2012 and extends through March 2019. Interest on loans drawn and other charges are paid on a monthly basis and commenced in March 2011. As of June 30, 2014 and December 31, 2013, the total outstanding loan balance under this credit facility was R$4.8 million (approximately US$2.2 million based on the exchange rate as of June 30, 2014) and R$5.2 million (approximately US$2.2 million based on exchange rate as of December 31, 2013), respectively.

The FINEP Credit Facility contains the following significant terms and conditions:

• the Company was required to share with FINEP the costs associated with the FINEP Project. At a minimum, the Company was required to contribute from its own funds approximately R$14.5 million (approximately US$6.6 million based on the exchange rate as of June 30, 2014) of which R$11.1 million was contributed prior to the release of the second disbursement. All four disbursements were completed and the Company has fulfilled all of its cost sharing obligations;

• after the release of the first disbursement, prior to any subsequent drawdown from the FINEP Credit Facility, the Company was required to provide bank letters of guarantee of up to R$3.3 million in aggregate (approximately US$1.5 million

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based on the exchange rate as of June 30, 2014). On December 17, 2012 and prior to release of the second disbursement on December 26, 2012, the Company obtained the required bank letter of guarantees from Banco ABC Brasil S.A. (or "ABC"); and

• amounts disbursed under the FINEP Credit Facility were required to be used towards the FINEP Project within 30 months after the contract execution.

BNDES Credit Facility

In December 2011, the Company entered into a credit facility with the Brazilian Development Bank (the bank is referred to as “BNDES” and the credit facility referred to as the “BNDES Credit Facility”) in the amount of R$22.4 million (approximately US$10.2 million based on the exchange rate as of June 30, 2014). This BNDES Credit Facility was extended as project financing for a production site in Brazil. The credit line is divided into an initial tranche of up to approximately R$19.1 million and an additional tranche of approximately R$3.3 million that becomes available upon delivery of additional guarantees. The credit line is available for 12 months from the date of the BNDES Credit Facility, subject to extension by the lender. The credit line was cancelled in 2013.

The principal of the loans under the BNDES Credit Facility is required to be repaid in 60 monthly installments, with the first installment paid in January 2013 and the last due in December 2017. Interest was due initially on a quarterly basis with the first installment due in March 2012. From and after January 2013, interest payments are due on a monthly basis together with principal payments. The loaned amounts carry interest of 7% per annum. Additionally, there is a credit reserve charge of 0.1% on the unused balance from each credit installment from the day immediately after it is made available through its date of use, when it is paid.

The BNDES Credit Facility is collateralized by a first priority security interest in certain of the Company's equipment and other tangible assets totaling R$24.9 million (approximately $11.3 million based on the exchange rate as of June 30, 2014). The Company is a parent guarantor for the payment of the outstanding balance under the BNDES Credit Facility. Additionally, the Company was required to provide a bank guarantee equal to 10% of the total approved amount (R$22.4 million in total debt) available under this Credit Facility. For advances of the second tranche (above R$19.1 million), the Company is required to provide additional bank guarantees equal to 90% of each such advance, plus additional Company guarantees equal to at least 130% of such advance. The BNDES Credit Facility contains customary events of default, including payment failures, failure to satisfy other obligations under this credit facility or related documents, defaults in respect of other indebtedness, bankruptcy, insolvency and inability to pay debts when due, material judgments, and changes in control of Amyris Brasil. If any event of default occurs, the Lender may terminate its commitments and declare immediately due all borrowings under the facility. As of June 30, 2014 and December 31, 2013, the Company had R$13.4 million (approximately US$6.1 million based on the exchange rate as of June 30, 2014) and R$15.3 million (approximately US$6.5 million based on the exchange rate as of December 31, 2013), respectively, in outstanding advances under the BNDES Credit Facility.

Hercules Loan Facility

In March 2014, the Company entered into a Loan and Security Agreement with Hercules Technology Growth Capital, Inc. (referred to as “Hercules”) to make available to Amyris a loan in the aggregate principal amount of up to $25.0 million (referred to as the "Hercules Loan Facility"). The original Hercules Loan Facility accrues interest at a rate per annum equal to the greater of either the prime rate reported in the Wall Street Journal plus 6.25% or 9.50%. The Company may repay the loaned amounts before the maturity date (generally February 1, 2017) if it pays an additional fee of 3% of the outstanding loans (1% if after the initial twelve-month period of the loan). The Company was also required to pay a 1% facility charge at the closing of the transaction, and is required to pay a 10% end of term charge. In connection with the original Hercules Loan Facility, Amyris agreed to certain customary representations and warranties and covenants, as well as certain covenants that were subsequently amended (as described below). The total available credit of $25.0 million under this facility was fully drawn down by the Company.

In June 2014, the Company and Hercules entered into a first amendment (referred to as the “Hercules Amendment”) of the Loan and Security Agreement entered into in March 2014. Pursuant to the Hercules Amendment, the parties agreed to adjust the term loan maturity date from May 31, 2015 to February 1, 2017 and remove (i) a requirement for the Company to pay a forbearance fee of $10.0 million in the event certain covenants were not satisfied, (ii) a covenant that the Company maintain positive cash flow commencing with the fiscal quarter beginning October 1, 2014, (iii) a covenant that, beginning with the fiscal quarter beginning July 1, 2014, the Company and its subsidiaries achieve certain projected cash product revenues and projected cash product gross profits, and (iv) an obligation for the Company to file a registration statement on Form S-3 with the SEC by no later than June 30, 2014 and complete an equity financing of more than $50.0 million by no later than September 30, 2014. The Company further agreed to include a new covenant requiring the Company to maintain unrestricted, unencumbered cash in an amount equal to at least 50% of the principal amount then outstanding under the Hercules Loan Facility and borrow an additional $5.0 million. The additional $5.0 million borrowing was completed in June 2014, and accrues interest at a rate per annum equal to the greater of

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either the prime rate reported in the Wall Street Journal plus 5.25% or 8.5%. The Hercules Loan Facility is secured by liens on the Company's assets, including on certain Company intellectual property. The Hercules Loan Facility includes customary events of default, including failure to pay amounts due, breaches of covenants and warranties, certain cross defaults and judgments, and insolvency. If an event of default occurs, Hercules may require immediate repayment of all amounts due.

As of June 30, 2014, $29.7 million was outstanding under the Hercules Loan Facility, net of discount of $0.3 million, and the Company maintains cash in excess of the approximately $15.0 million current minimum cash covenant described above.

Notes Payable

During the period between May 2008 and October 2008, the Company entered into notes payable agreements with the lessor of its headquarters under which it borrowed a total of $3.3 million for the purchase of tenant improvements, bearing an interest rate of 9.5% per annum and to be repaid over a period of 55 to 120 months. As of June 30, 2014 and December 31, 2013, no principal amount was outstanding under these notes payable. In June 2013, as part of the April 30, 2013 Amendment to the Company's operating lease for its headquarters, the Company recorded the elimination of these notes payable as a lease incentive and recorded approximately $1.4 million to deferred rent liability in the condensed consolidated balance sheet. The deferred rent liability is being amortized to expense over the remaining lease term.

Convertible Notes

Fidelity

In February 2012, the Company completed the sale of senior unsecured convertible promissory notes in an aggregate principal amount of $25.0 million pursuant to a securities purchase agreement, between the Company and certain investment funds affiliated with FMR LLC (referred to as the "Fidelity Securities Purchase Agreement"). The offering consisted of the sale of 3% senior unsecured convertible promissory notes with a March 1, 2017 maturity date and an initial conversion price equal to $7.0682 per share of the Company's common stock, subject to proportional adjustment for adjustments to outstanding common stock and anti-dilution provisions in case of dividends and distributions (referred to as the "Fidelity Notes"). As of June 30, 2014, the Fidelity Notes were convertible into an aggregate of up to 3,536,968 shares of the Company's common stock. Such note holders have a right to require repayment of 101% of the principal amount of the Fidelity Notes in an acquisition of the Company, and the notes provide for payment of unpaid interest on conversion following such an acquisition if the note holders do not require such repayment. The Fidelity Securities Purchase Agreement and Fidelity Notes include covenants regarding payment of interest, maintaining the Company's listing status, limitations on debt, maintenance of corporate existence, and filing of SEC reports. The Fidelity Notes include standard events of default resulting in acceleration of indebtedness, including failure to pay, bankruptcy and insolvency, cross-defaults, material adverse effect clauses and breaches of the covenants in the Fidelity Securities Purchase Agreement and Fidelity Notes, with default interest rates and associated cure periods applicable to the covenant regarding SEC reporting. Furthermore, the Fidelity Notes include restrictions on the amount of debt the Company is permitted to incur. With exceptions for certain existing debt, refinancing of such debt and certain other exclusions and waivers, the Fidelity Notes provide that the Company's total outstanding debt at any time cannot exceed the greater of $200.0 million or 50% of its consolidated total assets and its secured debt cannot exceed the greater of $125.0 million or 30% of its consolidated total assets. In connection with the Company’s closing of a short-term bridge loan for $35.0 million in October 2013, holders of the Fidelity Notes waived compliance with the debt limitations outlined above as to the $35.0 million bridge loan and the August 2013 Financing (defined below). In consideration for such waiver, the Company granted to holders of the Fidelity Notes or their affiliates, the right to purchase up to an aggregate of $7.6 million worth of convertible promissory notes in the first tranche of the August 2013 Financing.

In August 2013, the Company entered into that certain Securities Purchase Agreement, dated as of August 8, 2013 (referred to as the “August 2013 SPA”), for the sale of senior convertible promissory notes (referred to as the “August 2013 Notes”) to Maxwell (Mauritius) Pte Ltd (or “Temasek”) and Total, each of whom are existing stockholders of the Company. The August 2013 SPA contemplated the sale of up to an aggregate of $73.0 million in principal amount of the August 2013 Notes in a private placement (referred to as the “August 2013 Financing”) exempt from registration under the Securities Act of 1933, as amended, (the "Securities Act") in an initial tranche of $42.6 million in aggregate principal amount and a second tranche of $30.4 million in aggregate principal amount.

In October 2013, the Company amended the August 2013 SPA to include certain entities affiliated with FMR LLC (referred to as the “Fidelity Entities”) in the first tranche of the August 2013 Financing. Pursuant to the amended agreement the Company sold senior convertible notes with an aggregate principal amount of $7.6 million to the Fidelity Entities (referred to as the "Tranche I Notes"). The Tranche I Notes are due sixty months from the date of issuance and will be convertible into the Company’s common stock at a conversion price equal to $2.44, which represents a 15% discount to a trailing 60-day weighted-average closing price of the common stock on The NASDAQ Stock Market (or “NASDAQ”) through August 7, 2013, subject to adjustment as described

18

below. The Tranche I Notes are convertible at the option of the holder: (i) at any time after 18 months from the date of the August 2013 SPA, (ii) on a change of control of the Company and (iii) upon the occurrence of an event of default. The conversion price of the Tranche I Notes will be reduced to $2.15 if either (a)(i) a specified Company manufacturing plant had failed to achieve a total production of 1,000,000 liters within a run period of 45 days prior to June 30, 2014, or (ii) the Company fails to achieve gross margins from product sales of at least 5% prior to June 30, 2014, or (b) the Company reduces the conversion price of certain existing promissory notes held by Total prior to the repayment or conversion of the Tranche I Notes. In 2013, the Company achieved a total production of 1.0 million liters within a run period of 45 days in satisfaction of clause (a)(i) of the preceding sentence and the Company is currently evaluating the achievement of clause (a)(ii) of the preceding sentence. If either of the production and margin milestones in clause (a) above were to not occur, and the Company also reduces the conversion price of certain existing promissory notes held by Total prior to the repayment or conversion of the Tranche I Notes as set forth in clause (b) above, the conversion price of the Tranche I Notes would be reduced to $1.87. Each Tranche I Note accrues interest from the date of issuance until the earlier of the date that such Tranche I Note is converted into the Company’s common stock or is repaid in full. Interest accrues at a rate of 5% per six months, compounded semiannually (with graduated interest rates of 6.5% applicable to the first 180 days and 8% applicable thereafter as the sole remedy should the Company fail to maintain NASDAQ listing status or at 6.5% for all other defaults). Interest for the first 30 months is payable in kind and added to the principal every six-months and thereafter, the Company may continue to pay interest in kind by adding to the principal every six-months or may elect to pay interest in cash. The Tranche I Notes may be prepaid by the Company after 30 months from the issuance date and initial interest payment date; thereafter the Company has the option to prepay the Tranche I Notes every six months at the date of payment of the semi-annual coupon.

As of June 30, 2014 and December 31, 2013, principal amount of $29.3 million and $28.5 million, respectively, were outstanding under these convertible notes, net of debt discount of $3.7 million and $4.0 million, respectively. The debt discount is the result of the bifurcation of the conversion options that contain "make-whole" provisions or down round conversion price adjustment provisions associated with the outstanding debt.

Rule 144A Convertible Note Offering

In May 2014, the Company entered into a Purchase Agreement with Morgan Stanley & Co. LLC, as the initial purchaser (the “Initial Purchaser”), relating to the sale of $75.0 million aggregate principal amount of its 6.50% Convertible Senior Notes due 2019 (the "144A Notes") to the Initial Purchaser in a private placement, and for initial resale by the Initial Purchaser to certain qualified institutional buyers. In addition, the Company granted the Initial Purchaser an option to purchase up to an additional $15.0 million aggregate principal amount of notes, which option expired according to its terms. Under the terms of the Purchase Agreement, the Company agreed to customary indemnification of the Initial Purchaser against certain liabilities. The Notes were issued pursuant to an Indenture, dated as of May 29, 2014 (the “Indenture”), between the Company and Wells Fargo Bank, National Association, as trustee. The net proceeds from the offering of the Notes were approximately $72.0 million after payment of the Initial Purchaser’s discounts and offering expenses. In addition, in connection with obtaining a waiver from one of its existing investors, Total Energies Nouvelles Activités USA (“Total”), of its preexisting contractual right to exchange certain senior secured convertible notes previously issued by the Company for new notes issued in the offering, the Company has used approximately $9.7 million of the net proceeds to repay previously issued notes (representing the amount of 144A Notes purchased by Total from the Initial Purchaser). Certain of the Company's affiliated entities purchased $24.7 million in aggregate principal amount of Rule 144A Notes from the Initial Purchaser (described further below under "Related Party Convertible Notes"). The 144A Notes will bear interest at a rate of 6.50% per year, payable semiannually in arrears on May 15 and November 15 of each year, beginning November 15, 2014. The 144A Notes will mature on May 15, 2019 unless earlier converted or repurchased. The 144A Notes are convertible into shares of the Company's common stock at any time prior to the close of business day on May 15, 2019.The Notes will have an initial conversion rate of 267.0370 shares of Common Stock per $1,000 principal amount of 144A Notes (subject to adjustment in certain circumstances). This represents an initial effective conversion price of approximately $3.74 per share of common stock. For any conversion on or after May 15, 2015, in the event that the last reported sale price of the Company’s common stock for 20 or more trading days (whether or not consecutive) in a period of 30 consecutive trading days ending within five trading days immediately prior to the date the Company receives a notice of conversion exceeds the conversion price of $3.74 per share on each such trading day, the holders, in addition to the shares deliverable upon conversion, will be entitled to receive a cash payment equal to the present value of the remaining scheduled payments of interest that would have been made on the 144A Notes being converted from the conversion date to the earlier of the date that is three years after the date the Company receive such notice of conversion and maturity (May 15, 2019). In the event of a fundamental change, as defined in the Indenture, holders of the 144A Notes may require the Company to purchase all or a portion of the 144A Notes at a price equal to 100% of the principal amount of the 144A Notes, plus any accrued and unpaid interest to, but excluding, the fundamental change repurchase date. Holders of the 144A Notes who convert their 144A Notes in connection with a make-whole fundamental change will receive additional shares representing the present value of the remaining interest payments which will be computed using a discount rate of 0.75%. If a holder of 144A Notes elects to convert their 144A Notes prior to the effective date of any make-whole fundamental change, such holder will not be entitled to an increased conversion rate in connection with such conversion.

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Related Party Convertible Notes

Total R&D Convertible Notes

In July 2012, the Company entered into an agreement with Total that expanded Total's investment in the Biofene collaboration with the Company, provided new structure for a joint venture (referred to as the "Fuels JV") to commercialize the products encompassed by the diesel and jet fuel research and development program (or, the "Program"), and established a convertible debt structure for the collaboration funding from Total (referred to as the "July 2012 Agreements").

The purchase agreement for the notes related to the funding from Total (referred to as the "Total Purchase Agreement") provides for the sale of an aggregate of $105.0 million in notes as follows:

• As part of an initial closing under the purchase agreement (which initial closing was completed in two installments), (i) on July 30, 2012, the Company sold a 1.5% Senior Unsecured Convertible Note due March 2017 to Total in the face amount of $38.3 million, including $15.0 million in new funds and $23.3 million in previously-provided diesel research and development funding by Total, and (ii) on September 14, 2012, the Company sold another note (in the same form) for $15.0 million in new funds from Total.

• At a second closing under the Total Purchase Agreement (also completed in two installments) the Company sold additional notes for an aggregate of $30.0 million in new funds from Total ($10.0 million in June 2013 and $20.0 million in July 2013).

• The Total Purchase Agreement provides that additional notes may be sold in subsequent closings in July 2014 (for cash proceeds to the Company of $21.7 million, which would be settled in an initial installment of $10.85 million payable at such closing and a second installment of $10.85 million payable in January 2015).

The notes issued to Total pursuant to the Total Purchase Agreement have a maturity date of March 1, 2017, an initial conversion price equal to $7.0682 per share for the notes issued under the initial closing, an initial conversion price equal $3.08 per share for the notes issued under the second closing and an initial conversion price equal to $4.11 per share for the notes issued (and that remain to be issued) under the third closing. The notes bear interest of 1.5% per annum (with a default rate of 2.5%), accruing from the date of funding and payable at maturity or on conversion or a change of control where Total exercises the right to require the Company to repay the notes. Accrued interest is cancelled if the notes are cancelled based on a “Go” decision (see Note 8, "Significant Agreements"). The agreements contemplate that the research and development efforts under the Program may extend through 2016, with a series of “Go/No Go” decisions by Total through such date tied to funding by Total. The notes issuable under the third closing will be senior secured promissory notes, pursuant to the exchange agreed to by Total and the Company in December 2013.

The notes become convertible into the Company's common stock (i) within 10 trading days prior to maturity (if they are not cancelled as described above prior to their maturity date), (ii) on a change of control of the Company, (iii) if Total is no longer the largest stockholder of the Company following a “No-Go” decision (subject to a six-month lock-up with respect to any shares of common stock issued upon conversion), and (iv) on a default by the Company. If Total makes a final “Go” decision, then the notes will be exchanged by Total for equity interests in the Fuels JV, after which the notes will not be convertible and any obligation to pay principal or interest on the notes will be extinguished. In case of a “Go” decision only with respect to jet fuel, the parties would form an operational joint venture only for jet fuel (and the rights associated with diesel would terminate), 70% of the outstanding notes would remain outstanding and become payable by the Company, and 30% of the outstanding notes would be cancelled. If Total makes a “No-Go” decision, outstanding notes will remain outstanding and become payable at maturity.

In connection with a December 2012 private placement of the Company’s common stock involving certain existing stockholders of the Company, Total elected to participate in the private placement by exchanging approximately $5.0 million of its $53.3 million in senior unsecured convertible promissory notes into 1,677,852 shares of the Company's common stock at a price of $2.98 per share. As such, $5.0 million of Total's outstanding $53.3 million in senior unsecured convertible promissory notes was cancelled. The cancellation of the debt was treated as an extinguishment of debt in accordance with the guidance outlined in ASC 470-50. As a result of the exchange and cancellation of the $5.0 million debt the Company recorded a loss from extinguishment of debt of $0.9 million.

In March 2013, the Company entered into a letter agreement with Total (referred to as the "March 2013 Letter Agreement") under which Total agreed to waive its right to cease its participation in the parties' fuels collaboration at the July 2013 decision point and committed to proceed with the July 2013 funding tranche of $30.0 million (subject to the Company's satisfaction of the

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relevant closing conditions for such funding in the Total Purchase Agreement). As consideration for this waiver and commitment, the Company agreed to:

• reduce the conversion price for the senior unsecured convertible promissory notes to be issued in connection with such funding from $7.0682 per share to a price per share equal to the greater of (i) the consolidated closing bid price of the Company's common stock on the date of the March 2013 Letter Agreement, plus $0.01, and (ii) $3.08 per share, provided that the conversion price would not be reduced by more than the maximum possible amount permitted under the rules of NASDAQ such that the new conversion price would require the Company to obtain stockholder consent; and

• grant Total a senior security interest in the Company's intellectual property, subject to certain exclusions and subject to release by Total when the Company and Total enter into final documentation regarding the establishment of the Fuels JV.

In addition to the waiver by Total described above, Total also agreed that, at the Company's request and contingent upon the Company meeting its obligations described above, it would pay advance installments of the amounts otherwise payable at the July 2013 closing. Specifically, if the Company requested such advance installments, subject to certain closing conditions and delivery of certifications regarding the Company's cash levels, Total was obligated to fund $10.0 million no later than May 15, 2013, and an additional $10.0 million no later than June 15, 2013, with the remainder to be funded on the original July 2013 closing date.

In June 2013, the Company sold and issued a 1.5% Senior Unsecured Convertible Note to Total in the face amount of $10.0 million with a March 1, 2017 maturity date pursuant to the Total Purchase Agreement as discussed above. In accordance with the March 2013 Letter Agreement, this convertible note has an initial conversion price equal to $3.08 per share of the Company's common stock. The Company did not request the May advance of $10.0 million, but did request the June advance (as described above), under which this convertible note was issued.

In July 2013, the Company sold and issued a 1.5% Senior Unsecured Convertible Note to Total in the face amount of $20.0 million with a March 1, 2017 maturity date pursuant to the Total Purchase Agreement as discussed above. This purchase and sale completed Total's commitment to purchase $30.0 million of such notes by July 2013. In accordance with the March 2013 Letter Agreement, this convertible note has an initial conversion price equal to $3.08 per share of the Company's common stock.

The conversion prices of the notes issued under the Total Purchase Agreement are subject to adjustment for proportional adjustments to outstanding common stock and under anti-dilution provisions in case of certain dividends and distributions. Total has a right to require repayment of 101% of the principal amount of the notes in the event of a change of control of the Company and the notes provide for payment of unpaid interest on conversion following such a change of control if Total does not require such repayment. The Total Purchase Agreement and notes include covenants regarding payment of interest, maintenance of the Company's listing status, limitations on debt, maintenance of corporate existence, and filing of SEC reports. The notes include standard events of default resulting in acceleration of indebtedness, including failure to pay, bankruptcy and insolvency, cross-defaults, and breaches of the covenants in the purchase agreement and notes, with added default interest rates and associated cure periods applicable to the covenant regarding SEC reporting. Furthermore, the notes include restrictions on the amount of debt the Company is permitted to incur. With exceptions for certain existing debt, refinancing of such debt and certain other exclusions and waivers, the notes provide that the Company's total outstanding debt at any time cannot exceed the greater of $200.0 million or 50% of its consolidated total assets and its secured debt cannot exceed the greater of $125.0 million or 30% of its consolidated total assets. In connection with the Company’s closing of a short-term bridge loan for $35.0 million provided by Temasek in October 2013, Total waived compliance with the debt limitations outlined above as to the $35.0 million bridge loan and the August 2013 Financing.

In April 2014, the Company and Total entered into a letter agreement dated as of March 29, 2014 (referred to as the "March 2014 Letter Agreement") to amend the Amended and Restated Master Framework Agreement entered into as of December 2, 2013 (included as part of JV Documents, as defined below) and the Total Purchase Agreement. Under the March 2014 Letter Agreement, the Company agreed to, (i) amend the conversion price of the convertible notes to be issued in the third closing under the Total Purchase Agreement from $7.0682 to $4.11 subject to stockholder approval at the Company's 2014 annual meeting (which was attained in May 2014), (ii) extend the period during which Total may exchange for other Company securities certain outstanding convertible promissory notes issued under the July 2012 Agreements from June 30, 2014 to the later of December 31, 2014 and the date on which the Company shall have raised $75.0 million of equity and/or convertible debt financing (excluding any convertible promissory notes issued pursuant to the Total Purchase Agreement), (iii) eliminate the Company’s ability to qualify, in a disclosure letter to Total, certain of the representations and warranties that the Company must make at the closing of any third closing sale, and (iv) beginning on March 31, 2014, provide Total with monthly reporting on the Company’s cash, cash equivalents and short-term investments. In consideration of these agreements, Total agreed to waive its right not to consummate the closing of the issuance of the third closing notes if it decides not to proceed with the collaboration and makes a "No-Go" decision with respect thereto.

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JVCO Convertible Notes

In December 2013, in connection with the Company's entry into a Shareholders Agreement and License Agreement and related documents (collectively, referred to as the "JV Documents") with Total and Total Amyris BioSolutions B.V. (or "JVCO") relating to the establishment of JVCO (see Note 7, "Joint Venture and Noncontrolling Interest"), Amyris (i) exchanged the $69.0 million of the outstanding Total unsecured convertible notes issued pursuant to the Total Purchase Agreement and issued replacement 1.5% senior secured convertible notes, in principal amounts equal to the principal amount of each cancelled note (the “Replacement Notes”), (ii) granted to Total a security interest in and lien on all Amyris’s rights, title and interest in and to Amyris’s shares in the capital of JVCO and (iii) agreed that any securities to be purchased and sold at the third closing under the Total Purchase Agreement by Total will be 1.5%, senior secured convertible notes instead of senior unsecured convertible notes. As a consequence of executing the JV Documents and forming JVCO, the security interests in all of the Company’s intellectual property, granted by Amyris in favor of Total, Temasek, and certain Fidelity Entities pursuant the Restated Intellectual Property Security Agreement dated as of October 16, 2013, were automatically terminated effective as of December 2, 2013 upon Total’s and the Company’s joint written notice to Temasek.

As of June 30, 2014 and December 31, 2013, $40.3 million and $51.5 million, respectively, of Replacement Notes were outstanding, net of debt discount of $13.1 million and $17.6 million, respectively.

August 2013 Financing Convertible Notes and 2013 Bridge Loans

In connection with the August 2013 Financing, the Company entered into the August 2013 SPA with Total and Temasek to sell up to $73.0 million in convertible promissory notes in private placements, with such notes to be sold and issued over a period of up to 24 months from the date of signing. The August 2013 SPA provided for the August 2013 Financing to be divided into two tranches (the first tranche for $42.6 million and the second tranche for $30.4 million), each with differing closing conditions. Of the total possible purchase price in the financing, $60.0 million to be paid in the form of cash by Temasek ($35.0 million in the first tranche and up to $25.0 million in the second tranche) and $13.0 million to be paid by the exchange and cancellation of outstanding convertible promissory notes held by Total in connection with its exercise of pro rata rights ($7.6 million in the first tranche and $5.4 million in the second tranche). The August 2013 SPA included requirements that the Company meet certain production milestones before the second tranche would become available, obtain stockholder approval prior to completing any closing of the transaction, and issue a warrant to Temasek to purchase 1,000,000 shares of the Company's common stock at an exercise price of $0.01 per share, exercisable only if Total converts notes previously issued to Total in the second closing under the Total Purchase Agreement. In September 2013, prior to the initial closing of the August 2013 Financing, the Company's stockholders approved the issuance in the private placement of up to $110.0 million aggregate principal amount of senior convertible promissory notes, the issuance of a warrant to purchase 1,000,000 shares of the Company's common stock and the issuance of the common stock issuable upon conversion or exercise of such notes and warrant, which approval included the transactions contemplated by the August 2013 Financing.

In September 2013, the Company entered into a bridge loan agreement with an existing investor to provide additional cash availability of up to $5.0 million. As of June 30, 2014, the Company had not drawn any funds from the agreement and the facility expired in October 2013 in accordance with its terms.

In October 2013, the Company sold and issued a bridge note to Temasek (referred to as the “Temasek Bridge Note”) in exchange for a bridge loan of $35.0 million. The Temasek Bridge Note was due on February 2, 2014 and accrued interest at a rate of 5.5% quarterly from the October 4, 2013 date of issuance. The Temasek Bridge Note was cancelled on October 16, 2013 as payment for Temasek’s purchase of Tranche I Notes in the first tranche of the August 2013 Financing as further described below.

In October 2013, the Company amended the August 2013 SPA to include the Fidelity Entities in the first tranche of the August 2013 Financing with an investment amount of $7.6 million, and to proportionally increase the amount acquired by exchange and cancellation of outstanding convertible promissory notes held by Total in connection with its exercise of pro rata rights to $14.6 million ($9.2 million in the first tranche and up to $5.4 million in the second tranche). Also in October 2013, the Company completed the closing of the first tranche of the August 2013 Financing, issuing a total of $51.8 million in Tranche I Notes for cash proceeds of $7.6 million and cancellation of outstanding convertible promissory notes of $44.2 million, of which $35.0 million resulted from cancellation of the Temasek Bridge Note and the remaining $9.2 million from the exchange and cancellation of an outstanding convertible note held by Total. As a result of the exchange and cancellation of the $35.0 million Temasek Bridge Note and the $9.2 million Total convertible note for the Tranche I Notes, the Company recorded a loss from extinguishment of debt of $19.9 million. The Tranche I Notes are due sixty months from the date of issuance and will be convertible into the Company’s common stock at a conversion price equal to $2.44, which represents a 15% discount to a trailing 60-day weighted-average closing price of the common stock on NASDAQ through August 7, 2013, subject to adjustment as described below. The Tranche I Notes

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are convertible at the option of the holder: (i) at any time after 18 months from the date of the August 2013 SPA, (ii) on a change of control of the Company and (iii) upon the occurrence of an event of default. The conversion price of the Tranche I Notes would be reduced to $2.15 if (a)(i) a specified Company manufacturing plant had failed to achieve a total production of 1.0 million liters within a run period of 45 days prior to June 30, 2014, or (ii) the Company fails to achieve gross margins from product sales of at least 5% prior to June 30, 2014, or (b) the Company reduces the conversion price of certain existing promissory notes held by Total prior to the repayment or conversion of the Tranche I Notes. In 2013, the Company achieved a total production of 1.0 million liters within a run period of 45 days in satisfaction of clause (a)(i) of the preceding sentence and the Company is currently evaluating the achievement of clause (a)(ii) of the preceding sentence. If either of the production and margin milestones in clause (a) above were to occur, and the Company also reduces the conversion price of certain existing promissory notes held by Total prior to the repayment or conversion of the Tranche I Notes as set forth in clause (b) above, the conversion price of the Tranche I Notes will be reduced to $1.87. Each Tranche I Note accrues interest from the date of issuance until the earlier of the date that such Tranche I Note is converted into the Company’s common stock or is repaid in full. Interest accrues at a rate of 5% per six months, compounded semiannually (with graduated interest rates of 6.5% applicable to the first 180 days and 8% applicable thereafter as the sole remedy should the Company fail to maintain NASDAQ listing status or at 6.5% for all other defaults). Interest for the first 30 months is payable in kind and added to the principal every six-months and thereafter, the Company may continue to pay interest in kind by adding to the principal every six-months or may elect to pay interest in cash. The Tranche I Notes may be prepaid by the Company after 30 months from the issuance date and initial interest payment; thereafter the Company has the option to prepay the Tranche I Notes every six months at the date of payment of the semi-annual coupon.

In January 2014, the Company sold and issued, for face value, approximately $34.0 million of convertible promissory notes in the second tranche of the August 2013 Financing (referred to as the “Tranche II Notes”). At the closing, Temasek purchased $25.0 million of the Tranche II Notes and Wolverine Asset Management, LLC (referred to as “Wolverine”) purchased $3.0 million of the Tranche II Notes, each for cash. Total purchased approximately $6.0 million of the Tranche II Notes through cancellation of the same amount of principal of previously outstanding convertible promissory notes held by Total. As a result of the exchange and cancellation of the $6.0 million Total convertible note for the Tranche II Notes, the Company recorded a loss from extinguishment of debt of $9.4 million. The Tranche II Notes will be due sixty months from the date of issuance and will be convertible into shares of common stock at a conversion price equal to $2.87, which represents a trailing 60-day weighted-average closing price of the common stock on NASDAQ through August 7, 2013, subject to adjustment as described below. Specifically, the Tranche II Notes are convertible at the option of the holder (i) at any time 12 months after issuance, (ii) on a change of control of the Company, and (iii) upon the occurrence of an event of default. Each Tranche II Note will accrue interest from the date of issuance until the earlier of the date that such Tranche II Note is converted into common stock or repaid in full. Interest will accrue at a rate per annum equal to 10%, compounded annually (with graduated interest rates of 13% applicable to the first 180 days and 16% applicable thereafter as the sole remedy should the Company fail to maintain NASDAQ listing status or at 12% for all other defaults). Interest for the first 36 months shall be payable in kind and added to principal every year following the issue date and thereafter, the Company may continue to pay interest in kind by adding to principal on every year anniversary of the issue date or may elect to pay interest in cash.

In addition to the conversion price adjustments set forth above, the conversion prices of the Tranche I Notes and Tranche II Notes are subject to further adjustment (i) according to proportional adjustments to outstanding common stock of the Company in case of certain dividends and distributions, (ii) according to anti-dilution provisions, and (iii) with respect to notes held by any purchaser other than Total, in the event that Total exchanges existing convertible notes for new securities of the Company in connection with future financing transactions in excess of its pro rata amount. Notwithstanding the foregoing, holders of a majority of the principal amount of the notes outstanding at the time of conversion may waive any anti-dilution adjustments to the conversion price. The purchasers have a right to require repayment of 101% of the principal amount of the notes in the event of a change of control of the Company and the notes provide for payment of unpaid interest on conversion following such a change of control if the purchasers do not require such repayment. The August 2013 SPA, Tranche I Notes and Tranche II Notes include covenants regarding payment of interest, maintenance of the Company’s listing status, limitations on debt and on certain liens, maintenance of corporate existence, and filing of SEC reports. The notes include standard events of default resulting in acceleration of indebtedness, including failure to pay, bankruptcy and insolvency, cross-defaults, and breaches of the covenants in the August 2013 SPA, Tranche I Notes and Tranche II Notes, with default interest rates and associated cure periods applicable to the covenant.

As of June 30, 2014 and December 31, 2013, the related party convertible notes outstanding under the Tranche I and Tranche II Notes were $46.2 million and $37.9 million, respectively, net of debt discount of $31.6 million and $6.3 million, respectively. The debt discount is the result of the bifurcation of the conversion options that contain "make-whole" provisions or down round conversion price adjustment provisions associated with the outstanding debt.

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Rule 144A Convertible Notes Sold to Related Parties

As discussed above under “Rule 144A Convertible Note Offering”, the Company sold and issued $75.0 million aggregate principal amount of 144A Notes pursuant to Rule 144A of the Securities Act. In connection with obtaining a waiver from one of its existing investors, Total, of its preexisting contractual right to exchange certain senior secured convertible notes previously issued by Amyris pursuant to the Total Purchase Agreement for 144A Notes issued in the transaction, Amyris used approximately $9.7 million of the net proceeds to repay such amount of previously issued notes held by Total, which represented the amount of notes purchased by Total from the Initial Purchaser under the Rule 144A Convertible Note Offering. As a result of the settlement of the $9.7 million Total convertible notes, the Company recorded a loss from extinguishment of debt of $1.1 million.

Additionally, Foris Ventures, LLC (a fund affiliated with John Doerr) and Temasek each participated in the Rule 144A Convertible Note Offering and purchased $5.0 million and $10.0 million, respectively, of the convertible promissory notes sold thereunder.

As of June 30, 2014 the related party convertible notes outstanding under the 144A Notes were $14.0 million, net of discount of $10.7 million.

As of June 30, 2014 and December 31, 2013 the total related party convertible notes outstanding were $100.5 million and $89.5 million, respectively, net of discount of $55.3 million and $23.9 million, respectively. The Company recorded a loss from extinguishment of debt from the settlement, exchange and cancellation of related party convertible notes for the three months ended June 30, 2014 and 2013, of $1.1 million and zero, respectively, and $10.5 million and zero for the six months ended June 30, 2014 and 2013, respectively.

Loans Payable

In December 2009, the Company entered into a loans payable agreement with the lessor of its Emeryville, California pilot plant under which it borrowed a total of $0.3 million, bearing an interest rate of 10.0% per annum and to be repaid over a period of 96 months. As of June 30, 2014 and December 31, 2013, there was no amount outstanding under the loan. In June 2013, as part of the April 30, 2013 amendment entered into regarding the Company's operating lease for its headquarters, the Company recorded the elimination of this loan payable as a lease incentive and recorded approximately $0.2 million to deferred rent liability in the condensed consolidated balance sheet. The deferred rent liability is being amortized to expense over the remaining lease term.

In July 2012, the Company entered into a Note of Bank Credit and a Fiduciary Conveyance of Movable Goods Agreement (together, referred to as the "July 2012 Bank Agreements") with each of Nossa Caixa Desenvolvimento (or “Nossa Caixa”) and Banco Pine S.A. (or “Banco Pine”). Under the July 2012 Bank Agreements, the Company pledged certain farnesene production assets as collateral for the loans of R$52.0 million. The Company's total acquisition cost for such pledged assets was approximately R$68.0 million (approximately US$30.9 million based on the exchange rate as of June 30, 2014). The Company is also a parent guarantor for the payment of the outstanding balance under these loan agreements. Under the July 2012 Bank Agreements, the Company could borrow an aggregate of R$52.0 million (approximately US$23.6 million based on the exchange rate as of June 30, 2014) as financing for capital expenditures relating to the Company's manufacturing facility located in Brotas, Brazil. Specifically, Banco Pine, agreed to lend R$22.0 million and Nossa Caixa agreed to lend R$30.0 million. The funds for the loans are provided by BNDES, but are guaranteed by the lenders. The loans have a final maturity date of July 15, 2022 and bear a fixed interest rate of 5.5% per year. The loans are also subject to early maturity and delinquency charges upon occurrence of certain events including interruption of manufacturing activities at the Company's manufacturing facility in Brotas, Brazil for more than 30 days, except during sugarcane off-season. For the first two years that the loans are outstanding, the Company is required to pay interest only on a quarterly basis. After August 15, 2014, the Company is required to pay equal monthly installments of both principal and interest for the remainder of the term of the loans. As of June 30, 2014 and December 31, 2013, a principal amount of $23.6 million and $22.2 million, respectively, was outstanding under these loan agreements.

In October 2013, the Company borrowed $0.6 million from a third party lender to pay for the Company's current insurance premiums. The loan is payable in nine monthly installments of principal and interest. Interest accrues at a rate of 3.24% per annum. As of June 30, 2014 and December 31, 2013, the outstanding unpaid loan balance was zero and $0.4 million, respectively.

In February 2014, the Company borrowed $0.2 million from a third party lender to pay for the Company's consolidated VIE's current insurance premiums. The loan is payable in ten monthly installments of principal and interest. Interest accrues at a rate of 5.95% per annum. As of June 30, 2014 and December 31, 2013, the outstanding unpaid loan balance was $0.1 million and zero, respectively.

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In March 2013, the Company entered into a one-year-term export financing agreement with ABC for approximately $2.5 million to fund exports through March 2014. This loan is collateralized by future exports from the Company's subsidiary in Brazil. As of June 30, 2014, the loan was fully paid.

In March 2014, the Company entered into an additional one-year-term export financing agreement with ABC for approximately $2.2 million to fund exports through March 2015. This loan is collateralized by future exports from the Company's subsidiary in Brazil. As of June 30, 2014, the principal amount outstanding under this agreement was $2.2 million.The Company is also a parent guarantor for the payment of the outstanding balance under these loan agreements. 

Letters of Credit

In June 2012, the Company entered into a letter of credit agreement for $1.0 million under which it provided a letter of credit to the landlord of its headquarters in Emeryville, California, in order to cover the security deposit on the lease. This letter of credit is secured by a certificate of deposit. Accordingly, the Company has $1.7 million and $0.9 million as restricted cash as of June 30, 2014 and December 31, 2013.

Future minimum payments under the debt agreements as of June 30, 2014 are as follows (in thousands):

Years ending December 31:	Related Party Convertible Debt			Convertible Debt			Loans Payable			Credit Facility
2014 (remaining six months)	$	744		$	1,891		$	4,080		$	2,539
2015	1,606			4,020			4,114			15,426
2016	1,606			4,020			3,935			20,301
2017	58,849			28,715			3,772			7,822
2018	74,485			15,685			3,612			472
Thereafter	75,825			56,798			11,751			131
Total future minimum payments	213,115			111,129			31,264			46,691
Less: amount representing interest(1)	(112,635		)	(53,225		)	(5,265		)	(8,719		)
Present value of minimum debt payments	100,480			57,904			25,999			37,972
Less: current portion	—			—			(5,218		)	(4,705		)
Noncurrent portion of debt	$	100,480		$	57,904		$	20,781		$	33,267

______________ 

⁽¹⁾ Including debt discount of $83.9 million related to the embedded derivative associated with the related party and non-related party convertible debt which will be accreted to interest expense under the effective interest method over the term of the convertible debt.

6. Commitments and Contingencies

Lease Obligations

The Company leases certain facilities and finances certain equipment under operating and capital leases, respectively. Operating leases include leased facilities and capital leases include leased equipment (see Note 4, "Balance Sheet Components"). The Company recognizes rent expense on a straight-line basis over the non-cancellable lease term and records the difference between rent payments and the recognition of rent expense as a deferred rent liability. Where leases contain escalation clauses, rent abatements, and/or concessions, such as rent holidays and landlord or tenant incentives or allowances, the Company applies them as a straight-line rent expense over the lease term. The Company has non-cancellable operating lease agreements for office, research and development, and manufacturing space that expire at various dates, with the latest expiration in February 2031. Rent expense under operating leases was $1.3 million and $1.4 million for the three months ended June 30, 2014 and 2013, respectively, and was $2.7 million and $2.1 million for the six months ended June 30, 2014 and 2013, respectively.

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Future minimum payments under the Company's lease obligations as of June 30, 2014, are as follows (in thousands):

Years ending December 31:	Capital Leases			Operating Leases		Total Lease Obligations
2014 (remaining six months)	$	557		$	3,182	$	3,739
2015	462			6,606		7,068
2016	159			6,614		6,773
2017	—			6,588		6,588
2018	—			6,675		6,675
Thereafter	—			32,320		32,320
Total future minimum lease payments	1,178			$	61,985	$	63,163
Less: amount representing interest	(68		)
Present value of minimum lease payments	1,110
Less: current portion	(882		)
Long-term portion	$	228

GuarantorArrangements

The Company has agreements to indemnify its officers and directors for certain events or occurrences while the officers or directors are serving in their official capacities. The indemnification period remains enforceable for the officer's or director’s lifetime. The maximum potential amount of future payments the Company could be required to make under these indemnification agreements is unlimited; however, the Company has a director and officer insurance policy that limits its exposure and enables the Company to recover a portion of any future payments. As a result of its insurance policy coverage, the Company believes the estimated fair value of these indemnification agreements is minimal. Accordingly, the Company had no liabilities recorded for these agreements as of June 30, 2014 and December 31, 2013.

The Company entered into the FINEP Credit Facility to finance a research and development project on sugarcane-based biodiesel (see Note 5, "Debt"). The FINEP Credit Facility is guaranteed by a chattel mortgage on certain equipment of the Company. The Company's total acquisition cost for the equipment under this guarantee is approximately R$6.0 million (approximately US$2.7 million based on the exchange rate as of June 30, 2014).

The Company entered into the BNDES Credit Facility to finance a production site in Brazil (see Note 5, "Debt").The BNDES Credit Facility is collateralized by a first priority security interest in certain of the Company's equipment and other tangible assets with a total acquisition cost of R$24.9 million (approximately US$11.3 million based on the exchange rate as of June 30, 2014). The Company is a parent guarantor for the payment of the outstanding balance under the BNDES Credit Facility. Additionally, the Company is required to provide certain bank guarantees under the BNDES Credit Facility. Accordingly, the Company has a $0.8 million and $0.7 million as restricted cash as of June 30, 2014 and December 31, 2013, respectively.

The Company entered into loan agreements and security agreement where the Company pledged certain farnesene production assets as collateral (the fiduciary conveyance of movable goods) with each of Nossa Caixa and Banco Pine (see Note 5, "Debt"). The Company's total acquisition cost for the farnesene production assets pledged as collateral under these agreements is approximately R$68.0 million (approximately US$30.9 million based on the exchange rate as of June 30, 2014). The Company is also a parent guarantor for the payment of the outstanding balance under these loan agreements. 

The Company had an export financing agreement with ABC for approximately $2.5 million for a one year term to fund exports through March 2014. As of June 30, 2014, the loan was fully paid. The Company has entered into another export financing agreement with the same bank for approximately $2.2 million for a one year term to fund exports through March 2015. This loan is collateralized by future exports from Amyris Brasil. The Company is also a parent guarantor for the payment of the outstanding balance under these loan agreements. 

Under an operating lease agreement for its office facilities in Brazil, which commenced on November 15, 2011, the Company is required to maintain restricted cash or letters of credit equal to 3 months of rent of approximately R$0.2 million (approximately US$0.1 million based on the exchange rate as of June 30, 2014) in the aggregate as a guarantee that the Company will meet its performance obligations under such operating lease agreement.

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In October 2013, the Company entered into a letter agreement with Total relating to the Temasek Bridge Note and to the closing of the August 2013 Financing (referred to as the "Amendment Agreement") (see Note 5, "Debt"). In the August 2013 Financing, the Company was required to provide the purchasers under the August 2013 SPA with a security interest in the Company’s intellectual property if Total still held such security interest as of the initial closing of the August 2013 Financing. Under the terms of a previous Intellectual Property Security Agreement by and between the Company and Total (referred to as the "Security Agreement"), the Company had previously granted a security interest in favor of Total to secure the obligations of the Company under certain convertible promissory notes issued and issuable to Total under the Total Purchase Agreement. The Security Agreement provided that such security interest would terminate if Total and the Company entered into certain agreements relating to the formation of the Fuels JV. In connection with Total’s agreement to (i) permit the Company to grant the security interest under the Temasek Bridge Note and the August 2013 Financing and (ii) waive a secured debt limitation contained in the outstanding convertible promissory notes issued pursuant to the Total Purchase Agreement and held by Total (referred to as the “Total Securities”), the Company entered into the Amendment Agreement. Under the Amendment Agreement, the Company agreed to reduce, effective December 2, 2013, the conversion price for the Total Securities issued in 2012 (approximately $48.3 million of which are outstanding as of the date hereof) from $7.0682 per share to $2.20, the market price per share of the Company’s common stock as of the signing of the Amendment Agreement, as determined in accordance with applicable NASDAQ rules, unless the Company and Total entered into the JV Documents on or prior to December 2, 2013. The Company and Total entered into the JV agreements on December 2, 2013 and the Amendment Agreement and all security interests thereunder were automatically terminated and the conversion price of the Total Securities remained at $7.0682 per share.

In December 2013, in connection with the execution of JV Documents entered into by and among Amyris, Total and JVCO relating to the establishment of the JVCO (see Note 5, "Debt" and Note 7, "Joint Venture and Noncontrolling Interest"), Amyris agreed to exchange the $69.0 million outstanding Total unsecured convertible notes issued pursuant to the Total Purchase Agreement and issue replacement 1.5% senior secured convertible notes, in principal amounts equal to the principal amount of each Replacement Notes and grant a security interest to Total in and lien on all Amyris’s rights, title and interest in and to Amyris’s shares in the capital of the JVCO. Following execution of the JV Documents, all notes that have been issued and that remain to be issued in connection with the third closing under the Total Purchase Agreement (up to $21.7 million in the aggregate; with $10.85 million in principal amount of such remaining notes issued on July 31, 2014, and an additional $10.85 million in principal amount of such remaining notes to be issued by January 31, 2015) are senior secured convertible notes instead of senior unsecured convertible notes.

In March 2014, the Company and Hercules Technology Growth Capital, Inc. entered into a loan and security agreement to make available to the Company a loan in the aggregate principal amount of up to $25.0 million (see Note5 "Debt"). Loans under the facility are secured by various liens, including a lien on certain Company intellectual property. In connection with the Hercules loan, the Company agreed to certain customary representations and warranties and covenants, as well as certain covenants with respect to obtaining additional financing as described above and performance covenants related to revenues and cash flows starting with the third quarter of 2014. If the Company had not satisfied the equity financing covenant, a forbearance fee of $10.0 million would have become due and payable at the end of the initial term of the loan. The Company borrowed the full amount available under the facility and received the funds on March 31, 2014. In June 2014, the Company and Hercules entered into the Hercules Amendment of the Loan and Security Agreement entered into on March 29, 2014. Pursuant to the Hercules Amendment, the parties agreed to remove (i) a requirement for the Company to pay a forbearance fee of $10.0 million in the event certain covenants were not satisfied, (ii) a covenant that the Company maintain positive cash flow commencing with the fiscal quarter beginning October 1, 2014, (iii) a covenant that, beginning with the fiscal quarter beginning July 1, 2014, the Company and its subsidiaries achieve certain projected cash product revenues and projected cash product gross profits, and (iv) an obligation for the Company to file a registration statement on Form S-3 with the SEC by no later than June 30, 2014 and complete an equity financing of more than $50.0 million by no later than September 30, 2014. Under the Hercules Amendment, in connection with the amendments and modification or removal of the covenants described above, the Company agreed to include a new covenant requiring the Company to maintain unrestricted, unencumbered cash in an amount equal to at least 50% of the remaining principal amount then outstanding under the Hercules Loan Facility and borrow an additional tranche of $5.0 million, subject to obtaining specified third party consents under outstanding convertible promissory notes. The Hercules Loan Facility is collateralized by liens on the Company's assets, including on certain Company intellectual property.

Purchase Obligations

As of June 30, 2014, the Company had $6.8 million in purchase obligations which included $5.9 million in non-cancellable contractual obligations and construction commitments, of which $2.4 million have been accrued as loss on purchase commitments.

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Other Matters

Certain conditions may exist as of the date the financial statements are issued, which may result in a loss to the Company but will only be recorded when one or more future events occur or fail to occur. The Company's management assesses such contingent liabilities, and such assessment inherently involves an exercise of judgment. In assessing loss contingencies related to legal proceedings that are pending against and by the Company or unasserted claims that may result in such proceedings, the Company's management evaluates the perceived merits of any legal proceedings or unasserted claims as well as the perceived merits of the amount of relief sought or expected to be sought.

If the assessment of a contingency indicates that it is probable that a material loss has been incurred and the amount of the liability can be estimated, then the estimated liability would be accrued in the Company's financial statements. If the assessment indicates that a potential material loss contingency is not probable but is reasonably possible, or is probable but cannot be estimated, then the nature of the contingent liability, together with an estimate of the range of possible loss if determinable and material would be disclosed. Loss contingencies considered to be remote by management are generally not disclosed unless they involve guarantees, in which case the guarantee would be disclosed.

In May 2013, a securities class action complaint was filed against the Company and its CEO, John G. Melo, in the U.S. District Court for the Northern District of California. In October 2013, the lead plaintiffs filed a consolidated amended complaint. The complaint, as amended, sought unspecified damages on behalf of a purported class that would comprise all individuals who acquired the Company's common stock between April 29, 2011 and February 8, 2012. The complaint alleged securities law violations based on the Company's commercial projections during that period. In December 2013, the Company filed a motion to dismiss the complaint. In March 2014, the court issued an order granting the Company's motion to dismiss with leave to amend the complaint. The plaintiffs declined to amend their complaint further and, on June 12, 2014, the court issued an order (based on stipulation of the parties) dismissing the action with prejudice.

In August 2013, a complaint entitled Steve Shannon, derivatively on behalf of Amyris, Inc. v. John G. Melo et al and Amyris, Inc., was filed against the Company as nominal defendant in the United States District Court for the Northern District of California. The lawsuit sought unspecified damages on behalf of the Company from certain of its current and former officers, directors and employees and alleges these defendants breached their fiduciary duties to the Company and unjustly enriched themselves by making allegedly false and misleading statements and omitting certain material facts in the Company's securities filings. Because this purported stockholder derivative action is based on substantially the same facts as the securities class action described above, the two actions were related and were heard by the same judge. On June 23, 2014, following the dismissal of the related class action (discussed above), the court issued an order (based on stipulation of the parties) dismissing the action with prejudice.

The Company is subject to disputes and claims that arise or have arisen in the ordinary course of business and that have not resulted in legal proceedings or have not been fully adjudicated. Such matters that may arise in the ordinary course of business are subject to many uncertainties and outcomes are not predictable with assurance. Therefore, if one or more of these legal disputes or claims resulted in settlements or legal proceedings that were resolved against the Company for amounts in excess of management’s expectations, the Company’s consolidated financial statements for the relevant reporting period could be materially adversely affected.

7. Joint Ventures and Noncontrolling Interest

Novvi S.A.

In June 2011, the Company entered into joint venture agreements with Cosan Combustíveis e Lubrificantes S.A. and Cosan S.A. Industria e Comércio (such Cosan entities, collectively or individually, “Cosan”), related to the formation of a joint venture to focus on the worldwide development, production and commercialization of base oils made from Biofene for the automotive, commercial and industrial lubricants markets (referred to as the "Original JV Agreement"). The parties originally envisioned operating their joint venture through Novvi S.A., a Brazilian entity jointly owned by Cosan and Amyris Brasil.

Under the Original JV Agreement and related agreements, the Company and Cosan each owned 50% of the Novvi S.A. and each party would share equally in any costs and any profits ultimately realized by Novvi S.A. The joint venture agreement had an initial term of 20 years from the date of the Original JV Agreement, subject to earlier termination by mutual written consent or by a non-defaulting party in the event of specified defaults by the other party. The shareholders' agreement had an initial term of 10 years from the date of the agreement, subject to earlier termination if either the Company or Cosan ceases to own at least 10% of the voting stock of Novvi S.A. Since its formation, Novvi S.A. had minimal operating activities while the Company and

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Cosan continued to determine and finalize the strategy and operating activities for the joint venture. Upon determination by the Company and Cosan that the joint venture should be operated out of a U.S. entity, the operating activities of Novvi S.A. ceased. The Company has identified that Novvi S.A. is a VIE and determined that the power to direct activities, which most significantly impact the economic success of the joint venture, is equally shared between the Company and Cosan. Accordingly, the Company is not the primary beneficiary and therefore accounts for its investment in Novvi S.A. under the equity method of accounting.

In March 2013, the Company, Amyris Brasil and Cosan entered into a termination agreement to terminate the Original JV Agreement. In addition, Amyris Brasil agreed to sell, its 50% ownership in Novvi S.A. to Cosan for approximately R$22,000 (approximately US$9,989 based on the exchange rate as of June 30, 2014), which represented the current value of its 50% equity ownership in Novvi S.A., a now-dormant company. Upon the consummation of the transaction with the shares transferring from Amyris Brasil to Cosan, the Novvi S.A. shareholders agreement automatically terminated.

Novvi LLC

In September 2011, the Company and Cosan US, Inc. (or "Cosan U.S.") formed Novvi LLC, a U.S. entity that is jointly owned by the Company and Cosan U.S. (or "Novvi"). In March 2013, the Company and Cosan U.S. entered into agreements to (i) expand their base oils joint venture to also include additives and lubricants and (ii) operate their joint venture exclusively through Novvi. Specifically, the parties entered into an Amended and Restated Operating Agreement for Novvi (referred to as the "Operating Agreement"), which sets forth the governance procedures for Novvi and the joint venture and the parties' initial contribution. The Company also entered into an IP License Agreement with Novvi (referred to as the "IP License Agreement") under which the Company granted Novvi (i) an exclusive (subject to certain limited exceptions for the Company), worldwide, royalty-free license to develop, produce and commercialize base oils, additives, and lubricants derived from Biofene for use in automotive and industrial lubricants markets and (ii) a non-exclusive, royalty-free license, subject to certain conditions, to manufacture Biofene solely for its own products. In addition, both the Company and Cosan U.S. granted Novvi certain rights of first refusal with respect to alternative base oil and additive technologies that may be acquired by the Company or Cosan U.S. during the term of the IP License Agreement. Under these agreements, the Company and Cosan U.S. will each own 50% of Novvi and each party will share equally in any costs and any profits ultimately realized by the joint venture. Novvi is governed by a six member Board of Managers (or the "Board Managers"), with three managers represented by each investor. The Board of Managers appoints the officers of Novvi, who are responsible for carrying out the daily operating activities of Novvi as directed by the Board of Managers. The IP License Agreement has an initial term of 20 years from the date of the agreement, subject to standard early termination provisions such as uncured material breach or a party's insolvency. Under the terms of the Operating Agreement, Cosan U.S. is obligated to fund its 50% ownership share of Novvi in cash in the amount of $10.0 million and the Company is obligated to fund its 50% ownership share of Novvi through the granting of an IP License to develop, produce and commercialize base oils, additives, and lubricants derived from Biofene for use in the automotive, commercial and industrial lubricants markets which has been agreed upon by Cosan U.S. and Amyris valued at $10.0 million. In March 2013, the Company measured its initial contribution of intellectual property to Novvi at the Company's carrying value of the licenses granted under the IP License Agreement, which was zero. Additional funding requirements to finance the ongoing operations of Novvi are expected to happen through revolving credit or other loan facilities provided by unrelated parties (i.e. such as financial institutions); cash advances or other credit or loan facilities provided by the Company and Cosan U.S. or their affiliates; or additional capital contributions by the Company and Cosan U.S.

In April 2014, the Company subscribed and purchased Membership Units of Novvi for an aggregate purchase price of $0.2 million. Also in April 2014, the Company contributed $2.1 million in cash in exchange of receiving additional Membership Units in Novvi. Each member owns 50% of Novvi's issued and outstanding Membership Units. The Company recorded its investment in Novvi of $2.1 million under "Other Assets" in the condensed consolidated balance sheet.

The Company has identified Novvi as a VIE and determined that the power to direct activities, which most significantly impact the economic success of the joint venture (i.e. continuing research and development, marketing, sales, distribution and manufacturing of Novvi products), is equally shared between the Company and Cosan U.S. Accordingly, the Company is not the primary beneficiary and therefore accounts for its investment in Novvi under the equity method of accounting. The Company will continue to reassess its primary beneficiary analysis of Novvi if there are changes in events and circumstances impacting the power to direct activities that most significantly affect Novvi's economic success. Under the equity method, the Company's share of profits and losses are included in “Other income (expense), net” in the condensed consolidated statements of operations. For the three and six months ended June 30, 2014, the Company recorded $0.2 million of its share of Novvi's net loss. The Company recorded collaboration revenue of zero and $0.3 million for the three months ended June 30, 2014 and 2013, respectively, and zero and $2.8 million for the six months ended June 30, 2014 and 2013, respectively, from the research and development activities that it has performed on behalf of Novvi.

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Total Amyris BioSolutions B.V.

In November 2013, the Company and Total formed JVCO. The common equity of JVCO is jointly owned (50%/50%) by the Company and Total, and the preferred equity of JVCO is 100% owned by the Company. The Parties have agreed that JVCO’s purpose is limited to executing the License Agreement and maintaining such licenses under it, unless and until either (i) Total elects to go forward with either the full (diesel and jet fuel) JVCO commercialization program or the jet fuel component of the JVCO commercialization program (referred to as a “Go Decision”), (ii) Total elects to not continue its participation in the R&D Program and JVCO (referred to as a “No-Go Decision”), or (iii) Total exercises any of its rights to buy out the Company’s interest in JVCO. Following a Go Decision, the articles and shareholders’ agreement would be amended and restated to be consistent with the shareholders’ agreement contemplated by the July 2012 Agreements (see Note 5, "Debt" and Note 8, "Significant Agreements").

The JVCO has an initial capitalization of €0.1 million (approximately US$0.1 million based on the exchange rate as of June 30, 2014). The Company has identified JVCO as a VIE and determined that the Company is not the primary beneficiary and therefore accounts for its investment in JVCO under the equity method of accounting. Under the equity method, the Company's share of profits and losses are included in "Other income (expense), net" in the condensed consolidated statements of operations. No later than six months prior to July 31, 2016, the Company and Total shall amend the July 2012 Agreements to reflect the corporate structure of JVCO, amend and restate the articles of association of JVCO, finalize and agree on a five-year plan and an initial budget, maximize economic viability and value of JVCO and enter into the Total license agreement. The Company will reevaluate its assessment in 2016 based on the specific terms of the final shareholders' agreement.

SMA Indústria Química S.A.

In April 2010, the Company established SMA Indústria Química (or "SMA"), a joint venture with Sao Martinho S.A. (or "SMSA") (formerly Usina São Martinho S.A.), to build a production facility in Brazil. SMA is located at the SMSA mill in Pradópolis, São Paulo state. The joint venture agreements establishing SMA have a 20 year initial term.

 SMA is managed by a three member executive committee, of which the Company appoints two members, one of whom is the plant manager who is the most senior executive responsible for managing the construction and operation of the facility. SMA is governed by a four member board of directors, of which the Company and SMSA each appoint two members. The board of directors has certain protective rights which include final approval of the engineering designs and project work plan developed and recommended by the executive committee.

The joint venture agreements require the Company would fund the construction costs of the new facility and SMSA would reimburse the Company up to R$61.8 million (approximately US$28.1 million based on the exchange rate as of June 30, 2014) of the construction costs after SMA commences production. After commercialization, the Company would market and distribute Amyris renewable products produced by SMA and SMSA would sell feedstock and provide certain other services to SMA. The cost of the feedstock to SMA would be a price that is based on the average return that SMSA could receive from the production of its current products, sugar and ethanol. The Company would be required to purchase the output of SMA for the first four years at a price that guarantees the return of SMSA’s investment plus a fixed interest rate. After this four year period, the price would be set to guarantee a break-even price to SMA plus an agreed upon return.

Under the terms of the joint venture agreements, if the Company becomes controlled, directly or indirectly, by a competitor of SMSA, then SMSA has the right to acquire the Company’s interest in SMA. If SMSA becomes controlled, directly or indirectly, by a competitor of the Company, then the Company has the right to sell its interest in SMA to SMSA. In either case, the purchase price shall be determined in accordance with the joint venture agreements, and the Company would continue to have the obligation to acquire products produced by SMA for the remainder of the term of the supply agreement then in effect even though the Company would no longer be involved in SMA’s management.

The Company has a 50% ownership interest in SMA. The Company has identified SMA as a variable interest entity (or "VIE") pursuant to the accounting guidance for consolidating VIEs because the amount of total equity investment at risk is not sufficient to permit SMA to finance its activities without additional subordinated financial support, as well as because the related commercialization agreement provides a substantive minimum price guarantee. Under the terms of the joint venture agreement, the Company directs the design and construction activities, as well as production and distribution. In addition, the Company has the obligation to fund the design and construction activities until commercialization is achieved. Subsequent to the construction phase, both parties equally fund SMA for the term of the joint venture. Based on those factors, the Company was determined to have the power to direct the activities that most significantly impact SMA’s economic performance and the obligation to absorb losses and the right to receive benefits. Accordingly, the financial results of SMA are included in the Company’s consolidated financial statements and amounts pertaining to SMSA’s interest in SMA are reported as noncontrolling interests in subsidiaries.

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The Company completed a significant portion of the construction of the new facility in 2012. The Company suspended construction of the facility in order to focus on completing and operating the Company's smaller production facility in Brotas, Brazil. In February 2014, the Company entered into an amendment to the joint venture agreement with SMSA which updated and documented certain preexisting business plan requirements related to the start-up of construction at the joint venture operated plant and set forth, among other things, (i) the extension of the deadline for the commencement of operations at the joint venture operated plant to no later than 18 months following the construction of the plant, which shall occur no later than March 31, 2017, and (ii) the extension of an option held by SMSA to build a second large-scale farnesene production facility to no later than December 31, 2018 with the commencement of operations at such second facility to occur no later than April 1, 2019.

Glycotech

In January 2011, the Company entered into a production service agreement (referred to as the "Glycotech Agreement") with Glycotech, Inc. (or "Glycotech"), under which Glycotech provides process development and production services for the manufacturing of various Company products at its leased facility in Leland, North Carolina. The Company products manufactured by Glycotech are owned and distributed by the Company. Pursuant to the terms of the Glycotech Agreement, the Company is required to pay the manufacturing and operating costs of the Glycotech facility, which is dedicated solely to the manufacture of Amyris products. The initial term of the Glycotech Agreement was for a two year period commencing on February 1, 2011 and the Glycotech Agreement renews automatically for successive one-year terms, unless terminated by the Company. Concurrent with the Glycotech Agreement, the Company also entered into a Right of First Refusal Agreement with the lessor of the facility and site leased by Glycotech (referred to as the "ROFR Agreement"). Per conditions of the ROFR Agreement, the lessor agreed not to sell the facility and site leased by Glycotech during the term of the Glycotech Agreement. In the event that the lessor is presented with an offer to sell or decides to sell an adjacent parcel, the Company has the right of first refusal to acquire it.

The Company has determined that the arrangement with Glycotech qualifies as a VIE. The Company determined that it is the primary beneficiary of this arrangement since it has the power through the management committee over which it has majority control to direct the activities that most significantly impact Glycotech's economic performance. In addition, the Company is required to fund 100% of Glycotech's actual operating costs for providing services each month while the facility is in operation under the Glycotech Agreement. Accordingly, the Company consolidates the financial results of Glycotech. As of June 30, 2014, the carrying amounts of the consolidated VIE's assets and liabilities were not material to the Company's condensed consolidated financial statements.

The table below reflects the carrying amount of the assets and liabilities of the two consolidated VIEs for which the Company is the primary beneficiary. As of June 30, 2014, the assets include $22.9 million in property, plant and equipment, $4.1 million in other assets and $0.5 million in current assets. The liabilities include $0.2 million in accounts payable and accrued current liabilities and $0.1 million in loan obligations by Glycotech to its shareholders that are non-recourse to the Company. The creditors of each consolidated VIE have recourse only to the assets of that VIE.

	June 30,		December 31,
(In thousands)	2014		2013
Assets	$	27,509	$	25,730
Liabilities	$	421	$	229

The change in noncontrolling interest for the six months ended June 30, 2014 and 2013, is summarized below (in thousands):

	2014			2013
Balance at January 1	$	(584	)	$	(877	)
Foreign currency translation adjustment	(42		)	54
Gain (loss) attributable to noncontrolling interest	(60		)	261
Balance at June 30	$	(686	)	$	(562	)

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8. Significant Agreements

Collaboration Agreement with Michelin and Braskem

In September 2011, the Company entered into a collaboration agreement with Manufacture Francaise des Pneumatiques Michelin (or “Michelin”). Under the terms of the September 2011 collaboration agreement, the Company and Michelin agreed to collaborate on the development, production and worldwide commercialization of isoprene or isoprenol, generally for tire applications, using the Company's technology. Under the agreement, Michelin agreed to pay an upfront payment to the Company of $5.0 million.

In June 2014, the Company entered into a collaboration agreement with Braskem S.A. and Braskem America, Inc. (or “Braskem”) and Michelin to collaborate to develop the technology to produce and possibly commercialize renewable isoprene. The term of the collaboration agreement commenced on June 30, 2014 and will continue, unless earlier terminated in accordance with the agreement, until the first to occur of (i) the date that is three (3) years following the actual date on which a Work Plan is completed, which date is estimated to occur on or about December 30, 2020 or (ii) the date of the commencement of commissioning of a production plant for the production of renewable isoprene. The June 2014 collaboration agreement terminated and supersedes the September 2011 collaboration agreement with Michelin, and as a result of the signing of the June 2014 collaboration agreement, the upfront payment by Michelin of $5.0 million is being rolled into the new collaboration agreement between Michelin, Braskem and the Company as Michelin's collaboration funding towards the research and development activities to be performed. As of June 30, 2014, the $5.0 million from Michelin is still recorded as "Deferred Revenue" in the condensed consolidated balance sheet .

Collaboration Partner Joint Development and License Agreement

In April 2013, the Company entered into a joint development and license agreement with a collaboration partner. Under the terms of the multi-year agreement, the collaboration partner and the Company will jointly develop certain fragrance ingredients. The collaboration partner will have exclusive rights to these fragrance ingredients for applications in the flavors and fragrances field, and the Company will have exclusive rights in other fields. The collaboration partner and the Company will share in the economic value derived from these ingredients. The joint development and license agreement provided for up to $6.0 million in funding based upon the achievement of certain technical milestones which are considered substantive by the Company during the first phase of the collaboration.

In February 2014, the Company entered into an amendment to the joint development and license agreement with the collaboration partner noted in the preceding paragraph to proceed with the second phase of the collaboration and the development of a certain fragrance ingredient. The Company recognized revenue for the three and six months ended June 30, 2014 of $0.8 million and $1.0 million, respectively, and zero for the three and six months ended June 30, 2013, respectively, under this agreement.

Collaboration Partner Master Collaboration and Joint Development Agreement

In March 2013, the Company entered into a Master Collaboration Agreement with the collaboration partner to establish a collaboration for the development and commercialization of multiple renewable flavors and fragrances (referred to as "F&F") compounds. Under this agreement, except for rights granted under preexisting collaboration relationships, the Company granted the collaboration partner exclusive access for such compounds to specified Company intellectual property for the development and commercialization of F&F products in exchange for research and development funding and a profit sharing arrangement. The agreement superseded and expanded the prior collaboration agreement between the Company and the collaboration partner.

The agreement provides annual, up-front funding to the Company by the collaboration partner of $10.0 million for each of the first three years of the collaboration. The initial payment of $10.0 million was received by the Company in March 2013 and the second payment was received in March 2014. The Company recognized revenue under this agreement for the three months ended June 30, 2014 and 2013, of $2.5 million and $2.8 million, respectively, and for the six months ended June 30, 2014 and 2013, of $5.0 million and $3.2 million, respectively. The agreement contemplates additional funding by the collaboration partner of up to $5.0 million under three potential milestone payments, as well as additional funding by the collaboration partner on a discretionary basis.

Kuraray Collaboration Agreement and Securities Purchase Agreement

In March 2014, the Company entered into the Second Amended and Restated Collaboration Agreement with Kuraray Co., Ltd. (or “Kuraray”) in order to extend the term of the original agreement dated July 21, 2011 for an additional two years and add additional fields and products to the scope of development. In consideration for the Company’s agreement to extend the term of the original collaboration agreement and add additional fields and products, Kuraray will pay the Company $4.0 million in two

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(2) equal installments of $2.0 million. The first installment was paid on April 30, 2014 and the second installment is due on April 30, 2015. In connection with the collaboration agreement Kuraray signed a Securities Purchase Agreement in March 2014 to purchase 943,396 shares of the Company's common stock at a price per share of $4.24 per share. The Company issued 943,396 shares of its common stock at a price per share of $4.24 in April 2014 for aggregate cash proceeds of $4.0 million.

9. Goodwill and Intangible Assets

The following table presents the components of the Company's intangible assets (in thousands):

		June 30, 2014							December 31, 2013
	Useful Life in Years	Gross Carrying Amount		Accumulated Amortization			Net Carrying Value		Gross Carrying Amount		Accumulated Amortization			Net Carrying Value
In-process research and development	Indefinite	$	8,560	$	—		$	8,560	$	8,560	$	—		$	8,560
Acquired licenses and permits	2	772		(772		)	—		772		(772		)	—
Goodwill	Indefinite	560		—			560		560		—			560
		$	9,892	$	(772	)	$	9,120	$	9,892	$	(772	)	$	9,120

The following table presents the activity of intangible assets for the six months ended June 30, 2014 (in thousands):

	December 31, 2013								June 30, 2014
	Net Carrying Value		Additions		Adjustments		Amortization		Net Carrying Value
In-process research and development	$	8,560	$	—	$	—	$	—	$	8,560
Acquired licenses and permits	—		—		—		—		—
Goodwill	560		—		—		—		560
	$	9,120	$	—	$	—	$	—	$	9,120

The intangible assets acquired through the Draths Corporation acquisition in October 2011 of in-process research and development of $8.6 million and goodwill of $0.6 million are treated as indefinite lived intangible assets until completion or abandonment of the projects, at which time the assets will be amortized over the remaining useful life or written-off, as appropriate. If the carrying amount of the assets is greater than the measures of fair value, impairment is considered to have occurred and a write-down of the asset is recorded. Any finding that the value of its intangible assets has been impaired would require the Company to write-down the impaired portion, which could reduce the value of its assets and reduce (increase) its net income (loss) for the year in which the related impairment charges occur. As of June 30, 2014 and December 31, 2013, no impairment of the goodwill and intangible assets was recorded.    

Acquired licenses and permits are amortized using a straight-line method over its estimated useful life. Amortization expense for this intangible was zero and $32,000 for the six months ended June 30, 2014 and 2013, respectively. As of June 30, 2014, acquired licenses and permits were fully amortized.

10. Stockholders’ Deficit

Private Placement

In March 2014, the Company completed a private placement of 943,396 shares of its common stock at a price of $4.24 per share for aggregate proceeds of $4.0 million (see Note 8, "Significant Agreements").

Evergreen Shares for 2010 Equity Plan and 2010 ESPP

In January 2014, the Company's Board of Directors (or "Board") approved an increase to the number of shares available for issuance under the Company's 2010 Equity Incentive Plan (or "Equity Plan") and the 2010 Employee Stock Purchase Plan (or

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"ESPP"). These shares represent an automatic annual increase in the number of shares available for issuance under the Equity Plan and the ESPP of 3,833,141 and 766,628, respectively. These increases equal 5% and 1%, respectively, of 76,662,812 shares, the total outstanding shares of the Company’s common stock as of December 31, 2013. This automatic increase was effective as of January 1, 2014. Shares available for issuance under the Equity Plan and ESPP were initially registered on a registration statement on Form S-8 filed with the Securities and Exchange Commission on October 1, 2010 (Registration No. 333-169715). The Company filed registration statements on Form S-8 on April 14, 2014 (Registration No. 333-195259) with respect to the shares added by the automatic increase on January 1, 2014.

Common Stock

As of June 30, 2014, the Company was authorized to issue 300,000,000 shares of common stock pursuant to the Company’s amended and restated certificate of incorporation. Holders of the Company’s common stock are entitled to dividends as and when declared by the Board, subject to the rights of holders of all classes of stock outstanding having priority rights as to dividends. There have been no dividends declared to date. The holder of each share of common stock is entitled to one vote.

Preferred Stock

Pursuant to the Company’s amended and restated certificate of incorporation, the Company is authorized to issue 5,000,000 shares of preferred stock. The Board has the authority, without action by its stockholders, to designate and issue shares of preferred stock in one or more series and to fix the rights, preferences, privileges and restrictions thereof. As of June 30, 2014 and December 31, 2013, the Company had no convertible preferred stock outstanding.

Common Stock Warrants

In December 2011, in connection with a capital lease agreement, the Company issued warrants to purchase 21,087 shares of the Company's common stock at an exercise price of $10.67 per share. The Company estimated the fair value of these warrants as of the issuance date to be $0.2 million and recorded these warrants as other assets, amortizing them subsequently over the term of the lease. The fair value was based on the contractual term of the warrants of 10 years, risk free interest rate of 2%, expected volatility of 86% and zero expected dividend yield. These warrants remain unexercised and outstanding as of June 30, 2014.

In October 2013, in connection with the issuance of the Temasek Tranche I Notes (see Note 5, "Debt"), the Company issued contingently exercisable warrants to purchase 1,000,000 shares of the Company's common stock at an exercise price of $0.01 per share. The Company estimated the fair value of these warrants as of the issuance date at $1.3 million and recorded these warrants as debt issuance cost to be amortized over the term of the note. The fair-value was calculated using a Monte Carlo simulation valuation model based on the contractual term of the warrants of 3.4 years, risk free interest rate of 0.77%, expected volatility of 45% and zero expected dividend yield. These warrants remain unexercised and outstanding as of June 30, 2014.

Each of these warrants includes a cashless exercise provision which permits the holder of the warrant to elect to exercise the warrant without paying the cash exercise price, and receive a number of shares determined by multiplying (i) the number of shares for which the warrant is being exercised by (ii) the difference between the fair market value of the stock on the date of exercise and the warrant exercise price, and dividing such by (iii) the fair market value of the stock on the date of exercise. During six months ended June 30, 2014 and 2013, no warrants were exercised through the cashless exercise provision.

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11. Stock-Based Compensation

The Company’s stock option activity and related information for the six months ended June 30, 2014 was as follows:

		Number Outstanding		Weighted- Average Exercise Price		Weighted-Average Remaining Contractual Life (Years)	Aggregate Intrinsic Value
							(in thousands)
Outstanding - December 31, 2013		8,409,605		$	7.39	7.40	$	12,393
	Options granted	2,909,183		$	3.51
	Options exercised	(337,110	)	$	3.06
	Options cancelled	(485,971	)	$	7.09
Outstanding - June 30, 2014		10,495,707		$	6.47	7.72	$	3,709
Vested and Expected to vest after June 30, 2014		9,590,575		$	6.72	7.58	$	3,326
Exercisable at June 30, 2014		4,554,010		$	9.29	6.13	$	1,027

The aggregate intrinsic value of options exercised under all option plans was $33,000 and $0.1 million for the three months ended June 30, 2014 and 2013, respectively, and was $0.5 million and $0.3 million for the six months ended June 30, 2014 and 2013, respectively, determined as of the date of option exercise.

The Company’s restricted stock units (or RSUs) and restricted stock activity and related information for the six months ended June 30, 2014 was as follows:

	RSUs		Weighted-Average Grant-Date Fair Value		Weighted Average Remaining Contractual Life (Years)
Outstanding - December 31, 2013	2,316,437		$	4.30	0.88
Awarded	1,049,300		$	3.51	—
Vested	(1,158,585	)	$	4.68	—
Forfeited	(98,863	)	$	3.17	—
Outstanding - June 30, 2014	2,108,289		$	3.75	1.39
Expected to vest after June 30, 2014	1,803,053		$	3.75	1.31

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The following table summarizes information about stock options outstanding as of June 30, 2014:

	Options Outstanding				Options Exercisable
Exercise Price	Number of Options	Weighted- Average Remaining Contractual Life (Years)	Weighted-Average Exercise Price		Number of Options	Weighted-Average Exercise Price
$0.10—$2.79	1,580,682	8.20	$	2.66	476,896	$	2.52
$2.81—$2.94	1,056,600	8.94	$	2.88	279,097	$	2.87
$2.96—$3.44	945,057	8.55	$	3.14	304,429	$	3.07
$3.51—$3.51	2,489,199	9.75	$	3.51	—	$	—
$3.55—$3.93	1,700,908	5.75	$	3.88	1,247,160	$	3.89
$4.06—$16.00	1,555,854	5.94	$	10.11	1,281,705	$	9.88
$16.50—$24.50	724,345	5.97	$	20.10	625,057	$	20.11
$25.43—$25.43	15,000	7.07	$	25.43	15,000	$	25.43
$26.84—$26.84	368,062	6.64	$	26.84	264,666	$	26.84
$30.17—$30.17	60,000	6.71	$	30.17	60,000	$	30.17
$0.10—$30.17	10,495,707	7.72	$	6.47	4,554,010	$	9.29

Stock-Based Compensation Expense

Stock-based compensation expense related to options and restricted stock units granted to employees and nonemployees was allocated to research and development expense and sales, general and administrative expense as follows (in thousands):

	Three Months Ended June 30,				Six Months Ended June 30,
	2014		2013		2014		2013
Research and development	$	909	$	1,049	$	1,707	$	2,296
Sales, general and administrative	2,774		3,936		5,490		6,882
Total stock-based compensation expense	$	3,683	$	4,985	$	7,197	$	9,178

As of June 30, 2014, there was unrecognized compensation expense of $15.0 million related to stock options, and the Company expects to recognize this expense over a weighted average period of 2.93 years. As of June 30, 2014, there was unrecognized compensation expense of $4.9 million related to RSUs, and the Company expects to recognize this expense over a weighted average period of 2.07 years.

Stock-based compensation expense for RSUs is measured based on the closing fair market value of the Company's common stock on the date of grant. Stock-based compensation expense for stock options and employee stock purchase plan rights is estimated at the grant date and offering date, respectively, based on the fair-value using the Black-Scholes option pricing model. The fair value of employee stock options is being amortized on a straight-line basis over the requisite service period of the awards. The fair value of employee stock options was estimated using the following weighted-average assumptions:

	Three Months Ended June 30,				Six Months Ended June 30,
	2014		2013		2014		2013
Expected dividend yield	—	%	—	%	—	%	—	%
Risk-free interest rate	2	%	1	%	2	%	1	%
Expected term (in years)	6.09		6.10		6.10		6.10
Expected volatility	75	%	82	%	75	%	82	%

Expected Dividend Yield—The Company has never paid dividends and does not expect to pay dividends.

Risk-Free Interest Rate—The risk-free interest rate was based on the market yield currently available on United States Treasury securities with maturities approximately equal to the option’s expected term.

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Expected Term—Expected term represents the period that the Company’s stock-based awards are expected to be outstanding. The Company’s assumptions about the expected term have been based on that of companies that have similar industry, life cycle, revenue, and market capitalization and the historical data on employee exercises.

Expected Volatility—The expected volatility is based on a combination of historical volatility for the Company's stock and the historical stock volatilities of several of the Company’s publicly listed comparable companies over a period equal to the expected terms of the options, as the Company does not have a long trading history.

Forfeiture Rate—The Company estimates its forfeiture rate based on an analysis of its actual forfeitures and will continue to evaluate the adequacy of the forfeiture rate based on actual forfeiture experience, analysis of employee turnover behavior, and other factors. The impact from a forfeiture rate adjustment will be recognized in full in the period of adjustment, and if the actual number of future forfeitures differs from that estimated by the Company, the Company may be required to record adjustments to stock-based compensation expense in future periods.

Each of the inputs discussed above is subjective and generally requires significant management and director judgment.

Nonemployee Stock–Based Compensation

During the three months ended June 30, 2014 and 2013, there were no options granted to nonemployees, and for each of the six months ended June 30, 2014 and 2013, the Company granted options to purchase 20,000 shares of its common stock, respectively, to nonemployees in exchange for services. Compensation expense of $0.1 million and $8,000 was recorded for the three months ended June 30, 2014 and 2013, respectively, and $0.1 million and $22,000 was recorded for the six months ended June 30, 2014 and 2013, respectively, for stock-based options granted to nonemployees. The nonemployee options were valued using the Black-Scholes option pricing model.

During the three and six months ended June 30, 2014 and 2013, no restricted stock units, were granted to nonemployees. Stock-based compensation expense of $12,000 and $15,000 was recorded by the Company for the three months ended June 30, 2014 and 2013, respectively, and $9,000 and $39,000 for the six months ended June 30, 2014 and 2013, respectively, for the restricted stocks granted to nonemployees.

The fair value of nonemployee stock options was estimated using the following weighted-average assumptions:

	Three Months Ended June 30,				Six Months Ended June 30,
	2014		2013		2014		2013
Expected dividend yield	—	%	—	%	—	%	—	%
Risk-free interest rate	2	%	2	%	2	%	2	%
Expected term (in years)	5.80		6.10		5.94		6.40
Expected volatility	75	%	82	%	76	%	83	%

12. Employee Benefit Plan

The Company established a 401(k) Plan to provide tax deferred salary deductions for all eligible employees. Participants may make voluntary contributions to the 401(k) Plan up to 90% of their eligible compensation, limited by certain Internal Revenue Service (referred to as the "IRS") restrictions. Effective January 2014, the Company implemented a discretionary employer match plan whereby the Company will match employee contributions up to the IRS limit or 90% of compensation, with a minimum one year of service required for vesting. The total matching amount for the three and six months ended June 30, 2014 was $0.1 million and $0.2 million, respectively.

13. Related Party Transactions

Letter Agreements with Total

In March 2013 and March 2014, respectively, the Company entered into letter agreements with Total that reduced the respective conversion prices of certain convertible promissory notes issuable under the Total Purchase Agreement, as described under “Related Party Convertible Notes” in Note 5, "Debt."

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Related Party Financings

In March 2013, the Company completed a private placement of 1,533,742 shares of its common stock to an existing stockholder, Biolding Investment SA ("Biolding"), at a price of $3.26 per share for aggregate proceeds of $5.0 million. This private placement represented the final tranche of Biolding's preexisting contractual obligation to fund $15.0 million upon satisfaction by the Company of certain criteria associated with the commissioning of the Company's production plant in Brotas, Brazil.

In June 2013, the Company sold and issued a 1.5% Senior Unsecured Convertible Note to Total in the face amount of $10.0 million with a March 1, 2017 maturity date pursuant to the Total Purchase Agreement as discussed above under “Related Party Convertible Notes” in Note 5, “Debt."

In July 2013, the Company sold and issued a 1.5% Senior Unsecured Convertible Note to Total in the face amount of $20.0 million with a March 1, 2017 maturity date pursuant to the Total Purchase Agreement as discussed above under “Related Party Convertible Notes” in Note 5, “Debt."

In August 2013, the Company entered into a securities purchase agreement by and among the Company, Total and Temasek, each a beneficial owner of more than 5% of the Company's existing common stock at the time of the transaction, for a private placement of convertible promissory notes in an aggregate principal amount of $73.0 million. The initial closing of the August 2013 Financing was completed in October 2013 for the sale of approximately$42.6 million of these Tranche I Notes and the second closing of the August 2013 Financing for the sale of approximately $30.4 million of these Tranche II Notes was completed in January 2014.

In September 2013, the Company entered into a bridge loan agreement with an existing investor to provide additional cash availability of up to $5.0 million as needed before the initial closing of the August 2013 Financing. The Company did not use this facility and it expired in October 2013 in accordance with its terms.

In October 2013, the Company sold and issued a senior secured promissory note to Temasek for a bridge loan of $35.0 million. The note was due on February 2, 2014 and accrued interest at a rate of 5.5% each four months from October 4, 2013 (with a rate of 2% per month if a default occurred). The note was cancelled as payment for the investor’s purchase of Tranche I Notes in the August 2013 Financing.

In December 2013, the Company agreed to issue to Temasek $25.0 million of Tranche II Notes for cash. Total purchased approximately $6.0 million of Tranche II Notes through cancellation of the same amount of principal of previously outstanding convertible promissory notes held by Total (in respect of Total’s preexisting contractual right to maintain its pro rata ownership position through such cancellation). Such financing transactions closed in January 2014 (see Note 5, "Debt").

In December 2013, the Company agreed (i) to exchange the $69.0 million outstanding Total unsecured convertible notes and issue a replacement 1.5% senior secured convertible notes, in principal amounts equal to the principal amount of each cancelled note (see Note 5, "Debt") and (ii) that all notes issued in connection with a third closing under the Total Purchase Agreement will be senior secured convertible notes instead of senior unsecured convertible notes (see Note 5, "Debt").

In May 2014, the Company sold and issued 144A Notes pursuant to the Rule 144A Convertible Note Offering. In connection with obtaining a waiver from one of its existing investors, Total, of its preexisting contractual right to exchange certain senior secured convertible notes previously issued by Amyris for new notes issued in the Rule 144A Convertible Note Offering, Amyris used approximately $9.7 million of the net proceeds of the Rule 144A Convertible Note Offering to repay such amount of previously issued notes (representing the amount of notes purchased by Total from the Initial Purchaser under the Rule 144A Convertible Note Offering). Additionally, Foris Ventures, LLC (a fund affiliated with John Doerr) and Temasek each participated in the Rule 144A Convertible Note Offering and purchased $5.0 million and $10.0 million, respectively, of the convertible promissory notes sold thereunder (see Note 5, “Debt").

As of June 30, 2014 and December 31, 2013, convertible notes with related parties were outstanding in aggregate principal of $100.5 million and $89.5 million, respectively, net of debt discount of $55.3 million and $23.9 million, respectively. The Company recorded a loss from extinguishment of debt from the settlement, exchange and cancellation of related party convertible notes for the three months ended June 30, 2014 and 2013, of $1.1 million and zero, respectively, and $10.5 million and zero for the six months ended June 30, 2014 and 2013, respectively (see Note 5, "Debt").

The fair value of the derivative liability related to the related party convertible notes as of June 30, 2014 and December 31, 2013 is $107.2 million and $116.8 million, respectively. The Company recognized for the three months ended June 30, 2014 and

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2013, a $4.0 million loss from change in fair value of the derivative instruments and $1.4 million gain from change in fair value of the derivative instruments, respectively, and $53.1 million and $2.5 million gain from change in fair value of the derivative instruments for the six months ended June 30, 2014 and 2013, respectively, related to these derivative liabilities (see Note 3, "Fair Value of Financial Instruments").

Related Party Revenue

The Company recognized related party revenue from Novvi of zero and $0.3 million for the three months ended June 30, 2014 and 2013, respectively, and zero and $2.8 million for the six months ended June 30, 2014 and 2013, respectively, from the research and development activities that it has performed on behalf of Novvi. The related party accounts receivables from Novvi as of June 30, 2014 and December 31, 2013, was $20,604 and $0.3 million, respectively.

The Company recognized related party revenue from Total of $30,625 and $32,441 for the three months ended June 30, 2014 and 2013, respectively, and $33,250 and $35,294 for the six months ended June 30, 2014 and 2013, respectively, from product sales. The related party accounts receivables from Total as of June 30, 2014 and December 31, 2013, was $30,625 and $0.2 million, respectively.

Joint Venture

In November 2013, the Company and Total formed JVCO as discussed above under “Joint Venture and Noncontrolling Interest” in Note 7.

Pilot Plant Agreements

In May 2014, the Company received the final consents necessary for the Pilot Plant Services Agreement ("Pilot Plant Services Agreement") and a Sublease Agreement (the "Sublease Agreement"), each dated as of April 4, 2014 (collectively the “Pilot Plant Agreements”), between the Company and Total for a term of 5 years. Under the terms of the Pilot Plant Services Agreement, the Company will provide certain fermentation and downstream separations scale-up services and training to Total and will receive an aggregate annual fee payable by Total for all services in the amount of up to approximately $0.9 million. Under the Sublease Agreement, the Company will receive an annual base rent payable by Total of approximately $0.1 million. As of June 30, 2014, the Company received $0.3 million in cash under the Pilot Plant Agreements from Total which was recorded as "Other Current Liability" on the condensed consolidated balance sheet.

14. Income Taxes

For the three months ended June 30, 2014 and 2013, the Company recorded a provision for income taxes of $0.1 million and $0.2 million, respectively, and $0.2 million and $0.5 million for the six months ended June 30, 2014 and 2013, respectively. The provision for income taxes for the six months ended June 30, 2014 and 2013 consisted of an accrual of Brazilian withholding tax on intercompany interest liability. Other than the above mentioned provision for income tax, no additional provision for income taxes has been made, net of the valuation allowance, due to cumulative losses since the commencement of operations.

As of June 30, 2014, the US Internal Revenue Service (the "IRS") has completed its audit of the Company for tax year 2008 which concluded that there were no adjustments resulting from the audit. While the statutes are closed for tax year 2008, the US federal tax carryforwards (net operating losses and tax credits) may be adjusted by the IRS in the year in which the carryforward is utilized.

15. Reporting Segments

The chief operating decision maker for the Company is the chief executive officer. The chief executive officer reviews financial information presented on a consolidated basis, accompanied by information about revenue by geographic region, for purposes of allocating resources and evaluating financial performance. The Company has one business activity comprised of research and development and sales of fuels and farnesene-derived products and there are no segment managers who are held accountable for operations, operating results or plans for levels or components below the consolidated unit level. Accordingly, the Company has determined that it has a single reportable segment and operating segment structure.

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Revenues by geography are based on the location of the customer. The following tables set forth revenue and long-lived assets by geographic area (in thousands):

Revenues

	Three Months Ended June 30,				Six Months Ended June 30,
	2014		2013		2014		2013
United States	$	2,815	$	4,458	$	4,788	$	10,022
Brazil	1,402		1,259		2,050		2,077
Europe	2,985		4,005		6,338		4,230
Asia	2,105		1,127		2,172		2,389
Total	$	9,307	$	10,849	$	15,348	$	18,718

Long-Lived Assets

	June 30, 2014		December 31, 2013
United States	$	49,628	$	54,015
Brazil	90,375		85,891
Europe	653		685
Total	$	140,656	$	140,591

16. Comprehensive Income (Loss)

Comprehensive income (loss) represents all changes in stockholders’ equity (deficit) except those resulting from investments or contributions by stockholders. The Company’s foreign currency translation adjustments represent the components of comprehensive income (loss) excluded from the Company’s net loss and have been disclosed in the condensed consolidated statements of comprehensive loss for all periods presented.

The components of accumulated other comprehensive loss are as follows (in thousands):

	June 30, 2014			December 31, 2013
Foreign currency translation adjustment, net of tax	$	(15,634	)	$	(20,087	)
Total accumulated other comprehensive loss	$	(15,634	)	$	(20,087	)

17. Net Income (Loss) Attributable to Common Stockholders and Net Income (Loss) per Share

The Company computes net income (loss) per share in accordance with ASC 260, “Earnings per Share.” Basic net income (loss) per share of common stock is computed by dividing the Company’s net income (loss) attributable to Amyris, Inc. common stockholders by the weighted average number of shares of common stock outstanding during the period. Diluted net income (loss) per share of common stock is computed by giving effect to all potentially dilutive securities, including stock options, restricted stock units, common stock warrants, convertible promissory notes using the treasury stock method or the as converted method, as applicable. For the three months ended June 2014 and 2013 and for the six months ended June 30, 2013, basic net loss per share was the same as diluted net loss per share because the inclusion of all potentially dilutive securities outstanding was anti-dilutive. As such, the numerator and the denominator used in computing both basic and diluted net loss are the same.

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The following table presents the calculation of basic and diluted net loss per share of common stock attributable to Amyris, Inc. common stockholders (in thousands, except share and per share amounts):

	Three Months Ended June 30,						Six Months Ended June 30,
	2014			2013			2014			2013
Numerator:
Net loss attributable to Amyris, Inc. common stockholders	$	(35,479	)	$	(38,876	)	$	(19,094	)	$	(71,490	)
Interest on convertible debt	—			—			3,169			—
Accretion of debt discount	—			—			2,518			—
Gain from change in fair value of derivative instruments	—			—			(59,995		)	—
Net loss attributable to Amyris, Inc. common stockholders after assumed conversion	$	(35,479	)	$	(38,876	)	$	(73,402	)	$	(71,490	)
Denominator:
Weighted average shares of common stock outstanding for basic EPS	78,604,692			75,959,228			77,722,437			74,640,314
Basic loss per share	$	(0.45	)	$	(0.51	)	$	(0.25	)	$	(0.96	)
Weighted average shares of common stock outstanding	78,604,692			75,959,228			77,722,437			74,640,314
Effect of dilutive securities:
Convertible promissory notes	—			—			32,909,641			—
Weighted common stock equivalents	—			—			32,909,641			—
Diluted weighted-average common shares	78,604,692			75,959,228			110,632,078			74,640,314
Diluted loss per share	$	(0.45	)	$	(0.51	)	$	(0.66	)	$	(0.96	)

The following outstanding shares of potentially dilutive securities were excluded from the computation of diluted net loss per share of common stock because including them would have been anti-dilutive:

	Three Months Ended June 30,		Six Months Ended June 30,
	2014	2013	2014	2013
Period-end stock options to purchase common stock	10,495,707	8,803,300	10,495,707	8,803,300
Convertible promissory notes	69,727,211	13,617,144	36,643,102	13,617,144
Period-end common stock subject to repurchase	—	1	—	1
Period-end common stock warrants	1,021,087	21,087	1,021,087	21,087
Period-end restricted stock units	2,108,289	2,770,516	2,108,289	2,770,516
Total	83,352,294	25,212,048	50,268,185	25,212,048

18. Subsequent Events

In July 2014, the Company closed on the initial installment of the remaining $21.7 million in convertible notes to be issued to Total under the July 2012 Agreements as described in in Note 5, "Debt", in the amount of $10.85 million and expect the second installment to occur by January 2015.

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ITEM 2. MANAGEMENT’S DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION AND RESULTS OF OPERATIONS

Forward-Looking Statements

The following discussion and analysis should be read in conjunction with our condensed consolidated financial statements and the related notes that appear elsewhere in this Form 10-Q. These discussions contain forward-looking statements reflecting our current expectations that involve risks and uncertainties which are subject to safe harbors under the Securities Act of 1933, as amended, or the Securities Act, and the Securities Exchange Act of 1934, as amended, or the Exchange Act. These forward looking statements include, but are not limited to, statements concerning our strategy of achieving a significant reduction in net cash outflows in 2014, future production capacity and other aspects of our future operations, ability to improve our production efficiencies, future financial position, future revenues, projected costs, expectations regarding demand and acceptance for our technologies, growth opportunities and trends in the market in which we operate, prospects and plans and objectives of management. The words “anticipates,” “believes,” “estimates,” “expects,” “intends,” “may,” “plans,” “projects,” “will,” “would” and similar expressions are intended to identify forward-looking statements, although not all forward-looking statements contain these identifying words. We may not actually achieve the plans, intentions or expectations disclosed in our forward-looking statements and you should not place undue reliance on our forward looking statements. These forward-looking statements involve risks and uncertainties that could cause our actual results to differ materially from those in the forward-looking statements, including, without limitation, the risks set forth in Part II, Item 1A, “Risk Factors,” in this Quarterly Report on Form 10-Q and in our other filings with the Securities and Exchange Commission. We do not assume any obligation to update any forward-looking statements.

Trademarks

Amyris®, the Amyris logo, Biofene® and No Compromise® are trademarks or registered trademarks of Amyris, Inc. This report also contains trademarks and trade names of other businesses that are the property of their respective holders.

Overview

Amyris, Inc. (referred to as the Company, Amyris, we, us, or our) is a renewable products company focused on providing sustainable alternatives to a broad range of petroleum-sourced products. We developed innovative microbial engineering and screening technologies that modify the way microorganisms process sugars. We are using our proprietary industrial bioscience technology to design microbes, primarily yeast, and use them as living factories in established fermentation processes to convert plant-sourced sugars into renewable hydrocarbons. We are developing, and, in some cases, already commercializing, products from these hydrocarbons in several target industry sectors, including cosmetics, lubricants, flavors and fragrances, performance materials, and transportation fuels. We call these No Compromise products because we design them to perform comparably to or better than currently available products.

We have been applying our industrial bioscience technology platform to provide alternatives to a broad range of petroleum-sourced products. We have focused our development efforts on the production of Biofene, our brand of renewable farnesene, a long-chain, branched liquid hydrocarbon molecule. Using Biofene as a first commercial building block molecule, we are developing a wide range of renewable products for our target markets.

While our platform is able to utilize a wide variety of feedstocks, we are focusing our large-scale production plans primarily on the use of Brazilian sugarcane as our feedstock because of its abundance, low cost and relative price stability. We have also been able to produce Biofene through the use of other feedstocks such as sugar beets, corn dextrose, sweet sorghum and cellulosic sugars.

Our first purpose-built, large-scale Biofene production plant commenced operations in southeastern Brazil in December 2012. This plant is located in Brotas, in the state of São Paulo, Brazil, and is adjacent to an existing sugar and ethanol mill, Paraíso Bioenergia. We have also advanced initial construction of a second large-scale production plant in Brazil, located at the SMSA sugar and ethanol mill also in the state of São Paulo, Brazil, for which we intend to complete the construction when market developments support the start-up of that plant.

Our business strategy is focused on our commercialization efforts of specialty products while moving commodity products, including our fuels and base oil lubricants products, into joint venture arrangements with established industry leaders. We believe this approach will permit access to the capital and resources necessary to support large-scale production and global distribution for our products. Our initial renewable products efforts have been focused on cosmetics, niche fuel opportunities, fragrance oils, and performance materials sector.

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Total Relationship

In July 2012 and December 2013, we entered into a series of agreements to establish a research and development program and form a joint venture with Total Energies Nouvelles Activités USA (formerly known as Total Gas & Power USA, SAS, and referred to as Total) to produce and commercialize Biofene-based diesel and jet fuels, and successfully formed such joint venture in December 2013. With an exception for our fuels business in Brazil, the collaboration and joint venture established the exclusive means for us to develop, produce and commercialize fuels from Biofene. We granted the joint venture exclusive licenses under certain of our intellectual property to make and sell joint venture products. We also granted the joint venture, in the event of a buy-out of our interest in the joint venture by Total (which Total is entitled to do under certain circumstances described below), a non-exclusive license to optimize or engineer yeast strains used by us to produce farnesene for the joint venture’s diesel and jet fuels. As a result of these licenses, Amyris generally no longer has an independent right to make or sell Biofene fuels outside of Brazil without the approval of Total.

Our agreements with Total relating to our fuels collaboration created a convertible debt financing structure for funding the research and development program. The collaboration agreements contemplated approximately $105.0 million in financing for the collaboration, of which Total has funded approximately $94.2 million to date. Total is committed to fund the remaining $10.85 million by January 2015. If Total chooses not to continue participating at certain "Go/No-Go" decision points during the program, licenses to our technology would terminate, and the notes would remain outstanding and become payable at maturity unless otherwise converted in accordance with their terms. If Total chooses to continue the collaboration and makes a final decision to proceed with the joint venture only for jet fuel, Total is required to buy from Amyris 50% of the preferred shares of the joint venture in exchanges for the settlement of 30% of the principal and interest outstanding under the notes. The remaining notes would continue to be outstanding and payable upon maturity unless otherwise converted in accordance with the terms of the notes.

In April 2014, we and Total entered into a letter agreement dated as of March 29, 2014 (referred to as the "March 2014 Letter Agreement") to amend the Amended and Restated Master Framework Agreement entered into as of December 2, 2013 (included as part of documents entered into in connection with the Total joint venture). Under the March 2014 Letter Agreement, we agreed to (i) amend the conversion price of the remaining $21.7 million of convertible notes from $7.0682 to $4.11 (of which $10.85 million was funded in July 2014), (ii) extend the period during which Total may exchange for other Amyris securities certain outstanding convertible promissory notes issued under the July 2012 purchase agreement that we entered into with Total from June 30, 2014 to the later of December 31, 2014 and the date on which we shall have raised $75.0 million of equity and convertible debt financing (excluding any convertible promissory notes issued pursuant to the Total Purchase Agreement), (iii) eliminate our ability to qualify, in a disclosure letter to Total, certain of the representations and warranties that we must make at the third closing of any sale thereunder, and (iv) provide Total with monthly reporting on our cash, cash equivalents and short-term investments. In consideration of these agreements, Total agreed to waive its right not to consummate the closing of the issuance of the third closing notes if it decides not to proceed with the collaboration and makes a "No-Go" decision with respect thereto, subject to us obtaining stockholder approval of the issuance of the of securities at a third closing sale at the New Conversion Price.

Sales and Revenue

To commercialize our initial Biofene-derived product, squalane, in the cosmetics sector for use as an emollient, we have entered into certain marketing and distribution agreements in Europe, Asia, and North America. As an initial step towards commercialization of Biofene-based diesel, we have entered into agreements with municipal fleet operators in Brazil. Our diesel fuel is supplied to the largest Company in Brazil's fuel distribution segment which blends our product with petroleum diesel and sells to a number of bus fleet operators. Pursuant to our agreements with Total, future commercialization of our diesel and jet fuel products outside of Brazil would generally occur exclusively through JVCO. For the industrial lubricants market, we established a joint venture with Cosan for the worldwide development, production and commercialization of renewable base oils in the lubricant sector. In the second half of 2014, we expect to generate sales and revenue from our fragrance oils currently being produced at our Brotas facility in Brazil.

Financing

In 2013 through the second quarter of 2014, we completed multiple financings involving loans, convertible debt and equity offerings. We completed private placements of 6,567,299 shares of common stock in 2013 for aggregate proceeds of $20.0 million, of which $15.0 million was from the receipt of funds from a private placement that closed in December 2012. We raised $72.6 million in 2013 from an offering of senior unsecured convertible promissory notes pursuant to the August 2013 Financing and research and development funding from Total.

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In December 2012, we completed a private placement of 14,177,849 shares of common stock for aggregate proceeds of $37.2 million and the cancellation of $5.0 million worth of outstanding senior unsecured convertible promissory notes we previously issued to Total in exchange for approximately 1,677,852 shares of common stock. Under the December 2012 purchase agreement and related documents, the purchase of a portion of the shares, representing $15.0 million of the proceeds from that transaction, was settled in January 2013. Cash received as of December 31, 2012 in the December 2012 financing, net of the note conversion and the January 2013 settlement, was $22.2 million. In January 2013, we received the $15.0 million proceeds from the private placement offering that closed in December 2012. Consequently we issued 5,033,557 shares of the 14,177,849 shares of Amyris's common stock issuable pursuant to such private placement.

In March 2013, we completed a private placement of 1,533,742 of our common stock to Biolding Investment SA ("Biolding")for aggregate proceeds of $5.0 million. This private placement represented the final tranche of Biolding's preexisting contractual obligation to fund $15.0 million upon satisfaction by us of certain criteria associated with the commissioning of our production plant in Brotas, Brazil.

In March 2013, we entered into a letter agreement with Total (referred to as the "March 2013 Letter Agreement"). Under the March 2013 Letter Agreement, we sold and issued a $10.0 million senior unsecured convertible note to Total with an initial conversion price of $3.08 per share in June 2013. Subsequently, in July 2013, we sold and issued a $20.0 million senior unsecured convertible note to Total with the same initial conversion price of $3.08 per share as the note sold in June 2013. The July 2013 purchase and sale completed Total's commitment to purchase $30.0 million of such notes by July 2013. In April 2014, we entered into the March 2014 Letter Agreement. Under the March 2014 Letter Agreement, we agreed to sell and issue $21.7 million in senior unsecured convertible note to Total with an initial conversion price of $4.11 per share in a third closing to occur in two installments ($10.85 million was sold and issued in July 2014 and the second installment is to be sold and issued In January 2015). The January 2015 installment will complete Total's commitment to purchase $21.7 million of such notes by that date.

In October 2013, we completed an additional private placement of convertible promissory notes in the August 2013 Financing as described in more detail below under "Liquidity and Capital Resources."

In December 2013, we agreed to complete an additional private placement of a portion of the second tranche of convertible promissory notes in the August 2013 Financing as described in more detail below under "Liquidity and Capital Resources." On January 15, 2014, we completed the offering of convertible promissory notes in the second tranche of the August 2013 Financing.

In March 2014, we and Kuraray Co., Ltd. (or "Kuraray") entered into a securities purchase agreement under which we agreed to sell shares of our common stock at a price equal to the greater of $2.88 per share or the average daily closing prices per share on the NASDAQ Stock Market for the three month period ending March 27, 2014, for an aggregate purchase price of $4.0 million. On April 14, 2014, we completed the sale of common stock to Kuraray and issued 943,396 shares of our common stock at a price per share of $4.24 for aggregate proceeds of approximately $4.0 million.

In June 2014, we and Hercules Technology Growth Capital, Inc. (referred to as “Hercules”) entered into a first amendment (referred to as the "Hercules Amendment") of the Loan and Security Agreement entered into on March 29, 2014 (as amended, the "Hercules Loan Facility") under which we have received from Hercules, in two tranches, secured debt in the aggregate amount of $30.0 million. The Hercules Loan Facility is described in more detail below under "Liquidity and Capital Resources."

In May 2014, we sold and issued $75.0 million aggregate principal amount of 6.50% Convertible Senior Notes due 2019 to Morgan Stanley & Co. LLC as the initial purchaser (the "Initial Purchaser") in a private placement, and for initial resale by the Initial Purchaser to qualified institutional buyers pursuant to Rule 144A of the Securities Act int the rule 144A Convertible Note Offering. The Rule 144A Convertible Note Offering is described in more detail below under "Liquidity and Capital Resources."

In July 2014, we closed on the initial installment of the $21.7 million in convertible notes from Total under the July 2012 Agreements as described in more detail in Note 5, "Debt", in the amount of $10.85 million and expect the second installment to occur within six months of such initial installment.

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Liquidity

We have incurred significant losses since our inception and believe that we will continue to incur losses and negative cash flow from operations through at least 2014. As of June 30, 2014, we had an accumulated deficit of $840.5 million and had cash, cash equivalents and short term investments of $90.2 million. We have significant outstanding debt and contractual obligations related to purchase commitments, as well as capital and operating leases. As of June 30, 2014, our debt, net of discount of $83.9 million, totaled $222.4 million, of which $9.9 million matures within the next twelve months. Additionally, our debt agreements contain various covenants, including restrictions on business that could cause us to be at risk of defaults.

In addition to cash contributions from product sales and debt and equity financings, we also depend on collaboration funding to support our operating expenses. While part of this funding is committed based on existing collaboration agreements, we will need to identify and obtain funding under additional collaborations that are not yet subject to any definitive agreement or are not yet identified. In addition, some of our existing anticipated collaboration funding is subject to our achievement of milestones or other funding conditions. If we are unable to raise additional financing, or if other expected sources of funding are delayed or not received, we would take actions to support our liquidity needs that could have a material negative impact on our ability to continue our business as currently contemplated. See “Liquidity and Capital Resources” below in this section for additional detail regarding these contingency plans and their potential effects on our business.

Results of Operations

Comparison of Three Months Ended June 30, 2014 and 2013

Revenues

	Three Months Ended June 30,				Year-to  Year Change			Percentage Change
	2014		2013
	(Dollars in thousands)
Revenues
Renewable product sales	$	4,379	$	4,011	$	368		9%
Related party renewable product sales	31		174		(143		)	(82)%
Total product sales	4,410		4,185		225			5%
Grants and collaborations revenue	4,897		6,555		(1,658		)	(25)%
Related party grants and collaborations revenue	—		109		(109		)	(100)%
Total grants and collaborations revenue	4,897		6,664		(1,767		)	(27)%
Total revenues	$	9,307	$	10,849	$	(1,542	)	(14)%

Our total revenues decreased by $1.5 million to $9.3 million for the three months ended June 30, 2014 as compared to the same period in the prior year due to decreased revenues from grants and collaborations.

Product sales increased by $0.2 million to $4.4 million for the three months ended June 30, 2014 resulting primarily from an increase in squalane sales to existing and new customers compared to the same period in the prior year.

Grants and collaborations revenue decreased by $1.8 million to $4.9 million for the three months ended June 30, 2014 with such reduction resulting from a decrease of $0.8 million in government grant revenue from the National Renewable Energy Lab as a result of the project being completed during 2013 and the decrease in government grant revenue of $1.4 million under the DARPA Technology Investment Agreement with the Defense Advanced Research Projects Agency (referred to as “DARPA”) resulting mainly from the timing of the project's revenue milestones, partially offset by $0.3 million from the subcontract with Lawrence Berkeley National Laboratory.

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Cost and Operating Expenses

	Three Months Ended June 30,				Year-to  Year Change			Percentage Change
	2014		2013
	(Dollars in thousands)
Cost of products sold	$	7,511	$	8,853	$	(1,342	)	(15)%
Loss on purchase commitments and write-off of production assets	52		8,423		(8,371		)	(99)%
Research and development	12,175		13,992		(1,817		)	(13)%
Sales, general and administrative	13,971		14,718		(747		)	(5)%
Total cost and operating expenses	$	33,709	$	45,986	$	(12,277	)	(27)%

Cost of Products Sold

Our cost of products sold includes cost of raw materials, labor and overhead, amounts paid to contract manufacturers, period costs related to inventory write-downs resulting from applying lower of cost or market inventory valuations, and costs related to scale-up in production of such products. Our cost of products sold decreased by $1.3 million to $7.5 million for the three months ended June 30, 2014 as compared to the same period in prior year due to lower cost of production as a result of higher production volumes and overall manufacturing cost reduction efforts.

Loss on Purchase Commitments and Write Off of Production Assets

Our loss on purchase commitments and write off of production assets decreased by $8.4 million to $0.1 million for the three months ended June 30, 2014, mainly due to the loss related to the termination and settlement in 2013 of our existing agreement with Tate & Lyle, one of our contract manufacturers.

Research and Development Expenses

Our research and development expenses decreased by $1.8 million to $12.2 million for the three months ended June 30, 2014 compared to the same period in the prior year primarily as a result of our overall cost reduction efforts and lower spending to manage our operating costs. The decrease is attributable to a $0.6 million reduction in personnel-related expenses and lower stock-based compensation expenses due to lower headcount, a $0.6 million reduction in other overhead expenses, a $0.3 million reduction in lab supplies and product testing and a $0.3 million decrease in depreciation due to equipment disposal and fully depreciated assets. Research and development expenses included stock-based compensation expense of $0.9 million and $1.0 million during the three months ended June 30, 2014 and 2013, respectively.

Sales, General and Administrative Expenses

Our sales, general and administrative expenses decreased by $0.7 million to $14.0 million for the three months ended June 30, 2014 compared to the same period in the prior year primarily as a result of our overall cost reduction efforts and lower spending to manage our operating costs. The decrease is attributable to reduction in personnel-related expenses and lower stock-based compensation expenses due to lower headcount. Sales, general and administrative expenses included stock-based compensation expense of $2.8 million and $3.9 million during the three months ended June 30, 2014 and 2013, respectively.

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Other Income (Expense)

	Three Months Ended June 30,						Year-to  Year Change			Percentage Change
	2014			2013
	(Dollars in thousands)
Other income (expense):
Interest income	$	148		$	57		$	91		160%
Interest expense	(6,802		)	(1,558		)	(5,244		)	337%
Gain (loss) from change in fair value of derivative instruments	(3,252		)	(254		)	(2,998		)	1,180%
Income (loss) from extinguishment of debt	(1,082		)	—			(1,082		)	nm
Other income (expense), net	5			(1,776		)	1,781			(100)%
Total other expense	$	(10,983	)	$	(3,531	)	$	(7,452	)	211%

______________ 

nm= not meaningful

Total other expense increased by $7.5 million to $11.0 million for the three months ended June 30, 2014 compared to the same period in prior year. The increase was primarily attributable to an increase in interest expense of $5.2 million associated with our increased borrowings, an increase in loss from change in fair value of derivative instruments of $3.0 million due to a change in the fair value of our compound embedded derivative liability associated with our senior secured promissory notes as a result of the changes in the inputs used in the valuation models from one reporting period to another, such as stock price, credit risk rate and estimated stock volatility and the change in fair value of our interest rate swap derivative liability and a $1.1 million loss from extinguishment of debt from the settlement of Total convertible notes in connection with the Rule 144A Convertible Note Offering as described above under Overview. The increase was offset by $1.8 million decrease in other expense, net primarily due to an increase in realized gain on foreign currency transactions.

Comparison of Six Months Ended June  30, 2014 and 2013

Revenues

	Six Months Ended June 30,				Year-to  Year Change			Percentage Change
	2014		2013
	(Dollars in thousands)
Revenues
Renewable product sales	$	7,221	$	6,991	$	230		3%
Related party renewable product sales	34		177		(143		)	(81)%
Total product sales	7,255		$	7,168	87			1%
Grants and collaborations revenue	8,093		8,903		(810		)	(9)%
Related party grants and collaborations revenue	—		2,647		(2,647		)	(100)%
Total grants and collaborations revenue	8,093		11,550		(3,457		)	(30)%
Total revenues	$	15,348	$	18,718	$	(3,370	)	(18)%

Our total revenues decreased by $3.4 million to $15.3 million for the six months ended June 30, 2014 as compared to the same period in the prior year due to decreased revenues from grants and collaborations.

Product sales increased by $0.1 million to $7.3 million for the six months ended June 30, 2014 primarily from an increase in squalane sales to existing and new customers compared to the same period in the prior year.

Grants and collaborations revenue decreased by $3.5 million to $8.1 million for the six months ended June 30, 2014 with such reduction resulting from a decrease of $1.1 million in government grant revenue from the Department of Energy (referred to as "DOE"), a decrease of $1.5 million in government grant revenue from the National Renewable Energy Lab as a result of the project being completed during 2013, a decrease of $0.9 million in government grant revenue under the DARPA Technology Investment Agreement with the Defense Advanced Research Projects Agency (referred to as “DARPA”) resulting mainly from the timing of the project's revenue milestones and a decrease of $2.6 million in collaboration research services recognized for research and development activities performed on behalf of Novvi, offset by an increase of $2.4 million in collaborations revenue

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from the Master Collaboration, Joint Development and License Agreements with collaboration partners and a $0.3 million revenue from the subcontract with Lawrence Berkeley National Laboratory.

Cost and Operating Expenses

	Six Months Ended June 30,				Year-to  Year Change			Percentage Change
	2014		2013
	(Dollars in thousands)
Cost of products sold	$	13,747	$	17,813	$	(4,066	)	(23)%
Loss on purchase commitments and write-off of production assets	159		8,423		(8,264		)	(98)%
Research and development	25,161		29,746		(4,585		)	(15)%
Sales, general and administrative	27,370		29,545		(2,175		)	(7)%
Total cost and operating expenses	$	66,437	$	85,527	$	(19,090	)	(22)%

Cost of Products Sold

Our cost of products sold decreased by $4.1 million to $13.7 million for the six months ended June 30, 2014 as compared to the same period in the prior year due to lower cost of production, along with a reduction in current period lower of cost or market adjustments as a result of higher production volumes and overall manufacturing cost reduction efforts.

Loss on Purchase Commitments and Write Off of Production Assets

Our loss on purchase commitments and write off of production assets decreased by $8.3 million to $0.2 million for the six months ended June 30, 2014, mainly due to the loss related to the termination and settlement in 2013 of our existing agreement with Tate & Lyle, one of our contract manufacturers.

Research and Development Expenses

Our research and development expenses decreased by $4.6 million to $25.2 million for the six months ended June 30, 2014 compared to the same period in the prior year primarily as a result of our overall cost reduction efforts and lower spending to manage our operating costs. The decrease is attributable to a $2.5 million reduction in personnel-related expenses and lower stock-based compensation expenses due to lower headcount, a $0.9 million reduction in other overhead expenses, a $0.3 million reduction in product testing mainly due from the planned shut down of our Brotas facility for maintenance in early 2014 and $0.6 million decrease in depreciation due to equipment disposal and fully depreciated assets. Research and development expenses included stock-based compensation expense of $1.7 million and $2.3 million during the six months ended June 30, 2014 and 2013, respectively.

Sales, General and Administrative Expenses

Our sales, general and administrative expenses decreased by $2.2 million to $27.4 million for the six months ended June 30, 2014 compared to the same period in prior year primarily as a result of our overall cost reduction efforts and lower spending to manage our operating costs. The decrease is attributable to reduction in personnel-related expenses and lower stock-based compensation expenses due to lower headcount. Sales, general and administrative expenses included stock-based compensation expense of $5.5 million and $6.9 million during the six months ended June 30, 2014 and 2013, respectively.

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Other Income (Expense)

	Six Months Ended June 30,						Year-to  Year Change			Percentage Change
	2014			2013
	(Dollars in thousands)
Other income (expense):
Interest income	$	204		$	93		$	111		119%
Interest expense	(11,552		)	(3,120		)	(8,432		)	270%
Gain (loss) from change in fair value of derivative instruments	54,148			785			53,363			6,798%
Income (loss) from extinguishment of debt	(10,512		)	—			(10,512		)	nm
Other expense, net	(117		)	(1,696		)	1,579			(93)%
Total other income (expense)	$	32,171		$	(3,938	)	$	36,109		(917)%

______________ 

nm= not meaningful

Total other income increased by $36.1 million to $32.2 million for the six months ended June 30, 2014 compared to the same period in the prior year. The increase was primarily attributable to an increase in the gain from the change in fair value of derivative instruments of $53.4 million, this increase was due to a change in the fair value of our compound embedded derivative liability associated with our senior secured promissory notes as a result of the changes in the inputs used in the valuation models from one reporting period to another, such as stock price, credit risk rate and estimated stock volatility and the change in fair value of our interest rate swap derivative liability, and a $1.6 million decrease in other expense, net primarily due to an increase in realized gain on foreign currency transactions. The increase was offset by a $10.5 million loss on the extinguishment of debt related to Total’s conversion of a portion of their outstanding notes issued under the collaboration agreements with Total into the Tranche II Notes, as described below under Liquidity and Capital Resources and loss from extinguishment of Total convertible notes in connection with the Rule 144A Convertible Note Offering and an $8.4 million increase in interest expense associated with our increased borrowings to fund operations.

Liquidity and Capital Resources

	June 30, 2014			December 31, 2013
	(Dollars in thousands)
Working capital (deficit)	$	74,383		$	(382	)
Cash and cash equivalents and short-term investments	$	90,207		$	8,296
Debt and capital lease obligations	$	223,465		$	153,305
Accumulated deficit	$	(840,532	)	$	(821,438	)

	Six Months Ended June 30,
	2014			2013
	(Dollars in thousands)
Net cash used in operating activities	$	(35,827	)	$	(45,268	)
Net cash used in investing activities	$	(3,990	)	$	(5,141	)
Net cash provided by financing activities	$	122,143		$	30,023

Working Capital. Our working capital was $74.4 million at June 30, 2014, which represents an increase of $74.8 million compared to a working capital deficit of $0.4 million at December 31, 2013. The increase of $74.8 million in working capital during the six month ended June 30, 2014 was primarily due to cash provided by financing activities of $122.1 million related to the second tranche offering of convertible promissory notes of $28.0 million, draw down from the Hercules Loan Facility of $29.7 million and new 144A Convertible Note Offering amounting to $75.0 million, offset by the extinguishment of $9.7 million debt with Total. The cash provided by financing activities was offset by cash usage to fund our operating expenses and to a lesser extent, to service our other debt obligations.

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To support production of our products in contract manufacturing and dedicated production facilities, we have incurred, and we expect to continue to incur, capital expenditures as we invest in these facilities. We plan to continue to seek external debt and equity financing from U.S. and Brazilian sources to help fund our investment in these contract manufacturing and dedicated production facilities.

We expect to fund our operations for the foreseeable future with cash and investments currently on hand, with cash inflows from collaboration and grant funding, cash contributions from product sales, and with new debt and equity financings. Some of our anticipated financing sources, such as research and development collaborations and convertible debt financings, are subject to risk that we cannot meet milestones, are not yet subject to definitive agreements or mandatory funding commitments and, if needed, we may not be able to secure additional types of financing in a timely manner or on reasonable terms, if at all. Our planned 2014 working capital needs and our planned operating and capital expenditures for 2014 are dependent on significant inflows of cash from existing collaboration partners and from funds under existing convertible debt facilities, as well as additional funding from new collaborations, and may also require additional funding from debt or equity financings. We will continue to need to fund our research and development and related activities and to provide working capital to fund production, storage, distribution and other aspects of our business. Our operating plan contemplates capital expenditures of approximately $9.0 million in 2014.

Liquidity. We have incurred significant losses since our inception and believe that we will continue to incur losses and negative cash flow from operations through 2014. As of June 30, 2014, we had an accumulated deficit of $840.5 million and had cash, cash equivalents and short term investments of $90.2 million. We have significant outstanding debt and contractual obligations related to purchase commitments, as well as capital and operating leases. As of June 30, 2014, our debt, net of discount of $83.9 million, totaled $222.4 million, of which $9.9 million matures within the next twelve months. In addition, our debt agreements contain various covenants, including certain restrictions on our business that could cause us to be at risk of defaults.

Our operating plan for 2014 contemplates significant reduction in our net cash outflows, resulting from (i) revenue growth from sales of existing and new products with positive gross margins, (ii) reduced production costs compared to prior periods as a result of manufacturing and technical developments in 2013, (iii) cash inflows from collaborations consistent with levels achieved in 2013 and (iv) operating expenses maintained at reduced levels.

If we are unable to increase positive gross margin product sales or generate sufficient additional payments from existing and new collaboration partners, we may need to obtain additional funding from equity financings, credit facilities, loans or issue additional preferred and/or discounted equity, agree to burdensome covenants, grant further security interest in our assets, enter into collaboration and licensing arrangements that require us to relinquish commercial rights, or grant licenses on terms that are not favorable. If we fail to generate positive gross margin product sales or secure such funding, we could be forced to curtail our operations, which would have a material adverse effect on our ability to continue with our business plans.

Collaboration Funding. In March 2013, we signed a collaboration agreement with a collaboration partner that included a collaboration funding component and that resulted in an initial payment of $10.0 million in March 2013, and we obtained a commitment letter from Total with respect to additional convertible note funding (as described above under "Overview-Total Relationship") of which we received $10.0 million in proceeds in June 2013. We also received $20.0 million in funding through the sale of a convertible note in a private placement under an existing funding agreement with Total in July 2013. This purchase and sale completed Total's commitment to purchase $30.0 million of such notes by July 2013.

In addition to cash contributions from product sales and debt and equity financings, we depend on collaboration funding to support our operating expenses. While part of this funding is committed based on existing collaboration agreements, we will be required to identify and obtain funding under new collaborations. In addition, some of our existing collaboration funding is subject to our achievement of milestones or other funding conditions.

If we cannot secure sufficient collaboration funding to support our operating expenses in excess of cash contributions from product sales and existing debt and equity financings, we may need to issue additional preferred and/or discounted equity, agree to onerous covenants, grant further security interests in our assets, enter into collaboration and licensing arrangements that require us to relinquish commercial rights or grant licenses on terms that are not favorable to us. If we fail to secure such funding, we could be forced to curtail our operations, which would have a material adverse effect on our ability to continue with our business plans and on our status as a going concern.

Government Contracts. In 2010, we were awarded a $24.3 million “Integrated Bio-Refinery” grant from the DOE. Under this grant, we were required to fund an additional $10.6 million in cost sharing expenses. Our obligation for this cost share was contingent on reimbursement for project costs incurred. The “Integrated Bio-Refinery” project from DOE was completed in the first quarter of 2013.

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In August 2010, we were appointed as a subcontractor to NREL under a DOE grant awarded to the National Renewable Energy Laboratory (or “NREL”). Under this contract, we have the right to be reimbursed for up to $3.6 million, and are required to fund an additional $1.4 million in cost sharing expenses. As of December 31, 2013, we had recognized the entire $3.6 million in revenue under this grant, of which $0.2 million was received in cash during the six months ended June 30, 2014.

In June 2012, we entered into a Technology Investment Agreement with DARPA, under which we are performing certain research and development activities funded in part by DARPA. The work is to be performed on a cost-share basis, where DARPA funds 90% of the work and we fund the remaining 10% (primarily by providing specified labor). The agreement provided for funding of up to approximately $7.7 million over two years based on achievement of program milestones, and, accordingly, if fully funded, we would be responsible for contributions equivalent to approximately $0.9 million. The agreement had an initial term of one year and at DARPA's option, may be renewed for an additional year. The agreement was renewed by DARPA in May 2013. Through June 30, 2014, we had recognized $7.1 million in revenue under this agreement, of which $3.3 million was received in cash during the six months ended June 30, 2014.

In May 2014, we entered into a subcontract with Lawrence Berkeley National Laboratory for the 1000 Molecules program. The subcontract is for $0.6 million, with an expected completion date of September 30, 2014. Through June 30, 2014, we had recognized $0.3 million in revenue under this agreement.

Convertible Note Offerings. In February 2012, we sold $25.0 million in principal amount of senior unsecured convertible promissory notes due March 1, 2017 as described in more detail in Note 5, "Debt".

In July and September 2012, we issued $53.3 million worth of senior unsecured convertible notes to Total for an aggregate of $30.0 million in cash proceeds and our repayment of $23.3 million in previously-provided research and development funds as described in more detail in Note 5, "Debt". As part of the December 2012 private placement with Temasek, Biolding Investment SA, Naxyris SA, Foris Ventures, LLC, Sualk Capital Ltd, TPG Biotechnology Partners II, L.P. and Total, 1,677,852 shares of our common stock were issued in exchange for the cancellation of $5.0 million worth of an outstanding senior unsecured convertible promissory note held by Total. In December 2013, we exchanged all of such unsecured convertible notes (to the extent not previously used to purchase common stock) for secured notes.

In August 2013, we entered into an agreement with Total and Temasek to sell up to $73.0 million in convertible promissory notes in private placements over a period of up to 24 months from the date of signing as described in more detail in Note 5, "Debt" (such agreement referred to as the “August 2013 SPA” and such financing is referred to as the “August 2013 Financing”). The August 2013 Financing was divided into two tranches (one for $42.6 million and one for $30.4 million), each with differing closing conditions. Of the total possible purchase price in the financing, $60.0 million was to be paid in the form of cash by Temasek ($35.0 million in the first tranche and up to $25.0 million in the second tranche) and $13.0 million was to be paid by cancellation of outstanding convertible promissory notes held by Total in connection with its exercise of pro rata rights ($7.6 million in the first tranche and $5.4 million in the second tranche).

In September 2013, prior to the initial closing of the August 2013 Financing, our stockholders approved the issuance in the private placement of up to $110.0 million aggregate principal amount of senior convertible promissory notes, the issuance of a warrant to purchase 1,000,000 shares of our common stock and the issuance of the common stock issuable upon conversion or exercise of such notes and warrant, which approval included the transactions contemplated by the August 2013 Financing.

In September 2013, we entered into a bridge loan agreement with an existing investor to provide additional cash availability of up to $5.0 million as needed before the initial closing of the August 2013 Financing. The bridge loan agreement provided for the sale of up to $5.0 million in principal amount of unsecured convertible notes at any time prior to October 31, 2013 following the satisfaction of certain closing conditions, including that we pay an availability fee for the bridge loan. We did not use this facility and it expired in October 2013 in accordance with its terms.

In October 2013, we sold and issued a senior secured promissory note to Temasek for a bridge loan of $35.0 million (referred to as the "Temasek Bridge Note"). The Temasek Bridge Note was due on February 2, 2014 and accrued interest at a rate of 5.5% each four month period from October 4, 2013 (with a rate of 2% per month applicable if a default occurred). The Temasek Bridge Note was cancelled as payment for Temasek's purchase of a first tranche convertible note in the initial closing of the August 2013 Financing.

In October 2013, we amended the August 2013 SPA to include certain entities affiliated with FMR, LLC (or the "Fidelity Entities") in the first tranche in the principal amount of $7.6 million, and to proportionally increase the amount acquired by exchange and cancellation of outstanding convertible promissory notes by Total to $14.6 million ($9.2 million in the first tranche and up to

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$5.4 million in the second tranche). Also in October 2013, we completed the closing of the first tranche of notes contemplated by the August 2013 Financing (or the "Tranche I Notes") for cash proceeds of $7.6 million and cancellation of outstanding convertible promissory notes of $44.2 million, of which $35.0 million resulted from the cancellation of the Temasek Bridge Note. In December 2013, we agreed to place $3.0 million of senior convertible notes under the second tranche of the August 2013 Financing (or the "Tranche II Notes") to funds affiliated with Wolverine Asset Management (or Wolverine) and we elected to call $25.0 million in additional funds from Temasek pursuant to its previous commitment to purchase such amount of convertible promissory notes in the second tranche. Additionally, in December 2013, we agreed to sell approximately $6.0 million of convertible promissory notes in the second tranche to Total through cancellation of the same amount of principal of previously outstanding convertible notes held by Total (in respect of Total’s preexisting contractual right to maintain its pro rata ownership position through such cancellation of indebtedness). The closing of the sale of such Tranche II Notes occurred in January 2014. The August 2013 Financing is more fully described in Note 5, “Debt”.

In May 2014, we sold and issued $75.0 million aggregate principal amount of 144A Notes to Morgan Stanley & Co. LLC as the Initial Purchaser in a private placement, and for initial resale by the Initial Purchaser to qualified institutional buyers pursuant to Rule 144A of the Securities Act. The Rule 144A Convertible Note is described in more detail in Note 5, "Debt".

In July 2014, we closed on the initial installment of the $21.7 million in convertible notes from Total under the July 2012 Agreements as described in more detail in Note 5, "Debt", in the amount of $10.85 million and expect the second installment to occur within six months of such initial installment.

Export Financing with ABC Brasil. In March 2013, we entered into a one-year export financing agreement with ABC for approximately $2.5 million to fund exports through March 2014. This loan is collateralized by future exports from our subsidiary in Brazil. As of June 30, 2014, the loan was fully paid.

In March 2014, we entered into an additional one-year-term export financing agreement with ABC for approximately $2.2 million to fund exports through March 2015. This loan is collateralized by future exports from our subsidiary in Brazil. As of June 30, 2014, the principal amount outstanding under this agreement was $2.2 million.

Banco Pine/Nossa Caixa Financing. In July 2012, we entered into a Note of Bank Credit and a Fiduciary Conveyance of Movable Goods agreement with each of Nossa Caixa Desenvolvimento and Banco Pine. Under these instruments, we borrowed an aggregate of R$52.0 million (approximately US$23.6 million based on the exchange rate as of June 30, 2014) as financing for capital expenditures relating to our manufacturing facility in Brotas, Brazil. Under the loan agreements, Banco Pine agreed to lend R$22.0 million and Nossa Caixa agreed to lend R$30.0 million. The loans have a final maturity date of July 15, 2022 and bear a fixed interest rate of 5.5% per year. The loans are also subject to early maturity and delinquency charges upon occurrence of certain events including interruption of manufacturing activities at our manufacturing facility in Brotas, Brazil for more than 30 days, except during sugarcane off-season. The loans are secured by certain of our farnesene production assets at the manufacturing facility in Brotas, Brazil and we were required to provide parent guarantees to each of the lenders.

BNDES Credit Facility. In December 2011, we entered into the BNDES Credit Facility to finance a production site in Brazil. The BNDES Credit Facility was for R$22.4 million (approximately US$10.2 million based on the exchange rate as of June 30, 2014). This BNDES Credit Facility was extended as project financing for a production site in Brazil. The credit line is divided into an initial tranche for up to approximately R$19.1 million and an additional tranche of approximately R$3.3 million that becomes available upon delivery of additional guarantees. The credit line is available for 12 months from the date of the BNDES Credit Facility, subject to extension by the lender.

The principal of loans under the BNDES Credit Facility is required to be repaid in 60 monthly installments, with the first installment due in January 2013 and the last due in December 2017. Interest was initially due on a quarterly basis with the first installment due in March 2012. From and after January 2013, interest payments will be due on a monthly basis together with principal payments. The loaned amounts carry interest of 7% per year. Additionally, a credit reserve charge of 0.1% on the unused balance from each credit installment from the day immediately after it is made available through its date of use, when it is paid.

The BNDES Credit Facility is collateralized by first priority security interest in certain of our equipment and other tangible assets totaling R$24.9 million (approximately US$11.3 million based on the exchange rate as of June 30, 2014). We are a parent guarantor for the payment of the outstanding balance under the BNDES Credit Facility. Additionally, we were required to provide a bank guarantee equal to 10% of the total approved amount (R$22.4 million in total debt) available under the BNDES Credit Facility. For advances in the second tranche (above R$19.1 million ), we are required to provide additional bank guarantees equal to 90% of each such advance, plus additional Amyris guarantees equal to at least 130% of such advance. The BNDES Credit Facility contains customary events of default, including payment failures, failure to satisfy other obligations under the credit facility or related documents, defaults in respect of other indebtedness, bankruptcy, insolvency and inability to pay debts when due, material

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judgments, and changes in control of Amyris Brasil. If any event of default occurs, BNDES may terminate its commitments and declare immediately due all borrowings under the facility. As of June 30, 2014 and December 31, 2013, we had R$14.3 million (approximately US$6.5 million based on the exchange rate as of June 30, 2014) and R$15.3 million (approximately US$6.9 million based on the exchange rate as of June 30, 2014), respectively, in outstanding advances under the BNDES Credit Facility.

FINEP Credit Facility. In November 2010, we entered into a credit facility with Financiadora de Estudos e Projetos (or FINEP), a state-owned company subordinated to the Brazilian Ministry of Science and Technology (referred to as the "FINEP Credit Facility") to finance a research and development project on sugarcane-based biodiesel (referred to as the "FINEP Project") and provided for loans of up to an aggregate principal amount of R$6.4 million (approximately US$2.9 million based on the exchange rate as of June 30, 2014) which are secured by a chattel mortgage on certain equipment of Amyris as well as by bank letters of guarantee. All available credit under this facility was fully drawn.

Interest on loans drawn under the FINEP Credit Facility is fixed at 5.0% per annum. In case of default under, or non-compliance with, the terms of the agreement, the interest on loans will be dependent on the long-term interest rate as published by the Central Bank of Brazil (such rate, the TJLP). If the TJLP at the time of default is greater than 6%, then the interest will be 5.0% plus a TJLP adjustment factor otherwise the interest will be at 11.0% per annum. In addition, a fine of up to 10.0% will apply to the amount of any obligation in default. Interest on late balances will be 1.0% interest per month, levied on the overdue amount. Payment of the outstanding loan balance will be made in 81 monthly installments, which commenced in July 2012 and extends through March 2019. Interest on loans drawn and other charges are paid on a monthly basis and commenced in March 2011. As of June 30, 2014, total outstanding loan balance under this credit facility was R$5.0 million (approximately US$2.3 million based on the exchange rate as of June 30, 2014).

The FINEP Credit Facility contains the following significant terms and conditions:

• We are required to share with FINEP the costs associated with the FINEP Project. At a minimum, we are required to contribute approximately R$14.5 million (US$6.6 million based on the exchange rate as of June 30, 2014) of which R$11.1 million was contributed prior to the release of the second disbursement. All four disbursements have been completed and we have fulfilled all of our cost sharing obligations;

• After the release of the first disbursement, prior to any subsequent drawdown from the FINEP Credit Facility, we were required to provide bank letters of guarantee of up to R$3.3 million in aggregate (approximately US$1.5 million based on the exchange rate as of June 30, 2014) before receiving the second installment in December 2012. We obtained the bank letters of guarantee from ABC;

• Amounts disbursed under the FINEP Credit Facility were required to be used towards the FINEP Project within 30 months after the contract execution.

Hercules Loan Facility. In March 2014, we entered into a loan and security agreement with Hercules Technology Growth Capital, Inc. to make available a loan in the aggregate principal amount of up to $25.0 million (referred to as the "Hercules Loan Facility"). The original Hercules Loan Facility accrues interest at a rate per annum equal to the greater of either the prime rate reported in the Wall Street Journal plus 6.25% or 9.5%. We may repay the loaned amounts before the maturity date (generally February 1, 2017) if we pay an additional fee of 3% of the outstanding loans (1% if after the initial twelve-month period of the loan). We were also required to pay a 1% facility charge at the closing of the transaction, and are required to pay a 10% end of term charge. In connection with the original Hercules Loan Facility, Amyris agreed to certain customary representations and warranties and covenants, as well as certain covenants that were subsequently amended (as described below). The total available credit of $25.0 million under this facility was fully drawn down.

In June 2014, we and Hercules entered into a first amendment (referred to as “Hercules Amendment”) of the Loan and Security Agreement entered into in March 2014. Pursuant to the Hercules Amendment, the parties agreed to adjust the term loan maturity date from May 31, 2015 to February 1, 2017 and remove (i) a requirement for us to pay a forbearance fee of $10.0 million in the event certain covenants were not satisfied, (ii) a covenant that we maintain positive cash flow commencing with the fiscal quarter beginning October 1, 2014, (iii) a covenant that, beginning with the fiscal quarter beginning July 1, 2014, we and our subsidiaries achieve certain projected cash product revenues and projected cash product gross profits, and (iv) an obligation for us to file a registration statement on Form S-3 with the SEC by no later than June 30, 2014 and complete an equity financing of more than $50.0 million by no later than September 30, 2014. We further agreed to include a new covenant requiring us to maintain unrestricted, unencumbered cash in an amount equal to at least 50% of the principal amount then outstanding under the Hercules Loan Facility and borrow an additional $5.0 million. The additional $5.0 million borrowing was completed in June 2014, and accrues interest at a rate per annum equal to the greater of either the prime rate reported in the Wall Street Journal plus 5.25% or 8.5%. The Hercules Loan Facility is secured by liens on our assets, including on certain of our intellectual property. The Hercules Loan Facility includes customary events of default, including failure to pay amounts due, breaches of covenants and warranties,

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certain cross defaults and judgments, and insolvency. If an event of default occurs, Hercules may require immediate repayment of all amounts due. As of June 30, 2014, we maintain cash in excess of the approximately $15.0 million current minimum cash covenant described above.

The fair values of the notes payable, loan payable, convertible notes and credit facilities are based on the present value of expected future cash flows and assumptions about current interest rates and our creditworthiness that market participants would use in pricing the debt.

Common Stock Offerings. In December 2012, we completed a private placement of 14,177,849 shares of our common stock for aggregate proceeds of $37.2 million, of which $22.2 million in cash was received in December 2012 and $15.0 million in cash was received in January 2013. As part of this private placement, 1,677,852 of such shares were issued to Total in exchange for the cancellation of $5.0 million worth of an outstanding senior unsecured convertible promissory note we previously issued to Total.

In March 2013, we completed a private placement of 1,533,742 of our common stock to Biolding for aggregate proceeds of $5.0 million. This private placement represented the final tranche of Biolding's preexisting contractual obligation to fund $15.0 million upon satisfaction by us of certain criteria associated with the commissioning of our production plant in Brotas, Brazil.

In March 2014, we and Kuraray entered into a securities purchase agreement under which the we agreed to sell shares of our common stock at a price equal to the greater of $2.88 per share or the average daily closing prices per share on The NASDAQ Stock Market for the three month period ending March 27, 2014 for an aggregate purchase price of $4.0 million. In April 2014, we completed the sale of 943,396 shares of common stock to Kuraray at a price per share of $4.24 for aggregate proceeds of $4.0 million.

Cash Flows during the Six Months Ended June 30, 2014 and 2013

Cash Flows from Operating Activities

Our primary uses of cash from operating activities are cost of products sold and personnel-related expenditures offset by cash received from product sales, grants and collaborative research. Cash used in operating activities was $35.8 million and $45.3 million for the six months ended June 30, 2014 and 2013, respectively.

Net cash used in operating activities of $35.8 million for the six months ended June 30, 2014 was related to our net loss of $19.2 million and by a net non-cash charges of $25.0 million, offset by $8.4 million net change in our operating assets and liabilities. Net change in operating assets and liabilities of $8.4 million primarily consisted of a $7.4 million increase in deferred revenue related to the funds received under a collaboration agreement, a $3.6 million decrease in accounts receivable and related party accounts receivable mainly from collections of outstanding receivables, a $1.3 million increase in accounts payable and accrued other liabilities, offset by a $3.6 million increase in inventory, and a $0.3 million increase in prepaid expenses and other assets. Non-cash charges of $25.0 million consisted primarily of a $54.1 million change in the fair value of derivative instruments related to the embedded derivative liabilities associated with our senior secured convertible promissory notes and currency interest rate swap derivative liability, offset by $7.5 million of depreciation and amortization expenses, $7.2 million of stock-based compensation, $3.8 million of amortization of debt discount, $10.5 million loss associated with the extinguishment of convertible debt and $0.2 million loss on purchase commitments and write-off of production assets.

The largest component of the $45.3 million of cash used in our operations during the six months ended June 30, 2013 was related to our net loss of $71.2 million, offset by non-cash charges of $9.2 million of stock-based compensation, $8.5 million of depreciation and amortization expenses, an $8.4 million of loss on purchase commitments and write off of production assets related to a termination and settlement of our existing agreement with one of our contract manufacturers, and a $1.1 million amortization of debt discount. Significant operating cash inflows during the six months ended June 30, 2013 were derived primarily from sales of renewable products and from collaborative research services. Operating cash inflows also included an $8.5 million increase in deferred revenue primarily from the up-front collaboration payment from a collaboration partner.

Cash Flows from Investing Activities

Our investing activities consist primarily of capital expenditures and investment activities. Net cash used in investing activities of $4.0 million for the six months year ended June 30, 2014, was a result of $2.1 million of capital expenditures mainly due to maintenance and upgrades at our facility in Brotas, Brazil, and investments in the joint venture with Novvi of $2.1 million, offset by $0.1 million in net maturities of investments.

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For the six months ended June 30, 2013, cash used in investing activities was $5.1 million as a result of $3.7 million in capital expenditures on plant, property and equipment due principally to the construction of our production facility in Brotas and $1.4 million in net purchases of investments.

Cash Flows from Financing Activities

Net cash provided by financing activities of $122.1 million for the six months ended June 30, 2014, was a result of the net receipt of $126.2 million from debt and equity financing, which included $75.0 million from the 144A Convertible Note Offering, of which $24.7 million was sold to related parties, $29.7 million from the Hercules Loan Facility, $28.0 million financing from third parties in relation to the Tranche II Notes, $2.2 million from a one-year term export financing agreement with ABC and $4.0 million proceeds from issuance of common stock in private placements, offset in by payments of discount and expenses of $3.0 million and settlement of Total R&D Convertible Note of $9.7 million. These cash inflows were offset by other principal payments of debt of $3.6 million.

For the six months ended June 30, 2013, cash provided by financing activities was $30.0 million, primarily the result of the receipt of $20.0 million in proceeds from sales of common stock in private placements net of issuance cost and the net receipt of $12.6 million from debt financing. These cash inflows were offset in part by principal payments on debt and capital leases of $2.8 million.

Off-Balance Sheet Arrangements

We did not have during the periods presented, and we do not currently have, any material off-balance sheet arrangements, as defined under Securities and Exchange Commission ("SEC") rules, such as relationships with unconsolidated entities or financial partnerships, which are often referred to as structured finance or special purpose entities, established for the purpose of facilitating financing transactions that are not required to be reflected on our consolidated financial statements.

Contractual Obligations

The following is a summary of our contractual obligations as of June 30, 2014 (in thousands):

	Total		2014		2015		2016		2017		2018		Thereafter
Principal payments on long-term debt	$	306,290	$	4,591	$	15,435	$	21,852	$	86,502	$	58,040	$	119,870
Interest payments on long-term debt, fixed rate(1)	95,911		5,275		9,730		8,010		12,656		36,214		24,026
Operating leases	61,985		3,182		6,606		6,614		6,588		6,675		32,320
Principal payments on capital leases	1,110		521		438		151		—		—		—
Interest payments on capital leases	68		37		24		7		—		—		—
Terminal storage costs	87		53		34		—		—		—		—
Purchase obligations(2)	6,757		5,443		504		504		262		44		—
Total	$	472,208	$	19,102	$	32,771	$	37,138	$	106,008	$	100,973	$	176,216

____________________

⁽¹⁾  Does not include any obligations related to make-whole interest or downround provisions. The fixed interest rates are more fully described in Note 5, "Debt" of our consolidated financial statements.

⁽²⁾  Purchase obligations include noncancellable contractual obligations and construction commitments of $5.9 million, of which $2.4 million have been accrued as loss on purchase commitments.

This table does not reflect non-reimbursable expenses that we expect to incur in 2014 in connection with research activities under the NREL subcontract discussed above under the caption "Liquidity and Capital Resources - Government Contracts."

Additionally, this table does not reflect the expenses that we expect to incur in 2014 in connection with research activities under DARPA under which we will perform certain research and development activities funded in part by DARPA. The work is to be performed on a cost-share basis, where DARPA funds 90% of the work and we fund the remaining 10% (primarily by providing specified labor). Under the agreement, we will receive funding of up to approximately $7.7 million over two years based on achievement of program milestones, and, accordingly, we would be responsible for contributions equivalent to approximately $0.9 million.

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Recent Accounting Pronouncements

The information contained in Note 2 to the Unaudited Condensed Consolidated Financial Statements under the heading "Recent Accounting Pronouncements" is hereby incorporated by reference into this Part I, Item 2.

ITEM 3. QUANTITATIVE AND QUALITATIVE DISCLOSURES ABOUT MARKET RISK

The market risk inherent in our market risk sensitive instruments and positions is the potential loss arising from adverse changes in: commodity market prices, foreign currency exchange rates, and interest rates as described below.

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Interest Rate Risk

Our exposure to market risk for changes in interest rates relates primarily to our investment portfolio and our outstanding debt obligations. We generally invest our cash in investments with short maturities or with frequent interest reset terms. Accordingly, our interest income fluctuates with short-term market conditions. As of June 30, 2014, our investment portfolio consisted primarily of money market funds and certificates of deposit, all of which are highly liquid investments. Due to the short-term nature of our investment portfolio, our exposure to interest rate risk is minimal. Additionally, as of June 30, 2014, 100% of our outstanding debt is in fixed rate instruments.

Foreign Currency Risk

Most of our sales contracts are principally denominated in U.S. dollars and, therefore, our revenues are not currently subject to significant foreign currency risk. The functional currency of our wholly-owned consolidated subsidiary in Brazil is the local currency (Brazilian real) in which recurring business transactions occur. We do not use currency exchange contracts as hedges against amounts permanently invested in our foreign subsidiary. The amount we consider permanently invested in our foreign subsidiary and translated into U.S. dollars using the June 30, 2014 exchange rate is $156.7 million at June 30, 2014 and $145.2 million at December 31, 2013. The increase in the permanent investments in our foreign subsidiary between December 31, 2013 and June 30, 2014 is due to additional capital contributions made, the appreciation of the Brazilian real versus the U.S. dollar, offset by an increase in accumulated deficit of our wholly-owned consolidated subsidiary in Brazil. The potential loss in fair value, which would principally be recognized in Other Comprehensive Income (Loss), resulting from a hypothetical 10% adverse change in quoted Brazilian real exchange rates is $15.7 million and $14.5 million for June 30, 2014 and December 31, 2013, respectively. Actual results may differ.

We make limited use of derivative instruments, which includes currency interest rate swap agreements, to manage the Company's exposure to foreign currency exchange rate and interest rate related to the Company's Banco Pine loan. In June 2012, we entered into a currency interest rate swap arrangement with Banco Pine for R$22.0 million (approximately US$10.0 million based on the exchange rate as of June 30, 2014). The swap arrangement exchanges the principal and interest payments under the Banco Pine loan entered into in July 2012 for alternative principal and interest payments that are subject to adjustment based on fluctuations in the foreign exchange rate between the U.S. dollar and Brazilian real. The swap has a fixed interest rate of 3.94%. This arrangement hedges the fluctuations in the foreign exchange rate between the U.S. dollar and Brazilian real.

Commodity Price Risk

Our primary exposure to market risk for changes in commodity prices currently relates to our purchases of sugar feedstocks. When possible, we manage our exposure to this risk primarily through the use of supplier pricing agreements.

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ITEM 4. CONTROLS AND PROCEDURES

Disclosure Controls and Procedures

Our management, with the participation of our chief executive officer (or "CEO") and chief financial officer (or "CFO"), evaluated the effectiveness of our disclosure controls and procedures pursuant to Rules 13a-15 and 15d-15(e) under the Securities Exchange Act of 1934, as amended (or the "Exchange Act"), as of the end of the period covered by this Quarterly Report on Form 10-Q.  Based on this evaluation, our CEO and CFO concluded that, as of June 30, 2014, our disclosure controls and procedures are designed and are effective to provide reasonable assurance that information we are required to disclose in reports that we file or submit under the Exchange Act is recorded, processed, summarized, and reported within the time periods specified in the SEC's rules and forms, and that such information is accumulated and communicated to our management, including our CEO and CFO, as appropriate, to allow timely decisions regarding required disclosure.

Our management recognizes that any controls and procedures, no matter how well designed and operated, can provide only reasonable assurance of achieving their objectives and management necessarily applies its judgment in evaluating the cost-benefit relationship of possible controls and procedures.

Changes in Internal Control over Financial Reporting

There were no changes in our internal control over financial reporting identified in management’s evaluation pursuant to Rules 13a-15(d) or 15d-15(d) of the Exchange Act during our second fiscal quarter ended June 30, 2014 that materially affected, or are reasonably likely to materially affect, our internal control over financial reporting.

Inherent Limitations on the Effectiveness of Internal Controls

The effectiveness of any system of internal control over financial reporting, including ours, is subject to inherent limitations, including the exercise of judgment in designing, implementing, operating, and evaluating the controls and procedures, and the inability to eliminate misconduct completely. Accordingly, any system of internal control over financial reporting, including ours, no matter how well designed and operated, can only provide reasonable, not absolute assurances. In addition, projections of any evaluation of effectiveness to future periods are subject to the risk that controls may become inadequate because of changes in conditions, or that the degree of compliance with the policies or procedures may deteriorate. We intend to continue to monitor and upgrade our internal controls as necessary or appropriate for our business, but cannot assure you that such improvements will be sufficient to provide us with effective internal control over financial reporting.

PART II

ITEM 1. LEGAL PROCEEDINGS

In May 2013, a securities class action complaint was filed against Amyris and our CEO, John G. Melo, in the U.S. District Court for the Northern District of California. In October 2013, the lead plaintiffs filed a consolidated amended complaint. The complaint, as amended, sought unspecified damages on behalf of a purported class that would comprise all individuals who acquired our common stock between April 29, 2011 and February 8, 2012. The complaint alleged securities law violations based on the company's commercial projections during that period. In December 2013, we filed a motion to dismiss the complaint. In March 2014, the court issued an order granting our motion to dismiss with leave to amend the complaint. The plaintiffs declined to amend their complaint further and, on June 12, 2014, the court issued an order (based on a stipulation of the parties) dismissing the action with prejudice.

In August 2013, a complaint entitled Steve Shannon, derivatively on behalf of Amyris, Inc. v. John G. Melo et al and Amyris, Inc., was filed against Amyris as nominal defendant in the United States District Court for the Northern District of California. The lawsuit sought unspecified damages on behalf of Amyris from certain of our current and former officers, directors and employees and alleges these defendants breached their fiduciary duties to Amyris and unjustly enriched themselves by making allegedly false and misleading statements and omitting certain material facts in our securities filings. Because this purported stockholder derivative action is based on substantially the same facts as the securities class action described above, the two actions were related and were heard by the same judge. On June 23, 2014, following the dismissal of the related class action (discussed above), the court issued an order (based on a stipulation of the parties) dismissing the action with prejudice.

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We may be involved, from time to time, in legal proceedings and claims arising in the ordinary course of our business. Such matters are subject to many uncertainties and there can be no assurance that legal proceedings arising in the ordinary course of business or otherwise will not have a material adverse effect on our business, results of operations, financial position or cash flows.

ITEM 1A. RISK FACTORS

Investing in our common stock involves a high degree of risk. You should carefully consider the risks and uncertainties described below, together with all of the other information set forth in this Quarterly Report on Form 10-Q, which could materially affect our business, financial condition or future results. If any of the following risks actually occurs, our business, financial condition, results of operations and future prospects could be materially and adversely harmed. The trading price of our common stock could decline due to any of these risks, and, as a result, you may lose all or part of your investment.

Risks Related to Our Business

We have incurred losses to date, anticipate continuing to incur losses in the future and may never achieve or sustain profitability.

We have incurred significant losses in each year since our inception and believe that we will continue to incur losses and negative cash flow from operations through at least 2014. As of June 30, 2014, we had an accumulated deficit of $840.5 million and had cash, cash equivalents and short term investments of $90.2 million. We have significant outstanding debt and contractual obligations related to purchase commitments, as well as capital and operating leases. As of June 30, 2014, our debt totaled $222.4 million, net of discount of $83.9 million, of which $9.9 million matures within the next twelve months. In addition, our debt agreements contain various covenants, including restrictions on business that could cause us to be at risk of defaults. We expect to incur additional costs and expenses related to the continued development and expansion of our business, including construction and operation of our manufacturing facilities, contract manufacturing, research and development operations, and operation of our pilot plants and demonstration facility. There can be no assurance that we will ever achieve or sustain profitability on a quarterly or annual basis.

We have limited experience producing our products at commercial scale and may not be able to commercialize our products to the extent necessary to sustain and grow our current business.

To commercialize our products, we must be successful in using our yeast strains to produce target molecules at commercial scale and at a commercially viable cost. If we cannot achieve commercially-viable production economics for enough products to support our business plan, including through establishing and maintaining sufficient production scale and volume, we will be unable to achieve a sustainable integrated renewable products business. Virtually all of our production capacity is through a purpose-built, large-scale production plant in Brotas, Brazil. This plant commenced operations in 2013, and scaling and running the plant has been, and continues to be, a time-consuming, costly, uncertain and expensive process. Given our limited experience commissioning and operating our own manufacturing facilities and our limited financial resources, we cannot be sure that we will be successful in achieving production economics that allow us to meet our plans for commercialization of various products we intend to offer. In addition, until very recently we have only produced Biofene at the Brotas plant and are only in the beginning stages of producing our second molecule (for the flavors and fragrances market) at the Brotas plant. Our attempts to scale production of new molecules at the plant is subject to uncertainty and risk. For example, even to the extent we successfully complete product development in our laboratories and pilot and demonstration facilities, and at contract manufacturing facilities, we may be unable to translate such success to large-scale, purpose-built plants. If this occurs, our ability to commercialize our technology will be adversely affected and we may be unable to produce and sell any significant volumes of our products. Also, with respect to products that we are able to bring to market, we may not be able to lower the cost of production, which would adversely affect our ability to sell such products profitably.

We will require significant inflows of cash from financing and collaboration transactions to fund our anticipated operations and may not be able to obtain such financing and collaboration funding on favorable terms, if at all.

Though we recently completed a sale of $75.0 million of convertible senior notes in May 2014, our planned 2014 and 2015 working capital needs and our planned operating and capital expenditures for 2014 and 2015 are dependent on significant inflows of cash from existing and new collaboration partners and cash contributions from growth in renewable product sales, as well as additional funding from new joint ventures or other collaborations. We may also be required to obtain additional funding from equity financings, credit facilities or loans, especially to the extent that we are unable to increase positive gross margin product sales or generate sufficient additional payments from existing and new collaboration partners. We will continue to need to fund our research and development and related activities and to provide working capital to fund production, storage, distribution and other aspects of our business. Some of our anticipated financing sources, such as research and development collaborations, are

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subject to the risk that we cannot meet milestones or are not yet subject to definitive agreements or mandatory funding commitments and, if needed, we may not be able to secure additional types of financing in a timely manner or on reasonable terms, if at all.

If we are unable to increase positive gross margin product sales or generate sufficient additional payments from existing and new collaboration partners, we may need to obtain additional funding from equity financings, credit facilities, loans or issue additional preferred and/or discounted equity, agree to burdensome covenants, grant further security interest in our assets, enter into collaboration and licensing arrangements that require us to relinquish commercial rights, or grant licenses on terms that are not favorable, or any or all of these possibilities. If we fail to generate positive gross margins product sales or secure such funding, we could be forced to curtail our operations, which would have a material adverse effect on our ability to continue with our business plans.

Our existing financing arrangements may cause significant future dilution and other risks to our stockholders and may impact our ability to pursue certain transactions.

From January 2013 through the second quarter of 2014, we completed several equity and debt financings to provide us with cash resources to pursue our business plans. In August 2013, we entered into an agreement with Total Total Energies Nouvelles Activités USA (formerly known as Total Gas & Power USA, SAS, or Total) and Maxwell (Mauritius) Pte Ltd, (or Temasek), to sell up to $73.0 million in convertible promissory notes in private placements over a period of up to 24 months from the date of signing (referred to as the August 2013 Financing). The August 2013 Financing was divided into two tranches, the first of which closed in October 2013 and the second of which closed in January 2014. In the October 2013 closing, we issued a total of $51.8 million in convertible promissory notes for cash proceeds of $7.6 million and cancellation of outstanding promissory notes and convertible promissory notes of $44.2 million (including $35.0 million advanced by one of the investors as a bridge loan earlier in October 2013 and approximately $9.2 million canceled by Total in connection with its exercise of pro rata rights). In the January 2014 closing, we issued an additional $34.0 million in convertible promissory notes for cash proceeds of $28.0 million and cancellation of outstanding convertible promissory notes of approximately $6.0 million by Total in connection with its further exercise of pro rata rights.

In April 2014, we entered into a letter agreement dated as of March 29, 2014 (referred to as the March 2014 Letter Agreement) with Total to amend our Amended and Restated Master Framework Agreement (included as part of Shareholders Agreement and License Agreement and related documents (collectively, referred to as the JV Documents) entered into by and among Amyris, Total and Total Amyris BioSolutions B.V. (or JVCO) relating to the establishment of JVCO in In December 2013). Under the March 2014 Letter Agreement, we agreed to (i) amend the conversion price of convertible notes to be issued in 2014 and 2015 (for up to an aggregate of $21.7 million) from $7.0682 to $4.11 subject to stockholder approval at our 2014 annual meeting (to the extent required by applicable law or regulation), (ii) extend the period during which Total may exchange for other Amyris securities certain outstanding convertible promissory notes in connection with its exercise of its existing pro rata rights from June 30, 2014 to the later of December 31, 2014 and the date on which Amyris raises $75.0 million of equity and convertible debt financing (excluding any convertible promissory notes issued pursuant to that certain Securities Purchase Agreement dated July 30, 2012 by and between Amyris and Total), (iii) eliminate our ability to qualify, in a disclosure letter to Total, certain of the representations and warranties that we must make at the closing of the 2014 and 2015 note issuances, and (iv) provide Total with monthly reporting on our cash, cash equivalents and short-term investments. In consideration of these agreements, Total agreed to waive its right not to consummate the closing of the issuance of the notes to be issued in 2014 and 2015 if it decides not to proceed with the collaboration and makes a "No-Go" decision with respect thereto. In July 2014, we closed on the initial installment of the $21.7 million in convertible notes to be sold to Total in 2014 and 2015. Such first installment was in the amount of $10.85 million and we expect the second installment to occur in January 2015.

In May 2014, we entered into a Purchase Agreement (or the 144A Purchase Agreement) with Morgan Stanley & Co. LLC, as the initial purchaser (or the Initial Purchaser), relating to the sale of $75.0 million aggregate principal amount of its 6.50% Convertible Senior Notes due 2019 to the Initial Purchaser in a private placement, and for initial resale of such notes by the Initial Purchaser to qualified institutional buyers (such offering, the 144A Offering). In addition, we granted the Initial Purchaser an option to purchase up to an additional $15.0 million aggregate principal amount of notes, which option could have been exercised for 30 days after the date of the Purchase Agreement. Under the terms of the Purchase Agreement, we agreed to customary indemnification of the Initial Purchaser against certain liabilities. The notes were issued pursuant to an indenture, dated as of May 29, 2014 (or the Indenture), between Amyris and Wells Fargo Bank, National Association, as trustee.

In March 2014, we entered into a loan and security agreement with Hercules Technology Growth Capital, Inc. to make available to Amyris a loan in the aggregate principal amount of up to $25.0 million and in June 2014, we amended such loan and security agreement with Hercules to simplify and remove certain covenants under the original loan facility and we agreed to incur an additional tranche of debt in the aggregate principal amount of $5.0 million (such loan facility, as amended, is referred to as the Hercules Loan Facility). The Hercules Loan Facility generally becomes due on May 31, 2017. We may repay the loaned amounts

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before the maturity date if we pay an additional fee of 3% of the outstanding loans (1% if after the twelve-month period following the execution of the loan and security agreement in March 2014). With respect to the initial tranche of $25.0 million, we were also required to pay a 1% facility charge at the closing of such transaction and will be required to pay a 10% end of term charge. The Hercules Loan Facility contains customary covenants and also a covenant requiring the Company to maintain unrestricted, unencumbered cash in an amount equal to at least 50% of the remaining principal amount then outstanding under the Hercules Loan Facility. The Hercules Loan Facility includes customary events of default, including failure to pay amounts due, breaches of covenants and warranties, certain cross defaults and judgments, and insolvency. If an event of default occurs, Hercules may require immediate repayment of all amounts due.

The terms of the August 2013 Financing include significant potential reductions in the conversion price for the notes issued in the August 2013 Financing if we do not meet certain performance milestones and other conditions. These conditions, if triggered, could result in further reductions to the conversion price that would cause significant additional dilution to our stockholders if the notes are ultimately converted. Furthermore, if our outstanding convertible promissory notes (including those issued in the August 2013 Financing, those issued to Total in connection with our fuels collaboration and those issued pursuant to the 144A Offering) are not converted or cancelled, we may not have sufficient cash to repay the notes when they become due, which could result in insolvency and related issues. In addition, we were required to agree to significant covenants in connection with our debt financing transactions that have an impact on our ability to engage in certain transactions. For example, the purchase agreement for the August 2013 Financing (referred to as the August 2013 SPA) requires us to obtain the consent of a majority of the purchasers in the financing before completing any change-of-control transaction, or purchasing assets in one transaction or a series of related transactions in an amount greater than $20.0 million, in each case while the notes are outstanding. We also agreed to provide the purchasers in the August 2013 Financing with pro rata rights under which they could cancel up to the full amount of their outstanding notes to pay for new equity securities if we raise additional financing during the term of the notes, which could delay or prevent us from obtaining additional financing if the purchasers do not support it. Also, as discussed in more detail below, our outstanding convertible promissory notes (and related agreements) and the Hercules loan agreement include a minimum unrestricted, unencumbered cash covenant and other covenants that restrict us from raising additional financing through debt issuances without consent of these lenders; this could also slow down or limit our ability to pursue funding if the purchasers or Hercules do not support it. Additionally, under the notes issued in connection with the 144A Offering, under certain fundamental corporate transactions, such as a change of control, the conversion rate of the notes issued thereunder will be adjusted in favor of the holders of such notes and the holders have the option require us to purchase their notes. This could lead to, among other things, liquidity difficulties should we not have sufficient cash when holders elect to cause us to purchase the notes, significant dilution to our stockholders if the conversion rate is adjusted, or could delay or prevent a change of control, including a merger, consolidation or other business combination involving us, or discourage a potential acquirer from making a tender offer or otherwise attempting to obtain control, even if that change of control would benefit our other stockholders.

To the extent we issue convertible promissory notes or other debt instruments in the future, we would become subject to various covenants, including restrictions on our business, that could cause us to be at risk of defaults. For example, the convertible notes we issued in 2012, 2013 and early 2014 and the Hercules Loan Facility contain various covenants, including restrictions on the amount and type of debt we are permitted to incur, and any convertible notes or other debt we may issue in connection with future debt financings could contain similar covenants. There is no guarantee we will be able to obtain waivers to such covenants, to the extent necessary to undertake future financings.

To the extent we obtain funding through the issuance of additional equity securities, our existing stockholders will experience further dilution.

In 2014, we completed private placements of our common stock that resulted in the issuance of approximately 943,396 shares of our common stock. Also, in 2014, we issued approximately $109.0 million in senior convertible promissory notes that are or may become convertible into common stock. As of June 30, 2014, we had issued an aggregate a total of $239.2 million in senior convertible promissory notes that are or may become convertible into common stock. As of June 30, 2014, we had issued and outstanding $48.3 million of convertible promissory notes with a conversion price of $7.0682 to Fidelity and Total under agreements signed in 2012, including the arrangement with Total for research and development-related funding, $30.0 million of convertible promissory notes with a conversion price of $3.08 per share pursuant to our arrangement with Total for research and development-related funding, $51.8 million in convertible promissory notes that are convertible into common stock at an initial conversion price of $2.44 per share issued under the first tranche of the August 2013 Financing, $34.0 million in convertible promissory notes that are convertible into common stock at an initial conversion price of $2.87 per share issued under the second tranche of the August 2013 Financing, and $75.0 million in convertible promissory notes that are convertible into common stock at a conversion price of $3.74 issued in the144A Offering. In addition, in connection with the initial closing of the August 2013 Financing, we issued a warrant to Temasek to purchase 1,000,000 shares of our common stock at an exercise price of $0.01 per share, exercisable if and to the extent Total converts certain preexisting convertible promissory notes. In July 2014, we issued an additional convertible promissory note to Total in the face amount of $10.85 million with a conversion price of $4.11 as discussed above. Through 2015,

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we expect to issue up to an aggregate of $10.85 million in additional convertible promissory notes to Total (representing the second issuance of notes under the $21.7 million third closing), with a conversion price of $4.11 per share, under the agreements with Total described below under the risk factor, “Our relationship with our strategic partner, Total, has a substantial impact on our company.” We may undertake further equity or debt offerings in the future in order to grow our business or fund operations. To the extent we issue further common stock, convertible promissory notes or other equity instruments, such issuances may cause further dilution to our existing stockholders.

Our substantial leverage could adversely affect our ability to fulfill our obligations under our existing indebtedness and may place us at a competitive disadvantage in our industry.

As of June 30, 2014, we had $306.4 million of indebtedness outstanding, of which $117.5 million was secured indebtedness. The foregoing amount of indebtedness does not include approximately $0.4 million in aggregate principal amount of indebtedness of our subsidiaries that we have guaranteed and on which we are primarily liable. As previously described, we may incur additional indebtedness from time to time to finance working capital, product development efforts, strategic acquisitions, investments and alliances, capital expenditures or other general corporate purposes, subject to the restrictions contained in our existing indebtedness and in any other agreements under which we incur indebtedness. Our significant indebtedness and debt service requirements could adversely affect our ability to operate our business and may limit our ability to take advantage of potential business opportunities. For example, our high level of indebtedness presents the following risks:

• we will be required to use a substantial portion of our cash flow from operations to pay principal and interest on our indebtedness, thereby reducing the availability of our cash flow to fund working capital, capital expenditures, product development efforts, acquisitions, investments and strategic alliances and other general corporate requirements;

• our substantial leverage increases our vulnerability to economic downturns and adverse competitive and industry conditions and could place us at a competitive disadvantage compared to those of our competitors that are less leveraged;

• our debt service obligations could limit our flexibility in planning for, or reacting to, changes in our business and our industry and could limit our ability to pursue other business opportunities, borrow more money for operations or capital in the future and implement our business strategies; and

• our level of indebtedness and the covenants within our debt instruments may restrict us from raising additional financing on satisfactory terms to fund working capital, capital expenditures, product development efforts, strategic acquisitions, investments and alliances, and other general corporate requirements.

If we are at any time unable to generate sufficient cash flow from operations to service our indebtedness when payment is due, we may be required to attempt to renegotiate the terms of the instruments relating to the indebtedness, seek to refinance all or a portion of the indebtedness or obtain additional financing. There can be no assurance that we will be able to successfully renegotiate such terms, that any such refinancing would be possible or that any additional financing could be obtained on terms that are favorable or acceptable to us.

A failure to comply with the covenants and other provisions of our debt instruments, including any failure to make a payment when required, could result in events of default under such instruments, and which could permit acceleration of such indebtedness. If such indebtedness is accelerated, it could also constitute an event of default under our other outstanding indebtedness. Any required repayment of our indebtedness as a result of acceleration or otherwise would lower our current cash on hand such that we would not have those funds available for use in our business or for payment on the notes.

Servicing our indebtedness requires a significant amount of cash and our ability to generate cash may be affected by factors beyond our control.

Our business may not generate cash flow in an amount sufficient to enable us to pay the principal of, or interest on, our indebtedness, or to fund our other liquidity needs, including working capital, capital expenditures, product development efforts, strategic acquisitions, investments and alliances, and other general corporate requirements. Our ability to generate cash is subject to general economic, financial, competitive, legislative, regulatory and other factors that are beyond our control. There can be no assurance that:

• we will generate sufficient cash inflows from collaborations;

• our business will generate sufficient cash flow from operations;

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• we will realize cost savings, revenue growth and operating improvements resulting from the execution of our long-term plan; or

• future sources of funding will be available to us in amounts sufficient to enable us to fund our liquidity needs.

If we cannot fund our liquidity needs, we will have to take actions such as reducing or delaying capital expenditures, product development efforts, strategic acquisitions, investments and alliances, selling assets, restructuring or refinancing our indebtedness or seeking additional equity capital. Such actions could further negatively impact our ability to generate cash flows. We cannot assure you that any of these remedies could, if necessary, be effected on commercially reasonable terms, or at all, or that they would permit us to meet our scheduled debt service obligations. Our Hercules Loan Facility limits our ability to dispose of assets and, as a result, we may not be allowed, under that document or the terms of any indebtedness we may incur in the future, to engage in such dispositions to satisfy our debt service obligations. In addition, if we incur additional indebtedness, the risks associated with our substantial leverage, including the risk that we will be unable to service our indebtedness or generate enough cash flow to fund our liquidity needs, could intensify.

Restrictive covenants in our Hercules Loan Facility and the terms of our existing convertible notes, and the terms of any indebtedness we may incur in the future, may materially restrict our ability to operate.

The agreements governing our existing indebtedness, and any indebtedness we may incur in the future, contain, and may contain, affirmative and negative covenants that materially limit our ability to take certain actions, including our ability to incur indebtedness, pay dividends, make certain investments and other payments, enter into certain mergers and consolidations, and encumber and dispose of assets. The breach of any of these covenants or the failure by us to meet any of these conditions would result in a default under any or all of such indebtedness. If a default occurs under any such indebtedness, all of the outstanding obligations thereunder could become immediately due and payable. If such indebtedness is accelerated, it may result in a default under our other outstanding indebtedness and could lead to an acceleration of such other outstanding indebtedness. Our ability to comply with the provisions of our debt agreements, including debt agreements we may enter into in the future, can be affected by events beyond our control. A default under any debt instrument, if not cured or waived, could result in a material adverse effect on us. We may not have the cash available and may not be able to raise financing in an amount sufficient to pay the indebtedness due as a result of the default or any other indebtedness that may become due as a result of such acceleration.

Our GAAP operating results could fluctuate substantially due to the accounting for the early conversion payment features of the convertible promissory notes sold in the 144A Offering .

Holders of notes sold in the 144A Offering (the 144A Notes) who convert their 144A Notes on or after May 15, 2015, if the last reported sale price of our common stock for 20 or more trading days (whether or not consecutive) in a period of 30 consecutive trading days ending within five trading days immediately prior to the date we receive a notice of conversion exceeds the conversion price in effect on each such trading day, will receive an early conversion payment equal to the present value of the remaining scheduled payments of interest that would have been made on the 144A Notes being converted from the earlier of the date that is three years after the date we receive such notice of conversion and maturity. The early conversion payment feature of the 144A Notes will be accounted for under Accounting Standards Codification 815, Derivatives and Hedging (“ASC 815”) as an embedded derivative. ASC 815 requires companies to bifurcate conversion options from their host instruments and account for them as free standing derivative financial instruments according to certain criteria. The fair value of the derivative is remeasured to fair value at each balance sheet date, with a resulting non-cash gain or loss related to the change in the fair value of the derivative being charged to earnings (loss). We have determined that we must bifurcate and account for the Early Conversion Payment feature of the notes as an embedded derivative in accordance with ASC 815. We will record this embedded derivative liability as a non-current liability on our consolidated balance sheet with a corresponding debt discount at the date of issuance that is netted against the principal amount of the 144A Notes. The derivative liability will be remeasured to fair value at each balance sheet date, with a resulting non-cash gain or loss related to the change in the fair value of the derivative liability being recorded in other income and loss. We will estimate the fair value of these liabilities using a Monte Carlo simulation model. We cannot predict the effect that the accounting for the notes will have on our future GAAP financial results, the trading of our common stock and the trading price of the notes, which could be material.

If our major production facilities do not successfully commence or scale up operations, our customer relationships, business and results of operations may be adversely affected.

A substantial component of our planned production capacity in the near and long term depends on successful operations at our initial and planned large-scale production plants in Brazil. We are in the early stages of operating our first purpose-built, large-scale production plant in Brotas, Brazil and may complete construction of certain other facilities in the coming years. Delays or problems in the construction, start-up or operation of these facilities will cause delays in our ramp-up of production and hamper

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our ability to reduce our production costs. Delays in construction can occur due to a variety of factors, including regulatory requirements and our ability to fund construction and commissioning costs. Once our large-scale production facilities are built, we must successfully commission them and they must perform as we have designed them. If we encounter significant delays, cost overruns, engineering issues, contamination problems, equipment or raw material supply constraints, unexpected equipment maintenance requirements, safety issues, work stoppage or other serious challenges in bringing these facilities online and operating them at commercial scale, we may be unable to produce our initial renewable products in the time frame we have planned. For example, we have just begun using our plant at Brotas to produce molecules beyond Biofene. To date, we have only successfully produced Biofene at scale at the plant. In order to produce additional molecules at Brotas, we have been and will be required to perform thorough transition activities, and modify the design of the plant. Any modifications to the production plant could cause complications in the start-up and operations of the plant, which could result in delays or failures in production. We may also need to continue to use contract manufacturing sources more than we expect (e.g., if the modifications to the Brotas plant are not successful or have a negative impact on the plant's operations), which would reduce our anticipated gross margins and may prevent us from accessing certain markets for our products. Further, if our efforts to increase (or complete and commence, as the case may be) production at these facilities are not successful, other mill owners in Brazil or elsewhere may decide not to work with us to develop additional production facilities, demand more favorable terms or delay their commitment to invest capital in our production.

Our reliance on the large-scale production plant in Brotas, Brazil subjects us to execution and economic risks.

Our decision to focus our efforts for production capacity on the manufacturing facility in Brotas, Brazil means that we will have limited manufacturing sources for our products in 2014 and beyond. Accordingly, any failure to establish operations at that plant could have a significant negative impact on our business, including our ability to achieve commercial viability for our products. With the facility in Brotas, Brazil, we are, for the first time, operating a commercial fermentation and separation facility ourselves. We may face unexpected difficulties associated with the operation of the plant. For example, we have in the past, at certain contract manufacturing facilities and at the Brotas facility, encountered delays and difficulties in ramping up production based on contamination in the production process, problems with plant utilities, lack of automation and related human error, issues arising from process modifications to reduce costs and adjust product specifications or transition to producing new molecules, and other similar challenges. We cannot be certain that we will be able to remedy all of such challenges quickly or effectively enough to achieve commercially viable near-term production costs and volumes.

To the extent we secure collaboration arrangements with new or existing partners, we may be required to make significant capital investments at our existing or new facilities in order to produce molecules or other products for such collaborations. Any failure or difficulties in establishing, building up or retooling our operations for these new collaboration arrangements could have a significant negative impact on our business, including our ability to achieve commercial viability for our products, lead to the inability to meet our contractual obligations and could cause us to allocate capital, personnel and other resources from our organization which could adversely affect our business and reputation.

As part of our arrangement to build the plant in Brotas, Brazil we have an agreement with Paraíso Bioenergia to purchase from Paraíso Bioenergia sugarcane juice corresponding to a certain number of tons of sugarcane per year, along with specified water and vapor volumes. Until this annual volume is reached, we are restricted from purchasing sugarcane juice for processing in the facility from any third party, subject to limited exceptions, unless we pay the premium to Paraíso Bioenergia that we would have paid if we bought the juice from them. As such, we will be relying on Paraíso Bioenergia to supply such juice and utilities on a timely basis, in the volumes we need, and at competitive prices. If a third party can offer superior prices and Paraíso Bioenergia does not consent to our purchasing from such third party, we would be required to pay Paraíso Bioenergia the applicable premium, which would have a negative impact on our production cost. Furthermore, we agreed to pay a price for the juice that is based on the lower of the cost of two other products produced by Paraíso Bioenergia using such juice, plus a premium. Paraíso Bioenergia may not want to sell sugarcane juice to us if the price of one of the other products is substantially higher than the one setting the price for the juice we purchase. While the agreement provides that Paraíso Bioenergia would have to pay a penalty to us if it fails to supply the agreed-upon volume of juice for a given month, the penalty may not be enough to compensate us for the increased cost if third-party suppliers do not offer competitive prices. Also, if the prices of the other products produced by Paraíso Bioenergia increase, we could be forced to pay those increased prices for production without a related increase in the price at which we can sell our products, reducing or eliminating any margins we can otherwise achieve. If in the future these supply terms no longer provide a viable economic structure for the operation in Brotas, Brazil we may be required to renegotiate our agreement, which could result in manufacturing disruptions and delays.

Furthermore, as we continue to scale up production of our products, both through contract manufacturers and at our large-scale production plant in Brotas, Brazil, we may be required to store increasing amounts of our products for varying periods of time and under differing temperatures or other conditions that cannot be easily controlled, which may lead to a decrease in the quality of our products and their utility profiles and could adversely affect their value. If our stored products degrade in quality,

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we may suffer losses in inventory and incur additional costs in order to further refine our stored products or we may need to make new capital investments in shipping, improved storage or sales channels and related logistics.

Our joint venture with São Martinho S.A. subjects us to certain legal and financial terms that could adversely affect us.

We have various agreements with Sao Martinho S.A. (or SMSA) that contemplate construction of another large-scale manufacturing facility as a joint venture in Brazil. Under these agreements, we are responsible for designing and managing the construction project, and are responsible for the initial construction costs. We projected the construction costs of the project to be approximately $100.0 million. While we completed a significant portion of the construction of the plant before 2012, we delayed further construction and commissioning of the plant while we constructed and commissioned our production plant in Brotas, Brazil and we expect to continue to defer the project for SMA Indústria Química (or “SMA”), a joint venture with SMSA, for the near term based on economic considerations and to allow us to focus on operations at our production plant in Brotas, Brazil. We entered into an amendment to the joint venture agreement with SMSA in February 2014 which updated and documented certain preexisting business plan requirements related to the start-up of construction at the plant and set forth, among other things, (i) the extension of the deadline for the commencement of operations at the joint venture operated plant to no later than 18 months following the construction of the plant, which is required to occur no later than March 31, 2017, and (ii) the extension of an option held by SMSA to build a second large-scale farnesene production facility to no later than December 31, 2018 with the commencement of operations at such second facility to occur no later than April 1, 2019. While SMSA was obligated to contribute up to approximately R$61.8 million (approximately US$28.1 million based on the exchange rate as of June 30, 2014) to the construction of the original plant, such contributions depended on, among other things, successful commencement of operations at the plant. Notwithstanding the February 2014 amendment to the joint venture agreement, based on our shifting manufacturing priorities and uncertainty regarding financing availability, we cannot currently predict exactly when or if our facility at SMSA will be completed or commence commercial operations, which means that SMSA's anticipated contribution will continue to be delayed and may never occur. SMSA holds rights with respect to the termination and acquisition of our interests in SMA. For instance, if our Brazilian subsidiary, Amyris Brasil becomes controlled, directly or indirectly, by a competitor of SMSA, then SMSA has the right to acquire our interest in the joint venture and if SMSA becomes controlled, directly or indirectly, by a competitor of ours, then we have the right to sell our interest in the joint venture to SMSA. In either case, the purchase price is to be determined in accordance with the joint venture agreements, as amended, and we would continue to have the obligation to acquire products produced by the joint venture for the remainder of the term of the supply agreement then in effect even though we might no longer be involved in the joint venture's management.

If we are ultimately successful in establishing the plant at SMSA, the agreements governing the joint venture subject us to terms that may not be favorable to us under certain conditions. For example, we are required to purchase the output of the joint venture for the first four years at a price that guarantees the return of SMSA's investment plus a fixed surcharge rate. We may not be able to sell the output at a price that allows us to achieve anticipated, or any, level of profitability on the product we acquire under these terms. Similarly, the return that we are required to provide the joint venture for products after the first four years may have an adverse effect on the profitability we achieve from acquiring the mill's output. Additionally, we are required to purchase the output of the joint venture regardless of whether we have a customer for such output, and our results of operations and financial condition would be adversely affected if we are unable to sell the output that we are required to purchase.

Loss or termination of contract manufacturing relationships could harm our ability to meet our production goals.

As we have focused on building and commissioning our own plant and improving our production economics, we have reduced our use of contract manufacturing and have terminated relationships with some of our contract manufacturing partners. The failure to have multiple available supply options for farnesene or other target molecules could create a risk for us if a single source or a limited number of sources of manufacturing runs into operational issues. In addition, if we are unable to secure the services of contract manufacturers when and as needed, we may lose customer opportunities and the growth of our business may be impaired. We cannot be sure that contract manufacturers will be available when we need their services, that they will be willing to dedicate a portion of their capacity to our projects, or that we will be able to reach acceptable price and other terms with them for the provision of their production services. If we shift priorities and adjust anticipated production levels (or cease production altogether) at contract manufacturing facilities, such adjustments or cessations could also result in disputes or otherwise harm our business relationships with contract manufacturers. In addition, reducing or stopping production at one facility while increasing or starting up production at another facility generally results in significant losses of production efficiency, which can persist for significant periods of time. Also, in order for production to commence under our contract manufacturing arrangements, we generally must provide equipment, and we cannot be assured that such equipment can be ordered or installed on a timely basis, at acceptable costs, or at all. Further, in order to establish new manufacturing facilities, we need to transfer our yeast strains and production processes from lab to commercial plants controlled by third parties, which may pose technical or operational challenges that delay production or increase our costs.

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Our use of contract manufacturers exposes us to risks relating to costs, contractual terms and logistics.

While we have commenced commercial production at the Brotas, Brazil plant, we continue to commercially produce, process and manufacture some specialty molecules through the use of contract manufacturers, and we anticipate that we will continue to use contract manufacturers for the foreseeable future for chemical conversion and production of end-products and, to mitigate cost and volume risks at our large-scale production facilities. Establishing and operating contract manufacturing facilities requires us to make significant capital expenditures, which reduces our cash and places such capital at risk. For example, based on an evaluation of our assets associated with contract manufacturing facilities and anticipated levels of use of such facilities, we recorded a loss on purchase commitments and write off of production assets of approximately $0.2 million and $9.4 million for the six months ended June 30, 2014 and for the year ended December 31, 2013, respectively. Also, contract manufacturing agreements may contain terms that commit us to pay for capital expenditures and other costs incurred or expected to be earned by the plant operators and owners, which can result in contractual liability and losses for us even if we terminate a particular contract manufacturing arrangement or decide to reduce or stop production under such an arrangement. For example, in June 2013, we entered into a termination agreement with a contract manufacturer that required us to make payments totaling $8.8 million in 2013, of which $3.6 million was to satisfy outstanding obligations and $5.2 million was in lieu of additional payments otherwise owed.

The locations of contract manufacturers can pose additional cost, logistics and feedstock challenges. If production capacity is available at a plant that is remote from usable chemical finishing or distribution facilities, or from customers, we will be required to incur additional expenses in shipping products to other locations. Such costs could include shipping costs, compliance with export and import controls, tariffs and additional taxes, among others. In addition, we may be required to use feedstock from a particular region for a given production facility. The feedstock available in a particular region may not be the least expensive or most effective feedstock for production, which could significantly raise our overall production cost or reduce our product's quality until we are able to optimize the supply chain.

If we are unable to reduce our production costs, we may not be able to produce our products at competitive prices and our ability to grow our business will be limited.

In order to be competitive in the the market our products must have superior qualities or be competitively priced relative to alternatives available in the market. Currently, our costs of production are not low enough to allow us to offer some of our planned products at competitive prices relative to alternatives available in the market. Our production costs depend on many factors that could have a negative effect on our ability to offer our planned products at competitive prices, including, in particular, our ability to establish and maintain sufficient production scale and volume, and feedstock cost. For example, see "We have limited experience producing our products at commercial scale and may not be able to commercialize our products to the extent necessary to sustain and grow our current business," "Our manufacturing operations require sugar feedstock, and the inability to obtain such feedstock in sufficient quantities or in a timely manner, or at reasonable prices, may limit our ability to produce products profitably or at all," and "The price of sugarcane and other feedstocks can be volatile as a result of changes in industry policy and may increase the cost of production of our products."

We face financial risk associated with scaling up production to reduce our production costs. To reduce per-unit production costs, we must increase production to achieve economies of scale and to be able to sell our products with positive margins. However, if we do not sell production output in a timely manner or in sufficient volumes, our investment in production will harm our cash position and generate losses. Additionally, we may incur added costs in storage and we may face issues related to the decrease in quality of our stored products, which could adversely affect the value of such products. Since achieving competitive product prices generally requires increased production volumes and our manufacturing operations and cash flows from sales are in their early stages, we have had to produce and sell products at a loss in the past, and may continue to do so as we build our business. If we are unable to achieve adequate revenues from a combination of product sales and other sources, we may not be able to invest in production and we may not be able to pursue our business plans.

Key factors beyond production scale and feedstock cost that impact our production costs include yield, productivity, separation efficiency and chemical process efficiency. Yield refers to the amount of the desired molecule that can be produced from a fixed amount of feedstock. Productivity represents the rate at which our product is produced by a given yeast strain. Separation efficiency refers to the amount of desired product produced in the fermentation process that we are able to extract and the time that it takes to do so. Chemical process efficiency refers to the cost and yield for the chemical finishing steps that convert our target molecule into a desired product. In order to successfully enter transportation fuels and certain chemical markets, we must produce those products at significantly lower costs, which will require both substantially higher yields than we have achieved to date and other significant improvements in production efficiency, including in productivity and in separation and chemical process efficiencies. There can be no assurance that we will be able to make these improvements or reduce our production costs sufficiently to offer our planned products at competitive prices, and any such failure could have a material adverse impact on our business and prospects.

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Our ability to establish substantial commercial sales of our products is subject to many risks, any of which could prevent or delay revenue growth and adversely impact our customer relationships, business and results of operations.

There can be no assurance that our products will be approved or accepted by customers, that customers will choose our products over competing products, or that we will be able to sell our products profitably at prices and with features sufficient to establish demand. The markets we have entered first are primarily those for specialty chemical products used by large consumer products or specialty chemical companies. In entering these markets, we have sold and we intend to sell our products as alternatives to chemicals currently in use, and in some cases the chemicals that we seek to replace have been used for many years. The potential customers for our molecules generally have well developed manufacturing processes and arrangements with suppliers of the chemical components of their products and may have a resistance to changing these processes and components. These potential customers frequently impose lengthy and complex product qualification procedures on their suppliers, influenced by consumer preference, manufacturing considerations such as process changes and capital and other costs associated with transitioning to alternative components, supplier operating history, established business relationships and agreements, regulatory issues, product liability and other factors, many of which are unknown to, or not well understood by, us. Satisfying these processes may take many months or years. If we are unable to convince these potential customers (and the consumers who purchase products containing such chemicals) that our products are comparable to the chemicals that they currently use or that the use of our products is otherwise to their benefits, we will not be successful in entering these markets and our business will be adversely affected.

In order for our diesel fuel or jet fuel to be accepted in various countries around the world, a significant number of diesel engine and jet engine manufacturers or operators of large trucking or jet fleets, as the case may be, must determine that the use of our fuels in their equipment will not invalidate product warranties and that they otherwise regard our diesel fuel or jet fuel as an acceptable fuel so that our diesel and jet fuel will have appropriately large and accessible addressable markets. In addition, we must successfully demonstrate to these manufacturers that our fuel does not degrade the performance or reduce the life cycle of their engines or cause them to fail to meet applicable emissions standards. These certification processes include fuel analysis modeling and the testing of engines and their components to ensure that the use of our diesel fuel or jet fuel does not degrade performance or reduce the lifecycle of the engine or cause them to fail to meet applicable emissions standards.

Additionally, we may be subject to product safety testing and may be required to meet certain product safety standards. Meeting these suitability or safety standards can be a time consuming and expensive process, and we may invest substantial time and resources into such qualification efforts without ultimately securing approval. To date, our diesel fuel has achieved limited approvals from certain engine manufacturers, but we cannot be assured that other engine or vehicle manufacturers or fleet operators, will approve usage of our fuels. To distribute our diesel fuel, we must also meet requirements imposed by pipeline operators and fuel distributors. If these operators impose volume limitations on the transport of our fuels, our ability to sell our fuels may be impaired. Our ability to sell a jet fuel product is subject to similar types of qualification requirements as diesel (although the jet fuel qualification process is generally more rigorous, time consuming and expensive than for diesel).

Our ability to enter the fuels market is also dependent upon our ability to continue to achieve the required regulatory approvals in the global markets in which we will seek to sell our fuel products. These approvals primarily involve clearance by the relevant environmental agencies in the particular jurisdiction and are described below under the risk factors, "Our use of genetically-modified feedstocks and yeast strains to produce our products subjects us to risks of regulatory limitations and rejection of our products," "We may not be able to obtain regulatory approval for the sale of our renewable products," and "We may incur significant costs complying with environmental laws and regulations, and failure to comply with these laws and regulations could expose us to significant liabilities."

We expect to face competition for our specialty chemical and transportation fuels products from providers of petroleum-based products and from other companies seeking to provide alternatives to these products, and if we cannot compete effectively against these companies or products we may not be successful in bringing our products to market or further growing our business after we do so.

We expect that our renewable products will compete with both the traditional, largely petroleum-based specialty chemical and fuels products that are currently being used in our target markets and with the alternatives to these existing products that established enterprises and new companies are seeking to produce.

In the specialty chemical markets that we are initially entering, and in other chemical markets that we may seek to enter in the future, we will compete primarily with the established providers of chemicals currently used in products in these markets. Producers of these incumbent products include global oil companies, large international chemical companies and companies specializing in specific products, such as squalane or essential oils. We may also compete in one or more of these markets with products that are offered as alternatives to the traditional petroleum-based or other traditional products being offered in these markets.

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In the transportation fuels market, we expect to compete with independent and integrated oil refiners, advanced biofuels companies and biodiesel companies. Refiners compete with us by selling traditional fuel products and some are also pursuing hydrocarbon fuel production using non-renewable feedstocks, such as natural gas and coal, as well as processes using renewable feedstocks, such as vegetable oil and biomass. We also expect to compete with companies that are developing the capacity to produce diesel and other transportation fuels from renewable resources in other ways. These include advanced biofuels companies using specific enzymes that they have developed to convert cellulosic biomass, which is non-food plant material such as wood chips, corn stalks and sugarcane bagasse, into fermentable sugars. Similar to us, some companies are seeking to use engineered enzymes to convert sugars, in some cases from cellulosic biomass and in others from natural sugar sources, into renewable diesel and other fuels. Biodiesel companies convert vegetable oils and animal oils into diesel fuel and some are seeking to produce diesel and other transportation fuels using thermochemical methods to convert biomass into renewable fuels.

With the emergence of many new companies seeking to produce chemicals and fuels from alternative sources, we may face increasing competition from alternative fuels and chemicals companies. As they emerge, some of these companies may be able to establish production capacity and commercial partnerships to compete with us. If we are unable to establish production and sales channels that allow us to offer comparable products at attractive prices, we may not be able to compete effectively with these companies.

We believe the primary competitive factors in both the chemicals and fuels markets are:

• product price;

• product performance and other measures of quality;

• infrastructure compatibility of products;

• sustainability; and

• dependability of supply.

The oil companies, large chemical companies and well-established agricultural products companies with whom we compete are much larger than us, have, in many cases, well developed distribution systems and networks for their products, have valuable historical relationships with the potential customers we are seeking to serve and have much more extensive sales and marketing programs in place to promote their products. In order to be successful, we must convince customers that our products are at least as effective as the traditional products they are seeking to replace and we must provide our products on a cost basis that does not greatly exceed these traditional products and other available alternatives. Some of our competitors may use their influence to impede the development and acceptance of renewable products of the type that we are seeking to produce.

We believe that for our chemical products to succeed in the market, we must demonstrate that our products are comparable alternatives to existing products and to any alternative products that are being developed for the same markets based on some combination of product cost, availability, performance, and consumer preference characteristics. With respect to our diesel and other transportation fuels products, we believe that our product must perform as effectively as petroleum-based fuel, or alternative fuels, and be available on a cost basis that does not greatly exceed these traditional products and other available alternatives. In addition, with the wide range of renewable fuels products under development, we must be successful in reaching potential customers and convincing them that ours are effective and reliable alternatives.

Our relationship with our strategic partner, Total, has a substantial impact on our company.

We have a license, development, research and collaboration agreement with Total, under which we may develop, produce and commercialize products with Total. Under this agreement, Total has a right of first negotiation with us with respect to certain exclusive commercialization arrangements that we would propose to enter into with third parties, as well as the right to purchase any of our products on terms not less favorable than those offered to or received by us from third parties in any market where Total or its affiliates have a significant market position. These rights might inhibit potential strategic partners or potential customers from entering into negotiations with us about future business opportunities. Total also has the right to terminate this agreement if we undergo a sale or change of control to certain entities, which could discourage a potential acquirer from making an offer to acquire us.

Under certain other agreements with Total related to their original investment in our capital stock, for as long as Total owns 10% of our voting securities, it has rights to an exclusive negotiation period if our Board of Directors decides to sell our company.

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Total also has the right to designate one director to serve on our Board of Directors. Also, in connection with Total’s investments, our certificate of incorporation includes a provision that excludes Total from prohibitions on business combinations between Amyris and an “interested stockholder.” These provisions could have the effect of discouraging potential acquirers from making offers to acquire us, and give Total more access to Amyris than other stockholders if Total decides to pursue an acquisition.

Additionally, in connection with subsequent investments by Total in Amyris, we granted Total, among other investors, a right of first investment if we propose to sell securities in a private placement financing transaction. With these rights, Total and other investors may subscribe for a portion of any new financing and require us to comply with certain notice periods, which could discourage other investors from participating, or cause delays, in our ability to close such a financing. Further, Total and other holders of notes issued in the first and second tranches of the August 2013 Financing (or, the Tranche I Notes and Tranche II Notes, respectively) have a right to cancel certain outstanding Tranche I Notes and Tranche II Notes to exercise pro rata rights under the August 2013 SPA. To the extent Total or other investors exercise these rights, it will reduce the cash proceeds we may realize from the relevant financing. Additionally, under agreements originally signed in July 2012, as subsequently amended, Total previously had the right to cancel up to $30.0 million of certain outstanding convertible promissory notes. Total has since, in financings that closed in December 2012, October 2013, December 2013 and January 2014 used and extinguished approximately $20.3 million of such rights. The remaining approximately $9.7 million of such rights were extinguished by agreement of Amyris and Total in connection with the 144A Offering in May 2014 when we used approximately $9.7 million of the proceeds from the 144A Offering to repay certain senior secured convertible notes held by Total, which amount equaled the amount of Total’s participation in the 144A Offering.

Our joint venture with Total limits our ability to independently develop and commercialize Biofene-based diesel and jet fuels.

In July 2012 and December 2013, we entered into a series of agreements with Total to establish a research and development program and form a joint venture to produce and commercialize Biofene-based diesel and jet fuels. With an exception for our fuels business in Brazil, the collaboration and joint venture establish the exclusive means for us to develop, produce and commercialize fuels from Biofene. We granted the joint venture exclusive licenses under certain of our intellectual property to make and sell joint venture products. We also granted the joint venture, in the event of a buy-out of our interest in the joint venture by Total (which Total is entitled to do under certain circumstances described below) a non-exclusive license to optimize or engineer yeast strains used by us to produce farnesene for the joint venture’s diesel and jet fuels. As a result of these licenses, Amyris generally no longer has an independent right to make or sell Biofene fuels outside of Brazil without the approval of Total. If, for any reason, the joint venture is not fully supported or is not successful and the joint venture does not allow us to pursue Biofene-based fuels independently, this joint venture arrangement could impair our ability to develop and commercialize such fuels, which could have a material adverse effect on our business and long term prospects. For example, these arrangements could adversely affect our ability to enter or expand in these markets on terms that would otherwise be more favorable to us independently or with third parties.

In addition to granting the joint venture exclusive licenses, we also agreed that, if we encounter certain financial hardship situations, such as bankruptcy, insolvency and debt defaults, or upon a change of control of Amyris, Total has a right to buy out our interest in the joint venture at fair market value. The agreements also provide Total with a right to buy out our interest in the joint venture in the event of a “deadlock” in negotiating agreements to establish an operational fuels joint venture following a decision to proceed with the next phase of the joint venture. In a situation where Total buys out our interest in the joint venture, it also has rights to buy our Brazil fuels business at fair market value. If Total were to exercise these rights, we would, in effect, relinquish rights to intellectual property exclusively licensed to the joint venture, and our ability to seek future revenue from Biofene in the fuels market would be adversely affected (or completely prevented). This could significantly reduce the value of our product offerings, and have a material adverse effect on our ability to grow our business in future years.

Total’s collaboration funding is in the form of convertible promissory notes.

Our agreements with Total relating to our fuels collaboration created a convertible debt financing structure for funding the research and development program. The collaboration agreements contemplated approximately $105.0 million in financing for the collaboration, of which Total has funded approximately $94.2 million to date. Pursuant to the March 2014 Letter Agreement between Total and Amyris, we agreed to a reduced conversion price (from $7.0682 to $4.11) for $21.7 million in then unissued convertible promissory notes to be issued under the collaboration. In July 2014, the first issuance of notes with a conversion price of $4.11 occurred when we sold and issued $10.85 million of such notes. Total is expected to fund the remaining $10.85 million by January 2015. Total has a final opportunity to decide whether or not to proceed with the operational fuels joint venture program, with the decision to occur thirty days following the earlier to occur of the completion of the parties' research and development program and December 31, 2016. If, at such time, Total elects not to proceed with the operational fuels joint venture, then licenses to our technology would terminate, and the notes would remain outstanding and become payable at maturity unless otherwise converted in accordance with their terms. If Total chooses to continue the collaboration and makes a final decision to proceed with the operational fuels joint venture, Total is required to buy from Amyris 50% of the preferred shares (all of which are currently

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held by Amyris) of a related joint venture in exchange for full settlement of principal and interest outstanding under the notes. If Total chooses to continue the collaboration and makes a final decision to proceed with the joint venture only for jet fuel, Total is required to buy from Amyris 50% of the preferred shares of the joint venture in exchange for the settlement of 30% of the principal and interest outstanding under the notes. The remaining notes would continue to be outstanding and payable upon maturity unless otherwise converted in accordance with the terms of the notes.

We cannot be certain that Total will ultimately opt to participate in an operational fuels joint venture. If Total were to decide not to proceed with the operational fuels joint venture, the outstanding notes representing amounts paid by Total to date would remain outstanding and become payable or convertible into our common stock. If Total chooses to demand repayment of amounts funded under the notes following such a decision (or a portion of such notes based on a jet fuel-only decision), we may not be able to satisfy our obligations to repay the notes by the maturity date in March 2017, which could lead to defaults and our insolvency, and Total and other creditors could pursue collections claims against us. If the notes become convertible and Total chooses to convert them, the resulting issuance of common stock would be dilutive to other stockholders.

If we do not meet technical, development and commercial milestones in our collaboration agreements, our future revenue and financial results will be adversely impacted.

We have entered into a number of agreements regarding the further development of certain of our products and, in some cases, for ultimate sale of certain products to the customer under the agreement. None of these agreements affirmatively obligates the other party to purchase specific quantities of any products at this time, and most contain important conditions that must be satisfied before additional research and development funding or product purchases would occur. These conditions include research and development milestones and technical specifications that must be achieved to the satisfaction of our collaborators, which we cannot be certain we will achieve. If we do not achieve these contractual milestones, our revenues and financial results will be adversely affected.

We are subject to risks related to our reliance on collaboration arrangements to fund development and commercialization of our products.

For most product markets we are trying to address, we either have or are seeking collaboration partners to fund the research and development, commercialization and production efforts required for the target products. Typically we provide limited exclusive rights and revenue sharing with respect to the production and sale of particular types of products in specific markets in exchange for such up-front funding. These exclusivity, revenue-sharing and other similar terms limit our ability to commercialize our products and technology, and may impact the size of our business or our profitability in ways that we do not currently envision. In addition, revenues from these types of relationships are a key part of our cash plan for 2014 and beyond. If we fail to collect expected collaboration revenues, or to identify and add sufficient additional collaborations to fund our planned operations, we may be unable to fund our operations or pursue development and commercialization of our planned products. To achieve our collaboration revenue targets from year to year, we may be forced to enter into agreements that contain less favorable terms. As part of our current and future collaboration arrangements, we may be required to make significant capital investments at our existing or new facilities in order to produce molecules or other products for such collaborations. Any failure or difficulties in establishing, building up or retooling our operations for these collaboration arrangements could have a significant negative impact on our business, including our ability to achieve commercial viability for our products, lead to the inability to meet our contractual obligations and could cause us to allocate capital, personnel and other resources from our organization which could adversely affect our business and reputation.

Our manufacturing operations require sugar feedstock, and the inability to obtain such feedstock in sufficient quantities or in a timely manner, or at reasonable prices, may limit our ability to produce our products profitably, or at all.

We anticipate that the production of our products will require large volumes of feedstock. We have relied on a mixture of feedstock sources for use at our contract manufacturing operations, including cane sugar, corn-based dextrose and beet molasses. For our large-scale production facilities in Brazil, we are relying primarily on Brazilian sugarcane. We cannot predict the future availability or price of these various feedstocks, nor can we be sure that our mill partners, which we expect to supply the sugarcane feedstock necessary to produce our products in Brazil, will be able to supply it in sufficient quantities or in a timely manner. Furthermore, to the extent we are required to rely on sugar feedstock other than Brazilian sugarcane, the cost of such feedstock may be higher than we expect, increasing our anticipated production costs. Feedstock crop yields and sugar content depend on weather conditions, such as rainfall and temperature. Weather conditions have historically caused volatility in the ethanol and sugar industries by causing crop failures or reduced harvests. Excessive rainfall can adversely affect the supply of sugarcane and other sugar feedstock available for the production of our products by reducing the sucrose content and limiting growers' ability to harvest. Crop disease and pestilence can also occur from time to time and can adversely affect feedstock growth, potentially rendering useless or unusable all or a substantial portion of affected harvests. With respect to sugarcane, our initial primary feedstock,

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seasonal availability and price, the limited amount of time during which it keeps its sugar content after harvest, and the fact that sugarcane is not itself a traded commodity, increases these risks and limits our ability to substitute supply in the event of such an occurrence. If production of sugarcane or any other feedstock we may use to produce our products is adversely affected by these or other conditions, our production will be impaired, and our business will be adversely affected.

The price of sugarcane and other feedstocks can be volatile as a result of changes in industry policy and may increase the cost of production of our products.

In Brazil, Conselho dos Produtores de Cana, Açúcar e Álcool (Council of Sugarcane, Sugar and Ethanol Producers), or Consecana, an industry association of producers of sugarcane, sugar and ethanol, sets market terms and prices for general supply, lease and partnership agreements for sugarcane. If Consecana makes changes to such terms and prices, this could result in higher sugarcane prices and/or a significant decrease in the volume of sugarcane available for the production of our products. Furthermore, if Consecana were to cease to be involved in this process, such prices and terms could become more volatile. Similar principles apply to pricing of other feedstocks as well. Any of these events could adversely affect our business and results of operations.

Our large-scale commercial production capacity is centered in Brazil, and our business will be adversely affected if we do not operate effectively in that country.

For the foreseeable future, we will be subject to risks associated with the concentration of essential product sourcing and operations in Brazil. The Brazilian government has changed in the past, and may change in the future, monetary, taxation, credit, tariff, labor and other policies to influence the course of Brazil's economy. For example, the government's actions to control inflation have at times involved setting wage and price controls, adjusting interest rates, imposing taxes and exchange controls and limiting imports into Brazil. We have no control over, and cannot predict, what policies or actions the Brazilian government may take in the future. Our business, financial performance and prospects may be adversely affected by, among others, the following factors:

• delays or failures in securing licenses, permits or other governmental approvals necessary to build and operate facilities and use our yeast strains to produce products;

• rapid consolidation in the sugar and ethanol industries in Brazil, which could result in a decrease in competition;

• political, economic, diplomatic or social instability in or affecting Brazil;

• changing interest rates;

• tax burden and policies;

• effects of changes in currency exchange rates;

• exchange controls and restrictions on remittances abroad;

• inflation;

• land reform or nationalization movements;

• changes in labor related policies;

• export or import restrictions that limit our ability to move our products out of Brazil or interfere with the import of essential materials into Brazil;

• changes in, or interpretations of foreign regulations that may adversely affect our ability to sell our products or repatriate profits to the United States;

• tariffs, trade protection measures and other regulatory requirements;

• successful compliance with United States and foreign laws that regulate the conduct of business abroad;

• an inability, or reduced ability, to protect our intellectual property in Brazil including any effect of compulsory licensing imposed by government action; and

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• difficulties and costs of staffing and managing foreign operations. 

We cannot predict whether the current or future Brazilian government will implement changes to existing policies on taxation, exchange controls, monetary strategy, labor relations, social security and the like, nor can we estimate the impact of any such changes on the Brazilian economy or our operations.

Our international operations expose us to the risk of fluctuation in currency exchange rates and rates of foreign inflation, which could adversely affect our results of operations.

We currently incur significant costs and expenses in Brazilian real and may in the future incur additional expenses in foreign currencies and derive a portion of our revenues in the local currencies of customers throughout the world. As a result, our revenues and results of operations are subject to foreign exchange fluctuations, which we may not be able to manage successfully. During the past few decades, the Brazilian currency in particular has faced frequent and substantial exchange rate fluctuations in relation to the United States dollar and other foreign currencies. There can be no assurance that the Brazilian real will not significantly appreciate or depreciate against the United States dollar in the future. We also bear the risk that the rate of inflation in the foreign countries where we incur costs and expenses or the decline in value of the United States dollar compared to those foreign currencies will increase our costs as expressed in United States dollars. For example, future measures by the Central Bank of Brazil to control inflation, including interest rate adjustments, intervention in the foreign exchange market and actions to fix the value of the real, may weaken the United States dollar in Brazil. Whether in Brazil or otherwise, we may not be able to adjust the prices of our products to offset the effects of inflation or foreign currency appreciation on our cost structure, which could increase our costs and reduce our net operating margins. If we do not successfully manage these risks through hedging or other mechanisms, our revenues and results of operations could be adversely affected.

Our use of genetically-modified feedstocks and yeast strains to produce our products subjects us to risks of regulatory limitations and rejection of our products.

The use of genetically modified microorganisms (or GMMs), such as our yeast strains, is subject to laws and regulations in many countries, some of which are new and some of which are still evolving. Public attitudes about the safety and environmental hazards of, and ethical concerns over, genetic research and GMMs could influence public acceptance of our technology and products. In the United States, the Environmental Protection Agency (or EPA), regulates the commercial use of GMMs as well as potential products produced from the GMMs. Various states or local governments within the United States could choose to regulate products made with GMMs as well. While the strain of genetically modified yeast that we currently use for the development and anticipate using for the commercial production of our target molecules, S. cerevisiae, is eligible for exemption from EPA review because it is recognized as posing a low risk, we must satisfy certain criteria to achieve this exemption, including but not limited to use of compliant containment structures and safety procedures, and we cannot be sure that we will meet such criteria in a timely manner, or at all. If exemption of S. cerevisiae is not obtained, our business may be substantially harmed. In addition to S. cerevisiae, we may seek to use different GMMs in the future that will require EPA approval. If approval of different GMMs is not secured, our ability to grow our business could be adversely affected.

In Brazil, GMMs are regulated by the National Biosafety Technical Commission (or CTNBio). We have obtained approval from CTNBio to use GMMs in a contained environment in our Campinas facilities for research and development purposes as well as at a contract manufacturing facility in Brazil. In addition, we have obtained initial commercial approval from CTNBio for one of our current yeast strains. As we continue to develop new yeast strains and deploy our technology at new production facilities in Brazil, we will be required to obtain further approvals from CTNBio in order to use these strains in commercial production in Brazil. We may not be able to obtain approvals from relevant Brazilian authorities on a timely basis, or at all, and if we do not, our ability to produce our products in Brazil would be impaired, which would adversely affect our results of operations and financial condition.

In addition to our production operations in the United States and Brazil, we have been party to contract manufacturing agreements with parties in other production locations around the world, including Europe. The use of GMM technology is strictly regulated in the European Union, which has established various directives for member states regarding regulation of the use of such technology, including notification processes for contained use of such technology. We expect to encounter GMM regulations in most, if not all, of the countries in which we may seek to establish production capabilities and/or conduct sales to customers or end-use consumers, and the scope and nature of these regulations will likely be different from country to country. If we cannot meet the applicable requirements in other countries in which we intend to produce products using our yeast strains, or if it takes longer than anticipated to obtain such approvals, our business could be adversely affected.

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We may not be able to obtain regulatory approval for the sale of our renewable products.

Our renewable chemical products may be subject to government regulation in our target markets. In the United States, the EPA administers the Toxic Substances Control Act (or TSCA), which regulates the commercial registration, distribution, and use of many chemicals. Before an entity can manufacture or distribute significant volumes of a chemical, it needs to determine whether that chemical is listed in the TSCA inventory. If the substance is listed, then manufacture or distribution can commence immediately. If not, then in most cases a “Chemical Abstracts Service” number registration and pre-manufacture notice must be filed with the EPA, which has up to 180 days to review the filing. Some of the products we produce or plan to produce, such as farnesene (i.e., Biofene), farnesane (in diesel and new jet fuel applications) and squalane, are already in the TSCA inventory. We may not be able to expediently receive approval from the EPA to list future molecules we would like to make on the TSCA registry, resulting in delays or significant increases in testing requirements. A similar program exists in the European Union, called REACH. Under this program, we need to register our new products with the European Commission, and this process could cause delays or significant costs. To the extent that other geographies, such as Brazil, may rely on TSCA or REACH (or similar laws and programs) for chemical registration in their geographies, delays with the United States or European authorities may subsequently delay entry into these markets as well. In addition, some of our Biofene-derived products are sold for the cosmetics market, and some countries may impose additional regulatory requirements or permits for such uses, which could impair, delay or prevent sales of our products in those markets.

Our diesel and jet fuel is subject to regulation by various government agencies, including the EPA, and the California Air Resources Board (or CARB) in the United States and Agência Nacional do Petróleo, Gas Natural e Biocombustíveis (or ANP), in Brazil. To date, we have obtained registration with the EPA for the use of our diesel fuel in the United States at a 35% blend rate with petroleum diesel. In addition, ANP has authorized the use our diesel fuel at blend rates of 10% and 30% for specific transportation fleets. In Europe, we obtained REACH registration for importing/manufacturing up to 1,000 metric tons of our diesel fuel per year and are pursuing data validation for greater volumes. Registration with each of these bodies is required for the sale and use of our fuels within their respective jurisdictions. Jet fuel (aviation turbine fuel) validation and specifications are subject to the ASTM International industry consensus process and the Brazilian ANP national adoption process. While our jet fuel has been validated and supported by an applicable ASTM aviation turbine fuel standard, the ANP approval remains pending. Any failure to achieve required validation and certifications for our jet fuel could impair or delay our plans to introduce a jet fuel product in 2014, which would have a material adverse impact on our renewable product revenues for the year.In addition, for us to achieve full access to the United States fuels market for our fuel products, we will need to obtain EPA and CARB (and potentially other state agencies) certifications for our feedstock pathway and production facilities, including certification of a feedstock lifecycle analysis relating to greenhouse gas emissions. Any delay in obtaining these additional certifications could impair our ability to sell our renewable fuels to refiners, importers, blenders and other parties that produce transportation fuels as they comply with federal and state requirements to include certified renewable fuels in their products.

We expect to encounter regulations in most, if not all, of the countries in which we may seek to sell our renewable chemical and fuel products (and our customers may encounter similar regulations in selling end use products to consumers), and we cannot assure you that we (or our customers) will be able to obtain necessary approvals in a timely manner or at all. If our chemical and fuel products do not meet applicable regulatory requirements in a particular country or at all, then we (or our customers) may not be able to commercialize our products and our business will be adversely affected.

Changes in government regulations, including subsidies and economic incentives, could have a material adverse effect upon our business.

The market for renewable fuels is heavily influenced by foreign, federal, state and local government regulations and policies. Changes to existing or adoption of new domestic or foreign federal, state and local legislative initiatives that impact the production, distribution or sale of renewable fuels may harm our renewable fuels business. In the United States and in a number of other countries, regulations and policies encouraging production and use of alternative fuels have been modified in the past and may be modified again in the future. Any reduction in mandated requirements for fuel alternatives and additives to gasoline or diesel may cause demand for biofuels to decline and deter investment in the research and development of renewable fuels. The market uncertainty regarding this and future standards and policies may also affect our ability to develop new renewable products or to license our technologies to third parties and to sell products to our end customers. Any inability to address these requirements and any regulatory or policy changes could have a material adverse effect on our business, financial condition and results of operations.

Concerns associated with renewable fuels, including land usage, national security interests and food crop usage, continue to receive legislative, industry and public attention. This attention could result in future legislation, regulation and/or administrative action that could adversely affect our business. Any inability to address these requirements and any regulatory or policy changes could have a material adverse effect on our business, financial condition and results of operations.

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Furthermore, the production of our products will depend on the availability of feedstock, especially sugarcane. Agricultural production and trade flows are subject to government policies and regulations. Governmental policies affecting the agricultural industry, such as taxes, tariffs, duties, subsidies, incentives and import and export restrictions on agricultural commodities and commodity products, can influence the planting of certain crops, the location and size of crop production, whether unprocessed or processed commodity products are traded, the volume and types of imports and exports, and the availability and competitiveness of feedstocks as raw materials. Future government policies may adversely affect the supply of feedstocks, restrict our ability to use sugarcane or other feedstocks to produce our products, and negatively impact our future revenues and results of operations or could encourage the use of feedstocks more advantageous to our competitors which would put us at a commercial disadvantage.

We may incur significant costs complying with environmental laws and regulations, and failure to comply with these laws and regulations could expose us to significant liabilities.

We use hazardous chemicals and radioactive and biological materials in our business and such materials are subject to a variety of federal, state and local laws and regulations governing the use, generation, manufacture, storage, handling and disposal of these materials both in the United States and overseas. Although we have implemented safety procedures for handling and disposing of these materials and related waste products in an effort to comply with these laws and regulations, we cannot be sure that our safety measures will prevent accidental injury or contamination from the use, storage, handling or disposal of hazardous materials. In the event of contamination or injury, we could be held liable for any resulting damages, and any liability could exceed our insurance coverage. There can be no assurance that violations of environmental, health and safety laws will not occur in the future as a result of human error, accident, equipment failure or other causes. Compliance with applicable environmental laws and regulations may be expensive, and the failure to comply with past, present, or future laws could result in the imposition of fines, third party property damage, product liability and personal injury claims, investigation and remediation costs, the suspension of production, or a cessation of operations, and our liability may exceed our total assets. Liability under environmental laws can be joint and several, without regard to comparative fault and may be punitive in nature. Environmental laws could become more stringent over time, imposing greater compliance costs and increasing risks and penalties associated with violations, which could impair our research, development or production efforts and harm our business.

A decline in the price of petroleum and petroleum-based products may reduce demand for some of our renewable products and may otherwise adversely affect our business.

We anticipate that many of our renewable products, and in particular our fuels, will be marketed as alternatives to corresponding petroleum-based products. If the price of oil falls, we may be unable to produce products that are cost-effective alternatives to petroleum-based products. Declining oil prices, or the perception of a future decline in oil prices, may adversely affect the prices we can obtain from our potential customers or prevent potential customers from entering into agreements with us to buy our products. During sustained periods of lower oil prices we may be unable to sell some of our products, which could materially and adversely affect our operating results.

Our financial results could vary significantly from quarter to quarter and are difficult to predict.

Our revenues and results of operations could vary significantly from quarter to quarter because of a variety of factors, many of which are outside of our control. As a result, comparing our results of operations on a period-to-period basis may not be meaningful. Factors that could cause our quarterly results of operations to fluctuate include:

• achievement, or failure, with respect to technology, product development or manufacturing milestones needed to allow us to enter identified markets on a cost effective basis;

• delays or greater than anticipated expenses associated with the completion or commissioning of new production facilities,or the time to ramp up and stabilize production following completion of a new production facility or the transition to, and ramp up of, producing new molecules at our existing facilities;

• impairment of assets based on shifting business priorities and working capital limitations;

• disruptions in the production process at any manufacturing facility, including disruptions due to seasonal or unexpected downtime at our facilities as a result of feedstock availability, contamination, safety or other issues or other technical difficulties or the scheduled downtime at our facilities as a result of transitioning our equipment to the production of different molecules;

• losses associated with producing our products as we ramp to commercial production levels;

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• failure to recover value added tax (or VAT) that we currently reflect as recoverable in our financial statements (e.g., due to failure to meet conditions for reimbursement of VAT under local law);

• the timing, size and mix of sales to customers for our products;

• increases in price or decreases in availability of feedstock;

• the unavailability of contract manufacturing capacity altogether or at reasonable cost;

• exit costs associated with terminating contract manufacturing relationships;

• fluctuations in foreign currency exchange rates;

• gains or losses associated with our hedging activities;

• change in the fair value of derivative instruments;

• fluctuations in the price of and demand for sugar, ethanol, and petroleum-based and other products for which our products are alternatives;

• seasonal variability in production and sales of our products;

• competitive pricing pressures, including decreases in average selling prices of our products;

• unanticipated expenses associated with changes in governmental regulations and environmental, health, labor and safety requirements;

• reductions or changes to existing fuel and chemical regulations and policies;

• departure of executives or other key management employees resulting in transition and severance costs;

• our ability to use our net operating loss carryforwards to offset future taxable income;

• business interruptions such as earthquakes, tsunamis and other natural disasters;

• our ability to integrate businesses that we may acquire;

• our ability to successfully collaborate with business venture partners;

• risks associated with the international aspects of our business; and

• changes in general economic, industry and market conditions, both domestically and in our foreign markets.

As part of our operating plan for 2014, we are planning to keep our expenditures to be relatively consistent with prior years.

Due to the factors described above, among others, the results of any quarterly or annual period may not meet our expectations or the expectations of our investors and may not be meaningful indications of our future performance.

Loss of key personnel, including key management personnel, and/or failure to attract and retain additional personnel could delay our product development programs and harm our research and development efforts and our ability to meet our business objectives.

Our business involves complex, global operations across a variety of markets and requires a management team and employee workforce that is knowledgeable in the many areas in which we operate. As we continue to build our business, we will need to hire and retain qualified research and development, management and other personnel to succeed. The process of hiring, training and successfully integrating qualified personnel into our operations, in the United States, Brazil and other countries we may seek to operate in, is a lengthy and expensive one. The market for qualified personnel is very competitive because of the limited number of people available with the necessary technical skills and understanding of our technology and anticipated products, particularly

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in Brazil. Our failure to hire and retain qualified personnel could impair our ability to meet our research and development and business objectives and adversely affect our results of operations and financial condition.

The loss of any key member of our management or key technical and operational employees, or the failure to attract or retain such employees could prevent us from developing and commercializing our products for our target markets and executing our business strategy. We also may not be able to attract or retain qualified employees in the future due to the intense competition for qualified personnel among biotechnology and other technology-based businesses, particularly in the renewable chemicals and fuels area, or due to the availability of personnel with the qualifications or experience necessary for our business. In addition, reductions to our workforce as part of cost-saving measures may make it more difficult for us to attract and retain key employees. If we do not maintain the necessary personnel to accomplish our business objectives, we may experience staffing constraints that will adversely affect our ability to meet the demands of our collaborators and customers in a timely fashion or to support our internal research and development programs and operations. In particular, our product and process development programs are dependent on our ability to attract and retain highly skilled technical and operational personnel. Competition for such personnel from numerous companies and academic and other research institutions may limit our ability to do so on acceptable terms. All of our employees are at-will employees, which means that either the employee or we may terminate their employment at any time.

Growth may place significant demands on our management and our infrastructure.

We have experienced, and expect to continue to experience, expansion of our business as we continue to make efforts to develop and bring our products to market. We have grown from 18 employees at the end of 2005 to 391at June 30, 2014. Our growth and diversified operations have placed, and may continue to place, significant demands on our management and our operational and financial infrastructure. In particular, continued growth could strain our ability to:

• manage multiple research and development programs;

• operate multiple manufacturing facilities around the world;

• develop and improve our operational, financial and management controls;

• enhance our reporting systems and procedures;

• recruit, train and retain highly skilled personnel;

• develop and maintain our relationships with existing and potential business partners;

• maintain our quality standards; and

• maintain customer satisfaction.

Managing our growth will require significant expenditures and allocation of valuable management resources. If we fail to achieve the necessary level of efficiency in our organization as it grows, our business, results of operations and financial condition would be adversely impacted.

Our proprietary rights may not adequately protect our technologies and product candidates.

Our commercial success will depend substantially on our ability to obtain patents and maintain adequate legal protection for our technologies and product candidates in the United States and other countries. As of June 30, 2014, we had 272 issued United States and foreign patents and 330 pending United States and foreign patent applications that were owned by or licensed to us. We will be able to protect our proprietary rights from unauthorized use by third parties only to the extent that our proprietary technologies and future products are covered by valid and enforceable patents or are effectively maintained as trade secrets.

We apply for patents covering both our technologies and product candidates, as we deem appropriate. However, we may fail to apply for patents on important technologies or product candidates in a timely fashion, or at all. Our existing and future patents may not be sufficiently broad to prevent others from practicing our technologies or from developing competing products or technologies. In addition, the patent positions of companies like ours are highly uncertain and involve complex legal and factual questions for which important legal principles remain unresolved. No consistent policy regarding the breadth of patent claims has emerged to date in the United States and the landscape is expected to become even more uncertain in view of recent rule changes by the United States patent office (or, USPTO). The patent situation outside of the United States is even less predictable. As a result, the validity and enforceability of patents cannot be predicted with certainty. Moreover, we cannot be certain whether:

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• we or our licensors were the first to make the inventions covered by each of our issued patents and pending patent applications;

• we or our licensors were the first to file patent applications for these inventions;

• others will independently develop similar or alternative technologies or duplicate any of our technologies;

• any of our or our licensors' patents will be valid or enforceable;

• any patents issued to us or our licensors will provide us with any competitive advantages, or will be challenged by third parties;

• we will develop additional proprietary products or technologies that are patentable; or

• the patents of others will have an adverse effect on our business.

We do not know whether any of our patent applications or those patent applications that we license will result in the issuance of any patents. Even if patents are issued, they may not be sufficient to protect our technology or product candidates. The patents we own or license and those that may be issued in the future may be challenged, invalidated, rendered unenforceable, or circumvented, and the rights granted under any issued patents may not provide us with proprietary protection or competitive advantages. Moreover, third parties could practice our inventions in territories where we do not have patent protection or in territories where they could obtain a compulsory license to our technology where patented. Such third parties may then try to import products made using our inventions into the United States or other territories. Additional uncertainty may result from legal precedent by the United States Federal Circuit and Supreme Court as they determine legal issues concerning the scope and construction of patent claims and inconsistent interpretation of patent laws by the lower courts. Accordingly, we cannot ensure that any of our pending patent applications will result in issued patents, or even if issued, predict the breadth, validity and enforceability of the claims upheld in our and other companies' patents.

Unauthorized parties may attempt to copy or otherwise obtain and use our products or technology. Monitoring unauthorized use of our intellectual property is difficult, and we cannot be certain that the steps we have taken will prevent unauthorized use of our technology, particularly in certain foreign countries where the local laws may not protect our proprietary rights as fully as in the United States or may provide, today or in the future, for compulsory licenses. If competitors are able to use our technology, our ability to compete effectively could be harmed. Moreover, others may independently develop and obtain patents for technologies that are similar to, or superior to, our technologies. If that happens, we may need to license these technologies, and we may not be able to obtain licenses on reasonable terms, if at all, which could cause harm to our business.

We rely in part on trade secrets to protect our technology, and our failure to obtain or maintain trade secret protection could adversely affect our competitive business position.

We rely on trade secrets to protect some of our technology, particularly where we do not believe patent protection is appropriate or obtainable. However, trade secrets are difficult to maintain and protect. Our strategy for contract manufacturing and scale-up of commercial production requires us to share confidential information with our international business partners and other parties. Our product development collaborations with third parties, including with Total, require us to share confidential information, including with employees of Total who are seconded to Amyris during the term of the collaboration. While we use reasonable efforts to protect our trade secrets, our or our business partners' employees, consultants, contractors or scientific and other advisors may unintentionally or willfully disclose our proprietary information to competitors. Enforcement of claims that a third party has illegally obtained and is using trade secrets is expensive, time consuming and uncertain. In addition, foreign courts are sometimes less willing than United States courts to protect trade secrets. If our competitors independently develop equivalent knowledge, methods and know-how, we would not be able to assert our trade secrets against them.

We require new employees and consultants to execute confidentiality agreements upon the commencement of an employment or consulting arrangement with us. These agreements generally require that all confidential information developed by the individual or made known to the individual by us during the course of the individual's relationship with us be kept confidential and not disclosed to third parties. These agreements also generally provide that inventions conceived by the individual in the course of rendering services to us shall be our exclusive property. Nevertheless, our proprietary information may be disclosed, or these agreements may be unenforceable or difficult to enforce. Additionally, trade secret law in Brazil differs from that in the United States which requires us to take a different approach to protecting our trade secrets in Brazil. Some of these approaches to trade secret protection may be novel and untested under Brazilian law and we cannot guarantee that we would prevail if our trade secrets

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are contested in Brazil. If any of the above risks materializes, our failure to obtain or maintain trade secret protection could adversely affect our competitive business position.

Third parties may misappropriate our yeast strains.

Third parties, including contract manufacturers, sugar and ethanol mill owners, other contractors and shipping agents, often have custody or control of our yeast strains. If our yeast strains were stolen, misappropriated or reverse engineered, they could be used by other parties who may be able to reproduce the yeast strains for their own commercial gain. If this were to occur, it would be difficult for us to challenge and prevent this type of use, especially in countries where we have limited intellectual property protection or that do not have robust intellectual property law regimes.

If we are sued for infringing intellectual property rights or other proprietary rights of third parties, litigation could be costly and time consuming and could prevent us from developing or commercializing our future products.

Our commercial success depends on our ability to operate without infringing the patents and proprietary rights of other parties and without breaching any agreements we have entered into with regard to our technologies and product candidates. We cannot determine with certainty whether patents or patent applications of other parties may materially affect our ability to conduct our business. Our industry spans several sectors, including biotechnology, renewable fuels, renewable specialty chemicals and other renewable compounds, and is characterized by the existence of a significant number of patents and disputes regarding patent and other intellectual property rights. Because patent applications can take several years to issue, there may currently be pending applications, unknown to us, that may result in issued patents that cover our technologies or product candidates. We are aware of a significant number of patents and patent applications relating to aspects of our technologies filed by, and issued to, third parties. The existence of third-party patent applications and patents could significantly reduce the coverage of patents owned by or licensed to us and limit our ability to obtain meaningful patent protection. If we wish to make, use, sell, offer to sell, or import the technology or compound claimed in issued and unexpired patents owned by others, we will need to obtain a license from the owner, enter into litigation to challenge the validity of the patents or incur the risk of litigation in the event that the owner asserts that we infringe its patents. If patents containing competitive or conflicting claims are issued to third parties and these claims are ultimately determined to be valid, we may be enjoined from pursing research, development, or commercialization of products, or be required to obtain licenses to these patents, or to develop or obtain alternative technologies.

If a third-party asserts that we infringe upon its patents or other proprietary rights, we could face a number of issues that could seriously harm our competitive position, including:

• infringement and other intellectual property claims, which could be costly and time consuming to litigate, whether or not the claims have merit, and which could delay getting our products to market and divert management attention from our business;

• substantial damages for past infringement, which we may have to pay if a court determines that our product candidates or technologies infringe a third party's patent or other proprietary rights;

• a court prohibiting us from selling or licensing our technologies or future products unless the holder licenses the patent or other proprietary rights to us, which it is not required to do; and

• if a license is available from a third party, such third party may require us to pay substantial royalties or grant cross licenses to our patents or proprietary rights.

The industries in which we operate, and the biotechnology industry in particular, are characterized by frequent and extensive litigation regarding patents and other intellectual property rights. Many biotechnology companies have employed intellectual property litigation as a way to gain a competitive advantage. If any of our competitors have filed patent applications or obtained patents that claim inventions also claimed by us, we may have to participate in interference proceedings declared by the relevant patent regulatory agency to determine priority of invention and, thus, the right to the patents for these inventions in the United States These proceedings could result in substantial cost to us even if the outcome is favorable. Even if successful, an interference proceeding may result in loss of certain claims. Our involvement in litigation, interferences, opposition proceedings or other intellectual property proceedings inside and outside of the United States, to defend our intellectual property rights or as a result of alleged infringement of the rights of others, may divert management time from focusing on business operations and could cause us to spend significant resources, all of which could harm our business and results of operations.

Many of our employees were previously employed at universities, biotechnology, specialty chemical or oil companies, including our competitors or potential competitors. We may be subject to claims that these employees or we have inadvertently

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or otherwise used or disclosed trade secrets or other proprietary information of their former employers. Litigation may be necessary to defend against these claims. If we fail in defending such claims, in addition to paying monetary damages, we may lose valuable intellectual property rights or personnel and be enjoined from certain activities. A loss of key research personnel or their work product could hamper or prevent our ability to commercialize our product candidates, which could severely harm our business. Even if we are successful in defending against these claims, litigation could result in substantial costs and demand on management resources.

We may need to commence litigation to enforce our intellectual property rights, which would divert resources and management's time and attention and the results of which would be uncertain.

Enforcement of claims that a third party is using our proprietary rights without permission is expensive, time consuming and uncertain. Significant litigation would result in substantial costs, even if the eventual outcome is favorable to us and would divert management's attention from our business objectives. In addition, an adverse outcome in litigation could result in a substantial loss of our proprietary rights and we may lose our ability to exclude others from practicing our technology or producing our product candidates.

The laws of some foreign countries do not protect intellectual property rights to the same extent as do the laws of the United States. Many companies have encountered significant problems in protecting and defending intellectual property rights in certain foreign jurisdictions. The legal systems of certain countries, particularly certain developing countries, do not favor the enforcement of patents and other intellectual property protection, particularly those relating to biotechnology and/or bioindustrial technologies. This could make it difficult for us to stop the infringement of our patents or misappropriation of our other intellectual property rights. Proceedings to enforce our patent rights in foreign jurisdictions could result in substantial costs and divert our efforts and attention from other aspects of our business. Moreover, our efforts to protect our intellectual property rights in such countries may be inadequate.

We do not have exclusive rights to intellectual property we developed under U.S. federally funded research grants and contracts, including with DARPA and we could ultimately share or lose the rights we do have under certain circumstances.

Some of our intellectual property rights have been or may be developed in the course of research funded by the U.S. government, including under our agreements with DARPA. As a result, the U.S. government may have certain rights to intellectual property embodied in our current or future products pursuant to the Bayh-Dole Act of 1980. Government rights in certain inventions developed under a government-funded program include a non-exclusive, non-transferable, irrevocable worldwide license to use inventions for any governmental purpose. In addition, the U.S. government has the right to require us to grant exclusive licenses to any of these inventions to a third party if they determine that: (i) adequate steps have not been taken to commercialize the invention; (ii) government action is necessary to meet public health or safety needs; or (iii) government action is necessary to meet requirements for public use under federal regulations. The U.S. government also has the right to take title to these inventions if we fail to disclose the invention to the government and fail to file an application to register the intellectual property within specified time limits. In addition, the U.S. government may acquire title in any country in which a patent application is not filed within specified time limits. If any of our intellectual property becomes subject to any of the rights or remedies available to the U.S. government or third parties pursuant to the Bayh-Dole Act of 1980, this could impair the value of our intellectual property and could adversely affect our business.

Our products subject us to product-safety risks, and we may be sued for product liability.

The design, development, production and sale of our products involve an inherent risk of product liability claims and the associated adverse publicity. Our potential products could be used by a wide variety of consumers with varying levels of sophistication. Although safety is a priority for us, we are not always in control of the final uses and formulations of the products we supply or their use as ingredients. Our products could have detrimental impacts or adverse impacts we cannot anticipate. Despite our efforts, negative publicity about Amyris, including product safety or similar concerns, whether real or perceived, could occur, and our products could face withdrawal, recall or other quality issues. In addition, we may be named directly in product liability suits relating to our products, even for defects resulting from errors of our commercial partners, contract manufacturers, chemical finishers or customers or end users of our products. These claims could be brought by various parties, including customers who are purchasing products directly from us or other users who purchase products from our customers. We could also be named as co-parties in product liability suits that are brought against the contract manufacturers or Brazilian sugar and ethanol mills with whom we partner to produce our products. Insurance coverage is expensive, may be difficult to obtain and may not be available in the future on acceptable terms. We cannot be certain that our contract manufacturers or the sugar and ethanol producers who partner with us to produce our products will have adequate insurance coverage to cover against potential claims. Any insurance we do maintain may not provide adequate coverage against potential losses, and if claims or losses exceed our liability insurance

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coverage, our business would be adversely impacted. In addition, insurance coverage may become more expensive, which would harm our results of operations.

During the ordinary course of business, we may become subject to lawsuits or indemnity claims, which could materially and adversely affect our business and results of operations.

From time to time, we may in the ordinary course of business be named as a defendant in lawsuits, claims and other legal proceedings. These actions may seek, among other things, compensation for alleged personal injury, worker's compensation, employment discrimination, breach of contract, property damages, civil penalties and other losses of injunctive or declaratory relief. In the event that such actions or indemnities are ultimately resolved unfavorably at amounts exceeding our accrued liability, or at material amounts, the outcome could materially and adversely affect our reputation, business and results of operations. In addition, payments of significant amounts, even if reserved, could adversely affect our liquidity position.

If we fail to maintain an effective system of internal controls, we might not be able to report our financial results accurately or in a timely manner or prevent fraud; in that case, our stockholders could lose confidence in our financial reporting, which would harm our business and could negatively impact the price of our stock.

Effective internal controls are necessary for us to provide reliable financial reports and prevent fraud. In addition, Section 404 of the Sarbanes-Oxley Act of 2002 requires us and our independent registered public accounting firm to evaluate and report on our internal control over financial reporting. The process of implementing our internal controls and complying with Section 404 is expensive and time consuming, and requires significant attention of management. We cannot be certain that these measures will ensure that we maintain adequate controls over our financial processes and reporting in the future. In addition, to the extent we create joint ventures or have any variable interest entities and the financial statements of such entities are not prepared by us, we will not have direct control over their financial statement preparation. As a result, we will, for our financial reporting, depend on what these entities report to us, which could result in us adding monitoring and audit processes and increase the difficulty of implementing and maintaining adequate controls over our financial processes and reporting in the future and could lead to delays in our external reporting. This may be particularly true where we are establishing such entities with commercial partners that do not have sophisticated financial accounting processes in place, or where we are entering into new relationships at a rapid pace, straining our integration capacity. Additionally, if we do not receive the information from the joint venture or variable interest entity on a timely basis, this could cause delays in our external reporting. Even if we conclude, and our independent registered public accounting firm concurs, that our internal control over financial reporting provides reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with generally accepted accounting principles, because of its inherent limitations, internal control over financial reporting may not prevent or detect fraud or misstatements. Failure to implement required new or improved controls, or difficulties encountered in their implementation, could harm our results of operations or cause us to fail to meet our reporting obligations. If we or our independent registered public accounting firm discover a material weakness, the disclosure of that fact, even if quickly remedied, could reduce the market's confidence in our financial statements and harm our stock price. In addition, failure to comply with Section 404 could subject us to a variety of administrative sanctions, including SEC action, ineligibility for short form resale registration, the suspension or delisting of our common stock from the stock exchange on which it is listed, and the inability of registered broker-dealers to make a market in our common stock, which would further reduce our stock price and could harm our business.

If the value of our goodwill or other intangible assets becomes impaired, it could materially reduce the value of our assets and reduce our net income for the year in which the related impairment charges occur.

We apply the applicable accounting principles set forth in the United States Financial Accounting Standards Board's Accounting Standards Codification to our intangible assets (including goodwill), which prohibits the amortization of intangible assets with indefinite useful lives and requires that these assets be reviewed for impairment at least annually. There are several methods that can be used to determine the estimated fair value of the in-process research and development acquired in a business combination. We have used the “income method,” which applies a probability weighting that considers the risk of development and commercialization, to the estimated future net cash flows that are derived from projected sales revenues and estimated costs. These projections are based on factors such as relevant market size, pricing of similar products, and expected industry trends. The estimated future net cash flows are then discounted to the present value using an appropriate discount rate. These assets are treated as indefinite-lived intangible assets until completion or abandonment of the projects, at which time the assets will be amortized over the remaining useful life or written off, as appropriate.If the carrying amount of the assets is greater than the measures of fair value, impairment is considered to have occurred and a write-down of the asset is recorded. Any finding that the value of our intangible assets has been impaired would require us to write-down the impaired portion, which could reduce the value of our assets and reduce our net income for the year in which the related impairment charges occur. As of June 30, 2014, we had a net carrying value of approximately $9.1 million in in-process research and development and goodwill associated with our acquisition of Draths Corporation.

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Our ability to use our net operating loss carryforwards to offset future taxable income may be subject to certain limitations.

In general, under Section 382 of the Internal Revenue Code (or the Code), a corporation that undergoes an “ownership change” is subject to limitations on its ability to utilize its pre-change net operating loss carryforwards (or NOLs), to offset future taxable income. If the Internal Revenue Service challenges our analysis that our existing NOLs are not subject to limitations arising from previous ownership changes, or if we undergo an ownership change, our ability to utilize NOLs could be limited by Section 382 of the Code. Future changes in our stock ownership, some of which are outside of our control, could result in an ownership change under Section 382 of the Code. Furthermore, our ability to utilize NOLs of companies that we may acquire in the future may be subject to limitations. For these reasons, we may not be able to utilize a material portion of the NOLs carryforward as of June 30, 2014, even if we attain profitability.

Loss of, or inability to secure government contract revenues could impair our business.

We have contracts with various governmental agencies, including the United States Department of Energy (or the DOE) and The Defense Advanced Research Projects Agency (or DARPA). Generally, these agreements, as they may be amended or modified from time to time, have fixed terms and may be terminated, modified or be subject to recovery of payments by the government agency under certain conditions (such as failure to comply with detailed reporting and governance processes or failure to achieve milestones). Under these agreements, we are also subject to audits, which can result in corrective action plans and penalties up to and including termination. If these governmental agencies terminate these agreements with us, it could reduce our revenues which could harm our business. Additionally, we anticipate securing additional government contracts as part of our business plan for 2014 and beyond. If we are unable to secure such government contracts, it could harm our business.

Our headquarters and other facilities are located in an active earthquake zone, and an earthquake or other types of natural disasters affecting us or our suppliers could cause resource shortages and disrupt and harm our results of operations.

We conduct our primary research and development operations in the San Francisco Bay Area in an active earthquake and tsunami zone, and certain of our suppliers conduct their operations in the same region or in other locations that are susceptible to natural disasters. In addition, California and some of the locations where certain of our suppliers are located have experienced shortages of water, electric power and natural gas from time to time. The occurrence of a natural disaster, such as an earthquake, drought or flood, or localized extended outages of critical utilities or transportation systems, or any critical resource shortages, affecting us or our suppliers could cause a significant interruption in our business, damage or destroy our facilities, production equipment or inventory or those of our suppliers and cause us to incur significant costs or result in limitations on the availability of our raw materials, any of which could harm our business, financial condition and results of operations. The insurance we maintain against fires, earthquakes and other natural disasters may not be adequate to cover our losses in any particular case.

Risks Related to Ownership of Our Common Stock

Our stock price may be volatile.

The market price of our common stock has been, and we expect it to continue to be, subject to significant volatility, and it has declined significantly from our initial public offering price. As of June 30, 2014, the reported closing price for our common stock on the NASDAQ Global Select Market was $3.73 per share. Market prices for securities of early stage companies have historically been particularly volatile. Such fluctuations could be in response to, among other things, the factors described in this “Risk Factors” section or elsewhere in this report, or other factors, some of which are beyond our control, such as:

• fluctuations in our financial results or outlook or those of companies perceived to be similar to us;

• changes in estimates of our financial results or recommendations by securities analysts;

• changes in market valuations of similar companies;

• changes in the prices of commodities associated with our business such as sugar, ethanol and petroleum;

• changes in our capital structure, such as future issuances of securities or the incurrence of debt;

• announcements by us or our competitors regarding significant contracts, acquisitions or strategic alliances;

• regulatory developments in the United States, Brazil, and/or other foreign countries;

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• litigation involving us, our general industry or both;

• additions or departures of key personnel;

• investors' general perception of us; and

• changes in general economic, industry and market conditions.

Furthermore, stock markets have experienced price and volume fluctuations that have affected, and continue to affect, the market prices of equity securities of many companies. These fluctuations often have been unrelated or disproportionate to the operating performance of those companies. These broad market fluctuations, as well as general economic, political and market conditions, such as recessions, interest rate changes and international currency fluctuations, may negatively affect the market price of our common stock.

In the past, many companies that have experienced volatility and sustained declines in the market price of their stock have become subject to securities class action and derivative action litigation. We were involved in two such lawsuits, which have recently been dismissed, as described in more detail above in "Part II, Item 1 of this Quarterly Report on Form 10-Q, "Legal Proceedings", and we may be the target of similar litigation in the future. Securities litigation against us could result in substantial costs and divert our management's attention from other business concerns, which could seriously harm our business.

The concentration of our capital stock ownership with insiders will limit the ability to influence corporate matters.

As of July 31, 2014 :

• our executive officers and directors and their affiliates (including Total) together held approximately 39.5% of our outstanding common stock;

• Total held approximately 20.5% of our outstanding common stock; and

• the two largest holders of outstanding common stock after Total (Temasek and Biolding Investment SA (or Biolding), each of whom has a designee on our Board of Directors) together held approximately 25.9% of our outstanding common stock.

Furthermore, certain of our largest stockholders, including Total and Temasek, hold convertible promissory notes that under certain circumstances could be converted into common stock, thereby significantly increasing such holders' ownership concentration.

This significant concentration of share ownership may adversely affect the trading price for our common stock because investors often perceive disadvantages in owning stock in companies with controlling stockholders. Also, these stockholders, acting together, will be able to control our management and affairs and matters requiring stockholder approval, including the election of directors and the approval of significant corporate transactions, such as mergers, consolidations or the sale of substantially all of our assets. Consequently, this concentration of ownership may have the effect of delaying or preventing a change of control, including a merger, consolidation or other business combination involving us, or discouraging a potential acquirer from making a tender offer or otherwise attempting to obtain control, even if that change of control would benefit our other stockholders.

If securities or industry analysts do not publish or cease publishing research or reports about us, our business or our market, or if they change their recommendations regarding our stock adversely, our stock price and trading volume could decline.

The trading market for our common stock will be influenced by the research and reports that industry or securities analysts may publish about us, our business, our market or our competitors. If any of the analysts who cover us change their recommendation regarding our stock adversely, or provide more favorable relative recommendations about our competitors, our stock price would likely decline. If any analyst who may cover us were to cease coverage of our company or fail to regularly publish reports on us, we could lose visibility in the financial markets, which in turn could cause our stock price or trading volume to decline.

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We do not expect to declare any dividends in the foreseeable future.

We do not anticipate declaring any cash dividends to holders of our common stock in the foreseeable future. In addition, certain of our equipment leases and credit facilities currently restrict our ability to pay dividends. Consequently, investors may need to rely on sales of their common stock after price appreciation, which may never occur, as the only way to realize any future gains on their investment. Investors seeking cash dividends should not purchase our common stock.

Anti-takeover provisions contained in our certificate of incorporation and bylaws, as well as provisions of Delaware law, could impair a takeover attempt.

Our certificate of incorporation and bylaws contain provisions that could delay or prevent a change in control of our company. These provisions could also make it more difficult for stockholders to elect directors and take other corporate actions. These provisions include:

• a staggered board of directors;

• authorizing the board of directors to issue, without stockholder approval, preferred stock with rights senior to those of our common stock;

• authorizing the board of directors to amend our bylaws and to fill board vacancies until the next annual meeting of the stockholders;

• prohibiting stockholder action by written consent;

• limiting the liability of, and providing indemnification to, our directors and officers;

• eliminating the ability of our stockholders to call special meetings; and

• requiring advance notification of stockholder nominations and proposals. 

Section 203 of the Delaware General Corporation Law prohibits, subject to some exceptions, “business combinations” between a Delaware corporation and an “interested stockholder,” which is generally defined as a stockholder who becomes a beneficial owner of 15% or more of a Delaware corporation's voting stock, for a three-year period following the date that the stockholder became an interested stockholder. We have agreed to opt out of Section 203 through our certificate of incorporation, but our certificate of incorporation contains substantially similar protections to our company and stockholders as those afforded under Section 203, except that we have agreed with Total that it and its affiliates will not be deemed to be “interested stockholders” under such protections.

In addition, we have an agreement with Total, which provides that, so long as Total holds at least 10% of our voting securities, we must inform Total of any offer to acquire us or any decision of our Board of Directors to sell our company, and we must provide Total with information about the contemplated transaction. In such events, Total will have an exclusive negotiating period of fifteen business days in the event the Board of Directors authorizes us to solicit offers to buy Amyris, or five business days in the event that we receive an unsolicited offer to purchase us. This exclusive negotiation period will be followed by an additional restricted negotiation period of ten business days, during which we are obligated to continue to negotiate with Total and will be prohibited from entering into an agreement with any other potential acquirer.

These and other provisions in our amended and restated certificate of incorporation and our amended and restated bylaws that became effective upon the completion of our initial public offering under Delaware law and in our agreements with Total could discourage potential takeover attempts, reduce the price that investors might be willing to pay in the future for shares of our common stock and result in the market price of our common stock being lower than it would be without these provisions.

Conversion of our outstanding convertible promissory notes will dilute the ownership interest of existing stockholders or may otherwise depress the market price of our common stock.

The conversion of some or all of our outstanding convertible promissory notes will dilute the ownership interests of existing stockholders. Any sales in the public market of the shares of our common stock issuable upon such conversion could adversely affect prevailing market prices of our common stock. In addition, the existence of our outstanding convertible promissory notes, particularly the 144A Notes, may encourage short selling by market participants because the anticipated conversion of such notes into shares of our common stock could depress the market price of our common stock.

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ITEM 2. UNREGISTERED SALES OF EQUITY SECURITIES AND USE OF PROCEEDS

Not applicable.

ITEM 3. DEFAULTS UPON SENIOR SECURITIES

Not applicable.

ITEM 4. MINE SAFETY DISCLOSURES

Not applicable.

ITEM 5. OTHER INFORMATION

Not applicable.

ITEM 6. EXHIBITS

The exhibits listed in Exhibit Index immediately preceding the exhibits are filed (other than exhibits 32.01, 32.02 and

101) as part of this Quarterly Report on Form 10-Q and such Exhibit Index is incorporated herein by reference.

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(b) Exhibits.

The following table lists the exhibits filed as part of this report on Form 10-Q. In some cases, these exhibits are incorporated into this report by reference to exhibits to our other filings with the Securities and Exchange Commission. Where an exhibit is incorporated by reference, we have noted the type of form filed with the Securities and Exchange Commission, the

file number of that form, the date of the filing, and the number of the exhibit referenced in that filing.

Exhibit		Previously Filed				Filed
No.	Description	Form	File No.	Filing Date	Exhibit	Herewith
3.01	Restated Certificate of Incorporation	10-Q	001-34885	November 10, 2010	3.01
3.02	Certificate of Amendment to Restated Certificate of Incorporation dated May 12, 2014					X
3.03	Restated Bylaws	10-Q	001-34885	November 10, 2010	3.02
4.01a	Amended and Restated Letter Agreement re: Certain Registration Rights dated May 8, 2014 between registrant and the purchasers listed therein					X
4.02	6.5% Convertible Senior Note due 2019 dated May 29, 2014 issued by registrant to Morgan Stanley & Co. LLC					X
4.03c	6.5% Convertible Senior Note due 2019 dated May 29, 2014 issued by registrant to Maxwell (Mauritius) Pte Ltd.					X
4.04a	1.5% Unsecured Convertible Note dated May 29, 2014 issued by Registrant to Total Energies Nouvelles Activités USA					X
4.05	Indenture dated May 29, 2014 between registrant and Wells Fargo Bank, National Association, as Trustee.	8-K	001-34885	May 29, 2014	4.1
4.06	First Amendment to Loan and Security Agreement dated June 12, 2014 between registrant and Hercules Technology Growth Capital, Inc.					X
10.01a	Modification No. 10 dated April 11, 2014 to Technology Investment Agreement between registrant and The Defense Advanced Research Project Agency (DARPA)					X
10.02a	Modification No. 11 dated May 2, 2014 to Technology Investment Agreement between registrant and The Defense Advanced Research Project Agency (DARPA)					X
10.03a	Pilot Plant Sublease dated April 4, 2014 between registrant and Total New Energies USA, Inc.					X
10.04a	Pilot Plant Services Agreement dated April 4, 2014 between registrant and Total New Energies USA, Inc.					X
10.05bde	Consulting Agreement dated December 6, 2013, between registrant and Steven R. Mills					X
31.01	Certification of Chief Executive Officer pursuant to Securities Exchange Act Rules 13a-14(c) and 15d-14(a), as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002					X

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31.02	Certification of Chief Financial Officer pursuant to Securities Exchange Act Rules 13a-14(c) and 15d-14(a), as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002	X
32.01f	Certification of Chief Executive Officer pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002	X
32.02f	Certification of Chief Financial Officer pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002	X
101g	The following materials from Registrant's Quarterly Report on Form 10-Q for the fiscal quarter ended June 30, 2014, formatted in XBRL (Extensible Business Reporting Language): (i) the Consolidated Statements of Operations; (ii) the Consolidated Balance Sheets; (iii) the Consolidated Statements of Comprehensive Income; (iv) the Consolidated Statements of Convertible Preferred Stock, Redeemable Noncontrolling Interest and Equity (Deficit); (v) the Consolidated Statements of Cash Flows; and (vi) Notes to Consolidated Financial Statements	X

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a	Portions of this exhibit have been omitted pending a determination by the Securities and Exchange Commission as to whether these portions should be granted confidential treatment.
b	Portions of this exhibit, which have been granted confidential treatment by the Securities and Exchange Commission, have been omitted.
c	Registrant issued substantially identical 6.5% Senior Convertible Notes due 2019 (the “6.5% Notes”) to Maxwell (Mauritius) Pte Ltd. (“Temasek”), Total Gas & Power USA, SAS, and Foris Ventures, LLC on May 29, 2014. Registrant has filed the 6.5% Note issued to Temasek, and has included, with Exhibit 4.03, a schedule (Schedule A to Exhibit 4.03) identifying each of the 6.5% Notes and setting forth the material details in which the other 6.5% Notes differ from the filed 6.5% Note (i.e., the note number, the purchasers, and the amounts of the 6.5% Notes).
d	Indicates management contract or compensatory plan or arrangement.
e	Registrant previously filed Exhibit 10.05 in its Annual Report on Form 10-K for the Fiscal Year ending December 31, 2013 as Exhibit 10.66 thereto. Registrant has refiled such exhibit as Exhibit 10.05 to this Quarterly Report on Form 10-Q to correct an improperly routed hyperlink that previously was directed to the wrong exhibit on EDGAR.
f	This certification shall not be deemed “filed” for purposes of Section 18 of the Exchange Act or otherwise subject to the liability of that Section, nor shall it be deemed incorporated by reference into any filing under the Securities Act or the Exchange Act.
g	Pursuant to applicable securities laws and regulations, registrant is deemed to have complied with the reporting obligation relating to the submission of interactive data files in such exhibits and is not subject to liability under any anti-fraud provisions of the federal securities laws as long as registrant has made a good faith attempt to comply with the submission requirements and promptly amends the interactive data files after becoming aware that the interactive data files fails to comply with the submission requirements. These interactive data files are deemed not filed or part of a registration statement or prospectus for purposes of sections 11 or 12 of the Securities Act, are deemed not filed for purposes of section 18 of the Exchange Act and otherwise are not subject to liability under these sections.

(c) Financial statements and schedules.

Reference is made to Item 15(a) above.

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SIGNATURES

Pursuant to the requirements of the Securities Exchange Act of 1934, the registrant has duly caused this report to be signed on its behalf by the undersigned thereunto duly authorized.

Dated: August 8, 2014	AMYRIS, INC.
	/s/ JOHN G. MELO
	John G. Melo
	President and Chief Executive Officer
	(Principal Executive Officer)

Dated: August 8, 2014
	/s/ PAULO DINIZ
	Paulo Diniz
	Interim Chief Financial Officer
	(Principal Financial Officer)

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EXHIBIT INDEX

Exhibit		Previously Filed				Filed
No.	Description	Form	File No.	Filing Date	Exhibit	Herewith
3.01	Restated Certificate of Incorporation	10-Q	001-34885	November 10, 2010	3.01
3.02	Certificate of Amendment to Restated Certificate of Incorporation dated May 12, 2014					X
3.03	Restated Bylaws	10-Q	001-34885	November 10, 2010	3.02
4.01a	Amended and Restated Letter Agreement re: Certain Registration Rights dated May 8, 2014 between registrant and the purchasers listed therein					X
4.02	6.5% Convertible Senior Note due 2019 dated May 29, 2014 issued by registrant to Morgan Stanley & Co. LLC					X
4.03c	6.5% Convertible Senior Note due 2019 dated May 29, 2014 issued by registrant to Maxwell (Mauritius) Pte Ltd.					X
4.04a	1.5% Unsecured Convertible Note dated May 29, 2014 issued by Registrant to Total Energies Nouvelles Activités USA					X
4.05	Indenture dated May 29, 2014 between registrant and Wells Fargo Bank, National Association, as Trustee.	8-K	001-34885	May 29, 2014	4.1
4.06	First Amendment to Loan and Security Agreement dated June 12, 2014 between registrant and Hercules Technology Growth Capital, Inc.					X
10.01a	Modification No. 10 dated April 11, 2014 to Technology Investment Agreement between registrant and The Defense Advanced Research Project Agency (DARPA)					X
10.02a	Modification No. 11 dated May 2, 2014 to Technology Investment Agreement between registrant and The Defense Advanced Research Project Agency (DARPA)					X
10.03a	Pilot Plant Sublease dated April 4, 2014 between registrant and Total New Energies USA, Inc.					X
10.04a	Pilot Plant Services Agreement dated April 4, 2014 between registrant and Total New Energies USA, Inc.					X
10.05bde	Consulting Agreement dated December 6, 2013, between registrant and Steven R. Mills					X
31.01	Certification of Chief Executive Officer pursuant to Securities Exchange Act Rules 13a-14(c) and 15d-14(a), as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002					X
31.02	Certification of Chief Financial Officer pursuant to Securities Exchange Act Rules 13a-14(c) and 15d-14(a), as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002					X

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32.01f	Certification of Chief Executive Officer pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002	X
32.02f	Certification of Chief Financial Officer pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002	X
101g	The following materials from Registrant's Quarterly Report on Form 10-Q for the fiscal quarter ended June 30, 2014, formatted in XBRL (Extensible Business Reporting Language): (i) the Consolidated Statements of Operations; (ii) the Consolidated Balance Sheets; (iii) the Consolidated Statements of Comprehensive Income; (iv) the Consolidated Statements of Convertible Preferred Stock, Redeemable Noncontrolling Interest and Equity (Deficit); (v) the Consolidated Statements of Cash Flows; and (vi) Notes to Consolidated Financial Statements	X

a	Portions of this exhibit have been omitted pending a determination by the Securities and Exchange Commission as to whether these portions should be granted confidential treatment.
b	Portions of this exhibit, which have been granted confidential treatment by the Securities and Exchange Commission, have been omitted.
c	Registrant issued substantially identical 6.5% Senior Convertible Notes due 2019 (the “6.5% Notes”) to Maxwell (Mauritius) Pte Ltd. (“Temasek”), Total Gas & Power USA, SAS, and Foris Ventures, LLC on May 29, 2014. Registrant has filed the 6.5% Note issued to Temasek, and has included, with Exhibit 4.03, a schedule (Schedule A to Exhibit 4.03) identifying each of the 6.5% Notes and setting forth the material details in which the other 6.5% Notes differ from the filed 6.5% Note (i.e., the note number, the purchasers, and the amounts of the 6.5% Notes).
d	Indicates management contract or compensatory plan or arrangement.
e	Registrant previously filed Exhibit 10.05 in its Annual Report on Form 10-K for the Fiscal Year ending December 31, 2013 as Exhibit 10.66 thereto. Registrant has refiled such exhibit as Exhibit 10.05 to this Quarterly Report on Form 10-Q to correct an improperly routed hyperlink that previously was directed to the wrong exhibit on EDGAR.
f	This certification shall not be deemed “filed” for purposes of Section 18 of the Exchange Act or otherwise subject to the liability of that Section, nor shall it be deemed incorporated by reference into any filing under the Securities Act or the Exchange Act.
g	Pursuant to applicable securities laws and regulations, registrant is deemed to have complied with the reporting obligation relating to the submission of interactive data files in such exhibits and is not subject to liability under any anti-fraud provisions of the federal securities laws as long as registrant has made a good faith attempt to comply with the submission requirements and promptly amends the interactive data files after becoming aware that the interactive data files fails to comply with the submission requirements. These interactive data files are deemed not filed or part of a registration statement or prospectus for purposes of sections 11 or 12 of the Securities Act, are deemed not filed for purposes of section 18 of the Exchange Act and otherwise are not subject to liability under these sections.

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EX-3.02

CERTIFICATE OF AMENDMENT

OF THE

RESTATED CERTIFICATE OF INCORPORATION

OF

AMYRIS, INC.

Amyris, Inc., a corporation organized and existing under and by virtue of the General Corporation Law of the State of Delaware (the "Corporation"),

DOES HEREBY CERTIFY THE FOLLOWING:

FIRST: That the name of the Corporation is Amyris, Inc.

SECOND:     That the date on which the Certificate of Incorporation of the Corporation was originally filed with the Secretary of State of Delaware is April 15, 2010 under the name Amyris Biotechnologies, Inc.

THIRD: That, at a meeting of the Board of Directors of the Corporation (the "Board"),the Board duly adopted resolutions setting forth the following proposed amendment of the Restated Certificate of Incorporation of Corporation, declaring said amendment to be advisable and directing the Corporation to submit said amendment to the annual meeting of the stockholders of said Corporation for consideration thereof, and that, thereafter, pursuant to such resolutions, the Corporation submitted the amendment to the stockholders of the Corporation at the annual meeting of the stockholders of the Corporation duly called and held upon notice in accordance with Section 222 of the Delaware General Corporation Law at which meeting the necessary number of shares as required by statute were voted in favor of said amendment:

Section 1 of Article IV of the Corporation's Restated Certificate of Incorporation is hereby amended to read in its entirety as follows:

"1.    Total Authorized. The total number of shares of all classes of stock that the corporation has authority to issue is Three-Hundred and Five Million (305,000,000) shares, consisting of two classes: Three-Hundred Million (300,000,000) shares of Common Stock, $0.0001 par value per share, and Five Million (5,000,000) shares of Preferred Stock, $0.0001 par value per share."

FOURTH: That said amendment was duly adopted in accordance with the provisions of Section 242 of the Delaware General Corporation Law.

IN WITNESS WHEREOF, the Corporation has caused this Certificate of Amendment of the Restated Certificate of Incorporation to be signed by its Senior Vice President, General Counsel and Corporate Secretary this 12th day of May, 2014 and the foregoing facts stated herein are true and correct.

AMYRIS, INC.

By: /s. Nicholas Khadder    

Name: Nicholas Khadder

Title: SVP, General Counsel and Corporate Secretary

EX-4.01

CONFIDENTIAL TREATMENT REQUESTED. CERTAIN PORTIONS OF THIS DOCUMENT HAVE BEEN OMITTED PURSUANT TO A REQUEST FOR CONFIDENTIAL TREATMENT AND, WHERE APPLICABLE, HAVE BEEN MARKED WITH AN ASTERISK TO DENOTE WHERE OMISSIONS HAVE BEEN MADE. THE CONFIDENTIAL MATERIAL HAS BEEN FILED SEPARATELY WITH THE SECURITIES AND EXCHANGE COMMISSION.

May 8, 2014

Amended and Restated Letter Agreement

To the Purchasers Listed

On Schedule A hereto

Dear Purchasers:

In connection with that certain Securities Purchase Agreement, dated as of August 8, 2013, as amended by that Amendment No. 1 to Securities Purchase Agreement dated as of October 16, 2013 and as further amended by that Amendment No. 2 to Securities Purchase Agreement and Tranche I Note Amendment Agreement of even date herewith (as amended, the “Purchase Agreement”), by and among Amyris, Inc., a Delaware corporation (the “Company”), and the purchasers listed on Schedule I thereto (each, a “Purchaser”, and collectively, the “Purchasers”) and that certain Amended and Restated Investors’ Rights Agreement dated as of June 21, 2010, as amended by (i) Amendment No. 1 to Amended and Restated Investors’ Rights Agreement, dated as of February 23, 2012, (ii) Amendment No. 2 to Amended and Restated Investors’ Rights Agreement, dated as of December 24, 2012, (iii) Amendment No. 3 to Amended and Restated Investors’ Rights Agreement, dated as of March 27, 2013, (iv) Amendment No. 4 to Amended and Restated Investors’ Rights Agreement, dated as of October 16, 2013 and (v) Amendment No. 5 to Amended and Restated Investors’ Rights Agreement, dated as of December 24, 2013 (as amended, the “Rights Agreement”), by and among the Company and certain of its stockholders party thereto, and because the Company and the Purchasers wish to amend and restate that certain Letter Agreement dated as of December 24, 2013 by and among the Company and the Purchasers (the “Original Letter Agreement”), the Company and the Purchasers are hereby entering into this amended and restated Letter Agreement (this “A&R Letter Agreement”). Capitalized terms used herein but not otherwise defined shall have the meaning given to such terms in the Rights Agreement.

The Company and the undersigned Purchasers agree to the following:

1.Definitions. As used in this A&R Letter Agreement, the following terms shall have the following meanings:

(a)“Effectiveness Period” means the earlier of (i) such time as all of the Registrable Securities covered by the Registration Statement have been publicly sold by the Purchasers or (ii) the date that all Registrable Securities covered by the Registration Statement may be sold by non-affiliates without volume or manner-of-sale restrictions pursuant to Rule 144, without the requirement for the Company to be in compliance with the current public information requirement under Rule 144 as determined by counsel to the Company pursuant to a written opinion letter to such effect, addressed and reasonably acceptable to the Company’s transfer agent.

(b)“Prospectus” means the prospectus included in the Registration Statement (including, without limitation, a prospectus that includes any information previously omitted from a prospectus filed as part of an effective registration statement in reliance upon Rule 430A promulgated under the Act), as amended or supplemented by any prospectus supplement, with respect to the terms of the offering of any portion of the Registrable Securities covered by the Registration Statement, and all other amendments and supplements to the Prospectus, including post‑effective amendments, and all material incorporated by reference or deemed to be incorporated by reference in such Prospectus.

(c)“Rule 144” means Rule 144 promulgated by the SEC pursuant to the Act, as such Rule may be amended from time to time, or any similar rule or regulation hereafter adopted by the SEC having substantially the same effect as such Rule.

(d)“SEC Guidance” means (i) any publicly-available written or oral guidance, comments, requirements or requests of the SEC staff and (ii) the Act.

2.Registration. The Company, upon receipt of a written request from any Purchaser (a “Registration Request”), hereby agrees that it will (i) within five days of receipt thereof, give written notice of such request to all other Purchasers, and (ii) file a registration statement (the “Registration Statement”) with the SEC covering all of the shares of the Company’s Common Stock that may become issuable upon conversion of the Tranche I Notes (as defined in the Purchase Agreement) and the Tranche II Notes (as defined in the Purchase Agreement) issued pursuant to the Purchase Agreement (such shares of Common Stock, the “Registrable Securities”) by no later than thirty (30) calendar days following the date of receipt of the Registration Request (the “Filing Deadline”); provided, however, that if the Filing Deadline falls on a Saturday, Sunday or other day that the SEC is closed for business, the Filing Deadline shall be extended to the next business day. The Company shall use its commercially reasonable efforts to cause the Registration Statement to be declared effective by the SEC as soon as practicable and no later than the ninetieth (90^th) day following the date of the Registration Request (or, in the event the SEC reviews and has written comments to the Registration Statement, the one hundred twentieth (120^th) calendar day following the date of the Registration Request) (the “Effectiveness Deadline”); provided, however, that if the Effectiveness Deadline falls on a Saturday, Sunday or other day that the SEC is closed for business, the Effectiveness Deadline shall be extended to the next business day.

3.Applicable Provisions. The provisions of Sections 1.4, 1.5, 1.6, 1.9 and 1.10 of the Rights Agreement are hereby incorporated by reference, mutatis mutandis, and shall be deemed to be a part hereof as if restated herein in their entirety; provided, however, that for purposes of this A&R Letter Agreement the references in Section 1.4(a) of the Rights Agreement to “one hundred twenty (120) days” and “120-day period” shall be deemed to be “one hundred eighty (180) days” and “180-day period,” respectively.

4.Representations. The Company hereby represents and warrants to each of the Purchasers that this A&R Letter Agreement and the Rights Agreement are the only agreements pursuant to which registration rights exist in respect of the Registrable Securities.

2    

5.Liquidated Damages. If: (i) following the receipt by the Company of a Registration Request, the Registration Statement is not filed with the SEC on or prior to the Filing Deadline, (ii) following the receipt by the Company of a Registration Request, the Registration Statement is not declared effective by the SEC (or otherwise does not become effective) for any reason on or prior to the later of (x) the Effectiveness Deadline or (y) if SEC Guidance prohibits the Registration Statement from being declared effective until such time as the Company’s definitive proxy statement for the 2014 annual stockholder meeting has been filed, the date immediately following such filing and upon which SEC Guidance permits the Registration Statement to be declared effective, (iii) after the effective date of the Registration Statement (following the receipt by the Company of a Registration Request), (A) the Registration Statement ceases for any reason (including without limitation by reason of a stop order, or the Company’s failure to update the Registration Statement), to remain continuously effective as to all Registrable Securities included in such Registration Statement or (B) the Purchasers are not permitted to utilize the Prospectus therein to resell the Registrable Securities for any reason for more than an aggregate of twenty (20) consecutive calendar days or forty (40) calendar days (which need not be consecutive days) during any twelve (12) month period, or (iv) the Company fails to satisfy the current public information requirement pursuant to Rule 144(c)(1) as a result of which the Purchasers who are not affiliates are unable to sell the Registrable Securities without restriction under Rule 144 (or any successor thereto), (any such failure or breach in clauses (i) through (iv) above being referred to as an “Event,” and, for purposes of clauses (i), (ii) or (iv), the date on which such Event occurs, or for purposes of clause (iii), the date on which such twenty (20) or forty (40) calendar day period is exceeded, being referred to as an “Event Date”), then in addition to any other rights the Purchasers may have hereunder or under applicable law, on each such Event Date and on each 30-day anniversary (or pro rata portion thereof) of each such Event Date (if the applicable Event shall not have been cured by such date) until the earlier of (1) the applicable Event is cured or (2) the Registrable Securities are eligible for resale pursuant to Rule 144 without manner of sale or volume restrictions, the Company shall pay to each Purchaser an amount in cash, as partial liquidated damages and not as a penalty (“Liquidated Damages”), equal (x) on the Event Date and through the fifth 30-day anniversary thereafter, one-half percent (0.5%) of the aggregate purchase price paid by such Purchaser pursuant to the Purchase Agreement for the Securities (as defined in the Purchase Agreement) with respect to which any unregistered Registrable Securities are then held by such Purchaser or would be held by such Purchaser if the Securities held by such Purchaser were converted, and (y) from the sixth 30-day anniversary of the Event Date and thereafter, one percent (1.0%) of the aggregate purchase price paid by such Purchaser pursuant to the Purchase Agreement for the Securities with respect to which any unregistered Registrable Securities are then held by such Purchaser or would be held by such Purchaser if the Securities held by such Purchaser were converted. The parties agree that (1) notwithstanding anything to the contrary herein or in the Purchase Agreement, no Liquidated Damages shall be payable with respect to any period after the expiration of the Effectiveness Period (except in respect of an Event described in clause (iv) above), (it being understood that this sentence shall not relieve the Company of any Liquidated Damages accruing prior to the Effectiveness Deadline) and in no event shall the aggregate amount of Liquidated Damages (excluding Liquidated Damages payable in respect of an Event described in clause (iv) above) payable to a Purchaser exceed, in the aggregate, ten percent (10%) of the aggregate purchase price paid by such Purchaser pursuant to the Purchase Agreement (or twelve percent (12%) if the only Event is clause (iv)) and (2) in no event shall the

3    

Company be liable in any thirty (30) day period for Liquidated Damages under this Agreement in excess of, (x) with respect to the first five 30-day anniversaries after the Event Date, and including the Event Date, one-half percent (0.5%) of the aggregate purchase price paid by the Purchasers pursuant to the Purchase Agreement, and (y) with respect to the sixth 30-day anniversary and any date thereafter, one percent (1.0%) of the aggregate purchase price paid by the Purchasers pursuant to the Purchase Agreement. If the Company fails to pay any Liquidated Damages pursuant to this Section 5 in full within five (5) business days after the date payable, the Company will pay interest thereon at a rate of one and one-half percent (1.5%) per month (or such lesser maximum amount that is permitted to be paid by applicable law) to the Purchaser, accruing daily from the date such Liquidated Damages are due until such amounts, plus all such interest thereon, are paid in full. The Liquidated Damages pursuant to the terms hereof shall apply on a daily pro-rata basis for any portion of a month prior to the cure of an Event. Notwithstanding the foregoing, nothing shall preclude any Purchaser from pursuing or obtaining any available remedies at law, specific performance or other equitable relief with respect to this Section 5 in accordance with applicable law. In such case, the Liquidated Damages shall be calculated to only apply to the percentage of Registrable Securities which are permitted in accordance with SEC Guidance to be included in the Registration Statement.The Effectiveness Deadline for the Registration Statement shall be extended without default or Liquidated Damages hereunder in the event that the Company’s failure to obtain the effectiveness of the Registration Statement on a timely basis results from the failure of a Purchaser to timely provide the Company with information requested by the Company and necessary to complete the Registration Statement in accordance with the requirements of the Act (in which the Effectiveness Deadline would be extended with respect to Registrable Securities held by such Purchaser).

6.Amendment and Waiver.      No amendment, modification, termination or cancellation of this A&R Letter Agreement shall be effective unless it is in writing signed by the Company and each of the Purchasers party hereto. No waiver of any of the provisions of this A&R Letter Agreement shall be deemed or shall constitute a waiver of any other provisions hereof (whether or not similar) nor shall such waiver constitute a continuing waiver.

7.Entire Agreement.    This A&R Letter Agreement, the Purchase Agreement, the Rights Agreement and the agreements contemplated thereby set forth the entire understanding between the parties hereto relating to the subject matter hereof and supersedes and merges all previous written and oral negotiations, commitments, understandings and agreements relating to the subject matter hereof between the Company and the Purchasers, including, without limitation, the terms set forth in the Original Letter Agreement and the subsequent waivers pertaining thereto.

8.Assignment.    This A&R Letter Agreement may not be transferred or assigned (whether by operation of law or otherwise) by either party without the prior written consent of the other party.

9.Notices.    All notices, requests, and other communications hereunder shall be in writing and will be deemed to have been duly given and received (a) when personally delivered, (b) when sent by facsimile or e-mail upon confirmation of receipt, (c) one business day after the day on which the same has been delivered prepaid to a nationally recognized courier service, or

4    

(d) five business days after the deposit in the United States mail, registered or certified, return receipt requested, postage prepaid, in each case addressed, as to the Company, to Amyris, Inc., 5885 Hollis Street, Suite 100, Emeryville, CA 94608, Attn: General Counsel, facsimile number: [*], with a copy to Fenwick & West LLP, 801 California Street, Mountain View, CA 94041, Attn: [*], facsimile number: [*], and as to the Purchaser at the address, facsimile number and e-mail address set forth below the Purchaser’s signature on the signature pages of this A&R Letter Agreement. Any party hereto from time to time may change its address, facsimile number, or other information for the purpose of notices to that party by giving notice specifying such change to the other parties hereto. Each Purchaser and the Company may each agree in writing to accept notices and other communications to it hereunder by electronic communications pursuant to procedures reasonably approved by it; provided that approval of such procedures may be limited to particular notices or communications.

10.Governing Law.    

(a)This A&R Letter Agreement shall be governed by and construed in accordance with the laws of the State of Delaware applicable to contracts entered into therein, without reference to principles of choice of law or conflicts of laws that might lead to the application of laws other than the laws of the State of Delaware.

(b)Any and all disputes arising out of, or in connection with, the interpretation, performance, or nonperformance of this A&R Letter Agreement or any and all disputes arising out of, or in connection with, transactions in any way related to this A&R Letter Agreement and/or the relationship between the parties shall be resolved pursuant to Section 9.6 of the Purchase Agreement.

11.Counterparts. This A&R Letter Agreement may be executed in one or more counterparts, which shall together constitute one agreement.

Please indicate your agreement to the terms of this A&R Letter Agreement by executing the acknowledgement and agreement below and returning a copy to the attention of Nicholas Khadder, our General Counsel.

[Remainder of Page Intentionally Left Blank]

5    

                        Very truly yours,

AMYRIS, INC.

/s/ John G. Melo                        Name: John G. Melo                        Title: President and Chief Executive Officer

[Signature Page to Registration Rights A&R Letter Agreement]

Acknowledged and Agreed as

of the date first written above:

PURCHASERS:

	Maxwell (Mauritius) Pte Ltd
By:	/s/ Rohit Sipahimalani
	(signature)

Name:	Rohit Sipahimalani
	(printed name)
Title:	Authorized Signatory

Address: 60B Orchard Road #06-18 Tower 2, The Atrium @ Orchard Singapore 238891

Fax:

E-mail:

[Signature Page to Registration Rights A&R Letter Agreement]

Acknowledged and Agreed as

of the date first written above:

PURCHASERS:

	Total Energies Nouvelles Activités USA (f.k.a. Total Gas & Power USA, SAS)
By:	/s/ Bernard Clement
	(signature)

Name:	Bernard Clement
	(printed name)
Title:	President

Address:

Fax:

E-mail:

[Signature Page to Registration Rights A&R Letter Agreement]

Acknowledged and Agreed as

of the date first written above:

PURCHASERS:

PYRAMIS LIFECYCLE LARGE CAP STOCK COMMINGLED POOL

By: /s/ Dana Rancourt

Name: Dana Rancourt
Title: DIRECTOR

State Street Bank & Trust

PO Box 5756

Boston, Massachusetts 02206

Attn: FLAPPER CO. FBO Pyramis Lifecycle Large

Cap Stock Commingled Pool

Fax:                    

Email:                    

[Signature Page to Registration Rights A&R Letter Agreement]

Acknowledged and Agreed as

of the date first written above:

PURCHASERS:

VARIABLE INSURANCE PRODUCTS FUND III: GROWTH & INCOME PORTFOLIO

By: /s/ Adrien Deberghes

Name: Adrien Deberghes
Title: Deputy Treasurer

M.Gardiner & Co

C/O JPMorgan Chase Bank, N.A

P.O. Box 35308

Newark, NJ 07101-8006

Fax:                    

Email:                    

[Signature Page to Registration Rights A&R Letter Agreement]

Acknowledged and Agreed as

of the date first written above:

PURCHASERS:

FIDELITY SECURITIES FUND: FIDELITY GROWTH & INCOME PORTFOLIO

By: /s/ Adrien Deberghes

Name: Adrien Deberghes
Title: Deputy Treasurer

The Northern Trust Company

Attn: Trade Securities Processing, C-1N

801 South Canal Street

Chicago, IL 60607

Fidelity Securities Fund: Fidelity Growth &

Income Portfolio. Reference Account# [*]

Fax:                    

Email:                    

[Signature Page to Registration Rights A&R Letter Agreement]

Acknowledged and Agreed as

of the date first written above:

PURCHASERS:

FIDELITY COMMONWEALTH TRUST: FIDELITY LARGE CAP STOCK FUND

By: /s/ Adrien Deberghes

Name: Adrien Deberghes
Title: Deputy Treasurer

Brown Brothers Harriman & Co.

525 Washington Blvd

Jersey City NJ 07310

Attn: [*] 15th Floor

Corporate Actions

Fax:                    

Email:                    

[Signature Page to Registration Rights A&R Letter Agreement]

Acknowledged and Agreed as

of the date first written above:

PURCHASERS:

FIDELITY HASTINGS STREET TRUST: FIDELITY SERIES GROWTH & INCOME FUND

By: /s/ Adrien Deberghes

Name: Adrien Deberghes
Title: Deputy Treasurer

The Northern Trust Company

Attn: Trade Securities Processing, C-1N

801 South Canal Street

Chicago, IL 60607

Fidelity Securities Fund: Fidelity Growth &

Income Portfolio. Reference Account# [*]

Fax:                    

Email:                    

[Signature Page to Registration Rights A&R Letter Agreement]

Acknowledged and Agreed as

of the date first written above:

PURCHASERS:

FIDELITY HASTINGS STREET TRUST: FIDELITY ADVISOR SERIES GROWTH & INCOME FUND

By: /s/ Adrien Deberghes

Name: Adrien Deberghes
Title: Deputy Treasurer

The Northern Trust Company

Attn: Trade Securities Processing, C-1N

801 South Canal Street

Chicago, IL 60607

Fidelity Securities Fund: Fidelity Growth &

Income Portfolio. Reference Account# [*]

Fax:                    

Email:                    

[Signature Page to Registration Rights A&R Letter Agreement]

Acknowledged and Agreed as

of the date first written above:

PURCHASERS:

WOLVERINE FLAGSHIP FUND TRADING LIMITED

BY: WOLVERINE ASSET MANAGEMENT, LLC, ITS INVESTMENT MANAGER

By: /s/ Michael Adamski

Name: Michael Adamski
Title: Chief Legal Officer

c/o Wolverine Asset Management, LLC

175 West Jackson Blvd, Ste 340

Chicago, IL 60604

Fax:    [*]                

Email:    [*]

[Signature Page to Registration Rights A&R Letter Agreement]

Schedule A

Purchaser

Maxwell (Mauritius) Pte Ltd (“Temasek”)

Total Energies Nouvelles Activités USA (“Total”)

Pyramis Lifecycle Large Cap Stock Commingled Pool

Variable Insurance Products Fund III: Growth & Income Portfolio

Fidelity Securities Fund: Fidelity Growth & Income Portfolio

Fidelity Commonwealth Trust: Fidelity Large Cap Stock Fund

Fidelity Hastings Street Trust: Fidelity Series Growth & Income Fund

Fidelity Hastings Street Trust: Fidelity Advisor Series Growth & Income Fund

Wolverine Flagship Fund Trading Limited

EX-4.02

NO AFFILIATE (AS DEFINED IN RULE 144 UNDER THE SECURITIES ACT) OF THE COMPANY OR PERSON THAT HAS BEEN AN AFFILIATE (AS DEFINED IN RULE 144 UNDER THE SECURITIES ACT) OF THE COMPANY DURING THE IMMEDIATELY PRECEDING THREE MONTHS MAY RESELL THIS NOTE OR A BENEFICIAL INTEREST HEREIN.

THIS SECURITY IS A GLOBAL SECURITY WITHIN THE MEANING OF THE INDENTURE HEREINAFTER REFERRED TO AND IS REGISTERED IN THE NAME OF A DEPOSITARY OR A NOMINEE THEREOF. THIS SECURITY MAY NOT BE EXCHANGED IN WHOLE OR IN PART FOR A SECURITY REGISTERED, AND NO TRANSFER OF THIS SECURITY IN WHOLE OR IN PART MAY BE REGISTERED, IN THE NAME OF ANY PERSON OTHER THAN SUCH DEPOSITARY OR A NOMINEE THEREOF, EXCEPT IN THE LIMITED CIRCUMSTANCES DESCRIBED IN THE INDENTURE.

UNLESS THIS CERTIFICATE IS PRESENTED BY AN AUTHORIZED REPRESENTATIVE OF THE DEPOSITORY TRUST COMPANY (“DTC”), A NEW YORK CORPORATION, TO THE COMPANY OR ITS AGENT FOR REGISTRATION OF TRANSFER, EXCHANGE OR PAYMENT, AND ANY CERTIFICATE ISSUED IS REGISTERED IN THE NAME OF CEDE & CO. OR IN SUCH OTHER NAME AS IS REQUESTED BY AN AUTHORIZED REPRESENTATIVE OF DTC (AND ANY PAYMENT IS MADE TO CEDE & CO. OR TO SUCH OTHER ENTITY AS IS REQUESTED BY AN AUTHORIZED REPRESENTATIVE OF DTC), ANY TRANSFER, PLEDGE OR OTHER USE HEREOF FOR VALUE OR OTHERWISE BY OR TO ANY PERSON IS WRONGFUL IN AS MUCH AS THE REGISTERED OWNER HEREOF, CEDE & CO., HAS AN INTEREST HEREIN.

THIS SECURITY AND THE SHARES OF COMMON STOCK ISSUABLE UPON CONVERSION OF THIS SECURITY HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED (THE “SECURITIES ACT”), AND MAY NOT BE OFFERED, SOLD, PLEDGED OR OTHERWISE TRANSFERRED EXCEPT IN ACCORDANCE WITH THE FOLLOWING SENTENCE. BY ITS ACQUISITION HEREOF OR OF A BENEFICIAL INTEREST HEREIN, THE ACQUIRER:

(1) REPRESENTS THAT IT AND ANY ACCOUNT FOR WHICH IT IS ACTING IS A “QUALIFIED INSTITUTIONAL BUYER” (WITHIN THE MEANING OF RULE 144A UNDER THE SECURITIES ACT) AND THAT IT EXERCISES SOLE INVESTMENT DISCRETION WITH RESPECT TO EACH SUCH ACCOUNT, AND

(2) AGREES FOR THE BENEFIT OF AMYRIS, INC. (THE “COMPANY”) THAT IT WILL NOT OFFER, SELL, PLEDGE OR OTHERWISE TRANSFER THIS SECURITY OR ANY BENEFICIAL INTEREST HEREIN PRIOR TO THE DATE THAT IS THE LATER OF (X) ONE YEAR AFTER THE LAST ORIGINAL ISSUE DATE HEREOF OR SUCH SHORTER PERIOD OF TIME AS PERMITTED BY RULE 144 UNDER THE SECURITIES ACT OR ANY SUCCESSOR PROVISION THERETO, AND (Y) SUCH LATER DATE, IF ANY, AS MAY BE REQUIRED BY APPLICABLE LAW, EXCEPT:

(A) TO THE COMPANY OR ANY SUBSIDIARY THEREOF, OR

(B) PURSUANT TO A REGISTRATION STATEMENT WHICH HAS BECOME EFFECTIVE UNDER THE SECURITIES ACT, OR

(C) TO A QUALIFIED INSTITUTIONAL BUYER IN COMPLIANCE WITH RULE 144A UNDER THE SECURITIES ACT, OR

(D) PURSUANT TO AN EXEMPTION FROM REGISTRATION PROVIDED BY RULE 144 UNDER THE SECURITIES ACT OR ANY OTHER AVAILABLE EXEMPTION FROM THE REGISTRATION REQUIREMENTS OF THE SECURITIES ACT.

PRIOR TO THE REGISTRATION OF ANY TRANSFER IN ACCORDANCE WITH CLAUSE (2)(D) ABOVE, THE COMPANY AND THE TRUSTEE RESERVE THE RIGHT TO REQUIRE THE DELIVERY OF SUCH LEGAL OPINIONS, CERTIFICATIONS OR OTHER EVIDENCE AS MAY REASONABLY BE REQUIRED IN ORDER TO DETERMINE THAT THE PROPOSED TRANSFER IS BEING MADE IN COMPLIANCE WITH THE SECURITIES ACT AND APPLICABLE STATE SECURITIES LAWS. NO REPRESENTATION IS MADE AS TO THE AVAILABILITY OF ANY EXEMPTION FROM THE REGISTRATION REQUIREMENTS OF THE SECURITIES ACT.¹ 

¹The restricted legend shall be deemed removed from the face of this security without further action of the Company, the Trustee, or the Holders of this security at such time as the Company instructs the Trustee to remove such legend pursuant to Section 3.08 of the Indenture and upon such removal, the CUSIP No. shall be 03236M AC5.

AMYRIS, INC.

6.50% Convertible Senior Notes due 2019

No. R-1    U.S. $50,300,000

CUSIP NO.    03236M AB7

ISIN NO.    US03236MAB72

Amyris, Inc., a company duly incorporated and validly existing under the laws of the state of Delaware in the United States of America (herein called the “Company”), which term includes any successor corporation under the Indenture referred to on the reverse hereof), for value received hereby promises to pay to CEDE & CO., or registered assigns, the principal sum of FIFTY MILLION THREE HUNDRED THOUSAND UNITED STATES DOLLARS (U.S. $50,300,000) (which amount may from time to time be increased or decreased by adjustments made on the records of the Trustee, as custodian for the Depositary, in accordance with the rules and procedures of the Depositary and in accordance with the below referred Indenture) on May 29, 2019. The Principal Amount of Physical Notes and interest thereon, as provided on the reverse hereof, shall be payable at the Corporate Trust Office and at any other office or agency maintained by the Company for such purpose. The Paying Agent will pay principal of any Note and interest thereon, as provided on the reverse hereof, in immediately available funds to The Depository Trust Company or its nominee, as the case may be, as the registered holder of such global note, on each Interest Payment Date, Fundamental Change Purchase Date or other payment date, as the case may be.

Reference is made to the further provisions of this Note set forth on the reverse hereof, including, without limitation, provisions giving the Holder the right to convert this Note into shares of Common Stock of the Company and to the ability and obligation of the Company to purchase this Note upon certain events, in each case, on the terms and subject to the limitations referred to on the reverse hereof and as more fully specified in the Indenture. Such further provisions shall for all purposes have the same effect as though fully set forth at this place. Capitalized terms used but not defined herein shall have such meanings as are ascribed to such terms in the Indenture. In the case of any conflict between this Note and the Indenture, the provisions of the Indenture shall control.

This Note shall not be valid or become obligatory for any purpose until the certificate of authentication hereon shall have been manually signed by the Trustee or a duly authorized authenticating agent under the Indenture.

IN WITNESS WHEREOF, the Company has caused this instrument to be duly executed.

AMYRIS, INC.

By:     /s/ John Melo    

Name: John Melo

Title: President

Date: May 29, 2014

[Signature Page to Global Note (No. R-1)]

AMYRIS, INC.

6.50% Convertible Senior Notes due 2019

This Note is one of a duly authorized issue of Notes of the Company, designated as its 6.50% Convertible Senior Notes due 2019 (the “Notes”), initially limited in aggregate principal amount to $75,000,000 (or $90,000,000 if the Initial Purchaser exercises its option to purchase additional Notes pursuant to the Purchase Agreement), which amount may from time to time be increased or decreased by adjustments made on the records of the Trustee, as custodian for the Depositary, in accordance with the rules and procedures of the Depositary and in accordance with the below referred Indenture) all issued or to be issued under and pursuant to an Indenture dated as of May 29, 2014 (the “Indenture”) between the Company and Wells Fargo Bank, National Association, as Trustee (the “Trustee”), to which Indenture and all indentures supplemental thereto reference is hereby made for a description of the rights, limitations of rights, obligations, duties and immunities thereunder of the Trustee, the Company and the Holders of the Notes. The Indenture provides that Additional Notes may be issued thereunder, if certain conditions are met.

Interest. The Notes will bear interest at a rate of 6.50% per year. Interest on the Notes will accrue from, and including, May 29, 2014, or from the most recent date to which interest has been paid or duly provided for. Interest will be payable semiannually in arrears on each Interest Payment Date, beginning November 15, 2014. Pursuant to Section 8.03 of the Indenture, in certain circumstances, the Holders of Notes shall be entitled to receive Additional Interest. Payments of the Fundamental Change Repurchase Price, principal and interest that are not made when due will accrue interest per annum at the then-applicable interest rate for the Notes from the required date of payment.

Interest will be paid to the person in whose name a Note is registered at the Close of Business on the May 1 or November 1 (whether or not such date is a Business Day), as the case may be, immediately preceding the relevant Interest Payment Date. Interest on the Notes will be computed on the basis of a 360-day year composed of twelve 30-day months.

Interest will cease to accrue on a Note upon its maturity, conversion or repurchase in connection with a Fundamental Change.

Ranking. The Notes constitute a general unsecured and unsubordinated obligation of the Company.

No Redemption at the Option of the Company. The Notes may not be redeemed at the option of the Company and no sinking fund is provided for the Notes.

Purchase at the Option of the Holder Upon a Fundamental Change. Subject to the terms and conditions of the Indenture, the Company shall become obligated, at the option of the Holder, to repurchase the Notes if a Fundamental Change occurs at any time prior to the Maturity Date at 100% of the Principal Amount together with accrued and unpaid interest to, but excluding, the Fundamental Change Purchase Date, which amount will be paid in cash.

Withdrawal of Fundamental Change Purchase Notice. Holders have the right to withdraw, in whole or in part, any Fundamental Change Purchase Notice by delivering to the Paying Agent a written notice of withdrawal in accordance with the provisions of the Indenture, or in the case of Notes held in book entry form, in accordance with the Applicable Procedures of DTC. The right to withdraw the Fundamental Change Purchase Notice will terminate at the Close of Business on the Business Day immediately preceding the relevant Fundamental Change Purchase Date.

Payment of Fundamental Change Purchase Price. If money sufficient to pay the Fundamental Change Purchase Price of all Notes or portions thereof to be purchased on a Fundamental Change Purchase Date is deposited with the Paying Agent on the Fundamental Change Purchase Date, such Notes will cease to be outstanding and interest will cease to accrue on such Notes (or portions thereof) immediately after the Close of Business on such Fundamental Change Purchase Date, and the Holder thereof shall have no other rights as such (other than the right to receive the Fundamental Change Purchase Price upon surrender of such Note).

Conversion. Subject to and upon compliance with the provisions of the Indenture (including without limitation the conditions of conversion of this Note set forth in Article 6 thereof), the Holder hereof has the right, at its option, to convert the Principal Amount hereof or any portion of such principal which is $1,000 or an integral multiple of $1,000 in excess thereof, into shares of Common Stock at the Applicable Conversion Rate. The Conversion Rate is initially 267.0370 shares of Common Stock per $1,000 Principal Amount of Notes (equivalent to an initial Conversion Price of approximately $3.74), subject to adjustment in certain events described in the Indenture. Upon conversion, the Company will deliver shares of Common Stock and Early Conversion Payment, if applicable, as set forth in the Indenture. No fractional shares will be issued upon any conversion, but a payment in cash will be made, as provided in the Indenture, in respect of any fraction of a share which would otherwise be issuable upon the surrender of any Notes for conversion. Notes in respect of which a Holder is exercising its right to require repurchase on a Fundamental Change Purchase Date may be converted only if such Holder withdraws the related election to exercise such right in accordance with the terms of the Indenture.

In the event of a deposit or withdrawal of an interest in this Note, including an exchange, transfer, repurchase or conversion of this Note in part only, the Trustee, as custodian of the Depositary, shall make an adjustment on its records to reflect such deposit or withdrawal in accordance with the rules and procedures of the Depositary.

Acceleration of Maturity. Subject to certain exceptions in the Indenture, if an Event of Default shall occur and be continuing, the Principal Amount plus interest through such date on all the Notes may be declared due and payable in the manner and with the effect provided in the Indenture.

Supplement Indentures with Consent of Holders; Waiver of Past Defaults. The Indenture permits, with certain exceptions as therein provided, the amendment thereof and the modification of the rights and obligations of the Company and the rights of the Holders of the Notes under the Indenture at any time by the Company and the Trustee with the consent of the Holders of not less than a majority in aggregate Principal Amount of the outstanding Notes. The Indenture also contains provisions permitting the Holders of specified percentages in aggregate Principal Amount of the outstanding Notes, on behalf of the Holders of all the Notes, to waive compliance by the Company with certain provisions of the Indenture and certain past Defaults under the Indenture and their consequences. Any such consent or waiver by the Holder of any provision of or applicable to this Note shall be conclusive and binding upon such Holder and upon all future Holders of this Note and of any Note issued upon the registration of transfer hereof or in exchange herefor or in lieu hereof, whether or not notation of such consent or waiver is made upon this Note.

Registration of Transfer and Exchange. As provided in the Indenture and subject to certain limitations therein set forth, the transfer of this Note is registrable in the Register, upon surrender of this Note for registration of transfer at the office or agency of the Company in the United States, duly endorsed by, or accompanied by a written instrument of transfer in form satisfactory to the Company and the Registrar duly executed by, the Holder hereof or his attorney duly authorized in writing, and thereupon one or more new Notes, of authorized denominations and for the same aggregate Principal Amount, will be issued to the designated transferee or transferees.

No service charge shall be made for any such registration of transfer or exchange, but the Company and the Registrar may require payment of a sum sufficient to cover any tax or other governmental charge payable in connection therewith.

Prior to due presentment of this Note for registration of transfer, the Company, the Trustee and the Registrar and any agent of the Company or the Trustee may treat the Person in whose name this Note is registered as the owner hereof for all purposes, whether or not this Note be overdue, and neither the Company, the Trustee nor any such agent shall be affected by notice to the contrary.

Denominations. The Notes are issuable only in registered form in denominations of $1,000 and any integral multiple of $1,000 in excess thereof, as provided in the Indenture and subject to certain limitations therein set forth. Notes are exchangeable for a like aggregate Principal Amount of Notes of a different authorized denomination, as requested by the Holder surrendering the same.

This Note and any claim, controversy or dispute arising under or related to this Note shall be governed by and construed in accordance with the laws of the State of New York.

All terms used in this Note that are defined in the Indenture shall have the meanings assigned to them in the Indenture.

EX-4.03

THIS SECURITY AND THE SHARES ISSUABLE UPON CONVERSION OF THIS SECURITY HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED (THE “SECURITIES ACT”), AND MAY NOT BE OFFERED, SOLD, PLEDGED OR OTHERWISE TRANSFERRED EXCEPT IN ACCORDANCE WITH THE FOLLOWING SENTENCE.  BY ITS ACQUISITION HEREOF, THE ACQUIRER:

(1) REPRESENTS THAT IT AND ANY ACCOUNT FOR WHICH IT IS ACTING IS A “QUALIFIED INSTITUTIONAL BUYER” (WITHIN THE MEANING OF RULE 144A UNDER THE SECURITIES ACT) AND THAT IT EXERCISES SOLE INVESTMENT DISCRETION WITH RESPECT TO EACH SUCH ACCOUNT, AND

(2) AGREES FOR THE BENEFIT OF AMYRIS, INC. THAT IT WILL NOT OFFER, SELL, PLEDGE OR OTHERWISE TRANSFER THIS SECURITY OR ANY BENEFICIAL INTEREST HEREIN PRIOR TO THE DATE THAT IS THE LATER OF (X) ONE YEAR AFTER THE LAST ORIGINAL ISSUE DATE HEREOF OR SUCH SHORTER PERIOD OF TIME AS PERMITTED BY RULE 144 UNDER THE SECURITIES ACT OR ANY SUCCESSOR PROVISION THEREUNDER, AND (Y) SUCH LATER DATE, IF ANY, AS MAY BE REQUIRED BY APPLICABLE LAW, EXCEPT:

(A) AMYRIS, INC. OR ANY SUBSIDIARY THEREOF, OR

(B) PURSUANT TO A REGISTRATION STATEMENT WHICH HAS BECOME EFFECTIVE UNDER THE SECURITIES ACT.

THIS SECURITY AND THE COMMON STOCK ISSUABLE UPON CONVERSION OF THIS SECURITY ARE HELD BY AN AFFILIATE OF THE COMPANY AND ARE SUBJECT TO ADDITIONAL RESTRICTIONS ON TRANSFER UNDER RULE 144 UNDER THE SECURITIES ACT.

AMYRIS, INC.

6.50% Convertible Senior Notes due 2019

No. A-1    U.S. $10,000,000

Amyris, Inc., a company duly incorporated and validly existing under the laws of the state of Delaware in the United States of America (herein called the “Company”), which term includes any successor corporation under the Indenture referred to on the reverse hereof), for value received hereby promises to pay to Maxwell (Mauritius) Pte Ltd or registered assigns, the principal sum of TEN MILLION UNITED STATES DOLLARS (U.S. $10,000,000) on May 29, 2019. The Principal Amount of Physical Notes and interest thereon, as provided on the reverse hereof, shall be payable at the Corporate Trust Office and at any other office or agency maintained by the Company for such purpose. The Paying Agent will pay principal of any Note and interest thereon, as provided on the reverse hereof, in immediately available funds to the Holder on each Interest Payment Date, Fundamental Change Purchase Date or other payment date, as the case may be.

Reference is made to the further provisions of this Note set forth on the reverse hereof, including, without limitation, provisions giving the Holder the right to convert this Note into shares of Common Stock of the Company and to the ability and obligation of the Company to purchase this Note upon certain events, in each case, on the terms and subject to the limitations referred to on the reverse hereof and as more fully specified in the Indenture. Such further provisions shall for all purposes have the same effect as though fully set forth at this place. Capitalized terms used but not defined herein shall have such meanings as are ascribed to such terms in the Indenture. In the case of any conflict between this Note and the Indenture, the provisions of the Indenture shall control.

This Note shall not be valid or become obligatory for any purpose until the certificate of authentication hereon shall have been manually signed by the Trustee or a duly authorized authenticating agent under the Indenture.

IN WITNESS WHEREOF, the Company has caused this instrument to be duly executed.

AMYRIS, INC.

By:     /s/ John Melo    

Name: John Melo

Title: President

Date: May 29, 2014

[Signature Page to Affiliate Note (No A-1)]

AMYRIS, INC.

6.50% Convertible Senior Notes due 2019

This Note is one of a duly authorized issue of Notes of the Company, designated as its 6.50% Convertible Senior Notes due 2019 (the “Notes”), initially limited in aggregate principal amount to $75,000,000 (or $90,000,000 if the Initial Purchaser exercises its option to purchase additional Notes pursuant to the Purchase Agreement), which amount may from time to time be increased or decreased by adjustments made on the records of the Trustee, as custodian for the Depositary, in accordance with the rules and procedures of the Depositary and in accordance with the below referred Indenture) all issued or to be issued under and pursuant to an Indenture dated as of May 29, 2014 (the “Indenture”) between the Company and Wells Fargo Bank, National Association, as Trustee (the “Trustee”), to which Indenture and all indentures supplemental thereto reference is hereby made for a description of the rights, limitations of rights, obligations, duties and immunities thereunder of the Trustee, the Company and the Holders of the Notes. The Indenture provides that Additional Notes may be issued thereunder, if certain conditions are met.

Interest. The Notes will bear interest at a rate of 6.50% per year. Interest on the Notes will accrue from, and including, May 29, 2014, or from the most recent date to which interest has been paid or duly provided for. Interest will be payable semiannually in arrears on each Interest Payment Date, beginning November 15, 2014. Pursuant to Section 8.03 of the Indenture, in certain circumstances, the Holders of Notes shall be entitled to receive Additional Interest. Payments of the Fundamental Change Repurchase Price, principal and interest that are not made when due will accrue interest per annum at the then-applicable interest rate for the Notes from the required date of payment.

Interest will be paid to the person in whose name a Note is registered at the Close of Business on the May 1 or November 1 (whether or not such date is a Business Day), as the case may be, immediately preceding the relevant Interest Payment Date. Interest on the Notes will be computed on the basis of a 360-day year composed of twelve 30-day months.

Interest will cease to accrue on a Note upon its maturity, conversion or repurchase in connection with a Fundamental Change.

Ranking. The Notes constitute a general unsecured and unsubordinated obligation of the Company.

No Redemption at the Option of the Company. The Notes may not be redeemed at the option of the Company and no sinking fund is provided for the Notes.

Purchase at the Option of the Holder Upon a Fundamental Change. Subject to the terms and conditions of the Indenture, the Company shall become obligated, at the option of the Holder, to repurchase the Notes if a Fundamental Change occurs at any time prior to the Maturity Date at 100% of the Principal Amount together with accrued and unpaid interest to, but excluding, the Fundamental Change Purchase Date, which amount will be paid in cash.

Withdrawal of Fundamental Change Purchase Notice. Holders have the right to withdraw, in whole or in part, any Fundamental Change Purchase Notice by delivering to the Paying Agent a written notice of withdrawal in accordance with the provisions of the Indenture, or in the case of Notes held in

book entry form, in accordance with the Applicable Procedures of DTC. The right to withdraw the Fundamental Change Purchase Notice will terminate at the Close of Business on the Business Day immediately preceding the relevant Fundamental Change Purchase Date.

Payment of Fundamental Change Purchase Price. If money sufficient to pay the Fundamental Change Purchase Price of all Notes or portions thereof to be purchased on a Fundamental Change Purchase Date is deposited with the Paying Agent on the Fundamental Change Purchase Date, such Notes will cease to be outstanding and interest will cease to accrue on such Notes (or portions thereof) immediately after the Close of Business on such Fundamental Change Purchase Date, and the Holder thereof shall have no other rights as such (other than the right to receive the Fundamental Change Purchase Price upon surrender of such Note).

Conversion. Subject to and upon compliance with the provisions of the Indenture (including without limitation the conditions of conversion of this Note set forth in Article 6 thereof), the Holder hereof has the right, at its option, to convert the Principal Amount hereof or any portion of such principal which is $1,000 or an integral multiple of $1,000 in excess thereof, into shares of Common Stock at the Applicable Conversion Rate. The Conversion Rate is initially 267.0370 shares of Common Stock per $1,000 Principal Amount of Notes (equivalent to an initial Conversion Price of approximately $3.74), subject to adjustment in certain events described in the Indenture. Upon conversion, the Company will deliver shares of Common Stock and Early Conversion Payment, if applicable, as set forth in the Indenture. No fractional shares will be issued upon any conversion, but a payment in cash will be made, as provided in the Indenture, in respect of any fraction of a share which would otherwise be issuable upon the surrender of any Notes for conversion. Notes in respect of which a Holder is exercising its right to require repurchase on a Fundamental Change Purchase Date may be converted only if such Holder withdraws the related election to exercise such right in accordance with the terms of the Indenture.

In the event of a deposit or withdrawal of an interest in this Note, including an exchange, transfer, repurchase or conversion of this Note in part only, the Trustee, as custodian of the Depositary, shall make an adjustment on its records to reflect such deposit or withdrawal in accordance with the rules and procedures of the Depositary.

Acceleration of Maturity. Subject to certain exceptions in the Indenture, if an Event of Default shall occur and be continuing, the Principal Amount plus interest through such date on all the Notes may be declared due and payable in the manner and with the effect provided in the Indenture.

Supplement Indentures with Consent of Holders; Waiver of Past Defaults. The Indenture permits, with certain exceptions as therein provided, the amendment thereof and the modification of the rights and obligations of the Company and the rights of the Holders of the Notes under the Indenture at any time by the Company and the Trustee with the consent of the Holders of not less than a majority in aggregate Principal Amount of the outstanding Notes. The Indenture also contains provisions permitting the Holders of specified percentages in aggregate Principal Amount of the outstanding Notes, on behalf of the Holders of all the Notes, to waive compliance by the Company with certain provisions of the Indenture and certain past Defaults under the Indenture and their consequences. Any such consent or waiver by the Holder of any provision of or applicable to this Note shall be conclusive and binding upon such Holder and upon all future Holders of this Note and of any Note issued upon the registration of transfer hereof or in exchange herefor or in lieu hereof, whether or not notation of such consent or waiver is made upon this Note.

Registration of Transfer and Exchange. As provided in the Indenture and subject to certain limitations therein set forth, the transfer of this Note is registrable in the Register, upon surrender of this Note for registration of transfer at the office or agency of the Company in the United States, duly endorsed by, or accompanied by a written instrument of transfer in form satisfactory to the Company and the Registrar duly executed by, the Holder hereof or his attorney duly authorized in writing, and thereupon one or more new Notes, of authorized denominations and for the same aggregate Principal Amount, will be issued to the designated transferee or transferees.

No service charge shall be made for any such registration of transfer or exchange, but the Company and the Registrar may require payment of a sum sufficient to cover any tax or other governmental charge payable in connection therewith.

Prior to due presentment of this Note for registration of transfer, the Company, the Trustee and the Registrar and any agent of the Company or the Trustee may treat the Person in whose name this Note is registered as the owner hereof for all purposes, whether or not this Note be overdue, and neither the Company, the Trustee nor any such agent shall be affected by notice to the contrary.

Denominations. The Notes are issuable only in registered form in denominations of $1,000 and any integral multiple of $1,000 in excess thereof, as provided in the Indenture and subject to certain limitations therein set forth. Notes are exchangeable for a like aggregate Principal Amount of Notes of a different authorized denomination, as requested by the Holder surrendering the same.

This Note and any claim, controversy or dispute arising under or related to this Note shall be governed by and construed in accordance with the laws of the State of New York.

All terms used in this Note that are defined in the Indenture shall have the meanings assigned to them in the Indenture.

Schedule A

Notes Issued by Registrant

Note Number	Purchaser	Amount
A-1	Maxwell (Mauritius) Pte Ltd		$10,000,000
A-2	Total Energies Nouvelles Activités USA		$9,700,000
A-3	Foris Ventures LLC		$5,000,000

EX-4.04

CONFIDENTIAL TREATMENT REQUESTED. CERTAIN PORTIONS OF THIS DOCUMENT HAVE BEEN OMITTED PURSUANT TO A REQUEST FOR CONFIDENTIAL TREATMENT AND, WHERE APPLICABLE, HAVE BEEN MARKED WITH AN ASTERISK TO DENOTE WHERE OMISSIONS HAVE BEEN MADE. THE CONFIDENTIAL MATERIAL HAS BEEN FILED SEPARATELY WITH THE SECURITIES AND EXCHANGE COMMISSION.

1.5% SENIOR SECURED CONVERTIBLE NOTE

RS-6    May 29, 2014

U.S. $8,300,751.86

THE SECURITIES REPRESENTED BY THIS NOTE AND THE SECURITIES ISSUABLE UPON ITS CONVERSION HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED (THE “ACT”), OR SECURITIES LAWS OF ANY STATE AND MAY NOT BE OFFERED, SOLD, ASSIGNED, PLEDGED TRANSFERRED OR OTHERWISE DISPOSED OF IN THE ABSENCE OF AN EFFECTIVE REGISTRATION STATEMENT UNDER THE ACT AND APPLICABLE STATE SECURITIES LAWS OR PURSUANT TO AN AVAILABLE EXEMPTION FROM REGISTRATION UNDER THE ACT OR SUCH LAWS AND, IF REASONABLY REQUESTED BY THE COMPANY, UPON DELIVERY OF AN OPINION OF COUNSEL REASONABLY SATISFACTORY TO THE COMPANY THAT THE PROPOSED TRANSFER IS EXEMPT FROM THE ACT OR SUCH LAWS. THIS NOTE IS ALSO SUBJECT TO THE TRANSFER RESTRICTIONS CONTAINED IN THE SECURITIES PURCHASE AGREEMENT, DATED AS OF JULY 30, 2012, AMONG THE COMPANY AND TOTAL ENERGIES NOUVELLES ACTIVITÉS USA (FORMERLY KNOWN AS TOTAL GAS & POWER USA, SAS).

FOR VALUE RECEIVED, the undersigned, Amyris, Inc., a Delaware corporation (the “Company”), promises to pay to Total Energies Nouvelles Activités USA (formerly known as Total Gas & Power USA, SAS), a société par actions simplifiée organized under the laws of the Republic of France, or its Permitted Transferees pursuant to Section 13 of this Note (the “Investor”), in lawful money of the United States and in immediately available funds (or in shares of Common Stock as provided herein), U.S. $8,300,751.86 (the “Face Amount”), all in accordance with the provisions of this Note. The “Issue Date” of this Note is May 29, 2014.

This Note was issued pursuant to the Securities Purchase Agreement, dated as of July 30, 2012 (as amended from time to time, the “Agreement”), among the Company and the Investor. Unless the context otherwise requires, as used herein, “Note” means any of the Convertible Notes issued to the Investor pursuant to the Agreement and any other similar convertible notes issued by the Company in exchange for, or to effect a transfer of, any Note and “Notes” means all such Notes in the aggregate. This Note is issued as a replacement for RS-5, issued January 15, 2014 (the “Exchanged Note”), a portion of which was prepaid and cancelled on the date hereof. The Exchanged Note was issued in exchange for Note RS-4 originally issued on December 3, 2013 pursuant to the Agreement. Note RS-4 was issued in exchange for Note R-3 originally issued on December 24, 2012 pursuant to the Agreement. Note R-3 was initially issued in a principal amount equal to $33,300,001.04 in exchange for Note R-1 originally issued on July 30, 2012 (the “Original Issue Date”) pursuant to the Agreement. On October 16, 2013, a portion of Note R-3 was cancelled and a replacement Note was issued in a principal amount equal to $24,047,816.63. On January 15, 2014 a portion of Note R-4 was cancelled and the

Exchanged Note was issued as a replacement of the remaining principal amount equal to $18,005,751.86.

The Company’s liabilities, obligations and indebtedness to the Investor for monetary amounts, whether now or hereafter owing, arising, due or payable under this Note (collectively, the “Obligations”), are secured by a lien on all of the Company’s right, title and interests in and to the Company’s shares in the capital of Total Amyris BioSolutions B.V., a private company with limited liability organized under the laws of the Netherlands (besloten vennootschap met beperkte aansprakelijkheid) (“JVCO”), as well as certain additional collateral pursuant to a pledge agreement executed as a notarial deed as of as of December 2, 2013 before B.J. Kuck, civil law notary in Amsterdam, the Netherlands, or his deputy, by the Company in favor of the Investor, and in the presence of and acknowledged by JVCO, as amended from time to time.

1.Definitions. For purposes of this Note, the following definitions shall be applicable:

“Affiliate” of any specified person means any other person directly or indirectly controlling or controlled by or under direct or indirect common control with such specified person; for purposes of this definition, “control” (including, with correlative meanings, the terms “controlling,” “controlled by” and ‘under common control with”), as used with respect to any person, shall mean the possession, directly or indirectly, of the power to direct or cause the direction of the management or policies of such person, whether through the ownership of voting securities, by agreement or otherwise.

“Amyris License Agreement” has the meaning ascribed thereto in the Shareholders Agreement.

“Bankruptcy Law” means Title 11, U.S. Code or any similar federal or state law for the relief of debtors.

“Boardof Directors” means the board of directors of the Company.

“Business Day” means any day other than a Saturday, a Sunday or a day on which the Federal Reserve Bank of New York is authorized or required by law or executive order to close or be closed.

“Capital Lease Obligation” means, at the time any determination thereof is to be made, the amount of the liability in respect of a capital lease that would at such time be required to be capitalized on a balance sheet in accordance with GAAP.

“Certificate of Incorporation” means the Company’s Restated Certificate of Incorporation, as amended and as in effect on the date hereof.

“Change of Control” shall mean the occurrence of any of the following: (i) the consolidation of the Company with, or the merger of the Company with or into, another “person” (as such term is used in Rule 13d-3 and Rule 13d-5 of the Exchange Act), or the sale, lease, transfer, conveyance or other disposition, in one or a series of related transactions, of all or substantially all of the assets of the Company and its Subsidiaries taken as a whole, or the consolidation of another “person” with, or the merger of another “person” into, the Company,

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other than in each case pursuant to a transaction in which the “persons” that “beneficially owned” (as such term is defined in Rule 13d-3 and Rule 13d-5 under the Exchange Act), directly or indirectly, the Voting Shares of the Company immediately prior to the transaction “beneficially own”, directly or indirectly, Voting Shares representing at least a majority of the total voting power of all outstanding classes of voting stock of the surviving or transferee person; (ii) the adoption by the Company of a plan relating to the liquidation or dissolution of the Company; (iii) the consummation of any transaction (including, without limitation, any merger or consolidation) the result of which is that any “person” becomes the “beneficial owner” directly or indirectly, of more than 50% of the Voting Shares of the Company (measured by voting power rather than number of shares); or (iv) the first day on which a majority of the members of the Board of Directors does not consist of Continuing Directors.

“Class A Note” has the meaning ascribed thereto in the Shareholders Agreement.

“Closing Price” of the shares of Common Stock on any day means the last reported sale price regular way on such day or, in the case no such sale takes place on such day, the average of the reported closing bid and asked prices regular way of the shares of Common Stock, in each case as quoted on The NASDAQ Stock Market or such other principal securities exchange or inter-dealer quotation system on which the shares of Common Stock are then traded.

“Common Stock” means the Company’s common stock, $0.0001 par value per share (or such other security into which such Common Stock is exchanged for (or becomes) pursuant to the consummation of a Capital Reorganization (as defined in Section 3(g))).

“Continuing Director” shall mean, as of any date of determination, any member of the Board of Directors who (i) was a member of the Board of Directors on July 31, 2012 or (ii) was nominated for election or elected to the Board of Directors with the approval of a majority of the Continuing Directors who were members of the Board of Directors at the time of such nomination or election and who voted with respect to such nomination or election; provided that a majority of the members of the Board of Directors voting with respect thereto shall at the time have been Continuing Directors.

“Debt” shall mean, with respect to any person, any indebtedness of such person, whether or not contingent, in respect of borrowed money or evidenced by bonds, notes, debentures or similar instruments or letters of credit (or reimbursement agreements in respect thereof) or banker’s acceptances or representing Capital Lease Obligations or the balance deferred and unpaid of the purchase price of any property or representing any Hedging Obligations, except any such balance that constitutes an accrued expense or trade payable, if and to the extent any of the foregoing indebtedness (other than letters of credit and Hedging Obligations) would appear as a liability upon a balance sheet of such Person prepared in accordance with GAAP, as well as all Debt of others secured by a Lien on any asset of such Person (whether or not such Debt is assumed by such Person) and Lease Debt and, to the extent not otherwise included, the Guarantee by such Person of any Debt of any other Person. The indebtedness of the Company represented by this Note shall constitute Debt. The amount of any Debt outstanding as of any date shall be (i) the accreted value thereof, in the case of any Debt that does not require current payments of interest or (ii) the principal amount thereof, together with any interest thereon that is more than 30 days past due, in the case of any other Debt.

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“Default” means any event that is or with the passage of time or the giving of notice or both would be an Event of Default.

“Disqualified Stock” means any capital stock that, by its terms (or by the terms of any security into which it is convertible, or for which it is exchangeable, in each case, at the option of the holder of the capital stock), or upon the happening of any event, matures or is mandatorily redeemable, pursuant to a sinking fund obligation or otherwise, or redeemable at the option of the holder of the capital stock, in whole or in part, on or prior to the date that is 91 days after the date on which this Note matures. The amount of Disqualified Stock deemed to be outstanding at any time will be the maximum amount that the Company and its Subsidiaries may become obligated to pay upon the maturity of, or pursuant to any mandatory redemption provisions of, such Disqualified Stock, exclusive of accrued dividends.

“Exchange Act” means the Securities Exchange Act of 1934, as amended, and the rules and regulations thereunder.

“Final Go Decision Date” has the meaning ascribed thereto in the Shareholders Agreement.

“GAAP” means generally accepted accounting principles set forth in the opinions and pronouncements of the Accounting Principles Board of the American Institute of Certified Public Accountants and statements and pronouncements of the Financial Accounting Standards Board or in such other statements by such other entity as have been approved by a significant segment of the accounting profession in the United States, which are in effect from time to time.

“Guarantee” means a guarantee (other than by endorsement of negotiable instruments for collection in the ordinary course of business), direct or indirect, in any manner (including, without limitation, by way of a pledge of assets, letters of credit and reimbursement agreements in respect thereof), of all or any part of any Debt.

“Hedging Obligations” means, with respect to any person, the obligations of such person under (i) currency exchange or interest rate swap agreements, interest rate cap agreements and interest rate collar agreements and (ii) other agreements or arrangements designed to protect such person against fluctuations in interest rates or currency exchange rates.

“Intellectual Property” has the meaning ascribed thereto in the Agreement.

“Jet Go Decision” has the meaning ascribed thereto in the Master Framework Agreement.

“Larger Shareholder” shall mean any “person” or “group” (as each such term is used in Rule 13d-3 and Rule 13d-5 of the Exchange Act) who shall “beneficially own” (as such term is defined in Rule 13d-3 and Rule 13d-5 under the Exchange Act), directly or indirectly, Voting Shares of the Company (measured by voting power rather than number of shares) representing a larger number of Voting Shares than the number of Voting Shares of the Company (measured by voting power rather than number of shares) “beneficially owned”, directly or indirectly, by the Investor and its Affiliates, in each case as reported on (or required to have been reported on to the extent any “executive officer” (as such term is defined in Rule 3b-7 under the Exchange Act)

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of the Company has actual knowledge of the number of such “person” or “group’s” Voting Shares) the most recent Schedule 13D or Schedule 13G or an amendment to any such Schedule filed with the Securities and Exchange Commission by any such “person” or “group” or by the Investor or any of its Affiliates or as otherwise publicly announced by any such “person” or “group” or by the Investor or any of its Affiliates.

“Lease Debt” means, with respect to any Person, (i) the amount of any accrued and unpaid obligations of such Person arising under any lease or related document (including a purchase agreement, conditional sale or other title retention agreement) in connection with the lease of real property or improvement thereon (or any personal property included as part of any such lease) which provides that such Person is contractually obligated to purchase or cause a third party to purchase the leased property or pay an agreed upon residual value of the leased property to the lessor (whether or not such lease transaction is characterized as an operating lease or a capitalized lease in accordance with GAAP) and (ii) the guarantee, direct or indirect, in any manner (including, without limitation, letters of credit and reimbursement agreements in respect thereof), of any of the amounts set forth in (i) above.

“Lien” means, with respect to any asset, any mortgage, lien, pledge, charge, security interest or encumbrance of any kind in respect of such asset, whether or not filed, recorded or otherwise perfected under applicable law (including any conditional sale or other title retention agreement, any lease in the nature thereof, any option or other agreement to sell or give a security interest in and any filing of or agreement to give any financing statement under the Uniform Commercial Code (or equivalent statutes) of any jurisdiction). Notwithstanding the foregoing, (x) prior to either the No-Go Decision Date or the Final Go Decision Date, a license to any Intellectual Property for uses other than those set forth in the scope of the Amyris License Agreement shall not constitute a Lien hereunder, (y) following the No-Go Decision Date with respect to a particular JV Product or JV Products, a license to any Intellectual Property with respect to such JV Product or JV Products shall not constitute a Lien hereunder, and (z) following the Final Go Decision Date with respect to a particular JV Product or JV Products, a license to any Intellectual Property with respect to such JV Product or JV Products for uses other than those set forth in the scope of the Amyris License Agreement, shall not constitute a Lien hereunder.

“Master Framework Agreement” shall have the meaning specified in the Agreement.

“No-Go Decision Date” has the meaning ascribed thereto in the Master Framework Agreement.

“Permitted Transferees” shall mean any Affiliate of Total Energies Nouvelles Activités USA.

“Person” means any individual, corporation, limited liability company, partnership, joint venture, association, joint-stock company, trust, unincorporated organization or government or any agency or political subdivision thereof.

“Registration Rights Agreement” means that certain Registration Rights Agreement, dated July 30, 2012, by and among the Company and the Investor.

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“Securities Act” means the Securities Act of 1933, as amended, and the rules and regulations promulgated thereunder.

“Shareholders Agreement” means the Shareholders’ Agreement dated as of December 2, 2013, by and among the Company, the Investor and JVCO.

“Significant Subsidiary” means any Subsidiary of the Company that would be a “significant subsidiary” within the meaning specified in Rule 1-02(w) of Regulation S-X promulgated by the Commission under the Exchange Act..

“Subsidiary” means, with respect to any specified Person:

(1)    any corporation, association or other business entity of which more than 50% of the total voting power of shares of capital stock entitled (without regard to the occurrence of any contingency and after giving effect to any voting agreement or stockholders’ agreement that effectively transfers voting power) to vote in the election of directors, managers or trustees of the corporation, association or other business entity is at the time owned or controlled, directly or indirectly, by that Person or one or more of the other Subsidiaries of that Person (or a combination thereof); and

(2)    any partnership (a) the sole general partner or the managing general partner of which is such Person or a Subsidiary of such Person or (b) the only general partners of which are that Person or one or more Subsidiaries of that Person (or any combination thereof).

“Trading Day” means, with respect to the Common Stock, each Monday, Tuesday, Wednesday, Thursday and Friday, other than any day on which securities are not generally traded on The NASDAQ Stock Market (or its successor) or such other principal securities exchange or inter-dealer quotation system on which the shares of Common Stock are then traded.

“Transfer” means, directly or indirectly, to offer, sell (including any short sale), transfer, assign, pledge, encumber, hypothecate or similarly dispose of (by merger, testamentary disposition, operation of law or otherwise), either voluntarily or involuntarily, or enter into any contract, option or other arrangement or understanding with respect to the offer, sale (including any short sale), transfer, assignment, pledge, encumbrance, hypothecation or similar disposition of (by merger, testamentary disposition, operation of law or otherwise), any Conversion Shares “beneficially owned” (as such term is defined in Rule 13d-3 and Rule 13d-5 under the Exchange Act) by a Person or any interest (including any right to (x) all or any portion of the pecuniary interest in the security, including, without limitation, the right to receive dividends and distributions, proceeds upon liquidation and receive the proceeds of disposition or conversion (if applicable) of the security, or (y) direct the voting of the security with respect to any matter for which the security is entitled to vote) in any Conversion Shares beneficially owned by a Person. Whether or not treated as an offer or sale of the Conversion Shares under the Securities Act, “Transfer” shall also include any hedging or other transaction entered into after the date hereof, such as any purchase, sale (including any short sale) or grant of any right (including without limitation any put or call option) with respect to any of the Conversion Shares or with respect to

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any security that includes or derives any significant part of its value from such Conversion Shares.

“Voting Shares” of any person means capital shares or capital stock of such Person which ordinarily has voting power for the election of directors (or persons performing similar functions) of such person, whether at all times or only so long as no senior class of securities has such voting power by reason of any contingency.

2.Interest; Payment of Principal of Note; Cancellation of Note.

(a)Interest. This Note shall bear interest from the Issue Date on the Face Amount at a rate per annum equal to 1.50% (subject to Section 5(c)), it being understood and agreed that $841,781.57 in accrued and unpaid interest under the Exchanged Note as of the Issue Date is deemed to have accrued and is outstanding under this Note. Interest on this Note shall accrue daily and be due and payable in arrears on the Final Maturity Date and at such other times as may be specified herein. All computations of interest shall be made on the basis of a 360-day year and actual days elapsed (which results in more interest being paid than if computed on the basis of a 365-day year). Notwithstanding the foregoing, if an Event of Default shall have occurred and be continuing this Note shall bear interest on the Face Amount at a rate per annum equal to 2.50% (as may be further adjusted pursuant to Section 5(c)).

(b)Scheduled Payment of Principal. Unless paid, converted or cancelled and extinguished earlier in accordance with the terms hereof, the Company shall deliver to the Investor cash in the amount of the Face Amount, together with all accrued and unpaid interest on this Note, on March 1, 2017 (the “Final Maturity Date”).

(c)Final Go Decision Date After a Go Decision. Promptly following the occurrence of the Final Go Decision Date after a Go Decision, and concurrently with the execution and delivery of the Final Shareholders’ Agreement, the Company will repurchase this Note from the Investor at a price equal to 100% of the Face Amount of this Note, plus any accrued and unpaid interest thereon as of the date of the execution and delivery of the Final Shareholders’ Agreement.

(d)Final Go Decision Date After a Jet Go Decision. Promptly following the occurrence of the Final Go Decision Date after a Jet Go Decision, and concurrently with the execution and delivery of the Final Shareholders’ Agreement, (i) the Company will repurchase from the Investor 30% of the Debt represented by the Face Amount of this Note at a price equal to 30% of the Face Amount of this Note, plus any accrued and unpaid interest on this Note as of the date of the execution and delivery of the Final Shareholders’ Agreement and (ii) upon receipt of this Note from the Investor, the Company shall concurrently issue and deliver to the Investor a new Note in an aggregate principal amount equal to 70% of the Debt represented by the Face Amount.

3.Conversion Rights; Adjustments. The Investor shall have conversion rights as follows (the “Conversion Rights”):

(a)Investor’s Right to Convert. At any time (i) after the tenth Trading Day prior to the Final Maturity Date and prior to the fifth Trading Day prior to the Final Maturity

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Date, (ii) after the earlier to occur of (x) the occurrence of a Change of Control and (y) the date of the Company’s delivery of the Change of Control Notice pursuant to Section 4(b), and in each case and prior to the fifth Trading Day prior to the Final Maturity Date, (iii) when there shall then exist a Larger Shareholder after the No-Go Decision Date, or (iv) after the occurrence of an Event of Default, the Investor shall have the right to convert the Face Amount of this Note, in whole or in part, at the option of the Investor, at any time within the period specified above into a number of fully paid and nonassessable authorized but unissued Common Stock determined by dividing (x) the Face Amount proposed to be converted at such date by (y) the then effective Conversion Price on the Conversion Date (as defined in Section 3(c)(i)) (the “InvestorOptional Conversion”).

(b)The “Conversion Price” at which Common Stock shall be deliverable upon conversion of the Notes (the “Conversion Price”) shall initially be $7.0682. Such initial Conversion Price shall be subject to adjustment as provided below.

(c)Mechanics of Conversion.

(i)In order to exercise its rights pursuant to the Investor Optional Conversion, the Investor shall deliver written notice in the form of Exhibit 1 to the Company stating that the Investor elects to convert all or part of the Face Amount represented by this Note. Such notice shall state the Face Amount of Notes which the Investor seeks to convert and shall be accompanied within one (1) Trading Day by the Note or Notes subject to conversion. The date contained in the notice (which date shall be no earlier than the Trading Day immediately following the date of the notice) shall be the date of conversion of the Note (such date of conversion, the “Conversion Date”) and the Investor shall be deemed to be the beneficial owner of the underlying Common Stock as of such date.

(ii)The Investor shall be deemed to beneficially own the Common Stock underlying this Note as of the applicable Conversion Date. Not later than three (3) Trading Days following the Conversion Date, the Company shall promptly issue and deliver to the Investor a certificate or certificates for the number of shares of Common Stock to which the Investor is entitled and, in the case where only part of a Note is converted, the Company shall execute and deliver (at its own expense) a new Note of any authorized denomination as requested by the Investor in an aggregate principal amount equal to and in exchange for the unconverted portion of the principal amount of the Note so surrendered.

(iii)Upon conversion of this Note in whole or in part in accordance with the provision of Section 3(c) of this Note, the Company shall pay to the Investor, substantially concurrently with delivery of the shares of Common Stock issuable on such conversion (the “Conversion Shares”), any accrued and unpaid interest, through the day preceding the Conversion Date, on the portion of the Face Amount represented by this Note that has been so converted. In addition, upon conversion of this Note in whole or in part following a Change of Control the Company shall pay to the Investor, substantially concurrently with delivery of the Conversion Shares, an amount in cash equal to the interest that would have accrued at a rate per annum equal to 1.50% from such Conversion Date through the Final Maturity Date on the portion of the Face Amount represented by this Note that has been so converted if such Note (or portion of the Note) had not been converted (“Make-Whole

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Interest”). Notwithstanding the foregoing, in no event will the total amount of Make-Whole Interest exceed $4,143,447.52.

(iv)The Company shall at all times during which the Notes shall be outstanding, have and keep available out of its authorized but unissued shares, for the purpose of effecting the conversion of the outstanding Notes, such number of its duly authorized shares of Common Stock as shall from time to time be sufficient to effect the conversion of all outstanding Notes. In no event shall the Conversion Price be reduced to an amount less than the then par value of the Common Stock.

(v)No fractional shares of Common Stock shall be issued upon any conversion of the Notes pursuant to this Section 3. In lieu of fractional shares, the Company shall pay cash equal to such fraction multiplied by the Closing Price of the Common Stock on the Conversion Date.

(vi)All Notes (or the portions thereof) which shall have been surrendered for conversion as herein provided shall no longer be deemed to be outstanding and all rights with respect to such Notes, except only the right of the Investor to receive shares of Common Stock in exchange therefor, accrued and unpaid interest and Make-Whole Interest, if applicable, each as described in Section 3(b)(iii) and, if applicable, cash for any fractional shares of Common Stock. Any Notes, to the extent so converted, shall be retired and canceled.

(vii)If any conversion pursuant to this Section 3 is in connection with an underwritten offering of securities registered pursuant to the Securities Act, the conversion may, at the option of the Investor, be conditioned upon the closing with the underwriter of the sale of the Conversion Shares issuable to the Investor pursuant to such offering, in which event the Investor shall not be deemed to have converted such Notes until immediately prior to the closing of such sale of securities.

(d)Adjustment for Share Splits and Combinations. If the Company shall at any time or from time to time after July 31, 2012 effect a subdivision of the outstanding shares of Common Stock, the Conversion Price and Conversion Price Floor (as defined in Section 3(e)) then in effect immediately before that subdivision shall be proportionately decreased. If the Company shall at any time or from time to time after July 31, 2012 combine the outstanding shares of Common Stock, the Conversion Price and Conversion Price Floor then in effect immediately before the combination shall be proportionately increased. Any adjustment under this paragraph shall become effective at the close of business on the date the subdivision or combination becomes effective.

(e)Adjustment for Certain Dividends and Distributions. In the event the Company at any time or from time to time after July 31, 2012, shall make or issue a dividend or other distribution payable in (x) additional shares of Common Stock, then and in each such event the Conversion Price shall be decreased as of the time of such issuance, by multiplying such Conversion Price by a fraction, the numerator of which shall be the total number of shares of Common Stock outstanding immediately prior to such issuance and the denominator of which shall be the total number of shares of Common Stock outstanding immediately prior to such issuance plus the number of such additional shares of Common Stock issuable in payment of

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such dividend or distribution; (y) in cash, then and in each such event, the Conversion Price shall be decreased as of the time of such issuance, by multiplying such Conversion Price by a fraction, the numerator of which shall be the Closing Price of the Common Stock on the Trading Day immediately preceding the ex-dividend date for such dividend and distribution minus the amount in cash per share of Common Stock that the Company dividends or distributes, and the denominator of which shall be the Closing Price of the Common Stock on the Trading Day immediately preceding the ex-dividend date for such dividend and distribution; (z) shares of capital stock of the Company, evidences of indebtedness, or any other asset (collectively, the “Distributed Property”), then and in each such event, the Conversion Price shall be decreased as of the time of such issuance, by multiplying such Conversion Price by a fraction, the numerator of which shall be the Closing Price of the Common Stock on the Trading Day immediately preceding the ex-dividend date for such dividend and distribution minus the fair market value (as determined in good faith by the Company’s board of directors) of the Distributed Property distributed with respect to each share of Common Stock, and the denominator of which shall be the Closing Price of the Common Stock on the Trading Day immediately preceding the ex-dividend date for such dividend and distribution. Notwithstanding the foregoing, in no event shall the Conversion Price be reduced below $5.99 (as may be adjusted pursuant to Section 3(d), the “Conversion Price Floor”) pursuant to this clause (e). If a distribution or dividend would cause the Conversion Price to be below the Conversion Price Floor if not for the immediately preceding sentence, the Company shall allow the Investor to participate in the dividend or distribution as if it held the number of shares of Common Stock that this Note would be convertible into at the close of business on the day immediately preceding the ex-dividend date or effective date, as the case may be, for such distribution or dividend, and no adjustment shall be made to the Conversion Price as a result of such distribution or dividend.

(f)Adjustment for Reclassification, Exchange or Substitution. If at any time after July 31, 2012, shares of Common Stock of the Company shall be changed into the same or a different number of shares of any class or classes of shares, whether by reclassification, or otherwise (other than a subdivision or combination of shares, share dividend or reorganization, reclassification, merger, consolidation or asset sale provided for elsewhere in this Section 3), then and in each such event the Company shall enter into an amendment to supplement to this Note to provide that the Note will become convertible (subject to Section 3(a)) into the kind and amount of shares and other securities and property receivable upon such reorganization, reclassification, or other change, by holders of the number of shares of Common Stock into which this Note might have been converted immediately prior to such reorganization, reclassification, or change, all subject to further adjustment as provided herein or with respect to such other securities or property by the terms thereof.

(g)Reorganizations, Mergers, Consolidations or Asset Sales. If at any time after July 31, 2012 there is a tender offer, exchange offer, merger, consolidation, recapitalization, sale of all or substantially all of the Company’s assets or reorganization involving the shares of Common Stock (collectively, a “Capital Reorganization”) (other than a merger, consolidation, sale of assets, recapitalization, subdivision, combination, reclassification, exchange or substitution of shares provided for elsewhere in this Section 3), as part of such Capital Reorganization, the Company shall enter into an amendment or supplement to this Note to provide that the Note will become convertible (subject to Section 3(a)) into the number of shares or other securities or property of the Company to which a holder of the number of shares

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of Common Stock deliverable upon conversion immediately prior to such Capital Reorganization would have been entitled on such Capital Reorganization, subject to adjustment in respect to such shares or securities by the terms thereof. In any such case, appropriate adjustment will be made in the application of the provisions of this Section 3 with respect to the rights of the Investor after the Capital Reorganization to the end that the provisions of this Section 3 (including adjustment of the Conversion Price then in effect and the number of Conversion Shares) and the provisions of the Agreement and the Registration Rights Agreement will be applicable after that event and be as nearly equivalent as practicable. In the event that the Company is not the surviving entity of any such Capital Reorganization, each Note shall become Notes of such surviving entity, with the same powers, rights and preferences as provided herein.

(h)No Impairment. The Company will not, by amendment of its Certificate of Incorporation or through any reorganization, transfer of assets, consolidation, merger, dissolution, issue or sale of securities or any other voluntary action, avoid or seek to avoid the observance or performance of any of the terms to be observed or performed hereunder by the Company, but will at all times in good faith assist in the carrying out of all the provisions of this Section 3 and in the taking of all such action as may be necessary or appropriate in order to protect the conversion rights of the Investor against impairment to the extent required hereunder.

(i)Certificate as to Adjustments or Distributions. Upon the occurrence of each adjustment of the Conversion Price or distribution to holders pursuant to this Section 3, the Company at its expense shall promptly compute such adjustment or distribution in accordance with the terms hereof and furnish to the Investor a certificate setting forth the terms of such adjustment or distribution and showing in detail the facts upon which such adjustment or distribution are based and shall file a copy of such certificate with its corporate records.

(j)Notice of Record Date. In the event:

(i)that the Company declares a dividend (or any other distribution) on its Common Stock payable in shares of Common Stock, securities, or other assets, rights or properties;

(ii)that the Company subdivides or combines its outstanding shares of Common Stock;

(iii)of any reclassification of the shares of Common Stock (other than a subdivision or combination of the Company’s outstanding shares of Common Stock or a share dividend or share distribution thereon);

(iv)of any Capital Reorganization; or

(v)of the involuntary or voluntary dissolution, liquidation or winding up of the Company;

then the Company shall cause to be filed at its principal office, and shall cause to be mailed to the Investor, at least ten (10) days prior to the record date specified in (A) below or twenty (20) days prior to the date specified in (B) below, a notice stating:

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(A)the record date of such dividend, distribution, subdivision or combination, or, if a record is not to be taken, the date as of which the holders of shares of Common Stock of record to be entitled to such dividend, distribution, subdivision or combination are to be determined, or

(B)the date on which such reclassification, Capital Reorganization, dissolution, liquidation or winding up is expected to become effective, and the date as of which it is expected that holders of shares of Common Stock of record shall be entitled to exchange their shares of Common Stock for securities or other property deliverable upon such reclassification, Capital Reorganization, dissolution or winding up

(k)Notice of Adjustment to Conversion Price. The Company will provide notice to the Investor upon the occurrence of any adjustment to the Conversion Price.

(l)Lockup Agreement. In the event of an Investor Optional Conversion pursuant to clause (iii) of Section 3(a), the Investor shall not, without the prior written consent of the Company, Transfer any of the Conversion Shares other than as expressly permitted by, and in compliance with, the provisions of this Section 3(l):

(i)the Investor may Transfer any or all of its Conversion Shares to the Company or any of its Subsidiaries;

(ii)the Investor may Transfer all or any of its Conversion Shares in a transaction exempt from the registration requirements under the Securities Act to any of its Affiliates, so long as prior to or concurrent with any such Transfer such Affiliate agrees in writing to be bound by the terms hereunder as the “Investor” and such other terms hereunder applicable to the Investor, and agrees to transfer such Conversion Shares back to the Investor if it ceases to be an Affiliate of the Investor;

(iii)the Investor may Transfer all or any of its Conversion Shares pursuant to the terms of any tender offer, exchange offer, merger, reclassification, reorganization, recapitalization or other similar transaction in which stockholders of the Company are offered, permitted or required to participate as holders of Common Stock, provided that such tender offer, exchange offer, merger, reclassification, reorganization, recapitalization or other transaction has been approved or recommended by the Board of Directors (and which at the time of Transfer continues to be approved or recommended by the Board of Directors); or

(iv)following the date that is six (6) months after the date of such Investor Optional Conversion pursuant to clause (iii) of Section 3(a), the Investor may transfer all or any of its Conversion Shares pursuant to either an effective registration statement that is effective at the time of such transfer or pursuant to Rule 144 promulgated under the Securities Act, and any successor provision thereto.

Notwithstanding anything herein to the contrary, the restrictions set forth in this Article III shall terminate (i) upon the consummation of a Change of Control, or (ii) at such time as the Investor, together with its Affiliates, “beneficially owns” (as such term is defined in Rule 13d-3 and Rule 13d-5 under the Exchange Act) in the aggregate Voting Shares of the Company (measured by

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voting power rather than number of shares) representing less than five percent (5%) of the total voting power of all outstanding classes of voting stock of the Company.

4.Repurchase Right Upon a Change of Control.

(a)Upon the occurrence of a Change of Control, the Investor will have the right to require the Company to repurchase all or any part of its Notes pursuant to an offer as provided in this Section 4 (the “Change of Control Offer”) at an offer price in cash equal to 101% of the Face Amount of its Notes, plus any accrued and unpaid interest as of the Change of Control Payment Date (as defined in Section 4(b)(i)) (the “Change of Control Payment”), in addition to the Investor’s right to convert the Notes pursuant to Section 3 above.

(b)On or before the 30th day after a Change of Control, the Company shall give to the Investor notice (the “Change of Control Notice”) of the occurrence of the Change of Control and of the Investor’s right to receive the Change of Control Payment arising as a result thereof. Each notice of the Investor’s right to participate in the Change of Control Offer (the “Change of Control Repurchase Right”) shall be mailed to the Investor pursuant to Section 15 and shall state:

(i)the date on which the Notes shall be repurchased (the “Change of Control Payment Date”), which date shall be no earlier than 30 days and no later than 60 days from the date of the Company’s delivery of the Change of Control Notice;

(ii)the date by which the Change of Control Repurchase Right must be exercised, which date shall be no earlier than the close of business on the Trading Day immediately prior to the Change of Control Payment Date;

(iii)the amount of the Change of Control Payment;

(iv)a description of the procedure which the Investor must follow to exercise the Change of Control Repurchase Right, and the place or places where the Notes are to be surrendered for payment of the Change of Control Payment; and

(v)the Conversion Price then in effect and the place where such Notes may be surrendered for conversion.

No failure by the Company to give the Change of Control Notice and no defect in any Change of Control Notice shall limit the Investor’s right to exercise its Change of Control Repurchase Right or affect the validity of the proceedings for the repurchase of Notes. If any of the foregoing provisions or other provisions of this Section 4 are inconsistent with applicable law, such law shall govern.

(c)To exercise the Change of Control Repurchase Right, the Investor shall deliver to the Company, on or before the Trading Day immediately prior to the Change of Control Payment Date, (i) written notice of the Investor’s exercise of such right, which notice shall set forth the name of the Investor, the Face Amount of Notes held by the Investor to be repurchased, and a statement that an election to exercise the Change of Control Repurchase Right is being made thereby, and (ii) the Notes with respect to which the Change of Control

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Repurchase Right is being exercised. Such written notice shall be irrevocable, except that the right of the Investor to convert the Notes shall continue until midnight (Eastern Time) on the Trading Day immediately preceding the Change of Control Repurchase Date.

(d)On the Change of Control Payment Date, the Company will (i) accept for payment all Notes or portions thereof properly tendered pursuant to the Change of Control Offer and (ii) deliver cash in the amount of the Change of Control Payment to the Investor in respect of all Notes or portions thereof so tendered. All Notes repurchased by the Company shall be canceled immediately by the Company

(e)The Company shall publicly announce the results of the Change of Control Offer on or as soon as practicable after the Change of Control Payment Date.

(f)The Company will comply with the requirements of Rule 14e-1 under the Exchange Act and any other securities laws and regulations thereunder to the extent such laws and regulations are applicable in connection with the repurchase of the Notes as a result of a Change of Control.

(g)Any Note which is to be repurchased only in part shall be surrendered to the Company and the Company shall execute and make available for delivery to the Investor without service charge, a new Note or Notes, containing identical terms and conditions, each in an authorized denomination in aggregate principal amount equal to and in exchange for the unrepurchased portion of the principal of the Note so surrendered. Any Notes surrendered to the Company pursuant to the provisions of this Section 4 shall be retired and cancelled.

(h)The Company will not be required to make a Change of Control Offer upon a Change of Control if a third party makes the Change of Control Offer in the manner, at the times and otherwise in compliance with the requirements set forth in this Section 4 applicable to a Change of Control Offer made by the Company and purchases all Notes validly tendered and not withdrawn under such Change of Control Offer.

5.Events of Default. Definitions. For purposes of this Note, the following events shall constitute an “Event of Default”:

(i)default in payment when due (whether at the Final Maturity Date or upon an earlier repurchase) of the principal of, or premium, if any, on this Note;

(ii)default in the payment of an installment of interest on the Notes, which failure continues for thirty (30) days after the date when due;

(ii)failure by the Company for thirty (30) days after notice from the Investor to comply with the provisions of Section 4 or Section 6 of this Note;

(iv)failure by the Company for sixty (60) days after notice from the Investor to comply with any of its other agreements in this Note or the Agreement (other than Section 8.6(b) of the Agreement);

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(v)default under any mortgage, indenture or instrument under which there may be issued or by which there may be secured or evidenced any Debt for money borrowed by the Company (or the payment of which is guaranteed by the Company, whether such Debt or guarantee existed as of the Original Issue Date or is created after the Original Issue Date, which default (a) is caused by a failure to pay principal of or premium, if any, or interest on such Debt prior to the expiration of the grace period provided in such Debt on the date of such default or (b) results in the acceleration of such Debt prior to its express maturity and, in each case in clause (a) or (b), the principal amount of any such Debt, together with the principal amount of any other such Debt that has not been paid when due, or the maturity of which has been so accelerated, aggregates $10,000,000 or more;

(vi)failure by the Company to pay final judgments aggregating in excess of $10,000,000, which judgments are not paid, discharged or stayed for a period of sixty (60) days;

(vii)the Company:

(A)commences a voluntary case under any Bankruptcy Law,

(B)consents to the entry of an order for relief against it in an involuntary case under any Bankruptcy Law,

(C)consents to the appointment of a custodian of it or for all or substantially all of its property,

(D)makes a general assignment for the benefit of its creditors, or

(E)is unable to pay its debts as they become due; or

(viii)a court of competent jurisdiction enters an order or decree under any Bankruptcy Law that:

(A)is for relief against the Company;

(B)appoints a custodian of the Company or any of its Significant Subsidiaries or for all or substantially all of the property of the Company; or

(C)orders the liquidation of the Company and the order or decree remains unstayed and in effect for sixty (60) consecutive days; or

(ix)    failure by the Company to deliver when due the consideration deliverable upon conversion of this Note, which failure shall continue for a period of five days.

(b)Notice of Compliance. The Company shall be required to deliver to the Investor annually a statement regarding compliance with this Note, and the Company shall be required within five (5) days of becoming aware of any Default or Event of Default (or such earlier date as any such statement is provided to the holders of the Debt incurred pursuant to the

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Securities Purchase Agreement dated as of February 24, 2012) to deliver to the Investor a statement specifying such Default or Event of Default.

(c)Acceleration. If any Event of Default occurs and is continuing, the Investor may declare all the Notes to be due and payable immediately. Notwithstanding the foregoing, in the case of an Event of Default described in Section 5(vii) or (viii) with respect to the Company all outstanding Notes will become due and payable without further action or notice. The Investor may rescind an acceleration and its consequences if the rescission would not conflict with any judgment or decree. Notwithstanding the foregoing (or anything to the contrary in the Agreement), the sole remedy of the Investor for a failure by the Company to comply with Section 8.6(b) of the Agreement shall, for the first 365 days after the occurrence of such failure, be the right, by notice to the Company by the Investor, to increase in the rate of interest on this Note to 6% for the first 180 days of such failure, and to 9% thereafter (which increased interest shall constitute liquidated damages for such failure).

(d)Waiver of Past Defaults. The Investor may waive any existing Default or Event of Default and its consequences under this Note. Upon any such waiver, such Default shall cease to exist, and any Event of Default arising therefrom shall be deemed to have been cured for every purpose of this Note, but no such waiver shall extend to any subsequent or other default or impair any right consequent thereon.

(e)Rights of Investor to Receive Payment. Notwithstanding any other provision of this Note, the right of the Investor to receive payment of the principal of, and premium on, this Note, on or after the respective due dates expressed in the Note (including in connection with a redemption or an offer to purchase), or to bring suit for the enforcement of any such payment on or after such respective dates, shall not be impaired or affected without the consent of the Investor

6.Limitation on Debt and Liens. The Company will not, and will not permit its Subsidiaries to, directly or indirectly, create, incur, issue, assume, guarantee or otherwise become directly or indirectly liable, contingently or otherwise, with respect to any Debt, and the Company will not issue any Disqualified Stock and the Company will not permit its Subsidiaries to issue shares of preferred stock except for:

(a)Debt in an amount outstanding at any time not to exceed the greater of (i) $200 million in aggregate principal amount or (ii) 50% of the Company’s total consolidated assets (as set forth on its most recent balance sheet prepared in accordance with GAAP and filed with the Securities and Exchange Commission after giving effect to any reductions or additions to assets in accordance with GAAP since the date of such balance sheet) (the “Maximum Debt Amount”) (provided thatthat the Company and its Subsidiaries may incur (x) Debt in connection with the Notes issued by the Company under the Agreement and Debt in connection with the Class A Note, (y) Debt of Amyris Brasil Ltda. outstanding as of the December 2, 2013 and (z) Debt in connection with the senior convertible notes to be issued by the Company under that certain Securities Purchase Agreement, dated as of August 8, 2013, by and among the Company and the investors identified on Schedule I thereto, as amended as of October 16, 2013 and December 24, 2013 (such Debt described in clauses (x), (y) and (z) referred to herein as the “Existing Debt”), and provided further that upon incurring such Existing Debt, the Company and

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its Subsidiaries may have incurred Debt in excess of the Maximum Debt Amount, and so long as the Debt of the Company and its Subsidiaries exceeds the Maximum Debt Amount, the Company and its Subsidiaries shall not be permitted to incur any additional Debt in reliance on this clause (a) without Total’s consent) (and provided that Debt incurred pursuant to this clause (a) that is secured by a Lien on assets of the Company shall not exceed the greater of (i) $125 million in aggregate principal amount or (ii) 30% of the Company’s total consolidated assets (as set forth on its most recent balance sheet prepared in accordance with GAAP) (the “Maximum Secured Debt Amount”) (it being understood and agreed that the Notes issued by the Company under the Agreement shall reduce the available Maximum Secured Debt Amount)); provided that neither the Company nor any of its Subsidiaries shall incur any Debt pursuant to this clause 6(a) if the issuance of such Debt would prohibit the Company from issuing the maximum amount of Notes to be issued by the Company under the Agreement;

(b)Debt in existence on February 27, 2012;

(c)the incurrence by the Company or any of its Subsidiaries of Debt represented by Capital Lease Obligations, mortgage financings or purchase money obligations, in each case, incurred for the purpose of financing all or any part of the purchase price or cost of design, construction, installation or improvement of property, plant or equipment used in the business of the Company or any of its Subsidiaries.

(d)Debt of the Company that is (i) contractually subordinated in right of payment to the Notes, (ii) matures 91 days after the Notes and (iii) is less than $50 million in aggregate principal amount at any one time outstanding;

(e)Debt of the Company (A) in respect of performance, surety or appeal bonds or letters of credit in the ordinary course of business, or (B) under interest rate, currency, commodity or similar hedges, swaps and other derivatives entered into with one or more financial institutions that is designed to protect such the Company against fluctuations in interest rates or currency exchange rates, commodity prices or other market fluctuations and is not entered into for speculative purposes; and

(f)Debt which is exchanged for or the proceeds of which are used to refinance or refund, or any extension or renewal of (each a "refinancing"), (1) the Notes or (2) debt in existence on the Original Issue Date, and (3) Debt incurred pursuant to clause (c) of this paragraph, in each case in an aggregate principal amount not to exceed the principal amount of the Debt so refinanced (together with any accrued interest and any premium and other payment required to be made with respect to the Debt being refinanced or refunded, and any fees, costs, expenses, underwriting discounts or commissions and other payments paid or payable with respect to the Debt incurred pursuant to this clause (f)); provided, however, that (A) Debt, the proceeds of which are used to refinance the Notes, or Debt which is pari passu with the Notes (including Debt incurred pursuant to the Securities Purchase Agreement, dated as of February 24, 2012, among the Company and the purchasers named therein) or subordinate in right of payment to the Notes, shall only be permitted if (x) in the case of any refinancing of the Notes or Debt which is pari passu to the Notes (including Debt incurred pursuant to the Securities Purchase Agreement, dated as of February 24, 2012, among the Company and the purchasers named therein), the refinancing Debt is Incurred by the Company and made pari passu to the

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Notes or subordinated to the Notes, and (y) in the case of any refinancing of Debt which is subordinated to the Notes, the refinancing Debt is incurred by the Company and is subordinated to the Notes in a manner that is at least as favorable to the Investor as that of the Debt refinanced; (B) refinancing Debt with respect to Debt incurred pursuant to clause (c) of this paragraph shall not be secured by a Lien on any assets other than the assets securing the Debt so refinanced, and any improvements or additions thereto, and (C) the refinancing Debt by its terms, or by the terms of any agreement or instrument pursuant to which such Debt is issued, does not have a final maturity prior to the final maturity of the Debt being refinanced.

For purposes of determining compliance with this Section 6, in the event that an item of Debt meets the criteria of more than one of the types of Debt described in the above clauses the Company, in its sole discretion, shall classify, and from time to time may reclassify, such item of Debt.

(g)The Company will not create, incur, assume or suffer to exist any Lien of any kind on any asset now owned or hereafter acquired, except for (a) the Liens described in Section 6(a) and 6(c) (including the refinancing of Liens described in Section 6(c) pursuant to Section 6(f)), (b) Permitted Liens, and (c) any Liens in existence on the Original Issue Date (including the refinancing thereof pursuant to Section 6(f)). Notwithstanding the foregoing, without the prior written consent of the Investor, which consent shall not be unreasonably withheld, the Company will not create, incur, assume or suffer to exist any Lien of any kind on any of its Intellectual Property that is subject to or within the scope of the Amyris License Agreement, unless the secured party acknowledges in writing that its Lien shall not restrict the Company from granting and performing its obligations under any license agreement entered into in accordance with the Amyris License Agreement, and that the rights of the secured party under its Lien shall be subordinate and subject to the rights of the licensees under any such licenses, and (ii) there shall be no restriction on the ability of the Company to create, incur, assume or suffer to exist any Lien of any kind on any of its Intellectual Property that is not subject to or within the scope of the Amyris License Agreement.

As used herein, “Permitted Liens” means the following: (a) Liens for taxes, assessments and governmental charges or levies that are not overdue for a period of more than thirty (30) days or which are being contested in good faith; (b) Liens imposed by law, such as materialmen’s, mechanics’, carriers’, workmen’s and repairmen’s Liens and other similar Liens securing obligations that are not overdue for a period of more than thirty (30) days or that are being contested in good faith; (c) pledges or deposits to secure obligations under workers’ compensation laws or similar legislation or to secure public or statutory obligations; (d) easements, rights of way and other encumbrances on title to real property that do not render title to the property encumbered thereby unmarketable or materially adversely affect the use of such property for its present purposes; (e) Liens to secure the performance of bids, trade contracts, leases, statutory obligations, surety and appeal bonds, performance bonds and other obligations of a like nature; (f) landlords’ Liens under leases; (g) Liens consisting of leases, subleases, licenses or sublicenses granted to others and not interfering in any material respect with the business of the Company and its Subsidiaries, taken as a whole, and any interest or title of a lessor or licensor under any lease or license, as applicable; (h) Liens arising solely by virtue of any statutory or common law provision relating to banker’s Liens, rights of set-off or similar rights and remedies as to deposit accounts or other funds maintained with a creditor depository

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institution; and (i) Liens securing judgments for the payment of money not constituting an Event of Default under Section 5(a)(vi) or securing appeal or other surety bonds related to such judgments.

7.Successors.

(a)Merger, Consolidation or Sale of Assets. The Company shall not consolidate or merge with or into (whether or not the Company is the surviving corporation), or sell, assign, transfer, lease, convey or otherwise dispose of all or substantially all of its properties or assets in one or more related transactions, to another corporation, Person or entity unless:

(i)the entity or Person formed by or surviving any such consolidation or merger (if other than the Company), or the parent company thereof, or the entity or Person to which such sale, assignment, transfer, lease, conveyance or other disposition shall have been made assumes all the obligations of the Company under the Notes and the Agreement; and

(ii)immediately after such transaction no Default or Event of Default exists.

(b)Successor Corporation Substituted. Upon any consolidation or merger or any transfer of all or substantially all of the assets of the Company in accordance with Section 7(a) hereof, the successor Person formed by such consolidation or into which the Company is merged, or the parent company thereof, or to which such transfer is made shall succeed to and (except in the case of a lease) be substituted for (so that from and after the date of such consolidation, merger or transfer, the provisions of this Note, the Agreement and the Registration Rights Agreement referring to the “Company” shall refer instead to the successor Person and not to the Company), and may exercise every right and power of, the Company under this Note and the Agreement with the same effect as if such successor Person had been named herein as the Company, and (except in the case of a lease) the Company shall be released from the obligations under the Notes and the Agreement except with respect to any obligations that arise from, or are related to, such transaction.

8.Amendment and Waiver. Except as otherwise expressly provided herein, the provisions of this Note may be amended and the Company may take any action herein prohibited, or omit to perform any act herein required to be performed by it, only if the Company has obtained the written consent of the Investor.

9.Place of Payment. Payments of principal, interest, and premium, if any, consideration deliverable upon conversion of this Note (unless otherwise specified in the conversion notice) and all notices and other communications to the Investor hereunder or with respect hereto are to be delivered to the Investor at the address identified in the Agreement or to such other address or to the attention of such other person as specified by prior written notice to the Company, including any Permitted Transferee of this Note in accordance with Section 3 of this Note.

10. Costs of Collection. In the event that the Company fails to (a) pay when due (including, without limitation upon acceleration in connection with an Event of Default) the full amount of principal, interest and/or premium hereunder or (b) deliver when due the consideration

19

deliverable upon conversion of this Note, the Company shall indemnify and hold harmless the Investor of any portion of this Note from and against all reasonable costs and expenses incurred in connection with the enforcement of this provision or collection of such principal, interest, premium and/or consideration, including, without limitation, reasonable attorneys’ fees and expenses.

11.Waivers. The Company hereby waives presentment, demand, notice, protest and all other demands and notices in connection with the delivery, acceptance, performance, default or enforcement of this Note.

12.Benefits of the Agreement. The Investor and all transferees of this Note (to the extent such transfer is permitted by the Agreement) shall be entitled to the rights and benefits granted to them in the Agreement.

13.Registration of Transfer and Exchange Generally.

(a)Registration, Registration of Transfer and Exchange Generally. The Company shall keep at its principal executive offices a register (the register maintained in such being herein sometimes collectively referred to as the “Note Register”) in which the Company shall provide for the registration of Notes and of transfers and exchanges of Notes.

Subject to the provisions of the Agreement regarding restrictions on transfer and provided the Permitted Transferee agrees to be bound by the terms of this Note and the Agreement, upon surrender for registration of transfer of any Note at its principal executive office, the Company shall execute and deliver, in the name of the designated transferee or transferees, one or more new Notes in denominations requested by the transferee (which denominations shall not be less than $1,000,000 per Note (unless the transferor holds a lesser denomination, in which case no such restriction shall apply)), of a like aggregate principal amount and bearing such restrictive legends as may be required by law.

At the option of the Investor, Notes may be exchanged for other Notes of any authorized denominations, of a like aggregate principal amount and bearing such restrictive legends as may be required by law upon surrender of the Notes to be exchanged at the Company’s principal executive offices. Whenever any Notes are so surrendered for exchange, the Company shall execute and make available for delivery the Notes that the Investor making the exchange is entitled to receive.

All Notes issued upon any registration of transfer or exchange of Notes shall be the valid obligations of the Company, evidencing the same debt, and entitled to the same benefits as the Notes surrendered upon such registration of transfer or exchange.

Every Note presented or surrendered for registration of transfer or for exchange shall (if so required by the Company) be duly endorsed, or be accompanied by a written instrument of transfer in form satisfactory to the Company, duly executed by the Investor.

No service charge shall be made for any registration of transfer or exchange of Notes.

20

(b)Mutilated, Destroyed, Lost and Stolen Notes. If any mutilated Note is surrendered to the Company, the Company shall execute and make available for delivery in exchange therefor a new Note of like tenor and principal amount and bearing a number not contemporaneously outstanding.

If there shall be delivered to the Company (i) evidence to its reasonable satisfaction of the destruction, loss or theft of any Note and (ii) such indemnity as may be reasonably requested by the Company to save itself harmless, then, in the absence of notice to the Company that such Note has been acquired by a protected purchaser, the Company shall execute and make available for delivery, in lieu of any such destroyed, lost or stolen Note, a new Note of like tenor and principal amount and bearing a number not contemporaneously outstanding.

Every new Note issued pursuant to this Section 13 in lieu of any mutilated, destroyed, lost or stolen Note shall constitute an original additional contractual obligation of the Company, whether or not the destroyed, lost or stolen Note shall be at any time enforceable by anyone.

The provisions of this Section 13 are exclusive and shall preclude (to the extent lawful) all other rights and remedies with respect to the replacement or payment of mutilated, destroyed, lost or stolen Notes.

14.Governing Law.

(a)    THIS NOTE, AND THE PROVISIONS, RIGHTS, OBLIGATIONS, AND CONDITIONS SET FORTH HEREIN, AND THE LEGAL RELATIONS BETWEEN THE PARTIES HERETO, INCLUDING ALL DISPUTES AND CLAIMS, WHETHER ARISING IN CONTRACT, TORT, OR UNDER STATUTE, SHALL BE GOVERNED BY AND CONSTRUED IN ACCORDANCE WITH THE LAWS OF THE STATE OF NEW YORK WITHOUT GIVING EFFECT TO ITS CONFLICT OF LAW PROVISIONS.

(b)    Any and all disputes arising out of, or in connection with, the interpretation, performance, or nonperformance of this Note or any and all disputes arising out of, or in connection with, transactions in any way related to this Note and/or the relationship between the parties shall be litigated solely and exclusively before the United States District Court for the Southern District of New York. The parties consent to the in personam jurisdiction of said court for the purposes of any such litigation, and waive, fully and completely, any right to dismiss and/or transfer any action pursuant to 28 U.S.C. § 1404 or 1406 (or any successor statute). In the event the United States District Court for the Southern District of New York does not have subject matter jurisdiction of said matter, then such matter shall be litigated solely and exclusively before the appropriate state court of competent jurisdiction located in the state of New York.

15.Notices. All notices, requests, and other communications hereunder shall be in writing and will be deemed to have been duly given and received (a) when personally delivered, (b) when sent by facsimile upon confirmation of receipt, (c) one business day after the day on which the same has been delivered prepaid to a nationally recognized courier service, or (d) five business days after the deposit in the United States mail, registered or certified, return receipt requested, postage prepaid, in each case to the applicable address set forth below:

21

(i)if to the Company, to:

Amyris, Inc.

5885 Hollis Street, Suite 100

Emeryville, CA 94608

United States of America

Attn:     General Counsel

Fax. No.: [*]

with a copy (which shall not constitute notice) to:

Shearman & Sterling LLP
Four Embarcadero Center, Suite 3800
San Francisco, CA  94111-5994
United States of America
Attn:    [*]
Fax. No.: [*]

(ii)if to the Investor, to:

Total Energies Nouvelles Activités USA

24 Cours Michelet
92800 Puteaux

France

Attn:     [*]
Fax. No.: [*]

with copies (which shall not constitute notice) to:

Wilson Sonsini Goodrich & Rosati

Professional Corporation

650 Page Mill Road

Palo Alto, CA 94304

United States of America

Attn:     [*]

Fax No.: [*]

and

Jones Day
555 California Street, 26th Floor
San Francisco, CA 94104-1500
United States of America
Attn:     [*]
Fax No.: [*]

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

22

Any party hereto from time to time may change its address, facsimile number, or other information for the purpose of notices to that party by giving notice specifying such change to the other parties hereto. The Investor and the Company may each agree in writing to accept notices and other communications to it hereunder by electronic communications pursuant to procedures reasonably approved by it; provided that approval of such procedures may be limited to particular notices or communications.

[Signature Page Follows]

23

IN WITNESS WHEREOF, the Company has executed and delivered this Note on May 29, 2014.

AMYRIS, INC.
By:	/s/ John Melo
Name:		John Melo
Title:		President and Chief Executive Officer

[Signature Page to Note RS-6]

EXHIBIT 1

(To be Executed by Investor in order to Convert Note)

CONVERSION NOTICE
FOR
1.5% SENIOR SECURED CONVERTIBLE NOTE DUE 2017

The undersigned, as holder of the 1.5% Senior Secured Convertible Note due 2017 of AMYRIS, INC., (the “Company”), in the outstanding principal amount of U.S. $8,300,751.86 (the “Note”), hereby elects to convert that portion of the outstanding principal amount of the Note shown on the next page into shares of the Company’s common stock, $0.0001 par value per share (the “Common Stock”), of the Company, accrued and unpaid interest and Make-Whole Interest, if any, in accordance with and in compliance with the conditions of the Note, as of the date written below. The undersigned hereby requests that share certificates for the shares of Common Stock to be issued to the undersigned pursuant to this Conversion Notice be issued in the name of, and delivered to, the undersigned or its designee as indicated below. If shares are to be issued in the name of a person other than the undersigned, the undersigned will pay all transfer taxes payable with respect thereto. No fee will be charged to the Investor for any conversion, except for transfer taxes, if any.

Conversion Information:	TOTAL ENERGIES NOUVELLES ACTIVITÉS USA:
	By:
	Print Name:
	Print Title:
	Address:
	24 Cours Michelet 92800 PuteauxFrance Attn: [*] Fax. No.: [*]

	Issue Common Stock:
	at:
	Date of Conversion
	Applicable Conversion Price
[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

SFDOCS01/309503.1

THE COMPUTATION OF THE NUMBER OF SHARES OF COMMON STOCK TO
BE RECEIVED IS SET FORTH ON THE ATTACHED PAGE

Page 2 to Conversion Notice for: Total Energies Nouvelles Activités USA

COMPUTATION OF NUMBER OF COMMON SHARES TO BE RECEIVED

Face Amount converted:		$
Conversion Price		$
Number of shares of Common Stock =	Total dollar amount converted   =	$
	Conversion Price
Number of shares of Common Stock =
Please issue and deliver ___ certificate(s) for shares of Common Stock in the following amount(s):
Please issue and deliver ______ new Note(s) in the following amounts:

SFDOCS01/309503.1

EX-4.06

EXECUTION VERSION

FIRST AMENDMENT TO LOAN AND SECURITY AGREEMENT AND NOTE MODIFICATION

This FIRST AMENDMENT TO LOAN AND SECURITY AGREEMENT AND NOTE MODIFICATION (this “Amendment”), dated as of June 12, 2014, is among AMYRIS, INC., a Delaware corporation (the “Parent”), and each of its Subsidiaries that has delivered a Joinder Agreement (as defined herein) (each a “Subsidiary Guarantor” and collectively, the “Subsidiary Guarantors” and together with Parent, collectively, “Borrower”), the several banks and other financial institutions or entities from time to time parties to this Agreement (collectively, referred to as “Lender”) and HERCULES TECHNOLOGY GROWTH CAPITAL, INC., a Maryland corporation, in its capacity as administrative agent for itself and the Lender (in such capacity, the “Agent”).

RECITALS

A.    Parent, Subsidiary Guarantors, Lender and Agent have previously entered into that certain Loan and Security Agreement, dated as of March 29, 2014 (the “Loan and Security Agreement”), pursuant to which, among other things, Lender has provided a term loan to Borrower in the amount of Twenty-Five Million Dollars.

B.    Borrower has, among other things, requested that Lender provide an additional Five Million Dollar Term Loan.

C.    In response to the request of Borrower, and in reliance upon the representations made in support thereof, and the other terms and provisions of this Amendment, the parties hereto desire to amend the Loan and Security Agreement as set forth herein and on the terms and conditions contained herein.

NOW, THEREFORE, for good and valuable consideration (the receipt and sufficiency of which are hereby acknowledged), the parties hereto agree as follows:

1.    Defined Terms. Each capitalized term used but not otherwise defined herein has the meaning ascribed thereto in the Loan and Security Agreement.

2.    Amendments to Loan and Security Agreement. Subject to the satisfaction of the conditions precedent set forth in Section 3 of this Amendment and effective as of the First Amendment Effective Date (notwithstanding the date of execution of this Amendment), the Loan and Security Agreement is hereby amended as follows:

(a)    New definitions of “Additional Term Loan Advance”, “Additional Term Loan Interest Rate”, “First Amendment”, “First Amendment Effective Date”, “Closing Date Term Loan Advance Date” and “Closing Date Term Loan Interest Rate” are hereby inserted into Section 1 of the Loan and Security Agreement in appropriate alphabetical order:

“Additional Term Loan Advance” is defined in Section 2.2(a) of this Agreement.

“Additional Term Loan Interest Rate” means for any day a per annum rate of interest equal to the greater of either (i) the prime rate as reported in The Wall Street Journal plus 5.25% and (ii) 8.5%.

“First Amendment” means that certain First Amendment to Loan and Security Agreement, dated as of June 12, 2014, between Parent, the Subsidiary Guarantors, Lender and Agent.

“First Amendment Effective Date” means the date specified in Section 3 of the First Amendment.

“Closing Date Term Loan Advance” is defined in Section 2.2(a) of this Agreement.

“Closing Date Term Loan Interest Rate” means for any day a per annum rate of interest equal to the greater of either (i) the prime rate as reported in The Wall Street Journal plus 6.25%, and (ii) 9.5%.

(b)    The definitions of “Permitted Indebtedness”, “Term Loan Advance”, “Term Loan Interest Rate”, “Term Loan Maturity Date”, “Term Note” and “Threshold Amount” set forth in Section 1 of the Loan and Security Agreement are each hereby deleted in its entirety and the following are substituted therefor in appropriate alphabetical order:

“Permitted Indebtedness” means: (i) Indebtedness of Borrower in favor of Lender or Agent arising under this Agreement or any other Loan Document; (ii) Indebtedness existing on, or committed for but not yet outstanding as of, the Closing Date which is disclosed in Schedule 1A; (iii) Indebtedness of up to $10,000,000 outstanding at any time secured by a Lien described in clause (vii) of the defined term “Permitted Liens,” provided such Indebtedness does not exceed the lesser of the cost or fair market value of the Equipment financed with such Indebtedness; (iv) Indebtedness to trade creditors incurred in the ordinary course of business, including Indebtedness incurred in the ordinary course of business with corporate credit cards; (v) Indebtedness that also constitutes a Permitted Investment; (vi) Subordinated Indebtedness; (vii) reimbursement obligations in

- 2 -

connection with letters of credit that are secured by cash or cash equivalents and issued on behalf of the Borrower or a Subsidiary thereof in an amount not to exceed $200,000 at any time outstanding, (viii) Indebtedness incurred by Parent prior to the First Amendment Effective Date in an aggregate amount of up to $100,000,000 relating to unsecured convertible securities issued pursuant to Rule 144A under the Securities Act pursuant to a Purchase Agreement entered into between Parent and Morgan Stanley & Co. LLC; (ix) other unsecured Indebtedness in an amount not to exceed $15,000,000 at any time outstanding, and (x) extensions, refinancings and renewals of any items of Permitted Indebtedness, provided that the principal amount is not increased or the terms modified to impose materially more burdensome terms upon Borrower or its Subsidiary, as the case may be.

“Term Loan Advance” means any Loan funds advanced under this Agreement and includes, without limitation, the Closing Date Term Loan Advance and the Additional Term Loan Advance.

“Term Loan Maturity Date” means, subject to the provisions hereof, February 1, 2017.

“Term Note” means a Promissory Note in substantially the form of (i) Exhibit B with respect to the Closing Date Term Loan Advance and (ii) Exhibit B-1 with respect to the Additional Term Loan Advance.

“Threshold Amount” means an amount equal to fifty percent of the principal amount of then outstanding Advances under this Agreement.

(c)    The definitions of “Forbearance Fee”, “Specified Covenant”, “Specified Covenant Breach Date” and “Term Loan Interest Rate” set forth in Section 1 are hereby deleted in their entirety.

(d)    Section 2.2 of the Loan and Security Agreement is hereby deleted in its entirety and the following is substituted therefor:

2.2    Term Loans.

(a)    Advances. Subject to the terms and conditions of this Agreement, Lender will severally (and not jointly) make in an amount not to exceed its respective Term Commitment, and Borrower agrees to draw, (i) a Term Loan Advance of Twenty-Five Million Dollars ($25,000,000) on the Closing Date (the “Closing Date Term Loan Advance”) and (ii) subject to the effectiveness of the First Amendment, a Term Loan Advance of Five Million Dollars ($5,000,000) on the First Amendment Effective Date (the “Additional Term Loan Advance”).

(b)     Advance Request. To obtain a Term Loan Advance, Borrower shall complete, sign and deliver an Advance Request (at least one (1) Business Day before the applicable Advance Date) to Agent. Lender shall fund such Term Loan Advance in the manner requested by the applicable Advance Request

- 3 -

provided that each of the conditions precedent to such Term Loan Advance is satisfied as of the Closing Date or the First Amendment Effective Date, as applicable.

(c)    Interest. The principal balance of the Closing Date Term Loan Advance shall bear interest thereon from the Closing Date at the Closing Date Term Loan Interest Rate based on a year consisting of 360 days, with interest computed daily based on the actual number of days elapsed. The principal balance of the Additional Term Loan Advance shall bear interest thereon from the First Amendment Effective Date at the Additional Term Loan Interest Rate based on a year consisting of 360 days, with interest computed daily based on the actual number of days elapsed. The Closing Date Term Loan Interest Rate and the Additional Term Loan Interest Rate will float and change on the day the Prime Rate changes from time to time.

(d)    Payment. Borrower will pay interest on each Term Loan Advance on the first Business Day of each month, beginning the month after the (i) Closing Date with respect to the Closing Date Term Loan Advance and (ii) First Amendment Effective Date with respect to the Additional Term Loan Advance. Borrower shall repay the aggregate principal balance of all Term Loan Advances that are outstanding on the day immediately preceding the Amortization Date, in equal monthly installments of principal and interest (mortgage style) beginning on the Amortization Date and continuing on the first Business Day of each month thereafter until the Secured Obligations are repaid. The entire Term Loan Advance principal balance and all accrued but unpaid interest hereunder, shall be due and payable on Term Loan Maturity Date. Borrower shall make all payments under this Agreement without setoff, recoupment or deduction and regardless of any counterclaim or defense. Lender will initiate debit entries to the Borrower’s account as authorized on the ACH Authorization on each payment date of all periodic obligations payable to Lender under each Term Loan Advance.

(e)    Section 2.9 of the Loan and Security Agreement is hereby deleted in its entirety and the following is substituted therefor:

Section 2.9. [Intentionally omitted.]

(f)    Section 7.14 of the Loan and Security Agreement is hereby deleted in its entirety and the following is substituted therefor:

Section 7.14. Minimum Cash. So long as the Secured Obligations are outstanding, Borrower shall, as of any date, have at least the Threshold Amount of unrestricted, unencumbered Cash in one or more Deposit Accounts subject to an Account Control Agreement in favor of Agent.

(g)    Section 7.16 of the Loan and Security Agreement is hereby deleted in its entirety and the following is substituted therefor:

Section 7.16. [Intentionally omitted.]

- 4 -

(h)    Section 7.17 of the Loan and Security Agreement is hereby deleted in its entirety and the following is substituted therefor:

Section 7.17. [Intentionally omitted.]

(h)    Schedule 1.1 of the Loan and Security Agreement is hereby amended by deleting the references to “$25,000,000” and substituting in each place “$30,000,000” therefor.

(i)    Exhibit 1 to this Amendment is hereby inserted as Exhibit B-1 of the Loan and Security Agreement and shall, for all purposes, be the Exhibit B-1 referred to therein.

3.    Conditions to Effectiveness. The provisions of this Amendment shall become effective on the date, which date (if ever) shall be prior to June 25, 2014, that all of the following conditions precedent have been satisfied (the “First Amendment Effective Date”):

(a)    Agent shall have received (i) three original counterparts of this Amendment, duly executed and delivered by Parent and the Subsidiary Guarantor, (ii) one original of the Note relating to the Additional Term Loan Advance in substantially the form attached hereto as Exhibit 1 (if requested by Agent), and (iii) one original Advance Request relating to the Additional Term Loan Advance;

(b)    Each of the representations and warranties of Borrower in Section 5 of this Amendment shall be true, correct and accurate in all material respects as of the First Amendment Effective Date;

(c)    No Material Adverse Effect has occurred;

(d)    Borrower shall have received consents to the transactions contemplated by this Amendment from (i) the counterparties to the agreements listed on Schedule 5.3 to the Loan and Security Agreement and (ii) Total and Maxwell (Mauritius) Pte Ltd with respect to certain covenants contained in the Company’s Tranche I Notes (as defined on Schedule 5.14 of the Loan and Security Agreement) issued pursuant to that certain Securities Purchase Agreement dated as of August 8, 2013, as amended on October 16, 2013 and December 24, 2013, by and among the Company and the investors party thereto;

(e)    

(f)    No Default or Event of Default exists under the Loan and Security Agreement or any Loan Document;

(g)    Borrower shall have paid to Agent’s counsel all legal fees and out-of-pocket expenses incurred in connection with this Amendment; and

(h)    All legal matters incident to the execution and delivery of this Amendment shall be satisfactory to Agent and its counsel.

- 5 -

4.    Note Modification. Subject to the satisfaction of the terms and conditions set forth in Section 3 of this Amendment, the Secured Term Promissory Note, dated March 29, 2014, executed by Borrower to the order of Lender in the original principal amount of $25,000,000 (the “Existing Note”), is hereby modified to have a Maturity Date of February 1, 2017.

5.    Representations, Warranties and Agreements. Borrower hereby represents, warrants and agrees in favor of Agent and Lender as follows:

(a)    No Default or Event of Default has occurred and is continuing (or would result from the amendment of the Loan and Security Agreement contemplated hereby);

(b)    The execution, delivery and performance by Borrower of this Amendment has been duly authorized by all necessary corporate and/or other action and do not and will not require any registration with, consent or approval of, notice to or action by, any Person in order to be effective and enforceable. Each of the Loan and Security Agreement and the other Loan Documents to which Borrower is a party constitutes and continues to constitute the legally, valid and binding obligation of Borrower, in each case enforceable against Borrower in accordance with its terms;

(c)    All of the representations and warranties of Borrower contained in the Loan and Security Agreement and the other Loan Documents are true and correct in all material respects on and as of the date hereof and will be true and correct on the First Amendment Effective Date (except to the extent that such representations and warranties specifically refer to an earlier date, in which case they shall be true and correct as of such earlier date);

(d)    No Material Adverse Effect has occurred;

(e)    Borrower is entering into this Amendment on the basis of such Person’s own business judgment, without reliance upon Agent or Lender; and

(f)    Borrower acknowledges and agrees that the execution and delivery by Agent and Lender of this Amendment shall not be deemed to create a course of dealing or otherwise obligate Agent or Lender to execute similar agreements under the same or similar circumstances in the future. Neither Agent nor Lender has any obligation to Borrower or any other Person to further amend provisions of the Loan and Security Agreement or the other Loan Documents. Other than as specifically contemplated hereby, all of the terms, covenants and provisions of the Loan and Security Agreement (and the other Loan Documents) are and shall remain in full force and effect.

6.    General Provisions.

(a)    Upon the effectiveness of this Amendment, all references in the Loan and Security Agreement and in the other Loan Documents to the Loan and Security Agreement shall refer to the Loan and Security Agreement as modified hereby. This Amendment shall be deemed incorporated into, and a part of, the Loan and Security Agreement. This Amendment is a Related Document. THIS AMENDMENT IS EXPRESSLY SUBJECT TO THE PROVISIONS OF SECTION 11.8 (GOVERNING LAW), SECTION 11.9 (CONSENT TO JURISDICTION AND VENUE) AND SECTION 11.10 (MUTUAL WAIVER OF JURY TRIAL; JUDICIAL REFERENCE) OF THE LOAN AND SECURITY AGREEMENT, WHICH PROVISIONS ARE INCORPORATED HEREIN AND MADE APPLICABLE HERETO BY THIS REFERENCE.

- 6 -

(b)    This Amendment is made pursuant to Section 11.3(b) and 11.7 of the Loan and Security Agreement and shall be binding upon and inure to the benefit of the parties hereto and thereto and their respective successors and assigns. No third party beneficiaries are intended in connection with this Amendment.

(c)    This Amendment may be executed in counterparts (and by different parties hereto in different counterparts), each of which shall constitute an original, but all of which when taken together shall constitute a single contract. Delivery of an executed counterpart of a signature page of this Amendment by telecopy shall be effective as delivery of a manually executed counterpart of this Amendment.

(d)    Each provision of this Amendment shall be severable from every other provision of this Amendment for the purpose of determining the legal enforceability of any specific provision.

(e)    Borrower shall promptly pay to Agent’s counsel all attorneys’ fees and expenses incurred in connection with the preparation, negotiation and closing of this Amendment.

(f)    The appearing parties herein declare that all the terms and conditions of the Loan and Security Agreement continue to remain, as herein amended, in full force and effect and by these presents the appearing parties hereby ratify, reaffirm and confirm all the terms and conditions of the Loan and Security Agreement and further declare that it is their express intention that the transactions set forth in this Amendment shall in no way, manner or form be construed or be interpreted as an extinctive novation of any of the obligations and agreements set forth in the Loan and Security Agreement.

[Document continues with signature pages.]

- 7 -

IN WITNESS WHEREOF, the parties hereto have caused this First Amendment to Loan and Security Agreement to be duly executed and delivered as of the date first written above.

PARENT:

AMYRIS, INC.

By: /s/ John G. Melo

Print Name:     John G. Melo

Title: President and Chief Executive Office

Accepted in Palo Alto, California:    AGENT:

HERCULES TECHNOLOGY GROWTH CAPITAL, INC.

Signature: /s/ Ben Bang

Print Name: Ben Bang

Title: Senior Counsel

LENDER:

HERCULES TECHNOLOGY GROWTH CAPITAL, INC.

Signature: /s/ Ben Bang

Print Name: Ben Bang

Title: Senior Counsel

The undersigned Subsidiary Guarantor hereby acknowledges and consents (without implying the need for any such consent) to the First Amendment to Loan and Security Agreement and Note Modification as set forth above (the “First Amendment”). The undersigned confirms that the guaranty set forth in Section 11.19 of the Loan and Security Agreement and that all of the undersigned’s obligations thereunder remain in full force and effect, without set-off, defense or counterclaim, and that the obligations guaranteed thereunder include, without limitation, all amounts owing in respect of the Loan and Security Agreement and the Notes, each modified by the First Amendment to Loan and Security Agreement, dated as of June __, 2014

SUBSIDIARY GUARANTOR:

AMYRIS FUELS, LLC

By: /s/ John G. Melo    

Print Name: John G. Melo    

Title:        

EXHIBIT 1 TO FIRST AMENDMENT TO

LOAN AND SECURITY AGREEMENT AND NOTE MODIFICATION

EXHIBIT B-1 TO LOAN AND SECURITY AGREEMENT

ADDITIONAL SECURED TERM PROMISSORY NOTE

$5,000,000	Advance Date: June __, 2014
	Maturity Date: February 1, 2017

FOR VALUE RECEIVED, Amyris, Inc., a Delaware corporation, for itself and each of its Subsidiaries that has delivered a Joinder Agreement (the “Borrower”) hereby promises to pay to the order of Hercules Technology Growth Capital, Inc., a Maryland corporation or the holder of this Note (the “Lender”) at 400 Hamilton Avenue, Suite 310, Palo Alto, CA 94301 or such other place of payment as the holder of this Secured Term Promissory Note (this “Promissory Note”) may specify from time to time in writing, in lawful money of the United States of America, the principal amount of Five Million Dollars ($5,000,000) or such other principal amount as Lender has advanced to Borrower, together with interest at a fixed rate equal to the greater of (a) the prime rate as reported in the Wall Street Journal, and if not reported, then the prime rate next reported in the Wall Street Journal, plus 5.25% per annum and (b) 8.5% per annum, in each case based upon a year consisting of 360 days, with interest computed daily based on the actual number of days in each month.

This Promissory Note is a Term Note referred to in, and is executed and delivered in connection with, that certain Loan and Security Agreement dated March 29, 2014, by and among Borrower, Hercules Technology Growth Capital, Inc., a Maryland corporation (the “Agent”) and the several banks and other financial institutions or entities from time to time party thereto as lender (as the same may from time to time be amended, modified or supplemented in accordance with its terms, the “Loan Agreement”), and is entitled to the benefit and security of the Loan Agreement and the other Loan Documents (as defined in the Loan Agreement), to which reference is made for a statement of all of the terms and conditions thereof. All payments shall be made in accordance with the Loan Agreement. All terms defined in the Loan Agreement shall have the same definitions when used herein, unless otherwise defined herein. An Event of Default under the Loan Agreement shall constitute a default under this Promissory Note.

Borrower waives presentment and demand for payment, notice of dishonor, protest and notice of protest under the UCC or any applicable law. Borrower agrees to make all payments under this Promissory Note without setoff, recoupment or deduction and regardless of any counterclaim or defense. This Promissory Note has been negotiated and delivered to Lender and is payable in the State of California. This Promissory Note shall be governed by and construed and enforced in accordance with, the laws of the State of California, excluding any conflicts of law rules or principles that would cause the application of the laws of any other jurisdiction.

[Signature Page Follows]

BORROWER FOR ITSELF ANDON BEHALF OF THE SUBSIDIARIES
THAT HAVE DELIVERED A JOINDER
AGREEMENT:    AMYRIS, INC.

By:    /s/ John G. Melo

Name:    John G. Melo

Title:    President and Chief Executive Officer

- 2 -

EX-10.01

CONFIDENTIAL TREATMENT REQUESTED. CERTAIN PORTIONS OF THIS DOCUMENT HAVE BEEN OMITTED PURSUANT TO A REQUEST FOR CONFIDENTIAL TREATMENT AND, WHERE APPLICABLE, HAVE BEEN MARKED WITH AN ASTERISK TO DENOTE WHERE OMISSIONS HAVE BEEN MADE. THE CONFIDENTIAL MATERIAL HAS BEEN FILED SEPARATELY WITH THE SECURITIES AND EXCHANGE COMMISSION.

MODIFICATION

TO

TECHNOLOGY INVESTMENT AGREEMENT

BETWEEN

AMYRIS, INC.,

5885 HOLLIS STREET

SUITE 100

EMERYVILLE, CALIFORNIA 94608

AND

THE DEFENSE ADVANCED RESEARCH PROJECTS AGENCY

675 NORTH RANDOLPH STREET

ARLINGTON, VA 22203-2114

CONCERNING

IMPROVING DNA ASSEMBLY AND INTEGRATION ACROSS PLATFORMS WITH

BETTER SYSTEMS AND TOOLS

(LIVING FOUNDRIES)

Agreement No.: HR0011-12-3-0006

Modification No.: P00010

Purchase Request No.: N/A

Total Amount of the Agreement: $8,504,788

Phase 1: $3,358,334

Phase 2 (Option): $5,146,453

Total Estimated Government Funding: $7,654,309

Phase 1: $3,022,501

Phase 2 (Option): $4,631,808

Contactor Share Contribution: $850,479

Phase 1: $335,834

Phase 2 (Option): $514,645

Funds Obligated By This Modification: $0.00

Total Funds Obligated To Date: $6,300,819

Authority: Article III(C)(1)

HR0011-12-3-0006

P00010

Page 2 of 2

The purpose of this modification is to make minor technical edits to the Statement of Work (Agreement Attachment 1) and Payable Milestone Plan (Agreement Attachment 3). Accordingly, the following changes apply:

1. Attachment No. 1, “Statement of Work,” is modified to reflect changes to Phase II, Task F, “Metrics/Completion Criteria” and “Deliverable,” and Subtask F.1. “Transform Alternative Hosts with Mevalonate Pathway.” Changes are highlighted in yellow at Enclosure 1

2. The Attachment No. 3 “Schedule of Payments and Payable Milestones” is modified to reflect the changes to “Exit Criteria” for Milestone No. 14. Changes are highlighted in red at Enclosure 1.

3. A fully conformed version of Agreement No. HR0011-12-3-0006 though P00010, reflecting the changes summarized above, is provided as Enclosure 1 to this modification. All changes to the Modification P00010 conformed Agreement are highlighted as noted in Paragraphs 1 and 2 above.

4. Except as modified above, the terms and conditions of Agreement No. HR0011-12-3-006 shall remain unchanged and in full force and effect

FOR AMYRIS INC	FOR THE DEFENSE ADVANCED RESEARCH PRODUCTS AGENCY
/s/ Nicholas Khadder April 10, 2014	/s/Michael D. Blackstone April 11, 2014
(Signature & Date)	(Signature & Date)
Nicholas Khadder	Michael D. Blackstone
Vice President & General Counsel	Agreements Officer

TECHNOLOGY INVESTMENT AGREEMENT

BETWEEN

AMYRIS, INC.,

5885 HOLLIS STREET

SUITE 100

EMERYVILLE, CALIFORNIA 94608

AND

THE DEFENSE ADVANCED RESEARCH PROJECTS AGENCY

675 NORTH RANDOLPH STREET

ARLINGTON, VA 22203-2114

CONCERNING

IMPROVING DNA ASSEMBLY AND INTEGRATION ACROSS PLATFORMS WITH BETTER

SYSTEMS AND TOOLS

(LIVING FOUNDRIES)

Agreement No.: HR0011-12-3-0006

ARPA Order No.: S351/00, S351/01, S351/02, HR001133399, HR001146140, HR001147725

Total Amount of the Agreement: $8,504,788

Phase 1: $3,358,334

Phase 2 (Option): $5,146,453

Total Estimated Government Funding: $7,654,309

Phase 1: $3,022,501

Phase 2 (Option): $4,631,808

Contactor Share Contribution: $850,479

Phase 1: $335,834

Phase 2 (Option): $514,645

Total Funds Obligated: $6,300,819

Authority: 10 U.S.C. § 2371

Line of Appropriation – See Article V.

This Agreement is entered into between the United States of America, hereinafter called the Government, represented by The Defense Advanced Research Projects Agency (DARPA), and AMYRIS, INC., a corporation organized and existing under the laws of the State of Delaware with its principal place of business at 5885 Hollis Street, Suite 100, Emeryville, California 94608 pursuant to and under U.S. Federal law.

Enclosure 1 Conformed Copy P00010

Agreement HR0011-12-3-0006

FOR AMYRIS INC	FOR THE DEFENSE ADVANCED RESEARCH PRODUCTS AGENCY
//See Modification No. P00010//
(Signature & Date)	(Signature & Date)
	Michael D. Blackstone
	Agreements Officer
(Name, Title)	(Name, Title)

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TABLE OF CONTENTS

ARTICLES		PAGE
ARTICLE I	Scope of the Agreement	4
ARTICLE II	Term	7
ARTICLE III	Management of the Project	8
ARTICLE IV	Agreement Administration	9
ARTICLE V	Obligation and Payment	10
ARTICLE VI	Disputes	13
ARTICLE VII	Patent Rights	14
ARTICLE VIII	Data Rights	17
ARTICLE IX	Foreign Access to Technology	18
ARTICLE X	Title to and Disposition of Property	20
ARTICLE XI	Civil Rights Act	20
ARTICLE XII	Security	20
ARTICLE XIII	Subcontractors	21
ARTICLE XIV	Key Personnel	21
ARTICLE XV	Export Control	21
ARTICLE XVI	Order of Precedence	22
ARTICLE XVII	Execution	22
ARTICLE XVIII	Applicable Law	22
ARTICLE XIX	Severability	22
ARTICLE XX	Force Majeure	23
ATTACHMENTS
ATTACHMENT 1	Statement of Work
ATTACHMENT 2	Report Requirements
ATTACHMENT 3	Schedule of Payments and Payable Milestones
ATTACHMENT 4	Funding Schedule
ATTACHMENT 5	List of Intellectual Property Assertions

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ARTICLE I:    SCOPE OF THE AGREEMENT

A.    Background

Amyris has been a leader in the synthetic biology technologies, using living organisms as “factories” or “manufacturing systems” to produce compounds. Although the synthetic biology movement has been intermittently successful in certain directed endeavors, there has been insufficient effort toward standardizing and optimizing synthetic biology tools, procedures and platforms. By focusing on the same principles that made the United States the leaders in traditional manufacturing, namely consistent engineering and efficiency, Amyris seeks, through funding in this Agreement , to research and develop a state of the art development cycle for an enhanced engineering cycle to realize living foundries. Amyris aims to achieve these innovations by developing tools increasing the speed of engineered DNA and microbes while simultaneously expanding the scope of the living systems that are readily engineered. Engineering living systems is slow, expensive, and unreliable. Even for seemingly straightforward applications such as developing a fermentable microbe capable of turning sugar into higher value chemicals can take many hundreds of person-years of effort. For example, genetic engineering has enabled the microbial production of non-native natural products such as 1,3-propanediol made in engineered E. coli (~575 years of effort) or artemisinic acid made in engineered S. cerevisiae (~130 years of effort).

For microbes to become a routine manufacture paradigm, offering an alternative to traditional chemicals

and petroleum feedstocks, and for living systems eventually to enable novel commercial and military

applications (self-healing or corrosion-resistant materials) the effort and expense associated with

developing new applications must be reduced by an order of magnitude. This entire enterprise is in its

infancy and the work required to reduce the time and effort needed to develop a new microbe is risky and

at odds with the work also needed to bring a product to market in a one-off manner, the chief goal of any

company seeking to capitalize on the technology. This Agreement supports research with a long-term

perspective to support that entire industry by funding efforts that will enable everyone to do more with

less.

B.    Definitions

Agreement: The body of this Agreement and Attachments 1 – 4, which are expressly incorporated in

and made a part of the Agreement.

Collaborators: A third party in a contractual arrangement with the Performer whereby Amyris has agreed to jointly research, develop and/or commercialize and has an active role in such arrangement. For the avoidance of doubt, an “active role” by Amyris is a contractual relationship (1) that involves more than the mere transfer of intellectual property, and (2) where Amyris has a significant participation in decisionmaking and/or funding of the activities. Collaborators include all parties in collaborations with Amyris as of the effective date, even if the collaboration is modified or amended after the effective date.

Data: Recorded information, regardless of form or method of recording, which includes but is not limited to, technical data, software, and trade secrets. The term does not include financial, administrative, cost, pricing or management information and does not include Subject Inventions, included in Article VII.

Foreign Firm or Institution: A firm or institution organized or existing under the laws of a country other than the United States, its territories, or possessions. The term includes, for purposes of this

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Agreement, any agency or instrumentality of a foreign government; and firms, institutions or business organizations which are owned or substantially controlled by foreign governments, firms, institutions, or individuals.

Government: The United States of America, as represented by DARPA.

Government Purpose Rights: The rights to use, duplicate, or disclose Data, in whole or in part and in any manner, for Government purposes only, and to have or permit others to do so for Government purposes only.

Government Purpose: Any activity in which the United States Government is a party, including cooperative agreements with international or multi-national defense organizations or sales or transfers by the United States Government to foreign governments or international organizations. Government purposes include competitive procurement, but do not include the rights to use, modify, reproduce, release, perform, display, or disclose Data for commercial purposes or authorize others to do so.

Invention: Any invention or discovery which is or may be patentable or otherwise protectable under Title 35 of the United States Code.

Know-How: All information including, but not limited to discoveries, formulas, materials, Inventions, processes, ideas, approaches, concepts, techniques, methods, software, programs, documentation, procedures, firmware, hardware, technical data, specifications, devices, apparatus and machines.

Limited Rights: The rights to use, modifiy, reproduce, release, perform, display, or disclose Data, in whole or in part, within the Government. The Government may not, without the written permission of the party asserting limited rights, release or disclose the Data outside the Government.

Made: Relates to any Invention means the conception or first actual reduction to practice of such Invention.

Performer: AMYRIS, INC. a corporation organized and existing under the laws of the State of Delaware with its principal place of business at 5885 Hollis Street, Suite 100, Emeryville, California 94608

Practical Application: To manufacture, in the case of a composition of product; to practice, in the case of a process or method, or to operate, in the case of a machine or system; and, in each case, under such conditions as to establish that the Invention is capable of being utilized and that its benefits are, to the extent permitted by law or Government regulations, available to the public on reasonable terms. For the avoidance of doubt, the Parties acknowledge that “practical application” under this Agreement may not include actual commercialization of Subject Inventions hereunder because such Subject Inventions are likely to be research tools and platforms (e.g., it is envisioned that the tools and platforms resulting from the research carried out under this agreement will later – outside of this agreement - be used by the performer to develop commercial products).

Program: Research and development being conducted by the Performer, as set forth in Article I., paragraph C.

Property: Any tangible personal property other than property actually consumed during the execution of work under this agreement.

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Subject Invention: Any Invention conceived or first actually reduced to practice in the performance of work under this Agreement that is capable of use as a tool for making or altering a genetically modified organism, provided however, any Inventions, regardless when conceived or reduced to practice, covering the genetically modified organism, a strain, or any compound or product made by or from an organism or strain shall not be considered “Subject Inventions” hereunder. For the avoidance of doubt, no work performed prior to the effective date of this Agreement shall be considered performed “under this Agreement.”

Technology: Discoveries, innovations, Know-How and Inventions, whether patentable or not, including computer software, recognized under U.S. law as intellectual creations to which rights of ownership accrue, including, but not limited to, patents, trade secrets, and copyrights developed under this Agreement.

Unlimited Rights: Rights to use, duplicate, release, or disclose, Data in whole or in part, in any manner and for any purposes whatsoever, and to have or permit others to do so.

C.    Scope

1.    Amyris, Inc. (hereafter “the Performer”) shall perform a research and development program (Program) designed to develop improved DNA assembly and integration across platforms. The research shall be carried out in accordance with the Statement of Work incorporated in this Agreement as Attachment 1. The Performer shall submit or otherwise provide all documentation required by Attachment 2, Report Requirements.

2.    The Performer shall be paid for each Payable Milestone accomplished in accordance with the Schedule of Payments and Payable Milestones set forth in Attachment 3 and the procedures of Article V. Both the Schedule of Payments and the Funding Schedule set forth in Attachments 3 and 4 respectively may be revised or updated in accordance with Article III, subject to mutual agreement of the Parties.

3.    The Government and the Performer estimate that the Statement of Work of this Agreement can only be accomplished with a Performer aggregate resource contribution of

	Phase 1	Phase 2/ Option 1 (Exercised)	Total Costs if All Options Exercised
Government Share (90%)	$3,022,501	$4,631,808	$7,654,309
Performer Share (10%)	$335,834	$514,645	$850,479
Total Amount of the Agreement	$3,358,334	$5,146,453	$8,504,788

from the effective date of this Agreement, subject to the availability of funds. The Performer intends and, by entering into this Agreement, undertakes to cause these funds to be provided. The Performer’s contributions will be provided as detailed in the Funding Schedule set forth in Attachment 4. If either DARPA or the Performer is unable to provide its respective total contribution, the other Party may reduce its project funding by a proportional amount.

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D.    Goals / Objectives

1.    The goal of this Agreement is for the Government to fund a performance-based effort by the Performer to investigate and create platforms for increasing the speed of engineering DNA and microbes while simultaneously expanding the scope of the living systems that are readily engineered.

2.    The Government will have continuous involvement with the Performer. The Government will also obtain access to research results and certain rights in data and patents pursuant to Articles VII and VIII. DARPA and the Performer are bound to each other by a duty of good faith and best research effort in achieving the goals of the Program.

3.    This Agreement is an "other transaction" pursuant to 10 U.S.C. § 2371. The Parties agree that the principal purpose of this Agreement is for the Government to support and stimulate the Performer to provide their best effort in advanced research and technology development and not for the acquisition of property or services for the direct benefit or use of the Government. This Agreement can best be described as an accumulation of expenses approach with payments tied to Fixed Payable Milestones. The Performer will be paid for each Payable Milestone accomplished in accordance with the Schedule of Payments and Payable Milestones set forth in Attachment 3 and the procedures of Article V. The Schedule of Payments and Payable Milestones may be revised or updated in accordance with Article III. This Agreement is not intended to be, nor shall it be construed as, by implication or otherwise, a partnership, a corporation, or other business organization.

ARTICLE II:    TERM

A.    Term of this Agreement

The Program commences upon the date of the last signature hereon and continues for:

Phase 1 – Twelve (12) months.

Phase 2 (Exercised via P00005) – Twelve (12) months from date of option exercise.

If all funds are expended prior to the duration of any Phase of the Agreement, the Parties have no obligation to continue performance and may elect to cease development at that point.

Provisions of this Agreement, which, by their express terms or by necessary implication, apply for periods of time other than specified herein, shall be given effect, notwithstanding this Article.

B.    Termination Provisions

Subject to a reasonable determination that the program will not produce beneficial results commensurate with the expenditure of resources, either Party may terminate this Agreement by written notice to the other Party, provided that such written notice is preceded by consultation between the Parties. In the event of a termination of the Agreement, it is agreed that disposition of Data developed under this Agreement, shall be in accordance with the provisions set forth in Article VIII, Data Rights. The Government and the Performer will negotiate in good faith a reasonable and timely adjustment of all outstanding issues between the Parties as a result of termination. Failure of the Parties to agree to a reasonable adjustment will be resolved pursuant to Article VI, Disputes. The Government has no obligation to pay the Performer beyond the last completed and paid milestone if the Performer decides to terminate. For the avoidance of doubt, any such termination does not require repayment of milestone amounts already received by Performer.

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C. Extending the Term (Phase 2)

The Parties may extend by mutual written agreement the term of this Agreement if funding availability and research opportunities reasonably warrant. Any extension shall be formalized through modification of the Agreement by the Agreements Officer and the Performer’s Administrator.

(i) The Government may extend the term of this agreement by written notice to the Performer within 12 months; provided that the Government gives the Performer a preliminary written notice of its intent to extend at least 14 days before the agreement expires. The preliminary notice does not commit the Government to an extension.

(ii) If the Government exercises this option, the extended agreement shall be considered to include this article.

(iii) The total duration of this agreement, including the exercise of any options under this article, shall not exceed 24 months.

(End of clause)

ARTICLE III:    MANAGEMENT OF THE PROJECT

A.    Management and Program Structure

The Performer shall be responsible for the overall technical and program management of the Program, and technical planning and execution shall remain with the Performer. The DARPA Agreements Officer’s Representative shall provide recommendations to Program developments and technical collaboration and be responsible for the review and verification of the Payable Milestones.

B.    Program Management Planning Process

Program planning will consist of an Annual Program Plan with inputs and review from the Performer and DARPA management, containing the detailed schedule of research activities and payable milestones. The Annual Program Plan will consolidate quarterly adjustments in the research schedule, including revisions/modification to payable milestones.

1.    Initial Program Plan: The Performer will follow the initial program plan that is contained in the Statement of Work (Attachment 1), and the Schedule of Payments and Payable Milestones (Attachment 3).

2.    Overall Program Plan Annual Review

(a)    The Performer, with DARPA Agreements Officer’s Representative review, will prepare an overall Annual Program Plan in the first quarter of each Agreement year. (For this purpose, each consecutive twelve (12) month period from (and including) the month of execution of this Agreement during which this Agreement shall remain in effect shall be considered an “Agreement Year”.) The Annual Program Plan will be presented and reviewed at an annual site review which will be attended by the performer’s Key Personnel, the DARPA Agreements Officer’s Representative, Senior DARPA management as appropriate, and other DARPA program managers and personnel as appropriate. The Performer, with DARPA participation and review, will prepare a final Annual Program Plan.

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(b)    The Annual Program Plan provides a detailed schedule of research activities, commits the Performer to use its best efforts to meet specific performance objectives, includes forecasted expenditures and describes the Payable Milestones. The Annual Program Plan will consolidate all prior adjustments in the research schedule, including revisions/modifications to payable milestones. Recommendations for changes, revisions or modifications to the Agreement which result from the Annual Review shall be made in accordance with the provisions of Article III, Section C.

C.    Modifications

1.    As a result of quarterly meetings (in person or videoconference), annual reviews, or at any time during the term of the Agreement, research progress or results may indicate that a change in the Statement of Work and/or the Payable Milestones, would be beneficial to program objectives. Recommendations for modifications, including justifications to support any changes to the Statement of Work and/or the Payable Milestones, will be documented in a letter and submitted by the Performer to the DARPA Agreements Officer’s Representative with a copy to the DARPA Agreements Officer. This documentation letter will detail the technical, chronological, and financial impact of the proposed modification to the research program. The Performer shall approve any Agreement modification. The Government is not obligated to pay for additional or revised Payable Milestones until the Payable Milestones Schedule (Attachment 3) is formally revised by the DARPA Agreements Officer and made part of this Agreement.

2.    The DARPA Agreements Officer’s Representative shall be responsible for the review and verification of any recommendations to revise or otherwise modify the Agreement Statement of Work, Schedule of Payments or Payable Milestones, or other proposed changes to the terms and conditions of this Agreement.

3.    For minor or administrative Agreement modifications (e.g. changes in the paying office or appropriation data, changes to Government or the Performer’s personnel identified in the Agreement, etc.) no signature is required by the Performer.

ARTICLE IV:    AGREEMENT ADMINISTRATION

Unless otherwise provided in this Agreement, approvals permitted or required to be made by DARPA

may be made only by the DARPA Agreements Officer. Administrative and contractual matters under

this Agreement shall be referred to the following representatives of the parties:

A.    Government Points of Contact:

Agreements Officer:

[*]

[*]

[*]

DARPA Program Manager:

[*]

Program Manager

[*]

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

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[*]

Agreements Officer’s Representative (AOR):

[*]

[*]

[*]

Administrative Agreements Officer (AAO):

[*]

[*]

[*]

B.    Performer Points of Contact

Performer’s Administrative/Contracting:

[*]

General Counsel

[*]

[*]

Performer’s Program Manager:

[*]

Chief Science Officer

[*]

[*]

ARTICLE V:    OBLIGATION AND PAYMENT

A.    Obligation

1. The Government’s liability to make payments to the Performer is limited to only those funds obligated under the Agreement or by modification to the Agreement. DARPA may obligate funds to the Agreement incrementally.

2. If modification becomes necessary in performance of this Agreement, pursuant to Article III, paragraph B, the DARPA Agreements Officer and the Performer’s Administrator shall execute a revised Schedule of Payable Milestones consistent with the then current Program Plan.

B. Payments

1. The Performer has an established and agrees to maintain an established accounting system which complies with Generally Accepted Accounting Principles and the requirements of this Agreement, and shall ensure that appropriate arrangements have been made for receiving, distributing and accounting for all funding. An acceptable accounting system is one in which all cash receipts and disbursements are controlled and documented properly.

2. The Performer shall document the accomplishments of each Payable Milestone by submitting or otherwise providing the Payable Milestones Report required by Attachment 2, Part D.

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

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After written verification of the accomplishment of the Payable Milestone by the DARPA Agreements Officer’s Representative, and approval by the Agreements Officer, the associated invoice will be submitted to the payment office via Wide Area Workflow (WAWF), as detailed in paragraph B.6 of this Article. If deemed necessary by the Agreements Officer, payment approval for the final Payable Milestone will be made after reconciliation of DARPA funding with actual Performer contributions. Subject to change only through written Agreement modification, payment shall be made to the address of the Performer’s Administrator set forth below.

3. Address of Payee: AMYRIS, INC., 5885 Hollis Street, Suite 100, Emeryville, California 94608

4. Government funds shall be maintained in an interest-bearing account prior to disbursement. This account shall not be in U. S. Treasury Notes. Any interest earned shall be remitted annually to the DARPA Agreements Officer, or designee. Interest payments shall be made payable to the U. S. Treasury. Interest amounts less than $250 per year may be retained by the Performer for administrative expenses.

5. Payments will be made by the cognizant Defense Agencies Financial Services office, as indicated below, within thirty (30) calendar days of an accepted invoice in Wide Area Workflow (WAWF). Wide Area Workflow (WAWF) is a secure web-based system for electronic invoicing, receipt and acceptance. The WAWF application enables electronic form submission of invoices, government inspection, and acceptance documents in order to support DoD’s goal of moving to a paperless acquisition process. Authorized DoD users are notified of pending actions by e-mail and are presented with a collection of documents required to process the contracting or financial action. It uses Public Key Infrastructure (PKI) to electronically bind the digital signature to provide non-reputable proof that the user (electronically) signed the document with the contents. Benefits include online access and full spectrum view of document status, minimized re-keying and improving data accuracy, eliminating unmatched disbursements and making all documentation required for payment easily accessible.

The Performer is required to utilize the Wide Area Workflow system when processing invoices and receiving reports under this Agreement. The Performer shall (i) ensure an Electronic Business Point of Contact is designated in Central Contractor Registration at http://www.ccr.gov and (ii) register to use WAWF–RA at the https://wawf.eb.mil site, within ten (10) calendar days after award of this Agreement. Step by Step procedures to register are available at the https://wawf.eb.mil site. The Performer is directed to use the “2-in-1” format when processing invoices.

a. For the Issue By DoDAAC enter HR0011

b. For the Admin DoDAAC and Ship To fields, enter S0507A.

c. For the Service Acceptor field, enter HR0011, Extension 01.

d. Leave the Inspect by DoDAAC, Ship From Code DoDAAC and LPO DoDAAC fields blank unless otherwise directed by the Agreements Officer or Administrative Agreements Officer.

e. The following guidance is provided for invoicing processed under this Agreement through WAWF:

• The AOR identified at Article IV "Agreement Administration" shall continue to formally inspect and accept the deliverables/payable milestones. To the maximum extent practicable, the AOR shall review the deliverable(s)/payable milestone report(s) and either: 1) provide a written notice of rejection to the Performer which includes feedback

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regarding deficiencies requiring correction or 2) written notice of acceptance to the Administrative Agreements Officer (AAO), DARPA PM and Agreements Officer.

• Acceptance within the WAWF system shall be performed by the Agreements Officer upon receipt of a confirmation email, or other form of transmittal, from the AOR.

• The Performer shall send an email notice to the AOR and Agreements Officer upon submission of an invoice in WAWF (this can be done from within WAWF).

• Payments shall be made by DFAS-CO/WEST (HQ0339)

• The Performer agrees, when entering invoices entered in WAWF to utilize the CLINs associated with each payable milestone as delineated at Attachment 3. The description of the CLIN shall include reference to the associated milestone number along with other necessary descriptive information. The Performer agrees that the Government may reject invoices not submitted in accordance with this provision.

Note for DFAS: The Agreement shall be entered into the DFAS system by CLIN – Milestone association as delineated at Attachment 3. The Agreement is to be paid out by CLIN – Milestone association. Payments shall be made using the CLIN (MS)/ACRN association as delineated at Attachment 3.

6.    Payee Information: As identified at Central Contractor Registration.

• Cage Code: 47QN9

• DUNS: 185930182

• TIN: 55-0856151

7.    Limitation of Funds: In no case shall the Government’s financial liability exceed the

amount obligated under this Agreement.

8.    Payments shall be made in the amounts set forth in Attachment No. 3, provided the DARPA Agreements Officer’s Representative has verified the accomplishment of the Payable Milestones. It is recognized that the quarterly accounting of current expenditures reported in the “Quarterly Business Status Report” submitted in accordance with Attachment No. 2 is not necessarily intended or required to match the Payable Milestones until submission of the Final Report; however, payable milestones may be revised during the course of the program to reflect current and revised projected expenditures, subject to the requirements set forth in Article III.

account for all funding under this Agreement and shall maintain adequate records to account for the Performer’s funding provided under this Agreement. Upon completion or termination of this Agreement, whichever occurs earlier, the Performer’s Administrator shall furnish to the Agreements Officer a copy of the Final Report required by Attachment 2, Part E. The Performer’s relevant financial records are subject to examination or audit on behalf of DARPA by the Government for a period not to exceed three (3) years after expiration of the term of this Agreement. The Agreements Officer or designee shall have direct access to sufficient records and information of the Performer, to ensure full accountability for all funding under this Agreement. Such audit, examination, or access shall be performed during business hours on business days upon prior written notice and shall be subject to the security requirements of the audited party.

C.    Accounting and Appropriation Data

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AA    9720400 1320 S351 P2D10 2525 DPAC 2 5205 S12136 61101E    $3,022,501

AB    012199 097    0400 000 N 20132014 D 1320 HLIF6    2013.MBT-02.CORE.A

DARPA 255

$2,632,428

ACRN    AC: 012199 097    0400 000 N 20132014 D 1320 HTLM6    2013.MBT-02.CORE.A

DARPA        255

$645,890

ARTICLE VI:    DISPUTES

A.    General

The Parties shall communicate with one another in good faith and in a timely and cooperative manner

when raising issues under this Article.

B.    Dispute Resolution Procedures

1.    Any disagreement, claim or dispute between DARPA and the Performer concerning questions of fact or law arising from or in connection with this Agreement, and, whether or not involving an alleged breach of this Agreement, may be raised only under this Article.

2.    Whenever disputes, disagreements, or misunderstandings arise, the Parties shall attempt to resolve the issue(s) involved by discussion and mutual agreement as soon as practicable. In no event shall a dispute, disagreement or misunderstanding which arose more than three (3) months prior to the notification made under subparagraph B.3 of this article constitute the basis for relief under this article unless the Director of DARPA in the interests of justice waives this requirement.

3.    Failing resolution by mutual agreement, the aggrieved Party shall document the dispute, disagreement, or misunderstanding by notifying the other Party (through the DARPA Agreements Officer or the Performer’s Administrator, as the case may be) in writing of the relevant facts, identify unresolved issues, and specify the clarification or remedy sought. Within five (5) working days after providing notice to the other Party, the aggrieved Party may, in writing, request a joint decision by the DARPA Senior Procurement Executive, and senior executive (no lower than Vice President, Legal) appointed by the Performer. The other Party shall submit a written position on the matter(s) in dispute within thirty (30) calendar days after being notified that a decision has been requested. The DARPA Senior Procurement Executive, and the senior executive shall conduct a review of the matter(s) in dispute and render a decision in writing within thirty (30) calendar days of receipt of such written position. Any such joint decision is final and binding.

4.    In the absence of a joint decision, upon written request to the Director of DARPA, made within thirty (30) calendar days of the expiration of the time for a decision under subparagraph B.3 above, the dispute shall be further reviewed. The Director of DARPA may elect to conduct this review personally or through a designee or jointly with a senior executive (no lower than (Vice President, Legal) level) appointed by the Performer. Following the review, the Director of DARPA or designee will resolve the issue(s)and notify the Parties in writing. Such resolution is not subject to further administrative review and, to the extent permitted by law, shall be final and binding.

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C.    Limitation of Damages

Claims for damages of any nature whatsoever pursued under this Agreement shall be limited to direct damages only up to the aggregate amount of DARPA funding disbursed as of the time the dispute arises. In no event shall DARPA be liable for claims for consequential, punitive, special and incidental damages, claims for lost profits, or other indirect damages.

ARTICLE VII:    PATENT RIGHTS

A.    Allocation of Principal Rights

Unless the Performer shall have notified DARPA (in accordance with subparagraph B.2 below) that the Performer does not intend to retain title, the Performer shall retain the entire right, title, and interest throughout the world to each Subject Invention consistent with the provisions of this Article and 35 U.S.C. § 202. With respect to any Subject Invention in which the Performer retains title, DARPA shall have a nonexclusive, nontransferable, irrevocable, paid-up license to practice or have practiced on behalf of the United States the Subject Invention throughout the world.

B.    Invention Disclosure, Election of Title, and Filing of Patent Application

1.    The Performer shall disclose each Subject Invention to DARPA within four (4) months after the inventor discloses it in writing to his company personnel responsible for patent matters or, in the case of no internal writing from the inventor, within two (2) months after filing a provisional application, provided however that in the event the Performer does not file a provisional application, it shall disclose the Subject Invention to DARPA within two (2) months of determining that a particular set of experiments and or data qualify as a Subject Invention. The disclosure to DARPA shall be in the form of a written report and shall identify the Agreement under which the Subject Invention was made and the identity of the inventor(s). It shall be sufficiently complete in technical detail to convey a clear understanding to the extent known at the time of the disclosure, of the nature, purpose, operation, and the physical, chemical, biological, or electrical characteristics of the invention. The disclosure shall also identify any publication, sale, or public use of the invention and whether a manuscript describing the invention has been submitted for publication and, if so, whether it has been accepted for publication at the time of disclosure. The Performer shall also submit to DARPA an annual listing of Subject Inventions.

2.    If the Performer determines that it does not intend to retain title to any such Subject Invention, the Performer shall notify DARPA, in writing, within eight (8) months of disclosure to DARPA. However, in any case where publication, sale, or public use has initiated the one (1)-year statutory period wherein valid patent protection can still be obtained in the United States, the period for such notice may be shortened by DARPA to a date that is no more than sixty (60) calendar days prior to the end of the statutory period.

3.    The Performer shall file its initial patent application on a Subject Invention to which it elects to retain title within one (1) year after election of title or, if earlier, prior to the end of the statutory period wherein valid patent protection can be obtained in the United States after a publication, or sale, or public use. The Performer may elect to file patent applications in additional countries (including the European Patent Office and the Patent Cooperation Treaty) within either ten (10) months of the corresponding initial patent application or six (6) months from the date permission is granted by the

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Commissioner of Patents and Trademarks to file foreign patent applications, where such filing has been prohibited by a Secrecy Order.

4.    Requests for extension of the time for disclosure election, and filing under Article VII, paragraph C, may, at the discretion of DARPA, and after considering the position of the Performer, be granted.

C.    Conditions When the Government May Obtain Title

Upon DARPA’s written request, the Performer shall convey title to any Subject Invention to DARPA under any of the following conditions:

1.    If the Performer fails to disclose or elects not to retain title to the Subject Invention within the times specified in paragraph C of this Article; provided, that DARPA may only request title within sixty (60) calendar days after learning of the failure of the Performer to disclose or elect within the specified times.

2.    In those countries in which the Performer fails to file patent applications within the times specified in paragraph B of this Article; provided, that if the Performer has filed a patent application in a country after the times specified in paragraph B of this Article, but prior to its receipt of the written request by DARPA, the Performer shall continue to retain title in that country; or

3.    In any country in which the Performer decides not to continue the prosecution of any application for, to pay the maintenance fees on, or defend in reexamination or opposition proceedings on, a patent on a Subject Invention.

D.    Minimum Rights to the Performer and Protection of the Performer’s Right to File

1.    The Performer shall retain a nonexclusive, royalty-free license throughout the world in each Subject Invention to which the Government obtains title, except if the Performer fails to disclose the invention within the times specified in paragraph B of this Article. The Performer’s license extends to subsidiaries and affiliates and Collaborators, if any, within the corporate structure of which the Performer is a party and includes the right to grant licenses of the same scope to the extent that the Performer was legally obligated to do so at the time the Agreement was awarded. The license is transferable only with the approval of DARPA, except when transferred to the successor of that part of the business to which the invention pertains. DARPA approval for license transfer shall not be unreasonably withheld.

2.    The Performer’s license may be revoked or modified by DARPA to the extent necessary to achieve expeditious practical application of the Subject Invention pursuant to an application for an exclusive license submitted consistent with appropriate provisions at 37 CFR Part 404. This license shall not be revoked at any time when the Performer continues to practice the general technology developed hereunder in pursuit of commercial goals, including the goal of making the products derived from such platforms reasonably accessible to the public.

3     Before revocation or modification of the license, DARPA shall furnish the Performer a written notice of its intention to revoke or modify the license, and the Performer shall be allowed thirty (30) calendar days (or such other time as may be authorized for good cause shown) after the notice to show cause why the license should not be revoked or modified.

E.    Action to Protect the Government’s Interest

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1.    The Performer agrees to execute or to have executed and promptly deliver to DARPA all instruments necessary to (i) establish or confirm the rights the Government has throughout the world in those Subject Inventions to which the Performer elects to retain title, and (ii) convey title to DARPA when requested under paragraph D of this Article and to enable the Government to obtain patent protection throughout the world in that Subject Invention.

2.    The Performer agrees to require, by written agreement, its employees, other than clerical and non-technical employees, to disclose promptly in writing to personnel identified as responsible for the administration of patent matters and in a format suggested by the Performer each Subject Invention made under this Agreement in order that the Performer can comply with the disclosure provisions of paragraph C of this Article. The Performer shall instruct employees, through employee agreements or other suitable educational programs, on the importance of reporting inventions in sufficient time to permit the filing of patent applications prior to U. S. or foreign statutory bars.

3.    The Performer shall notify DARPA of any decisions not to continue the prosecution of a patent application, pay maintenance fees, or defend in a reexamination or opposition proceedings on a patent, in any country, not less than thirty (30) calendar days before the expiration of the response period required by the relevant patent office.

4.    The Performer shall include, within the specification of any United States patent application and any patent issuing thereon covering a Subject Invention, the following statement: “This invention was made with Government support under Agreement HR0011-12-3-0006, awarded by DARPA. The Government has certain rights in the invention.”

F.    Lower Tier Agreements

The Performer shall include this Article, suitably modified, to identify the Parties, in all subcontracts or lower tier agreements, regardless of tier, for experimental, developmental, or research work.

G.    Reporting on Utilization of Subject Inventions

1. The Performer agrees to submit, during the term of the Agreement, an annual report on the general subject matter research at Performer or its Collaborators, licensees or assignees in connection with utilization of a Subject Invention or on efforts at obtaining such utilization that is being made by the Performer or its Collaborators, licensees or assignees. Such reports shall include information regarding the general fields of potential products where such Subject Inventions may ultimately assist in commercial sales. The Performer also agrees to provide additional reports as may be requested by DARPA in connection with any march-in proceedings undertaken by DARPA in accordance with paragraph J of this Article. Consistent with 35 U.S.C. § 202(c)(5), DARPA agrees it shall not disclose such information to persons outside the Government without permission of the Performer.

2 All required reporting shall be accomplished, to the extent possible, using the i-Edison reporting website: https://s-edison.info.nih.gov/iEdison/. To the extent any such reporting cannot be carried out by use of i-Edison, reports and communications shall be submitted to the Agreements Officer and Administrative Agreements Officer.

H.    Preference for American Industry

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Notwithstanding any other provision of this clause, the Performer agrees that it shall not grant to any person the exclusive right to use or sell any Subject Invention in the United States or Canada unless such person agrees that any product embodying the Subject Invention or produced through the use of the Subject Invention shall be manufactured substantially in the United States or Canada except when such

such rights are in connection with a Collaborator. However, in individual cases, the requirements for such an agreement beyond what is contemplated herein may be waived by DARPA upon a showing by the Performer (1) that reasonable but unsuccessful efforts have been made to grant licenses on similar terms to potential licensees that would be likely to manufacture substantially in the United States or (2) that, under the circumstances, domestic manufacture is not commercially feasible.

I.    March-in Rights

The Performer agrees that, with respect to any Subject Invention in which it has retained title, DARPA has the right to require the Performer, an assignee, or exclusive licensee of a Subject Invention to grant a non-exclusive license to a responsible applicant or applicants, upon terms that are reasonable under the circumstances, and if the Performer, assignee, or exclusive licensee refuses such a request, DARPA has the right to grant such a license itself if DARPA determines that:

1.    Such action is necessary because the Performer or assignee has not taken effective steps, consistent with the intent of this Agreement, to achieve practical application of the Subject Invention;

2.    Such action is necessary to alleviate health or safety needs which are not reasonably satisfied by the Performer, assignee, or their licensees;

3.    Such action is necessary to meet requirements for public use and such requirements are not reasonably satisfied by the Performer, assignee, or licensees; or

4.    Such action is necessary because the agreement required by paragraph (I) of this Article has not been obtained or waived or because a licensee of the exclusive right to use or sell any Subject Invention in the United States is in breach of such Agreement.

ARTICLE VIII: DATA RIGHTS

A.    Allocation of Principal Rights

1.    This Agreement shall be performed with mixed Government and Performer funding. The Parties agree that in consideration for Government funding, the Performer intends to reduce to practical application items, components and processes developed under this Agreement.

2.    The Performer agrees to retain and maintain in good condition until two (2) years after completion or termination of this Agreement, all Data necessary to achieve practical application. In the event of exercise of the Government’s March-in Rights as set forth under Article VII or subparagraph A.3 of this article, the Performer agrees, upon written request from the Government, to deliver at no additional cost to the Government, all Data necessary to achieve practical application within sixty (60) calendar days from the date of the written request. The Government shall retain Unlimited Rights, as defined in paragraph A above, to this delivered Data.

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3.    The Performer agrees that, with respect to Data necessary to achieve practical application, DARPA has the right to require the Performer to deliver all such Data to DARPA in accordance with its reasonable directions if DARPA determines that:

(a)    Such action is necessary because the Performer or assignee has not taken effective steps, consistent with the intent of this Agreement, to achieve practical application of the technology developed during the performance of this Agreement;

(b)    Such action is necessary to alleviate health or safety needs which are not reasonably satisfied by the Performer, assignee, or their licensees; or

(c)    Such action is necessary to meet requirements for public use and such requirements are not reasonably satisfied by the Performer, assignee, or licensees.

4.    With respect to Data developed, generated or delivered under this Agreement, the Government shall receive Government Purpose Rights, except as noted in subparagraph (5) of this article.

5.    With respect to all Data delivered, in the event of the Government’s exercise of its right under subparagraph B.2 of this article, the Government shall receive Unlimited Rights.

6.    Any pre-existing Data to be utilized and delivered under this Agreement shall be delivered with restrictions as delineated in the Performer Identification and Assertion of Use, Release, or Disclosure Restrictions provided in Attachment 5.

B.    Marking of Data

Pursuant to paragraph B above, any Data delivered under this Agreement shall be marked with the following legend:

Use, duplication, or disclosure is subject to the restrictions as stated in Agreement HR0011-12-3- 0006 between the Government and the Performer.

C.     Lower Tier Agreements

The Performer shall include this Article, suitably modified to identify the Parties, in all subcontracts or lower tier agreements, regardless of tier, for experimental, developmental, or research work.

ARTICLE IX: FOREIGN ACCESS TO TECHNOLOGY

This Article shall remain in effect during the term of the Agreement and for two (2) years thereafter.

A.    General

The Parties agree that research findings and technology developments arising under this Agreement may constitute a significant enhancement to the national defense, and to the economic vitality of the United States. Accordingly, access to important technology developments under this Agreement by Foreign Firms or Institutions must be carefully controlled. The controls contemplated in this Article are in addition to, and are not intended to change or supersede, the provisions of the International Traffic in

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Arms Regulation (22 CFR pt. 121 et seq.), the DoD Industrial Security Regulation (DoD 5220.22-R) and the Department of Commerce Export Regulation (15 CFR pt. 770 et seq.)

B.    Restrictions on Sale or Transfer of Technology to Foreign Firms or Institutions

1.    In order to promote the national security interests of the United States and to effectuate the policies that underlie the regulations cited above, the procedures stated in subparagraphs C.2, C.3, and C.4 below shall apply to any transfer of Technology. For purposes of this paragraph, a transfer includes a sale of the company, and sales or licensing of Technology. Transfers do not include:

(a) sales of products or components, or

(b) licenses of software or documentation related to sales of products or components, or

(c) transfer to foreign subsidiaries of the Performer for purposes related to this Agreement or to Collaborators, or

(d) transfer which provides access to Technology to a Foreign Firm or Institution which is an approved source of supply or source for the conduct of research under this Agreement provided that such transfer shall be limited to that necessary to allow the firm or institution to perform its approved role under this Agreement.

2.    The Performer shall provide timely notice to DARPA of any proposed transfers which occur after the effective date of this agreement from the Performer of Technology developed under this Agreement to Foreign Firms or Institutions. If DARPA determines that the transfer may have adverse consequences to the national security interests of the United States, the Performer, its vendors, and DARPA shall jointly endeavor to find alternatives to the proposed transfer which obviate or mitigate potential adverse consequences of the transfer but which provide substantially equivalent benefits to the Performer.

3.    In any event, the Performer shall provide written notice to the DARPA Agreements Officer’s Representative and Agreements Officer of any proposed transfer to a foreign firm or institution at least sixty (60) calendar days prior to the proposed date of transfer. Such notice shall cite this Article and shall state specifically what is to be transferred and the general terms of the transfer. Within thirty (30) calendar days of receipt of the Performer’s written notification, the DARPA Agreements Officer shall advise the Performer whether it consents to the proposed transfer. In cases where DARPA does not concur or sixty (60) calendar days after receipt and DARPA provides no decision, the Performer may utilize the procedures under Article VI, Disputes. No transfer shall take place until a decision is rendered.

4. In the event a transfer of Technology to Foreign Firms or Institutions which is NOT approved by DARPA takes place, the Performer shall (a) refund to DARPA funds paid for the development of the Technology and (b) the Government shall have a non-exclusive, nontransferable, irrevocable, paid-up license to practice or have practiced on behalf of the United States the Technology throughout the world for Government and any and all other purposes, particularly to effectuate the intent of this Agreement. Upon request of the Government, the Performer shall provide written confirmation of such licenses.

C.    Lower Tier Agreements

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The Performer shall include this Article, suitably modified, to identify the Parties, in all subcontracts or lower tier agreements, regardless of tier, for experimental, developmental, or research work.

ARTICLE X:    TITLE TO AND DISPOSITION OF PROPERTY

A.    Title to Property

The Performer will acquire property with an acquisition value greater than $5,000 under this Agreement as set forth in Attachment * to this Agreement which is necessary to further the research and development goals of this Program and is not for the direct benefit of the Government. Title to this property shall vest in the Performer upon acquisition. Title to any other items of property acquired under this Agreement with an acquisition value of $5,000 or less shall vest in the Performer upon acquisition with no further obligation of the Parties unless otherwise determined by the Agreements Officer. Should any other item of property with an acquisition value greater than $5,000 be required, the Performer shall obtain prior written approval of the Agreements Officer. Title to this property shall also vest in the Performer upon acquisition. The Performer shall be responsible for the maintenance, repair, protection, and preservation of all property at its own expense.

B.    Disposition of Property

At the completion of the term of this Agreement, items of property set forth in Attachment * or any other items of property with an acquisition value greater than $5,000 shall be disposed of in the following manner:

1.    Purchased by the Performer at an agreed-upon price, the price to represent fair market value, with the proceeds of the sale being returned to DARPA; or

2.    Transferred to a Government research facility with title and ownership being transferred to the Government; or

3.    Donated to a mutually agreed University or technical learning center for research purposes; or

4. Any other DARPA-approved disposition procedure.

ARTICLE XI: CIVIL RIGHTS ACT

This Agreement is subject to the compliance requirements of Title VI of the Civil Rights Act of 1964 as amended (42 U.S.C. 2000-d) relating to nondiscrimination in Federally assisted programs. The Performer has signed an Assurance of Compliance with the nondiscriminatory provisions of the Act.

ARTICLE XII: SECURITY

The Government does not anticipate the need for the Performer to develop and/or handle classified information in the performance of this Agreement. No DD254 is currently required for this Agreement.

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ARTICLE XIII: SUBCONTRACTORS

The Performer shall make every effort to satisfy the intent of competitive bidding of sub-agreements to the maximum extent practical. The Performer may use foreign entities or nationals as subcontractors, subject to compliance with the requirements of this Agreement and to the extent otherwise permitted by law.

ARTICLE XIV: KEY PERSONNEL

A. The Performer shall notify the Agreements Officer in writing prior to making any change in key personnel. The following individuals are designated as key personnel for the purposes of this Agreement:

Name	Role/Title	% of time
Jack Newman	Chief Science Officer	60%
Sunil Chandran	Team Leader	100%

B. When replacing any of the personnel identified above, the Performer must demonstrate that the qualifications of the prospective personnel are acceptable to the Government as reasonably determined by the Program Manager. Substitution of key personnel shall be documented by modification to the Agreement made in accordance with the procedures outlined in Article III, paragraph C.

ARTICLE XV: EXPORT CONTROL

(a) Definition. “Export-controlled items,” as used in this clause, means items subject to the Export Administration Regulations (EAR) (15 CFR Parts 730-774) or the International Traffic in Arms Regulations (ITAR) (22 CFR Parts 120-130). The term includes:

1) “Defense items,” defined in the Arms Export Control Act, 22 U.S.C. 2778(j)(4)(A), as defense articles, defense services, and related technical data, and further defined in the ITAR, 22 CFR Part 120.

2) “Items,” defined in the EAR as “commodities”, “software”, and “technology,” terms that are also defined in the EAR, 15 CFR 772.1.

(b) The Performer shall comply with all applicable laws and regulations regarding export-controlled items, including, but not limited to, the requirement for contractors to register with the Department of State in accordance with the ITAR. The Performer shall consult with the Department of State regarding any questions relating to compliance with the ITAR and shall consult with the Department of Commerce regarding any questions relating to compliance with the EAR.

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(c) The Performer's responsibility to comply with all applicable laws and regulations regarding export-controlled items exists independent of, and is not established or limited by, the information provided by this clause.

(d) Nothing in the terms of this contract adds, changes, supersedes, or waives any of the requirements of applicable Federal laws, Executive orders, and regulations,

including but not limited to—

(1) The Export Administration Act of 1979, as amended (50 U.S.C. App. 2401, et seq.);

(2) The Arms Export Control Act (22 U.S.C. 2751, et seq.);

(3) The International Emergency Economic Powers Act (50 U.S.C. 1701, et seq.);

(4) The Export Administration Regulations (15 CFR Parts 730-774);

(5) The International Traffic in Arms Regulations (22 CFR Parts 120-130);

and

(6) Executive Order 13222, as extended;

(e) The Performer shall include the substance of this clause, including this paragraph (e), in all subawards.

ARTICLE XVI: ORDER OF PRECEDENCE

In the event of any inconsistency between the terms of this Agreement and language set forth in the Attachments, the inconsistency shall be resolved by giving precedence in the following order: (1) The Agreement, and (2) all Attachments to the Agreement.

ARTICLE XVII: EXECUTION

This Agreement constitutes the entire agreement of the Parties and supersedes all prior and contemporaneous agreements, understandings, negotiations and discussions among the Parties, whether oral or written, with respect to the subject matter hereof. This Agreement may be revised only by written consent of the Performer and the DARPA Agreements Officer. This Agreement, or modifications thereto, may be executed in counterparts each of which shall be deemed as original, but all of which taken together shall constitute one and the same instrument.

ARTICLE XVIII: APPLICABLE LAW

United States federal law will apply to the construction, interpretation, and resolution of any disputes arising out of or in connection with this Agreement.

ARTICLE XIX: SEVERABILITY

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In the event that any one or more of the provisions contained herein shall, for any reason, be held to be invalid, illegal or unenforceable in any respect, such invalidity, illegality or unenforceability shall not affect any other provisions of this Agreement, but this Agreement shall be construed as if such invalid, illegal or unenforceable provisions had never been contained herein, unless the deletion of such provision or provisions would result in such a material change so as to cause completion of the transactions contemplated herein to be unreasonable.

ARTICLE XX: FORCE MAJEURE

Performer shall not be liable for delays or non-performance hereunder if such delay or non-performance is from causes beyond the control and without the fault or negligence of the Performer or its subcontractors, and is due, directly, to fire or other casualty; act of God; strike or labor dispute; war or other violence, or to acts of the Government in either its sovereign or contractual capacity.

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Agreement No. HR0011-12-3-0006 Attachment 1

Amyris, Inc.

Statement of Work

For

Living Foundries

Improving DNA Assembly and Integration Across Platforms with Better Systems and Tools

30 May 2012

(Amended through 9 April 2014)

Advanced Tools and Capabilities for Generalizable Platforms (ATCG) Program Background

Current approaches to engineering biology rely on an ad hoc, laborious, trial-and-error process, wherein one successful project often does not translate to enabling subsequent new designs. As a result, the state of the art development cycle for engineering a new biologically manufactured product often takes 7+ years and tens to hundreds of millions of dollars (e.g. microbial production of artemisinic acid for the treatment of malaria and the non-petroleum-based production 1, 3-propanediol). The impact of current approaches is two-fold. First, the number of new entrants and innovators into the biomanufacturing space is immediately limited – few have the expertise, capital and/or time necessary to develop and engineer a new product. Second, combined with the complexity of biological systems, an ad hoc approach results in one-off efforts limited to modifying only a small set of genes and constructing simple, isolated genetic circuits and metabolic pathways. Consequently, while progress has been made, industry is constrained to producing only a tiny fraction of the vast number of possible chemicals, materials, and functional systems that would be enabled by the ability to truly engineer biology. A new approach is needed.

This new approach is Living Foundries: develop and apply an engineering framework to biology that decouples biological design from fabrication, yields design rules and tools, and manages biological complexity through abstraction and standardization. One analogy is that Living Foundries aims to do for biological design what very large-scale integration (VLSI) did for integrated circuits. Applying an engineering framework to biology will remove barriers to researchers outside the biological sciences, bringing diverse expertise and new methods to biological design. The best innovations will introduce new architectures and tools that will form the foundational technology for engineering biology.

The vision of Living Foundries is one where new and multiple cellular functions are readily constructed, combined, and controlled by an integrated genetic circuitry. The ultimate effect of which will be to open up the full space of biologically produced materials and systems. To achieve this, new tools, technologies and methodologies that directly address our current limitations and expand our capabilities must be developed. The outcome should be an open technology platform that integrates these tools and capabilities, allowing new designs to rapidly move from conception to execution.

Advanced Tools and Capabilities for Generalizable Platforms, (ATCG) seeks translatable tools that can serve as parts of an “end-to-end platform” to support rapid, specific in its goals: DARPA seeks new technology to enable low-cost and rapid DNA synthesis and assembly, especially to shorten the design-test cycle surrounding the ambitious constructs that characterize the broadest visions in modern synthetic biology.

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Agreement No. HR0011-12-3-0006 Attachment 1

Research Tasks

Task A

[*]

Task A. [*] (Jed Dean, Amyris)

Task Objective:[*]

[*]

Milestone: [*]

Metrics/Completion Criteria:[*]

Deliverables: [*]

Subtask A.1.[*]

Subtask A.2. [*]

Subtask A.3.[*]

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

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[*]

This subtask completes the Milestone outlined above.

Task C

[*]

Task C. [*] (Sunil Chandran, Amyris)

Task Objective: [*]

[*]

Phase I

Milestone: [*]

Metrics/Completion Criteria: [*]

Deliverable: [*]

Subtask C.1 [*]

[*]

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

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Agreement No. HR0011-12-3-0006 Attachment 1

Subtask C.2 [*]

[*]

Subtask C.3 [*]

[*]

Subtask C.4 [*]

[*]

This subtask completes the Milestone outlined above.

Phase II

Milestone (CIIa): [*]

Metrics/Completion Criteria: [*]

Subtask C.5 [*]

[*]

Subtask C.6 [*]

[*]

These subtasks complete the Milestone outlined above.

Milestone (CIIb): [*]

Metrics/Completion Criteria: [*]

Deliverable: [*]

Subtask C.7[*]

[*]

[*]

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

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Agreement No. HR0011-12-3-0006 Attachment 1

Milestone (CIIc): [*]

Metrics/Completion Criteria:[*]

Deliverable:[*]

Subtask C.8 [*]

[*]

Task D

[*]

Task D. [*] (Sunil Chandran, Amyris)

Task D. [*] (Sunil Chandran, Amyris)

Task Objective: [*]

[*]

Phase I

Milestone: [*]

Metrics/Completion Criteria: [*]

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

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Agreement No. HR0011-12-3-0006 Attachment 1

Deliverable: [*]

Subtask D.1 [*]

Subtask D.2 [*]

[*]

Subtask D.3 [*]

[*]

Subtask D.4 [*]

[*]

Phase II

Milestone (DIIa): [*]

Metrics/Completion Criteria: [*]

Subtask D.5 [*]

[*]

Subtask D.6 [*]

[*]

Milestone (DIIb): [*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

Subtask D.7 [*]

[*]

Subtask D.8 [*]

[*]

This subtask completes the Milestone outlined above.

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

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Agreement No. HR0011-12-3-0006 Attachment 1

Task E

[*]

Task E. [*] (Sunil Chandran, Amyris)

Task Objective: [*]

Phase IA

Milestone: [*]

Metrics/Completion Criteria: [*]

Deliverable: [*]

Subtask E.1. [*]

[*]

This subtask completes the Milestone outlined above.

Phase IB

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

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Agreement No. HR0011-12-3-0006 Attachment 1

Milestone: [*]

Metrics/Completion Criteria: [*]

Deliverable: [*]

Subtask E.3 [*]

[*]

This subtask completes the Milestone outlined above.

Phase II

Milestone (EIIa): [*].

Metrics/Completion Criteria: [*]

Deliverable: [*]

Subtask E.5 [*]

[*]

Milestone (EIIb): [*]

Metrics/Completion Criteria: [*]

Deliverable:[*]

Subtask E.6 [*]

[*]

This subtask completes the Milestone outlined above.

Milestone (EIIc):[*]

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

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Agreement No. HR0011-12-3-0006 Attachment 1

Metrics/Completion Criteria: [*]

Deliverable: [*]

Subtask E.7 [*]

[*]

Subtask E.8 [*]

[*]

This subtask completes the Milestone outlined above.

Task F

[*]

Task F.[*](Sunil Chandran, Amyris)

Task objective: [*]

Phase II

Milestone: [*]

Metrics/Completion Criteria: [*]

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

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Agreement No. HR0011-12-3-0006 Attachment 1

[*]

Deliverable: [*]

Subtask F.1. [*]

[*]

Subtask F.2. [*]

[*]

Task G (Bio-safety/Security)

Task Background: The research and engineering depicted in this Statement of Work seeks to make existing capabilities (e.g. genetic modification of microbes to produce commodity chemicals) more efficient with the intended purpose of speeding the development of Living Foundries. The goal of this research is to make better engineering tools, and not to produce microbes that may have Dual-Use potential. As noted in the performer’s technical proposal, a review of the research activities identified within this Statement of Work determined that this project will not enable technologies that are related to human, animal, or plant health. The performer’s choice of potential chassis or hosts will be made from amongst the list of microbes that, prior to genetic modification, are designated safely handled in a Biosafety Level 1 facility. Additionally, the resulting genetically modified organisms have no selective advantage in the environment.

Metrics/Completion Criteria: The performer shall demonstrate throughout the program that all methods and demonstrations of capability comply with national guidance for manipulation of genes and organisms and follow all guidance for biological safety and biosecurity. Demonstrations and testbeds must meet any applicable regulations designed to protect human health and the environment promulgated by the Environmental Protection Agency, National Institutes of Health, or other relevant agencies of the Federal Government. The performer shall use, store, and destroy biological material in accordance with all applicable regulations.

Deliverable: Include as part of the required monthly technical status reports an on-going status of efforts to develop and/or carry out their Advanced Tools and Capabilities for Generalizable Platforms (ATCG) Bio-Safety and Security plan.

Task H (Intellectual Property and Data Sharing)

Task Background: It is the goal of the Defense Advanced Research Projects Agency (DARPA) that its investment in the tools and capabilities developed under the ATCG program to be multiplied many-fold by adoption and improvement by researchers across the United States. In order to achieve this vision, the Living Foundries program aims to facilitate interoperability and open the field to new entrants.

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

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Agreement No. HR0011-12-3-0006 Attachment 1

Metrics/Completion Criteria: To facilitate interoperability, all applicable design tools and databases developed under the ATCG program should be compatible with Synthetic Biology Open Language (SBOL) core data model. The Performer shall make available the technologies developed under the ATCG effort to the broader synthetic biology community by presenting its ATCG research data at public meetings/conferences/workshops and publishing results in peer-reviewed journal articles. At a minimum, the types of information that will be made available to the broader synthetic biology community are as discussed below:

(i) Data and analysis necessary to evaluate the utility of the technologies, as well as standard operating procedures and design specifications enabling others to reconstitute the equipment, set up, and approaches developed.

(ii) The results of Design of Experiment work to arrive at the conditions for the best performance for untested or early stage technologies, describing the correlation between:

• DNA ligase cycling parameters and the complexity, size, and success rate of the assembled full length DNA constructs.

• Reaction parameters and the success and cost of performing sequencing QC on DNA assemblies.

• Designer nuclease number, type, and targeting site and the integration efficiency in to the chassis genome.

(iii) Details required for both technical evaluation and transfer, including: full protocols, technical drawings of equipment built and specifications met, data on accuracy and precision of these systems, and results on procedures performed against large number of samples to investigate the robustness and readiness of the approaches for broader distribution – providing a trained reader with the information needed to recapitulate the methods and results described. In addition, the Principal Investigator shall be available to consult with third parties seeking to replicate the results.

If the work performed under this Statement of Work results in one or more patents, the Performer shall grant licenses on a royalty-free basis to academic and non-profit institutions. Additionally, the Performer shall make licenses available to commercial entities outside its key business areas.

Deliverable/s: The Performer shall include as part of required monthly technical status reports an on-going status of efforts to develop and/or carry out their proposed ATCG Intellectual Property and Data Sharing plan. Reporting shall include a summary of data sharing activities that have taken place during the reporting period and any data sharing activities planned to take place within three months of the reporting period. Reporting shall include a listing of the performers Subject Invention disclosures, Subject Invention patent applications and a brief discussion summarizing plans, if any, to license the resulting technology (e.g., intent and rationale regarding whether the performer intends to seek non-exclusive licensing, exclusive licensing for a particular field of use, or exclusive licensing across the board, etc.).

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Agreement No. HR0011-12-3-0006 Attachment 2

ATTACHMENT 2:

REPORT REQUIREMENTS

A.     TECHNICAL STATUS REPORT

On or before sixty (60) calendar days after the effective date of the Agreement and monthly thereafter throughout the term of the Agreement, the Performer shall submit, via email, a monthly Technical Status Report to the DARPA Program Manager, DARPA Agreements Officer, Agreement Officer’s Representative (AOR), and DARPA/ADPM. The technical status report will detail technical progress to date and report on all problems, technical issues, major developments, and the status of external collaborations during the reporting period. Technical Status Reports shall be marked with Distribution Statement B:

“DISTRIBUTION STATEMENT B. Distribution authorized to U.S. Government agencies only due to the inclusion of proprietary information. Other requests for this document shall be referred to DARPA Public Release Center (PRC) via email at PRC@darpa.mil.”

B.    BUSINESS STATUS REPORT

On or before ninety (90) calendar days after the effective date of the Agreement and quarterly thereafter throughout the term of the Agreement, the Performer shall submit, via email, a quarterly Business Status Report to the DARPA Program Manager, DARPA Agreements Officer, Agreement Officer’s Representative (AOR), and DARPA/ADPM. The business status report shall provide summarized details of the resource status of this Agreement, including the status of the Performer’s contributions. This report will include a quarterly accounting of current expenditures as outlined in the Annual Program Plan. Any major deviations, over plus or minus 10%, shall be explained along with discussions of the adjustment actions proposed. The report will also include an accounting of any interest earned on Government funds. The Performer is reminded that interest in amounts greater than $250 per year is not expected to accrue under this Agreement. In the event that this interest does accrue on Government funds, the Performer is required to provide an explanation for the accrual in the business report. Depending on the circumstances, the Payable Milestones may require adjustment. Business Status Reports shall be marked with Distribution Statement B:

“DISTRIBUTION STATEMENT B. Distribution authorized to U.S. Government agencies only due to the inclusion of proprietary information. Other requests for this

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Agreement No. HR0011-12-3-0006 Attachment 2

document shall be referred to DARPA Public Release Center (PRC) via email at PRC@darpa.mil.

C.    ANNUAL PROGRAM PLAN DOCUMENT

The Performer shall submit via email or otherwise provide to the DARPA Agreements Officer’s Representative, DARPA Program Manager and DARPA Agreements Officer one (1) copy each of a report which describes the Annual Program Plan as described in Article III, Section B. This document shall be submitted not later than thirty (30) calendar days following the Annual Site Review as described in Article III, Section B. Annual Program Plans shall be marked with Distribution Statement B:

“DISTRIBUTION STATEMENT B. Distribution authorized to U.S. Government agencies only due to the inclusion of proprietary information. Other requests for this document shall be referred to DARPA Public Release Center (PRC) via email at PRC@darpa.mil.”

D.    SPECIAL TECHNICAL REPORTS

The Performer shall submit via email or otherwise provide to the DARPA Agreements Officer’s Representative, the DARPA Program Manager and DARPA Agreements Officer one (1) copy each of special technical reports on significant events such as significant target accomplishments by the Performer, significant tests, experiments, or symposia, as discussed in the Attachment No. 1 Statement of Work. Special Technical Reports shall be marked with Distribution Statement B:

“DISTRIBUTION STATEMENT B. Distribution authorized to U.S. Government agencies only due to the inclusion of proprietary information. Other requests for this document shall be referred to DARPA Public Release Center (PRC) via email at PRC@darpa.mil.”

E.    SCIENTIFIC PAPERS

The performer shall publish scientific papers in accordance with the Attachment No. Statement of Work. One (1) copy of each published scientific paper shall be submitted via email or otherwise provided to the DARPA Agreements Officer’s Representative, DARPA Program Manager, and DARPA Agreements Officer. Scientific Papers shall be marked with Distribution Statement A:

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Agreement No. HR0011-12-3-0006 Attachment 2

"Approved for public release; distribution is unlimited.”

E.    PAYABLE MILESTONES REPORTS

The Performer shall submit via email or otherwise provide to the DARPA Agreements Officer’s Representative, the DARPA Program Manager and DARPA Agreements Officer documentation describing the extent of accomplishment of Payable Milestones. This information shall be as required by Article V, paragraph B and shall be sufficient for the DARPA Agreements Officer’s Representative to reasonably verify the accomplishment of the milestone in accordance with the Attachment No. 1 Statement of Work and Attachment No. 3 Payable Milestone Plan. Payable Milestone Reports shall be marked with Distribution Statement B:

“DISTRIBUTION STATEMENT B. Distribution authorized to U.S. Government agencies only due to the inclusion of proprietary information. Other requests for this document shall be referred to DARPA Public Release Center (PRC) via email at PRC@darpa.mil.”

F.    FINAL REPORT    (NOTE: The Final Report is included in the last Payable Milestone for the completed Agreement)

1. The Performer shall submit or otherwise provide a Final Report making full disclosure of all major developments by the Performer upon completion of the Agreement or within sixty (60) calendar days of termination of this Agreement. With the approval of the DARPA Agreements Officer’s Representative, reprints of published articles may be attached to the Final Report. The Final Report shall be submitted via email to the DARPA Program Manager, DARPA Agreements Officer, Agreement Officer’s Representative (AOR), DARPA/ADPM, and the Defense Technical Information Center.

2. The Final Report shall be marked with a distribution statement to denote the extent of its availability for distribution, release, and disclosure without additional approvals or authorizations. The Final Report shall be marked on the front page in a conspicuous place with the following marking:

“DISTRIBUTION STATEMENT B. Distribution authorized to U.S. Government agencies only due to the inclusion of proprietary information. Other requests for this document shall be referred to DARPA Public Release Center (PRC) via email at PRC@darpa.mil.”

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Agreement No. HR0011-12-3-0006 Attachment 2

G.    FINAL REPORT MARKINGS

(1) The cover or title page of each of the above reports or publications prepared, will have the following citation:

Sponsored by

Defense Advanced Research Projects Agency

Microsystems Technology Office (MTO)

Program: Living Foundries

Issued by DARPA/CMO under Agreement No. HR0011-12-3-0006

(2) The title page shall include a disclaimer worded substantially as follows:

“The views and conclusions contained in this document are those of the authors and should not be interpreted as representing the official policies, either expressly or implied, of the Defense Advanced Research Projects Agency or the U.S. Government.”

(3) The Final Report shall include a Standard Form 298, August 1998.

(4) All reports shall be marked with the below Distribution Statement and Data Rights statements:

(a) Distribution Statement designations are listed above for each individual type of report.

(b) Government Purpose Rights.

“GOVERNMENT PURPOSE RIGHTS

Agreement Number: HR0011-12-3-0006

Contractor Name: Amyris, Inc.”

In accordance with Article VIII, as applicable, contained in the above identified Agreement, the Government has the right to use, duplicate, or disclose Data, in whole or in part and in any manner, for Government purposes only, and to have or permit others to do so for Government purposes only.”

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Agreement No. HR0011-12-3-0006 Attachment 2

(c) Limited Rights.

“LIMITED RIGHTS

Agreement Number: HR0011-12-3-0006

Contractor Name: Amyris, Inc.”

In accordance with Article VIII, as applicable, contained in the above identified

Agreement, the Government has the right to use, modify, reproduce, release, perform,

display, or disclose Data, in whole or in part, within the Government. The Government

may not, without the written permission of the party asserting limited rights, release or

disclose the Data outside the Government.

H. EXECUTIVE SUMMARY

The Performer shall submit a one to two page executive-level summary of the major

accomplishments of the Agreement and the benefits of using the “other transactions”

authority pursuant to 10 U.S.C. § 2371 upon completion of the Agreement. This

summary shall include a discussion of the actual or planned benefits of the technologies

for both the military and commercial sectors. Two (2) copies shall be submitted to the

DARPA Agreements Officer.

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Agreement No. HR1100-12-3-0006 Attachment 3

MILESTONE	Task	Month	Payable Milestones	Exit Criteria	Performer Payment	DARPA Payment	SUBLCIN/ ACRN
	Phase I
1	[*]	[*]	[*]	[*]	[*]	[*]	00101/AA
2	[*]	[*]	[*]	[*]	[*]	[*]	00201/AA
3	[*]	[*]	[*]	[*]	[*]	[*]	00301/AA
4	[*]	[*]	[*]	[*]	[*]	[*]	00401/AA
5	[*]	[*]	[*]	[*]	[*]	[*]	00501/AA
Total					$335,834	$3,022,501
	Phase 2
6	[*]	[*]	[*]	[*]	[*]	[*]	00601/AB
7	[*]	[*]	[*]	[*]	[*]	[*]	00701/AB
8	[*]	[*]	[*]	[*]	[*]	[*]	00801/AB
[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

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Agreement No. HR1100-12-3-0006 Attachment 3

9	[*]	[*]	[*]	[*]	[*]	[*]	00901/AB
10	[*]	[*]	[*]	[*]	[*]	[*]	01001/AB
11	[*]	[*]	[*]	[*]	[*]	[*]	001101/AC
12	[*]	[*]	[*]	[*]	[*]	[*]	001201/AC
13	[*]	[*]	[*]	[*]	[*]	[*]
14	[*]	[*]	[*]	[*]	[*]	[*]
15	[*]	[*]	[*]	[*]	[*]	[*]
Total					$514,645	$4,631,808
	Phase 1 & Phase 2
Total					$850,479	$7,654,309

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

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Agreement No. HR0011-12-3-0006 Attachment 4

ATTACHMENT 4:

FUNDING SCHEDULE

A.    PROJECTED PROGRAM FUNDING COMMITMENTS

	DARPA Performer		Funding Contribution
Base (Phase I)
FY 12 (At time of award)	$3,595,518		$399,501
FY 13 (on or about November 2012)	$370,411		$41,158
Modification P00007 Reduction	($943,428)		($104,825)
Phase 1 Totals	$3,022,501		$335,834
Option (Phase 2)
FY 13 (At time of Exercise)	$2,079,497		$231,055
FY 13 (Modification P00008)	$552,931		$61,437
FY13 (Modification P00009)	$645,890		$71,765
FY 14 (TBD)	$	1,353.490	$	150,388
Phase 2 Totals	$4,631,808		$514,645
AGREEMENT TOTALS	$7,654,309		$850,479

DARPA funding shall be applied toward the following expenses: Direct labor, to include indirect costs thereof, and direct materials/equipment purchases, to include indirect costs thereof, as included in Amyrsis’s Living Foundries proposal dated 3 May 2012 (as amended).

B.    PERFORMER CONTRIBUTION

	Total Contribution	Cash*	In-kind**
Phase 1	$335,834	$335,834	$0
Phase 2	$514,645	$514,645	$0
Total	$850,479	$850,479	$0

*Cash contributions consist of: Direct labor, to include indirect costs thereof, and direct materials/equipment purchases, to include indirect costs thereof, as included in Amyrsis’s Living Foundries proposal dated 3 May 2012 (as amended). The aforementioned are considered cash contributions made by Amyris in support of the Living Foundries research program.

**In-kind contributions consist of: N/A

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Agreement No. HR001112-3-0006 Attachment 5

List of Intellectual Property Assertions

Technical Data Computer Software to be Furnished with Restrictions	Basis for Assertion	Asserted Rights Category	Name of Person Asserting Restrictions
Production of Isoprenoids, Application US 11/754,235, Patent No. US 7,659,097 (US 20080274523)	Developed exclusively at private expense	Restricted Rights	Amyris, Inc.
Production of Isoprenoids, ApplicationUS 12/638,771, Patent No. (US2011/0287476)	Developed exclusively at private expense	Restricted Rights	Amyris, Inc.
Production of Isoprenoids, Application PCT/US2007/069807, Patent No. (WO2007/140339)	Developed exclusively at private expense	Restricted Rights	Amyris, Inc.
Nucleic Acids, Compositions and Methods for the Excision of Target Nucleic Acids, Application US 12/978,061, Patent No. US 7,919,605	Developed exclusively at private expense	Restricted Rights	Amyris, Inc.
Nucleic Acids, Compositions and Methods for the Excision of Target Nucleic Acids, Application US 13/220,553, Patent No. (US 2012/0052582)	Developed exclusively at private expense	Restricted Rights	Amyris, Inc.
Nucleic Acids, Compositions and Methods for the Excision of Target Nucleic Acids, Application PCT/US2011/049615, Patent No. (WO 2012/030747)	Developed exclusively at private expense	Restricted Rights	Amyris, Inc.
Compositions and Methods for the Rapid Assembly of Polynucleotides, Developed exclusively at private expense Application US 12/622,401, Patent No. (US 2010/0136633)	Developed exclusively at private expense	Restricted Rights	Amyris, Inc.
Compositions and Methods for the Rapid Assembly of Polynucleotides, Application US 12/684,874, Patent No. US 8,110,360 (US 2010/0124768)	Developed exclusively at private expense	Restricted Rights	Amyris, Inc.
[*]	Developed exclusively at private expense	Restricted Rights	Amyris, Inc.
[*]	Developed exclusively at private expense	Restricted Rights	Amyris, Inc.
[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

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Technical Data Computer Software to be Furnished with Restrictions	Basis for Assertion	Asserted Rights Category	Name of Person Asserting Restrictions
[*]
[*]	Developed exclusively at private expense	Restricted Rights	Amyris, Inc.
[*]	Developed exclusively at private expense	Restricted Rights	Amyris, Inc.
[*]	Developed exclusively at private expense	Restricted Rights	Amyris, Inc.
[*]	Developed exclusively at private expense	Restricted Rights	Amyris, Inc.
[*]	Developed exclusively at private expense	Restricted Rights	Amyris, Inc.
[*]	Developed exclusively at private expense	Restricted Rights	Amyris, Inc.
[*]	Software suites were developed exclusively with private funding.	Limited Rights	Amyris, Inc.
[*]	Software suites were Developed exclusively with private funding	Limited Rights	Amyris, Inc.

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Agreement No. HR001112-3-0006 Attachment 5

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.
Technical Data Computer Software to be Furnished with Restrictions	Basis for Assertion	Asserted Rights Category	Name of Person Asserting Restrictions
[*]
[*]	Amyris has generated extensive information related to the isoprenoid pathways which will be used as a benchmark to assess performance of this proposal but the underlying comparative data was developed exclusively with private funding.	Restricted Rights	Amyris, Inc.

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

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EX-10.02

CONFIDENTIAL TREATMENT REQUESTED. CERTAIN PORTIONS OF THIS DOCUMENT HAVE BEEN OMITTED PURSUANT TO A REQUEST FOR CONFIDENTIAL TREATMENT AND, WHERE APPLICABLE, HAVE BEEN MARKED WITH AN ASTERISK TO DENOTE WHERE OMISSIONS HAVE BEEN MADE. THE CONFIDENTIAL MATERIAL HAS BEEN FILED SEPARATELY WITH THE SECURITIES AND EXCHANGE COMMISSION.

MODIFICATION

TO

TECHNOLOGY INVESTMENT AGREEMENT

BETWEEN

AMYRIS, INC.,

5885 HOLLIS STREET

SUITE 100

EMERYVILLE, CALIFORNIA 94608

AND

THE DEFENSE ADVANCED RESEARCH PROJECTS AGENCY

675 NORTH RANDOLPH STREET

ARLINGTON, VA 22203-2114

CONCERNING

IMPROVING DNA ASSEMBLY AND INTEGRATION ACROSS PLATFORMS WITH

BETTER SYSTEMS AND TOOLS

(LIVING FOUNDRIES)

Agreement No.: HR0011-12-3-0006

Modification No.: P00011

Purchase Request No.: N/A

Total Amount of the Agreement: $8,504,788

Phase 1: $3,358,334

Phase 2 (Option): $5,146,453

Total Estimated Government Funding: $7,654,309

Phase 1: $3,022,501

Phase 2 (Option): $4,631,808

Contactor Share Contribution: $850,479

Phase 1: $335,834

Phase 2 (Option): $514,645

Funds Obligated By This Modification: $0.00

Total Funds Obligated To Date: $6,300,819

Authority: Article III(C)(1)

HR0011-12-3-0006

P00011

Page 2 of 3

The purpose of this modification is to apply funding to Milestones 13 through 15. Accordingly, the following changes apply:

1. Article V, “Obligation and Payment,” paragraph C, “Accounting and Appropriation Data,” is revised to reflect the inclusion of the $834,797 (PR No. HR001149922, Control No. 9922, ACRN AD) provided to Milestone 13, $428,693 (PR No. HR001149922, Control No. 9922, ACRN AD @ $76,747, and PR No. HR001149891, Control No. 9891, ACRN AC @ $351,946) to Milestone 14, and $90,000 (PR No. HR001149891, Control No. 9891, ACRN AC) to Milestone 15. The Lines of Accounting are shown in Enclosure 1 and below:

ACRN AC: 012199 097     0400 000 N 20132014 D 1320 HLTM6         2013.MBT-

02.CORE.A DARPA 255

$441,946

(Milestone 14 and 15)

(PR No. HR001149891)

ACRN AD: 012199 097     0400 000 N 20142015 D 1320 BLTM6         2014.MBT-

02.CORE.A DARPA 255

$911,544

(Milestones 13 and 14)

(PR No. HR001149922)

2. The “Total Funds Obligated To Date” is hereby increased from $6,300,890 by $1,353,490 to $7,654,309.

3. The Attachment No. 3, “Schedule of Payments and Payable Milestones” is modified to reflect the funding added to the Agreement via P00011. See Enclosure 1.

4. The Attachment No. 4, “Funding Schedule” is modified to reflect the current funding profile. See Enclosure 1.

5. A fully conformed version of Agreement No. HR0011-12-3-0006 through P00011, reflecting the changes summarized above, is provided as Enclosure 1 to this modification. All changes to the Modification No. P00011 conformed Agreement are highlighted in yellow.

HR0011-12-3-0006

P00011

Page 3 of 3

FOR AMYRIS INC	FOR THE DEFENSE ADVANCED RESEARCH PRODUCTS AGENCY
(Signature & Date)	(Signature & Date)
Nicholas Khadder	Michael D. Blackstone
Vice President & General Counsel	Agreements Officer

Agreement HR0011-12-3-0006

TECHNOLOGY INVESTMENT AGREEMENT

BETWEEN

AMYRIS, INC.,

5885 HOLLIS STREET

SUITE 100

EMERYVILLE, CALIFORNIA 94608

AND

THE DEFENSE ADVANCED RESEARCH PROJECTS AGENCY

675 NORTH RANDOLPH STREET

ARLINGTON, VA 22203-2114

CONCERNING

IMPROVING DNA ASSEMBLY AND INTEGRATION ACROSS PLATFORMS WITH BETTER

SYSTEMS AND TOOLS

(LIVING FOUNDRIES)

Agreement No.: HR0011-12-3-0006

ARPA Order No.: S351/00, S351/01, S351/02, HR001133399, HR001146140, HR001147725

HR001149922, and HR001149891

Total Amount of the Agreement: $8,504,788

Phase 1: $3,358,334

Phase 2 (Option): $5,146,453

Total Estimated Government Funding: $7,654,309

Phase 1: $3,022,501

Phase 2 (Option): $4,631,808

Contactor Share Contribution: $850,479

Phase 1: $335,834

Phase 2 (Option): $514,645

Total Funds Obligated: $7,654,309

Authority: 10 U.S.C. § 2371

Line of Appropriation – See Article V.

This Agreement is entered into between the United States of America, hereinafter called the Government, represented by The Defense Advanced Research Projects Agency (DARPA), and AMYRIS, INC., a corporation organized and existing under the laws of the State of Delaware with its principal place of business at 5885 Hollis Street, Suite 100, Emeryville, California 94608 pursuant to and under U.S. Federal law.

Enclosure 1 Conformed Copy P00011

Agreement HR0011-12-3-0006

FOR AMYRIS INC	FOR THE DEFENSE ADVANCED RESEARCH PRODUCTS AGENCY
//See Modification No. P00011//
(Signature & Date)	(Signature & Date)
	Michael D. Blackstone
	Agreements Officer
(Name, Title)	(Name, Title)

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Agreement HR0011-12-3-0006

TABLE OF CONTENTS

ARTICLES		PAGE
ARTICLE I	Scope of the Agreement	4
ARTICLE II	Term	7
ARTICLE III	Management of the Project	8
ARTICLE IV	Agreement Administration	9
ARTICLE V	Obligation and Payment	10
ARTICLE VI	Disputes	13
ARTICLE VII	Patent Rights	14
ARTICLE VIII	Data Rights	17
ARTICLE IX	Foreign Access to Technology	18
ARTICLE X	Title to and Disposition of Property	20
ARTICLE XI	Civil Rights Act	20
ARTICLE XII	Security	20
ARTICLE XIII	Subcontractors	21
ARTICLE XIV	Key Personnel	21
ARTICLE XV	Export Control	21
ARTICLE XVI	Order of Precedence	22
ARTICLE XVII	Execution	22
ARTICLE XVIII	Applicable Law	22
ARTICLE XIX	Severability	22
ARTICLE XX	Force Majeure	23
ATTACHMENTS
ATTACHMENT 1	Statement of Work
ATTACHMENT 2	Report Requirements
ATTACHMENT 3	Schedule of Payments and Payable Milestones
ATTACHMENT 4	Funding Schedule
ATTACHMENT 5	List of Intellectual Property Assertions

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ARTICLE I:    SCOPE OF THE AGREEMENT

A.    Background

Amyris has been a leader in the synthetic biology technologies, using living organisms as “factories” or “manufacturing systems” to produce compounds. Although the synthetic biology movement has been intermittently successful in certain directed endeavors, there has been insufficient effort toward standardizing and optimizing synthetic biology tools, procedures and platforms. By focusing on the same principles that made the United States the leaders in traditional manufacturing, namely consistent engineering and efficiency, Amyris seeks, through funding in this Agreement , to research and develop a state of the art development cycle for an enhanced engineering cycle to realize living foundries. Amyris aims to achieve these innovations by developing tools increasing the speed of engineered DNA and microbes while simultaneously expanding the scope of the living systems that are readily engineered. Engineering living systems is slow, expensive, and unreliable. Even for seemingly straightforward applications such as developing a fermentable microbe capable of turning sugar into higher value chemicals can take many hundreds of person-years of effort. For example, genetic engineering has enabled the microbial production of non-native natural products such as 1,3-propanediol made in engineered E. coli (~575 years of effort) or artemisinic acid made in engineered S. cerevisiae (~130 years of effort).

For microbes to become a routine manufacture paradigm, offering an alternative to traditional chemicals

and petroleum feedstocks, and for living systems eventually to enable novel commercial and military

applications (self-healing or corrosion-resistant materials) the effort and expense associated with

developing new applications must be reduced by an order of magnitude. This entire enterprise is in its

infancy and the work required to reduce the time and effort needed to develop a new microbe is risky and

at odds with the work also needed to bring a product to market in a one-off manner, the chief goal of any

company seeking to capitalize on the technology. This Agreement supports research with a long-term

perspective to support that entire industry by funding efforts that will enable everyone to do more with

less.

B.    Definitions

Agreement: The body of this Agreement and Attachments 1 – 4, which are expressly incorporated in

and made a part of the Agreement.

Collaborators: A third party in a contractual arrangement with the Performer whereby Amyris has agreed to jointly research, develop and/or commercialize and has an active role in such arrangement. For the avoidance of doubt, an “active role” by Amyris is a contractual relationship (1) that involves more than the mere transfer of intellectual property, and (2) where Amyris has a significant participation in decisionmaking and/or funding of the activities. Collaborators include all parties in collaborations with Amyris as of the effective date, even if the collaboration is modified or amended after the effective date.

Data: Recorded information, regardless of form or method of recording, which includes but is not limited to, technical data, software, and trade secrets. The term does not include financial, administrative, cost, pricing or management information and does not include Subject Inventions, included in Article VII.

Foreign Firm or Institution: A firm or institution organized or existing under the laws of a country other than the United States, its territories, or possessions. The term includes, for purposes of this

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Agreement, any agency or instrumentality of a foreign government; and firms, institutions or business organizations which are owned or substantially controlled by foreign governments, firms, institutions, or individuals.

Government: The United States of America, as represented by DARPA.

Government Purpose Rights: The rights to use, duplicate, or disclose Data, in whole or in part and in any manner, for Government purposes only, and to have or permit others to do so for Government purposes only.

Government Purpose: Any activity in which the United States Government is a party, including cooperative agreements with international or multi-national defense organizations or sales or transfers by the United States Government to foreign governments or international organizations. Government purposes include competitive procurement, but do not include the rights to use, modify, reproduce, release, perform, display, or disclose Data for commercial purposes or authorize others to do so.

Invention: Any invention or discovery which is or may be patentable or otherwise protectable under Title 35 of the United States Code.

Know-How: All information including, but not limited to discoveries, formulas, materials, Inventions, processes, ideas, approaches, concepts, techniques, methods, software, programs, documentation, procedures, firmware, hardware, technical data, specifications, devices, apparatus and machines.

Limited Rights: The rights to use, modifiy, reproduce, release, perform, display, or disclose Data, in whole or in part, within the Government. The Government may not, without the written permission of the party asserting limited rights, release or disclose the Data outside the Government.

Made: Relates to any Invention means the conception or first actual reduction to practice of such Invention.

Performer: AMYRIS, INC. a corporation organized and existing under the laws of the State of Delaware with its principal place of business at 5885 Hollis Street, Suite 100, Emeryville, California 94608

Practical Application: To manufacture, in the case of a composition of product; to practice, in the case of a process or method, or to operate, in the case of a machine or system; and, in each case, under such conditions as to establish that the Invention is capable of being utilized and that its benefits are, to the extent permitted by law or Government regulations, available to the public on reasonable terms. For the avoidance of doubt, the Parties acknowledge that “practical application” under this Agreement may not include actual commercialization of Subject Inventions hereunder because such Subject Inventions are likely to be research tools and platforms (e.g., it is envisioned that the tools and platforms resulting from the research carried out under this agreement will later – outside of this agreement - be used by the performer to develop commercial products).

Program: Research and development being conducted by the Performer, as set forth in Article I., paragraph C.

Property: Any tangible personal property other than property actually consumed during the execution of work under this agreement.

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Subject Invention: Any Invention conceived or first actually reduced to practice in the performance of work under this Agreement that is capable of use as a tool for making or altering a genetically modified organism, provided however, any Inventions, regardless when conceived or reduced to practice, covering the genetically modified organism, a strain, or any compound or product made by or from an organism or strain shall not be considered “Subject Inventions” hereunder. For the avoidance of doubt, no work performed prior to the effective date of this Agreement shall be considered performed “under this Agreement.”

Technology: Discoveries, innovations, Know-How and Inventions, whether patentable or not, including computer software, recognized under U.S. law as intellectual creations to which rights of ownership accrue, including, but not limited to, patents, trade secrets, and copyrights developed under this Agreement.

Unlimited Rights: Rights to use, duplicate, release, or disclose, Data in whole or in part, in any manner and for any purposes whatsoever, and to have or permit others to do so.

C.    Scope

1.    Amyris, Inc. (hereafter “the Performer”) shall perform a research and development program (Program) designed to develop improved DNA assembly and integration across platforms. The research shall be carried out in accordance with the Statement of Work incorporated in this Agreement as Attachment 1. The Performer shall submit or otherwise provide all documentation required by Attachment 2, Report Requirements.

2.    The Performer shall be paid for each Payable Milestone accomplished in accordance with the Schedule of Payments and Payable Milestones set forth in Attachment 3 and the procedures of Article V. Both the Schedule of Payments and the Funding Schedule set forth in Attachments 3 and 4 respectively may be revised or updated in accordance with Article III, subject to mutual agreement of the Parties.

3.    The Government and the Performer estimate that the Statement of Work of this Agreement can only be accomplished with a Performer aggregate resource contribution of

	Phase 1	Phase 2/ Option 1 (Exercised)	Total Costs if All Options Exercised
Government Share (90%)	$3,022,501	$4,631,808	$7,654,309
Performer Share (10%)	$335,834	$514,645	$850,479
Total Amount of the Agreement	$3,358,334	$5,146,453	$8,504,788

from the effective date of this Agreement, subject to the availability of funds. The Performer intends and, by entering into this Agreement, undertakes to cause these funds to be provided. The Performer’s contributions will be provided as detailed in the Funding Schedule set forth in Attachment 4. If either DARPA or the Performer is unable to provide its respective total contribution, the other Party may reduce its project funding by a proportional amount.

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D.    Goals / Objectives

1.    The goal of this Agreement is for the Government to fund a performance-based effort by the Performer to investigate and create platforms for increasing the speed of engineering DNA and microbes while simultaneously expanding the scope of the living systems that are readily engineered.

2.    The Government will have continuous involvement with the Performer. The Government will also obtain access to research results and certain rights in data and patents pursuant to Articles VII and VIII. DARPA and the Performer are bound to each other by a duty of good faith and best research effort in achieving the goals of the Program.

3.    This Agreement is an "other transaction" pursuant to 10 U.S.C. § 2371. The Parties agree that the principal purpose of this Agreement is for the Government to support and stimulate the Performer to provide their best effort in advanced research and technology development and not for the acquisition of property or services for the direct benefit or use of the Government. This Agreement can best be described as an accumulation of expenses approach with payments tied to Fixed Payable Milestones. The Performer will be paid for each Payable Milestone accomplished in accordance with the Schedule of Payments and Payable Milestones set forth in Attachment 3 and the procedures of Article V. The Schedule of Payments and Payable Milestones may be revised or updated in accordance with Article III. This Agreement is not intended to be, nor shall it be construed as, by implication or otherwise, a partnership, a corporation, or other business organization.

ARTICLE II:    TERM

A.    Term of this Agreement

The Program commences upon the date of the last signature hereon and continues for:

Phase 1 – Twelve (12) months.

Phase 2 (Exercised via P00005) – Twelve (12) months from date of option exercise.

If all funds are expended prior to the duration of any Phase of the Agreement, the Parties have no obligation to continue performance and may elect to cease development at that point.

Provisions of this Agreement, which, by their express terms or by necessary implication, apply for periods of time other than specified herein, shall be given effect, notwithstanding this Article.

B.    Termination Provisions

Subject to a reasonable determination that the program will not produce beneficial results commensurate with the expenditure of resources, either Party may terminate this Agreement by written notice to the other Party, provided that such written notice is preceded by consultation between the Parties. In the event of a termination of the Agreement, it is agreed that disposition of Data developed under this Agreement, shall be in accordance with the provisions set forth in Article VIII, Data Rights. The Government and the Performer will negotiate in good faith a reasonable and timely adjustment of all outstanding issues between the Parties as a result of termination. Failure of the Parties to agree to a reasonable adjustment will be resolved pursuant to Article VI, Disputes. The Government has no obligation to pay the Performer beyond the last completed and paid milestone if the Performer decides to terminate. For the avoidance of doubt, any such termination does not require repayment of milestone amounts already received by Performer.

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C. Extending the Term (Phase 2)

The Parties may extend by mutual written agreement the term of this Agreement if funding availability and research opportunities reasonably warrant. Any extension shall be formalized through modification of the Agreement by the Agreements Officer and the Performer’s Administrator.

(i) The Government may extend the term of this agreement by written notice to the Performer within 12 months; provided that the Government gives the Performer a preliminary written notice of its intent to extend at least 14 days before the agreement expires. The preliminary notice does not commit the Government to an extension.

(ii) If the Government exercises this option, the extended agreement shall be considered to include this article.

(iii) The total duration of this agreement, including the exercise of any options under this article, shall not exceed 24 months.

(End of clause)

ARTICLE III:    MANAGEMENT OF THE PROJECT

A.    Management and Program Structure

The Performer shall be responsible for the overall technical and program management of the Program, and technical planning and execution shall remain with the Performer. The DARPA Agreements Officer’s Representative shall provide recommendations to Program developments and technical collaboration and be responsible for the review and verification of the Payable Milestones.

B.    Program Management Planning Process

Program planning will consist of an Annual Program Plan with inputs and review from the Performer and DARPA management, containing the detailed schedule of research activities and payable milestones. The Annual Program Plan will consolidate quarterly adjustments in the research schedule, including revisions/modification to payable milestones.

1.    Initial Program Plan: The Performer will follow the initial program plan that is contained in the Statement of Work (Attachment 1), and the Schedule of Payments and Payable Milestones (Attachment 3).

2.    Overall Program Plan Annual Review

(a)    The Performer, with DARPA Agreements Officer’s Representative review, will prepare an overall Annual Program Plan in the first quarter of each Agreement year. (For this purpose, each consecutive twelve (12) month period from (and including) the month of execution of this Agreement during which this Agreement shall remain in effect shall be considered an “Agreement Year”.) The Annual Program Plan will be presented and reviewed at an annual site review which will be attended by the performer’s Key Personnel, the DARPA Agreements Officer’s Representative, Senior DARPA management as appropriate, and other DARPA program managers and personnel as appropriate. The Performer, with DARPA participation and review, will prepare a final Annual Program Plan.

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(b)    The Annual Program Plan provides a detailed schedule of research activities, commits the Performer to use its best efforts to meet specific performance objectives, includes forecasted expenditures and describes the Payable Milestones. The Annual Program Plan will consolidate all prior adjustments in the research schedule, including revisions/modifications to payable milestones. Recommendations for changes, revisions or modifications to the Agreement which result from the Annual Review shall be made in accordance with the provisions of Article III, Section C.

C.    Modifications

1.    As a result of quarterly meetings (in person or videoconference), annual reviews, or at any time during the term of the Agreement, research progress or results may indicate that a change in the Statement of Work and/or the Payable Milestones, would be beneficial to program objectives. Recommendations for modifications, including justifications to support any changes to the Statement of Work and/or the Payable Milestones, will be documented in a letter and submitted by the Performer to the DARPA Agreements Officer’s Representative with a copy to the DARPA Agreements Officer. This documentation letter will detail the technical, chronological, and financial impact of the proposed modification to the research program. The Performer shall approve any Agreement modification. The Government is not obligated to pay for additional or revised Payable Milestones until the Payable Milestones Schedule (Attachment 3) is formally revised by the DARPA Agreements Officer and made part of this Agreement.

2.    The DARPA Agreements Officer’s Representative shall be responsible for the review and verification of any recommendations to revise or otherwise modify the Agreement Statement of Work, Schedule of Payments or Payable Milestones, or other proposed changes to the terms and conditions of this Agreement.

3.    For minor or administrative Agreement modifications (e.g. changes in the paying office or appropriation data, changes to Government or the Performer’s personnel identified in the Agreement, etc.) no signature is required by the Performer.

ARTICLE IV:    AGREEMENT ADMINISTRATION

Unless otherwise provided in this Agreement, approvals permitted or required to be made by DARPA

may be made only by the DARPA Agreements Officer. Administrative and contractual matters under

this Agreement shall be referred to the following representatives of the parties:

A.    Government Points of Contact:

Agreements Officer:

[*]

[*]

DARPA Program Manager:

[*]

Program Manager

[*]

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

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[*]

Agreements Officer’s Representative (AOR):

[*]

[*]

[*]

Administrative Agreements Officer (AAO):

[*]

[*]

[*]

B.    Performer Points of Contact

Performer’s Administrative/Contracting:

[*]

General Counsel

[*]

[*]

Performer’s Program Manager:

[*]

Chief Science Officer

[*]

[*]

ARTICLE V:    OBLIGATION AND PAYMENT

A.    Obligation

1. The Government’s liability to make payments to the Performer is limited to only those funds obligated under the Agreement or by modification to the Agreement. DARPA may obligate funds to the Agreement incrementally.

2. If modification becomes necessary in performance of this Agreement, pursuant to Article III, paragraph B, the DARPA Agreements Officer and the Performer’s Administrator shall execute a revised Schedule of Payable Milestones consistent with the then current Program Plan.

B. Payments

1. The Performer has an established and agrees to maintain an established accounting system which complies with Generally Accepted Accounting Principles and the requirements of this Agreement, and shall ensure that appropriate arrangements have been made for receiving, distributing and accounting for all funding. An acceptable accounting system is one in which all cash receipts and disbursements are controlled and documented properly.

2. The Performer shall document the accomplishments of each Payable Milestone by submitting or otherwise providing the Payable Milestones Report required by Attachment 2, Part D.

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

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After written verification of the accomplishment of the Payable Milestone by the DARPA Agreements Officer’s Representative, and approval by the Agreements Officer, the associated invoice will be submitted to the payment office via Wide Area Workflow (WAWF), as detailed in paragraph B.6 of this Article. If deemed necessary by the Agreements Officer, payment approval for the final Payable Milestone will be made after reconciliation of DARPA funding with actual Performer contributions. Subject to change only through written Agreement modification, payment shall be made to the address of the Performer’s Administrator set forth below.

3. Address of Payee: AMYRIS, INC., 5885 Hollis Street, Suite 100, Emeryville, California 94608

4. Government funds shall be maintained in an interest-bearing account prior to disbursement. This account shall not be in U. S. Treasury Notes. Any interest earned shall be remitted annually to the DARPA Agreements Officer, or designee. Interest payments shall be made payable to the U. S. Treasury. Interest amounts less than $250 per year may be retained by the Performer for administrative expenses.

5. Payments will be made by the cognizant Defense Agencies Financial Services office, as indicated below, within thirty (30) calendar days of an accepted invoice in Wide Area Workflow (WAWF). Wide Area Workflow (WAWF) is a secure web-based system for electronic invoicing, receipt and acceptance. The WAWF application enables electronic form submission of invoices, government inspection, and acceptance documents in order to support DoD’s goal of moving to a paperless acquisition process. Authorized DoD users are notified of pending actions by e-mail and are presented with a collection of documents required to process the contracting or financial action. It uses Public Key Infrastructure (PKI) to electronically bind the digital signature to provide non-reputable proof that the user (electronically) signed the document with the contents. Benefits include online access and full spectrum view of document status, minimized re-keying and improving data accuracy, eliminating unmatched disbursements and making all documentation required for payment easily accessible.

The Performer is required to utilize the Wide Area Workflow system when processing invoices and receiving reports under this Agreement. The Performer shall (i) ensure an Electronic Business Point of Contact is designated in Central Contractor Registration at http://www.ccr.gov and (ii) register to use WAWF–RA at the https://wawf.eb.mil site, within ten (10) calendar days after award of this Agreement. Step by Step procedures to register are available at the https://wawf.eb.mil site. The Performer is directed to use the “2-in-1” format when processing invoices.

a. For the Issue By DoDAAC enter HR0011

b. For the Admin DoDAAC and Ship To fields, enter S0507A.

c. For the Service Acceptor field, enter HR0011, Extension 01.

d. Leave the Inspect by DoDAAC, Ship From Code DoDAAC and LPO DoDAAC fields blank unless otherwise directed by the Agreements Officer or Administrative Agreements Officer.

e. The following guidance is provided for invoicing processed under this Agreement through WAWF:

• The AOR identified at Article IV "Agreement Administration" shall continue to formally inspect and accept the deliverables/payable milestones. To the maximum extent practicable, the AOR shall review the deliverable(s)/payable milestone report(s) and either: 1) provide a written notice of rejection to the Performer which includes feedback

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regarding deficiencies requiring correction or 2) written notice of acceptance to the Administrative Agreements Officer (AAO), DARPA PM and Agreements Officer.

• Acceptance within the WAWF system shall be performed by the Agreements Officer upon receipt of a confirmation email, or other form of transmittal, from the AOR.

• The Performer shall send an email notice to the AOR and Agreements Officer upon submission of an invoice in WAWF (this can be done from within WAWF).

• Payments shall be made by DFAS-CO/WEST (HQ0339)

• The Performer agrees, when entering invoices entered in WAWF to utilize the CLINs associated with each payable milestone as delineated at Attachment 3. The description of the CLIN shall include reference to the associated milestone number along with other necessary descriptive information. The Performer agrees that the Government may reject invoices not submitted in accordance with this provision.

Note for DFAS: The Agreement shall be entered into the DFAS system by CLIN – Milestone association as delineated at Attachment 3. The Agreement is to be paid out by CLIN – Milestone association. Payments shall be made using the CLIN (MS)/ACRN association as delineated at Attachment 3.

6.    Payee Information: As identified at Central Contractor Registration.

• Cage Code: 47QN9

• DUNS: 185930182

• TIN: 55-0856151

7.    Limitation of Funds: In no case shall the Government’s financial liability exceed the

amount obligated under this Agreement.

8.    Payments shall be made in the amounts set forth in Attachment No. 3, provided the DARPA Agreements Officer’s Representative has verified the accomplishment of the Payable Milestones. It is recognized that the quarterly accounting of current expenditures reported in the “Quarterly Business Status Report” submitted in accordance with Attachment No. 2 is not necessarily intended or required to match the Payable Milestones until submission of the Final Report; however, payable milestones may be revised during the course of the program to reflect current and revised projected expenditures, subject to the requirements set forth in Article III.

account for all funding under this Agreement and shall maintain adequate records to account for the Performer’s funding provided under this Agreement. Upon completion or termination of this Agreement, whichever occurs earlier, the Performer’s Administrator shall furnish to the Agreements Officer a copy of the Final Report required by Attachment 2, Part E. The Performer’s relevant financial records are subject to examination or audit on behalf of DARPA by the Government for a period not to exceed three (3) years after expiration of the term of this Agreement. The Agreements Officer or designee shall have direct access to sufficient records and information of the Performer, to ensure full accountability for all funding under this Agreement. Such audit, examination, or access shall be performed during business hours on business days upon prior written notice and shall be subject to the security requirements of the audited party.

C.    Accounting and Appropriation Data

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AA    9720400 1320 S351 P2D10 2525 DPAC 2 5205 S12136 61101E    $3,022,501

AB    012199 097    0400 000 N 20132014 D 1320 HLIF6    2013.MBT-02.CORE.A

DARPA 255

$2,632,428

ACRN AC:    012199 097    0400 000 N 20132014 D 1320 HTLM6    2013.MBT-02.CORE.A

DARPA        255

$1,087,836

ACRN AD:     012199 097    0400 000 N 20142015 D 1320 BLTM6    2014.MBT-02.CORE.A

DARPA 255

$911,544

ARTICLE VI:    DISPUTES

A.    General

The Parties shall communicate with one another in good faith and in a timely and cooperative manner

when raising issues under this Article.

B.    Dispute Resolution Procedures

1.    Any disagreement, claim or dispute between DARPA and the Performer concerning questions of fact or law arising from or in connection with this Agreement, and, whether or not involving an alleged breach of this Agreement, may be raised only under this Article.

2.    Whenever disputes, disagreements, or misunderstandings arise, the Parties shall attempt to resolve the issue(s) involved by discussion and mutual agreement as soon as practicable. In no event shall a dispute, disagreement or misunderstanding which arose more than three (3) months prior to the notification made under subparagraph B.3 of this article constitute the basis for relief under this article unless the Director of DARPA in the interests of justice waives this requirement.

3.    Failing resolution by mutual agreement, the aggrieved Party shall document the dispute, disagreement, or misunderstanding by notifying the other Party (through the DARPA Agreements Officer or the Performer’s Administrator, as the case may be) in writing of the relevant facts, identify unresolved issues, and specify the clarification or remedy sought. Within five (5) working days after providing notice to the other Party, the aggrieved Party may, in writing, request a joint decision by the DARPA Senior Procurement Executive, and senior executive (no lower than Vice President, Legal) appointed by the Performer. The other Party shall submit a written position on the matter(s) in dispute within thirty (30) calendar days after being notified that a decision has been requested. The DARPA Senior Procurement Executive, and the senior executive shall conduct a review of the matter(s) in dispute and render a decision in writing within thirty (30) calendar days of receipt of such written position. Any such joint decision is final and binding.

4.    In the absence of a joint decision, upon written request to the Director of DARPA, made within thirty (30) calendar days of the expiration of the time for a decision under subparagraph B.3 above, the dispute shall be further reviewed. The Director of DARPA may elect to conduct this review

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personally or through a designee or jointly with a senior executive (no lower than (Vice President, Legal) level) appointed by the Performer. Following the review, the Director of DARPA or designee will resolve the issue(s)and notify the Parties in writing. Such resolution is not subject to further administrative review and, to the extent permitted by law, shall be final and binding.

C.    Limitation of Damages

Claims for damages of any nature whatsoever pursued under this Agreement shall be limited to direct damages only up to the aggregate amount of DARPA funding disbursed as of the time the dispute arises. In no event shall DARPA be liable for claims for consequential, punitive, special and incidental damages, claims for lost profits, or other indirect damages.

ARTICLE VII:    PATENT RIGHTS

A.    Allocation of Principal Rights

Unless the Performer shall have notified DARPA (in accordance with subparagraph B.2 below) that the Performer does not intend to retain title, the Performer shall retain the entire right, title, and interest throughout the world to each Subject Invention consistent with the provisions of this Article and 35 U.S.C. § 202. With respect to any Subject Invention in which the Performer retains title, DARPA shall have a nonexclusive, nontransferable, irrevocable, paid-up license to practice or have practiced on behalf of the United States the Subject Invention throughout the world.

B.    Invention Disclosure, Election of Title, and Filing of Patent Application

1.    The Performer shall disclose each Subject Invention to DARPA within four (4) months after the inventor discloses it in writing to his company personnel responsible for patent matters or, in the case of no internal writing from the inventor, within two (2) months after filing a provisional application, provided however that in the event the Performer does not file a provisional application, it shall disclose the Subject Invention to DARPA within two (2) months of determining that a particular set of experiments and or data qualify as a Subject Invention. The disclosure to DARPA shall be in the form of a written report and shall identify the Agreement under which the Subject Invention was made and the identity of the inventor(s). It shall be sufficiently complete in technical detail to convey a clear understanding to the extent known at the time of the disclosure, of the nature, purpose, operation, and the physical, chemical, biological, or electrical characteristics of the invention. The disclosure shall also identify any publication, sale, or public use of the invention and whether a manuscript describing the invention has been submitted for publication and, if so, whether it has been accepted for publication at the time of disclosure. The Performer shall also submit to DARPA an annual listing of Subject Inventions.

2.    If the Performer determines that it does not intend to retain title to any such Subject Invention, the Performer shall notify DARPA, in writing, within eight (8) months of disclosure to DARPA. However, in any case where publication, sale, or public use has initiated the one (1)-year statutory period wherein valid patent protection can still be obtained in the United States, the period for such notice may be shortened by DARPA to a date that is no more than sixty (60) calendar days prior to the end of the statutory period.

3.    The Performer shall file its initial patent application on a Subject Invention to which it elects to retain title within one (1) year after election of title or, if earlier, prior to the end of the statutory

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period wherein valid patent protection can be obtained in the United States after a publication, or sale, or public use. The Performer may elect to file patent applications in additional countries (including the European Patent Office and the Patent Cooperation Treaty) within either ten (10) months of the corresponding initial patent application or six (6) months from the date permission is granted by the Commissioner of Patents and Trademarks to file foreign patent applications, where such filing has been prohibited by a Secrecy Order.

4.    Requests for extension of the time for disclosure election, and filing under Article VII, paragraph C, may, at the discretion of DARPA, and after considering the position of the Performer, be granted.

C.    Conditions When the Government May Obtain Title

Upon DARPA’s written request, the Performer shall convey title to any Subject Invention to DARPA under any of the following conditions:

1.    If the Performer fails to disclose or elects not to retain title to the Subject Invention within the times specified in paragraph C of this Article; provided, that DARPA may only request title within sixty (60) calendar days after learning of the failure of the Performer to disclose or elect within the specified times.

2.    In those countries in which the Performer fails to file patent applications within the times specified in paragraph B of this Article; provided, that if the Performer has filed a patent application in a country after the times specified in paragraph B of this Article, but prior to its receipt of the written request by DARPA, the Performer shall continue to retain title in that country; or

3.    In any country in which the Performer decides not to continue the prosecution of any application for, to pay the maintenance fees on, or defend in reexamination or opposition proceedings on, a patent on a Subject Invention.

D.    Minimum Rights to the Performer and Protection of the Performer’s Right to File

1.    The Performer shall retain a nonexclusive, royalty-free license throughout the world in each Subject Invention to which the Government obtains title, except if the Performer fails to disclose the invention within the times specified in paragraph B of this Article. The Performer’s license extends to subsidiaries and affiliates and Collaborators, if any, within the corporate structure of which the Performer is a party and includes the right to grant licenses of the same scope to the extent that the Performer was legally obligated to do so at the time the Agreement was awarded. The license is transferable only with the approval of DARPA, except when transferred to the successor of that part of the business to which the invention pertains. DARPA approval for license transfer shall not be unreasonably withheld.

2.    The Performer’s license may be revoked or modified by DARPA to the extent necessary to achieve expeditious practical application of the Subject Invention pursuant to an application for an exclusive license submitted consistent with appropriate provisions at 37 CFR Part 404. This license shall not be revoked at any time when the Performer continues to practice the general technology developed hereunder in pursuit of commercial goals, including the goal of making the products derived from such platforms reasonably accessible to the public.

3     Before revocation or modification of the license, DARPA shall furnish the Performer a written notice of its intention to revoke or modify the license, and the Performer shall be allowed thirty

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(30) calendar days (or such other time as may be authorized for good cause shown) after the notice to show cause why the license should not be revoked or modified.

E.    Action to Protect the Government’s Interest

1.    The Performer agrees to execute or to have executed and promptly deliver to DARPA all instruments necessary to (i) establish or confirm the rights the Government has throughout the world in those Subject Inventions to which the Performer elects to retain title, and (ii) convey title to DARPA when requested under paragraph D of this Article and to enable the Government to obtain patent protection throughout the world in that Subject Invention.

2.    The Performer agrees to require, by written agreement, its employees, other than clerical and non-technical employees, to disclose promptly in writing to personnel identified as responsible for the administration of patent matters and in a format suggested by the Performer each Subject Invention made under this Agreement in order that the Performer can comply with the disclosure provisions of paragraph C of this Article. The Performer shall instruct employees, through employee agreements or other suitable educational programs, on the importance of reporting inventions in sufficient time to permit the filing of patent applications prior to U. S. or foreign statutory bars.

3.    The Performer shall notify DARPA of any decisions not to continue the prosecution of a patent application, pay maintenance fees, or defend in a reexamination or opposition proceedings on a patent, in any country, not less than thirty (30) calendar days before the expiration of the response period required by the relevant patent office.

4.    The Performer shall include, within the specification of any United States patent application and any patent issuing thereon covering a Subject Invention, the following statement: “This invention was made with Government support under Agreement HR0011-12-3-0006, awarded by DARPA. The Government has certain rights in the invention.”

F.    Lower Tier Agreements

The Performer shall include this Article, suitably modified, to identify the Parties, in all subcontracts or lower tier agreements, regardless of tier, for experimental, developmental, or research work.

G.    Reporting on Utilization of Subject Inventions

1. The Performer agrees to submit, during the term of the Agreement, an annual report on the general subject matter research at Performer or its Collaborators, licensees or assignees in connection with utilization of a Subject Invention or on efforts at obtaining such utilization that is being made by the Performer or its Collaborators, licensees or assignees. Such reports shall include information regarding the general fields of potential products where such Subject Inventions may ultimately assist in commercial sales. The Performer also agrees to provide additional reports as may be requested by DARPA in connection with any march-in proceedings undertaken by DARPA in accordance with paragraph J of this Article. Consistent with 35 U.S.C. § 202(c)(5), DARPA agrees it shall not disclose such information to persons outside the Government without permission of the Performer.

2 All required reporting shall be accomplished, to the extent possible, using the i-Edison reporting website: https://s-edison.info.nih.gov/iEdison/. To the extent any such reporting cannot be

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carried out by use of i-Edison, reports and communications shall be submitted to the Agreements Officer and Administrative Agreements Officer.

H.    Preference for American Industry

Notwithstanding any other provision of this clause, the Performer agrees that it shall not grant to any person the exclusive right to use or sell any Subject Invention in the United States or Canada unless such person agrees that any product embodying the Subject Invention or produced through the use of the Subject Invention shall be manufactured substantially in the United States or Canada except when such such rights are in connection with a Collaborator. However, in individual cases, the requirements for such an agreement beyond what is contemplated herein may be waived by DARPA upon a showing by the Performer (1) that reasonable but unsuccessful efforts have been made to grant licenses on similar terms to potential licensees that would be likely to manufacture substantially in the United States or (2) that, under the circumstances, domestic manufacture is not commercially feasible.

I.    March-in Rights

The Performer agrees that, with respect to any Subject Invention in which it has retained title, DARPA has the right to require the Performer, an assignee, or exclusive licensee of a Subject Invention to grant a non-exclusive license to a responsible applicant or applicants, upon terms that are reasonable under the circumstances, and if the Performer, assignee, or exclusive licensee refuses such a request, DARPA has the right to grant such a license itself if DARPA determines that:

1.    Such action is necessary because the Performer or assignee has not taken effective steps, consistent with the intent of this Agreement, to achieve practical application of the Subject Invention;

2.    Such action is necessary to alleviate health or safety needs which are not reasonably satisfied by the Performer, assignee, or their licensees;

3.    Such action is necessary to meet requirements for public use and such requirements are not reasonably satisfied by the Performer, assignee, or licensees; or

4.    Such action is necessary because the agreement required by paragraph (I) of this Article has not been obtained or waived or because a licensee of the exclusive right to use or sell any Subject Invention in the United States is in breach of such Agreement.

ARTICLE VIII: DATA RIGHTS

A.    Allocation of Principal Rights

1.    This Agreement shall be performed with mixed Government and Performer funding. The Parties agree that in consideration for Government funding, the Performer intends to reduce to practical application items, components and processes developed under this Agreement.

2.    The Performer agrees to retain and maintain in good condition until two (2) years after completion or termination of this Agreement, all Data necessary to achieve practical application. In the event of exercise of the Government’s March-in Rights as set forth under Article VII or subparagraph A.3 of this article, the Performer agrees, upon written request from the Government, to deliver at no additional cost to the Government, all Data necessary to achieve practical application within sixty (60)

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calendar days from the date of the written request. The Government shall retain Unlimited Rights, as defined in paragraph A above, to this delivered Data.

3.    The Performer agrees that, with respect to Data necessary to achieve practical application, DARPA has the right to require the Performer to deliver all such Data to DARPA in accordance with its reasonable directions if DARPA determines that:

(a)    Such action is necessary because the Performer or assignee has not taken effective steps, consistent with the intent of this Agreement, to achieve practical application of the technology developed during the performance of this Agreement;

(b)    Such action is necessary to alleviate health or safety needs which are not reasonably satisfied by the Performer, assignee, or their licensees; or

(c)    Such action is necessary to meet requirements for public use and such requirements are not reasonably satisfied by the Performer, assignee, or licensees.

4.    With respect to Data developed, generated or delivered under this Agreement, the Government shall receive Government Purpose Rights, except as noted in subparagraph (5) of this article.

5.    With respect to all Data delivered, in the event of the Government’s exercise of its right under subparagraph B.2 of this article, the Government shall receive Unlimited Rights.

6.    Any pre-existing Data to be utilized and delivered under this Agreement shall be delivered with restrictions as delineated in the Performer Identification and Assertion of Use, Release, or Disclosure Restrictions provided in Attachment 5.

B.    Marking of Data

Pursuant to paragraph B above, any Data delivered under this Agreement shall be marked with the following legend:

Use, duplication, or disclosure is subject to the restrictions as stated in Agreement HR0011-12-3- 0006 between the Government and the Performer.

C. Lower Tier Agreements

The Performer shall include this Article, suitably modified to identify the Parties, in all subcontracts or lower tier agreements, regardless of tier, for experimental, developmental, or research work.

ARTICLE IX: FOREIGN ACCESS TO TECHNOLOGY

This Article shall remain in effect during the term of the Agreement and for two (2) years thereafter.

A.    General

The Parties agree that research findings and technology developments arising under this Agreement may constitute a significant enhancement to the national defense, and to the economic vitality of the United

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States. Accordingly, access to important technology developments under this Agreement by Foreign Firms or Institutions must be carefully controlled. The controls contemplated in this Article are in addition to, and are not intended to change or supersede, the provisions of the International Traffic in Arms Regulation (22 CFR pt. 121 et seq.), the DoD Industrial Security Regulation (DoD 5220.22-R) and the Department of Commerce Export Regulation (15 CFR pt. 770 et seq.)

B.    Restrictions on Sale or Transfer of Technology to Foreign Firms or Institutions

1.    In order to promote the national security interests of the United States and to effectuate the policies that underlie the regulations cited above, the procedures stated in subparagraphs C.2, C.3, and C.4 below shall apply to any transfer of Technology. For purposes of this paragraph, a transfer includes a sale of the company, and sales or licensing of Technology. Transfers do not include:

(a) sales of products or components, or

(b) licenses of software or documentation related to sales of products or components, or

(c) transfer to foreign subsidiaries of the Performer for purposes related to this Agreement or to Collaborators, or

(d) transfer which provides access to Technology to a Foreign Firm or Institution which is an approved source of supply or source for the conduct of research under this Agreement provided that such transfer shall be limited to that necessary to allow the firm or institution to perform its approved role under this Agreement.

2.    The Performer shall provide timely notice to DARPA of any proposed transfers which occur after the effective date of this agreement from the Performer of Technology developed under this Agreement to Foreign Firms or Institutions. If DARPA determines that the transfer may have adverse consequences to the national security interests of the United States, the Performer, its vendors, and DARPA shall jointly endeavor to find alternatives to the proposed transfer which obviate or mitigate potential adverse consequences of the transfer but which provide substantially equivalent benefits to the Performer.

3.    In any event, the Performer shall provide written notice to the DARPA Agreements Officer’s Representative and Agreements Officer of any proposed transfer to a foreign firm or institution at least sixty (60) calendar days prior to the proposed date of transfer. Such notice shall cite this Article and shall state specifically what is to be transferred and the general terms of the transfer. Within thirty (30) calendar days of receipt of the Performer’s written notification, the DARPA Agreements Officer shall advise the Performer whether it consents to the proposed transfer. In cases where DARPA does not concur or sixty (60) calendar days after receipt and DARPA provides no decision, the Performer may utilize the procedures under Article VI, Disputes. No transfer shall take place until a decision is rendered.

4. In the event a transfer of Technology to Foreign Firms or Institutions which is NOT approved by DARPA takes place, the Performer shall (a) refund to DARPA funds paid for the development of the Technology and (b) the Government shall have a non-exclusive, nontransferable, irrevocable, paid-up license to practice or have practiced on behalf of the United States the Technology throughout the world for Government and any and all other purposes, particularly to effectuate the intent

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of this Agreement. Upon request of the Government, the Performer shall provide written confirmation of such licenses.

C.    Lower Tier Agreements

The Performer shall include this Article, suitably modified, to identify the Parties, in all subcontracts or lower tier agreements, regardless of tier, for experimental, developmental, or research work.

ARTICLE X:    TITLE TO AND DISPOSITION OF PROPERTY

A.    Title to Property

The Performer will acquire property with an acquisition value greater than $5,000 under this Agreement as set forth in Attachment * to this Agreement which is necessary to further the research and development goals of this Program and is not for the direct benefit of the Government. Title to this property shall vest in the Performer upon acquisition. Title to any other items of property acquired under this Agreement with an acquisition value of $5,000 or less shall vest in the Performer upon acquisition with no further obligation of the Parties unless otherwise determined by the Agreements Officer. Should any other item of property with an acquisition value greater than $5,000 be required, the Performer shall obtain prior written approval of the Agreements Officer. Title to this property shall also vest in the Performer upon acquisition. The Performer shall be responsible for the maintenance, repair, protection, and preservation of all property at its own expense.

B.    Disposition of Property

At the completion of the term of this Agreement, items of property set forth in Attachment * or any other items of property with an acquisition value greater than $5,000 shall be disposed of in the following manner:

1.    Purchased by the Performer at an agreed-upon price, the price to represent fair market value, with the proceeds of the sale being returned to DARPA; or

2.    Transferred to a Government research facility with title and ownership being transferred to the Government; or

3.    Donated to a mutually agreed University or technical learning center for research purposes; or

4. Any other DARPA-approved disposition procedure.

ARTICLE XI: CIVIL RIGHTS ACT

This Agreement is subject to the compliance requirements of Title VI of the Civil Rights Act of 1964 as amended (42 U.S.C. 2000-d) relating to nondiscrimination in Federally assisted programs. The Performer has signed an Assurance of Compliance with the nondiscriminatory provisions of the Act.

ARTICLE XII: SECURITY

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The Government does not anticipate the need for the Performer to develop and/or handle classified information in the performance of this Agreement. No DD254 is currently required for this Agreement.

ARTICLE XIII: SUBCONTRACTORS

The Performer shall make every effort to satisfy the intent of competitive bidding of sub-agreements to the maximum extent practical. The Performer may use foreign entities or nationals as subcontractors, subject to compliance with the requirements of this Agreement and to the extent otherwise permitted by law.

ARTICLE XIV: KEY PERSONNEL

A. The Performer shall notify the Agreements Officer in writing prior to making any change in key personnel. The following individuals are designated as key personnel for the purposes of this Agreement:

Name	Role/Title	% of time
Jack Newman	Chief Science Officer	60%
Sunil Chandran	Team Leader	100%

B. When replacing any of the personnel identified above, the Performer must demonstrate that the qualifications of the prospective personnel are acceptable to the Government as reasonably determined by the Program Manager. Substitution of key personnel shall be documented by modification to the Agreement made in accordance with the procedures outlined in Article III, paragraph C.

ARTICLE XV: EXPORT CONTROL

(a) Definition. “Export-controlled items,” as used in this clause, means items subject to the Export Administration Regulations (EAR) (15 CFR Parts 730-774) or the International Traffic in Arms Regulations (ITAR) (22 CFR Parts 120-130). The term includes:

1) “Defense items,” defined in the Arms Export Control Act, 22 U.S.C. 2778(j)(4)(A), as defense articles, defense services, and related technical data, and further defined in the ITAR, 22 CFR Part 120.

2) “Items,” defined in the EAR as “commodities”, “software”, and “technology,” terms that are also defined in the EAR, 15 CFR 772.1.

(b) The Performer shall comply with all applicable laws and regulations regarding export-controlled items, including, but not limited to, the requirement for contractors to register with the Department of State in accordance with the ITAR. The Performer shall consult with the Department of State regarding

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any questions relating to compliance with the ITAR and shall consult with the Department of Commerce regarding any questions relating to compliance with the EAR.

(c) The Performer's responsibility to comply with all applicable laws and regulations regarding export-controlled items exists independent of, and is not established or limited by, the information provided by this clause.

(d) Nothing in the terms of this contract adds, changes, supersedes, or waives any of the requirements of applicable Federal laws, Executive orders, and regulations,

including but not limited to—

(1) The Export Administration Act of 1979, as amended (50 U.S.C. App. 2401, et seq.);

(2) The Arms Export Control Act (22 U.S.C. 2751, et seq.);

(3) The International Emergency Economic Powers Act (50 U.S.C. 1701, et seq.);

(4) The Export Administration Regulations (15 CFR Parts 730-774);

(5) The International Traffic in Arms Regulations (22 CFR Parts 120-130);

and

(6) Executive Order 13222, as extended;

(e) The Performer shall include the substance of this clause, including this paragraph (e), in all subawards.

ARTICLE XVI: ORDER OF PRECEDENCE

In the event of any inconsistency between the terms of this Agreement and language set forth in the Attachments, the inconsistency shall be resolved by giving precedence in the following order: (1) The Agreement, and (2) all Attachments to the Agreement.

ARTICLE XVII: EXECUTION

This Agreement constitutes the entire agreement of the Parties and supersedes all prior and contemporaneous agreements, understandings, negotiations and discussions among the Parties, whether oral or written, with respect to the subject matter hereof. This Agreement may be revised only by written consent of the Performer and the DARPA Agreements Officer. This Agreement, or modifications thereto, may be executed in counterparts each of which shall be deemed as original, but all of which taken together shall constitute one and the same instrument.

ARTICLE XVIII: APPLICABLE LAW

United States federal law will apply to the construction, interpretation, and resolution of any disputes arising out of or in connection with this Agreement.

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ARTICLE XIX: SEVERABILITY

In the event that any one or more of the provisions contained herein shall, for any reason, be held to be invalid, illegal or unenforceable in any respect, such invalidity, illegality or unenforceability shall not affect any other provisions of this Agreement, but this Agreement shall be construed as if such invalid, illegal or unenforceable provisions had never been contained herein, unless the deletion of such provision or provisions would result in such a material change so as to cause completion of the transactions contemplated herein to be unreasonable.

ARTICLE XX: FORCE MAJEURE

Performer shall not be liable for delays or non-performance hereunder if such delay or non-performance is from causes beyond the control and without the fault or negligence of the Performer or its subcontractors, and is due, directly, to fire or other casualty; act of God; strike or labor dispute; war or other violence, or to acts of the Government in either its sovereign or contractual capacity.

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Amyris, Inc.

Statement of Work

For

Living Foundries

Improving DNA Assembly and Integration Across Platforms with Better Systems and Tools

30 May 2012

(Amended through 9 April 2014)

Advanced Tools and Capabilities for Generalizable Platforms (ATCG) Program Background

Current approaches to engineering biology rely on an ad hoc, laborious, trial-and-error process, wherein one successful project often does not translate to enabling subsequent new designs. As a result, the state of the art development cycle for engineering a new biologically manufactured product often takes 7+ years and tens to hundreds of millions of dollars (e.g. microbial production of artemisinic acid for the treatment of malaria and the non-petroleum-based production 1, 3-propanediol). The impact of current approaches is two-fold. First, the number of new entrants and innovators into the biomanufacturing space is immediately limited – few have the expertise, capital and/or time necessary to develop and engineer a new product. Second, combined with the complexity of biological systems, an ad hoc approach results in one-off efforts limited to modifying only a small set of genes and constructing simple, isolated genetic circuits and metabolic pathways. Consequently, while progress has been made, industry is constrained to producing only a tiny fraction of the vast number of possible chemicals, materials, and functional systems that would be enabled by the ability to truly engineer biology. A new approach is needed.

This new approach is Living Foundries: develop and apply an engineering framework to biology that decouples biological design from fabrication, yields design rules and tools, and manages biological complexity through abstraction and standardization. One analogy is that Living Foundries aims to do for biological design what verylarge-scale integration (VLSI) did for integrated circuits. Applying an engineering framework to biology will remove barriers to researchers outside the biological sciences, bringing diverse expertise and new methods to biological design. The best innovations will introduce new architectures and tools that will form the foundational technology for engineering biology.

The vision of Living Foundries is one where new and multiple cellular functions are readily constructed, combined, and controlled by an integrated genetic circuitry. The ultimate effect of which will be to open up the full space of biologically produced materials and systems. To achieve this, new tools, technologies and methodologies that directly address our current limitations and expand our capabilities must be developed. The outcome should be an open technology platform that integrates these tools and capabilities, allowing new designs to rapidly move from conception to execution.

Advanced Tools and Capabilities for Generalizable Platforms, (ATCG) seeks translatable tools that can serve as parts of an “end-to-end platform” to support rapid, specific in its goals: DARPA seeks new technology to enable low-cost and rapid DNA synthesis and assembly, especially to shorten the design-test cycle surrounding the ambitious constructs that characterize the broadest visions in modern synthetic biology.

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Research Tasks

Task A

[*]

Task A. [*] (Jed Dean, Amyris)

Task Objective: [*]

[*]

Milestone: [*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

Subtask A.1. [*]

[*]

Subtask A.2. [*]

[*]

Subtask A.3. [*]

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

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[*]

This subtask completes the Milestone outlined above.

Task C

[*]

Task C. [*](Sunil Chandran, Amyris)

Task Objective: [*]

[*]

Phase I

Milestone: (12 months) [*]

Metrics/Completion Criteria: [*]

Deliverable: [*]

Subtask C.1[*]

[*]

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

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Subtask C.2 [*]

[*]

Subtask C.3 [*]

[*]

Subtask C.4 [*]

[*]

This subtask completes the Milestone outlined above.

Phase II

Milestone (CIIa): [*]

Metrics/Completion Criteria: [*]

Subtask C.5 [*]

[*]

Subtask C.6 [*]

[*]

These subtasks complete the Milestone outlined above.

Milestone (CIIb): [*]

Metrics/Completion Criteria: [*]

Deliverable:[*]

Subtask C.7 [*]

[*]

[*]

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

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Milestone (CIIc): [*]

Metrics/Completion Criteria: [*]

Deliverable: [*]

Subtask C.8 [*]

[*]

Task D

[*]

Task D. [*] (Sunil Chandran, Amyris)

Task D. [*] (Sunil Chandran, Amyris)

Task Objective: [*]

[*]

Phase I

Milestone: [*]

Metrics/Completion Criteria: [*]

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

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Deliverable: [*]

Subtask D.1 [*]

Subtask D.2 [*]

[*]

Subtask D.3 [*]

[*]

Subtask D.4 [*]

[*]

Phase II

Milestone (DIIa): [*]

Metrics/Completion Criteria: [*]

Subtask D.5 [*]

[*]

Subtask D.6 [*]

[*]

Milestone (DIIb): [*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

Subtask D.7 [*]

[*]

Subtask D.8 [*]

[*]

This subtask completes the Milestone outlined above.

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

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Task E

[*]

Task E. [*] (Sunil Chandran, Amyris)

Task Objective: [*]

Phase IA

Milestone: [*]

Metrics/Completion Criteria: [*]

Deliverable: [*]

Subtask E.1.[*]

[*]

This subtask completes the Milestone outlined above.

Phase IB

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

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Milestone: [*]

Metrics/Completion Criteria: [*]

Deliverable: [*]

Subtask E.3 [*]

[*]

This subtask completes the Milestone outlined above.

Phase II

Milestone (EIIa): [*]

Metrics/Completion Criteria: [*]

Deliverable: [*]

Subtask E.5 [*]

[*]

Milestone (EIIb): [*]

Metrics/Completion Criteria: [*]

Deliverable: [*]

Subtask E.6 [*]

[*]

This subtask completes the Milestone outlined above.

Milestone (EIIc): [*]

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

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Metrics/Completion Criteria: [*]

Deliverable: [*]

Subtask E.7 [*]

[*]

Subtask E.8 [*]

[*]

This subtask completes the Milestone outlined above.

Task F

Task F.[*](Sunil Chandran, Amyris)

Task objective: [*]

Phase II

Milestone: [*]

Metrics/Completion Criteria: [*]

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

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[*]

Deliverable: [*]

Subtask F.1. [*]

[*]

Subtask F.2. [*]

[*]

Task G (Bio-safety/Security)

Task Background: The research and engineering depicted in this Statement of Work seeks to make existing capabilities (e.g. genetic modification of microbes to produce commodity chemicals) more efficient with the intended purpose of speeding the development of Living Foundries. The goal of this research is to make better engineering tools, and not to produce microbes that may have Dual-Use potential. As noted in the performer’s technical proposal, a review of the research activities identified within this Statement of Work determined that this project will not enable technologies that are related to human, animal, or plant health. The performer’s choice of potential chassis or hosts will be made from amongst the list of microbes that, prior to genetic modification, are designated safely handled in a Biosafety Level 1 facility. Additionally, the resulting genetically modified organisms have no selective advantage in the environment.

Metrics/Completion Criteria: The performer shall demonstrate throughout the program that all methods and demonstrations of capability comply with national guidance for manipulation of genes and organisms and follow all guidance for biological safety and biosecurity. Demonstrations and testbeds must meet any applicable regulations designed to protect human health and the environment promulgated by the Environmental Protection Agency, National Institutes of Health, or other relevant agencies of the Federal Government. The performer shall use, store, and destroy biological material in accordance with all applicable regulations.

Deliverable: Include as part of the required monthly technical status reports an on-going status of efforts to develop and/or carry out their Advanced Tools and Capabilities for Generalizable Platforms (ATCG) Bio-Safety and Security plan.

Task H (Intellectual Property and Data Sharing)

Task Background: It is the goal of the Defense Advanced Research Projects Agency (DARPA) that its investment in the tools and capabilities developed under the ATCG program to be multiplied many-fold by adoption and improvement by researchers across the United States. In order to achieve this vision, the Living Foundries program aims to facilitate interoperability and open the field to new entrants.

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

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Agreement No. HR0011-12-3-0006 Attachment 1

Metrics/Completion Criteria: To facilitate interoperability, all applicable design tools and databases developed under the ATCG program should be compatible with Synthetic Biology Open Language (SBOL) core data model. The Performer shall make available the technologies developed under the ATCG effort to the broader synthetic biology community by presenting its ATCG research data at public meetings/conferences/workshops and publishing results in peer-reviewed journal articles. At a minimum, the types of information that will be made available to the broader synthetic biology community are as discussed below:

(i) Data and analysis necessary to evaluate the utility of the technologies, as well as standard operating procedures and design specifications enabling others to reconstitute the equipment, set up, and approaches developed.

(ii) The results of Design of Experiment work to arrive at the conditions for the best performance for untested or early stage technologies, describing the correlation between:

• DNA ligase cycling parameters and the complexity, size, and success rate of the assembled full length DNA constructs.

• Reaction parameters and the success and cost of performing sequencing QC on DNA assemblies.

• Designer nuclease number, type, and targeting site and the integration efficiency in to the chassis genome.

(iii) Details required for both technical evaluation and transfer, including: full protocols, technical drawings of equipment built and specifications met, data on accuracy and precision of these systems, and results on procedures performed against large number of samples to investigate the robustness and readiness of the approaches for broader distribution – providing a trained reader with the information needed to recapitulate the methods and results described. In addition, the Principal Investigator shall be available to consult with third parties seeking to replicate the results.

If the work performed under this Statement of Work results in one or more patents, the Performer shall grant licenses on a royalty-free basis to academic and non-profit institutions. Additionally, the Performer shall make licenses available to commercial entities outside its key business areas.

Deliverable/s: The Performer shall include as part of required monthly technical status reports an on-going status of efforts to develop and/or carry out their proposed ATCG Intellectual Property and Data Sharing plan. Reporting shall include a summary of data sharing activities that have taken place during the reporting period and any data sharing activities planned to take place within three months of the reporting period. Reporting shall include a listing of the performers Subject Invention disclosures, Subject Invention patent applications and a brief discussion summarizing plans, if any, to license the resulting technology (e.g., intent and rationale regarding whether the performer intends to seek non-exclusive licensing, exclusive licensing for a particular field of use, or exclusive licensing across the board, etc.).

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Agreement No. HR0011-12-3-0006 Attachment 2

ATTACHMENT 2:

REPORT REQUIREMENTS

A.     TECHNICAL STATUS REPORT

On or before sixty (60) calendar days after the effective date of the Agreement and monthly thereafter throughout the term of the Agreement, the Performer shall submit, via email, a monthly Technical Status Report to the DARPA Program Manager, DARPA Agreements Officer, Agreement Officer’s Representative (AOR), and DARPA/ADPM. The technical status report will detail technical progress to date and report on all problems, technical issues, major developments, and the status of external collaborations during the reporting period. Technical Status Reports shall be marked with Distribution Statement B:

“DISTRIBUTION STATEMENT B. Distribution authorized to U.S. Government agencies only due to the inclusion of proprietary information. Other requests for this document shall be referred to DARPA Public Release Center (PRC) via email at PRC@darpa.mil.”

B.    BUSINESS STATUS REPORT

On or before ninety (90) calendar days after the effective date of the Agreement and quarterly thereafter throughout the term of the Agreement, the Performer shall submit, via email, a quarterly Business Status Report to the DARPA Program Manager, DARPA Agreements Officer, Agreement Officer’s Representative (AOR), and DARPA/ADPM. The business status report shall provide summarized details of the resource status of this Agreement, including the status of the Performer’s contributions. This report will include a quarterly accounting of current expenditures as outlined in the Annual Program Plan. Any major deviations, over plus or minus 10%, shall be explained along with discussions of the adjustment actions proposed. The report will also include an accounting of any interest earned on Government funds. The Performer is reminded that interest in amounts greater than $250 per year is not expected to accrue under this Agreement. In the event that this interest does accrue on Government funds, the Performer is required to provide an explanation for the accrual in the business report. Depending on the circumstances, the Payable Milestones may require adjustment. Business Status Reports shall be marked with Distribution Statement B:

“DISTRIBUTION STATEMENT B. Distribution authorized to U.S. Government agencies only due to the inclusion of proprietary information. Other requests for this

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Agreement No. HR0011-12-3-0006 Attachment 2

document shall be referred to DARPA Public Release Center (PRC) via email at PRC@darpa.mil.

C.    ANNUAL PROGRAM PLAN DOCUMENT

The Performer shall submit via email or otherwise provide to the DARPA Agreements Officer’s Representative, DARPA Program Manager and DARPA Agreements Officer one (1) copy each of a report which describes the Annual Program Plan as described in Article III, Section B. This document shall be submitted not later than thirty (30) calendar days following the Annual Site Review as described in Article III, Section B. Annual Program Plans shall be marked with Distribution Statement B:

“DISTRIBUTION STATEMENT B. Distribution authorized to U.S. Government agencies only due to the inclusion of proprietary information. Other requests for this document shall be referred to DARPA Public Release Center (PRC) via email at PRC@darpa.mil.”

D.    SPECIAL TECHNICAL REPORTS

The Performer shall submit via email or otherwise provide to the DARPA Agreements Officer’s Representative, the DARPA Program Manager and DARPA Agreements Officer one (1) copy each of special technical reports on significant events such as significant target accomplishments by the Performer, significant tests, experiments, or symposia, as discussed in the Attachment No. 1 Statement of Work. Special Technical Reports shall be marked with Distribution Statement B:

“DISTRIBUTION STATEMENT B. Distribution authorized to U.S. Government agencies only due to the inclusion of proprietary information. Other requests for this document shall be referred to DARPA Public Release Center (PRC) via email at PRC@darpa.mil.”

E.    SCIENTIFIC PAPERS

The performer shall publish scientific papers in accordance with the Attachment No. Statement of Work. One (1) copy of each published scientific paper shall be submitted via email or otherwise provided to the DARPA Agreements Officer’s Representative, DARPA Program Manager, and DARPA Agreements Officer. Scientific Papers shall be marked with Distribution Statement A:

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Agreement No. HR0011-12-3-0006 Attachment 2

"Approved for public release; distribution is unlimited.”

E.    PAYABLE MILESTONES REPORTS

The Performer shall submit via email or otherwise provide to the DARPA Agreements Officer’s Representative, the DARPA Program Manager and DARPA Agreements Officer documentation describing the extent of accomplishment of Payable Milestones. This information shall be as required by Article V, paragraph B and shall be sufficient for the DARPA Agreements Officer’s Representative to reasonably verify the accomplishment of the milestone in accordance with the Attachment No. 1 Statement of Work and Attachment No. 3 Payable Milestone Plan. Payable Milestone Reports shall be marked with Distribution Statement B:

“DISTRIBUTION STATEMENT B. Distribution authorized to U.S. Government agencies only due to the inclusion of proprietary information. Other requests for this document shall be referred to DARPA Public Release Center (PRC) via email at PRC@darpa.mil.”

F.    FINAL REPORT    (NOTE: The Final Report is included in the last Payable Milestone for the completed Agreement)

1. The Performer shall submit or otherwise provide a Final Report making full disclosure of all major developments by the Performer upon completion of the Agreement or within sixty (60) calendar days of termination of this Agreement. With the approval of the DARPA Agreements Officer’s Representative, reprints of published articles may be attached to the Final Report. The Final Report shall be submitted via email to the DARPA Program Manager, DARPA Agreements Officer, Agreement Officer’s Representative (AOR), DARPA/ADPM, and the Defense Technical Information Center.

2. The Final Report shall be marked with a distribution statement to denote the extent of its availability for distribution, release, and disclosure without additional approvals or authorizations. The Final Report shall be marked on the front page in a conspicuous place with the following marking:

“DISTRIBUTION STATEMENT B. Distribution authorized to U.S. Government agencies only due to the inclusion of proprietary information. Other requests for this document shall be referred to DARPA Public Release Center (PRC) via email at PRC@darpa.mil.”

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Agreement No. HR0011-12-3-0006 Attachment 2

G.    FINAL REPORT MARKINGS

(1) The cover or title page of each of the above reports or publications prepared, will have the following citation:

Sponsored by

Defense Advanced Research Projects Agency

Microsystems Technology Office (MTO)

Program: Living Foundries

Issued by DARPA/CMO under Agreement No. HR0011-12-3-0006

(2) The title page shall include a disclaimer worded substantially as follows:

“The views and conclusions contained in this document are those of the authors and should not be interpreted as representing the official policies, either expressly or implied, of the Defense Advanced Research Projects Agency or the U.S. Government.”

(3) The Final Report shall include a Standard Form 298, August 1998.

(4) All reports shall be marked with the below Distribution Statement and Data Rights statements:

(a) Distribution Statement designations are listed above for each individual type of report.

(b) Government Purpose Rights.

“GOVERNMENT PURPOSE RIGHTS

Agreement Number: HR0011-12-3-0006

Contractor Name: Amyris, Inc.”

In accordance with Article VIII, as applicable, contained in the above identified Agreement, the Government has the right to use, duplicate, or disclose Data, in whole or in part and in any manner, for Government purposes only, and to have or permit others to do so for Government purposes only.”

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Agreement No. HR0011-12-3-0006 Attachment 2

(c) Limited Rights.

“LIMITED RIGHTS

Agreement Number: HR0011-12-3-0006

Contractor Name: Amyris, Inc.”

In accordance with Article VIII, as applicable, contained in the above identified

Agreement, the Government has the right to use, modify, reproduce, release, perform,

display, or disclose Data, in whole or in part, within the Government. The Government

may not, without the written permission of the party asserting limited rights, release or

disclose the Data outside the Government.

H. EXECUTIVE SUMMARY

The Performer shall submit a one to two page executive-level summary of the major

accomplishments of the Agreement and the benefits of using the “other transactions”

authority pursuant to 10 U.S.C. § 2371 upon completion of the Agreement. This

summary shall include a discussion of the actual or planned benefits of the technologies

for both the military and commercial sectors. Two (2) copies shall be submitted to the

DARPA Agreements Officer.

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Agreement No. HR0011-12-3-0006 Attachment 3

MILESTONE	Task	Month	Payable Milestones	Exit Criteria	Performer Payment	DARPA Payment	SUBLCIN/ ACRN
	Phase I
1	[*]	[*]	[*]	[*]	[*]	[*]	00101/AA
2	[*]	[*]	[*]	[*]	[*]	[*]	00201/AA
3	[*]	[*]	[*]	[*]	[*]	[*]	00301/AA
4	[*]	[*]	[*]	[*]	[*]	[*]	00401/AA
5	[*]	[*]	[*]	[*]	[*]	[*]	00501/AA
Total					$335,834	$3,022,501
	Phase 2
6	[*]	[*]	[*]	[*]	[*]	[*]	00601/AB
7	[*]	[*]	[*]	[*]	[*]	[*]	00701/AB
8	[*]	[*]	[*]	[*]	[*]	[*]	00801/AB
[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

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Agreement No. HR0011-12-3-0006 Attachment 3

9	[*]	[*]	[*]	[*]	[*]	[*]	00901/AB
10	[*]	[*]	[*]	[*]	[*]	[*]	01001/AB
11	[*]	[*]	[*]	[*]	[*]	[*]	001101/AC
12	[*]	[*]	[*]	[*]	[*]	[*]	001201/AC
13	[*]	[*]	[*]	[*]	[*]	[*]	001301/AD
14	[*]	[*]	[*]	[*]	[*]	[*]	001401/AD @ $76,747 001402/AC @ $351,946
15	[*]	[*]	[*]	[*]	[*]	[*]	001501/AC
Total					$514,645	$4,631,808
	Phase 1 & Phase 2
Total					$850,479	$7,654,309

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

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Agreement No. HR0011-12-3-0006 Attachment 4

ATTACHMENT 4:

FUNDING SCHEDULE

A.    PROJECTED PROGRAM FUNDING COMMITMENTS

	DARPA Performer	Funding Contribution
Base (Phase I)
FY 12 (At time of award)	$3,595,518	$399,501
FY 13 (on or about November 2012)	$370,411	$41,158
Modification P00007 Reduction	($943,428)	($104,825)
Phase 1 Totals	$3,022,501	$335,834
Option (Phase 2)
FY 13 (At time of Exercise)	$2,079,497	$231,055
FY 13 (Modification P00008)	$552,931	$61,437
FY13 (Modification P00009)	$645,890	$71,765
FY 14 (Modification P00011)	$1,353.490	$150,388
Phase 2 Totals	$4,631,808	$514,645
AGREEMENT TOTALS	$7,654,309	$850,479

DARPA funding shall be applied toward the following expenses: Direct labor, to include indirect costs thereof, and direct materials/equipment purchases, to include indirect costs thereof, as included in Amyrsis’s Living Foundries proposal dated 3 May 2012 (as amended).

B.    PERFORMER CONTRIBUTION

	Total Contribution	Cash*	In-kind**
Phase 1	$335,834	$335,834	$0
Phase 2	$514,645	$514,645	$0
Total	$850,479	$850,479	$0

*Cash contributions consist of: Direct labor, to include indirect costs thereof, and direct materials/equipment purchases, to include indirect costs thereof, as included in Amyrsis’s Living Foundries proposal dated 3 May 2012 (as amended). The aforementioned are considered cash contributions made by Amyris in support of the Living Foundries research program.

**In-kind contributions consist of: N/A

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Agreement No. HR0011-12-3-0006 Attachment 5

List of Intellectual Property Assertions

Technical Data Computer Software to be Furnished with Restrictions	Basis for Assertion	Asserted Rights Category	Name of Person Asserting Restrictions
Production of Isoprenoids, Application US 11/754,235, Patent No. US 7,659,097 (US 20080274523)	Developed exclusively at private expense	Restricted Rights	Amyris, Inc.
Production of Isoprenoids, ApplicationUS 12/638,771, Patent No. (US2011/0287476)	Developed exclusively at private expense	Restricted Rights	Amyris, Inc.
Production of Isoprenoids, Application PCT/US2007/069807, Patent No. (WO2007/140339)	Developed exclusively at private expense	Restricted Rights	Amyris, Inc.
Nucleic Acids, Compositions and Methods for the Excision of Target Nucleic Acids, Application US 12/978,061, Patent No. US 7,919,605	Developed exclusively at private expense	Restricted Rights	Amyris, Inc.
Nucleic Acids, Compositions and Methods for the Excision of Target Nucleic Acids, Application US 13/220,553, Patent No. (US 2012/0052582)	Developed exclusively at private expense	Restricted Rights	Amyris, Inc.
Nucleic Acids, Compositions and Methods for the Excision of Target Nucleic Acids, Application PCT/US2011/049615, Patent No. (WO 2012/030747)	Developed exclusively at private expense	Restricted Rights	Amyris, Inc.
Compositions and Methods for the Rapid Assembly of Polynucleotides, Developed exclusively at private expense Application US 12/622,401, Patent No. (US 2010/0136633)	Developed exclusively at private expense	Restricted Rights	Amyris, Inc.
Compositions and Methods for the Rapid Assembly of Polynucleotides, Application US 12/684,874, Patent No. US 8,110,360 (US 2010/0124768)	Developed exclusively at private expense	Restricted Rights	Amyris, Inc.
[*]	Developed exclusively at private expense	Restricted Rights	Amyris, Inc.
[*]	Developed exclusively at private expense	Restricted Rights	Amyris, Inc.
[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

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Technical Data Computer Software to be Furnished with Restrictions	Basis for Assertion	Asserted Rights Category	Name of Person Asserting Restrictions
[*]
[*]	Developed exclusively at private expense	Restricted Rights	Amyris, Inc.
[*]	Developed exclusively at private expense	Restricted Rights	Amyris, Inc.
[*]	Developed exclusively at private expense	Restricted Rights	Amyris, Inc.
[*]	Developed exclusively at private expense	Restricted Rights	Amyris, Inc.
[*]	Developed exclusively at private expense	Restricted Rights	Amyris, Inc.
[*]	Developed exclusively at private expense	Restricted Rights	Amyris, Inc.
[*]	Software suites were developed exclusively with private funding.	Limited Rights	Amyris, Inc.
[*]	Software suites were Developed exclusively with private funding	Limited Rights	Amyris, Inc.
[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

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Technical Data Computer Software to be Furnished with Restrictions	Basis for Assertion	Asserted Rights Category	Name of Person Asserting Restrictions
[*]
[*]	Amyris has generated extensive information related to the isoprenoid pathways which will be used as a benchmark to assess performance of this proposal but the underlying comparative data was developed exclusively with private funding.	Restricted Rights	Amyris, Inc.

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

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EX-10.03

CONFIDENTIAL TREATMENT REQUESTED. CERTAIN PORTIONS OF THIS DOCUMENT HAVE BEEN OMITTED PURSUANT TO A REQUEST FOR CONFIDENTIAL TREATMENT AND, WHERE APPLICABLE, HAVE BEEN MARKED WITH AN ASTERISK TO DENOTE WHERE OMISSIONS HAVE BEEN MADE. THE CONFIDENTIAL MATERIAL HAS BEEN FILED SEPARATELY WITH THE SECURITIES AND EXCHANGE COMMISSION.

SUBLEASE

THIS SUBLEASE (this “Sublease”), dated as of April 4, 2014 (the “Effective Date”), is entered into by and between AMYRIS, INC., a Delaware corporation(“Amyris”), and TOTAL NEW ENERGIES USA, INC., a Delaware corporation (“TOTAL”).

Amyris is the tenant under the Master Lease (defined below) for the Master Premises (as defined in the Master Lease). Amyris desires to sublease to TOTAL, and TOTAL desires to sublease from Amyris, certain portions of the Master Premises, on terms and conditions set forth in this Sublease.

1. DEFINITIONS.

1.1    Sublease Premises:

(a) The “Sublease Premises” means the Master Premises, except for the Amyris Dedicated Area (as defined below), as depicted on Exhibit A hereto. The Sublease Premises is comprised of two areas: (i) an area dedicated to, and accessible only by, TOTAL (the “TOTAL Dedicated Area”) and (ii) a common area that will be shared, as described in this Sublease, by TOTAL and Amyris (the “OCT Facilities”). The TOTAL Dedicated Area is comprised of approximately 3,671 rentable square feet of space, as outlined in red on Exhibit A hereto. The OCT Facilities are comprised of approximately 18,350 square feet of space, including a fermentation area, media sterilization, a warehouse (including a “cold room” located therein), restrooms, shower, waste treatment, water treatment, a clean in place system, and a dish room, all as outlined on Exhibit A hereto, and includes all of the equipment and furniture located in those areas that is used to perform such functions. All of the Sublease Premises are located on the first (1st) floor of the building located at, and commonly known as, 5850 Hollis Street, Emeryville, California 94608 (the “Building”). The “Amyris Dedicated Area” is the portion(s) of the Master Premises outlined in blue on Exhibit A hereto, which is comprised of approximately 544 rentable square feet of space. The Amyris Dedicated Area will be entirely dedicated to Amyris Employees with no access by TOTAL without the express prior written consent of the OCT Manager (as defined in the Services Agreement).

(b) On or prior to the one year anniversary of the Commencement Date (defined below), and provided that this Sublease is then in full force and effect and TOTAL is not then in Default under this Sublease, TOTAL shall have the right to notify Amyris in writing (the “Cold Room Notice”) that TOTAL requires additional cold room space. Upon receipt of the Cold Room Notice, TOTAL and Amyris shall work together, in good faith, to reconfigure a new cold room space located in the warehouse, including moving shelving, and creating a separate cold room adjacent to the current cold room located in the warehouse, provided any physical construction work to accomplish the foregoing shall be the responsibility of TOTAL at TOTAL’s sole cost and expense and such physical construction work shall be subject to, and performed in accordance with, the terms of Section 11 below. The new separate cold room shall be for the sole use of TOTAL and shall constitute part of the TOTAL Dedicated Area under this Sublease. TOTAL shall pay to Amyris , prior to commencement of any construction in connection with the separate cold room, a one-time payment of $10,000 to defray any cost to Amyris of reconfiguring the existing cold room as contemplated in this paragraph. The Base Rent payable hereunder shall not be increased in connection with the new cold room. TOTAL’s failure to timely deliver the Cold Room Notice shall be deemed TOTAL’s determination that it does not require additional cold room space.

1.2    Master Landlord: EmeryStation Triangle, LLC, a California limited liability company.

1.3    Master Lease: Lease dated as of April 25, 2008 (the “Original Lease”), as amended by a letter agreement dated April 25, 2008, a Second Amendment to Lease dated as of February 5, 2010, and a

1    

Third Amendment to Lease dated as of May 1, 2013 (the Original Lease, as so amended, is referred to herein as the “Master Lease”).

1.4    Sublease Term: The term of this Sublease (the “Sublease Term”) shall begin on the Commencement Date and shall end on the Expiration Date, unless terminated earlier in accordance with the terms and conditions of this Sublease.

1.5    Commencement Date and Delivery Date:As used in this Sublease, the “Commencement Date” shall be the latest of (i) the Effective Date, and (ii) the date Master Landlord gives its consent to this Subleaseand (iii) the date TOTAL has furnished to Amyris all certificates of insurance required under Section 9.1 below; and the “Delivery Date” shall be the date Amyris delivers the Sublease Premises to TOTAL, provided, in no event shall the Delivery Date occur prior to the Commencement Date. As used in this Sublease, “delivery of the Sublease Premises” shall mean delivery of the TOTAL Dedicated Area and access to the OCT Facilities. Notwithstanding the foregoing, pursuant to and in accordance with the terms of the Services Agreement (defined below), TOTAL shall have early access to the OCT Facilities upon the later of (i) the Commencement Date and (i) execution of an acceptable SOW (as defined in the Services Agreement) by Amyris and TOTAL, and the parties agree that such early access to the OCT Facilities prior to Amyris delivering the Sublease Premises to TOTAL shall not cause the Delivery Date to have occurred.

1.6    Expiration Date: As used in this Sublease, “Expiration Date” means the day immediately preceding the fifth (5th) anniversary of the Effective Date.

1.7    Base Rent: The annual base rent (“Base Rent”) payable by TOTAL to Amyris with respect to the Sublease Premises shall be as follows:

ANNUAL BASE RENT
2014	$104,673
2015	$108,656
2016	$112,799
2017	$117,419
2018	$121,561
2019	$	—

1.8    Move Payment. TOTAL will pay to Amyris the Move Payment (as defined in Section 7.1 below), not later than thirty (30) days following receipt of an invoice therefor, together with reasonable supporting documentation.

1.9    Permitted Use: As used in this Sublease, “Permitted Use” means general office, warehouse, laboratory and research and development, with associated administration, including but not limited to, operation and administration of a fermentation research and scale-up pilot plant, all of which is subject to the limitations on use set forth in Section 7.1 of the Master Lease.

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1.10 TOTAL’s Address:    The Sublease Premises
Attn: Denis Giorno
Email: [*]

1.11 Amyris’s Address:    5885 Hollis Street, Suite 100
Emeryville, CA 94608
Attn: Legal Department
Email: generalcounsel@amyris.com

1.12    Definitions: Each of the terms in Section 1 is used in this Sublease as a defined term and has the meaning given in such Section. Other capitalized words and phrases for which no definition or incorporated reference is given in this Sublease shall have the meanings given them in the Master Lease. Unless otherwise indicated, all section references are to the sections of this Sublease. The Sublease includes Exhibits A, B, C, D, E and F,attached hereto and incorporated herein by this reference.

2. DEMISE OF SUBLEASE PREMISES.

2.1    In consideration for Rent (as defined in Section 4.1), Amyris hereby subleases the Sublease Premises to TOTAL, and TOTAL hereby subleases the Sublease Premises from Amyris, subject to the terms and conditions of this Sublease. TOTAL shall have no right to expand or contract the Sublease Premises and no right of first refusal or offer or other expansion rights as to any other premises, other than as provided in Section 10.2 below.

2.2    TOTAL shall have no right to use or access the Amyris Dedicated Area, without the express prior written consent of Amyris, and, except as otherwise expressly provided in this Sublease, the TOTAL Dedicated Area will be entirely dedicated to use and access by TOTAL employees, contractors and guests, with no access by Amyris or any other party without the express prior written consent of TOTAL. However, in the event of an emergency, emergency staff from the Building property manager and the Amyris emergency response team, may access the TOTAL Dedicated Area as reasonably required. Amyris shall advise TOTAL in writing, prior to the Effective Date, of the identity of Amyris’s emergency response team, together with current contact information for all persons on that team, and shall advise TOTAL promptly in writing of any changes to the members of the team or their contact information. Additionally, janitorial and other maintenance personnel may enter the TOTAL Dedicated Area as needed to perform routine janitorial and maintenance functions without additional consent from, or cost to, TOTAL.

2.3    All activities performed in the OCT Facilities by either party shall be subject to the OCT Policies set forth in Pilot Plant Services Agreement executed between the parties as of the Effective Date (including the exhibits thereto, the “Services Agreement”). Prior to entering the OCT Facilities, TOTAL shall request access from the OCT Manager (as defined in the Services Agreement), which consent may be withheld only during such times as Amyris is entitled to exclusive use of the OCT Facilities pursuant to the Services Agreement. Amyris shall cause the OCT Manager to be reasonably available during normal business hours to coordinate and provide such access to TOTAL. TOTAL acknowledges that OCT Personnel (as required in the Services Agreement) are required to accompany TOTAL at all times that TOTAL is within the OCT Facilities. Further, the OCT Manager shall not permit Amyris Employees (defined in the Services Agreement) to have access to the OCT Facilities without appropriate escort by OCT Personnel. Any dispute between the parties regarding TOTAL’s right to access the OCT Facilities in accordance with the terms of this Sublease, shall be resolved by the Joint Oversight Team (as defined in the Services Agreement) and pursuant to Section 23.12.1 below. If any such dispute is ultimately submitted to arbitration, as provided in Section 23.12.1, TOTAL’s obligation to pay Base Rent shall be suspended during the period of the arbitration and, if (but only if) it is determined that TOTAL was not

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

24

entitled to access to the OCT Facilities, TOTAL shall promptly pay to Amyris an amount equal to the suspended Base Rent. If it is determined that TOTAL was entitled to access to the OCT Facilities, TOTAL shall have no obligation to pay to Amyris any portion of the suspended Base Rent.

2.4    TOTAL acknowledges that the OCT Facilities portion of the Sublease Premises are not separately demised nor subject to exclusive use by TOTAL hereunder and that the OCT Facilities are comprised of common areas and shared lab and other space that Amyris retains the right to use, jointly with TOTAL during the Sublease Term, in accordance with the terms of this Sublease. TOTAL and Amyris shall cooperate in good faith and take commercially reasonable actions to mitigate interference with the business operations of the other party arising from the lack of demising walls and use of shared space. At least thirty (30) days prior to each anniversary of the effective date of the Services Agreement, TOTAL and Amyris will agree on the projected workload and utilization of the OCT Facilities by Amyris and TOTAL for the following year. Scheduling of OCT Facilities and utilization of the OCT Facilities will be coordinated by the OCT Manager in collaboration with a single point of contact designated by TOTAL (“TOTAL BPP Coordinator”). Notwithstanding the preceding sentence, for the first year of the Services Agreement, the parties will agree on such projected workload within thirty (30) days after the Effective Date. Scheduling of Campaigns (as defined in the Services Agreement) will be mutually agreed upon by the OCT Manager and the TOTAL BPP Coordinator at least thirty (30) days prior to the beginning of each calendar quarter.

2.5    Amyris hereby grants TOTAL a non-exclusive license (the “License”) to use, together with Amyris, Amyris’s furniture, trade fixtures and equipment located in the OCT Facilities (collectively, the “Furniture and Equipment”). Amyris shall not revoke the License during the Sublease Term. Amyris covenants to keep the Furniture and Equipment in reasonably good and working condition. A list of all of the material Furniture and Equipment is set forth in Exhibit C to this Sublease; provided, the parties acknowledge that Exhibit C does not contain an exhaustive list of the Furniture and Equipment. If additional equipment is required in order to execute the Services in the OCT Facilities, the parties will jointly determine whether such new equipment is to be purchased and owned by TOTAL or Amyris (or jointly owned), as well as any use rights and limitations. If such equipment is to be owned by TOTAL, it shall be labeled as owned by TOTAL, and Amyris shall take all actions and execute those instruments reasonably requested by TOTAL to evidence such ownership. The OCT Manager and the TOTAL BPP Coordinator shall review Exhibit C during their regular quarterly meeting and shall update Exhibit C, if necessary, to reflect any new or replaced material Furniture and Equipment. Shared use of the Furniture and Equipment is considered by the parties to be an integrated right under this Sublease and shall be considered appurtenant to the Sublease Premises for all purposes, including without limitation, as contemplated in Section 365(h) of the Bankruptcy Code. There shall be no additional charge for use of the Furniture and Equipment, except that TOTAL shall be responsible for any costs and expenses to repair or replace any Furniture and Equipment damaged by TOTAL or TOTAL’s agents, employees, contractors, or invitees (not including normal wear and tear). Amyris shall have the right to grant liens on or security interests in the Furniture and Equipment, in connection with a financing and the License shall be subordinate to any such liens; provided, with respect to the Furniture and Equipment listed under the “Utilities” heading on Exhibit C (the “Utilities Equipment”), and any replacements thereof, (i) Amyris shall give TOTAL prior written notice before granting any lien on the Utilities Equipment (or any replacements thereof), which notice shall include the name and contact information of the prospective lienholder (the “Lienholder”), and TOTAL shall have the right to contact any such prospective Lienholder, (ii) the Lienholder must agree to give TOTAL notice and the right (but TOTAL shall not have any obligation) to cure any default by Amyris that would entitle the Lienholder to exercise remedies and take title to any of the Utilities Equipment, and (iii) if TOTAL does cure any such default(s) by Amyris, or replaces any Utilities Equipment that is removed by a Lienholder, or purchases any of the Utilities Equipment from a Lienholder (i.e., in lieu of, or in connection with, a foreclosure of the Lienholder’s lien on the Utilities Equipment), all costs incurred by TOTAL in so doing, may be offset by TOTAL against

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the Base Rent Installment Payment next coming due under this Sublease, and any subsequent Base Rent Installment Payments until satisfied; and further provided, with respect to the balance of the Furniture and Equipment listed on Exhibit C hereto, and any replacements thereof, Amyris shall give TOTAL prior written notice before granting any lien on such Furniture and Equipment (or any replacements thereof). Subject to the rights of Amyris to encumber the Furniture and Equipment as provided above, Amyris shall not remove the Furniture and Equipment identified on Exhibit C (or any replacements thereof) from the OCT Facility during the Sublease Term, except with advance written notice to TOTAL and unless it is promptly replaced by other Furniture and Equipment of equal or better quality and utility. If Amyris removes any Furniture and Equipment identified on Exhibit C in violation of the covenant in the immediately preceding sentence, TOTAL shall have the right to replace such removed Furniture and Equipment and all costs incurred by TOTAL in so doing may be offset by TOTAL against the Base Rent Installment Payment next coming due under this Sublease.

2.6     The OCT Facilities equipment will be accessible by each party’s respective IT network, but it will only be accessible by one party’s network at a time, which sharing requires OCT Personnel to disconnect certain OCT Facilities equipment from one party’s network and attach it to the other party’s network when, for example shifting from executing a Campaign on behalf of TOTAL to Amyris conducting work for Amyris (and vice versa). The OCT Personnel shall take all actions necessary to ensure that all data is deleted from any OCT Facilities equipment prior to attaching such equipment to the other party’s network. In the event that a party inadvertently acquires or is given access to the other party’s data residing on OCT Facilities equipment, such party shall promptly notify the other party in writing by contacting the relevant OCT Manager or TOTAL BPP Coordinator, shall not use and shall promptly destroy such data.

2.7    All SOPs (as described in the Services Agreement) applicable to the OCT Facilities equipment shall be fully and accurately documented in writing by OCT Personnel and copies will be provided to TOTAL upon request.

2.8    Amyris is responsible for (i) training OCT Personnel and TOTAL employees to applicable health safety and environmental (“HSE”) standards for the Sublease Premises, (ii) reporting any safety incidence in the Sublease Premises, (iii) maintenance of OCT Facilities’ equipment and utilities, and (iv) organizing the workload of project operation and doing a hazard and operability study, if necessary. A copy of the HSE standards are set forth in Schedule 4 to the Services Agreement. However, for purposes of confirming HSE compliance in the TOTAL Dedicated Area, or as requested by TOTAL, the parties shall employ a mutually agreed upon third party who shall determine whether TOTAL has complied with all applicable HSE standards, and shall report to Amyris such compliance (or failure) but shall not disclose any details relating to the operation or use of such area or equipment.

2.9    In the scope of operations needed for the bioprocess development, some operations conducted by TOTAL might be subcontracted to specialists having specific pieces of equipment not available in the OCT Facilities. The use of such subcontractors who access the OCT Facilities must be reviewed and approved by the OCT Manager before any subcontractor may enter the OCT Facilities. In addition, TOTAL will ensure that any such subcontractors that enter the OCT Facilities will abide by the confidentiality provisions of the Services Agreement.

3. SUBLEASE TERM AND TERMINATION.

3.1    As noted in Section 1.4, the Sublease Term shall commence on the Commencement Date and Amyris shall deliver the Sublease Premises to TOTAL on the Delivery Date. If for any reason Amyris is delayed in delivery of the Sublease Premises to TOTAL after the occurrence of the Commencement Date, Amyris shall not be liable therefor, nor shall such failure affect the validity of this Sublease or the

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obligations of TOTAL hereunder, provided, however, that TOTAL’s obligation to pay Base Rent shall be subject to daily abatement, as provided in Section 4.2 below.

3.2    Unless sooner terminated pursuant to the terms of this Sublease, including without limitation pursuant to Sections 3.4, 12 or 14, the Sublease shall end on the Expiration Date.

3.3    The Sublease may be terminated prior to the Expiration Date if the Master Lease, either with respect to the entire Master Premises or with respect to any portion of the Master Premises which includes the Sublease Premises, is terminated for any cause whatsoever (and Master Landlord does not require TOTAL to attorn).

3.4    TOTAL may terminate this Sublease at any time upon ninety (90) days’ prior written notice, provided that as a condition precedent to TOTAL’s effective exercise of this early termination right, it will pay Amyris on or prior to the effective date of termination (i) all Rent accruing hereunder for the period up to and including the effective date of such early termination and (ii) an amount equal to one additional year of Base Rent for the twelve-month period following the date of early termination (with an appropriate proration for any month at the beginning or end of such twelve-month period that falls within a Base Rent Installment Payment period).

3.5    Amyris may terminate this Sublease for a Total Default, as set forth herein.

3.6    This Sublease may be terminated per the terms of Section 12.1.

3.7    Neither TOTAL nor Amyris shall have any further rights or obligations under this Sublease upon the Expiration Date or the effective date of any earlier termination of this Sublease, except for those that expressly survive termination of this Sublease.

4. RENT.

4.1    The rent (“Rent”) payable by TOTAL for the Sublease Premises shall consist of (i) the Base Rent and (ii) the Excess Utility Charges (defined below). Unless otherwise agreed in writing by Amyris, TOTAL shall make all payments due to Amyris pursuant to this Sublease by wire transfer or ACH of immediately available funds to:

Bank: Bank of the West

Bank address: 180 Montgomery Street, San Francisco, CA 94104

Checking Account No: [*]

ABA: [*]

Swift Code: [*]

or to such other bank account as is designated in writing by Amyris from time to time. Except as encompassed within Rent, TOTAL shall have no obligation to pay rent or other charges for services, utilities, equipment usage, security or other items to Amyris, including, without limitation, any Operating Expenses or Taxes (as such terms are defined in the Master Lease).

4.2    TOTAL shall pay to Amyris in advance, and without notice, demand, deduction or offset, the applicable Base Rent each calendar year during the Sublease Term through three (3) equal installments as set forth below (each such installment payment, a “Base Rent Installment Payment”):

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

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March 1        July 1            November 1

2014 US$34,891**        US$34,891        US$34,891

2015 US$36,219        US$36,219        US$36,219

2016 US$37,600        US$37,600        US$37,600

2017 US$39,140        US$39,140        US$39,140

2018 US$40,520        US$40,520        US$40,520

2019        US$0            N/A            N/A

**The parties agree that first Base Rent Installment Payment for 2014 will be due and payable within fifteen (15) days after the Effective Date, rather than on March 1, 2014.

The third Base Rent Installment Payment (and, if necessary to utilize the entire reduction, subsequent Base Rent Installment Payments) will be reduced by $282 for each day after the later of (i) the Commencement Date, and (ii) August 1, 2014, until the Delivery Date.

4.2.1    In the event of an early termination of this Sublease for any reason other than at TOTAL’s election pursuant to Section 3.4 above or pursuant to Section 12 below, any Rent amounts paid in advance by TOTAL for a period occurring after the effective date of the termination shall be reimbursed by Amyris promptly following such termination date.

4.3    The Base Rent for each calendar year in the Sublease Team was set by the parties assuming that the charges paid by Amyris (either directly or to the Master Landlord) for electricity, natural gas and treatment of effluents (including waste water and plant steam condensate, etc.) for the Master Premises for any 12-month calendar year during the Sublease Term (the “Actual Charges”) would not be greater than the sum of US$50,000 plus the charges paid by Amyris (either directly or to the Master Landlord) for electricity, natural gas and treatment of effluents for the Master Premises for 2013 (such sum, the “Baseline Utility Charges”) due to TOTAL’s operations in the TOTAL Dedicated Area. Consequently, if, in any calendar year during the Sublease Term, the Actual Charges are greater than the Baseline Utility Charges due to TOTAL’s operations in the TOTAL Dedicated Area, then, in addition to the applicable Base Rent, TOTAL shall pay to Amyris, the amount by which the Actual Charges for that calendar year exceeded the Baseline Utility Charges (the “ExcessUtility Charges”). Payment for the Excess Utility Charges shall be made once annually by TOTAL within thirty (30) days following receipt by TOTAL of an invoice therefor, which shall include such back-up information as is necessary for TOTAL to verify that the Excess Utility Charges being invoiced are accurate. Except for the Excess Utility Charges that TOTAL is required to pay pursuant to this subsection, Base Rent shall include all of the Building services and utilities provided to Amyris under the Master Lease with respect to both the TOTAL Dedicated Area and the OCT Facilities. Amyris shall, at its sole cost, be responsible for providing TOTAL with treatment of all effluents (including waste water and plant steam condensate, etc.).

With Master Landlord’s prior written consent, TOTAL shall be entitled, at any time during the Sublease Term and at its expense, to have separate meters installed for the electricity, natural gas and treatment of effluents that is provided by Amyris to the TOTAL Dedicated Area, and, to the extent the separately metered charges show that TOTAL’s operations in the TOTAL Dedicated Area resulted in the Actual Charges for any calendar year exceeding the Baseline Utility Charges, then the Excess Utility Charges shall be that excess for such calendar year.

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Except for the Excess Utility Charges that TOTAL is required to pay pursuant to this Section, TOTAL shall have no obligation to pay utility or other charges (other than as included in the Base Rent provided for in this Sublease) for its use of the OCT Facilities under this Sublease.

4.4    If any Rent is not paid within ten (10) business days of when due, TOTAL acknowledges that Amyris will incur additional administrative expenses and costs which are difficult or economically impractical to ascertain. In addition to any late charges and interest payable under the Master Lease, TOTAL shall pay an administrative charge to Amyris equal to two percent (2%) of the delinquent amount. Neither demand for nor receipt of any late charge called for under this Sublease shall (i) operate to waive any default by TOTAL or provide a substitute for TOTAL’s full and timely performance of the obligation to pay Rent, or (ii) limit the exercise of any other right or remedy Amyris may have under this Sublease in case of TOTAL’s default

4.5    If, during the Sublease Term, Amyris shall actually receive an abatement of rent under the Master Lease as to the Sublease Premises, then TOTAL shall be entitled to receive from Amyris a proportionate share of such abatement, calculated based on the ratio that the square footage of the TOTAL Dedicated Area bears to the portion of the Master Premises to which the abatement applies, multiplied by the total amount of the abatement, and shall be applied to reduce the next Base Rent Installment Payment(s) coming due.

5.     REPRESENTATIONS AND WARRANTIES.

5.1    TOTAL represents and warrants to Amyris that: (i) TOTAL is familiar with the provisions of the Master Lease insofar as it pertains to the Sublease Premises and TOTAL’s use and occupation thereof under this Sublease; (ii) TOTAL has the right and power to execute and deliver this Sublease and to perform its obligations hereunder; (iii) the person or persons executing this Sublease for TOTAL are fully authorized to so act and no other action, other than the parties obtaining Master Landlord’s consent to this Sublease, is required to bind TOTAL to this Sublease; and (iv) TOTAL is duly organized and in good standing in its state of formation and is authorized to conduct business in the state where the Sublease Premises are located.

5.2    Amyris represents and warrants to TOTAL that, as of the Effective Date: (i) a true and complete copy of the Master Lease is attached hereto as Exhibit F; (ii) the Master Lease is in full force and effect and Amyris has not received written notice that it is in default thereunder, and Amyris is not aware of any condition or event that could ripen into a default by Amyris thereunder; (iii) to Amyris’s knowledge, the Master Landlord is not in default under the Master Lease; (iv) Amyris has the right and power to execute and deliver this Sublease and to perform its obligations hereunder; (v) the person or persons executing this Sublease for Amyris are fully authorized to so act and no other action, other than the parties obtaining Master Landlord’s consent to this Sublease, is required to bind Amyris to this Sublease; (vi) attached Exhibit C is a true and correct description of all material Furniture and Equipment that is currently located in the OCT Facilities (and as such, is not an exhaustive list); (vii) Amyris owns the Furniture and Equipment listed on Exhibit C; (viii) Amyris is duly organized and in good standing in its state of formation and is authorized to conduct business in the state where the Sublease Premises are located; (ix) Amyris has not encumbered any portion of the Master Premises leasehold, and there is no leasehold deed of trust recorded with respect to such premises; (x) and Amyris has and is in compliance in all material respects with all governmental permits, licenses, authorizations, approvals, and entitlements with respect to its use and occupancy of the Master Premises (copies of all such governmental permits, licenses, authorizations, approvals, and entitlements are attached hereto as Exhibit D).

6.     PARKING. There are no parking spaces or rights provided to TOTAL under this Sublease.

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7. POSSESSION AND USE; SIGNAGE.

7.1    As soon as reasonably practical following the Effective Date, and in any event not later than August 1, 2014, Amyris will have moved all of its personnel, furniture, equipment and personal property out of the TOTAL Dedicated Area and will deliver the TOTAL Dedicated Area to TOTAL broom clean and with all utilities which are the obligation of Amyris to maintain under the Master Lease in good working condition. Commencing on the Delivery Date (but subject to any early access rights that may be granted to TOTAL pursuant to Section 1.5 above, Amyris shall provide TOTAL with continuing access to the OCT Facilities. Time is of the essence with respect to the timing of Amyris’s move and delivery of the TOTAL Dedicated Area to TOTAL and, if the TOTAL Dedicated Area is not delivered at the time and in the condition described above in this Section 7.1, Base Rent shall be subject to daily abatement during the period of delay, as provided in Section 4.2 above. Other than as set forth in this Section, Amyris has no obligation to prepare, modify or alter the Sublease Premises, and Amyris subleases the Sublease Premises to TOTAL, and TOTAL accepts the Sublease Premises, strictly in their present “as-is” and “with all faults” condition. As provided in Section 1.8 above, TOTAL will pay to Amyris, no later than thirty (30) days following receipt of an invoice and reasonable supporting documentation evidencing such costs, an amount not to exceed $150,000, for one-half of the out-of-pocket expenses incurred by Amyris in connection with the move described above (the “Move Payment”).

7.2    The Sublease Premises shall be used and occupied by TOTAL solely for the Permitted Use. TOTAL’s use of the Sublease Premises shall comply with the relevant provisions of the Master Lease and all laws, rules, regulations, restrictions, statutes, codes, ordinances and permits of, or issued by, any municipal or governmental entity (“Laws”) applicable to its use of the Sublease Premises.

7.3    TOTAL shall have the right, during the Sublease Term, to have its logo on the door of the TOTAL Dedicated Area. Amyris, at no cost to Amyris, will cooperate with TOTAL to have such logo installed in compliance with the Master Lease.

8. SERVICES, MAINTENANCE AND REPAIR OBLIGATIONS.

8.1     Amyris grants to TOTAL the right to receive, during the Sublease Term, all of the services and benefits with respect to the Sublease Premises that are to be provided by Master Landlord under the Master Lease. If any services pertaining to the Sublease Premises are contracted for directly by Amyris, TOTAL shall also have the right to receive the benefit of those services through Amyris at no additional charge, except as otherwise expressly provided in this Sublease. Amyris shall not be required to provide any services or to perform any maintenance or repairs or work or obtain any insurance which Master Landlord is or may be required to provide or perform under the Master Lease. Amyris shall have no responsibility for or be liable to TOTAL for any default, failure or delay on the part of Master Landlord in the performance or observance by Master Landlord of any of its obligations under the Master Lease, nor shall such default by Master Landlord affect this Sublease or waive or defer the performance of any of TOTAL’s obligations under this Sublease, including without limitation the obligation to pay Rent, except to the extent a default by Master Landlord that affects the Sublease Premises results in a waiver or deferral of Amyris’s obligations under the Master Lease that are to be performed by TOTAL under this Sublease or to the extent Amyris receives an abatement of rent under the Master Lease as set forth in Section 4.5 above. TOTAL hereby expressly waives (i) the provisions of any statute, ordinance or judicial decision, now or hereafter in effect, which would give TOTAL the right to make repairs at the expense of Amyris or Master Landlord, or (ii) to claim any actual or constructive eviction by virtue of any interruption in access, services or utilities to, or any failure to make repairs in or to, the Sublease Premises or the Building, including without limitation, any rights under California Civil Code Section 1932(1) and 1931(2), 1933 (4), 1941 or 1942. Notwithstanding the foregoing, the parties do contemplate that Master Landlord will, in fact, perform its obligations under the Master Lease and in the event of any default or failure of such

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performance by Master Landlord, Amyris agrees that it will, upon notice from TOTAL, take all commercially reasonable actions necessary to cause Master Landlord to perform its obligations under the Master Lease. Amyris, however, shall have no obligation to sue Master Landlord on TOTAL’s behalf or to terminate the Master Lease as a result of any such default or failure by Master Landlord. Notwithstanding the foregoing, if Master Landlord’s default or failure to perform its obligations under the Master Lease interferes with or adversely affects TOTAL’s use of the Sublease Premises and Amyris’ efforts to enforce the Master Lease do not result in Master Landlord curing the default or failure within the time period provided to Master Landlord under the Master Lease to cure such default or failure, Amyris shall not be deemed to be in default of its obligations hereunder, but in such event TOTAL, at TOTAL’s expense, shall have the right to institute legal proceedings in Amyris’ name (i.e., by naming Amyris as the plaintiff) and Amyris shall reasonably cooperate with TOTAL, without expense to Amyris, as necessary or desirable in connection with such proceedings. TOTAL shall provide Amyris with copies of any pleadings or other documents TOTAL proposes to file in any such legal proceedings prior to filing thereof. TOTAL shall protect, indemnify, defend and hold Amyris harmless from and against all Losses (as defined in Section 9.3) arising from any legal proceeding brought by TOTAL pursuant to this Section 8.1, except to the extent caused by the gross negligence or willful misconduct of Amyris.

8.2    TOTAL shall maintain the TOTAL Dedicated Area in a clean and orderly manner and condition, and Amyris shall maintain the OCT Facilities in a clean and orderly manner and condition, in each case, to the extent that Amyris is required to maintain the Sublease Premises under the Master Lease. In addition, Amyris shall maintain the Furniture and Equipment such that it is maintained in accordance with all SOPs.

8.3    Notwithstanding anything herein or in the Master Lease to the contrary, in no event shall TOTAL be responsible for making or paying for improvements to bring the Sublease Premises into compliance with Laws, including, without limitation, disability access laws, unless (A) (i) the applicable Laws become effective after the Commencement Date, and (ii) the improvements are necessitated solely by reason of TOTAL’s unique and specific use of the TOTAL Dedicated Area (i.e., other than for the uses contemplated by Section 1.9 above); or (B) the improvements are necessitated solely by the improvements constructed by or for TOTAL, pursuant to Section 11 below; provided, however, TOTAL shall be responsible for compliance with all Laws (including disability access laws) related to TOTAL’s employees and the arrangement of any furniture, equipment or personal property in the TOTAL Dedicated Area.

8.4    TOTAL shall comply with all Hazardous Materials Laws and terms and conditions of the Master Lease (including without limitation, Section 7.1(d) thereof) with respect to any Hazardous Materials (including any Permitted Hazardous Materials) handled by TOTAL in and about the TOTAL Dedicated Area. Amyris consents to TOTAL’s Handling of the Hazardous Materials listed on Exhibit B attached hereto, subject to Master Landlord’s approval of such list. Upon Master Landlord’s approval of the items listed on Exhibit B, such items shall be deemed Permitted Hazardous Materials (as defined in the Master Lease). Notwithstanding Section 7.1(d)(5) of the Master Lease, the proviso in the third sentence of that section that imposes the burden of proof on TOTAL (i) shall only apply to the TOTAL Dedicated Area and (ii) shall not apply if the Hazardous Materials that are the subject of a Release (as defined in the Master Lease) are used by both TOTAL and Amyris. Further, the obligation to complete an environmental study, as required by Section 7.1(d)(10) of the Master Lease, shall not apply to TOTAL.

9. TOTAL’S INSURANCE AND INDEMNITY.

9.1    Throughout the Sublease Term, TOTAL shall procure and maintain, at its own cost and expense, such workers’ compensation, commercial general liability insurance and any other coverages as are required to be carried by the tenant under the Master Lease, and such property insurance as is required to be carried by the tenant under the Master Lease to the extent such property insurance pertains to the

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TOTAL Dedicated Area, all naming Amyris (and any of its designees), as well as Master Landlord any other party designated by Master Landlord, pursuant to the Master Lease, from time to time, as additional insureds and loss payees in the manner required in the Master Lease. If the Master Lease requires the tenant under the Master Lease to insure leasehold improvements or alterations, then Amyris shall continue to insure such leasehold improvements that are located in the Sublease Premises as of the Effective Date during the Sublease Term. TOTAL shall be responsible for insuring any alterations in the Sublease Premises made by TOTAL. TOTAL's and Amyris’s general liability policies shall provide cross-liability coverage for both TOTAL and Amyris (and their designees), and the coverage afforded to one must be as broad as that afforded to the party carrying such insurance. TOTAL shall furnish to Amyris certificates, in form and substance reasonably satisfactory to Amyris and Master Landlord, of TOTAL’s insurance required under this Section 9.1 on or before the Commencement Date. Within five (5) business days after any renewal (or such earlier date as may be requested pursuant to the Master Lease), TOTAL shall furnish Amyris certificates of insurance evidencing maintenance and renewal of the required coverage on form reasonably acceptable to Amyris, and a copy of the endorsement to TOTAL’s liability policy showing the additional insureds and loss payees.

9.2    Each of TOTAL and Amyris hereby waives, on behalf of itself and on behalf of its insurers, any and all rights of recovery against the other, against Master Landlord, and their respective officers, employees, agents and representatives on account of loss or damage occasioned by the waiving party or its property or the properties of others under its control caused by fire or any of the extended coverage risks described hereunder, to the extent that such loss or damage is insured under any insurance policy in force at the time of such loss or damage or required to be carried hereunder. If necessary for its effectiveness, each party shall give notice to its insurance carrier of the foregoing waiver of subrogation.

9.3    To the fullest extent permitted by Law, Amyris waives all claims against TOTAL for economic damages, damage to any property or injury or death of any person in, on or about the Amyris Dedicated Area and the OCT Facilities arising at any time or from any cause other than to the extent resulting directly from the gross negligence or willful misconduct of TOTAL. Amyris agrees to protect, defend, indemnify and hold TOTAL harmless from all liabilities, claims, losses, obligations, damages, penalties, actions, costs, liens, charges and expenses, including, without limitation, reasonable attorneys’ fees and other professional fees (if and to the extent permitted by Law) (collectively, “Losses”) which TOTAL may incur, or for which TOTAL may be liable to Master Landlord arising from (a) the use, modification or occupancy of the Amyris Dedicated Area and the OCT Facilities or anything contained therein, (b) the acts or omissions of Amyris, its employees, agents, contractors, invitees or licensees (other than TOTAL), and (c) any acts or events occurring in or about the Amyris Dedicated Area and the OCT Facilities during the Sublease Term. Amyris’s obligations to protect, defend, indemnify and hold harmless TOTAL under this subsection are in no way conditioned upon either (i) Amyris’s acts or omissions being a cause of any underlying claim, demand, action, liability, expense, loss or damage, or (ii) TOTAL being free of negligence or wrongful conduct in connection therewith; provided, however, that Amyris shall not be required to indemnify or hold TOTAL harmless to the extent it is established that TOTAL’s gross negligence or willful misconduct is the cause of any Losses. Amyris’s indemnity obligations set forth in this subsection shall survive the expiration or earlier termination of this Sublease.

9.4    To the fullest extent permitted by Law, TOTAL waives all claims against Amyris for economic damages, damage to any property or injury or death of any person in, on or about the TOTAL Dedicated Area arising at any time or from any cause other than to the extent resulting directly from the gross negligence or willful misconduct of Amyris. TOTAL agrees to protect, defend, indemnify and hold Amyris harmless from all Losses which Amyris may incur, or for which Amyris may be liable to Master Landlord, arising from (a) the use, modification or occupancy of the TOTAL Dedicated Area or anything contained therein, (b) the acts or omissions of TOTAL, its employees, agents or contractors, invitees or licensees, and (c) any acts or events occurring in or about the TOTAL Dedicated Area during the Sublease

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Term. TOTAL’s obligations to protect, defend, indemnify and hold harmless Amyris under this subsection are in no way conditioned upon either (i) TOTAL’s acts or omissions being a cause of any underlying claim, demand, action, liability, expense, loss or damage, or (ii) Amyris being free of negligence or wrongful conduct in connection therewith; provided, however, that TOTAL shall not be required to indemnify or hold Amyris harmless to the extent it is established that Amyris’s gross negligence or willful misconduct is the cause of any Losses. TOTAL’s indemnity obligations set forth in this subsection shall survive the expiration or earlier termination of this Sublease.

10. ASSIGNMENT AND SUBLETTING.

10.1    TOTAL shall have the right to assign its entire interest in this Sublease or to sublet its entire interest in the Sublease Premises in each case to an entity that controls, is controlled by or is under common control with TOTAL (a “TOTAL Affiliate”), without the consent of Amyris, provided that (i) TOTAL shall give Amyris written notice at least five (5) business days prior to the effective date of the proposed transfer and the TOTAL Affiliate shall expressly assume TOTAL’s obligations hereunder, (ii) Master Landlord has given its written consent to such transfer, and (iii), TOTAL shall not be released from its obligations under this Sublease by reason of any such assignment or subletting to a TOTAL Affiliate. The foregoing right is personal to TOTAL and to any TOTAL Affiliate that takes an assignment of TOTAL’s entire interest in this Sublease or subleases TOTAL’s entire interest in this Sublease. Except as provided above, TOTAL shall not voluntarily, involuntarily or by operation of law: (a) assign, convey or mortgage this Sublease or any interest under it; (b) allow any transfer thereof or any lien upon TOTAL’s interest by operation of law; (c) sublet the Sublease Premises or any part thereof; or (d) permit the occupancy of the Sublease Premises or any part thereof by anyone other than TOTAL.

10.2    In the event that Amyris seeks to assign its entire interest in the Master Lease during the Sublease Term to anyone other than Master Landlord or any assignee pursuant to an assignment for which Master Landlord’s consent is not required under the Master Lease, including without limitation in connection with any sale or assignment in bankruptcy, such assignment shall be expressly subject to the terms and conditions of this Sublease, and provided TOTAL is not then in Default under this Sublease, before Amyris may consummate such assignment, it shall give TOTAL written notice (the “ROFO Notice”) setting forth the material terms of such assignment, including the rent and other consideration to be paid by the assignee, and TOTAL shall have fifteen (15) business days after receipt of that notice to elect, by giving written notice to Amyris, to acquire Amyris’s interest in the Master Lease on the terms set forth in the ROFO Notice, provided in all events any such assignment to TOTAL shall be subject to Master Landlord’s consent to such assignment pursuant to and in accordance with the terms and conditions of the Master Lease. If such election by TOTAL shall not be timely made, then Amyris may conclude such assignment on terms that are not materially more favorable to the prospective assignee than those set forth in the ROFO Notice. If the terms upon which the assignment will be made change from those set forth in the ROFO Notice, in a manner that is materially more favorable to the prospective assignee, then Amyris shall give TOTAL another ROFO Notice and the provisions of this section shall again apply. The foregoing right is personal to TOTAL and any TOTAL Affiliate to which TOTAL’s entire interest in this Sublease has been assigned in accordance with Section 10.1 above.

11. ALTERATIONS.

11.1    Other than as set forth below, TOTAL shall not make any alterations in or additions to the Sublease Premises (“Alterations”) without Amyris’s prior written consent, which shall not be unreasonably withheld. If Amyris consents thereto, Amyris shall use reasonable efforts, at no material cost to Amyris, to obtain the consent of Master Landlord if such consent is required under the Master Lease. If Alterations by TOTAL are permitted or consented to, TOTAL shall comply with all of the covenants of Amyris, as Tenant, contained in the Master Lease pertaining to the installation and removal of such

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Alterations. TOTAL shall indemnify, defend and hold Amyris harmless against any and all Losses imposed on Amyris arising out of the installation and/or removal of Alterations by TOTAL. At the time consent is given, Amyris shall advise TOTAL, in writing, if removal of the Alterations will be required by Amyris at the end of the Sublease Term. Amyris shall advise TOTAL at the time of its approval of any Alterations, whether Master Landlord has notified Amyris that such Alterations constitute Required Removables under the terms of the Master Lease. Provided any such Alterations would not otherwise be Required Removables under the terms of the Master Lease, TOTAL will not be required to remove such approved Alterations at the end of the Sublease Term unless Amyris advised TOTAL at the time of giving consent that removal will be required. Amyris shall not require TOTAL to remove the Initial Alterations (defined below) at the end of the Sublease Term.

11.2    Notwithstanding Section 11.1 above, (i) TOTAL intends to construct certain improvements in the TOTAL Dedicated Area (the “Initial Alterations”), as generally described on Exhibit E hereto, and Amyris hereby approves such general description and the Initial Alterations, subject to Master Landlord’s approval of same pursuant to the terms and conditions of the Master Lease, (ii) Amyris acknowledges that there may be reasonable interference with utilities and Amyris’s ability to use the OCT Facilities and the Amyris Dedicated Area during construction of the Initial Alterations, and confirms that the indemnity in Section 11.1 shall not apply to that reasonable interference, and (iii) TOTAL agrees to use reasonable efforts to minimize interference with operations in the OCT Facilities and the Amyris Dedicated Area in connection with the construction of the Initial Alterations. Amyris acknowledges that the description of the Initial Alterations may change, and Amyris shall have reasonable rights to approve all such changes, in addition to Master Landlord’s approval of the same, to the extent required by the Master Lease. The Initial Alterations shall be constructed in accordance with Article 9 of the Master Lease. Subject to Sections 1.5 and 2.3 above, TOTAL shall have full access to, and shared use of, the OCT Facilities during the period that the Initial Alterations are being constructed.

11.3    If TOTAL performs any Alterations (including the Initial Alterations), TOTAL shall be obligated to insure all such Alterations during the Sublease Term for their full replacement cost value.

12. CASUALTY OR EMINENT DOMAIN.

12.1    In the event of a fire or other casualty affecting the Building or the Sublease Premises, or of a taking of all or a part of the Building or the Sublease Premises under the power of eminent domain, Amyris shall be entitled to exercise any right it may have to terminate the Master Lease without first obtaining the consent or approval of TOTAL, except as provided in Section 18.4 below. If the Master Lease imposes on Amyris the obligation to repair or restore the Sublease Premises, the Building, or any leasehold improvements or alterations, (i) TOTAL shall be responsible for repair or restoration of the TOTAL Dedicated Area, and any leasehold improvements or alterations within the TOTAL Dedicated Area, to the extent Amyris, as tenant under the Master Lease, is obligated under the Master Lease, and (ii) Amyris shall be responsible for repair or restoration of the OCT Facilities and the Amyris Dedicated Area, and any leasehold improvements or alterations within the OCT Facilities and the Amyris Dedicated Area. If the Master Lease is terminated by reason of a casualty or a taking, this Sublease shall terminate on the date the Master Lease terminates.

12.2     As between TOTAL and Amyris, to the extent permitted by the Master Lease, each party shall be entitled to seek an award or compensation in any condemnation proceeding, whether for a total or partial taking, for damage to its respective business, loss of goodwill, relocation costs, and the cost of any Alterations paid for by it.

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12.3    Amyris and TOTAL hereby waive and release each and all of their respective common law and statutory rights inconsistent herewith, whether now or hereafter in effect, including without limitation, Section 1265.130 of the California Code of Civil Procedure, as amended from time to time.

13. SURRENDER.

13.1    On the Expiration Date or any earlier termination of the Sublease or of TOTAL’s right to possession of the Sublease Premises, TOTAL will at once surrender and deliver up the Sublease Premises, together with all improvements thereon (other than those which TOTAL is required to remove pursuant to Section 11 above), to Amyris in substantially the same condition as when delivered to TOTAL, reasonable wear and tear, casualty, and damage by Amyris to the OCT Facilities excepted. Conditions existing because of TOTAL’s failure to perform maintenance, repairs or replacements as required of TOTAL under this Sublease shall not be deemed “reasonable wear and tear.” TOTAL shall surrender to Amyris all keys and electronic access cards to the Sublease Premises.

13.2    All Alterations in or upon the Sublease Premises made by TOTAL and not removed or required to be removed hereunder shall become a part of and shall remain upon the Sublease Premises upon such termination. If removal of any Alterations is required pursuant to Section 11 above, TOTAL shall restore the Sublease Premises to their condition prior to the making of any Alterations and repair any damage caused by such removal or restoration. If TOTAL is permitted or required to remove any Alteration or a portion thereof, and TOTAL does not complete such removal in accordance with this Section, Amyris may remove the same (and repair any damage occasioned thereby), and dispose thereof, or at its election, warehouse the same. TOTAL shall pay the costs of such removal, repair and warehousing, plus an administrative fee equal to five percent (5%) of such costs, on demand.

13.3    On or prior to the Expiration Date or any earlier termination of the Sublease or of TOTAL’s right to possession of the Sublease Premises, TOTAL shall remove TOTAL’s personal property that is not affixed to the Sublease Premises and TOTAL’s trade fixtures, and TOTAL shall repair any damage to the Sublease Premises which may result from such removal. If TOTAL does not remove TOTAL’s trade fixtures or personal property from the Sublease Premises on or before the Expiration Date or the earlier termination of the Sublease or of TOTAL’s right to possession, Amyris may, at its option, remove the same (and repair any damage occasioned thereby and restore the Sublease Premises as aforesaid) and dispose thereof or warehouse the same, and TOTAL shall pay the cost of such removal, repair, restoration or warehousing, plus as administrative fee equal to five percent (5%) of such costs, to Amyris on demand.

14. TOTAL’S DEFAULT.

14.1    Any one or more of following events shall be considered a “Default” by TOTAL:

14.1.1    TOTAL shall be adjudged an involuntary bankrupt, or a decree or order approving, as properly filed, a petition or answer filed against TOTAL asking reorganization of TOTAL under the federal bankruptcy laws as now or hereafter amended, or under the laws of any state, shall be entered, and any such decree or judgment or order shall not have been vacated or stayed or set aside within thirty (30) days from the date of the entry or granting thereof; or

14.1.2    TOTAL shall file, or admit the jurisdiction of the court and the material allegations contained in, any petition in bankruptcy, or any petition pursuant or purporting to be pursuant to the federal Bankruptcy laws now or hereafter amended, or TOTAL shall institute any proceedings for relief of TOTAL under any bankruptcy or insolvency laws or any laws relating to the relief of debtors, readjustment of indebtedness, re-organization, arrangements, composition or extension; or

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14.1.3    TOTAL fails to make any payment of Rent required to be made by TOTAL within ten (10) days of the date it is due; or

14.1.4    The occurrence of any of the following: (i) TOTAL shall make a general assignment for the benefit of creditors; (ii) TOTAL shall admit in writing to its creditors its inability to generally pay its debts as they come due; (iii) TOTAL’s interest in the Sublease Premises are levied on by any revenue officer or similar officer and such levy shall not have been removed within thirty (30) days from the date levied; or (iv) a decree or order appointing a receiver of the property of TOTAL shall be made and such decree or order shall not have been vacated, stayed or set aside within thirty (30) days from the date of entry or granting thereof; or

14.1.5    TOTAL fails to perform and comply with any of its other covenants, agreements, obligations and use restrictions contained in this Sublease (including the incorporated Master Lease provisions which are to be compiled with by TOTAL hereunder), and such failure continues for more than five (5) business days after notice thereof in writing to TOTAL; or

14.1.6    TOTAL violates the provisions of Section 10 of this Sublease; or

14.1.7    Any of the representations and warranties provided herein by TOTAL shall prove to be false or misleading in any material respect; or

14.1.8    TOTAL shall be in monetary default beyond any applicable cure period under the terms of the Services Agreement.

14.2    Upon the occurrence of any one or more Defaults by TOTAL, Amyris may exercise any remedy against, and recover such amounts from, TOTAL as Master Landlord may exercise or be entitled to for default by Tenant under the Master Lease, (including without limitation, the right to terminate this Sublease), which provisions of the Master Lease are hereby incorporated herein by reference. Without limiting the generality of the foregoing, Amyris may exercise the damage remedies available under California Civil Code Sections 1951.2 and 1951.4 or any similar or successor statute which provides that a lessor may continue a lease in effect and recover damages as they become due.

15. AMYRIS’S DEFAULT.

15.1    Any one or more of the following events shall be considered a “Default” by Amyris under this Sublease:

15.1.1    Amyris shall be adjudged an involuntary bankrupt, or a decree or order approving, as properly filed, a petition or answer filed against Amyris asking reorganization of Amyris under the federal bankruptcy laws as now or hereafter amended, or under the laws of any state, shall be entered, and any such decree or judgment or order shall not have been vacated or stayed or set aside within thirty (30) days from the date of the entry or granting thereof; or

15.1.2    Amyris shall file, or admit the jurisdiction of the court and the material allegations contained in, any petition in bankruptcy, or any petition pursuant or purporting to be pursuant to the federal Bankruptcy laws now or hereafter amended, or Amyris shall institute any proceedings for relief of Amyris under any bankruptcy or insolvency laws or any laws relating to the relief of debtors, readjustment of indebtedness, re-organization, arrangements, composition or extension; or

15.1.3    Amyris shall fail to perform and comply with any of its covenants, agreements, obligations and use restrictions contained in this Sublease (including the incorporated Master Lease provisions which are to be complied with by Amyris hereunder), and such failure continues for more than

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fifteen (15) days after notice thereof in writing to Amyris; provided the cure period in this section shall not apply to any dispute between the parties regarding TOTAL’s right to access the OCT Facilities in accordance with the terms of this Sublease, which shall be resolved as provided in Sections 2.3 and 23.12 hereof; or

15.1.4    The occurrence of any of the following: (i) Amyris shall make any assignment for the benefit of creditors; (ii) Amyris shall admit in writing to its creditors its inability to generally pay its debts as they come due; (iii) Amyris’s interest in the Master Premises are levied on by any revenue officer or similar officer and such levy shall not have been removed within thirty (30) days from the date levied; or (iv) a decree or order appointing a receiver of the property of Amyris shall be made and such decree or order shall not have been vacated, stayed or set aside within thirty (30) days from the date of entry or granting thereof; or

15.1.5    Subject to Amyris’ termination rights under this Sublease, Amyris shall fail to preserve its leasehold estate and interests in and to the Master Lease; or

15.1.6    Any of the representations and warranties provided herein by Amyris shall prove to be false or misleading in any material respect; or

15.1.7    Amyris shall fail to obtain, maintain and preserve and take all necessary action to timely renew all permits, licenses, authorizations, approvals and entitlements necessary or appropriate for it to use and occupy the Master Premises; or

15.1.8     Amyris shall be in default beyond any applicable cure period under the terms of the Services Agreement.

15.2    Upon and during the continuance of any Default by Amyris hereunder, in addition to any other rights or remedies provided for hereunder, TOTAL shall have the right to withhold Base Rent until such Default is cured, and to the extent such Default is incapable of being cured, or is not cured within fifteen (15) days of notice of such Default to Amyris, to offset the value of any damages caused by such Default against the Base Rent reserved for the balance of the Sublease Term.

16. HOLDING OVER.

16.1    TOTAL has no right to occupy the Sublease Premises or any portion thereof after the Expiration Date or after the termination of this Sublease or of TOTAL’s right to possession hereunder. In the event TOTAL or any party claiming by, through or under TOTAL holds over, Amyris may exercise any and all remedies available to it at law or in equity to recover possession of the Sublease Premises, and to recover the damages specified in Section 16.2 below by reason of such holdover. For clarity, the License terminates on the earliest of (i) the Expiration Date, or (ii) early termination of the Sublease.

16.2    Without limiting Amyris’s rights under Section 16.1, for each and every month that TOTAL or any party claiming by, through or under TOTAL remains in occupancy of all or any portion of the Sublease Premises after the Expiration Date or after the earlier termination of this Sublease or of TOTAL’s right to possession, TOTAL shall pay, in addition to the Excess Utility Charges payable hereunder, monthly rental at a rate equal to 125% of the rate of Base Rent payable by TOTAL hereunder immediately prior to the Expiration Date or earlier termination of this Sublease or of TOTAL’s right to possession; provided, however, if the Expiration Date or the date of any earlier termination of this Sublease or of TOTAL’s right to possession occurs during 2019, the rate of Base Rent payable by TOTAL hereunder immediately prior to the Expiration Date or earlier termination of this Sublease or of TOTAL’s right to possession shall be deemed to mean the rate of Base Rent payable hereunder during 2018. The

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acceptance by Amyris of any lesser sum shall be construed as payment on account and not in satisfaction of damages for such holding over. In addition to the payment of the amounts provided herein, in the event TOTAL or any party claiming by, through or under TOTAL holds over, TOTAL shall also be (i) liable to Amyris for actual damages payable by Amyris to Master Landlord by reason of such holdover, and (ii) liable to Amyris for its actual damages,including,those incurred by Amyris or payable by Amyris to Amyris’s proposed assignee or subtenant, in the event Amyris has entered into a binding agreement for the assignment of the Master Lease (including any assignment which is not subject to Section 10.2 above) or for the sublease of either the entire Master Premises or any portion of the Master Premises which includes any portion of the Sublease Premises), if TOTAL’s holdover prevents or delays Amyris from delivering the Master Premises or applicable portion thereof as required.

17. ENCUMBERING TITLE.

17.1    TOTAL shall not do any act which in any way encumbers the title of Master Landlord in and to the Building nor shall the interest or estate of Master Landlord or Amyris be in any way subject to any claim by way of lien or encumbrance, whether by operation of law or by virtue of any express or implied contract by TOTAL, or by reason of any other act or omission of TOTAL. Any claim to, or lien upon, the Sublease Premises or the Building arising from any act or omission of TOTAL shall accrue only against the estate of TOTAL and shall be subject and subordinate to the paramount title and rights of Master Landlord and Amyris.

17.2    Without limiting the generality of Section 16.1, TOTAL shall not permit the Sublease Premises or the Building to become subject to any mechanics’, laborers’ or materialmen’s lien on account of labor or material furnished to or at the request of TOTAL in connection with work of any character performed on the Sublease Premises by, or at the direction or sufferance of, TOTAL. If TOTAL fails to do so within fifteen (15) days following written notice from Amyris, Amyris may cause such liens to be released by any means it deems proper, including payment, at TOTAL’s expense and without affecting Amyris’s rights.

18. PROVISIONS REGARDING MASTER LEASE.

18.1    This Sublease and all rights of the parties hereunder are subject and subordinate to the Master Lease. The parties hereby acknowledge that it is not practical in this Sublease to enumerate all of the rights and obligations of the various parties under the Master Lease and specifically to allocate those rights and obligations in this Sublease. Accordingly, in order to afford to TOTAL the benefits of this Sublease and of those provisions of the Master Lease which by their nature are intended to benefit the party in possession of the Sublease Premises, and in order to protect Amyris against a Default by TOTAL which might cause a default by Amyris under the Master Lease, Amyris and TOTAL covenant and agree as set forth in this Section 18.

18.2    Except as herein otherwise expressly provided, and except those that by their nature or purpose are inapplicable to the subleasing of the Sublease Premises pursuant to this Sublease or are inconsistent with or modified by any of the terms, covenants or conditions of this Sublease, and except for tenant’s obligations to pay rent and all other amounts due under the Master Lease, and except to the extent applicable solely to the Amyris Dedicated Area, all of the terms and conditions contained in the Master Lease are incorporated herein by reference as terms and conditions of this Sublease. Amyris and TOTAL agree to each refrain from any act or omission that would result in a Default (as defined in the Master Lease) on the part of the tenant under the Master Lease. Except as set forth in this Section above or otherwise excluded herein, the provisions of the Master Lease are hereby expressly incorporated into this Sublease with the term “Amyris” substituted for Landlord, the term “TOTAL” substituted for Tenant, the term “Sublease” substituted for Lease and, without limiting any of Amyris’s obligations hereunder

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(including pursuant to the incorporated terms of the Master Lease) with respect to the OCT Facilities, including the maintenance thereof, the term “Sublease Premises” substituted for “Premises,” as the context requires.

18.3    Except as otherwise expressly provided in this Sublease, TOTAL shall perform all affirmative covenants and shall refrain from performing any act that is prohibited by the negative covenants of the Master Lease, where the obligation to perform or refrain from performing is by its nature imposed upon the party in possession of the TOTAL Dedicated Area. Other than covenants regarding use and restrictions on use, and other than the obligation to refrain from performing any act that is prohibited by the negative covenants of the Master Lease (all which shall be performed and observed by both Amyris and TOTAL with respect to the OCT Facilities), Amyris shall be responsible for performing all affirmative covenants of the Master Lease, where the obligation to perform is by its nature imposed upon the party in possession of the OCT Facilities. If Amyris should Default (as defined in the Master Lease) under the Master Lease, and provided such Default was not caused by TOTAL, TOTAL shall have the right, but not the obligation, to cure such Default(s) on behalf of Amyris and all costs incurred by TOTAL in so doing may be offset by TOTAL against the Base Rent Installment Payment next coming due under this Sublease, and any subsequent Base Rent Installment Payment until satisfied.

18.4    It is expressly agreed that: (a) if the Master Lease should terminate prior to the Expiration Date, Amyris shall have no liability to TOTAL except in respect of a breach of Amyris’ covenants contained herein; and (b) to the extent the Master Lease grants Amyris any discretionary right to terminate the Master Lease (either as to the entire Master Premises or as to any portion of the Master Premises which includes the Sublease Premises), whether due to casualty, condemnation, by election by Amyris or otherwise, Amyris shall be entitled to exercise or not exercise such right in its sole and absolute discretion, without liability to TOTAL; provided, however, so long as TOTAL is not then in Default under this Sublease, Amyris shall not elect to terminate the Master Lease as to the Sublease Premises under any discretionary right to terminate the Master Lease without the prior written consent of TOTAL, which consent shall not be unreasonably withheld, conditioned or delayed.

18.5    Any non-liability, release, indemnity or hold harmless provision in the Master Lease for the benefit of Master Landlord shall be deemed to apply under this Sublease and inure to the benefit of both Amyris and Master Landlord. Any non-liability, release, indemnity or hold harmless provision in the Master Lease for the benefit of Amyris, as Tenant, shall be deemed to apply under this Sublease and inure to the benefit of TOTAL. Amyris shall cooperate and use commercially reasonable efforts to ensure that TOTAL receives such benefit.

18.6    If TOTAL desires to take any action that requires the consent of Master Landlord under the terms of the Master Lease, then, notwithstanding anything to the contrary herein: (i) Amyris, independently, shall have a reasonable right of approval or disapproval; (ii) TOTAL shall not take any such action until it obtains the consent of both Amyris and Master Landlord; and (iii) TOTAL shall request that Amyris obtain Master Landlord’s consent on TOTAL’s behalf and Amyris shall use commercially reasonable efforts to obtain such consent. TOTAL shall pay all costs reasonably incurred by Amyris in seeking or procuring Master Landlord’s consent. Any approval or consent required of Amyris conclusively shall be deemed reasonably withheld if approval or consent also is required of Master Landlord, and Master Landlord fails to give Master Landlord’s approval or consent.

18.7    Amyris agrees to forward to TOTAL, (a) a copy of any notices relating to the Sublease Premises that Amyris delivers to the Master Landlord, and (b) upon receipt thereof by Amyris, (i) a copy of each notice of default received by Amyris in its capacity as tenant under the Master Lease, and (ii) a copy of each notice of default or non-payment received by Amyris from any utility or other service providers to the Master Premises. Upon the full execution of this Sublease, Amyris shall request that

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Master Landlord simultaneously forward to TOTAL, at TOTAL’s notice address provided in this Sublease, a copy of any default notices from Master Landlord to Amyris. TOTAL agrees to forward to Amyris, upon receipt thereof, copies of any notices received by TOTAL with respect to the Sublease Premises from the Master Landlord.

18.8    As between Amyris and TOTAL, in the event of a conflict between the provisions of the Master Lease and the provisions of this Sublease, the provisions of this Sublease shall control.

18.9    Amyris will perform all of the obligations of the tenant pursuant to the Master Lease, except those expressly undertaken by TOTAL pursuant to this Sublease, to the extent failure to perform the same could adversely affect the rights of TOTAL hereunder. So long as TOTAL is not in Default under this Sublease, Amyris will not consent to any amendment of the Master Lease that could adversely affects the rights of TOTAL hereunder, without the prior written consent of TOTAL, which may be given or withheld in TOTAL’s sole discretion (provided that the foregoing shall not be construed to limit or otherwise restrict Master Landlord from exercising any rights it has under the Master Lease or, except as provided in Section 18.4 above, Amyris from exercising any termination right it has under the Master Lease, including in the event of casualty, condemnation or as a result of any default by Master Landlord, without the need for consent of TOTAL).

18.10    Notwithstanding anything to the contrary contained herein, the following provisions of the Master Lease shall not apply to the benefit of TOTAL and are not, and shall not be deemed to be, incorporated by reference into this Sublease: (a) the following provisions of the Master Lease: Sections 1.1, 1.3 (but only to the extent the defined terms are used only in provisions that are otherwise not applicable to this Sublease), 2.1(b), 2.2, 2.3, 2.4, 2.5, 2.6, 2.7, 2.8, 3.1, 4.1, 4.2, 4.3, 6.6, 9.1(a)(1) (but only pertaining to Tenant’s right to undertake Decoration Work), 9.3, 11.4, 12,1, 16.3, 20.1(b) (except to the extent Amyris is required to provide to Master Landlord financial statements of TOTAL pursuant to Section 20.1(b) of the Master Lease), 25.1, 25.8, 25.10; Articles 5, 13, 14, 15, 21 and 22; Exhibits A and B; Riders 1 and 2, and Schedule 1 to Exhibit B; and all of the Lease Amendments (other than solely for the purpose of establishing the Master Premises leased under the Master Lease to the extent such Master Premises comprise part of the Sublease Premises and establishing the Expiration Date of the Master Lease). With respect to Section 8.1 of the Original Lease, all references to “Landlord” shall, for purposes of incorporation herein, mean Master Landlord and not Amyris. Notwithstanding that Section 16.3 of the Master Lease is stated not to be incorporated into this Sublease, Amyris and TOTAL agree that:

a.    to the extent any proceeds of Master Landlord’s insurance are paid to Amyris during the Sublease Term for restoration of any portion of the TOTAL Dedicated Area or the OCT Facilities, then (i) any such proceeds paid to Amyris with respect to any damage to the OCT Facilities shall be utilized for the repair and maintenance of the OCT Facilities, to the extent Amyris has the obligation to repair and maintain the OCT Facilities under this Sublease, and (ii) any such proceeds paid to Amyris with respect to any damage to the TOTAL Dedicated Area shall be paid to and utilized by TOTAL for the repair and maintenance of the TOTAL Dedicated Area in accordance with TOTAL’s obligations under this Sublease with respect to the TOTAL Dedicated Area; and

b.    to the extent any proceeds of Master Landlord’s insurance are paid for Landlord’s liability relating to matters or events occurring in the Sublease Premises during the Sublease Term, then any such proceeds shall be paid to the appropriate claimant(s) or, if the claimant(s) has already been compensated, then the proceeds shall be divided between Amyris and TOTAL in the percentages reflecting their respective liability to the claimant(s).

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19.    MASTER LANDLORD’S CONSENT. This Sublease and the obligations of the parties hereunder are expressly conditioned upon the written consent hereto by Master Landlord in a form reasonably acceptable to TOTAL and Amyris, and receipt by TOTAL of a separate agreement between Master Landlord and TOTAL, in a form acceptable to TOTAL. Amyris and TOTAL hereby agree, for the benefit of Master Landlord, that this Sublease and Master Landlord’s consent hereto shall not: (a) create privity of contract between Master Landlord and TOTAL; (b) be deemed to have amended the Master Lease in any regard (unless Master Landlord shall have expressly agreed in writing to such amendment); or (c) be construed as a waiver of Master Landlord’s right to consent to any assignment of the Master Lease by Amyris or any further subletting of the Sublease Premises, or as a waiver of Master Landlord’s right to consent to any assignment by TOTAL of this Sublease or any subletting of the Sublease Premises or any part thereof.

20. PRESERVATION OF THE LEASEHOLD ESTATE.

20.1    Amyris acknowledges that pursuant to Section 365 of the Bankruptcy Code, it is possible that a trustee in bankruptcy of the Master Landlord, its successors and assigns, or as debtor-in possession, could reject the Master Lease, in which case Amyris, as lessee, would have the election described in Bankruptcy Code Section 365(h) (the “Election”) to treat the Master Lease as terminated by such rejection, or, in the alternative, to remain in possession for the balance of the term of the Master Lease and any renewal or extension thereof that is enforceable by Amyris under applicable non-bankruptcy law. Provided TOTAL is not then in Default under this Sublease, Amyris covenants that Amyris will not suffer or permit the termination of the Master Lease by exercise of the Election or otherwise without the prior written consent of TOTAL. Amyris acknowledges that given the potential negative effect to its rights under this Sublease, TOTAL does not anticipate that it would consent to the termination of the Master Lease under such circumstances and shall not be obligated to give such consent. In order to secure the covenant made in this subsection, Amyris hereby assigns the Election to TOTAL. Amyris acknowledges and agrees that the Election is in the nature of a remedy, and to the extent made in favor of retaining Amyris’s rights under the Master Lease, Amyris shall bear all responsibility for complying with any of its obligations thereunder.

21. RIGHTS IN BANKRUPTCY.

21.1    Amyris acknowledges and agrees that this Sublease is a lease of real property as contemplated by Bankruptcy Code Section 365(h). Upon the filing of a case by or against Amyris under the Bankruptcy Code, Amyris shall continue to perform all of its obligations under this Sublease, including without limitation, by providing TOTAL with use and access (including, without limitation, access codes and keys) of the (a) OCT Facilities, and (b) Furniture and Equipment,subject to the rights of Lienholders, consistent with the provisions of this Sublease, and, in each case, without the need for any further request from TOTAL, or notice and hearing. To the extent Amyris rejects this Agreement under the Bankruptcy Code and TOTAL elects to retain its rights, (x) TOTAL shall have the full rights provided to it under Bankruptcy Code Section 365(h)(1)(A)(ii), (y) the value of any damage caused by such rejection shall include, in addition to those caused by the non-performance hereunder, the value of any damages resulting from Amyris’s rejection of the Services Agreement in such bankruptcy (including any loss to use of the Furniture and Equipment), should such agreement also be rejected, given the parties’ agreement that the services thereunder relate to Amyris’s obligations hereunder, and (z) TOTAL shall have full and complete use of and access to the OCT Facilities and the right to use the Furniture and Equipment that is then located in the OCT Facilities, without any requirement of Amyris, OCT Manager or OCT Personnel permission, cooperation or supervision (with TOTAL hereby acknowledging that some or all of the Furniture and Equipment listed on Exhibit C may not then be located in the OCT Facilities, by reason of the foreclosure of liens that Amyris is permitted to grant on the Furniture and Equipment). TOTAL will indemnify, defend and hold harmless Amyris from any Losses arising from TOTAL’s use of the OCT

24

Facilities, or any Furniture and Equipment during the Sublease Term, pursuant to subsection (z) above. The foregoing indemnity will survive the expiration or earlier termination of the Sublease Term.

21.2    Upon the filing of a case by or against Amyris under the Bankruptcy Code, TOTAL is entitled to relief from the automatic stay imposed by Bankruptcy Code Section 362, or otherwise, to allow TOTAL to exercise its rights and remedies under this Sublease, and as otherwise provided by law. Amyris unconditionally and irrevocably waives the benefit of such automatic stay and shall not, in any manner, oppose or otherwise delay any motion filed by TOTAL for relief from the automatic stay.

22. NOTICES.

22.1    All notices that may or are required to be given by either party to the other shall be in writing and shall be deemed given when received or refused if personally delivered, or if sent by United States registered or certified mail, postage prepaid, return receipt requested, or if sent by a nationally recognized overnight commercial courier service providing receipted delivery, in any such case (a) if to TOTAL, addressed to TOTAL at the address specified in Section 1.10 or at such other place as TOTAL may from time to time designate by notice in writing to Amyris or (b) if to Amyris, addressed to Amyris at the address specified in Section 1.11 or at such other place as Amyris may from time to time designate by notice in writing to TOTAL. Notices may also be given by email (and shall be deemed received if made by 5:00 p.m. Pacific time on the business day transmitted, and if after such time, then on the next business day), provided they are also given by one of the other methods permitted above. Each party agrees promptly to deliver to the other party a copy of any notice, demand, request, consent or approval received from Master Landlord.

23. MISCELLANEOUS.

23.1    Each party warrants to the other that it has had no dealings with any broker or agent in connection with this Sublease. Each party covenants to protect, defend, indemnify and hold harmless the other party from and against any and all costs (including reasonable attorneys’ fees), expense or liability for any compensation, commission and charges claimed by any broker or other agent with respect to this Sublease or the negotiation thereof on behalf of the indemnifying party.

23.2    In the event that any action or proceeding is brought by either party to enforce the terms of this Sublease, the prevailing party shall be entitled to reasonable attorneys' fees and costs.

23.3    This Sublease, including Exhibits A, B, C, D, E and F hereto, is the entire agreement between the parties regarding its subject matter and supersedes any prior oral or written agreements among them regarding the subject matter contained herein.

23.4    No waiver of any provision of this Sublease or consent to any action shall constitute a waiver of any other provision of this Sublease or consent to any other action. No waiver or consent shall constitute a continuing waiver or consent, or commit a party to provide a future waiver, unless such provision is expressly set forth in writing. Any waiver given by a party shall be void if the party requesting such waiver has not provided a full and complete disclosure of all material facts relevant to the waiver requested.

23.5    The terms of this Sublease have been negotiated by the parties hereto and the language used in this Sublease shall be deemed to be the language chosen by the parties hereto to express their mutual intent. The parties acknowledge and agree that each party and its counsel have reviewed and revised this Sublease and that no rule of construction to the effect that any ambiguities are to be resolved against the drafting party shall be employed in the interpretation of this Sublease.

24

23.6    This Sublease is subject to amendment only by a writing that makes reference to this Sublease and is signed by all parties hereto.

23.7    This Sublease may be executed in counterparts, each of which shall constitute an original, but all of which together shall constitute one and the same instrument.

23.8    In case of any default by Amyris of its obligations to TOTAL under this Sublease, TOTAL shall have no right or recourse to property or assets of any officer, member, director, employee, shareholder, or agent of Amyris to recover such loss or damage. In no event shall Amyris be liable under any legal or equitable theory of liability for any indirect, special, incidental, consequential or punitive damages, however caused and on any theory of liability, arising out of this Sublease or any other subject matter of this Sublease. In case of any default by TOTAL of its obligations under this Sublease, Amyris shall have no right or recourse to property or assets of any officer, member, director, employee, shareholder, or agent of TOTAL to recover such loss or damage. In no event shall TOTAL be liable under any legal or equitable theory of liability for any indirect, special, incidental, consequential or punitive damages, however caused and on any theory of liability, arising out of this Sublease or any other subject matter of this Sublease. Without limiting the foregoing, Amyris and TOTAL agree that, in no event, shall either party have liability to the other for any matter arising out of this Sublease, whether in the context of litigation or otherwise, in excess of one million dollars ($1,000,000) in the aggregate, other than for matters caused by the gross negligence or willful misconduct of such party.

23.9    All provisions of this Sublease that require the payment of money, performance of obligations or the delivery of property after the termination of this Sublease, or require any party to indemnify, defend or hold the other party harmless, shall survive the expiration or earlier termination of this Sublease.

23.10        Neither Amyris nor TOTAL shall record this Sublease nor any memorandum hereof without the written consent of the other and any attempt by TOTAL to do the same shall constitute an immediate and uncurable Default by TOTAL under this Sublease. All provisions of the Master Lease which require Amyris, as tenant, to submit, exhibit to, supply or provide Master Landlord with evidence, certificates, or any other matter or thing shall be deemed to require TOTAL to submit, exhibit to, supply or provide, the same to both Master Landlord and Amyris.

23.11    This Sublease shall be governed by the laws of the State of California as such laws are applied to contracts entered into and to be performed with such state, without regard to any conflict of laws provisions.

23.12     Dispute Resolution.

23.12.1     Excluding (i) actions by Amyris for unlawful detainer following a Default by TOTAL under Sections 14.1.1, 14.1.2, 14.1.3, 14.1.4 or 14.1.8, and/or actions to recover Rent due under this Sublease, whether following the termination of this Sublease, an action pursuant to Civil Code Section 1951.4 or otherwise, (ii) the rights granted to TOTAL in Section 2.5 above to offset against Base Rent the cost of replacing Furniture and Equipment or of curing defaults of Amyris under any financing arrangement with a Lienholder regarding any of the Utilities Equipment), (iii) the rights granted to TOTAL in Section 15.2 above to offset against Base Rent the value of any damages to TOTAL caused by Amyris’s Default under this Sublease, (iv) the rights granted to TOTAL in Section 18.3 above to offset against Base Rent the costs incurred by TOTAL of curing a Default (as defined in the Master Lease) by Amyris under the Master Lease, (v) the rights granted to TOTAL in Sections 4.2 and 7.1 above to daily Base Rent abatement in the event of delay in the Delivery Date, and (vi) the rights of TOTAL to receive its proportionate share of, or the benefit of, any abatement pursuant to Section 4.5 above, if there is a

24

dispute between the Amyris and TOTAL arising out of this Sublease, the Joint Oversight Team shall, upon written request by either party, review and attempt to informally resolve, as provided in Section 7(a) of the Services Agreement. If the Joint Oversight Team does not resolve such dispute to the satisfaction of both parties within five (5) business days from the date of the initial notice of a dispute to the Joint Oversight Team, the parties shall each escalate such dispute to their respective officers, who shall meet (by phone or in person within ten (10) business days from the date of the initial notice to the Joint Oversight Team and endeavor to resolve such dispute. If such Officers are unable to resolve such dispute within thirty (30) business days from the date of the initial notice to the Joint Oversight Team, the parties shall submit the problem or dispute to arbitration in accordance with Sections 7(b) and 7(c) of the Services Agreement (for purposes of Section 7(b) of the Services Agreement, the last day of such thirty (30) business day period shall be the “Arbitration Date”). If any right of TOTAL to offset or abate Base Rent under this Sublease is required to be submitted to the process described in this Section 23.12.1 and the right of TOTAL to so offset or abate Base Rent is ultimately submitted to arbitration pursuant to this Section 23.12.1, then TOTAL’s obligation to pay Base Rent shall be suspended during the period of the arbitration and, if (but only if) it is determined that TOTAL was not entitled to abate or offset against its obligation to pay Base Rent, TOTAL shall promptly pay to Amyris an amount equal to the suspended Base Rent. If it is determined that TOTAL was entitled to abate or offset against its obligation to pay Base Rent, TOTAL shall have no obligation to pay to Amyris any portion of the suspended Base Rent.

23.12.2    Any dispute referred to arbitration as provided above, shall be referred to and be finally settled in accordance with the Arbitration Rules and Procedures of JAMS then in effect, (the “Rules”), without recourse to the ordinary courts of law, by three arbitrators with substantial experience in resolving complex commercial contract disputes. Each of the parties shall nominate an arbitrator, and the two so nominated shall, once their appointment is confirmed by JAMS, nominate the third arbitrator, who shall act as Chairperson of the arbitral tribunal. If, however, the two arbitrators nominated by TOTAL and Amyris cannot agree upon a third arbitrator within thirty (30) days of their confirmation, the third arbitrator shall be chosen by JAMS in accordance with the Rules. The seat or legal place of arbitration shall be New York City (United States). The language shall to be used in the arbitral proceedings shall be English. Notwithstanding anything to the contrary, either party may seek injunctive or other forms of equitable relief at any time from any court of competent jurisdiction.

23.13    Pursuant to California Civil Code Section 1938, Amyris hereby notifies TOTAL that as of the Effective Date, Amyris has not obtained an inspection of the Sublease Premises by a "Certified Access Specialist" to determine whether the Sublease Premises meet all applicable construction-related accessibility standards under California Civil Code Section 55.53.

[SIGNATURES ON FOLLOWING PAGE]

24

IN WITNESS WHEREOF, Amyris and TOTAL have executed this Sublease, as of the Effective Date.

AMYRIS:		TOTAL:
AMYRIS, INC., a Delaware corporation		TOTAL NEW ENGERGIES USA, INC., a Delaware corporation
By:	/s/ John Melo	By:
Name:	John Melo	Name:
Its:	C.E.O.	Its:

24

IN WITNESS WHEREOF, Amyris and TOTAL have executed this Sublease, as of the Effective Date.

AMYRIS:	TOTAL:
AMYRIS, INC., a Delaware corporation	TOTAL NEW ENGERGIES USA, INC., a Delaware corporation
By:	By:	/s/ Denis Giorno
Name:	Name:	Denis Giorno
Its:	Its:	President & CEO

EXHIBIT A

DEPICTION OF SUBLEASE PREMISES

24

EXHIBIT B

LIST OF HAZARDOUS MATERIALS

Material	Health	Fire	Reactivity
[*]	X
[*]	X
[*]	X		X
[*]	X
[*]	X
[*]	X	X
[*]	X	X
[*]	X		X
[*]	X
[*]	X
[*]	X
[*]	X	X
[*]	X
[*]	X
[*]	X	X
[*]	X	X
[*]	X	X
[*]	X	X	X
[*]	X	X
[*]	X	X
[*]	X	X
[*]	X	X
[*]	X	X
[*]	X	X
[*]	X
[*]	X
[*]	X	X
[*]	X

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

B-1

EXHIBIT C

LIST OF MATERIAL FURNITURE AND EQUIPMENT

- Ferrmentation:

[*]

- Centrifugation:

[*]

- General:

[*]

- Analytical:

[*]

- Utilities :

[*]

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

C-1

[*]

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

EXHIBIT D

PERMITS, APPROVALS AND AUTHORIZATIONS

SEE FOLLOWING PAGES

D-1

EXHIBIT E

GENERAL DESCRIPTION OF INITIAL IMPROVEMENTS

This exhibit aims at defining the needs for adaptation of the TOTAL Dedicated Area to comply with TOTAL’s needs, and will be used for the Architectual design package. It is based in a conceptual study realized in 2013 with the help of TOTAL’s engineering firm Clark, Richardson & Biskup Consulting Engineers, Inc..

The requirements have been defined across the following functional areas (FA’s):

- Strain handling and storage (FA1)

- Fermentation laboratory (FA2)

- Recovery laboratory (FA3)

- Fermentation pilot (FA4)

- Recovery pilot (FA5)

- Physico-Chemical Analytics (FA6)

- Offices and general areas (FA7)

- Utilities, storage and Waste treatment (FA8)

For each Functional area, the following section will specify:

- Narrative summary of the activities to be led within the functional area

- Envisioned floor space

- List of main equipment

- list of bench / hoods

- Utilities requirements

- Specific details (modularity, access restriction, co-location with others activities, air control, security access…)

Different scenarios for TOTAL Dedicated Area configuration/implantation have been studied during the conceptual study, and Scenario 4 (as represented on figure A) has been jointly selected with Amyris. In this scenario, all the functional areas are located in place of the current following existing areas : Office area (PP-101), Conference room (PP-104), Copy area (PP-105), Break Area (PP-106), Kitchen (PP-107), Toilets and Shower (PP108 & PP-109). In addition, the toilets are relocated next to the entrance.

To accommodate this new area, Amyris will have to relocate its offices area in the warehouse, this will be handle independently by Amyris.

A proposed conceptual layout of the TOTAL Dedicated Area is given in Figure A, and a general view of the pilot is given in Figure C. The TOTAL Dedicated Area represent a total area of 3671 sf; both represented in green in the layouts. A layout of the existing condition of the premises is given in figure B, where the area to be demolished is represented in red.

This conceptual layout may evolve during the design phase realized to be done by a contracted Architectural company.

Strain handling and storage (FA1)

1.1 Narrative summary of activities

[*]

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

E-1    

[*]

1.2 Itemized Description of FA1

v Stand-alone/larger items

[*]

v Bench-top items

[*]

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

E-2

[*]

v Benches & Storage

[*]

1.3 Specifics

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

E-3

[*]

Fermentation laboratory (FA2)

2.1 Narrative summary of activities

[*]

2.2 Itemized Description of FA2

v Stand-alone/larger items

[*]

E-4

v Bench-top items

[*]

v Benches & Storage

[*]

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

E-5

2.3 Specifics

[*]

Recovery laboratory (FA3) and Physical-Chemical Analytics (FA6)

Narrative summary of activities

[*]

FA3:

[*]

FA6:

[*]

Itemized description of FA3 & FA6

v Bench-top items

[*]

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

E-6

[*]

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

E-7

[*]

v Benches, Hood & Storage

[*]

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

E-8

[*]

Specifics

[*]

Fermentation pilot (FA4)

Narrative summary of activities

[*

Itemized description of FA4

[*]

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

E-9

[*]

Specifics

[*]

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

E-10

-

[*]

Recovery pilot (FA5)

Narrative summary of activities

[*]

Itemized description of FA5

[*]

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

E-11

[*]

Specifics

[*]

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

E-12

[*}

Offices and general areas (FA7)

7.1 Narrative summary of FA7

[*]

7.2 Itemized description of FA7

[*]

7.3 Specifics

[*]

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

E-13

8. Utilities, storage and Waste treatment (FA8)

[*]

Figure A

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

E-14

Figure B

Figure C

E-15

EXHIBIT F

MASTER LEASE

(See following pages)

EX-10.04

CONFIDENTIAL TREATMENT REQUESTED. CERTAIN PORTIONS OF THIS DOCUMENT HAVE BEEN OMITTED PURSUANT TO A REQUEST FOR CONFIDENTIAL TREATMENT AND, WHERE APPLICABLE, HAVE BEEN MARKED WITH AN ASTERISK TO DENOTE WHERE OMISSIONS HAVE BEEN MADE. THE CONFIDENTIAL MATERIAL HAS BEEN FILED SEPARATELY WITH THE SECURITIES AND EXCHANGE COMMISSION.

PILOT PLANT SERVICES AGREEMENT

THIS PILOT PLANT SERVICES AGREEMENT (“Agreement”) is made and entered into as of April 4, 2014 (the “Effective Date”) by and between Amyris, Inc., having its principal place of business located at 5885 Hollis St, Suite 100, Emeryville, CA 94608 (“Amyris”), and TOTAL New Energies USA, Inc., a corporation incorporated under the laws of the state of Delaware, having its principal place of business located at 5858 Horton Street, Emeryville, CA 94608 (“TOTAL”). Amyris and TOTAL may each be referred to herein individually as a “Party” and collectively as the “Parties.”

WHEREAS, TOTAL desires to receive pilot plant scale fermentation process development services, fermentation and downstream separations scale-up services, and training for certain of its employees on the aforementioned technologies in order to support its projects in the field of industrial biotechnology.

WHEREAS, Amyris has a fermentation pilot plant facility (the “Pilot Plant”) and personnel with fermentation and downstream separations scale-up expertise and agrees to provide certain fermentation and downstream separations scale-up services and training to TOTAL as outlined below; and

WHEREAS, Amyris has agreed to allow TOTAL to occupy certain portions of the Pilot Plant pursuant to that certain Sublease, entered into as of even date herewith, between Amyris and TOTAL (the “Sublease”);

NOW, THEREFORE, in consideration of the foregoing promises and the mutual covenants contained herein, the Parties agree as follows:

1. Services and Joint Oversight Team.

(a)Amyris agrees to perform the fermentation and downstream separations scale-up activities and training at the Pilot Plant for TOTAL as set forth on Exhibit A hereto (the “Services”), which exhibit is incorporated herein by reference. The Services and other terms and conditions set forth in Exhibit A may be supplemented and/or amended from time to time upon the execution of a revised Exhibit, signed by both Parties. Such revised Exhibit shall be subject to all the terms and conditions of this Agreement.

(b)At all times during the Term, TOTAL and Amyris shall each designate and maintain two (2) individuals to constitute a “Joint Oversight Team” for all Services to be performed under this Agreement. The Joint Oversight Team shall review from time to time the overall progress of the Services and shall, upon request by either Party, review and attempt to informally resolve, as provided in Section 7(a) of the Agreement, any problems or disputes that may arise pertaining to such Services. At the Effective Date, TOTAL’s representatives shall be its Head of Biotech, R&D and its Head of the Biotechnology Department, Technology, Operations & Projects Division, and Amyris’s representatives shall be its President of Research and Development and its Director of Fermentation. TOTAL and Amyris may each change the persons it designates to serve as its representative

GDSVF&H\1814591    Page 1 of 46     CONFIDENTIAL

on the Joint Oversight Team at any time and from time-to-time during the Term at its discretion.

2.Service Fees and Expenses; Recordkeeping and Inspection.

(a)Payment for Services. The annual fee payable by TOTAL to Amyris for all Services within a calendar year is $ 895,327 (each year’s fee being the applicable “Annual Fee” for such year). This Annual Fee will include the total cost of the Services, including, without limitation, all costs associated with staff, lab equipment, leasehold improvements, nutrients, sugar, materials, chemicals, consumables and other items required to perform the Services.

(b)No Adjustments. The Annual Fee is fixed as provided above and is not subject to adjustment.

(c)Payment Terms. The Annual Fee is due in three (3) equal installments payable on March 1, July 1 and November 1 of each year during the Term. The Parties agree that first Annual Fee payment for 2014 will be due and payable within fifteen (15) days after the Effective Date, rather than on March 1, 2014 (and Amyris shall generate and submit to TOTAL an electronic invoice on the Effective Date for such amount). After the first Annual Fee payment, and for all subsequent payment, Amyris shall generate an electronic invoice to be submitted to TOTAL thirty (30) days prior to the each installment due date. Each installment will be paid in U.S. Dollars by wire transfer in immediately available funds to an account designated in writing in advance by Amyris.

(d)Reports. Amyris shall create and maintain complete and accurate records, and raw data files in accordance with Amyris’s standard record keeping policies, which fully and properly reflect all Services performed by it and the results thereof, including, but not limited to, the time and date equipment in the OCT Facilities is utilized to conduct each Campaign, the amount of time expended by each OCT Personnel to perform each of the Services (including, without limitation, the time expended on each step of each Campaign) (the “Records”). The Records shall include, without limitation, appropriate detail for intellectual property and regulatory purposes and such information, data and materials as are required to be maintained pursuant to any applicable law, ordinance, rule, regulation or guideline and Exhibit A.

(e)Recordkeeping. All Records shall be kept separately from documentation, records, and materials associated with other Amyris activities. Amyris shall maintain the Records for one (1) year after expiration or earlier termination of the Agreement or such other longer amount of time as is required by any law, ordinance, rule, regulation or guideline applicable with respect to the Services. Prior to destroying any Records, Amyris shall give TOTAL at least sixty (60) days’ prior written notice of Amyris’s intention to destroy such Records and include with such notice a summary of such Records proposed to be destroyed containing sufficient detail for TOTAL to determine the content of such Records. Upon TOTAL’s written request, and at TOTAL’s expense, Amyris shall deliver to

GDSVF&H\1814591    Page 2 of 46     CONFIDENTIAL

TOTAL all original Records, or if requested by TOTAL, certified or authenticated complete legible copies of such Records.

(f)Records Access. Access to all Records, for inspection and copying, shall be made available by Amyris to TOTAL and/or TOTAL’s designees at any time during normal business hours at Amyris’s Emeryville offices upon five (5) business days’ prior notice.

(g)To the extent that an item in the Records relates exclusively to a Service, such item shall not be used by Amyris for any purpose other than performing the Services or as otherwise expressly required by this Agreement, and shall be deemed TOTAL Confidential Information (as defined below).

3.Confidentiality.

(a)Definition. “Confidential Information” means the information and material that either Amyris or TOTAL or their respective Affiliates (in such disclosing capacity, the “Disclosing Party”)has disclosed or may disclose per this Agreement to the other Party or its Affiliates (the “Receiving Party”) relating to the Disclosing Party’s business, including without limitation trade secrets, processes, formulae, data and know-how, improvements, inventions, chemical or biological materials, techniques, standard operating procedures (“SOP”), methods for making compounds, target compounds, product development plans, marketing plans, strategies, customer lists, or other information that has been created, discovered, or developed by the Disclosing Party, or has otherwise become known or provided to the Disclosing Party, or which proper rights have been assigned to the Disclosing Party, as well as any other information and materials that are deemed confidential or proprietary to or by the Disclosing Party (which may include, without limitation, information and materials of the Disclosing Party’s customers and consultants and other third parties). For clarity, all information disclosed, whether in oral, written, graphic or electronic form, pursuant to an SOW (as defined in Exhibit A) shall be considered Confidential Information of TOTAL and all other information will be considered Confidential Information of the Disclosing Party if the Disclosing Party has provided a non-confidential summary (which may be written or oral) of the items proposed to be disclosed between the Disclosing Party and the Receiving Party and the Receiving Party has agreed to accept such information and such acceptance is reflected by the parties in writing. However, SOPs pertaining to the operation of equipment in the OCT Facilities (as defined in the Sublease) shall not be deemed as Confidential Information of either Party. For purposes of this Agreement, an “Affiliate” of a Party means an entity directly or indirectly controlling, controlled by or under common control with that Party where controlling, controlled or control means the ownership or control, directly or indirectly, of at least fifty percent (50%) (or the maximum ownership or control permitted under applicable law, if lower) of all of the voting power of the shares (or other securities or rights) entitled to vote for the election of directors or other governing authority, as of the date of this Agreement or hereafter during the Term; provided that such entity shall be considered an Affiliate only for the time during which such control exists.

(b)Use. Except with the prior written consent of the Disclosing Party or as

GDSVF&H\1814591    Page 3 of 46     CONFIDENTIAL

contemplated by this Agreement, each Receiving Party agrees to:

(i)protect, maintain in confidence any and all Confidential Information of the Disclosing Party, including any information derived therefrom;

(ii)not to disassemble, reverse engineer, decompile, reproduced or distributed in whole or in part any Confidential Information of the Disclosing Party;

(iii)only disclose the Confidential Information of the Disclosing Party to each Affiliate, employee, officer, director, consultant or agent of the Receiving Party who has a legitimate “need to know” and who is bound by written agreements with the Receiving Party to restrictions substantially similar to the restrictions herein. For the avoidance of doubt, Amyris shall not disclose any TOTAL Confidential Information to anyone except (1) OCT Personnel, (2) Amyris’ members of the Joint Oversight Team and/or officers as needed to resolve disputes pursuant to Section 7(a) below, (3) members of Amyris’ legal department or outside counsel, or (4) as required by applicable law or regulation, without the express prior written consent of TOTAL;

(iv)take all reasonable precautions to prevent disclosure to, and use by, any person or entity of any Confidential Information of the Disclosing Party;

(v)not to make use of the Confidential Information of the Disclosing Party except in performance of its obligations or executing its rights hereunder;

(vi)notify the Disclosing Party, promptly and in writing, of any actual or suspected misappropriation or unauthorized use or disclosure of the Confidential Information that may come to the Receiving Party’s attention; and

(vii)notify the Disclosing Party in the event that the Pilot Plant Manager or TOTAL BPP Coordinator, as the case may be, has authorized disclosure of the Disclosing Party’s Confidential Information as set forth in Schedules 1 or 1A, as applicable.

(c)Exceptions. The Disclosing Party agrees that the restrictions set forth in this Section 3 above shall not apply with respect to any information that the Receiving Party can document (i) is or (through no improper action or inaction by the Receiving Party or any Affiliate, agent, consultant or employee) becomes generally available or known to the public, (ii) was rightfully in its possession or known by it prior to receipt from the Disclosing Party, (iii) was rightfully disclosed to it by a third party having no obligation of confidentiality, or (iv) was independently developed without use of any Confidential Information of the Disclosing Party. The Receiving Party may make disclosures of Confidential Information that are required by court order or applicable law provided the Receiving Party promptly notifies the Disclosing Party of any such request, demand, or requirement for disclosure and uses diligent efforts to limit disclosure and to obtain, if applicable, confidential treatment or a protective order and has allowed the Disclosing Party to participate in the proceeding. Notwithstanding the foregoing, all Confidential Information designated as owned by or assigned to TOTAL in connection with this

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Agreement shall be deemed Confidential Information of TOTAL disclosed by TOTAL to Amyris and exceptions (ii) and (iv) above will not be applicable thereto.

(d)Return of Materials. Except as otherwise provided herein, immediately upon a written request by the Disclosing Party at any time, the Receiving Party will turn over to the Disclosing Party all Confidential Information of the Disclosing Party and all documents or media containing any such Confidential Information and any and all copies or extracts thereof. Notwithstanding this Section 3(d), nothing herein shall prevent either Party from retaining copies of Confidential Information of the Disclosing Party as necessary to comply with applicable law and regulation, provided that such copies shall only be accessed by members of the Receiving Party’s legal counsel and internal finance group, and for no other use.

(e)Remedies. The Parties acknowledge that their obligations under this Section 3 are necessary and reasonable to protect the Confidential Information and expressly agree that monetary damages would be inadequate to compensate the Disclosing Party for the breach of any of the terms and conditions of this Section 3. In addition to any other remedies that may be available, in law, in equity, or otherwise, the Disclosing Party is entitled to seek appropriate equitable relief as set forth in Section 7 below.

4.Intellectual Property.

(a)Existing Intellectual Property. Each Party will retain all of its right, title and interest in and to its own intellectual property in existence prior to the Effective Date.

(b)Inventions. “Inventions” shall mean any and all inventions, discoveries, data and information, whether or not copyrightable or patentable, conceived, reduced to practice, made, observed or developed by a Party or its Affiliates, together with all intellectual property, industrial or other proprietary rights related thereto.

(c)Ownership of Work Product Inventions. All Inventions arising or developed pursuant to the performance of Services under an SOW that comprise improvements or modifications to either equipment or operating procedures for such equipment or sample preparations for farnesene that are owned, controlled or licensed by Amyris and used by Amyris in the performance of the Services under an SOW shall be exclusively owned by Amyris (“Amyris Inventions”); provided, that Amyris hereby grants TOTAL a nonexclusive, irrevocable, perpetual, non-transferable, royalty-free license to exploit and exercise all such Amyris Inventions in support of TOTAL’s exercise or exploitation of the TOTAL Inventions (including any modifications, improvements and derivatives of any of them). If Amyris rejects this Agreement under the Bankruptcy Code and TOTAL elects to retain its rights, (x) the waivers under Bankruptcy Code Section 365(n)(2)(C) shall apply only to rights of setoff and administrative claims arising solely out of this Section 4(c), and not to any other rights under this Agreement, or any other agreements or instruments; and (z) Amyris shall, without need for notice or hearing, provide to TOTAL a copy of any intellectual property (including any embodiments) held by Amyris or its Affiliates comprising the Amyris Inventions to enable Total to exercise its non-exclusive license in and to the Amyris

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Inventions, and shall not interfere with the rights of TOTAL to such intellectual property (including any embodiments) including any right to obtain such intellectual property (and embodiments) from any Affiliate. Except as provided in Section 4(d) below, all other Inventions arising or developed pursuant to the performance of Services under an SOW shall be exclusively owned by TOTAL (“TOTAL Inventions”). Amyris shall (and shall cause each of its Affiliates and each of their respective representatives, employees or agents) to assign, and hereby does assign to TOTAL (or an entity designated by TOTAL in writing), all rights, title and interest in and to such TOTAL Inventions.

(d)Ownership under the Biofene Program. Notwithstanding Section 4(c), all Inventions arising or developed pursuant to the performance of Services under a SOW for Campaigns to be operated pursuant to the Technology License, Development, Research and Collaboration Agreement, dated June 21, 2010 as amended by that a certain first Amendment dated as of November 23, 2011 and by a certain second amendment to the Technology, License, Development, Research and Collaboration dated as of July 30, 2012 the Second Amendment, by and between Amyris and TOTAL Energies Nouvelles Activités USA, SAS (the “Collaboration Agreement”) shall be governed by the terms of the Collaboration Agreement.

(e)No Rights Granted. Neither Party, pursuant to this Agreement, either expressly or by implication, grants to the other Party any type of rights or licenses to use any of its intellectual property (including its Confidential Information and Inventions) other than as set forth in this Agreement.

5.Indemnification and Insurance.

(a)TOTAL agrees to indemnify and hold harmless Amyris from any and all liability, loss (including attorneys’ fees), or damage they may suffer as the result of claims, demands, costs, or judgments against them (collectively, “Damages”) to the extent arising out of (i) any actions or omissions of TOTAL or its subcontractors with respect to the performance of the Services, (ii) gross negligence or willful misconduct on the part of TOTAL or its subcontractors with respect to the performance of the Services, (iii) actual or alleged infringement or misappropriation of a third party’s intellectual property through use of material (including cells and strains) provided by or on behalf of TOTAL or its Affiliates to Amyris for use in the Services, or (iv) a breach of any applicable federal, state or local law by TOTAL or its subcontractors.

(b) Amyris agrees to indemnify and hold harmless TOTAL from any and all Damages to the extent arising out of any (i) actions or omissions of Amyris or its subcontractors with respect to the performance of the Services, (ii) gross negligence or willful misconduct on the part of Amyris or its subcontractors with respect to the performance of the Services or (iii) a breach of any applicable federal, state or local law by Amyris or its subcontractors.

(c)For the avoidance of doubt, this Section does not cover or address any liability that could be an indemnifiable claim under the Sublease.

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(d)Each Party’s agreement to indemnify and hold the other harmless is conditioned on the indemnified Party (i) providing written notice to the indemnifying Party of any claim, demand or action (“Claim”) arising out of the indemnified activities within thirty (30) days after the indemnified Party has knowledge of such Claim; (ii) permitting the indemnifying Party to assume full responsibility to investigate, prepare for and defend against any such Claim; (iii) assisting the indemnifying Party, at the indemnifying Party’s reasonable expense, in the investigation of, preparation for and defense of any such Claim; and (iv) not compromising or settling such Claim without the indemnifying Party’s written consent. The indemnifying Party shall not settle a Claim in any manner that admits fault on behalf of the indemnified Party or imposes injunctive relief on the indemnified Party without such Party’s prior written consent.

(e)Each of TOTAL and Amyris shall maintain the following insurance coverage provided by an admitted insurer with an AM Best rating of A and a financial size rating of VII or greater:

(i)Workers’ Compensation insurance including Occupational Disease coverage in accordance with the laws of the federal, state and local governments having jurisdiction(s) over Emeryville, CA and Employers’ Liability Insurance (including Borrowed Servant and Voluntary Compensation) with a limit of not less than $1,000,000 for each accident;

(ii)Commercial General Liability Insurance with a combined single limit of $1,000,000 per occurrence and shall include, but not be limited to, coverage for death, bodily injury and property damage, and products-completed operations coverage applicable to bodily injury, sickness or death and for loss of or damage to property;

(iii)Automobile Liability Coverage for owned, non-owned, hired and all other vehicles used by Company, its employees and agents with a combined single limit of $1,000,000 applicable to bodily injury, sickness or death of any person, or loss of or damage to property for any one occurrence;

(iv)Umbrella liability insurance with a limit of $5,000,000 per occurrence providing liability insurance excess of the coverages listed above; and

(v)All policies shall provide a waiver of subrogation in favor of the other Party. The Commercial General Liability policy shall name the other Party as additional insured solely for the liabilities assumed in this agreement. Each Party shall be notified of material change or cancellation of insurance according to the policy provisions. Upon request, the Parties shall provide certificates of insurance evidencing compliance with this agreement.

6.Term and Termination.

(a)This Agreement will commence on the Effective Date and will continue for a five (5) year period or the earlier date of termination as provided below (the “Term”).

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(b)TOTAL may terminate this Agreement for convenience at any time upon ninety (90) days’ prior written notice, provided that TOTAL will, as Amyris’s sole and exclusive remedy, the effective date upon of such termination, pay Amyris (i) any fee(s) due under Exhibit A for the Services provided up to and including the effectivedate of notification of such termination, and (ii) an additional payment equal to the amount due for the Annual Fee for the next year of Services.

(c)In addition to any other rights or remedies it may have, TOTAL may terminate this Agreement upon sixty (60) days’ written notice (i) if Amyris materially breaches any of the terms or conditions of this Agreement, and such breach is not cured within such sixty (60) day period, or (ii) upon the occurrence of any event that is a “Default” under Sections 15.1.1, 15.1.2, 15.1.3 (but only if a default under that subsection results in a termination of the Sublease), 15.1.4, 15.1.5, and 15.1.7 of the Sublease.

(d)Amyris may terminate this Agreement (i) upon forty five (45) days’ written notice if TOTAL fails to pay any undisputed invoice when due, and such invoice is not paid within such forty five (45) day period, or (ii) upon sixty (60) days’ written notice if TOTAL materially breaches Section 3 or 5(a) of this Agreement, and such breach is not cured within such sixty (60) day period.

(e)Sections 3, 4, 5, 7, 6(e), 8 and 9 shall survive any termination or expiration of this Agreement in accordance with their respective terms.

7.Dispute Resolution.

(a)If there is a dispute between the Parties arising out of or in connection with this Agreement, including, but not limited to, any actual or alleged breach of the Agreement the OCT Manager and the TOTAL BPP Coordinator will negotiate in good faith to resolve it amicably within five (5) business days. If no solution is found by such date, either Party may give written notice of such dispute to the Joint Oversight Team, and the Joint Oversight Team shall then negotiate in good faith to resolve the dispute. If the Joint Oversight Team does not resolve such dispute to the satisfaction of both Parties within five (5) business days from the date of the initial notice of a dispute to the Joint Oversight Team, the Parties shall each escalate such dispute to their respective officers, who shall meet by phone or in person within ten (10) business days from the date of the initial notice to the Joint Oversight Team and endeavor to resolve such dispute. If (and only if) the respective officers are unable to resolve such dispute, and such dispute is not related to an actual or alleged breach by TOTAL, TOTAL shall be entitled to suspend payment of any amounts that may become due hereunder until such dispute is resolved to the mutual satisfaction of the Parties

(b)In the event that any such dispute between the Parties about a breach or alleged breach of this Agreement cannot be resolved pursuant to the process described in Section 7(a) within a period of sixty (60) days after the initial notice to the Joint Oversight Team (the last day of such sixty (60) day period being herein referred to as the “Arbitration Date”), such dispute shall be referred to and be finally settled in accordance with the Rules

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and Procedures of JAMS then in effect (the “Rules”), without recourse to the ordinary courts of law, by three arbitrators with substantial experience in resolving complex commercial contract disputes. Each of the Parties shall nominate an arbitrator, and the two so nominated shall, once their appointment is confirmed by JAMS, nominate the third arbitrator, who shall act as Chairperson of the arbitral tribunal. If, however, the two arbitrators nominated by TOTAL and Amyris cannot agree upon a third arbitrator within thirty (30) days of their confirmation, the third arbitrator shall be chosen by JAMS in accordance with the Rules. The seat or legal place of arbitration shall be New York City (United States). The language shall to be used in the arbitral proceedings shall be English. For clarity, disputes arising pursuant to the Services shall initially be addressed by the dispute resolution section in Exhibit A. In the event a dispute regarding the Services cannot be resolved by mutual agreement of the Parties under the Joint Oversight Team section in Exhibit A, then this provision will govern. Notwithstanding anything to the contrary, either Party may seek injunctive or other forms of equitable relief without the necessity of proving actual damages at any time from any court of competent jurisdiction.

(c)The Parties intend that these provisions will be valid, binding, enforceable, and irrevocable and will survive any termination of this Agreement and shall be the sole and exclusive set of procedures for the resolution of any dispute between the Parties arising out of or in connection with this Agreement.

8.Representations, Warranties and Covenants.

(a)Amyris represents, warrants and covenants that:

(i)the Services will be performed in a professional and workmanlike manner and in full compliance with all applicable laws and regulations, Exhibit A and the applicable SOW;

(ii) none of the Services or any part of this Agreement is or will be inconsistent with any obligation Amyris may have to others; all work under this Agreement shall be performed by OCT Personnel, and to the best of Amyris’s knowledge, such work will not infringe or misappropriate any intellectual property rights of Amyris, any of its Affiliates nor any third party; Amyris has the full right to provide TOTAL with the assignments and rights provided for herein; and

(i)in performing the Services, Amyris will not, without TOTAL’s prior written consent, disclose to TOTAL or use for its benefit any trade secret or proprietary or confidential information of any third party.

(b)Each Party represents and warrants to the other that: (i) it is duly organized, validly existing and in good standing under the laws of its jurisdiction of incorporation or formation, and has all requisite corporate power and authority to enter into this Agreement and to carry out the provisions hereof; (ii) it is duly authorized to execute and deliver this Agreement and to perform its obligations hereunder, and the person or persons executing this Agreement on its behalf has been duly authorized to do so by all requisite corporate or partnership action; (iii) this Agreement is legally binding upon it, enforceable against it in

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accordance with its terms, except as enforcement may be limited or affected by applicable bankruptcy, insolvency, moratorium, reorganization or other laws of general application relating to or affecting creditors' rights generally in accordance with its terms; and (iv) execution of this Agreement does not conflict with any agreement, instrument or understanding, oral or written, to which it is a Party or by which it may be bound, nor violate any material law or regulation of any court, governmental body or administrative or other agency having jurisdiction over it.

(c)Each Party understands and agrees that except as expressly provided herein, the Services, training and any materials provided hereunder are provided AS IS WITHOUT REPRESENTATION OR WARRANTY, INCLUDING WARRANTY OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE OR ANY OTHER WARRANTY, EXPRESS OR IMPLIED.

(d)EXCEPT FOR VIOLATIONS OF SECTION 3, IN NO EVENT WILL EITHER PARTY BE LIABLE UNDER ANY LEGAL OR EQUITABLE THEORY OF LIABILITY FOR ANY INDIRECT, SPECIAL, INCIDENTAL, CONSEQUENTIAL OR PUNITIVE DAMAGES, HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, ARISING OUT OF THE SERVICES OR ANY OTHER SUBJECT MATTER OF THIS AGREEMENT.

(e) EXCEPT FOR VIOLATIONS OF SECTION 3, IN NO EVENT WILL EITHER PARTY BE LIABLE UNDER ANY LEGAL OR EQUITABLE THEORY OF LIABILITY FOR ANY DIRECT DAMAGES, HOWEVER CAUSED, ARISING OUT OF THE SERVICES OR ANY OTHER SUBJECT MATTER OF THIS AGREEMENT IN EXCESS OF AMOUNT EQUAL TO THE MAXIMUM ANNUAL FEE PAID FOR ANY CALENDAR YEAR UNDER THIS AGREEMENT.

9.General Provisions.

(a)The Parties will perform their obligations under this Agreement as independent contractors and nothing contained in this Agreement will be construed to be inconsistent with such relationship or status. This Agreement will not constitute, create or in any way be interpreted as an employment or agency relationship or a joint venture or partnership of any kind.

(b)This Agreement will be governed by the laws of the State of New York, as such laws are applied to contracts entered into and to be performed within such state, without regard to any conflicts of laws provisions.

(c)This Agreement, including Exhibit A and any SOWs executed thereunder, are intended by the Parties to be one, integrated non-severable set of transactions, and set forth the entire agreement and understanding between Amyris and TOTAL relating to the subject matter herein and therein, and supersedes all prior discussions between the Parties. In the event of a conflict between or among this Agreement, Exhibit A, an SOW and any other schedule or Exhibit, the following order of precedence shall govern: Exhibit A, this Agreement, an SOW, and, if any, all other Exhibits and Schedules. No modification of or amendment to this Agreement, Exhibit A or any SOW, nor any waiver of any rights

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hereunder or thereunder will be effective unless executed in writing and signed by both Parties.

(d)All notices required or given herewith shall be addressed to Amyris or TOTAL at the designated addresses shown below by registered mail, special delivery, or by certified courier service:

If to TOTAL: TOTAL New Energies USA, Inc. 5858 Horton Street Emeryville, CA, 94608 Attn: Chief Executive Officer Email: ____________________________ If to Amyris: Amyris, Inc. 5885 Hollis St, Suite 100 Emeryville, CA 94608 Attn: Legal Department Email: generalcounsel@amyris.com

(e)The headings used in this Agreement are for the convenience of the Parties and for reference purposes only and shall not form a part or affect the interpretation of this Agreement.

(f)If one or more of the provisions in this Agreement are deemed void by law, then the remaining provisions will continue in full force and effect.

(g)Neither this Agreement nor any right or obligation hereunder or interest herein may be assigned, delegated, or transferred by either Party by operation of law or otherwise without the express prior written consent of an officer of the other Party, provided, however, that (i) either Party may assign this Agreement upon written notice to the other Party to the purchaser of its entire business, and (ii) TOTAL may assign or transfer this Agreement to any Affiliate. This Agreement will be binding upon the assignor’s heirs, executors, administrators and other legal representatives.

(h)If any action at law or in equity is necessary to enforce or interpret the terms of this Agreement, the prevailing Party shall be entitled to reasonable attorneys’ fees, costs, and necessary disbursements, in addition to any other relief to which the Party may be entitled.

(i)Amyris is committed to the provisions outlined in the Equal Opportunity Clauses of Executive Order 11246, (41 CFR 60-1.4), section 503 of the Rehabilitation Act of 1973, (41 CFR 60-741.5(a)), section 402 of the Vietnam Era Veterans Readjustment Act of 1974, (41 CFR 60-250.5(a)), and, the Jobs for Veterans Act of 2003, (41 CFR 60-300.5(a)) as well as any other regulations pertaining to these orders.

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IN WITNESS WHEREOF, and intending to be bound by the provisions hereof, the Parties hereto have caused this Agreement to be executed personally or by their duly authorized representatives, to be effective as of the Effective Date.

AMYRIS, INC.	TOTAL NEW ENERGIES USA, INC.
Signature: /s/ John Melo _______________	Signature:_________________________
By: John Melo__________________	By:___________________________________                (print name)
Title: C.E.O.___________________	Title:__________________________________

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IN WITNESS WHEREOF, and intending to be bound by the provisions hereof, the Parties hereto have caused this Agreement to be executed personally or by their duly authorized representatives, to be effective as of the Effective Date.

AMYRIS, INC.	TOTAL NEW ENERGIES USA, INC.
Signature:______________________________	Signature:/s/ Denis Giorno
By:___________________________________	By: Denis Giorno                (print name)
Title: ____________________________	Title: President and CEO

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EXHIBIT A

I.OVERVIEW

Pursuant to Section 1 of the Agreement, this Exhibit A describes and sets forth the terms and conditions under which Amyris shall perform certain Services for TOTAL as described below and as requested by TOTAL. All capitalized terms used herein and not otherwise defined shall have the meaning set forth in the Agreement. For purpose of this Exhibit A, the “OCT Facilities” shall have the meaning given to it in the Sublease.

II.OPERATING CORE TEAM (OCT) – MANAGEMENT OF THE OCT FACILITIES

a)OCT Personnel. Amyris will designate at least six (6) Amyris employees who will be exclusively authorized to operate the OCT Facility and perform all Services hereunder, including executing the Campaigns (as defined below) (the “OCT Personnel”). Amyris will endeavor to staff the OCT Facility with at least ten (10) OCT Personnel during the term of the Agreement. Amyris shall ensure that the OCT Personnel are qualified to use all equipment and tools in the OCT Facilities required for the performance of the Services. Throughout this Exhibit A, the term “Amyris Employees” means any and all employees of Amyris that are not OCT Personnel. Amyris will maintain a list of the names of all OCT Personnel which can be reviewed by TOTAL on an as-needed basis upon reasonable request. Amyris will notify TOTAL when it actually replaces an OCT Personnel, identifying the individual to be replaced and the replacement.

b)OCT Policies. All OCT Personnel will be required to follow a set of policies (including additional confidentiality restrictions) that apply to performance of the Services, and each OCT Employee shall acknowledge in writing that he/she has reviewed, understood and agreed to abide by such policies. Any TOTAL employees that are being trained as part of the Services or otherwise participating or observing the Services in the Pilot Plant will need permission of the OCT Manager to be in the OCT Facilities and will be required to follow the same policies while in the OCT Facilities, and sign substantially the same acknowledgement. In addition, Amyris employees executing SOWs on behalf of Amyris also shall sign agree to such acknowledgement as it applies to the non-use and nondisclosure obligations described therein. A copy of the policies is set forth in Schedule 1 hereto. The OCT Personnel shall treat any information regarding any activities being conducted by TOTAL or any of the Services as Confidential Information as set forth in the Agreement, and shall not share any such information, except as set forth in Section 3(b) of the Agreement. Notwithstanding the foregoing, the OCT Personnel shall not be restricted from sharing any such information with any Amyris Employees regarding (i) Amyris activities in the OCT Facilities that are not related to the Services or TOTAL Confidential Information, or (ii) the scheduling (but not the content or subject matter) of the Services. In addition, the OCT Personnel may disclose issues of safety within the Pilot Plant to the appropriate Amyris Employees responsible for safety and emergency management in the Pilot Plant.

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c)OCT Manager. The OCT Personnel will include one Amyris employee who will serve as one of the OCT Personnel and will manage the other OCT Personnel and the Services (the “OCT Manager”). The OCT Manager will be the primary contact for TOTAL and will represent and be authorized to take all decisions and exercise authority on behalf of Amyris in performing the Services. The OCT Manager will be responsible for tracking the OCT Personnel person-hours utilized for the Services to confirm compliance with the Annual Hours Commitment provided by Amyris as set forth below, provided that the time spent by the OCT Manager managing the OCT Personnel or tracking person–hours shall not constitute Services. For the avoidance of doubt, all OCT Personnel (including the OCT Manager) are employees of Amyris, reporting to Amyris’s management, shall be performing the Services as employees of Amyris, and shall not at any time act or take any action as an agent of TOTAL.

III.SERVICES

a)Services; Statement of Work (“SOW”); Scheduling. As used in this Exhibit, “Services” includes the following: (i) training TOTAL employees in the operation of the Pilot Plant, (ii) conducting and documenting Campaigns (as defined below) for TOTAL; and (iii) the following “Other Services”: (1) performing other fermentation and downstream separations scale-up services and such other tasks which may include the following: recovery operations, seed train fermentation on [*] and [*] (potentially [*] also) and (2) for the [*] fermenter, preparation and sterilization of feedstock, preparation and sterilization of media, support for fermentation operations, support for sterilization and cleaning of equipment or materials, support for sample analytical preparation as provided in Section III(e) below. Services will be performed only by OCT Personnel. During the performance of Services, TOTAL employees shall have access to the OCT Facilities, including the right to operate the equipment included in the OCT Facilities under the supervision of the OCT Personnel only while being trained under Section III(a)(i) above or conducting some Other Services as listed in Section III(a)(iii) above. For clarity, TOTAL shall have no right to operate any equipment in the OCT Facilities while Amyris is operating a Campaign for TOTAL.

If TOTAL desires Services, the OCT Manager and a single point of contact designated by TOTAL (“TOTAL BPP Coordinator”) will jointly determine the allocation of OCT Personnel person-hours for Services, including the amount of time spent on training, type of Campaign (e.g., Long Run Campaign or Short Run Campaign) or any Other Services, and the estimated number of OCT Personnel person-hours needed during each calendar quarter. The OCT Manager and TOTAL BPP Coordinator will meet and agree on the schedule for a calendar quarter at least thirty (30) days prior to the beginning of each calendar quarter. At this meeting, OCT Personnel person-hours to be expended on Services shall be allocated for such calendar quarter. The OCT Manager and TOTAL BPP Coordinator will target to schedule an approximate range between 500 OCT Personnel person-hours and 1500 OCT Personnel person-hours for the calendar quarter. In the event that the OCT Manager and TOTAL BPP Coordinator cannot agree on the schedule and/or associated OCT Personnel person-hours to be expended for a calendar quarter, the Parties agree to escalate the matter to the Joint Oversight Team as set forth in Section 7(a) of the Agreement. For the

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

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first year of the Agreement, the Parties will agree on such projected workload within thirty (30) days after the Effective Date.

For each specific Service, the OCT Manager and TOTAL BPP Coordinator will execute a SOW detailing the tasks to be performed and the estimated number of OCT Personnel and person-hours. Once the Services are completed, the OCT Manager and the TOTAL BPP Coordinator will meet in order to validate the person-hours duly spent to execute the Service described in the corresponding SOW. The information included in a SOW shall constitute TOTAL Confidential Information. A template SOW for use with Campaigns where a farnesene process is included is set forth in Schedule 5. For Campaigns that do not include a farnesene process and for Other Services, the Parties agree that to use as much as possible the SOW template set forth in Schedule 5. In any event, for the Campaigns operated pursuant to the Technology License, Development, Research and Collaboration Agreement, the SOW corresponding to such Campaigns shall clearly indicate that such Campaigns will be operated pursuant to the Collaboration Agreement.

b)Annual Maximum Number of Hours of Services. In consideration for the Annual Fee, Amyris shall cause the OCT Personnel to perform up to three thousand one hundred seventy eight (3,178) person-hours of Services each “Contract Year” (i.e., the twelve month period commencing on the Effective Date and then again each anniversary of it thereafter during the Term; such amount being the “Annual Hours Commitment”). In the event the Services agreed upon by the Parties in any Contract Year exceeds the Annual Hours Commitment, then TOTAL will be charged $281.73 for each additional hour of Services. In addition, TOTAL may request additional OCT Personnel person-hours in any Contract Year at the same rate. Amyris, in its discretion, can agree to accept the request for additional OCT Personnel person-hours and such acceptance will be documented in the related SOW. For clarity, “Services” do not include, and no hours shall be attributed to, analytical work performed by Amyris unless such work is identified in a SOW, maintenance of the equipment in the OCT Facilities or any management of OCT Personnel. The Annual Hours Commitment will be allocated each Contract Year to the performance of the Services agreed upon by the Parties as set forth herein and for no other purpose. The OCT Personnel will be required to record their time used to work on Services separately from their time spent on Amyris activities. Within 15 days after the end of each Contract Year, the Joint Oversight Team will determine whether Amyris has completed the Annual Hours Commitment during such Contract Year. In the event that the Joint Oversight Team cannot agree on the number of OCT Personnel person–hours expended in such Contract Year, the Parties agree to escalate the matter as set forth in Section 7(a) of the Agreement. If, in a Contract Year, TOTAL fails to use all of the Annual Hours Commitment, then the Parties agree that, except under the circumstances set forth below, TOTAL will not be entitled to receive a refund of the applicable Annual Fee or a reduction of a future Annual Fee with respect to those unused person-hours. If the Annual Hours Commitment during any Contract Year is not met by Amyris as a result of Amyris failure to perform Services as requested by TOTAL in accordance with the terms of the Agreement, including this Exhibit and any executed SOWs, and such failure results in Amyris failing to meet the Annual Hours Commitment, then the Parties agree as follows:

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Failure after Contract Year 1: All unused OCT Personnel person-hours will “roll over” to Contract Year 2 and will be added to the Annual Hours Commitment for Contract Year 2.

Failure after Contract Years 2-4: TOTAL will have the choice, at its discretion, to either (a) roll over any unused OCT Personnel person-hours to the Annual Hours Commitment for the following Contract Year or (b) reduce the Annual Fee for such following Contract Year by an amount equal to (i) the number of unused OCT Personnel person-hours from the previous Contract Year multiplied by (ii) $281.73, thereby eliminating all existing roll over hours.

Failure after Contract Year 5: Amyris will reimburse TOTAL the pro-rata portion of the Annual Fee equal to (i) the number of OCT Personnel person-hours that were unused at the end of Contract Year 5 multiplied by (ii) $281.73.

In addition, in the event the roll over hours OCT Personnel person-hours exceed, in the aggregate, 1,500 hours at the end of any Contract Year after Contract Year 1, Amyris will be considered in material breach of the Agreement and TOTAL may terminate in accordance with Section 6(c) of the Agreement.

c)Training of TOTAL Employees. As part of the Services, if requested by TOTAL, Amyris will provide TOTAL employees with training on how to operate equipment and generally process fermentation campaigns in the Pilot Plant. Most such training will occur through a “side-by-side” process, where TOTAL employees first accompany and then perform with supervision from the OCT Personnel, the tasks of running a Campaign as set forth below. As part of such training Services, the OCT Personnel shall provide the TOTAL employees access to all relevant documentation and equipment as needed to complete the Campaign training, as well as, if requested by TOTAL, access to a farnesene strain to be used in the fermentation processes to be carried out in such Campaign.

d)Campaigns.

(i)Definition

If requested by TOTAL under this Exhibit, Amyris will conduct Campaigns (as defined below) for TOTAL as part of the Services. A “Campaign” is defined by the completion of all the following steps: feedstock preparation and sterilization, media preparation and sterilization, flask culture, seed train fermentation, main fermentation (in fermentors from [*] to [*] capacity), product recovery, sampling and sample preparation, cleaning and handling, data collection and analysis, and reporting. For clarity and instance, a Campaign might be either a “Long Run Campaign” or a “Short Run Campaign”.

A typical Long Run Campaign means a fermentation process in the OCT Facility that typically includes the steps listed in Schedule 2 hereto. The Parties estimate will require approximately [*] OCT Personnel person-hours and associated utilization of equipment in

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

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the OCT Facilities to complete. Such campaign requires [*] of fermentation in MFA after inoculation. A simplified task schedule starting from the IFA task is provided on Figure 3 with number of working days per equipment. The red cells represent the inoculation day and the green ones the harvests days.

[*]

Figure 3 – [*]

A typical Short Run Campaign means a fermentation process in the OCT Facility that typically requires fewer technical steps and fewer estimated OCT Personnel person-hours to complete than a Long Run Campaign.

The Parties estimate a Short Run Campaign will typically require approximately 121 OCT Personnel person-hours and associated utilization of equipment in the OCT Facilities to complete. A simplified task schedule starting from the IFA task is provided on Figure 4 with number of working days per equipment.

[*]

Figure 4 – [*]

Measuring Success in Campaigns

•Key Parameters. In each SOW, TOTAL and Amyris will define the objectives to be reached when executing the Campaign. Among those objectives, no more than two objectives will be identified as “Key Parameters” by the Parties. If the Key Parameters are met, the Campaign will be considered a “Successful Campaign” and will be accepted by TOTAL.

•Process. Once the Campaign is terminated (at any time for any reason, including completion), the TOTAL BPP Coordinator and the OCT Manager shall meet to evaluate if the results (recorded data, analysis, etc.) are sufficient to meet the Key Parameters. The decision on whether Key Parameters are met will be at TOTAL BPP

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

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Coordinator’s discretion. However, if the Key Objectives are not met, an ABGD System (as defined below) analysis shall be performed by the OCT Personnel and upon TOTAL’s request, the TOTAL BPP Coordinator (or its designee) shall be entitled both to participate in such analysis, and to access the conclusions of the report of such analysis.

•The ABGD System. Amyris operates a batch quality system (the alpha beta gamma delta or ABGD system) which evaluates each batch by operational execution and outcome events as the basis for establishing whether a Campaign is a Successful Campaign. A detailed description of the ABGD system is set forth in Schedule 6. Alpha-Gamma, Alpha-Delta and Beta-Gamma outcomes will not result in an Attempted Campaign (as defined below).

•Attempted Campaign. A Campaign that does not meet the Key Parameters at termination and is categorized as Beta-Delta through the ABGD System is defined as an “Attempted Campaign”. An Attempted Campaign shall not be deemed a performance breach by Amyris, and Amyris will not deduct from the Annual Hours Commitment any OCT Personnel person-hours expended by Amyris on an Attempted Campaign. Within thirty (30) days after such Attempted Campaign, Amyris shall re-execute the Campaign, up to a maximum of two additional times, and TOTAL shall not be charged any additional OCT Personnel person-hours or cost for concluding such re-executed Campaign. In the event an Attempted Campaign occurs (up to a maximum of two Attempted Campaigns in a row) and the re-executed Campaign results in a Successful Campaign, TOTAL will be charged OCT Personnel person-hours for the Successful Campaign only.

•Failed Campaign. Three Attempted Campaigns on the same Campaign SOW is defined as a “Failed Campaign”. If three or more Failed Campaigns occur during a twelve month period, then TOTAL may thereafter terminate this Agreement without cause pursuant to Section 6(b) without, however, any obligation to pay the amount specified in Section 6(b) (ii).

•Root Cause Analysis. Amyris shall perform a root-cause analysis of each Attempted Campaign to identify the operational cause of the failure if applicable and report such analysis to TOTAL within thirty (30) days after the date of each Attempted Campaign, and resolve such failure within sixty (60) days after the basis for such Attempted Campaign has been identified.

e)Other Services. From time to time TOTAL may request the OCT Personnel to perform Other Services. If some of the Other Services are to be performed using equipment in the Total Dedicated Area, the SOW shall identify such equipment. The OCT Personnel person-hours incurred to perform such Services shall apply against the Annual Hours Commitment available in the Contract Year. Once an Other Service is terminated, the TOTAL BPP Coordinator and the OCT Manager shall meet to evaluate if the results (if any) established in the SOW for such Other Services have been achieved. The OCT Manager and the TOTAL BPP Coordinator shall agree on the Key Parameters (if any) and anticipated results to be achieved for any Other Services on the associated SOW prior to execution of the related Services. If the results are not achieved, the tasks described in such SOW will be

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re-executed by the OCT Personnel, TOTAL shall not be charged any additional OCT Personnel person-hours or cost for concluding such re-executed SOW within thirty (30) days after such termination.

f)Right to Lockout. Upon forty (40) days’ prior written notice and up to four (4) times each Contract Year, TOTAL may inform Amyris that Amyris will not be allowed to have any non-OCT Personnel visit or occupy the OCT Facilities during the operation of a specific Campaign or Service. Amyris will have the same right to exclude TOTAL and any associated employees, guest or partners from the OCT Facilities for the same number of days each year upon the same notice. Notwithstanding the foregoing, members of the Amyris emergency response team will at all times have access to the OCT Facilities in order to respond to any emergency situations on an as needed basis.

g)Information Technology. The OCT Facilities equipment will be accessible by each Party’s respective IT Networks, but it will only be accessible by one Party’s network at any time. The OCT Manager shall ensure that OCT Personnel disconnect certain OCT Facilities equipment from one Party’s network and attaching it to the other Party’s network when shifting from executing a Campaign to conducting work for Amyris (and vice versa). The OCT Personnel shall take all actions necessary to ensure that all Campaign data is deleted from any OCT Facilities equipment prior to reattaching such equipment to the Amyris network (and vice versa). In the event that a Party inadvertently acquires or is given access to the other Party’s data residing on OCT Facilities equipment, such Party shall promptly notify the other Party, shall not use and shall promptly destroy such data.

IV.DOCUMENTATION

a)Campaign/Service Report. For each Campaign or Other Service performed by Amyris, the OCT Personnel will prepare and provide a written report addressing the items specified in Schedule 3 as altered by mutually agreement of the OCT Manager and the TOTAL BPP Coordinator, or in the applicable SOW. The OCT Manager shall deliver such report to TOTAL not later than one (1) month after the end date designated in such SOW. The OCT Manager shall make the OCT Personnel involved with such Service reasonably available to answer TOTAL’s questions generated from review of each report. All time Amyris spends preparing such reports and subsequently answering questions about such reports will be deducted from the Annual Hours Commitment. For the avoidance of doubt, such report shall be deemed to be the property and Confidential Information of TOTAL for the purposes of this Agreement; however Amyris may keep a reference copy of such report in accordance with Section 3(d) of the Agreement.

b)Batch Records. The OCT Personnel shall maintain during the execution of each Campaign or other Service (as applicable) a batch record (in the form and including the details specified in the SOW for such Campaign) to keep track of all events and parameter settings used during the Campaign. Within five (5) business days after the conclusion of each Campaign or other Service (including Campaigns and Services terminated prior to completion), Amyris will provide a copy of the batch record to TOTAL. For the avoidance of doubt, such records shall be deemed to be the property and

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Confidential Information of TOTAL for the purposes of this Agreement; however Amyris will keep a reference copy of such records in accordance with its then current standard record keeping procedures, provided that such copy may only be used in relation to disputes between Amyris and TOTAL with respect to the performance of the Campaign or Service (as applicable) that was the subject of the report.

c)Raw Data. For each Campaign or other Service performed hereunder, the OCT Personnel shall maintain the raw data files that are generated by the analysers and fermenters used for execution of such Campaign or other Service (as applicable), and shall deliver such raw data files in a format reasonably requested by TOTAL within five (5) days after the conclusion of each Campaign or other Service (including Campaigns and Services terminated prior to completion). For the avoidance of doubt, such raw data files shall be deemed to be Confidential Information of TOTAL for the purposes of this Agreement; however Amyris may keep copies of such raw data files in accordance with Section 3(d) of the Agreement.

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SCHEDULE 1

OCT FACILITIES POLICIES

Amyris and TOTAL have entered into an agreement under which Amyris will provide fermentation and downstream separations scale-up services as well as training and related services to TOTAL employees at 5850 Hollis Street, Emeryville, California (the “Pilot Plant”).

You are one of the Amyris employees who will perform such services at the Pilot Plant. The services will be performed at the request of TOTAL under the oversight of Amyris’ Pilot Plant Manager in coordination with TOTAL (TOTAL manager referred to as the “TOTAL BPP Coordinator”). Employees of TOTAL also will be using and working in the Pilot Plant.

You will be interacting with TOTAL employees and materials belonging to TOTAL and may learn about or become exposed to confidential information belonging to TOTAL or its partners. It also is important to remember that you may possess confidential information belonging to Amyris or some of its other partners and need to ensure that you do not disclose this information to the TOTAL employees.

It is important to Amyris and TOTAL that you understand your obligations in regard to that information. As a consequence, Amyris and TOTAL have established the following policies to help guard against improper disclosure of confidential information and to help guide interactions between you and TOTAL employees. Note that this policy does not affect your obligations to Amyris under your Proprietary Information and Inventions Agreement. By signing this policy below, you hereby confirm and agree that:

• You will only disclose to TOTAL employees information about Amyris projects, materials or personnel (whether marked “confidential” or “proprietary” or communicated in oral, written, graphic or electronic form) if you are specifically instructed to do so by the Pilot Plant Manager.

• You will not disclose anything you learn about TOTAL’s projects, materials or personnel (whether marked “confidential” or “proprietary” or communicated in oral, written, graphic or electronic form) to any Amyris employee or consultant unless you are specifically instructed to do so by the Pilot Plant Manager.

• You will comply with all policies and procedures generally governing personnel working at the Pilot Plant, including Amyris safety policies.

• If you know or suspect there has been a security or safety incident in the Pilot Plant, you will report it immediately and directly to the Pilot Plant Manager.

• You will keep accurate records of any time spent conducting services on each TOTAL project and will accurately report all such time to the Pilot Plant Manager by the deadlines and in the form required by the Pilot Plant Manager.

Please see the Pilot Plant Manager if you have any questions related to this policy.

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Please acknowledge your agreement to the terms of this policy by signing and dating in the space below and returning the signed copy to the Pilot Plant Manager.

Signature: ______________________________________________________________

Printed Name: _________________________________________________________

Date: ____________________________________________________________________

Acknowledged: TOTAL New Energies USA, Inc.

Signature: _____________________________________________________________

Printed Name and Title: _____________________________________________

Date: ___________________________________________________________________

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SCHEDULE 1A

OCT FACILITIES POLICIES

Amyris and TOTAL have entered into an agreement under which Amyris will provide fermentation and downstream separations scale-up services as well as training and related services to TOTAL employees at 5850 Hollis Street, Emeryville, California (the “Pilot Plant”).

You are one of the TOTAL employees who will be engaged with such services at the Pilot Plant. The services will be performed at the request of TOTAL under the oversight of Amyris’ Pilot Plant Manager in coordination with TOTAL (TOTAL manager referred to as the “TOTAL BPP Coordinator”). Employees of TOTAL also will be using and working in the Pilot Plant.

You will be interacting with Amyris employees and materials belonging to Amyris and may learn about or become exposed to confidential information belonging to Amyris or its partners. It also is important to remember that you may possess confidential information belonging to TOTAL or some of its other partners and need to ensure that you do not disclose this information to the Amyris employees.

It is important to Amyris and TOTAL that you understand your obligations in regard to that information. As a consequence, Amyris and TOTAL have established the following policies to help guard against improper disclosure of confidential information and to help guide interactions between you and Amyris employees. Note that this policy does not affect your obligations to TOTAL under your employment contract and/or any policy or agreement issued by TOTAL and applicable to you concerning proprietary information and inventions management. By signing this policy below, you hereby confirm and agree that:

• You will only disclose to Amyris employees information about TOTAL projects, materials or personnel (whether marked “confidential” or “proprietary” or communicated in oral, written, graphic or electronic form) if you are specifically instructed to do so by the TOTAL BPP Coordinator.

• You will not disclose anything you learn about Amyris’s projects, materials or personnel (whether marked “confidential” or “proprietary” or communicated in oral, written, graphic or electronic form) to any TOTAL employee or consultant unless you are specifically instructed to do so by the TOTAL BPP Coordinator.

• You will comply with all policies and procedures generally governing personnel working at the Pilot Plant, including Amyris safety policies.

• If you know or suspect there has been a security or safety incident in the Pilot Plant, you will report it immediately and directly to the TOTAL BPP Coordinator.

Please see the TOTAL BPP Coordinator r if you have any questions related to this policy.

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Please acknowledge your agreement to the terms of this policy by signing and dating in the space below and returning the signed copy to the TOTAL BPP Coordinator.

Signature: ______________________________________________________________

Printed Name: _________________________________________________________

Date: ____________________________________________________________________

Acknowledged: Amyris, Inc.

Signature: _____________________________________________________________

Printed Name and Title: _____________________________________________

Date: ___________________________________________________________________

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SCHEDULE 2

FARNESENE LONG RUN CAMPAIGN STEPS AND PROJECTED TIME

Task Name	OCT hours
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[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

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[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

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[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

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[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

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[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

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SCHEDULE 3

CAMPAIGN REPORT REQUIREMENTS

Each Campaign report will address the following subject areas (provided that the Parties may adjust the subject areas for a particular Campaign and capture the new Campaign Report Requirements in the SOW for such Campaign or as mutually agreed) in detail reasonably acceptable to TOTAL:

• Report Executive Summary (Summary of the main observations, results and conclusions)

• Overview (Recap of the main objectives of the campaign including the Key Parameters, recall of main process conditions including strain and feedstock used)

• Experimental Plan (Recap of the original experimental plan and comparison with experiments actually performed, it could be a table with the main process conditions that has been varied along the Campaign + the main process fixed conditions that are of importance) :

◦ Varied process parameters

◦ Main fixed parameters

◦ Description of the adjustments Made between the original and the actual plan

• Experiment Chronology (Date and runtime of each activity (e.g. inoc transfer, draw, addition) with short description of activity including quantities and OD measurement when applicable, and main critical observation / operating issue when applicable)

• Process Description (including material and methods / Protocols used)

o Sterilization (e.g. Feedstock composition, set up conditions)

o Seed train (e.g. for each step : Vessel Size and type, Post-Inoc Volume, Volume of Innoc, Harvest OD, Feed composition, Media composition, Fermentation recipe)

o Fermentation (e.g. Vessel Size and type, Post-Inoc Volume, Volume of Inoc, Feed composition, Media composition, Fermentation recipe, Antifoam, PH control, Air flowrate & OTR, agitation, Pressure, Feed strategy)

o Downstream processes Operating Conditions

▪ L/S setup conditions if applicable

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▪ L/L setup conditions if applicable

▪ Polishing setup conditions if applicable

▪ Or any others setup conditions in case of a different recovery unit operation than centrifugation

o Sampling Plan (Identification of all samples taken and their frequency, and results acquired during all the steps of the Campaign, either captured on the batch record or in an electronic format)

o Analytical Plan (SOP used for sample preparation, SOP used for analytical work)

o Formulas Used for Calculation (Yield and mass balances)

• Results (one paragraph by Step or Process section)

◦ Sterilization (e.g. Composition, Brix analysis, Vapor consumption, Temperature profile)

◦ Fermentation (e.g. with MFCS profile for OTR, OUR, Temp, pH, RQ, Press, Residual Sugar, EtOH, Volume, Product titers )

◦ Downstream (e.g. capillary assay results, titers results in the broth and each stream along the recovery process, Centrifuges heavy and discharge phases if applicable)

◦ Mass Balances in case a template is provided in the SOW (For each draw : global and fene balance)

◦ Yields Calculation in case a template is provided in the SOW (e.g. Product yield, Productivity, L/S yield if applicable, L/L yield if applicable, Recovery Yield)

◦ Operational Observations

◦ Batch record and/or any others raw data files attached to the report)

• Data Analysis (If applicable and described in the SOW)

• Conclusions and Recommendations on an operational standpoint

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SCHEDULE 4

HSE STANDARDS

1. The Company's safety plans include, but are not limited to:

a. Ergonomics

b. Personal Protective Equipment (PPE)

c. Hazardous Waste Management

d. Radiation Safety

e. Chemical Hygiene Plan (CHP)

f. Biological Safety

g. Emergency Action Plan/Fire Prevention Plan

h. Risk Assessment Procedures

i. Safe Operating Guidelines (SOGs)

j. Lockout/tagout

k. Safety Orientation

l. Emergency Response

m. Hearing Conservation

n. Respiratory Protection

o. Contractor Safety

p. Contract Manufacturing Safe Operations

2. Training

a. OCT Personnel and TOTAL Employees

Amyris has established a program of training for all OCT Personnel and TOTAL employees so that they will be aware of the hazards and potential hazards. Training will be conducted by Amyris’ safety program administrator, the OCT Manager, knowledgeable and qualified Amyris employees, or outside consultants. The training may either be carried out in a classroom or through an online system. A schedule for various types of training can be obtained by contacting the OCT Manager.

All OCT Personnel and TOTAL Employees are required to attend mandated Amyris training sessions and meetings and to read and comply with Amyris notices, warnings, and memos/emails, if applicable.

3. Training Schedule

a. Initial Training.

OCT Personnel and TOTAL Employees will receive safety training prior to being granted access to the OCT Facilities.

b. Previously Unrecognized Hazards.

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OCT Personnel and TOTAL Employees shall receive additional training whenever a previously unrecognized potential hazard is identified or, for example, when new or different information is given on a Material Safety Data Sheet.

c. Emergency Training.

OCT Personnel and TOTAL Employees shall receive training in Emergency Action/Fire Prevention Program. In addition, certain OCT Personnel and TOTAL Employees may receive first aid/CPR training as needed.

d. Potentially Hazardous Non-Routine Tasks.

OCT Personnel and TOTAL Employees shall receive training and/or information before potentially hazardous non-routine tasks are undertaken. Depending on the circumstances, this training may be included in a regularly scheduled training session by the OCT Manager or through a task safety analysis or process safety review.

e. Annual Training.

Certain training such as biological, chemical, ergonomic and radiation safety will be done annually, as needed.

4. Training Records

a. Safety related training sessions will be documented using an Amyris training list sign-up sheet, highlighting the class. The Amyris training list sign-up sheet should give the name of the training class, the date and time of the session, and the name and signature of the OCT Personnel or TOTAL Employee.

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SCHEDULE 5

SOW TEMPLATE

The SOW should include the following:

• Objectives

• Key Parameters identified with acceptable deviation range as the trigger to qualify the failure of the Campaign (Alpha – Beta qualification)

• Recall of the main process description and parameters

• Expected results from smaller scale extrapolation

• Materials to be used for each process step, including Protocols / SOP applicable (equipment, sample preparation, etc.)

• Description of the work:

◦ Synoptic

◦ Process description for each process step if applicable

◦ Operating conditions for each process step (including if applicable a mention for Fixed Parameters vs Variables)

◦ Data to be recorded with a template of a Batch Record if applicable

◦ Sampling strategy

◦ Analytical strategy

◦ Performances expected

◦ Special requests

• A template for Data analysis, calculations, graphs plotting, if applicable

• Formulas for calculation, if applicable

• Content of the Campaign Report (and graphs to be plotted)

• Timing/Scheduling of the Campaign

• Estimated person-hours for the performance of the Campaign

• OCT Personnel responsible for the performance of the Campaign

• Safety constraints and Emergency Response Team in place

Every SOW must be signed by both the TOTAL BPP Coordinator and the OCT Manager prior to execution in order to be valid. The Parties agree to use as much as possible the template set forth below:

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SOW Form Request Amyris/Total under Pilot Plant Services Agreement
Date
Requester
Estimated person-hours
OCT Personnel responsible
Signatures
TOTAL	Amyris
Name: Signature Date	Name: Signature Date

Main Objectives of the Run:

Strain performance, recovery performance, samples production, robustness……

Purpose:

Description:

Strain number:

Feedstock:

Training Run: □Yes □No

Biofene Program: □Yes □No

1. Fermentation Step

1.1. Preparation

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[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

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1.2. Fermentation Culture Conditions

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1.3. Performances expected

Yield, growth rate, feed, OUR, lab scale graph

1.4. Special Requests - Comments :

What we need to focus on, issues that can happen

2. Recovery Step

2.1. Parameters for L/S separation

Equipment: Alfa-Laval DX203 centrifuge

Parameter	Standard	Required
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[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

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*The pump speed will be adjusted to maintain the split ratio closed to the target.

Comments / Special requests:

2.2. Parameters for L/L separation

Please choose:

a) Alfa-Laval LAPX404

b) Gyro

If LAPX chosen:

Parameter	Standard	Required
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Comments / Special requests:

If a surfactant is required, please specify:

• Type:

• Concentration:

• Mixing type and time:

2.3. Parameters for polishing

Please choose:

a) Alfa-Laval DX203

b) Filtration

If DX203 is chosen:

Parameter	Standard	Required
	Fene
[*]	[*]

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

GDSVF&H\1814591    Page 40 of 46     CONFIDENTIAL

[*]	[*]
[*]	[*]
[*]	[*]

Comments / Special requests:

If Filtration is chosen, describe the set-up and type of filters.

If a stabilizator is added, please specify:

• Type:

• Concentration:

3. Storage of Crude Products

How:

Where:

Duration:

If no polishing is done on the crude product, please specify if stabilizator addition is required:

• Type:

• Concentration:

4. Analytics

Please review our standard analysis, and add comments or precisions if required.

	Feedstock
[*]
[*]
[*]
[*]
[*]
[*]
[*]

	Daily Fermentation
	IFA, SFA	MFA
[*]
[*]
[*]
[*]
[*]
[*]
[*]
[*]

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

GDSVF&H\1814591    Page 41 of 46     CONFIDENTIAL

[*]

[*]

	DSP
[*]
[*]
[*]
[*]
[*]
[*]
[*]
[*]

	Type of streams
	Fene
[*]
[*]
[*]
[*]
[*]
[*]
[*]
[*]
[*]
[*]
[*]
[*]
[*]

5. Data Reporting

6. Special Samples and Requests

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

GDSVF&H\1814591    Page 42 of 46     CONFIDENTIAL

SCHEDULE 6

THE ABGD SYSTEM

Amyris Fermentation Process Quality Assignment – ABGD (αβγd) System

Background

The ABDG system is an acronym for Alpha (correct execution), Beta (incorrect execution), Gamma (meets specifications), Delta (Failed specifications). It is a data classification tool that identifies correct process control and experimental data sets. The purpose of applying the tool is to enable calculation of operational performance (control) and process robustness (capability). The system provides clarity across a number of projects, programs, and facilities.

Application of ABDG

Fermentation processes are performed by following a set of instructions. These instructions are in the form of written description in the scope of work. The instructions must include the key process variables and their target set points, acceptable ranges, and concern limits. The key parameters are monitored throughout the process and any deviations are noted. This assessment may be manual or be automated. In Amyris’s fermentation lab and pilot plant we are operating mainly an auto tagging system that is based on the MFCS process control system measurements and the process parameter targets. There are also a small number of manual assessments that are inputted by the operations team. These operational events or discrepancies in execution, or deviations from target, are referred to as tags.

In addition to the operational execution tagging there is a further level of assessment of the batch outcomes. This evaluates the ability of the method executed to deliver data and product quality that is within agreed range according to the specifications. The overall system is illustrated in Figure 1.

[*]

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

GDSVF&H\1814591    Page 43 of 46     CONFIDENTIAL

Figure 1: Categorization of process quality

In summary an alpha lot is a batch that has the following basic elements:-

• Equipment was set up correctly

• The correct raw materials were used

• The process operations were conducted correctly

• No mechanical issues

Beta lots would be batches that exhibit the following elements:-

• Contamination

• Excursions from set points

• Noisy measurements leading to poor control

• Equipment or electronic failures

• Utility failures leading to excursions

Setting Rules and Specifications

Process operational and outcome rules are listed and agreed through a review process. The review requires sign off from fermentation managers and project/ program stakeholders. The agreed rules sets and specifications are recorded in a versioned controlled document. By way of illustration only, Table 1 shows the typical listing of rules for alpha/beta and delta assignments:

GDSVF&H\1814591    Page 44 of 46     CONFIDENTIAL

Level	Set	Version	Current	Speciation Name
[*]	[*]		[*]	[*]
[*]	[*]		[*]	[*]
[*]	[*]		[*]	[*]
[*]	[*]		[*]	[*]
[*]	[*]		[*]	[*]
[*]	[*]		[*]	[*]
[*]	[*]		[*]	[*]
[*]	[*]		[*]	[*]
[*]	[*]		[*]	[*]
[*]	[*]		[*]	[*]
[*]	[*]		[*]	[*]
[*]	[*]		[*]	[*]
[*]	[*]		[*]	[*]
[*]	[*]		[*]	[*]
[*]	[*]		[*]	[*]
[*]	[*]		[*]	[*]
[*]	[*]		[*]	[*]
[*]	[*]		[*]	[*]
[*]	[*]		[*]	[*]
[*]	[*]		[*]	[*]
[*]	[*]		[*]	[*]
[*]	[*]		[*]	[*]
[*]	[*]		[*]	[*]
[*]	[*]		[*]	[*]
[*]	[*]		[*]	[*]
[*]	[*]		[*]	[*]
[*]	[*]		[*]	[*]
[*]	[*]		[*]	[*]
[*]	[*]		[*]	[*]
[*]	[*]		[*]	[*]
[*]	[*]		[*]	[*]
[*]	[*]		[*]	[*]
[*]	[*]		[*]	[*]
[*]	[*]		[*]	[*]
[*]	[*]		[*]	[*]
[*]	[*]		[*]	[*]
[*]	[*]		[*]	[*]
[*]	[*]		[*]	[*]
[*]	[*]		[*]	[*]
[*]	[*]		[*]	[*]
[*]	[*]		[*]	[*]
[*]	[*]		[*]	[*]
[*]	[*]		[*]	[*]
[*]	[*]		[*]	[*]
[*]	[*]		[*]	[*]
[*]	[*]		[*]	[*]
[*]	[*]		[*]	[*]
[*]	[*]		[*]	[*]
[*]	[*]		[*]	[*]
[*]	[*]		[*]	[*]
[*]	[*]		[*]	[*]
[*]	[*]		[*]	[*]

Table 1 Summarization of Rule Sets

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

GDSVF&H\1814591    Page 45 of 46     CONFIDENTIAL

Typical examples of beta delta events would be contamination resulting from operator error, process control failures, and incorrect media or batch recipe if the run request was not properly. For clarity, it is understood that the specific parameters to determine/define the ABDG status of a batch should be defined on a case by case basis and reviewed within the Scope of Work process

Assignment

A batch would be assigned a status once all the parameters have been assessed. The alpha/ beta assignment is completed by the OCT manager. The gamma/ delta specification assignment is made by the TOTAL BPP coordinator. Final assessment of the batch as gamma or delta requires completion of process assays and quality review of the data. Table 2 provides a summary of the four categories that are assignable:

Categorization	Description	Example
[*]	[*]	[*]
[*]	[*]	[*]
[*]	[*]	[*]
[*]	[*]	[*]

Table 2: Assignment of ABDG

Follow Up

The goal is to minimize the beta-delta rate to less than [*]. Beta-delta operational events are categorized by failure type in a Pareto analysis. A root cause analysis (RCA) process is performed on the major failure events to establish the basis for corrective and preventative action (CAPA). The impact of CAPA is monitored by measuring and comparing the frequency of that event over time. This is the process of continuous improvement.

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

GDSVF&H\1814591    Page 46 of 46     CONFIDENTIAL

EX-10.05

CONFIDENTIAL TREATMENT REQUESTED. CERTAIN PORTIONS OF THIS DOCUMENT HAVE BEEN OMITTED PURSUANT TO A REQUEST FOR CONFIDENTIAL TREATMENT AND, WHERE APPLICABLE, HAVE BEEN MARKED WITH AN ASTERISK TO DENOTE WHERE OMISSIONS HAVE BEEN MADE. THE CONFIDENTIAL MATERIAL HAS BEEN FILED SEPARATELY WITH THE SECURITIES AND EXCHANGE COMMISSION.

AMYRIS, INC

CONSULTING AGREEMENT

THIS CONSULTING AGREEMENT (“Agreement”) is made and entered into as of December 6, 2013, (the “Effective Date”) by and between Amyris, Inc., having its principal place of business located at 5885 Hollis Street, Suite 100 Emeryville, CA 94608 (the “Company”), and Steve Mills, an individual residing in the State of [*] with a principal place of residence at [*] (“Consultant”). The Company desires to retain Consultant as an independent contractor to perform consulting services for the Company, and Consultant is willing to perform such services, on terms set forth more fully below.

WHEREAS, the parties previously entered into that certain Consulting Agreement (“Prior Agreement”) dated April 9, 2012 and the parties wish to expressly terminate that Prior Agreement and supersede the terms with this Agreement.

NOW, THEREFORE, in consideration of the foregoing promises and the mutual covenants contained herein, the parties agree as follows:

1. Services. Consultant agrees to render consulting services (the “Services”) set forth on Exhibit A hereto. The Services and other terms and conditions set forth in Exhibit A may be amended from time to time upon the execution of a revised Exhibit A, signed by both parties. Such revised Exhibit A shall be subject to all the terms and conditions of this Agreement.

2.Compensation. During the term of this Agreement, as compensation for the Services rendered and other obligations undertaken by Consultant hereunder, Consultant shall be entitled to the compensation described on Exhibit A hereto.

3.Independent Contractor.

(a)It is the express intention of the parties to this Agreement that Consultant is an independent contractor, and is classified by the Company as such for all employee benefit purposes and is not an employee, agent, joint venturer, or partner of the Company. Nothing in this Agreement shall be interpreted or construed as creating or establishing an employment relationship between the Company and Consultant.

(b)Consultant acknowledges and agrees that Consultant is obligated to report as income all compensation received by Consultant pursuant to this Agreement and that Consultant is solely responsible for all taxes, withholdings, and other similar statutory obligations including, but not limited to, self-employment tax and Workers’ Compensation Insurance.

4.Consultant’s Obligations.

(a)Consultant’s performance under this Agreement shall be conducted with due diligence and in full compliance with the highest professional standards of practice in the industry. Consultant shall comply with all applicable laws and the Company safety rules in the course of performing the Services. If Consultant’s work requires a license, Consultant shall or has obtained that license and the license will be or is in full force and effect.

(b)Consultant certifies that Consultant has no outstanding agreement or obligation that is in conflict with any of the provisions of this Agreement, or that would preclude Consultant from

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

CONFIDENTIAL 1 of 6

complying with the provisions hereof and further certifies that Consultant will not enter into any such conflicting agreement during the term of this Agreement.

5.Confidentiality.

(a)“Confidential Information” means any Company proprietary information, technical data, trade secrets or know-how, including, but not limited to, research, product plans, products or components thereof, services, customer lists and customers (including, but not limited to, customers of the Company on whom Consultant called or with whom Consultant became acquainted during the term of this Agreement), software, developments, inventions, processes, formulas, technology, designs, drawings, engineering, hardware configuration information or marketing, financial or other business information disclosed to Consultant by the Company either directly or indirectly in writing, orally, or by drawings or observation of parts or equipment.

(b)Consultant will not use the Company’s Confidential Information for any purpose whatsoever other than the performance of the Services on behalf of the Company or disclose the Company’s Confidential Information to any third party. It is understood that said Confidential Information shall remain the sole property of the Company. Consultant further agrees to take all reasonable precautions to prevent any unauthorized disclosure of such Confidential Information. Confidential Information does not include information which (i) is known to Consultant at the time of disclosure to Consultant by the Company as evidenced by written records of Consultant, (ii) has become publicly known and made generally available through no improper action or inaction by Consultant or any agent or affiliate of Consultant, or (iii) has been rightfully received by Consultant from a third party who is authorized to make such disclosure. Without the Company’s prior written approval, Consultant will not directly or indirectly disclose to anyone the existence or terms of this Agreement or the fact that Consultant has this arrangement with the Company.

(c)Consultant agrees that Consultant will not, during the term of this Agreement, improperly use or disclose any proprietary information or trade secrets of any former or current client or other person, organization or entity with which Consultant has an agreement or duty to keep in confidence information acquired by Consultant, if any, and that Consultant will not bring onto the premises of the Company any unpublished document or proprietary information belonging to such client, person, organization or entity unless consented to in writing by such client, person, organization or entity.

(d)Consultant recognizes that the Company has received and in the future will receive from third parties their confidential or proprietary information subject to a duty on the Company’s part to maintain the confidentiality of such information and to use it only for certain limited purposes. Consultant agrees that Consultant owes the Company and such third parties, during the term of this Agreement and thereafter, a duty to hold all such confidential or proprietary information in the strictest confidence and not to disclose it to any person, organization or entity or to use it except as necessary in carrying out the Services for the Company consistent with the Company’s agreement with such third party.

(e)Upon the termination of this Agreement, or upon Company’s earlier request, Consultant will deliver to the Company (and will not recreate or deliver to anyone else) all of the Company’s property or Confidential Information that Consultant may have in Consultant’s possession or control.

CONFIDENTIAL 2 of 6

6.Ownership.

(a)Consultant agrees that all intellectual property, including without limitation, all copyrightable material, notes, records, drawings, designs, inventions (whether patentable or not), technology, know how, source and object code, algorithms, ideas, improvements, developments, discoveries and trade secrets (collectively, “Intellectual Property”) conceived, made or discovered by Consultant, solely or in collaboration with others, during the term of this Agreement which relate in any manner to the business of the Company that Consultant may be directed to undertake, investigate or experiment with, or which Consultant may become associated with in work, investigation or experimentation in the line of business of Company in performing the Services hereunder, and any and all patents, patent rights, copyrights, mask work rights, trade secret rights and other intellectual property rights anywhere in the world (collectively “Rights”) shall be the sole property of the Company. Consultant further agrees to assign (or cause to be assigned) and does hereby assign fully to the Company all Intellectual Property and Rights.

(b)Consultant shall not, without the Company’s prior written consent, incorporate into Intellectual Property developed by Consultant in the course of performing the Services for the Company (“Company IP”) any invention, improvement, development, concept, discovery or other proprietary information that is either owned by Consultant or in which Consultant has an interest (“Consultant IP”). In the event Consultant does knowingly incorporate any Consultant IP into Company IP without the Company’s prior written consent, Consultant hereby grants the Company a nonexclusive, fully paid up, royalty-free, perpetual, irrevocable, worldwide license to make, have made, modify, use, offer for sale, sell or import such Consultant IP as part of or in connection with such Company IP.

(c)Consultant shall not, without the Company’s prior written consent, incorporate into Company IP any invention, improvement, development, concept, discovery or other proprietary information that Consultant knows is owned by their current employer, any previous employer or any other third party (“Third Party IP”). To the extent Consultant does incorporate any Third Party IP into Company IP without the Company’s prior written consent, Consultant shall use their best efforts to cause the third part(y)(ies) who own or have the power to control the disposition of such Third Party IP to grant the Company a license of the same scope as that set forth in subsection (g) above.

7.Term and Termination.

(a)This Agreement will commence on the Effective Date and will continue until final completion of the Services unless earlier terminated as provided below.

(b)Either party may terminate this Agreement effective immediately upon written notice in the event the other party breaches or defaults under any provision of this Agreement.

(c)Either party may terminate this Agreement for convenience effective upon thirty (30) days written notice to the other party.

(d)Sections 3, 5, 6, 7(d), 8 and 9 shall survive termination of this Agreement.

8.Arbitration.

(a)The Company and Consultant agree to arbitrate any and all disputes, demands, claims, or controversies (collectively, “claims”) they may have against one another (and in the case of Consultant, including claims against current or former agents, owners, officers, directors or

CONFIDENTIAL 3 of 6

employees of the Company), arising from the consulting relationship between Consultant and Company, whether in tort, contract, or pursuant to a statute, regulation, or ordinance now in existence or which may in the future be enacted or amended or recognized at common law. The parties understand and agree that arbitration shall be the sole and exclusive method of resolving any and all existing and future claims, subject to this Agreement, that arise out of Consultant’s retention by the Company or the termination of their relationship, except that (i) Consultant shall not be precluded from filing an administrative charge or complaint with, or from participating in, an administrative investigation of a charge or complaint before any government agency, and (ii) neither party shall be relieved from any obligation it may have to exhaust administrative remedies before arbitrating any claim under this Agreement.

(b)The parties agree that arbitration shall be conducted in San Francisco, California in accordance with the national rules for the resolution of employment disputes of the American Arbitration Association (“AAA Rules”) then in effect. However, the parties shall be allowed discovery authorized by applicable law in arbitration proceedings.

(c)The parties agree that arbitration shall be conducted before a single, neutral arbitrator selected by mutual agreement of the parties, but who need not be a panel member of the American Arbitration Association (“AAA”). However, if the parties cannot agree to such arbitrator, arbitration shall be conducted before a single, neutral arbitrator selected from AAA panel members in accordance with AAA National Rules for the Resolution of Employment Disputes.

(d)The parties agree that the arbitrator shall issue a written award that sets forth the essential findings and conclusions on which the award is based. The arbitrator shall have the authority to award any relief authorized by law in connection with the asserted claims or defenses, and the arbitrator’s award shall be subject to correction, confirmation, or vacation, as provided by any applicable law setting forth the standard of judicial review of arbitration awards.

(e)The parties understand and agree that arbitration of claims under this Agreement shall be instead of a trial before a court or jury and that they are expressly waiving any and all rights to a trial before a court or a jury regarding any claims subject to this Agreement that either now has against the other or that either may in the future have against the other.

9.General Provisions.

(a)This Agreement will be governed by and construed under the laws of the State of California and the United States without regard to the conflicts of laws provisions thereof

(b)This Agreement sets forth the entire agreement and understanding between the Company and Consultant relating to the subject matter herein and supersedes all prior discussions, including the Prior Agreement, between the parties. No modification of or amendment to this Agreement, nor any waiver of any rights under this Agreement, will be effective unless executed in writing and signed by both parties.

(c)All notices required or given herewith shall be addressed to the Company or Consultant at the designated addresses shown below by registered mail, special delivery, or by certified courier service:

If to Consultant: Steve Mills [*]	If to Company: Amyris, Inc. 5885 Hollis St, Suite 100 Emeryville, CA 94608 Attn: Legal Department
[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

CONFIDENTIAL 4 of 6

Fax: [*]

Email:[*]

(d)The headings used in this Agreement are for the convenience of the parties and for reference purposes only and shall not form a part or affect the interpretation of this Agreement.

(e)If one or more of the provisions in this Agreement are deemed void by law, then the remaining provisions will continue in full force and effect.

(f)Neither this Agreement nor any right hereunder or interest herein may be assigned or transferred by Consultant without the express prior written consent of an officer of the Company provided, however, that either party may assign this Agreement upon notice to the other party in connection with a reincorporation, including but not limited to a reincorporation by merger. This Agreement will be binding upon Consultant’s heirs, executors, administrators and other legal representatives and will be for the benefit of the Company, its successors, and its assigns.

(g)If any action at law or in equity is necessary to enforce or interpret the terms of this Agreement, the prevailing party shall be entitled to reasonable attorneys’ fees, costs, and necessary disbursements, in addition to any other relief to which the party may be entitled.

IN WITNESS WHEREOF, the parties hereto have executed this Agreement as of the day and year first above written.

AMYRIS, INC.	CONSULTANT
By: /s/ Karen D. Rohde	By: /s/ Steven Mills
Name: Karen D. Rohde	Name: Steven Mills 12/6/13
Title: CHRO	Title:

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

CONFIDENTIAL 5 of 6

EXHIBIT A

Services and Compensation

1. Contact: Consultant’s principal Company contact:

Name:John Melo

Title:Chief Executive Officer

Telephone:    [*]

2. Services: Consultant shall perform the following “Services” for the Company:

• Act as an advisor to the Chief Executive Officer and the Company’s Board of Directors as requested in the areas of efficiency and process improvements, cost structure and overall strategy for the Company.

• Provide general support of the Company’s Finance group.

• Provide general support for the interim Chief Financial Officer.

3. Time Commitment: Consultant shall provide consulting Services on an ad-hoc basis commencing with the Effective Date and ending on June 1, 2014 (the “Term”). Services will be requested on an as-needed basis by the Chief Executive Officer during the Term. The Term of this Exhibit A may be renewed or extended in writing upon mutual consent of the parties. Upon request by the Company, Consultant shall provide the Company with a written record of current accrued hourly billings.

4. Expenses: The Company shall reimburse Consultant for all travel expenses incurred in connection with this Agreement upon submission and verification of customary receipts and vouchers. Unless otherwise agreed by the Company in advance, all air travel for flights lasting shorter than two (2) hours shall be economy class. First Class is permitted for all flights in excess of two (2) hours.

5. Compensation: The Company shall pay Consultant the following “Compensation” to performing the Services:

• Consultant shall receive three hundred fifty dollars ($350.00) per hour for the work performed. Consultant shall bill the Company on a monthly basis for the Services performed.

6. Payments:Consultant shall submit to the Company a reasonably detailed invoice for all Services rendered. Within forty-five (45) days of receipt of Consultant’s invoice, payment will be made by the Company for each hour in which Consultant has satisfactorily provided Services. The foregoing fees are Consultant’s sole compensation for rendering Services to the Company.

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

CONFIDENTIAL 6 of 6

EX-31.01

Exhibit 31.01

CERTIFICATION OF CHIEF EXECUTIVE OFFICER

PURSUANT TO RULE 13a-14(c) and 15d-(14(a) OF THE SECURITIES EXCHANGE ACT OF 1934

I, John Melo, certify that:

1. I have reviewed this Quarterly Report on Form 10-Q of Amyris, Inc.;

2. Based on my knowledge, this report does not contain any untrue statement of a material fact or omit to state a material fact necessary to make the statements made, in light of the circumstances under which such statements were made, not misleading with respect to the period covered by this report;

3. Based on my knowledge, the financial statements, and other financial information included in this report, fairly present in all material respects the financial condition, results of operations and cash flows of the registrant as of, and for, the periods presented in this report;

4. The registrant's other certifying officer and I are responsible for establishing and maintaining disclosure controls and procedures (as defined in Exchange Act Rules 13a-15(e) and 15d-15(e)) and internal control over financial reporting (as defined in Exchange Act Rules 13a-15(f) and 15d-15(f)) for the registrant and have:

a) Designed such disclosure controls and procedures, or caused such disclosure controls and procedures to be designed under our supervision, to ensure that material information relating to the registrant, including its consolidated subsidiaries, is made known to us by others within those entities, particularly during the period in which this report is being prepared;

b) Designed such internal control over financial reporting, or caused such internal control over financial reporting to be designed under our supervision, to provide reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with generally accepted accounting principles;

c) Evaluated the effectiveness of the registrant's disclosure controls and procedures and presented in this report our conclusions about the effectiveness of the disclosure controls and procedures, as of the end of the period covered by this report based on such evaluation; and

d) Disclosed in this report any change in the registrant's internal control over financial reporting that occurred during the registrant's most recent fiscal quarter (the registrant's fourth fiscal quarter in the case of an annual report) that has materially affected, or is reasonably likely to materially affect, the registrant's internal control over financial reporting; and

5. The registrant's other certifying officer and I have disclosed, based on our most recent evaluation of internal control over financial reporting, to the registrant's auditors and the audit committee of the registrant's board of directors (or persons performing the equivalent functions):

a) All significant deficiencies and material weaknesses in the design or operation of internal control over financial reporting which are reasonably likely to adversely affect the registrant's ability to record, process, summarize and report financial information; and

b) Any fraud, whether or not material, that involves management or other employees who have a significant role in the registrant's internal control over financial reporting.

Date: August 8, 2014	/s/ JOHN MELO
	John Melo
	President and Chief Executive Officer

EX-31.02

Exhibit 31.02

CERTIFICATION OF CHIEF FINANCIAL OFFICER

PURSUANT TO RULE 13a-14(c) and 15d-(14(a) OF THE SECURITIES EXCHANGE ACT OF 1934

I, Paulo Diniz, certify that:

1. I have reviewed this Quarterly Report on Form 10-Q of Amyris, Inc.;

2. Based on my knowledge, this report does not contain any untrue statement of a material fact or omit to state a material fact necessary to make the statements made, in light of the circumstances under which such statements were made, not misleading with respect to the period covered by this report;

3. Based on my knowledge, the financial statements, and other financial information included in this report, fairly present in all material respects the financial condition, results of operations and cash flows of the registrant as of, and for, the periods presented in this report;

4. The registrant's other certifying officer and I are responsible for establishing and maintaining disclosure controls and procedures (as defined in Exchange Act Rules 13a-15(e) and 15d-15(e)) and internal control over financial reporting (as defined in Exchange Act Rules 13a-15(f) and 15d-15(f)) for the registrant and have:

a) Designed such disclosure controls and procedures, or caused such disclosure controls and procedures to be designed under our supervision, to ensure that material information relating to the registrant, including its consolidated subsidiaries, is made known to us by others within those entities, particularly during the period in which this report is being prepared;

b) Designed such internal control over financial reporting, or caused such internal control over financial reporting to be designed under our supervision, to provide reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with generally accepted accounting principles;

c) Evaluated the effectiveness of the registrant's disclosure controls and procedures and presented in this report our conclusions about the effectiveness of the disclosure controls and procedures, as of the end of the period covered by this report based on such evaluation; and

d) Disclosed in this report any change in the registrant's internal control over financial reporting that occurred during the registrant's most recent fiscal quarter (the registrant's fourth fiscal quarter in the case of an annual report) that has materially affected, or is reasonably likely to materially affect, the registrant's internal control over financial reporting; and

5. The registrant's other certifying officer and I have disclosed, based on our most recent evaluation of internal control over financial reporting, to the registrant's auditors and the audit committee of the registrant's board of directors (or persons performing the equivalent functions):

a) All significant deficiencies and material weaknesses in the design or operation of internal control over financial reporting which are reasonably likely to adversely affect the registrant's ability to record, process, summarize and report financial information; and

b) Any fraud, whether or not material, that involves management or other employees who have a significant role in the registrant's internal control over financial reporting.

Date: August 8, 2014	/s/ PAULO DINIZ
	Paulo Diniz
	Interim Chief Financial Officer

EX-32.01

Exhibit 32.01

Certification of CEO Furnished Pursuant to 18 U.S.C. Section 1350,

As Adopted Pursuant To

Section 906 of The Sarbanes-Oxley Act of 2002

In connection with the Quarterly Report of Amyris, Inc. (the “Company”) on Form 10-Q for the quarterly period ended June 30, 2014, as filed with the Securities and Exchange Commission on the date hereof, I, John Melo, Chief Executive Officer of the Company, certify for the purposes of section 1350 of chapter 63 of title 18 of the United States Code, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002, that, to the best of my knowledge,

(i) the Quarterly Report of the Company on Form 10-Q for the quarterly period ended June 30, 2014 (the “Report”), fully complies with the requirements of section 13(a) or 15(d) of the Securities Exchange Act of 1934, and

(ii) the information contained in the Report fairly presents, in all material respects, the financial condition and results of operations of the Company.

Date: August 8, 2014	/s/ JOHN MELO
	John Melo
	President and Chief Executive Officer
	(Principal Executive Officer)

EX-32.02

Exhibit 32.02

Certification of CFO Furnished Pursuant to 18 U.S.C. Section 1350,

As Adopted Pursuant To

Section 906 of The Sarbanes-Oxley Act of 2002

In connection with the Quarterly Report of Amyris, Inc. (the “Company”) on Form 10-Q for the quarterly period ended June 30, 2014, as filed with the Securities and Exchange Commission on the date hereof, I, Paulo Diniz, Interim Chief Financial Officer of the Company, certify for the purposes of section 1350 of chapter 63 of title 18 of the United States Code, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002, that, to the best of my knowledge,

(i) the Quarterly Report of the Company on Form 10-Q for the quarterly period ended June 30, 2014 (the “Report”), fully complies with the requirements of section 13(a) or 15(d) of the Securities Exchange Act of 1934, and

(ii) the information contained in the Report fairly presents, in all material respects, the financial condition and results of operations of the Company.

Date: August 8, 2014	/s/ PAULO DINIZ
	Paulo Diniz
	Interim Chief Financial Officer
	(Principal Financial Officer)

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Fair Value of Financial Instruments - Hierarchy (Details) (Fair Value, Measurements, Recurring [Member], USD $) In Thousands, unless otherwise specified	Jun. 30, 2014		Dec. 31, 2013
Quoted Prices in Active Markets for Identical Assets (Level 1) [Member]
Financial Assets
Money market funds	$ 74,765		$ 398
Certificates of deposit	1,453		1,428
Total financial assets	76,218		1,826
Financial Liabilities
Loans payable	0	[1]	0
Credit facilities	0	[1]	0
Convertible notes	0	[1]	0
Compound embedded derivative liability	0		0
Currency interest rate swap derivative liability	0		0
Total financial liabilities	0		0
Other Observable Inputs (Level 2) [Member]
Financial Assets
Money market funds	0		0
Certificates of deposit	0		0
Total financial assets	0		0
Financial Liabilities
Loans payable	20,360	[1]	18,491
Credit facilities	39,864	[1]	7,571
Convertible notes	0	[1]	0
Compound embedded derivative liability	0		0
Currency interest rate swap derivative liability	2,808		3,600
Total financial liabilities	63,032		29,662
Significant Unobservable Inputs (Level 3) [Member]
Financial Assets
Money market funds	0		0
Certificates of deposit	0		0
Total financial assets	0		0
Financial Liabilities
Loans payable	0	[1]	0
Credit facilities	0	[1]	0
Convertible notes	227,638	[1]	131,952
Compound embedded derivative liability	145,032		131,117
Currency interest rate swap derivative liability	0		0
Total financial liabilities	372,670		263,069
Balance as of June 30 [Member]
Financial Assets
Money market funds	74,765		398
Certificates of deposit	1,453		1,428
Total financial assets	76,218		1,826
Financial Liabilities
Loans payable	20,360	[1]	18,491
Credit facilities	39,864	[1]	7,571
Convertible notes	227,638	[1]	131,952
Compound embedded derivative liability	145,032		131,117
Currency interest rate swap derivative liability	2,808		3,600
Total financial liabilities	$ 435,702		$ 292,731

[1] These liabilities are carried on the condensed consolidated balance sheet on a historical basis.

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Debt - Convertible Notes (Details) (USD $)	3 Months Ended				0 Months Ended					0 Months Ended					1 Months Ended		3 Months Ended		1 Months Ended			0 Months Ended	1 Months Ended
	Jun. 30, 2014	May 22, 2014	Dec. 31, 2013	Jan. 31, 2014 First Tranche [Member] August 2013 Convertible Notes [Member]	Dec. 02, 2013 Unsecured Senior Convertible Promissory Notes [Member]	Mar. 31, 2014 Unsecured Senior Convertible Promissory Notes [Member]	Dec. 31, 2013 Unsecured Senior Convertible Promissory Notes [Member]	Sep. 30, 2013 Unsecured Senior Convertible Promissory Notes [Member]	Feb. 29, 2012 Unsecured Senior Convertible Promissory Notes [Member] Fidelity [Member]	Jul. 30, 2012 Related Party Convertible Notes [Member]	Jun. 30, 2014 Related Party Convertible Notes [Member]	Dec. 31, 2013 Related Party Convertible Notes [Member]	Dec. 02, 2013 Related Party Convertible Notes [Member]	Oct. 31, 2013 Related Party Convertible Notes [Member]	Oct. 31, 2013 Related Party Convertible Notes [Member] August 2013 Convertible Notes [Member]	Aug. 31, 2013 Related Party Convertible Notes [Member] August 2013 Convertible Notes [Member]	Jun. 30, 2014 Related Party Convertible Notes [Member] Rule 144A Convertible Notes [Member]	Jun. 30, 2014 Related Party Convertible Notes [Member] First Tranche [Member]	Oct. 31, 2013 Related Party Convertible Notes [Member] First Tranche [Member] August 2013 Convertible Notes [Member] l	Aug. 31, 2013 Related Party Convertible Notes [Member] First Tranche [Member] August 2013 Convertible Notes [Member]	Dec. 31, 2013 Related Party Convertible Notes [Member] Second Tranche [Member]	Dec. 02, 2013 Related Party Convertible Notes [Member] Second Tranche [Member] August 2013 Convertible Notes [Member]	Jan. 31, 2014 Related Party Convertible Notes [Member] Second Tranche [Member] August 2013 Convertible Notes [Member]	Aug. 31, 2013 Related Party Convertible Notes [Member] Second Tranche [Member] August 2013 Convertible Notes [Member]	May 22, 2014 Rule 144A Convertible Notes [Member]	Oct. 31, 2013 Maximum [Member] Related Party Convertible Notes [Member] August 2013 Convertible Notes [Member]	Aug. 31, 2013 Maximum [Member] Related Party Convertible Notes [Member] August 2013 Convertible Notes [Member]	Dec. 24, 2012 Private Placement [Member] Related Party Convertible Notes [Member]	Jul. 31, 2013 Initial Installment [Member] Related Party Convertible Notes [Member]	Jun. 30, 2013 Initial Installment [Member] Related Party Convertible Notes [Member]	Jul. 30, 2012 Initial Installment [Member] Related Party Convertible Notes [Member]
Debt Instrument [Line Items]
Convertible Note Offering		$ 15,000,000																							$ 75,000,000
Proceeds from Convertible Debt	72,000,000																24,700,000
Debt Instrument, Unamortized Discount	83,900,000										83,900,000							31,600,000			6,300,000
Debt Instrument, Convertible Promissory Note, Held by Third Party					48,300,000
Future Proceeds from Convertible Debt										21,700,000						60,000,000	9,700,000			35,000,000		6,000,000	6,000,000	25,000,000
Convertible Note Offering [Abstract]
Debt Instrument, Face Amount				34,000,000					25,000,000	105,000,000										42,600,000			3,000,000	30,400,000		51,800,000	73,000,000		20,000,000	10,000,000	30,000,000
Debt Instrument, Interest Rate, Stated Percentage									3.00%
Debt Instrument, Convertible, Conversion Price					$ 2.20			$ 7.0682		$ 7.0682									$ 2.44				$ 2.87		$ 3.74			$ 2.98			$ 3.08
Debt Instrument, Convertible, Common Stock, Shares									3,536,968																			1,677,852
Percentage of Principal Amount of Notes, Required to Be Repaid In An Acquisition									101.00%
Debt Instrument, Debt Convenant, Outstanding Debt, Maximum									200,000,000
Debt Instrument, Debt Convenant, Percentage of Consolidated Total Assets, Maximum									50.00%
Debt Instrument, Debt Convenant, Outstanding Secured Debt, Maximum										125,000,000
Debt Instrument, Debt Convenant, Secured Debt, Percentage of Consolidated Total Assets, Maximum										30.00%
Bridge Loan														35,000,000
Debt Instrument, Amended Additional Investor Amount																				7,600,000
Long-term Debt	222,355,000		152,062,000			29,300,000	28,500,000				100,480,000	89,499,000	25,000,000					46,200,000			37,900,000
Future Cancellation Of Debt, Amount															44,200,000	13,000,000								5,400,000
Debt Instrument, Trailing Sixty Day Discount																			15.00%
Debt Instrument, Convertible, Conversion Price, Event Date Price																			$ 2.15
Plant Manufacturing Production, Volume																			1,000,000
Plant Manufacturing Production, Period																			45 days
Plant Manufacturing Production, Product Sales, Percentage																			5.00%
Debt Instrument, Convertible, Conversion Price, Milestone Price																			$ 1.87
Debt Instrument, Convertible, Conversion Price, Interest Accrued for Six Months																			5.00%
Debt Instrument, Convertible, Conversion Price, Interest Accrued for Three Months																			6.50%				13.00%
Debt Instrument, Convertible, Conversion Price, Interest Period																			30 months				36 months
Debt Instrument, Convertible, Conversion Price, Interest Accrued Thereafter																			8.00%				16.00%
Debt Instrument, Unamortized Discount (Premium), Net						$ 3,700,000	$ 4,000,000

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Balance Sheet Components - Derivative Liability (Details) (USD $) In Thousands, unless otherwise specified	Jun. 30, 2014		Dec. 31, 2013
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Fair market value of swap obligation	$ 2,808		$ 3,600
Fair value of compound embedded derivative liability(1)	145,032	[1]	131,117	[1]
Total derivative liability	$ 147,840		$ 134,717

[1] The compound embedded derivative liability represents the fair value of the bifurcated conversion options that contain "make-whole" provisions or down round conversion price adjustment provisions included in the outstanding Total Notes, Tranche I Notes, Tranche II Notes and the Rule 144A Convertible Note Offering (see Note 3, "Fair value of financial instruments" and Note 5, "Debt").

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Stock-Based Compensation - Nonemployee Stock-Based Compensation (Details) (Non Employee Share Based Compensation [Member], USD $)	3 Months Ended		6 Months Ended
	Jun. 30, 2014	Jun. 30, 2013	Jun. 30, 2014	Jun. 30, 2013
Stock Options [Member]
Share-based Goods and Nonemployee Services Transaction [Line Items]
Granted options to purchase, common stock			20,000	20,000
Compensation expense	$ 97,226	$ 8,000	$ 138,900	$ 22,000
Expected dividend yield	0.00%	0.00%	0.00%	0.00%
Risk-free interest rate	2.00%	2.00%	2.00%	2.00%
Expected term (in years)	5 years 9 months 18 days	6 years 1 month 6 days	5 years 11 months 9 days	6 years 4 months 24 days
Expected volatility	75.00%	82.00%	76.00%	83.00%
Restricted Stock Units (RSUs) [Member]
Share-based Goods and Nonemployee Services Transaction [Line Items]
Compensation expense	$ 12,000	$ 15,000	$ 9,000	$ 39,000

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Debt - Related Party Convertible Notes (Details)	3 Months Ended		6 Months Ended																0 Months Ended	1 Months Ended							1 Months Ended		3 Months Ended											3 Months Ended				0 Months Ended				1 Months Ended				0 Months Ended	1 Months Ended					1 Months Ended											3 Months Ended
	Jun. 30, 2014 USD ($)	Jun. 30, 2013 USD ($)	Jun. 30, 2014 USD ($)	Jun. 30, 2013 USD ($)	Mar. 31, 2014 USD ($)	Dec. 31, 2013 USD ($)	Jun. 30, 2014 Pine and Nossa Caixa Loan Agreement [Member] USD ($)	Jul. 13, 2012 Pine and Nossa Caixa Loan Agreement [Member] BRL	Jun. 30, 2014 Loans Payable [Member] USD ($)	Mar. 31, 2014 Loans Payable [Member] USD ($)	Dec. 31, 2013 Loans Payable [Member] USD ($)	Oct. 31, 2012 Loans Payable [Member]	Mar. 31, 2014 Loans Payable [Member] Pine and Nossa Caixa Loan Agreement [Member] USD ($)	Dec. 31, 2013 Loans Payable [Member] Pine and Nossa Caixa Loan Agreement [Member] USD ($)	Mar. 31, 2014 Unsecured Senior Convertible Promissory Notes [Member] USD ($)	Dec. 31, 2013 Unsecured Senior Convertible Promissory Notes [Member] USD ($)	Dec. 02, 2013 Unsecured Senior Convertible Promissory Notes [Member] USD ($)	Sep. 30, 2013 Unsecured Senior Convertible Promissory Notes [Member] USD ($)	Jul. 30, 2012 Related Party Convertible Notes [Member] USD ($)	Jan. 31, 2014 Related Party Convertible Notes [Member] USD ($)	Jun. 30, 2014 Related Party Convertible Notes [Member] USD ($)	Dec. 31, 2013 Related Party Convertible Notes [Member] USD ($)	Dec. 02, 2013 Related Party Convertible Notes [Member] USD ($)	Oct. 31, 2013 Related Party Convertible Notes [Member] USD ($)	Dec. 24, 2012 Related Party Convertible Notes [Member] USD ($)	Oct. 31, 2013 Related Party Convertible Notes [Member] Temasek Bridge Note [Member] USD ($)	Oct. 31, 2013 Related Party Convertible Notes [Member] August 2013 Convertible Notes [Member] USD ($)	Aug. 31, 2013 Related Party Convertible Notes [Member] August 2013 Convertible Notes [Member] USD ($)	Jun. 30, 2014 Related Party Convertible Notes [Member] Rule 144A Convertible Notes [Member] USD ($)	Jun. 30, 2014 Related Party Convertible Notes [Member] Unsecured Debt [Member] USD ($)	Mar. 31, 2014 Related Party Convertible Notes [Member] Unsecured Debt [Member] USD ($)	Dec. 31, 2013 Related Party Convertible Notes [Member] Unsecured Debt [Member] USD ($)	Sep. 14, 2012 Related Party Convertible Notes [Member] Unsecured Senior Convertible Notes 1.5% Due 2017 [Member] USD ($)	Jul. 30, 2012 Related Party Convertible Notes [Member] Unsecured Senior Convertible Notes 1.5% Due 2017 [Member]	Jul. 26, 2013 Related Party Convertible Notes [Member] July 2013 Convertible Notes [Member] USD ($)	Jun. 06, 2013 Related Party Convertible Notes [Member] July 2013 Convertible Notes [Member] USD ($)	Dec. 31, 2013 Loans Payable Lessor Emeryville Plant [Member] USD ($)	Dec. 31, 2010 Loans Payable Lessor Emeryville Plant [Member] USD ($)	Dec. 24, 2012 Private Placement [Member] Related Party Convertible Notes [Member] USD ($)	Dec. 31, 2013 Private Placement [Member] Related Party Convertible Notes [Member] Unsecured Senior Convertible Notes 1.5% Due 2017 [Member] USD ($)	Jul. 31, 2013 Initial Installment [Member] Related Party Convertible Notes [Member] USD ($)	Jun. 30, 2013 Initial Installment [Member] Related Party Convertible Notes [Member] USD ($)	Jul. 30, 2012 Initial Installment [Member] Related Party Convertible Notes [Member] USD ($)	Jul. 30, 2012 Initial Installment [Member] Related Party Convertible Notes [Member] July 2014 Convertible Notes [Member] USD ($)	Jul. 30, 2012 Second Installment [Member] Related Party Convertible Notes [Member] January 2015 Convertible Notes [Member] USD ($)	Jan. 31, 2014 First Tranche [Member] August 2013 Convertible Notes [Member] USD ($)	Jun. 30, 2014 First Tranche [Member] Related Party Convertible Notes [Member] USD ($)	Jan. 31, 2014 First Tranche [Member] Related Party Convertible Notes [Member] August 2013 Convertible Notes [Member] USD ($)	Oct. 31, 2013 First Tranche [Member] Related Party Convertible Notes [Member] August 2013 Convertible Notes [Member] USD ($) l	Aug. 31, 2013 First Tranche [Member] Related Party Convertible Notes [Member] August 2013 Convertible Notes [Member] USD ($)	Dec. 31, 2013 Second Tranche [Member] Related Party Convertible Notes [Member] USD ($)	Dec. 02, 2013 Second Tranche [Member] Related Party Convertible Notes [Member] August 2013 Convertible Notes [Member] USD ($)	Jan. 31, 2014 Second Tranche [Member] Related Party Convertible Notes [Member] August 2013 Convertible Notes [Member] USD ($)	Aug. 31, 2013 Second Tranche [Member] Related Party Convertible Notes [Member] August 2013 Convertible Notes [Member] USD ($)	Oct. 31, 2013 First and Second Tranche [Member] Related Party Convertible Notes [Member] August 2013 Convertible Notes [Member]	Mar. 24, 2013 May 15th 2013 [Member] Related Party Convertible Notes [Member] USD ($)	Mar. 24, 2013 June 15th 2013 [Member] Related Party Convertible Notes [Member] USD ($)	Aug. 31, 2013 Maximum [Member] Related Party Convertible Notes [Member] August 2013 Convertible Notes [Member] USD ($)	Oct. 31, 2013 Maximum [Member] Related Party Convertible Notes [Member] August 2013 Convertible Notes [Member] USD ($)	Aug. 31, 2013 Common Stock [Member] Related Party Convertible Notes [Member] August 2013 Convertible Notes [Member]	Aug. 31, 2013 Common Stock [Member] Private Placement [Member] Related Party Convertible Notes [Member] August 2013 Convertible Notes [Member] USD ($)	Feb. 29, 2012 Fidelity [Member] Unsecured Senior Convertible Promissory Notes [Member] USD ($)	Oct. 31, 2013 Related Party Financings [Member] Temasek Bridge Note [Member]	Sep. 30, 2013 Related Party Financings [Member] August 2013 Convertible Notes [Member] USD ($)	Aug. 31, 2013 Related Party Financings [Member] August 2013 Convertible Notes [Member] USD ($)	Jul. 31, 2013 Related Party Financings [Member] Unsecured Senior Convertible Promissory Notes [Member] July 2013 Convertible Notes [Member] USD ($)	Jun. 30, 2013 Related Party Financings [Member] Unsecured Senior Convertible Promissory Notes [Member] July 2013 Convertible Notes [Member] USD ($)	Jun. 30, 2012 Bridge Loan [Member] Banco Pine S.A Loan Agreement June 2012 [Member] BRL	Jun. 30, 2014 Related Party Financings [Member] Related Party Convertible Notes [Member] Rule 144A Convertible Notes [Member] USD ($)	Jun. 30, 2014 Related Party Financings [Member] Temasek [Member] Related Party Convertible Notes [Member] Rule 144A Convertible Notes [Member] USD ($)	Jun. 30, 2014 Related Party Financings [Member] Total [Member] Related Party Convertible Notes [Member] Rule 144A Convertible Notes [Member] USD ($)
Debt Instrument [Line Items]
Debt Instrument, Face Amount							$ 23,600,000	52,000,000		$ 600,000									$ 105,000,000												$ 69,000,000		$ 15,000,000		$ 20,000,000	$ 10,000,000		$ 0		$ 5,000,000	$ 20,000,000	$ 10,000,000	$ 30,000,000			$ 34,000,000				$ 42,600,000			$ 3,000,000	$ 30,400,000				$ 73,000,000	$ 51,800,000		$ 110,000,000	$ 25,000,000			$ 73,000,000	$ 20,000,000	$ 10,000,000	52,000,000
Collateral Provided By Company, Certain Equipment and Other Tangible Assets, Amount							30,900,000	68,000,000
Debt Instrument, Interest Rate, Stated Percentage								5.50%				3.24%																			1.50%			1.50%				10.00%																								3.00%	5.50%			1.50%	1.50%
Proceeds from Convertible Debt	72,000,000																												24,700,000																																								5,000,000	10,000,000	9,700,000
Future Proceeds from Convertible Debt																			21,700,000									60,000,000	9,700,000															10,850,000	10,850,000					35,000,000		6,000,000	6,000,000	25,000,000
Debt Instrument, Convertible, Conversion Price																	$ 2.20	$ 7.0682	$ 7.0682												$ 4.11				$ 3.08				$ 2.98				$ 3.08						$ 2.44				$ 2.87
Convertible Debt																															75,000,000
Debt Instrument, Convertible, Common Stock, Shares																																							1,677,852																							3,536,968
Collaboration Agreement, Funding Obligation Advanced Installments																																																								10,000,000	10,000,000
Private Placement Convertible Notes, Period																																																										24 months
Debt Instrument, Closing Price Plus Incremental Rate																			$ 0.01
Debt Instrument, Interest Rate, Default Rate, Stated Percentage																			2.50%
Debt Instrument, Convertible, Period Prior to Maturity to Eligible For Conversion																			10 days
Period of Lock-up Upon Conversion of Debt																			6 months
Loss from extinguishment of debt	(1,100,000)	0	(10,512,000)	0																(9,400,000)																				900,000								(19,900,000)
Convertible Debt, Amount Outstanding																									53,300,000
Debt Instrument, Early Repayment, Percentage of Principal																			101.00%
Debt Instrument, Debt Convenant, Outstanding Debt, Maximum																																																														200,000,000
Debt Instrument, Debt Convenant, Percentage of Consolidated Total Assets, Maximum																																																														50.00%
Debt Instrument, Debt Convenant, Outstanding Secured Debt, Maximum																			125,000,000
Debt Instrument, Debt Convenant, Secured Debt, Percentage of Consolidated Total Assets, Maximum																			30.00%
Bridge Loan																								35,000,000		35,000,000																																						5,000,000
Debt Instrument, Amended Additional Investor Amount																																																		7,600,000
Debt Instrument, Amended Promissory Note, Amount																											14,600,000																						9,200,000
Future Cancellation Of Debt, Amount																											44,200,000	13,000,000																										5,400,000
Class of Warrant or Right, Number of Securities Called by Warrants or Rights																																																												1,000,000
Class of Warrant or Right, Exercise Price of Warrants or Rights																																																												0.01
Export Financing Agreement					2,200,000
Long-term Debt	222,355,000		222,355,000			152,062,000			25,999,000		25,259,000		23,600,000	22,200,000	29,300,000	28,500,000					100,480,000	89,499,000	25,000,000							40,300,000		51,500,000					0										46,200,000				37,900,000
Debt Instrument, Unamortized Discount																					(55,300,000)	23,900,000
Debt Instrument, Unamortized Discount	$ 83,900,000		$ 83,900,000																		$ 83,900,000									$ 13,100,000		$ 17,600,000															$ 31,600,000				$ 6,300,000
Debt Instrument, Convertible, Conversion Price, Event Date Price																																																	$ 2.15
Plant Manufacturing Production, Volume																																																	1,000,000
Plant Manufacturing Production, Period																																																	45 days
Plant Manufacturing Production, Product Sales, Percentage																																																	5.00%
Debt Instrument, Convertible, Conversion Price, Milestone Price																																																	$ 1.87
Debt Instrument, Convertible, Conversion Price, Interest Accrued for Six Months																																																	5.00%
Debt Instrument, Convertible, Conversion Price, Interest Accrued for Three Months																																																	6.50%				13.00%
Debt Instrument, Convertible, Conversion Price, Interest Period																																																	30 months				36 months
Debt Instrument, Convertible, Conversion Price, Interest Accrued Thereafter																																																	8.00%				16.00%
Debt Instrument, Term																																																					12 months
Debt Instrument, Convertible, Conversion Price, Interest Accrued																																																					10.00%
Debt Instrument, Convertible, Conversion Price, Interest Accrued for Defaults																																																					12.00%
Percentage of Principal Amount of Notes, Required to Be Repaid In Change of Control																																																							101.00%

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Balance Sheet Components - Other Assets (Details) (USD $)	Jun. 30, 2014		Dec. 31, 2013
Deposits on property and equipment, including taxes	$ 2,095,000		$ 1,970,000
Recoverable taxes from Brazilian government entities	9,064,000		6,599,000
Debt issuance cost (2)	978,000	[1]	454,000	[1]
Investments in joint venture (1)	2,170,000	[2]	68,000	[2]
Other (2)	1,519,000	[1]	1,494,000	[1]
Total other assets	15,826,000		10,585,000
Novvi LLC [Member]
Investments in joint venture (1)	2,100,000		0
Total Amyris Biosolutions B.V [Member]
Investments in joint venture (1)	$ 100,000		$ 100,000

[1] Certain classifications of prior period amounts have been made to conform to the current period presentation. Such reclassifications did not materially change previously reported consolidated financial statements.

[2] The investments in joint venture represents the Company's investments in the joint venture with Novvi LLC and Total Amyris Biosolutions B.V. of $2.1 million and $0.1 million as of June 30, 2014, respectively, and zero and $0.1 million as of December 31, 2013, respectively.

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Stock-Based Compensation (Tables)

6 Months Ended

Jun. 30, 2014

Share-based Compensation Arrangement by Share-based Payment Award [Line Items]

Schedule of Share-based Compensation, Stock Options and Stock Appreciation Rights Award Activity

The Company’s stock option activity and related information for the six months ended June 30, 2014 was as follows:

		Number Outstanding		Weighted- Average Exercise Price		Weighted-Average Remaining Contractual Life (Years)	Aggregate Intrinsic Value
							(in thousands)
Outstanding - December 31, 2013		8,409,605		$	7.39	7.40	$	12,393
	Options granted	2,909,183		$	3.51
	Options exercised	(337,110	)	$	3.06
	Options cancelled	(485,971	)	$	7.09
Outstanding - June 30, 2014		10,495,707		$	6.47	7.72	$	3,709
Vested and Expected to vest after June 30, 2014		9,590,575		$	6.72	7.58	$	3,326
Exercisable at June 30, 2014		4,554,010		$	9.29	6.13	$	1,027

Schedule of Share-based Compensation, Restricted Stock and Restricted Stock Units Activity

The Company’s restricted stock units (or RSUs) and restricted stock activity and related information for the six months ended June 30, 2014 was as follows:

	RSUs		Weighted-Average Grant-Date Fair Value		Weighted Average Remaining Contractual Life (Years)
Outstanding - December 31, 2013	2,316,437		$	4.30	0.88
Awarded	1,049,300		$	3.51	—
Vested	(1,158,585	)	$	4.68	—
Forfeited	(98,863	)	$	3.17	—
Outstanding - June 30, 2014	2,108,289		$	3.75	1.39
Expected to vest after June 30, 2014	1,803,053		$	3.75	1.31

Schedule of Share-based Compensation, Shares Authorized under Stock Option Plans, by Exercise Price Range

The following table summarizes information about stock options outstanding as of June 30, 2014:

	Options Outstanding				Options Exercisable
Exercise Price	Number of Options	Weighted- Average Remaining Contractual Life (Years)	Weighted-Average Exercise Price		Number of Options	Weighted-Average Exercise Price
$0.10—$2.79	1,580,682	8.20	$	2.66	476,896	$	2.52
$2.81—$2.94	1,056,600	8.94	$	2.88	279,097	$	2.87
$2.96—$3.44	945,057	8.55	$	3.14	304,429	$	3.07
$3.51—$3.51	2,489,199	9.75	$	3.51	—	$	—
$3.55—$3.93	1,700,908	5.75	$	3.88	1,247,160	$	3.89
$4.06—$16.00	1,555,854	5.94	$	10.11	1,281,705	$	9.88
$16.50—$24.50	724,345	5.97	$	20.10	625,057	$	20.11
$25.43—$25.43	15,000	7.07	$	25.43	15,000	$	25.43
$26.84—$26.84	368,062	6.64	$	26.84	264,666	$	26.84
$30.17—$30.17	60,000	6.71	$	30.17	60,000	$	30.17
$0.10—$30.17	10,495,707	7.72	$	6.47	4,554,010	$	9.29

Schedule of Employee Service Share-based Compensation, Allocation of Recognized Period Costs

Stock-based compensation expense related to options and restricted stock units granted to employees and nonemployees was allocated to research and development expense and sales, general and administrative expense as follows (in thousands):

	Three Months Ended June 30,				Six Months Ended June 30,
	2014		2013		2014		2013
Research and development	$	909	$	1,049	$	1,707	$	2,296
Sales, general and administrative	2,774		3,936		5,490		6,882
Total stock-based compensation expense	$	3,683	$	4,985	$	7,197	$	9,178

Employee Share Based Compensation [Member]

Share-based Compensation Arrangement by Share-based Payment Award [Line Items]

Schedule of Share-based Payment Award, Stock Options, Valuation Assumptions

Stock-based compensation expense for RSUs is measured based on the closing fair market value of the Company's common stock on the date of grant. Stock-based compensation expense for stock options and employee stock purchase plan rights is estimated at the grant date and offering date, respectively, based on the fair-value using the Black-Scholes option pricing model. The fair value of employee stock options is being amortized on a straight-line basis over the requisite service period of the awards. The fair value of employee stock options was estimated using the following weighted-average assumptions:

	Three Months Ended June 30,				Six Months Ended June 30,
	2014		2013		2014		2013
Expected dividend yield	—	%	—	%	—	%	—	%
Risk-free interest rate	2	%	1	%	2	%	1	%
Expected term (in years)	6.09		6.10		6.10		6.10
Expected volatility	75	%	82	%	75	%	82	%

Non Employee Share Based Compensation [Member]

Share-based Compensation Arrangement by Share-based Payment Award [Line Items]

Schedule of Share-based Payment Award, Stock Options, Valuation Assumptions

The fair value of nonemployee stock options was estimated using the following weighted-average assumptions:

	Three Months Ended June 30,				Six Months Ended June 30,
	2014		2013		2014		2013
Expected dividend yield	—	%	—	%	—	%	—	%
Risk-free interest rate	2	%	2	%	2	%	2	%
Expected term (in years)	5.80		6.10		5.94		6.40
Expected volatility	75	%	82	%	76	%	83	%

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Income Taxes (Details) (USD $) In Thousands, unless otherwise specified	3 Months Ended		6 Months Ended
	Jun. 30, 2014	Jun. 30, 2013	Jun. 30, 2014	Jun. 30, 2013
Income Tax Disclosure [Abstract]
Income Tax Expense (Benefit), Continuing Operations	$ 125	$ 246	$ 236	$ 482

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Debt - Letters of Credit (Details) (USD $)	Jun. 30, 2014	Dec. 31, 2013	Jun. 30, 2012
Debt Instrument [Line Items]
Restricted cash	$ 1,721,000	$ 1,648,000
Letter of Credit [Member]
Debt Instrument [Line Items]
Letters of Credit Outstanding, Amount			1,000,000
Restricted cash	$ 1,700,000	$ 900,000

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Net Income (Loss) Attributable to Common Stockholders and Net Income (Loss) per Share (Details) (USD $) In Thousands, except Share data, unless otherwise specified	3 Months Ended		6 Months Ended
	Jun. 30, 2014	Jun. 30, 2013	Jun. 30, 2014	Jun. 30, 2013
Earnings Per Share [Abstract]
Net loss attributable to Amyris, Inc. common stockholders	$ (35,479)	$ (38,876)	$ (19,094)	$ (71,490)
Interest on convertible debt	0	0	3,169	0
Accretion of debt discount	0	0	2,518	0
Gain from change in fair value of derivative instruments	0	0	(59,995)	0
Net loss attributable to Amyris, Inc. common stockholders after assumed conversion	$ (35,479)	$ (38,876)	$ (73,402)	$ (71,490)
Weighted average shares of common stock outstanding for basic EPS (in shares)	78,604,692	75,959,228	77,722,437	74,640,314
Basic earnings (loss) per share (in dollars per share)	$ (0.45)	$ (0.51)	$ (0.25)	$ (0.96)
Effect of dilutive securities:
Convertible promissory notes	0	0	32,909,641	0
Weighted common stock equivalents	0	0	32,909,641	0
Diluted weighted-average common shares	78,604,692	75,959,228	110,632,078	74,640,314
Diluted earnings (loss) per share (in dollars per share)	$ (0.45)	$ (0.51)	$ (0.66)	$ (0.96)
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive Securities Excluded from Computation of Earnings Per Share, Amount (in shares)	83,352,294	25,212,048	50,268,185	25,212,048
Stock Options to Purchase Common Stock [Member]
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive Securities Excluded from Computation of Earnings Per Share, Amount (in shares)	10,495,707	8,803,300	10,495,707	8,803,300
Convertible Promissory Notes [Member]
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive Securities Excluded from Computation of Earnings Per Share, Amount (in shares)	69,727,211	13,617,144	36,643,102	13,617,144
Common Stock Subject to Repurchase [Member]
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive Securities Excluded from Computation of Earnings Per Share, Amount (in shares)	0	1	0	1
Common Stock Warrants [Member]
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive Securities Excluded from Computation of Earnings Per Share, Amount (in shares)	1,021,087	21,087	1,021,087	21,087
Restricted Stock Units [Member]
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive Securities Excluded from Computation of Earnings Per Share, Amount (in shares)	2,108,289	2,770,516	2,108,289	2,770,516

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Subsequent Events (Details) (Related Party Convertible Notes [Member], USD $) In Millions, unless otherwise specified	0 Months Ended		1 Months Ended
	Jul. 30, 2012	Jul. 30, 2012 Initial Installment [Member] July 2014 Convertible Notes [Member]	Jul. 31, 2014 Subsequent Event [Member] July 2014 Convertible Notes [Member]	Jul. 31, 2014 Subsequent Event [Member] Initial Installment [Member] July 2014 Convertible Notes [Member]
Subsequent Event [Line Items]
Future Proceeds from Convertible Debt	$ 21.70	$ 10.85	$ 21.70	$ 10.85

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Employee Benefit Plan (Details) (USD $) In Millions, unless otherwise specified	3 Months Ended		6 Months Ended
	Jun. 30, 2014	Mar. 31, 2014	Jun. 30, 2014
Compensation and Retirement Disclosure [Abstract]
401K Voluntary Contributions, Percentage of Eligible Compensation		90.00%
Defined Contribution Plan, Minimum Service Vesting Period		1 year
Defined Contribution Plan, Employer Discretionary Contribution Amount	$ 0.1		$ 0.2

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Subsequent Events

6 Months Ended

Jun. 30, 2014

Subsequent Events [Abstract]

Subsequent Events

Subsequent Events

In July 2014, the Company closed on the initial installment of the remaining $21.7 million in convertible notes to be issued to Total under the July 2012 Agreements as described in in Note 5, "Debt", in the amount of $10.85 million and expect the second installment to occur by January 2015.

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Debt - FINEP Credit Facility (Details) (FINEP Credit Facility [Member]) In Millions, unless otherwise specified	0 Months Ended	6 Months Ended		6 Months Ended
	Nov. 30, 2010	Jun. 30, 2014	Nov. 30, 2010 Minimum [Member]	Jun. 30, 2014 Maximum [Member]	Jun. 30, 2014 FINEP Project [Member] USD ($)	Nov. 30, 2010 FINEP Project [Member] BRL	Jun. 30, 2014 Chattel Mortgage [Member] USD ($)	Jun. 30, 2014 Chattel Mortgage [Member] BRL	Dec. 31, 2013 Chattel Mortgage [Member] USD ($)	Dec. 31, 2013 Chattel Mortgage [Member] BRL	Nov. 30, 2010 Chattel Mortgage [Member] BRL
Line of Credit Facility [Line Items]
Line of Credit Facility, Maximum Borrowing Capacity							$ 2.9				6.4
Debt Instrument, Interest Rate, Stated Percentage	5.00%
Long-term Debt, Percentage Bearing Fixed Interest, Percentage Rate			6.00%
Debt Instrument, Basis Spread on Variable Rate		5.00%
Long-term Debt, Percentage Bearing Variable Interest, Percentage Rate	11.00%
Debt Instrument Debt Default Fine Percentage	10.00%
Debt Instrument Interest On Late Balance Percentage Per Month	1.00%
Period Credit Line Is Available				81 months
Line of Credit Facility, Amount Outstanding							2.2	4.8	2.2	5.2
Research and Development Project, Amount To Be Contributed From Company Funds					6.6	14.5
Research and Development Project Amount To Be Contributed From Company Prior To Release Of Second Tranche						11.1
Guaranty Liabilities							$ 1.5				3.3
Period Of Time Amounts Released Must Be Used	30 months

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- Derivative Disclosures (Details) (USD $) In Thousands, unless otherwise specified					3 Months Ended				6 Months Ended				3 Months Ended		6 Months Ended				6 Months Ended
	Jun. 30, 2014	Dec. 31, 2013	Jun. 30, 2014 Future [Member] Not Designated as Hedging Instrument [Member] Currency interest rate swap, included as net liability in other long term liability [Member] Contracts	Dec. 31, 2013 Future [Member] Not Designated as Hedging Instrument [Member] Currency interest rate swap, included as net liability in other long term liability [Member] Contracts	Jun. 30, 2014 Currency interest rate swap [Member] Not Designated as Hedging Instrument [Member] Other income (expense), net [Member]		Jun. 30, 2013 Currency interest rate swap [Member] Not Designated as Hedging Instrument [Member] Other income (expense), net [Member]		Jun. 30, 2014 Currency interest rate swap [Member] Not Designated as Hedging Instrument [Member] Other income (expense), net [Member]		Jun. 30, 2013 Currency interest rate swap [Member] Not Designated as Hedging Instrument [Member] Other income (expense), net [Member]		Jun. 30, 2014 Derivative Liability - Compound Embedded Derivatives [Member]	Jun. 30, 2013 Derivative Liability - Compound Embedded Derivatives [Member]	Jun. 30, 2014 Derivative Liability - Compound Embedded Derivatives [Member]	Jun. 30, 2013 Derivative Liability - Compound Embedded Derivatives [Member]	Jun. 30, 2014 Significant Unobservable Inputs (Level 3) [Member] Derivative Liability - Compound Embedded Derivatives [Member]	Dec. 31, 2013 Significant Unobservable Inputs (Level 3) [Member] Derivative Liability - Compound Embedded Derivatives [Member]	Jun. 30, 2014 Derivative Financial Instruments, Liabilities [Member] Significant Unobservable Inputs (Level 3) [Member] Derivative Liability - Compound Embedded Derivatives [Member]		Jun. 30, 2014 Fair Value Measurement [Domain] Significant Unobservable Inputs (Level 3) [Member] Derivative Liability - Compound Embedded Derivatives [Member]
Derivative [Line Items]
Quantity of Short Contracts (in contracts)			1	1
Fair Value	$ (2,808)	$ (3,600)	$ 2,808	$ 3,600
Derivative contracts, gain (loss)					722	[1]	(1,639)	[1]	1,056	[1]	(1,651)	[1]
Fair value, beginning of period																	145,032	131,117
Transfer in to Level 3 net of cancellation														1,400	1,100				86,551	[2]
Total (income) loss from change in fair value of derivative liability													4,000		(53,100)	(2,500)					72,636
Fair value, end of period																	$ 145,032	$ 131,117

[1] Certain classifications of prior period amounts have been made to conform to the current period presentation. Such reclassifications did not materially change previously reported consolidated financial statements.

[2] Includes $1.1 million removal of derivative liability related to debt extinguishment.

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Comprehensive Income (Loss) (Details) (USD $) In Thousands, unless otherwise specified	Jun. 30, 2014	Dec. 31, 2013
Equity [Abstract]
Foreign currency translation adjustment, net of tax	$ (15,634)	$ (20,087)
Total accumulated other comprehensive loss	$ (15,634)	$ (20,087)

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The Company (Details) (USD $)	6 Months Ended
	Jun. 30, 2014	Dec. 31, 2013
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Expected Capital Expenditures During Next Fiscal Year	$ 9,000,000
Retained Earnings (Accumulated Deficit)	(840,532,000)	(821,438,000)
Cash, Cash Equivalents, and Short-term Investments	90,200,000
Debt Instrument, Unamortized Discount	83,900,000
Long-term Debt	222,355,000	152,062,000
Debt, current portion	$ 9,923,000	$ 6,391,000

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Debt - Hercules Loan Facility (Details) (USD $)	6 Months Ended
	Jun. 30, 2014	May 29, 2014	Mar. 31, 2014
Line of Credit Facility [Line Items]
Debt Instrument, Unamortized Discount	$ 83,900,000
Hercules Loan Facility [Member]
Line of Credit Facility [Line Items]
Loans Payable			25,000,000
Debt Instrument, Interest Rate, Stated Percentage		9.50%
Debt Instrument, Covenant Compliance	15.0
Debt Instrument, Financing Transaction, Additional Cash Proceeds		50,000,000
Debt Instrument, End of Term Fee Amount, Percentage		10.00%
Forbearance Fee Due		10,000,000	10,000,000
Prime Rate [Member] | Hercules Loan Facility [Member]
Line of Credit Facility [Line Items]
Debt Instrument, Interest Rate, Stated Percentage		6.25%
Funding Tranche [Domain] | Hercules Loan Facility [Member]
Line of Credit Facility [Line Items]
Debt Instrument, Interest Rate, Stated Percentage	8.50%
Convertible Notes Payable	29,700,000
Debt Instrument, Unamortized Discount	273,000
Debt Instrument, Financing Transaction, Additional Cash Proceeds	$ 5,000,000
Funding Tranche [Domain] | Prime Rate [Member] | Hercules Loan Facility [Member]
Line of Credit Facility [Line Items]
Debt Instrument, Interest Rate, Stated Percentage	5.25%

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Stock-Based Compensation - Stock Option Activity (Details) (USD $)	3 Months Ended		6 Months Ended			12 Months Ended	3 Months Ended	6 Months Ended	3 Months Ended	6 Months Ended	3 Months Ended	6 Months Ended	3 Months Ended	6 Months Ended	3 Months Ended	6 Months Ended	3 Months Ended	6 Months Ended	3 Months Ended	6 Months Ended	3 Months Ended	6 Months Ended	3 Months Ended	6 Months Ended	3 Months Ended	6 Months Ended	3 Months Ended	6 Months Ended
	Jun. 30, 2014	Jun. 30, 2013	Jun. 30, 2014	Jun. 30, 2013	Jun. 30, 2014 Employee Stock Option [Member]	Dec. 31, 2013 Employee Stock Option [Member]	Mar. 31, 2014 Employee Stock Option [Member] $0.10—$2.79	Jun. 30, 2014 Employee Stock Option [Member] $0.10—$2.79	Mar. 31, 2014 Employee Stock Option [Member] $2.81—$2.94	Jun. 30, 2014 Employee Stock Option [Member] $2.81—$2.94	Mar. 31, 2014 Employee Stock Option [Member] $2.96—$3.44	Jun. 30, 2014 Employee Stock Option [Member] $2.96—$3.44	Mar. 31, 2014 Employee Stock Option [Member] $3.51—$3.51	Jun. 30, 2014 Employee Stock Option [Member] $3.51—$3.51	Mar. 31, 2014 Employee Stock Option [Member] $3.55—$3.93	Jun. 30, 2014 Employee Stock Option [Member] $3.55—$3.93	Mar. 31, 2014 Employee Stock Option [Member] $4.06—$16.00	Jun. 30, 2014 Employee Stock Option [Member] $4.06—$16.00	Mar. 31, 2014 Employee Stock Option [Member] $16.50—$24.50	Jun. 30, 2014 Employee Stock Option [Member] $16.50—$24.50	Mar. 31, 2014 Employee Stock Option [Member] $25.43—$25.43	Jun. 30, 2014 Employee Stock Option [Member] $25.43—$25.43	Mar. 31, 2014 Employee Stock Option [Member] $26.84—$26.84	Jun. 30, 2014 Employee Stock Option [Member] $26.84—$26.84	Mar. 31, 2014 Employee Stock Option [Member] $30.17—$30.17	Jun. 30, 2014 Employee Stock Option [Member] $30.17—$30.17	Mar. 31, 2014 Employee Stock Option [Member] $0.10—$30.17	Jun. 30, 2014 Employee Stock Option [Member] $0.10—$30.17
Share-based Compensation Arrangement by Share-based Payment Award, Options, Outstanding [Roll Forward]
Options Oustanding, Beginning Balance					8,409,605
Options Outstanding, Options granted					2,909,183
Options Outstanding, Options exercised					(337,110)
Options Outstanding, Options cancelled					(485,971)
Options Outstanding, Ending Balance					10,495,707	8,409,605		1,580,682		1,056,600		945,057		2,489,199		1,700,908		1,555,854		724,345		15,000		368,062		60,000		10,495,707
Share-based Compensation Arrangement by Share-based Payment Award, Options, Outstanding, Weighted Average Exercise Price [Roll Forward]
Options Outstanding, Weighted Average Exercise Price, Beginning Balance					$ 7.39
Options Outstanding, Weighted Average Exercise Price, Options granted					$ 3.51
Options Outstanding, Weighted Average Exercise Price, Options exercised					$ 3.06
Options Outstanding, Weighted Average Exercise Price, Options cancelled					$ 7.09
Options Outstanding, Weighted Average Exercise Price, Ending Balance					$ 6.47	$ 7.39		$ 2.66		$ 2.88		$ 3.14		$ 3.51		$ 3.88		$ 10.11		$ 20.10		$ 25.43		$ 26.84		$ 30.17		$ 6.47
Options Outstanding, Weighted Average Remaining Contractual Life (Years)					7 years 8 months 19 days	7 years 4 months 24 days		8 years 2 months 12 days		8 years 11 months 9 days		8 years 6 months 18 days		9 years 9 months		5 years 9 months		5 years 11 months 9 days		5 years 11 months 19 days		7 years 0 months 26 days		6 years 7 months 21 days		6 years 8 months 16 days		7 years 8 months 19 days
Options Outstanding, Aggregate Intrinsic Value					$ 3,709,000	$ 12,393,000
Options, Vested and Expected to Vest, Number Outstanding					9,590,575
Options, Vested and Expected to Vest, Weighted Average Exercise Price					$ 6.72
Options, Vested and Expected to Vest, Weighted Average Remaining Contractual Life (Years)					7 years 6 months 29 days
Options, Vested and Expected to Vest, Aggregate Intrinsic Value					3,326,000
Options, Exercisable, Number Outstanding					4,554,010			476,896		279,097		304,429		0		1,247,160		1,281,705		625,057		15,000		264,666		60,000		4,554,010
Options, Exercisable, Weighted Average Exercise Price					$ 9.29			$ 2.52		$ 2.87		$ 3.07		$ 0.00		$ 3.89		$ 9.88		$ 20.11		$ 25.43		$ 26.84		$ 30.17		$ 9.29
Options, Exercisable, Weighted Average Remaining Contractual Life (Years)					6 years 1 month 17 days
Options, Exercisable, Aggregate Intrinsic Value					1,027,000
Aggregate intrinsic value of options exercised under all option plans	$ 0	$ 100,000	$ 500,000	$ 300,000
Exercise Price Range, Lower Range Limit							$ 0.10		$ 2.81		$ 2.96		$ 3.51		$ 3.55		$ 4.06		$ 16.5		$ 25.43		$ 26.84		$ 30.17		$ 0.10
Exercise Price Range, Upper Range Limit							$ 2.79		$ 2.94		$ 3.44		$ 3.51		$ 3.93		$ 16.00		$ 24.5		$ 25.43		$ 26.84		$ 30.17		$ 30.17

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Joint Ventures and Noncontrolling Interest - Variable Interest Entity (Details)	3 Months Ended			6 Months Ended						3 Months Ended			1 Months Ended						0 Months Ended	6 Months Ended	3 Months Ended		6 Months Ended
	Jun. 30, 2014 USD ($)		Jun. 30, 2013 USD ($)	Jun. 30, 2014 USD ($) consolidated_VIE		Jun. 30, 2013 USD ($)	Mar. 31, 2014 EUR (€)	Dec. 31, 2013 USD ($)		Mar. 31, 2014 Variable Interest Entity, Primary Beneficiary [Member] USD ($) consolidated_VIE	Jun. 30, 2014 Variable Interest Entity, Primary Beneficiary [Member] USD ($)	Dec. 31, 2013 Variable Interest Entity, Primary Beneficiary [Member] USD ($)	Jan. 31, 2011 Glycotech Agreement [Member]	Jan. 31, 2011 Glycotech Agreement [Member] Variable Interest Entity, Primary Beneficiary [Member]	Jun. 30, 2014 Glycotech Agreement [Member] Variable Interest Entity, Primary Beneficiary [Member] USD ($)	Mar. 26, 2013 Joint Venture with Cosan [Member] USD ($)	Mar. 26, 2013 Joint Venture with Cosan [Member] Corporate Joint Venture [Member]	Jun. 30, 2011 Joint Venture with Cosan [Member] Corporate Joint Venture [Member]	Mar. 26, 2013 Joint Venture with Cosan [Member] Amyris Brasil S.A. Subsidiary [Member] BRL	Jun. 30, 2014 Joint Venture with Cosan [Member] Amyris Brasil S.A. Subsidiary [Member] BRL	Jun. 30, 2014 Novvi LLC [Member] USD ($)	Jun. 30, 2013 Novvi LLC [Member] USD ($)	Jun. 30, 2014 Novvi LLC [Member] USD ($)	Jun. 30, 2013 Novvi LLC [Member] USD ($)	Dec. 31, 2013 Novvi LLC [Member] USD ($)	Apr. 14, 2010 SMA Industria Quimica S.A. [Member] Corporate Joint Venture [Member]	Jun. 30, 2014 SMA Industria Quimica S.A. [Member] Maximum [Member] Corporate Joint Venture [Member] USD ($)	Mar. 31, 2014 SMA Industria Quimica S.A. [Member] Maximum [Member] Corporate Joint Venture [Member] BRL	Jun. 30, 2014 Novvi LLC [Member] USD ($)
Variable Interest Entity [Line Items]
Equity Method Investment Ownership Percentage Required																		10.00%
Equity Method Investment, Ownership Percentage																	50.00%	50.00%								50.00%
Agreement to Sell Equity Ownership																			22,000	9,989
Due from Joint Ventures																											28,100,000	61,800,000
Variable Interest Entity, Consolidated, Carrying Amount, Assets										27,509,000		25,730,000
Period of Initial Term of Collaboration Agreement													2 years
Additional Year Periods of Collaboration Agreement													1 year
Variable Interest Entity, Financial or Other Support, Percentage														100.00%
Variable Interest Entity Number of Entities (in VIEs)				2						2
Variable Interest Entity, Consolidated, Carrying Amount, Other Assets											4,100,000
Variable Interest Entity, Consolidated, Carrying Amount, Current Assets										500,000
Variable Interest Entity, Consolidated, Carrying Amount, Accounts Payable And Accrued Liabilities											200,000
Variable Interest Entity, Consolidated, Carrying Amount, Loan Obligations															100,000
Assets											22,900,000
Liabilities										421,000		229,000
Obligation to Fund Agreement, Cash Portion																10,000,000
Investments in joint venture (1)	2,170,000	[1]		2,170,000	[1]			68,000	[1]												2,100,000		2,100,000		0				200,000
Equity Method Investment, Summarized Financial Information, Gross Profit (Loss)																							0
Related party grants and collaborations revenue	0		109,000	0		2,647,000															0	300,000	0	2,800,000
Capitalization, Long-term Debt and Equity							€ 100,000

[1] The investments in joint venture represents the Company's investments in the joint venture with Novvi LLC and Total Amyris Biosolutions B.V. of $2.1 million and $0.1 million as of June 30, 2014, respectively, and zero and $0.1 million as of December 31, 2013, respectively.

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Balance Sheet Components - Accrued and Other Current Liabilities (Details) (USD $) In Thousands, unless otherwise specified	Jun. 30, 2014	Dec. 31, 2013
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Professional services	$ 2,093	$ 2,279
Accrued vacation	2,516	2,274
Payroll and related expenses	3,939	5,066
Tax-related liabilities	157	825
Deferred rent, current portion	1,111	1,111
Accrued interest	1,246	3,176
Contractual obligations to contract manufacturers	853	4,241
Other	846	2,249
Total accrued and other current liabilities	$ 12,761	$ 21,221

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Summary of Significant Accounting Policies

6 Months Ended

Jun. 30, 2014

Accounting Policies [Abstract]

Summary of Significant Accounting Policies

Summary of Significant Accounting Policies

Basis of Presentation

The accompanying interim condensed consolidated financial statements have been prepared in accordance with the accounting principles generally accepted in the United States of America (“GAAP”) and with the instructions for Form 10-Q and Regulation S-X. Accordingly, they do not include all of the information and notes required for complete financial statements. These interim condensed consolidated financial statements should be read in conjunction with the consolidated financial statements and notes thereto contained in the Company’s Form 10-K filed with the Securities and Exchange Commission (“SEC”) on April 2, 2014. The unaudited condensed consolidated financial statements include the accounts of the Company and its consolidated subsidiaries. All intercompany accounts and transactions have been eliminated in consolidation.

Principles of Consolidation

The Company has interests in joint venture entities that are variable interest entities (“VIEs”). Determining whether to consolidate a variable interest entity requires judgment in assessing (i) whether an entity is a VIE and (ii) if the Company is the entity’s primary beneficiary and thus required to consolidate the entity. To determine if the Company is the primary beneficiary of a VIE, the Company evaluates whether it has (i) the power to direct the activities that most significantly impact the VIE’s economic performance and (ii) the obligation to absorb losses or the right to receive benefits of the VIE that could potentially be significant to the VIE. The Company’s evaluation includes identification of significant activities and an assessment of its ability to direct those activities based on governance provisions and arrangements to provide or receive product and process technology, product supply, operations services, equity funding and financing and other applicable agreements and circumstances. The Company’s assessment of whether it is the primary beneficiary of its VIEs requires significant assumptions and judgment.

The condensed consolidated financial statements of the Company include the accounts of Amyris, Inc., its subsidiaries and two consolidated VIEs with respect to which the Company is considered the primary beneficiary, after elimination of intercompany accounts and transactions. Disclosure regarding the Company’s participation in the VIEs is included in Note 7, "Joint Ventures and Noncontrolling Interest."

Use of Estimates

In preparing the unaudited condensed consolidated financial statements, management must make estimates and assumptions that affect the reported amounts of assets and liabilities and disclosure of contingent assets and liabilities as of the date of the unaudited condensed consolidated financial statements and the reported amounts of revenue and expenses during the reporting period. Actual results could differ from those estimates.

Unaudited Interim Financial Information

The accompanying interim condensed consolidated financial statements and related disclosures are unaudited, have been prepared on the same basis as the annual consolidated financial statements and, in the opinion of management, reflect all adjustments, which include only normal recurring adjustments, necessary for a fair statement of the results of operations for the periods presented.

The year-end condensed consolidated balance sheet data was derived from audited financial statements, but does not include all disclosures required by GAAP. The condensed consolidated results of operations for any interim period are not necessarily indicative of the results to be expected for the full year or for any other future year or interim period.

Recent Accounting Pronouncements

In July 2013, the Financial Accounting Standards Board ("FASB") issued an amended accounting standard update on the financial statement presentation of unrecognized tax benefits. The amended guidance provides that a liability related to an unrecognized tax benefit would be presented as a reduction of a deferred tax asset for a net operating loss carryforward, a similar tax loss or a tax credit carryforward if such settlement is required or expected in the event the uncertain tax position is disallowed. The new guidance became effective for the Company on January 1, 2014 and will be applied prospectively to unrecognized tax benefits that exist at the effective date with retrospective applications permitted. The Company's current presentation of unrecognized tax benefits conforms with the amended guidance. Accordingly, there was no significant impact to the Company resulting from the guidance.

In May 2014, the FASB issued a new guidance related to revenue recognition. This new standard will replace all current GAAP guidance on this topic and eliminate all industry-specific guidance. The new revenue recognition standard provides a unified model to determine how revenue is recognized. The core principle of the guidance is that an entity should recognize revenue to depict the transfer of promised goods or services to customers in an amount that reflects the consideration to which the entity expects to be entitled in exchange for those goods or services. This guidance will be effective for the Company beginning January 1, 2017 and can be applied either retrospectively to each period presented or as a cumulative-effect adjustment as of the date of adoption. The Company is currently assessing the impact of adopting this new accounting standard on its financial statements.

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Joint Ventures and Noncontrolling Interest - Noncontrolling Interest (Details) (USD $)	3 Months Ended		6 Months Ended		3 Months Ended		6 Months Ended	3 Months Ended	1 Months Ended
	Jun. 30, 2014	Jun. 30, 2013	Jun. 30, 2014 consolidated_VIE	Jun. 30, 2013	Mar. 31, 2014 Noncontrolling Interest [Member]	Mar. 31, 2013 Noncontrolling Interest [Member]	Jun. 30, 2014 Noncontrolling Interest [Member]	Mar. 31, 2014 Variable Interest Entity, Primary Beneficiary [Member] consolidated_VIE	Jan. 31, 2011 Variable Interest Entity, Primary Beneficiary [Member] Glycotech Agreement [Member]	Apr. 14, 2010 SMA Industria Quimica S.A. [Member] Corporate Joint Venture [Member] member
Noncontrolling Interest [Line Items]
Equity Method Investment Number of Members of Executive Committee that are Senior Executive										1
Variable Interest Entity, Consolidated, Carrying Amount, Current Assets								$ 500,000
Variable Interest Entity Number of Entities (in VIEs)			2					2
Variable Interest Entity, Financial or Other Support, Percentage									100.00%
Stockholders' Equity Attributable to Noncontrolling Interest [Roll Forward]
Beginning Balance			(584,000)		(584,000)	(877,000)	(584,000)
Foreign currency translation adjustment			4,411,000		(42,000)	54,000	(42,000)
Income (loss) attributable to noncontrolling interest	31,000	38,000	60,000	(261,000)	60,000	(261,000)
Ending Balance	$ (686,000)		$ (686,000)		$ (686,000)	$ (562,000)

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Balance Sheet Components - Inventory (Details) (USD $) In Thousands, unless otherwise specified	Jun. 30, 2014	Dec. 31, 2013
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Raw materials	$ 2,468	$ 1,796
Work-in-process	6,536	7,292
Finished goods	5,749	1,800
Inventories, net	$ 14,753	$ 10,888

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Debt (Tables)

6 Months Ended

Jun. 30, 2014

Debt Disclosure [Abstract]

Schedule of Debt

Debt is comprised of the following (in thousands):

	June 30, 2014			December 31, 2013
Credit facilities	$	37,972		$	8,767
Convertible notes	57,904			28,537
Related party convertible notes	100,480			89,499
Loans payable	25,999			25,259
Total debt	222,355			152,062
Less: current portion	(9,923		)	(6,391		)
Long-term debt	$	212,432		$	145,671

Schedule of Long-term Debt Instruments

Future minimum payments under the debt agreements as of June 30, 2014 are as follows (in thousands):

Years ending December 31:	Related Party Convertible Debt			Convertible Debt			Loans Payable			Credit Facility
2014 (remaining six months)	$	744		$	1,891		$	4,080		$	2,539
2015	1,606			4,020			4,114			15,426
2016	1,606			4,020			3,935			20,301
2017	58,849			28,715			3,772			7,822
2018	74,485			15,685			3,612			472
Thereafter	75,825			56,798			11,751			131
Total future minimum payments	213,115			111,129			31,264			46,691
Less: amount representing interest(1)	(112,635		)	(53,225		)	(5,265		)	(8,719		)
Present value of minimum debt payments	100,480			57,904			25,999			37,972
Less: current portion	—			—			(5,218		)	(4,705		)
Noncurrent portion of debt	$	100,480		$	57,904		$	20,781		$	33,267

______________ 

⁽¹⁾ Including debt discount of $83.9 million related to the embedded derivative associated with the related party and non-related party convertible debt which will be accreted to interest expense under the effective interest method over the term of the convertible debt.

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Balance Sheet Components (Tables)

6 Months Ended

Jun. 30, 2014

Organization, Consolidation and Presentation of Financial Statements [Abstract]

Schedule of Inventory, Current

Inventories are stated at the lower of cost or market and consist of the following (in thousands):

	June 30, 2014		December 31, 2013
Raw materials	$	2,468	$	1,796
Work-in-process	6,536		7,292
Finished goods	5,749		1,800
Inventories, net	$	14,753	$	10,888

Schedule of Prepaid and Other Current Assets

Prepaid expenses and other current assets is comprised of the following (in thousands):

	June 30, 2014		December 31, 2013
Maintenance (1)	$	393	$	258
Prepaid insurance(1)	603		894
Manufacturing catalysts	1,715		1,536
Recoverable VAT and other taxes	2,776		5,125
Other (1)	1,651		1,705
Prepaid expenses and other current assets	$	7,138	$	9,518

______________ 

⁽¹⁾  Certain classifications of prior period amounts have been made to conform to the current period presentation. Such reclassifications did not materially change previously reported consolidated financial statements.

Property, Plant and Equipment

Property, plant and equipment, net is comprised of the following (in thousands):

	June 30, 2014			December 31, 2013
Leasehold improvements	$	39,208		$	39,034
Machinery and equipment	101,383			96,585
Computers and software	8,946			8,509
Furniture and office equipment	2,584			2,535
Buildings	7,606			7,148
Vehicles	436			488
Construction in progress	44,635			41,387
	204,798			195,686
Less: accumulated depreciation and amortization	(64,142		)	(55,095		)
Property, plant and equipment, net	$	140,656		$	140,591

Schedule of Other Assets, Noncurrent

Other assets are comprised of the following (in thousands):

	June 30, 2014		December 31, 2013
Deposits on property and equipment, including taxes	$	2,095	$	1,970
Recoverable taxes from Brazilian government entities	9,064		6,599
Debt issuance cost (2)	978		454
Investments in joint venture (1)	2,170		68
Other (2)	1,519		1,494
Total other assets	$	15,826	$	10,585

Schedule Of Accrued And Other Current Liabilities

Accrued and other current liabilities are comprised of the following (in thousands):

	June 30, 2014		December 31, 2013
Professional services	$	2,093	$	2,279
Accrued vacation	2,516		2,274
Payroll and related expenses	3,939		5,066
Tax-related liabilities	157		825
Deferred rent, current portion	1,111		1,111
Accrued interest	1,246		3,176
Contractual obligations to contract manufacturers	853		4,241
Other	846		2,249
Total accrued and other current liabilities	$	12,761	$	21,221

Schedule of Derivative Liability

Derivative liability is comprised of the following (in thousands):

	June 30, 2014		December 31, 2013
Fair market value of swap obligation	$	2,808	$	3,600
Fair value of compound embedded derivative liability(1)	145,032		131,117
Total derivative liability	$	147,840	$	134,717

______________ 

⁽¹⁾  The compound embedded derivative liability represents the fair value of the bifurcated conversion options that contain "make-whole" provisions or down round conversion price adjustment provisions included in the outstanding Total Notes, Tranche I Notes, Tranche II Notes and the Rule 144A Convertible Note Offering (see Note 3, "Fair value of financial instruments" and Note 5, "Debt").

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Debt - Loans Payable (Details)					1 Months Ended											1 Months Ended				0 Months Ended	3 Months Ended
	Jun. 30, 2014 USD ($)	Mar. 31, 2014 USD ($)	Dec. 31, 2013 USD ($)	Jun. 30, 2012 Banco Pine S.A Loan Agreement June 2012 [Member] Bridge Loan [Member] BRL	Jul. 31, 2012 Pine and Nossa Caixa Loan Agreement [Member]	Jun. 30, 2014 Pine and Nossa Caixa Loan Agreement [Member] USD ($)	Jul. 13, 2012 Pine and Nossa Caixa Loan Agreement [Member] BRL	Jul. 30, 2012 Banco Pine July 2012 Loan Agreement [Member] BRL	Jul. 30, 2012 Nossa Caixa Loan Agreement [Member] BRL	Jun. 30, 2014 Loans Payable [Member] USD ($)	Mar. 31, 2014 Loans Payable [Member] USD ($)	Dec. 31, 2013 Loans Payable [Member] USD ($)	Oct. 31, 2012 Loans Payable [Member]	Mar. 31, 2014 Loans Payable [Member] Pine and Nossa Caixa Loan Agreement [Member] USD ($)	Dec. 31, 2013 Loans Payable [Member] Pine and Nossa Caixa Loan Agreement [Member] USD ($)	Dec. 31, 2009 Loans Payable Lessor Emeryville Plant [Member]	Dec. 31, 2013 Loans Payable Lessor Emeryville Plant [Member] USD ($)	Dec. 31, 2010 Loans Payable Lessor Emeryville Plant [Member] USD ($)	Jun. 30, 2014 Interest Rate Swap [Member] Banco Pine July 2012 Loan Agreement [Member]	Mar. 18, 2013 ABC Brasil Agreement [Member] USD ($)	Mar. 31, 2014 ABC Brasil Agreement [Member] USD ($)
Debt Instrument [Line Items]
Debt Instrument, Face Amount				52,000,000		$ 23,600,000	52,000,000	22,000,000	30,000,000		$ 600,000							$ 0
Debt Instrument, Interest Rate, Stated Percentage							5.50%						3.24%					10.00%
Repayment Period																96 months
Long-term Debt	222,355,000		152,062,000							25,999,000		25,259,000		23,600,000	22,200,000		0
Derivative, Fixed Interest Rate																			3.94%
Collateral Provided By Company, Certain Equipment and Other Tangible Assets, Amount						30,900,000	68,000,000
Debt Instrument, Period of Interest Only Quarterly Payments					2 years
Loans Payable to Bank										0		400,000
Other Loans Payable	100,000	200,000	0
Export Financing Agreement		$ 2,200,000																		$ 2,500,000	$ 2,200,000
Export Funding Agreement, Term																				1 year	1 year

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Balance Sheet Components - Prepaid and Other Current Assets (Details) (USD $) In Thousands, unless otherwise specified	Jun. 30, 2014		Dec. 31, 2013
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Maintenance (1)	$ 393	[1]	$ 258	[1]
Prepaid insurance(1)	603	[1]	894	[1]
Manufacturing catalysts	1,715		1,536
Recoverable VAT and other taxes	2,776		5,125
Other (1)	1,651	[1]	1,705	[1]
Prepaid expenses and other current assets	$ 7,138		$ 9,518

[1] Certain classifications of prior period amounts have been made to conform to the current period presentation. Such reclassifications did not materially change previously reported consolidated financial statements.

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Commitments and Contingencies (Tables)

6 Months Ended

Jun. 30, 2014

Commitments and Contingencies Disclosure [Abstract]

Schedule of Future Minimum Payments For Lease Obligations

Future minimum payments under the Company's lease obligations as of June 30, 2014, are as follows (in thousands):

Years ending December 31:	Capital Leases			Operating Leases		Total Lease Obligations
2014 (remaining six months)	$	557		$	3,182	$	3,739
2015	462			6,606		7,068
2016	159			6,614		6,773
2017	—			6,588		6,588
2018	—			6,675		6,675
Thereafter	—			32,320		32,320
Total future minimum lease payments	1,178			$	61,985	$	63,163
Less: amount representing interest	(68		)
Present value of minimum lease payments	1,110
Less: current portion	(882		)
Long-term portion	$	228

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Joint Ventures and Noncontrolling Interest (Tables)

6 Months Ended

Jun. 30, 2014

Joint Ventures and Noncontrolling Interest [Abstract]

Schedule of Variable Interest Entities

The table below reflects the carrying amount of the assets and liabilities of the two consolidated VIEs for which the Company is the primary beneficiary. As of June 30, 2014, the assets include $22.9 million in property, plant and equipment, $4.1 million in other assets and $0.5 million in current assets. The liabilities include $0.2 million in accounts payable and accrued current liabilities and $0.1 million in loan obligations by Glycotech to its shareholders that are non-recourse to the Company. The creditors of each consolidated VIE have recourse only to the assets of that VIE.

	June 30,		December 31,
(In thousands)	2014		2013
Assets	$	27,509	$	25,730
Liabilities	$	421	$	229

Noncontrolling Interest

The change in noncontrolling interest for the six months ended June 30, 2014 and 2013, is summarized below (in thousands):

	2014			2013
Balance at January 1	$	(584	)	$	(877	)
Foreign currency translation adjustment	(42		)	54
Gain (loss) attributable to noncontrolling interest	(60		)	261
Balance at June 30	$	(686	)	$	(562	)

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The Company

6 Months Ended

Jun. 30, 2014

Organization, Consolidation and Presentation of Financial Statements [Abstract]

The Company

The Company

Amyris, Inc. (the “Company”) was incorporated in California on July 17, 2003 and reincorporated in Delaware on June 10, 2010 for the purpose of leveraging breakthroughs in industrial bioscience technology to develop and provide renewable compounds for a variety of markets. The Company is currently applying its industrial bioscience technology platform to provide alternatives to select petroleum-sourced products used in consumer care, specialty chemical and transportation fuel markets worldwide. The Company's first commercialization efforts have been focused on a renewable hydrocarbon molecule called farnesene (Biofene®), which forms the basis for a wide range of products including emollients, fragrance oils and diesel fuel. While the Company's platform is able to use a wide variety of feedstocks, the Company is initially focused on Brazilian sugarcane. In addition, the Company has entered into various contract manufacturing agreements to support commercial production. The Company has established two principal operating subsidiaries, Amyris Brasil Ltda. (formerly Amyris Brasil S.A., or "Amyris Brasil") for production in Brazil, and Amyris Fuels, LLC (or "Amyris Fuels").

The Company's renewable products business strategy is to focus on direct commercialization of specialty products while moving established commodity products into joint venture arrangements with leading industry partners. To commercialize its products, the Company must be successful in using its technology to manufacture its products at commercial scale and on an economically viable basis (i.e., low per unit production costs). The Company is building its experience producing renewable products at commercial scale. The Company's prospects are subject to risks, expenses and uncertainties frequently encountered by companies in this stage of development.

The Company expects to fund its operations for the foreseeable future with cash and cash equivalents and investments currently on hand, with cash inflows from collaboration and grant funding, cash contributions from product sales, and with new debt and equity financings. The Company's planned 2014 and 2015 working capital needs and its planned operating and capital expenditures are dependent on significant inflows of cash from new and existing collaboration partners and from cash contributions from growth in renewable product sales, as well as additional funding from new joint ventures or other collaborations, and may also require additional funding from debt or equity financings. The Company will continue to need to fund its research and development and related activities and to provide working capital to fund production, storage, distribution and other aspects of its business. The Company's operating plan contemplates capital expenditures of approximately $9.0 million in 2014 and the Company expects to continue to incur costs in connection with its existing contract manufacturing arrangements.

Liquidity

The Company has incurred significant losses since its inception and believes that it will continue to incur losses and negative cash flow from operations through 2014. As of June 30, 2014, the Company had an accumulated deficit of $840.5 million and had cash, cash equivalents and short term investments of $90.2 million. The Company has significant outstanding debt and contractual obligations related to purchase commitments, as well as capital and operating leases. As of June 30, 2014, the Company's debt, net of discount of $83.9 million, totaled $222.4 million, of which $9.9 million matures within the next twelve months. In addition, the Company's debt agreements contain various covenants, including restrictions on the Company's business that could cause the Company to be at risk of defaults. Please refer to Note 5, “Debt” and Note 6, “Commitments and Contingencies” for further details regarding the Company's debt obligations and commitments.

The Company’s operating plan for 2014 contemplates significant reduction in the Company’s net cash outflows, resulting from (i) revenue growth from sales of existing and new products, (ii) reduced production costs compared to prior periods as a result of manufacturing and technical developments in 2013, (iii) cash inflows from collaborations consistent with levels achieved in 2013 and (iv) operating expenses maintained at reduced levels. Achieving a reduction in net cash outflows from these factors is subject to risks and uncertainties, including those set forth in Part II, Item 1A of this Quarterly Report on Form 10-Q, “Risk Factors.”

In addition to cash contributions from product sales and debt and equity financings, the Company also depends on collaboration funding to support its operating expenses. While part of this funding is committed based on existing collaboration agreements, the Company will need to identify and obtain funding under additional collaborations that are not yet subject to any definitive agreement or are not yet identified. In addition, some of the Company’s existing collaboration funding is subject to achievement by the Company of milestones or other funding conditions.

If the Company is unable to increase positive gross margin product sales or generate sufficient additional payments from existing and new collaboration partners, it may need to obtain additional funding from equity financings, credit facilities, loans or issue additional preferred and/or discounted equity, agree to burdensome covenants, grant further security interest in its assets, enter into collaboration and licensing arrangements that require it to relinquish commercial rights, or grant licenses on terms that are not favorable. If the Company fails to generate positive gross margins product sales or secure such funding, the Company could be forced to curtail its operations, which would have a material adverse effect on the Company's ability to continue with its business plans.

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Goodwill and Intangible Assets (Tables)

6 Months Ended

Jun. 30, 2014

Goodwill and Intangible Assets Disclosure [Abstract]

Schedule of Intangible Assets and Goodwill

The following table presents the components of the Company's intangible assets (in thousands):

		June 30, 2014							December 31, 2013
	Useful Life in Years	Gross Carrying Amount		Accumulated Amortization			Net Carrying Value		Gross Carrying Amount		Accumulated Amortization			Net Carrying Value
In-process research and development	Indefinite	$	8,560	$	—		$	8,560	$	8,560	$	—		$	8,560
Acquired licenses and permits	2	772		(772		)	—		772		(772		)	—
Goodwill	Indefinite	560		—			560		560		—			560
		$	9,892	$	(772	)	$	9,120	$	9,892	$	(772	)	$	9,120

The following table presents the activity of intangible assets for the six months ended June 30, 2014 (in thousands):

	December 31, 2013								June 30, 2014
	Net Carrying Value		Additions		Adjustments		Amortization		Net Carrying Value
In-process research and development	$	8,560	$	—	$	—	$	—	$	8,560
Acquired licenses and permits	—		—		—		—		—
Goodwill	560		—		—		—		560
	$	9,120	$	—	$	—	$	—	$	9,120

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Fair Value of Financial Instruments - Fair Value Using Significant Unobservable Inputs (Level 3) (Details) (Convertible Notes Payable [Member], Significant Unobservable Inputs (Level 3) [Member], USD $) In Thousands, unless otherwise specified	6 Months Ended
	Jun. 30, 2014
Convertible Notes Payable [Member] | Significant Unobservable Inputs (Level 3) [Member]
Fair Value, Liabilities Measured on Recurring Basis, Unobservable Input Reconciliation, Calculation [Roll Forward]
Fair value, beginning of period	$ 131,952
Additions to convertible notes	93,295
Change in fair value of convertible notes	2,391
Fair value, end of period	$ 227,638

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Debt - Notes Payable (Details) (Notes Payable, Other Payables-Lessor [Member], USD $) In Millions, unless otherwise specified		0 Months Ended
	Oct. 31, 2008	Apr. 30, 2013 Amendment of Lease Agreement - Emeryville [Member]
Debt Instrument [Line Items]
Debt Instrument, Face Amount	$ 3.3
Debt Instrument, Interest Rate, Stated Percentage	9.50%
Lease Incentive, Elimination of Debt, Amount		$ 1.4

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Related Party Transactions (Details) (USD $)	3 Months Ended		6 Months Ended				3 Months Ended		6 Months Ended				3 Months Ended		6 Months Ended			6 Months Ended			0 Months Ended	1 Months Ended							1 Months Ended						3 Months Ended								1 Months Ended	3 Months Ended			1 Months Ended			0 Months Ended	1 Months Ended					1 Months Ended	3 Months Ended		6 Months Ended
	Jun. 30, 2014	Jun. 30, 2013	Jun. 30, 2014	Jun. 30, 2013	Apr. 04, 2014	Dec. 31, 2013	Jun. 30, 2014 Novvi LLC [Member]	Jun. 30, 2013 Novvi LLC [Member]	Jun. 30, 2014 Novvi LLC [Member]	Jun. 30, 2013 Novvi LLC [Member]	Jun. 30, 2014 Novvi LLC [Member]	Dec. 31, 2013 Novvi LLC [Member]	Jun. 30, 2014 Total Gas And Power USA Biotech Agreement [Member]	Jun. 30, 2013 Total Gas And Power USA Biotech Agreement [Member]	Jun. 30, 2014 Total Gas And Power USA Biotech Agreement [Member]	Jun. 30, 2013 Total Gas And Power USA Biotech Agreement [Member]	Dec. 31, 2013 Total Gas And Power USA Biotech Agreement [Member]	Jun. 30, 2014 Common Stock [Member]	Mar. 31, 2014 Unsecured Senior Convertible Promissory Notes [Member]	Dec. 31, 2013 Unsecured Senior Convertible Promissory Notes [Member]	Jul. 30, 2012 Related Party Convertible Notes [Member]	Jan. 31, 2014 Related Party Convertible Notes [Member]	Jun. 30, 2014 Related Party Convertible Notes [Member]	Dec. 31, 2013 Related Party Convertible Notes [Member]	Dec. 02, 2013 Related Party Convertible Notes [Member]	Oct. 31, 2013 Related Party Convertible Notes [Member]	Jul. 26, 2013 Related Party Convertible Notes [Member] July 2013 Convertible Notes [Member]	Jun. 06, 2013 Related Party Convertible Notes [Member] July 2013 Convertible Notes [Member]	Oct. 31, 2013 Related Party Convertible Notes [Member] August 2013 Convertible Notes [Member]	Aug. 31, 2013 Related Party Convertible Notes [Member] August 2013 Convertible Notes [Member]	Oct. 31, 2013 Related Party Convertible Notes [Member] Temasek Bridge Note [Member]	Jun. 30, 2014 Related Party Convertible Notes [Member] Unsecured Debt [Member]	Mar. 31, 2014 Related Party Convertible Notes [Member] Unsecured Debt [Member]	Dec. 31, 2013 Related Party Convertible Notes [Member] Unsecured Debt [Member]	Jun. 30, 2014 Related Party Convertible Notes [Member] Rule 144A Convertible Notes [Member]	Jun. 30, 2014 Related Party Convertible Notes [Member] Rule 144A Convertible Notes [Member] Related Party Financings [Member]	Jun. 30, 2014 Total [Member] Related Party Convertible Notes [Member] Rule 144A Convertible Notes [Member] Related Party Financings [Member]	Sep. 30, 2013 Related Party Financings [Member] August 2013 Convertible Notes [Member]	Aug. 31, 2013 Related Party Financings [Member] August 2013 Convertible Notes [Member]	Oct. 31, 2013 Related Party Financings [Member] Temasek Bridge Note [Member]	Jul. 31, 2013 Related Party Financings [Member] Unsecured Senior Convertible Promissory Notes [Member] July 2013 Convertible Notes [Member]	Jun. 30, 2013 Related Party Financings [Member] Unsecured Senior Convertible Promissory Notes [Member] July 2013 Convertible Notes [Member]	Oct. 31, 2013 Related Party Financings [Member] Cancellation of the Temasek Bridge Note [Member] Temasek Bridge Note [Member]	Jun. 30, 2014 Temasek [Member] Related Party Convertible Notes [Member] Rule 144A Convertible Notes [Member] Related Party Financings [Member]	Jan. 31, 2014 First Tranche [Member] August 2013 Convertible Notes [Member]	Jun. 30, 2014 First Tranche [Member] Related Party Convertible Notes [Member]	Jan. 31, 2014 First Tranche [Member] Related Party Convertible Notes [Member] August 2013 Convertible Notes [Member]	Aug. 31, 2013 First Tranche [Member] Related Party Convertible Notes [Member] August 2013 Convertible Notes [Member]	Dec. 31, 2013 Second Tranche [Member] Related Party Convertible Notes [Member]	Dec. 02, 2013 Second Tranche [Member] Related Party Convertible Notes [Member] August 2013 Convertible Notes [Member]	Jan. 31, 2014 Second Tranche [Member] Related Party Convertible Notes [Member] August 2013 Convertible Notes [Member]	Aug. 31, 2013 Second Tranche [Member] Related Party Convertible Notes [Member] August 2013 Convertible Notes [Member]	Mar. 31, 2013 Private Placement [Member] Biolding Investment SA [Member]	Mar. 26, 2013 Private Placement [Member] Biolding Investment SA [Member]	Aug. 31, 2013 Private Placement [Member] Related Party Convertible Notes [Member] Common Stock [Member] August 2013 Convertible Notes [Member]	Aug. 31, 2013 Private Placement [Member] Related Party Financings [Member] Common Stock [Member]	Jun. 30, 2014 Derivative Liability - Compound Embedded Derivatives [Member]	Jun. 30, 2013 Derivative Liability - Compound Embedded Derivatives [Member]	Jun. 30, 2014 Derivative Liability - Compound Embedded Derivatives [Member]	Jun. 30, 2013 Derivative Liability - Compound Embedded Derivatives [Member]	Jun. 30, 2014 Derivative Liability - Compound Embedded Derivatives [Member] Significant Unobservable Inputs (Level 3) [Member]	Dec. 31, 2013 Derivative Liability - Compound Embedded Derivatives [Member] Significant Unobservable Inputs (Level 3) [Member]	Jun. 30, 2014 Derivative Liability - Compound Embedded Derivatives [Member] Significant Unobservable Inputs (Level 3) [Member] Wolverine [Member]	Dec. 31, 2013 Derivative Liability - Compound Embedded Derivatives [Member] Significant Unobservable Inputs (Level 3) [Member] Wolverine [Member]
Related Party Transaction [Line Items]
Stock Issued During Period, Shares, New Issues																		943,396																																			1,533,742
Stock Issued During Period, Price Per Share, New Issues																																																					$ 3.26
Proceeds from issuance of common stock in private placements, net of issuance costs			$ 4,000,000	$ 19,980,000																																																	$ 5,000,000
Commitment to purchase company common stock																																																						15,000,000
Benefical Owner, Ownership Percentage of Common Stock																																																								5.00%
Debt Instrument, Interest Rate, Stated Percentage																																	1.50%							5.50%	1.50%	1.50%
Debt Instrument, Face Amount																					105,000,000						20,000,000	10,000,000					69,000,000						73,000,000		20,000,000	10,000,000			34,000,000			42,600,000			3,000,000	30,400,000			110,000,000
Bridge Loan																										35,000,000					35,000,000							5,000,000
Future Cancellation Of Debt, Amount																													44,200,000	13,000,000													35,000,000									5,400,000
Debt Instrument, Interest Rate, Stated Default Percentage																																								2.00%
Future Proceeds from Convertible Debt																					21,700,000									60,000,000					9,700,000													35,000,000		6,000,000	6,000,000	25,000,000
Proceeds from Convertible Debt	72,000,000																																		24,700,000	5,000,000	9,700,000							10,000,000
Long-term Debt	222,355,000		222,355,000			152,062,000													29,300,000	28,500,000			100,480,000	89,499,000	25,000,000							40,300,000		51,500,000												46,200,000			37,900,000
Debt Instrument, Unamortized Discount																							(55,300,000)	23,900,000
Gains (Losses) on Extinguishment of Debt	(1,100,000)	0	(10,512,000)	0																		(9,400,000)																									(19,900,000)
Fair Value, Measurement with Unobservable Inputs Reconciliations, Recurring Basis, Liability Value																																																													145,032,000	131,117,000	107,200,000	116,800,000
Fair Value, Measurement with Unobservable Inputs Reconciliation, Liability, Transfers Into Level 3																																																										1,400,000	1,100,000
Fair Value, Measurement with Unobservable Inputs Reconciliation, Recurring Basis, Liability, Gain (Loss) Included in Earnings																																																									(4,000,000)		53,100,000	2,500,000
Related party grants and collaborations revenue	0	109,000	0	2,647,000			0	300,000	0	2,800,000
Revenue from Related Parties													30,625	32,441	33,250	35,294
Related party accounts receivable											20,604	300,000	30,625		30,625		200,000
Pilot plant service agreement					900,000
Sublease agreement					100,000
Accrued Liabilities	$ 300,000		$ 300,000

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Condensed Consolidated Balance Sheets (USD $) In Thousands, unless otherwise specified	Jun. 30, 2014	Dec. 31, 2013
Current assets:
Cash and cash equivalents	$ 88,828	$ 6,868
Short-term investments	1,379	1,428
Accounts receivable, net of allowance of $479 and $479, respectively	4,675	7,734
Related party accounts receivable	51	484
Inventories, net	14,753	10,888
Prepaid expenses and other current assets	7,138	9,518
Total current assets	116,824	36,920
Property, plant and equipment, net	140,656	140,591
Restricted cash	1,721	1,648
Other assets	15,826	10,585
Goodwill and intangible assets	9,120	9,120
Total assets	284,147	198,864
Current liabilities:
Accounts payable	8,503	6,512
Deferred revenue	10,372	2,222
Accrued and other current liabilities	12,761	21,221
Capital lease obligation, current portion	882	956
Debt, current portion	9,923	6,391
Total current liabilities	42,441	37,302
Capital lease obligation, net of current portion	228	287
Long-term debt, net of current portion	111,952	56,172
Related party debt	100,480	89,499
Deferred rent, net of current portion	10,223	10,191
Deferred revenue, net of current portion	4,100	5,000
Derivative liability	147,840	134,717
Other liabilities	6,560	1,544
Total liabilities	423,824	334,712
Commitments and contingencies (Note 6)
Stockholders’ deficit:
Preferred stock - $0.0001 par value, 5,000,000 shares authorized, none issued and outstanding	0	0
Common stock - $0.0001 par value, 300,000,000 and 200,000,000 shares authorized as of June 30, 2014 and December 31, 2013; 78,914,451 and 76,662,812 shares issued and outstanding as of June 30, 2014 and December 31, 2013, respectively	8	8
Additional paid-in capital	717,167	706,253
Accumulated other comprehensive loss	(15,634)	(20,087)
Accumulated deficit	(840,532)	(821,438)
Total Amyris, Inc. stockholders’ deficit	(138,991)	(135,264)
Noncontrolling interest	(686)	(584)
Total stockholders' deficit	(139,677)	(135,848)
Total liabilities and stockholders' deficit	$ 284,147	$ 198,864

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Balance Sheet Components - Property, Plant and Equipment, net (Details) (USD $)	6 Months Ended		12 Months Ended																			3 Months Ended		6 Months Ended
	Jun. 30, 2014	Jun. 30, 2013	Dec. 31, 2013	Jun. 30, 2014 Capital Lease Obligations [Member]	Dec. 31, 2013 Capital Lease Obligations [Member]	Jun. 30, 2014 Leasehold improvements [Member]	Dec. 31, 2013 Leasehold improvements [Member]	Jun. 30, 2014 Machinery and equipment [Member]	Dec. 31, 2013 Machinery and equipment [Member]	Jun. 30, 2014 Computer and software [Member]	Dec. 31, 2013 Computer and software [Member]	Jun. 30, 2014 Furniture and office equipment [Member]	Dec. 31, 2013 Furniture and office equipment [Member]	Jun. 30, 2014 Buildings [Member]	Dec. 31, 2013 Buildings [Member]	Jun. 30, 2014 Vehicles [Member]	Dec. 31, 2013 Vehicles [Member]	Jun. 30, 2014 Construction in progress [Member]	Dec. 31, 2013 Construction in progress [Member]	Jun. 30, 2014 Machinery and Equipment and Furniture and Office Equipment Under Capital Lease [Member] Capital Lease Obligations [Member]	Dec. 31, 2013 Machinery and Equipment and Furniture and Office Equipment Under Capital Lease [Member] Capital Lease Obligations [Member]	Jun. 30, 2014 Property Plant and Equipment Including Capital Leases [Member]	Jun. 30, 2013 Property Plant and Equipment Including Capital Leases [Member]	Jun. 30, 2014 Property Plant and Equipment Including Capital Leases [Member]	Jun. 30, 2013 Property Plant and Equipment Including Capital Leases [Member]
Property, Plant and Equipment [Line Items]
Property, Plant and Equipment, Gross	$ 204,798,000		$ 195,686,000			$ 39,208,000	$ 39,034,000	$ 101,383,000	$ 96,585,000	$ 8,946,000	$ 8,509,000	$ 2,584,000	$ 2,535,000	$ 7,606,000	$ 7,148,000	$ 436,000	$ 488,000	$ 44,635,000	$ 41,387,000	$ 3,800,000	$ 3,400,000
Less: accumulated depreciation and amortization	(64,142,000)		(55,095,000)	(1,800,000)	(1,500,000)
Property, plant and equipment, net	140,656,000		140,591,000
Depreciation and amortization expense	7,539,000	8,491,000																				3,700,000	4,100,000	7,500,000	8,500,000
Interest Costs Capitalized	$ 500,000		$ 500,000

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Condensed Consolidated Statements of Stockholders' Deficit (USD $) In Thousands, except Share data, unless otherwise specified	Total	Common Stock [Member]	Additional Paid-in Capital [Member]	Accumulated Deficit [Member]	Accumulated Other Comprehensive Income (Loss) [Member]	Noncontrolling Interest [Member]
Beginning Balance at Dec. 31, 2013						$ (584)
Increase (Decrease) in Stockholders' Equity [Roll Forward]
Foreign currency translation adjustment, net of tax						(42)
Ending Balance at Mar. 31, 2014
Beginning Balance at Dec. 31, 2013	(135,848)	8	706,253	(821,438)	(20,087)	(584)
Beginning Balance, shares at Dec. 31, 2013	76,662,812	76,662,812
Increase (Decrease) in Stockholders' Equity [Roll Forward]
Stock Issued During Period, Shares, Employee Stock Purchase Plans		551,707
Issuance of common stock upon exercise of stock options	1,507		1,507
Shares issued under restricted stock unit settlement, shares		756,536
Shares issued under restricted stock unit settlement	(1,790)		(1,790)
Issuance of common stock in a private placement, shares		943,396
Issuance of common stock in a private placement	4,000	4,000	4,000
Stock-based compensation	7,197		7,197
Foreign currency translation adjustment, net of tax	4,411				4,453	(42)
Net loss attributable to Amyris, Inc. common stockholders	(19,094)			(19,094)
Net loss	(19,154)					(60)
Ending Balance at Jun. 30, 2014	$ (139,677)	$ 8	$ 717,167	$ (840,532)	$ (15,634)	$ (686)
Ending Balance, shares at Jun. 30, 2014	78,914,451	78,914,451

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Commitments and Contingencies - Guarantor Arrangements/Purchase Obligations and Other Matters (Details) In Millions, except Per Share data, unless otherwise specified				3 Months Ended		0 Months Ended										0 Months Ended						0 Months Ended	3 Months Ended
	Jun. 30, 2014 USD ($)	Mar. 31, 2014 USD ($)	Nov. 30, 2010 FINEP Credit Facility [Member]	Jun. 30, 2014 FINEP Credit Facility [Member] Chattel Mortgage [Member] USD ($)	Mar. 31, 2014 FINEP Credit Facility [Member] Chattel Mortgage [Member] BRL	Nov. 15, 2011 Performance Guarantee [Member]	Mar. 31, 2014 Performance Guarantee [Member] Payment Guarantee [Member] USD ($)	Dec. 31, 2013 Performance Guarantee [Member] Payment Guarantee [Member] USD ($)	Nov. 15, 2011 Performance Guarantee [Member] Payment Guarantee [Member] USD ($)	Nov. 15, 2011 Performance Guarantee [Member] Payment Guarantee [Member] BRL	Jun. 30, 2014 BNDES Credit Facility [Member] BNDES [Member] USD ($)	Mar. 31, 2014 BNDES Credit Facility [Member] BNDES [Member] BRL	Dec. 31, 2011 BNDES Credit Facility [Member] BNDES [Member]	Jun. 30, 2014 Pine and Nossa Caixa Loan Agreement [Member] USD ($)	Jul. 13, 2012 Pine and Nossa Caixa Loan Agreement [Member] BRL	Dec. 02, 2013 Unsecured Senior Convertible Promissory Notes [Member] USD ($)	Sep. 30, 2013 Unsecured Senior Convertible Promissory Notes [Member] USD ($)	Jul. 30, 2012 Related Party Convertible Notes [Member] USD ($)	Mar. 31, 2014 Related Party Convertible Notes [Member] Unsecured Debt [Member] USD ($)	May 29, 2014 Hercules Loan Facility [Member] USD ($)	Mar. 31, 2014 Hercules Loan Facility [Member] USD ($)	Mar. 18, 2013 ABC Brasil Agreement [Member] USD ($)	Mar. 31, 2014 ABC Brasil Agreement [Member] USD ($)
Loss Contingencies [Line Items]
Research and Development Asset Acquired Other than Through Business Combination, Fair Value Acquired				$ 2.7	6.0
Collateral Provided By Company, Certain Equipment and Other Tangible Assets, Amount											11.3	24.9		30.9	68.0
Export Financing Agreement		2.2																				2.5	2.2
Export Funding Agreement, Term																						1 year	1 year
Period Required For Restricted Cash						3 months
Restricted Cash and Cash Equivalents							0.8	0.7	0.1	0.2
Debt Instrument, Convertible Promissory Note, Held by Third Party																48.3
Debt Instrument, Convertible, Conversion Price																$ 2.20	$ 7.0682	$ 7.0682	$ 4.11
Debt Instrument, Face Amount														23.6	52.0			105.0	69.0
Debt Instrument, Interest Rate, Stated Percentage			5.00%										7.00%		5.50%				1.50%	9.50%
Loans Payable																					25.0
Purchase Obligation	6.8																		21.7
Purchase Obligation, Due in Second Year																			10.85
Forbearance Fee Due																				10.0	10.0
Debt Instrument, Financing Transaction, Additional Cash Proceeds																				50.0
Contractual Obligation	5.9
Loss on Purchase Commitments	$ 2.4

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Comprehensive Income (Loss) (Tables)

6 Months Ended

Jun. 30, 2014

Equity [Abstract]

Schedule of Accumulated Other Comprehensive Income (Loss)

The components of accumulated other comprehensive loss are as follows (in thousands):

	June 30, 2014			December 31, 2013
Foreign currency translation adjustment, net of tax	$	(15,634	)	$	(20,087	)
Total accumulated other comprehensive loss	$	(15,634	)	$	(20,087	)

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Stockholders' Deficit (Details) (USD $) In Thousands, except Share data, unless otherwise specified	3 Months Ended	6 Months Ended			1 Months Ended		1 Months Ended		6 Months Ended			3 Months Ended
	Mar. 31, 2014 votes	Jun. 30, 2014	Dec. 31, 2013	Sep. 30, 2010	Jan. 31, 2014 Equity Incentive Plan, 2010 [Member]	Dec. 31, 2013 Equity Incentive Plan, 2010 [Member]	Jan. 31, 2014 Employee Stock Purchase Plan, 2010 [Member]	Dec. 31, 2013 Employee Stock Purchase Plan, 2010 [Member]	Jun. 30, 2014 Additional Paid-in Capital [Member]	Jun. 30, 2014 Common Stock [Member]	Dec. 31, 2013 Common Stock [Member]	Mar. 31, 2014 Kuraray Securities Purchase Agreement [Member] Common Stock [Member]
Class of Stock [Line Items]
Issuance of common stock in a private placement, shares										943,396
Stock Issued During Period, Price Per Share, New Issues												$ 4.24
Issuance of common stock in a private placement		$ 4,000							$ 4,000	$ 4,000
Share-based Compensation Arrangement by Share-based Payment Award, Number of Additional Shares Authorized					3,833,141		766,628
Share-based Compensation Arrangement by Share-based Payment Award, Number of Additional Shares Authorized, Percentage Increase of Common Stock, Shares, Outstanding								1.00%
Shares Available For Issuance Percentage Of Total Outstanding Shares						5.00%
Common Stock, Shares, Outstanding		78,914,451	76,662,812							78,914,451	76,662,812
Common stock, shares authorized		300,000,000	200,000,000
Common Stock, Number of Votes Entitled to Holder of each share	1
Preferred stock, shares authorized		5,000,000	5,000,000	5,000,000

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Reporting Segments

6 Months Ended

Jun. 30, 2014

Segment Reporting [Abstract]

Reporting Segments

Reporting Segments

The chief operating decision maker for the Company is the chief executive officer. The chief executive officer reviews financial information presented on a consolidated basis, accompanied by information about revenue by geographic region, for purposes of allocating resources and evaluating financial performance. The Company has one business activity comprised of research and development and sales of fuels and farnesene-derived products and there are no segment managers who are held accountable for operations, operating results or plans for levels or components below the consolidated unit level. Accordingly, the Company has determined that it has a single reportable segment and operating segment structure.

Revenues by geography are based on the location of the customer. The following tables set forth revenue and long-lived assets by geographic area (in thousands):

Revenues

	Three Months Ended June 30,				Six Months Ended June 30,
	2014		2013		2014		2013
United States	$	2,815	$	4,458	$	4,788	$	10,022
Brazil	1,402		1,259		2,050		2,077
Europe	2,985		4,005		6,338		4,230
Asia	2,105		1,127		2,172		2,389
Total	$	9,307	$	10,849	$	15,348	$	18,718

Long-Lived Assets

	June 30, 2014		December 31, 2013
United States	$	49,628	$	54,015
Brazil	90,375		85,891
Europe	653		685
Total	$	140,656	$	140,591

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Net Income (Loss) Attributable to Common Stockholders and Net Income (Loss) per Share (Tables)

6 Months Ended

Jun. 30, 2014

Earnings Per Share [Abstract]

Schedule of Calculation of Basic and Diluted Net Loss Per Share of Common Stock Attributable to Amyris, Inc. Common Stockholders

The following table presents the calculation of basic and diluted net loss per share of common stock attributable to Amyris, Inc. common stockholders (in thousands, except share and per share amounts):

	Three Months Ended June 30,						Six Months Ended June 30,
	2014			2013			2014			2013
Numerator:
Net loss attributable to Amyris, Inc. common stockholders	$	(35,479	)	$	(38,876	)	$	(19,094	)	$	(71,490	)
Interest on convertible debt	—			—			3,169			—
Accretion of debt discount	—			—			2,518			—
Gain from change in fair value of derivative instruments	—			—			(59,995		)	—
Net loss attributable to Amyris, Inc. common stockholders after assumed conversion	$	(35,479	)	$	(38,876	)	$	(73,402	)	$	(71,490	)
Denominator:
Weighted average shares of common stock outstanding for basic EPS	78,604,692			75,959,228			77,722,437			74,640,314
Basic loss per share	$	(0.45	)	$	(0.51	)	$	(0.25	)	$	(0.96	)
Weighted average shares of common stock outstanding	78,604,692			75,959,228			77,722,437			74,640,314
Effect of dilutive securities:
Convertible promissory notes	—			—			32,909,641			—
Weighted common stock equivalents	—			—			32,909,641			—
Diluted weighted-average common shares	78,604,692			75,959,228			110,632,078			74,640,314
Diluted loss per share	$	(0.45	)	$	(0.51	)	$	(0.66	)	$	(0.96	)

Schedule of Antidilutive Securities Excluded from Computation of Earnings Per Share

The following outstanding shares of potentially dilutive securities were excluded from the computation of diluted net loss per share of common stock because including them would have been anti-dilutive:

	Three Months Ended June 30,		Six Months Ended June 30,
	2014	2013	2014	2013
Period-end stock options to purchase common stock	10,495,707	8,803,300	10,495,707	8,803,300
Convertible promissory notes	69,727,211	13,617,144	36,643,102	13,617,144
Period-end common stock subject to repurchase	—	1	—	1
Period-end common stock warrants	1,021,087	21,087	1,021,087	21,087
Period-end restricted stock units	2,108,289	2,770,516	2,108,289	2,770,516
Total	83,352,294	25,212,048	50,268,185	25,212,048

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Net Income (Loss) Attributable to Common Stockholders and Net Income (Loss) per Share

6 Months Ended

Jun. 30, 2014

Earnings Per Share [Abstract]

Net Income (Loss) Attributable to Common Stockholders and Net Income (Loss) per Share

Net Income (Loss) Attributable to Common Stockholders and Net Income (Loss) per Share

The Company computes net income (loss) per share in accordance with ASC 260, “Earnings per Share.” Basic net income (loss) per share of common stock is computed by dividing the Company’s net income (loss) attributable to Amyris, Inc. common stockholders by the weighted average number of shares of common stock outstanding during the period. Diluted net income (loss) per share of common stock is computed by giving effect to all potentially dilutive securities, including stock options, restricted stock units, common stock warrants, convertible promissory notes using the treasury stock method or the as converted method, as applicable. For the three months ended June 2014 and 2013 and for the six months ended June 30, 2013, basic net loss per share was the same as diluted net loss per share because the inclusion of all potentially dilutive securities outstanding was anti-dilutive. As such, the numerator and the denominator used in computing both basic and diluted net loss are the same.

The following table presents the calculation of basic and diluted net loss per share of common stock attributable to Amyris, Inc. common stockholders (in thousands, except share and per share amounts):

	Three Months Ended June 30,						Six Months Ended June 30,
	2014			2013			2014			2013
Numerator:
Net loss attributable to Amyris, Inc. common stockholders	$	(35,479	)	$	(38,876	)	$	(19,094	)	$	(71,490	)
Interest on convertible debt	—			—			3,169			—
Accretion of debt discount	—			—			2,518			—
Gain from change in fair value of derivative instruments	—			—			(59,995		)	—
Net loss attributable to Amyris, Inc. common stockholders after assumed conversion	$	(35,479	)	$	(38,876	)	$	(73,402	)	$	(71,490	)
Denominator:
Weighted average shares of common stock outstanding for basic EPS	78,604,692			75,959,228			77,722,437			74,640,314
Basic loss per share	$	(0.45	)	$	(0.51	)	$	(0.25	)	$	(0.96	)
Weighted average shares of common stock outstanding	78,604,692			75,959,228			77,722,437			74,640,314
Effect of dilutive securities:
Convertible promissory notes	—			—			32,909,641			—
Weighted common stock equivalents	—			—			32,909,641			—
Diluted weighted-average common shares	78,604,692			75,959,228			110,632,078			74,640,314
Diluted loss per share	$	(0.45	)	$	(0.51	)	$	(0.66	)	$	(0.96	)

The following outstanding shares of potentially dilutive securities were excluded from the computation of diluted net loss per share of common stock because including them would have been anti-dilutive:

	Three Months Ended June 30,		Six Months Ended June 30,
	2014	2013	2014	2013
Period-end stock options to purchase common stock	10,495,707	8,803,300	10,495,707	8,803,300
Convertible promissory notes	69,727,211	13,617,144	36,643,102	13,617,144
Period-end common stock subject to repurchase	—	1	—	1
Period-end common stock warrants	1,021,087	21,087	1,021,087	21,087
Period-end restricted stock units	2,108,289	2,770,516	2,108,289	2,770,516
Total	83,352,294	25,212,048	50,268,185	25,212,048

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Stock-Based Compensation - Restricted Stock Units and Restricted Stock Activity (Details) (Restricted Stock Units (RSUs) [Member], USD $)	6 Months Ended	12 Months Ended
	Jun. 30, 2014	Dec. 31, 2013
Restricted Stock Units (RSUs) [Member]
Share-based Compensation Arrangement by Share-based Payment Award, Equity Instruments Other than Options, Nonvested, Number of Shares [Roll Forward]
RSU's Outstanding, Beginning Balance	2,316,437
RSU's Oustanding, Units awarded	1,049,300
RSU's Outstanding, Units vested	(1,158,585)
RSU's Outstanding, Units forfeited	(98,863)
RSU's Outstanding, Ending Balance	2,108,289	2,316,437
Share-based Compensation Arrangement by Share-based Payment Award, Equity Instruments Other than Options, Nonvested, Weighted Average Grant Date Fair Value [Roll Forward]
RSU's Outstanding, Weighted Average Grant Date Fair Value, Beginning Balance	$ 4.30
Share-based Compensation Arrangement by Share-based Payment Award, Equity Instruments Other than Options, Grants in Period, Weighted Average Grant Date Fair Value	$ 3.51
Share-based Compensation Arrangement by Share-based Payment Award, Equity Instruments Other than Options, Vested in Period, Weighted Average Grant Date Fair Value	$ 4.68
Share-based Compensation Arrangement by Share-based Payment Award, Equity Instruments Other than Options, Forfeited in Period, Weighted Average Grant Date Fair Value	$ 3.17
RSU's Outstanding, Weighted Average Grant Date Fair Value, Ending Balance	$ 3.75	$ 4.30
RSU's Outstanding, Weighted Average Remaining Contractual Life (Years)	1 year 4 months 21 days	10 months 17 days
RSU's Outstanding, Expected to Vest	1,803,053
RSU's Outstanding, Expected to Vest, Weighted Average Grant Date Fair Value	$ 3.75
RSU's Outstanding, Expected to Vest , Weighted Average Remaining Contractual Life (Years)	1 year 3 months 22 days

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Condensed Consolidated Statements of Cash Flows (USD $)	6 Months Ended
	Jun. 30, 2014	Jun. 30, 2013
Operating activities
Net loss	$ (19,154,000)	$ (71,229,000)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation and amortization	7,539,000	8,491,000
Loss (gain) on disposal of property, plant and equipment	57,000	(38,000)
Stock-based compensation	7,197,000	9,178,000
Amortization of debt discount	3,763,000	1,061,000
Loss on extinguishment of debt	10,512,000	0
Loss on purchase commitments and write-off of production assets	159,000	8,423,000
Change in fair value of derivative instruments	(54,148,000)	(719,000)
Other non-cash expenses	(113,000)	213,000
Changes in assets and liabilities:
Accounts receivable	3,423,000	(3,812,000)
Related party accounts receivable	147,000	345,000
Inventories, net	(3,570,000)	1,150,000
Prepaid expenses and other assets	(323,000)	1,098,000
Accounts payable	1,879,000	(1,912,000)
Accrued and other liabilities	(608,000)	(5,619,000)
Deferred revenue	7,380,000	8,549,000
Deferred rent	33,000	(447,000)
Net cash used in operating activities	(35,827,000)	(45,268,000)
Investing activities
Purchase of investments	(883,000)	(1,763,000)
Maturities of investments	1,032,000	334,000
Change in restricted cash	0	(1,000)
Investment in joint venture	(2,075,000)	0
Purchases of property and equipment, net of disposals	(2,064,000)	(3,711,000)
Net cash used in investing activities	(3,990,000)	(5,141,000)
Financing activities
Proceeds from issuance of common stock, net of repurchases	71,000	167,000
Proceeds from issuance of common stock in private placements, net of issuance costs	4,000,000	19,980,000
Principal payments on capital leases	(515,000)	(867,000)
Proceeds from debt issued, net of issuance costs	83,171,000	2,645,000
Proceeds from debt issued to related party	39,012,000	10,000,000
Principal payments on debt	(3,596,000)	(1,902,000)
Net cash provided by financing activities	122,143,000	30,023,000
Effect of exchange rate changes on cash and cash equivalents	(366,000)	1,297,000
Net increase (decrease) in cash and cash equivalents	81,960,000	(19,089,000)
Cash and cash equivalents at beginning of period	6,868,000	30,592,000
Cash and cash equivalents at end of period	88,828,000	11,503,000
Supplemental disclosures of cash flow information:
Cash paid for interest	1,847,000	1,004,000
Income Taxes Paid, Net	0	0
Supplemental disclosures of non-cash investing and financing activities:
Acquisitions of property, plant and equipment under accounts payable, accrued liabilities and notes payable	(226,000)	307,000
Financing of insurance premium under notes payable	(318,000)	147,000
Receivable of proceeds for options exercised	(355,000)	0
Accrued offering cost of common stock in private placement	0	(19,000)
Capitalized interest	2,812,000	0
Non-cash investment in joint venture	$ (237,000)	$ 0

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Consolidated Balance Sheets (Parentheticals) (USD $) In Thousands, except Share data, unless otherwise specified	Jun. 30, 2014	Dec. 31, 2013
Allowance for Doubtful Accounts	$ 479	$ 479
Stockholders' Equity:
Preferred stock, par value	$ 0.0001	$ 0.0001
Preferred stock, shares authorized	5,000,000	5,000,000
Preferred stock, shares issued	0	0
Preferred stock, shares outstanding	0	0
Common stock, par value	$ 0.0001	$ 0.0001
Common stock, shares authorized	300,000,000	200,000,000
Common stock, shares issued	78,914,451	76,662,812
Common Stock, Shares, Outstanding	78,914,451	76,662,812

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Stockholders' Deficit

6 Months Ended

Jun. 30, 2014

Stockholders' Equity Note [Abstract]

Stockholders' Deficit

Stockholders’ Deficit

Private Placement

In March 2014, the Company completed a private placement of 943,396 shares of its common stock at a price of $4.24 per share for aggregate proceeds of $4.0 million (see Note 8, "Significant Agreements").

Evergreen Shares for 2010 Equity Plan and 2010 ESPP

In January 2014, the Company's Board of Directors (or "Board") approved an increase to the number of shares available for issuance under the Company's 2010 Equity Incentive Plan (or "Equity Plan") and the 2010 Employee Stock Purchase Plan (or "ESPP"). These shares represent an automatic annual increase in the number of shares available for issuance under the Equity Plan and the ESPP of 3,833,141 and 766,628, respectively. These increases equal 5% and 1%, respectively, of 76,662,812 shares, the total outstanding shares of the Company’s common stock as of December 31, 2013. This automatic increase was effective as of January 1, 2014. Shares available for issuance under the Equity Plan and ESPP were initially registered on a registration statement on Form S-8 filed with the Securities and Exchange Commission on October 1, 2010 (Registration No. 333-169715). The Company filed registration statements on Form S-8 on April 14, 2014 (Registration No. 333-195259) with respect to the shares added by the automatic increase on January 1, 2014.

Common Stock

As of June 30, 2014, the Company was authorized to issue 300,000,000 shares of common stock pursuant to the Company’s amended and restated certificate of incorporation. Holders of the Company’s common stock are entitled to dividends as and when declared by the Board, subject to the rights of holders of all classes of stock outstanding having priority rights as to dividends. There have been no dividends declared to date. The holder of each share of common stock is entitled to one vote.

Preferred Stock

Pursuant to the Company’s amended and restated certificate of incorporation, the Company is authorized to issue 5,000,000 shares of preferred stock. The Board has the authority, without action by its stockholders, to designate and issue shares of preferred stock in one or more series and to fix the rights, preferences, privileges and restrictions thereof. As of June 30, 2014 and December 31, 2013, the Company had no convertible preferred stock outstanding.

Common Stock Warrants

In December 2011, in connection with a capital lease agreement, the Company issued warrants to purchase 21,087 shares of the Company's common stock at an exercise price of $10.67 per share. The Company estimated the fair value of these warrants as of the issuance date to be $0.2 million and recorded these warrants as other assets, amortizing them subsequently over the term of the lease. The fair value was based on the contractual term of the warrants of 10 years, risk free interest rate of 2%, expected volatility of 86% and zero expected dividend yield. These warrants remain unexercised and outstanding as of June 30, 2014.

In October 2013, in connection with the issuance of the Temasek Tranche I Notes (see Note 5, "Debt"), the Company issued contingently exercisable warrants to purchase 1,000,000 shares of the Company's common stock at an exercise price of $0.01 per share. The Company estimated the fair value of these warrants as of the issuance date at $1.3 million and recorded these warrants as debt issuance cost to be amortized over the term of the note. The fair-value was calculated using a Monte Carlo simulation valuation model based on the contractual term of the warrants of 3.4 years, risk free interest rate of 0.77%, expected volatility of 45% and zero expected dividend yield. These warrants remain unexercised and outstanding as of June 30, 2014.

Each of these warrants includes a cashless exercise provision which permits the holder of the warrant to elect to exercise the warrant without paying the cash exercise price, and receive a number of shares determined by multiplying (i) the number of shares for which the warrant is being exercised by (ii) the difference between the fair market value of the stock on the date of exercise and the warrant exercise price, and dividing such by (iii) the fair market value of the stock on the date of exercise. During six months ended June 30, 2014 and 2013, no warrants were exercised through the cashless exercise provision.

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Document and Entity Information	6 Months Ended
	Jun. 30, 2014	Jul. 31, 2014
Document and Entity Information [Abstract]
Entity Registrant Name	AMYRIS, INC.
Entity Central Index Key	0001365916
Current Fiscal Year End Date	--12-31
Entity Filer Category	Accelerated Filer
Document Type	10-Q
Document Period End Date	Jun. 30, 2014
Document Fiscal Year Focus	2014
Document Fiscal Period Focus	Q2
Amendment Flag	false
Entity Common Stock, Shares Outstanding		78,914,505

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Stock-Based Compensation

6 Months Ended

Jun. 30, 2014

Disclosure of Compensation Related Costs, Share-based Payments [Abstract]

Stock-Based Compensation Plans

Stock-Based Compensation

The Company’s stock option activity and related information for the six months ended June 30, 2014 was as follows:

		Number Outstanding		Weighted- Average Exercise Price		Weighted-Average Remaining Contractual Life (Years)	Aggregate Intrinsic Value
							(in thousands)
Outstanding - December 31, 2013		8,409,605		$	7.39	7.40	$	12,393
	Options granted	2,909,183		$	3.51
	Options exercised	(337,110	)	$	3.06
	Options cancelled	(485,971	)	$	7.09
Outstanding - June 30, 2014		10,495,707		$	6.47	7.72	$	3,709
Vested and Expected to vest after June 30, 2014		9,590,575		$	6.72	7.58	$	3,326
Exercisable at June 30, 2014		4,554,010		$	9.29	6.13	$	1,027

The aggregate intrinsic value of options exercised under all option plans was $33,000 and $0.1 million for the three months ended June 30, 2014 and 2013, respectively, and was $0.5 million and $0.3 million for the six months ended June 30, 2014 and 2013, respectively, determined as of the date of option exercise.

The Company’s restricted stock units (or RSUs) and restricted stock activity and related information for the six months ended June 30, 2014 was as follows:

	RSUs		Weighted-Average Grant-Date Fair Value		Weighted Average Remaining Contractual Life (Years)
Outstanding - December 31, 2013	2,316,437		$	4.30	0.88
Awarded	1,049,300		$	3.51	—
Vested	(1,158,585	)	$	4.68	—
Forfeited	(98,863	)	$	3.17	—
Outstanding - June 30, 2014	2,108,289		$	3.75	1.39
Expected to vest after June 30, 2014	1,803,053		$	3.75	1.31

The following table summarizes information about stock options outstanding as of June 30, 2014:

	Options Outstanding				Options Exercisable
Exercise Price	Number of Options	Weighted- Average Remaining Contractual Life (Years)	Weighted-Average Exercise Price		Number of Options	Weighted-Average Exercise Price
$0.10—$2.79	1,580,682	8.20	$	2.66	476,896	$	2.52
$2.81—$2.94	1,056,600	8.94	$	2.88	279,097	$	2.87
$2.96—$3.44	945,057	8.55	$	3.14	304,429	$	3.07
$3.51—$3.51	2,489,199	9.75	$	3.51	—	$	—
$3.55—$3.93	1,700,908	5.75	$	3.88	1,247,160	$	3.89
$4.06—$16.00	1,555,854	5.94	$	10.11	1,281,705	$	9.88
$16.50—$24.50	724,345	5.97	$	20.10	625,057	$	20.11
$25.43—$25.43	15,000	7.07	$	25.43	15,000	$	25.43
$26.84—$26.84	368,062	6.64	$	26.84	264,666	$	26.84
$30.17—$30.17	60,000	6.71	$	30.17	60,000	$	30.17
$0.10—$30.17	10,495,707	7.72	$	6.47	4,554,010	$	9.29

Stock-Based Compensation Expense

Stock-based compensation expense related to options and restricted stock units granted to employees and nonemployees was allocated to research and development expense and sales, general and administrative expense as follows (in thousands):

	Three Months Ended June 30,				Six Months Ended June 30,
	2014		2013		2014		2013
Research and development	$	909	$	1,049	$	1,707	$	2,296
Sales, general and administrative	2,774		3,936		5,490		6,882
Total stock-based compensation expense	$	3,683	$	4,985	$	7,197	$	9,178

As of June 30, 2014, there was unrecognized compensation expense of $15.0 million related to stock options, and the Company expects to recognize this expense over a weighted average period of 2.93 years. As of June 30, 2014, there was unrecognized compensation expense of $4.9 million related to RSUs, and the Company expects to recognize this expense over a weighted average period of 2.07 years.

Stock-based compensation expense for RSUs is measured based on the closing fair market value of the Company's common stock on the date of grant. Stock-based compensation expense for stock options and employee stock purchase plan rights is estimated at the grant date and offering date, respectively, based on the fair-value using the Black-Scholes option pricing model. The fair value of employee stock options is being amortized on a straight-line basis over the requisite service period of the awards. The fair value of employee stock options was estimated using the following weighted-average assumptions:

	Three Months Ended June 30,				Six Months Ended June 30,
	2014		2013		2014		2013
Expected dividend yield	—	%	—	%	—	%	—	%
Risk-free interest rate	2	%	1	%	2	%	1	%
Expected term (in years)	6.09		6.10		6.10		6.10
Expected volatility	75	%	82	%	75	%	82	%

Expected Dividend Yield—The Company has never paid dividends and does not expect to pay dividends.

Risk-Free Interest Rate—The risk-free interest rate was based on the market yield currently available on United States Treasury securities with maturities approximately equal to the option’s expected term.

Expected Term—Expected term represents the period that the Company’s stock-based awards are expected to be outstanding. The Company’s assumptions about the expected term have been based on that of companies that have similar industry, life cycle, revenue, and market capitalization and the historical data on employee exercises.

Expected Volatility—The expected volatility is based on a combination of historical volatility for the Company's stock and the historical stock volatilities of several of the Company’s publicly listed comparable companies over a period equal to the expected terms of the options, as the Company does not have a long trading history.

Forfeiture Rate—The Company estimates its forfeiture rate based on an analysis of its actual forfeitures and will continue to evaluate the adequacy of the forfeiture rate based on actual forfeiture experience, analysis of employee turnover behavior, and other factors. The impact from a forfeiture rate adjustment will be recognized in full in the period of adjustment, and if the actual number of future forfeitures differs from that estimated by the Company, the Company may be required to record adjustments to stock-based compensation expense in future periods.

Each of the inputs discussed above is subjective and generally requires significant management and director judgment.

Nonemployee Stock–Based Compensation

During the three months ended June 30, 2014 and 2013, there were no options granted to nonemployees, and for each of the six months ended June 30, 2014 and 2013, the Company granted options to purchase 20,000 shares of its common stock, respectively, to nonemployees in exchange for services. Compensation expense of $0.1 million and $8,000 was recorded for the three months ended June 30, 2014 and 2013, respectively, and $0.1 million and $22,000 was recorded for the six months ended June 30, 2014 and 2013, respectively, for stock-based options granted to nonemployees. The nonemployee options were valued using the Black-Scholes option pricing model.

During the three and six months ended June 30, 2014 and 2013, no restricted stock units, were granted to nonemployees. Stock-based compensation expense of $12,000 and $15,000 was recorded by the Company for the three months ended June 30, 2014 and 2013, respectively, and $9,000 and $39,000 for the six months ended June 30, 2014 and 2013, respectively, for the restricted stocks granted to nonemployees.

The fair value of nonemployee stock options was estimated using the following weighted-average assumptions:

	Three Months Ended June 30,				Six Months Ended June 30,
	2014		2013		2014		2013
Expected dividend yield	—	%	—	%	—	%	—	%
Risk-free interest rate	2	%	2	%	2	%	2	%
Expected term (in years)	5.80		6.10		5.94		6.40
Expected volatility	75	%	82	%	76	%	83	%

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Condensed Consolidated Statements of Operations (USD $) In Thousands, except Share data, unless otherwise specified	3 Months Ended		6 Months Ended
	Jun. 30, 2014	Jun. 30, 2013	Jun. 30, 2014	Jun. 30, 2013
Revenues
Renewable product sales	$ 4,379	$ 4,011	$ 7,221	$ 6,991
Related party renewable product sales	31	174	34	177
Total product sales	4,410	4,185	7,255	7,168
Grants and collaborations revenue	4,897	6,555	8,093	8,903
Related party grants and collaborations revenue	0	109	0	2,647
Total grants and collaborations revenue	4,897	6,664	8,093	11,550
Total revenues	9,307	10,849	15,348	18,718
Cost and operating expenses
Cost of products sold	7,511	8,853	13,747	17,813
Loss on purchase commitments and write-off of production assets	52	8,423	159	8,423
Research and development	12,175	13,992	25,161	29,746
Sales, general and administrative	13,971	14,718	27,370	29,545
Total cost and operating expenses	33,709	45,986	66,437	85,527
Loss from operations	(24,402)	(35,137)	(51,089)	(66,809)
Other income (expense):
Interest income	148	57	204	93
Interest expense	(6,802)	(1,558)	(11,552)	(3,120)
Gain (loss) from change in fair value of derivative instruments	(3,252)	(254)	54,148	785
Loss from extinguishment of debt	(1,100)	0	(10,512)	0
Other income (expense), net	5	(1,776)	(117)	(1,696)
Total other income (expense)	(10,983)	(3,531)	32,171	(3,938)
Loss before income taxes	(35,385)	(38,668)	(18,918)	(70,747)
Provision for income taxes	(125)	(246)	(236)	(482)
Net loss	(35,510)	(38,914)	(19,154)	(71,229)
Net income (loss) attributable to noncontrolling interest	31	38	60	(261)
Net loss attributable to Amyris, Inc. common stockholders	$ (35,479)	$ (38,876)	$ (19,094)	$ (71,490)
Net income (loss) per share attributable to common stockholders:
Basic (in dollars per share)	$ (0.45)	$ (0.51)	$ (0.25)	$ (0.96)
Diluted (in dollars per share)	$ (0.45)	$ (0.51)	$ (0.66)	$ (0.96)
Weighted-average shares of common stock outstanding used in computing net loss per share of common stock:
Basic (in shares)	78,604,692	75,959,228	77,722,437	74,640,314
Diluted (in shares)	78,604,692	75,959,228	110,632,078	74,640,314

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Debt

6 Months Ended

Jun. 30, 2014

Debt Disclosure [Abstract]

Debt

Debt

Debt is comprised of the following (in thousands):

	June 30, 2014			December 31, 2013
Credit facilities	$	37,972		$	8,767
Convertible notes	57,904			28,537
Related party convertible notes	100,480			89,499
Loans payable	25,999			25,259
Total debt	222,355			152,062
Less: current portion	(9,923		)	(6,391		)
Long-term debt	$	212,432		$	145,671

FINEP Credit Facility

In November 2010, the Company entered into a credit facility with Financiadora de Estudos e Projetos (referred to as the “FINEP Credit Facility”). The FINEP Credit Facility was extended to partially fund expenses related to the Company’s research and development project on sugarcane-based biodiesel (“FINEP Project”) and provided for loans of up to an aggregate principal amount of R$6.4 million (approximately US$2.9 million based on the exchange rate as of June 30, 2014), which is secured by a chattel mortgage on certain equipment of the Company as well as by bank letters of guarantee. All available credit under this facility is fully drawn.

Interest on loans drawn under the FINEP Credit Facility is fixed at 5% per annum. In case of default under or non-compliance with the terms of the agreement, the interest on loans will be dependent on the long-term interest rate as published by the Central Bank of Brazil (such rate, the “TJLP”). If the TJLP at the time of default is greater than 6%, then the interest will be 5% plus a TJLP adjustment factor, otherwise the interest will be at 11% per annum. In addition, a fine of up to 10% shall apply to the amount of any obligation in default. Interest on late balances will be 1% interest per month, levied on the overdue amount. Payment of the outstanding loan balance is being made in 81 monthly installments, which commenced in July 2012 and extends through March 2019. Interest on loans drawn and other charges are paid on a monthly basis and commenced in March 2011. As of June 30, 2014 and December 31, 2013, the total outstanding loan balance under this credit facility was R$4.8 million (approximately US$2.2 million based on the exchange rate as of June 30, 2014) and R$5.2 million (approximately US$2.2 million based on exchange rate as of December 31, 2013), respectively.

The FINEP Credit Facility contains the following significant terms and conditions:

• the Company was required to share with FINEP the costs associated with the FINEP Project. At a minimum, the Company was required to contribute from its own funds approximately R$14.5 million (approximately US$6.6 million based on the exchange rate as of June 30, 2014) of which R$11.1 million was contributed prior to the release of the second disbursement. All four disbursements were completed and the Company has fulfilled all of its cost sharing obligations;

• after the release of the first disbursement, prior to any subsequent drawdown from the FINEP Credit Facility, the Company was required to provide bank letters of guarantee of up to R$3.3 million in aggregate (approximately US$1.5 million based on the exchange rate as of June 30, 2014). On December 17, 2012 and prior to release of the second disbursement on December 26, 2012, the Company obtained the required bank letter of guarantees from Banco ABC Brasil S.A. (or "ABC"); and

• amounts disbursed under the FINEP Credit Facility were required to be used towards the FINEP Project within 30 months after the contract execution.

BNDES Credit Facility

In December 2011, the Company entered into a credit facility with the Brazilian Development Bank (the bank is referred to as “BNDES” and the credit facility referred to as the “BNDES Credit Facility”) in the amount of R$22.4 million (approximately US$10.2 million based on the exchange rate as of June 30, 2014). This BNDES Credit Facility was extended as project financing for a production site in Brazil. The credit line is divided into an initial tranche of up to approximately R$19.1 million and an additional tranche of approximately R$3.3 million that becomes available upon delivery of additional guarantees. The credit line is available for 12 months from the date of the BNDES Credit Facility, subject to extension by the lender. The credit line was cancelled in 2013.

The principal of the loans under the BNDES Credit Facility is required to be repaid in 60 monthly installments, with the first installment paid in January 2013 and the last due in December 2017. Interest was due initially on a quarterly basis with the first installment due in March 2012. From and after January 2013, interest payments are due on a monthly basis together with principal payments. The loaned amounts carry interest of 7% per annum. Additionally, there is a credit reserve charge of 0.1% on the unused balance from each credit installment from the day immediately after it is made available through its date of use, when it is paid.

The BNDES Credit Facility is collateralized by a first priority security interest in certain of the Company's equipment and other tangible assets totaling R$24.9 million (approximately $11.3 million based on the exchange rate as of June 30, 2014). The Company is a parent guarantor for the payment of the outstanding balance under the BNDES Credit Facility. Additionally, the Company was required to provide a bank guarantee equal to 10% of the total approved amount (R$22.4 million in total debt) available under this Credit Facility. For advances of the second tranche (above R$19.1 million), the Company is required to provide additional bank guarantees equal to 90% of each such advance, plus additional Company guarantees equal to at least 130% of such advance. The BNDES Credit Facility contains customary events of default, including payment failures, failure to satisfy other obligations under this credit facility or related documents, defaults in respect of other indebtedness, bankruptcy, insolvency and inability to pay debts when due, material judgments, and changes in control of Amyris Brasil. If any event of default occurs, the Lender may terminate its commitments and declare immediately due all borrowings under the facility. As of June 30, 2014 and December 31, 2013, the Company had R$13.4 million (approximately US$6.1 million based on the exchange rate as of June 30, 2014) and R$15.3 million (approximately US$6.5 million based on the exchange rate as of December 31, 2013), respectively, in outstanding advances under the BNDES Credit Facility.

Hercules Loan Facility

In March 2014, the Company entered into a Loan and Security Agreement with Hercules Technology Growth Capital, Inc. (referred to as “Hercules”) to make available to Amyris a loan in the aggregate principal amount of up to $25.0 million (referred to as the "Hercules Loan Facility"). The original Hercules Loan Facility accrues interest at a rate per annum equal to the greater of either the prime rate reported in the Wall Street Journal plus 6.25% or 9.50%. The Company may repay the loaned amounts before the maturity date (generally February 1, 2017) if it pays an additional fee of 3% of the outstanding loans (1% if after the initial twelve-month period of the loan). The Company was also required to pay a 1% facility charge at the closing of the transaction, and is required to pay a 10% end of term charge. In connection with the original Hercules Loan Facility, Amyris agreed to certain customary representations and warranties and covenants, as well as certain covenants that were subsequently amended (as described below). The total available credit of $25.0 million under this facility was fully drawn down by the Company.

In June 2014, the Company and Hercules entered into a first amendment (referred to as the “Hercules Amendment”) of the Loan and Security Agreement entered into in March 2014. Pursuant to the Hercules Amendment, the parties agreed to adjust the term loan maturity date from May 31, 2015 to February 1, 2017 and remove (i) a requirement for the Company to pay a forbearance fee of $10.0 million in the event certain covenants were not satisfied, (ii) a covenant that the Company maintain positive cash flow commencing with the fiscal quarter beginning October 1, 2014, (iii) a covenant that, beginning with the fiscal quarter beginning July 1, 2014, the Company and its subsidiaries achieve certain projected cash product revenues and projected cash product gross profits, and (iv) an obligation for the Company to file a registration statement on Form S-3 with the SEC by no later than June 30, 2014 and complete an equity financing of more than $50.0 million by no later than September 30, 2014. The Company further agreed to include a new covenant requiring the Company to maintain unrestricted, unencumbered cash in an amount equal to at least 50% of the principal amount then outstanding under the Hercules Loan Facility and borrow an additional $5.0 million. The additional $5.0 million borrowing was completed in June 2014, and accrues interest at a rate per annum equal to the greater of either the prime rate reported in the Wall Street Journal plus 5.25% or 8.5%. The Hercules Loan Facility is secured by liens on the Company's assets, including on certain Company intellectual property. The Hercules Loan Facility includes customary events of default, including failure to pay amounts due, breaches of covenants and warranties, certain cross defaults and judgments, and insolvency. If an event of default occurs, Hercules may require immediate repayment of all amounts due.

As of June 30, 2014, $29.7 million was outstanding under the Hercules Loan Facility, net of discount of $0.3 million, and the Company maintains cash in excess of the approximately $15.0 million current minimum cash covenant described above.

Notes Payable

During the period between May 2008 and October 2008, the Company entered into notes payable agreements with the lessor of its headquarters under which it borrowed a total of $3.3 million for the purchase of tenant improvements, bearing an interest rate of 9.5% per annum and to be repaid over a period of 55 to 120 months. As of June 30, 2014 and December 31, 2013, no principal amount was outstanding under these notes payable. In June 2013, as part of the April 30, 2013 Amendment to the Company's operating lease for its headquarters, the Company recorded the elimination of these notes payable as a lease incentive and recorded approximately $1.4 million to deferred rent liability in the condensed consolidated balance sheet. The deferred rent liability is being amortized to expense over the remaining lease term.

Convertible Notes

Fidelity

In February 2012, the Company completed the sale of senior unsecured convertible promissory notes in an aggregate principal amount of $25.0 million pursuant to a securities purchase agreement, between the Company and certain investment funds affiliated with FMR LLC (referred to as the "Fidelity Securities Purchase Agreement"). The offering consisted of the sale of 3% senior unsecured convertible promissory notes with a March 1, 2017 maturity date and an initial conversion price equal to $7.0682 per share of the Company's common stock, subject to proportional adjustment for adjustments to outstanding common stock and anti-dilution provisions in case of dividends and distributions (referred to as the "Fidelity Notes"). As of June 30, 2014, the Fidelity Notes were convertible into an aggregate of up to 3,536,968 shares of the Company's common stock. Such note holders have a right to require repayment of 101% of the principal amount of the Fidelity Notes in an acquisition of the Company, and the notes provide for payment of unpaid interest on conversion following such an acquisition if the note holders do not require such repayment. The Fidelity Securities Purchase Agreement and Fidelity Notes include covenants regarding payment of interest, maintaining the Company's listing status, limitations on debt, maintenance of corporate existence, and filing of SEC reports. The Fidelity Notes include standard events of default resulting in acceleration of indebtedness, including failure to pay, bankruptcy and insolvency, cross-defaults, material adverse effect clauses and breaches of the covenants in the Fidelity Securities Purchase Agreement and Fidelity Notes, with default interest rates and associated cure periods applicable to the covenant regarding SEC reporting. Furthermore, the Fidelity Notes include restrictions on the amount of debt the Company is permitted to incur. With exceptions for certain existing debt, refinancing of such debt and certain other exclusions and waivers, the Fidelity Notes provide that the Company's total outstanding debt at any time cannot exceed the greater of $200.0 million or 50% of its consolidated total assets and its secured debt cannot exceed the greater of $125.0 million or 30% of its consolidated total assets. In connection with the Company’s closing of a short-term bridge loan for $35.0 million in October 2013, holders of the Fidelity Notes waived compliance with the debt limitations outlined above as to the $35.0 million bridge loan and the August 2013 Financing (defined below). In consideration for such waiver, the Company granted to holders of the Fidelity Notes or their affiliates, the right to purchase up to an aggregate of $7.6 million worth of convertible promissory notes in the first tranche of the August 2013 Financing.

In August 2013, the Company entered into that certain Securities Purchase Agreement, dated as of August 8, 2013 (referred to as the “August 2013 SPA”), for the sale of senior convertible promissory notes (referred to as the “August 2013 Notes”) to Maxwell (Mauritius) Pte Ltd (or “Temasek”) and Total, each of whom are existing stockholders of the Company. The August 2013 SPA contemplated the sale of up to an aggregate of $73.0 million in principal amount of the August 2013 Notes in a private placement (referred to as the “August 2013 Financing”) exempt from registration under the Securities Act of 1933, as amended, (the "Securities Act") in an initial tranche of $42.6 million in aggregate principal amount and a second tranche of $30.4 million in aggregate principal amount.

In October 2013, the Company amended the August 2013 SPA to include certain entities affiliated with FMR LLC (referred to as the “Fidelity Entities”) in the first tranche of the August 2013 Financing. Pursuant to the amended agreement the Company sold senior convertible notes with an aggregate principal amount of $7.6 million to the Fidelity Entities (referred to as the "Tranche I Notes"). The Tranche I Notes are due sixty months from the date of issuance and will be convertible into the Company’s common stock at a conversion price equal to $2.44, which represents a 15% discount to a trailing 60-day weighted-average closing price of the common stock on The NASDAQ Stock Market (or “NASDAQ”) through August 7, 2013, subject to adjustment as described below. The Tranche I Notes are convertible at the option of the holder: (i) at any time after 18 months from the date of the August 2013 SPA, (ii) on a change of control of the Company and (iii) upon the occurrence of an event of default. The conversion price of the Tranche I Notes will be reduced to $2.15 if either (a)(i) a specified Company manufacturing plant had failed to achieve a total production of 1,000,000 liters within a run period of 45 days prior to June 30, 2014, or (ii) the Company fails to achieve gross margins from product sales of at least 5% prior to June 30, 2014, or (b) the Company reduces the conversion price of certain existing promissory notes held by Total prior to the repayment or conversion of the Tranche I Notes. In 2013, the Company achieved a total production of 1.0 million liters within a run period of 45 days in satisfaction of clause (a)(i) of the preceding sentence and the Company is currently evaluating the achievement of clause (a)(ii) of the preceding sentence. If either of the production and margin milestones in clause (a) above were to not occur, and the Company also reduces the conversion price of certain existing promissory notes held by Total prior to the repayment or conversion of the Tranche I Notes as set forth in clause (b) above, the conversion price of the Tranche I Notes would be reduced to $1.87. Each Tranche I Note accrues interest from the date of issuance until the earlier of the date that such Tranche I Note is converted into the Company’s common stock or is repaid in full. Interest accrues at a rate of 5% per six months, compounded semiannually (with graduated interest rates of 6.5% applicable to the first 180 days and 8% applicable thereafter as the sole remedy should the Company fail to maintain NASDAQ listing status or at 6.5% for all other defaults). Interest for the first 30 months is payable in kind and added to the principal every six-months and thereafter, the Company may continue to pay interest in kind by adding to the principal every six-months or may elect to pay interest in cash. The Tranche I Notes may be prepaid by the Company after 30 months from the issuance date and initial interest payment date; thereafter the Company has the option to prepay the Tranche I Notes every six months at the date of payment of the semi-annual coupon.

As of June 30, 2014 and December 31, 2013, principal amount of $29.3 million and $28.5 million, respectively, were outstanding under these convertible notes, net of debt discount of $3.7 million and $4.0 million, respectively. The debt discount is the result of the bifurcation of the conversion options that contain "make-whole" provisions or down round conversion price adjustment provisions associated with the outstanding debt.

Rule 144A Convertible Note Offering

In May 2014, the Company entered into a Purchase Agreement with Morgan Stanley & Co. LLC, as the initial purchaser (the “Initial Purchaser”), relating to the sale of $75.0 million aggregate principal amount of its 6.50% Convertible Senior Notes due 2019 (the "144A Notes") to the Initial Purchaser in a private placement, and for initial resale by the Initial Purchaser to certain qualified institutional buyers. In addition, the Company granted the Initial Purchaser an option to purchase up to an additional $15.0 million aggregate principal amount of notes, which option expired according to its terms. Under the terms of the Purchase Agreement, the Company agreed to customary indemnification of the Initial Purchaser against certain liabilities. The Notes were issued pursuant to an Indenture, dated as of May 29, 2014 (the “Indenture”), between the Company and Wells Fargo Bank, National Association, as trustee. The net proceeds from the offering of the Notes were approximately $72.0 million after payment of the Initial Purchaser’s discounts and offering expenses. In addition, in connection with obtaining a waiver from one of its existing investors, Total Energies Nouvelles Activités USA (“Total”), of its preexisting contractual right to exchange certain senior secured convertible notes previously issued by the Company for new notes issued in the offering, the Company has used approximately $9.7 million of the net proceeds to repay previously issued notes (representing the amount of 144A Notes purchased by Total from the Initial Purchaser). Certain of the Company's affiliated entities purchased $24.7 million in aggregate principal amount of Rule 144A Notes from the Initial Purchaser (described further below under "Related Party Convertible Notes"). The 144A Notes will bear interest at a rate of 6.50% per year, payable semiannually in arrears on May 15 and November 15 of each year, beginning November 15, 2014. The 144A Notes will mature on May 15, 2019 unless earlier converted or repurchased. The 144A Notes are convertible into shares of the Company's common stock at any time prior to the close of business day on May 15, 2019.The Notes will have an initial conversion rate of 267.0370 shares of Common Stock per $1,000 principal amount of 144A Notes (subject to adjustment in certain circumstances). This represents an initial effective conversion price of approximately $3.74 per share of common stock. For any conversion on or after May 15, 2015, in the event that the last reported sale price of the Company’s common stock for 20 or more trading days (whether or not consecutive) in a period of 30 consecutive trading days ending within five trading days immediately prior to the date the Company receives a notice of conversion exceeds the conversion price of $3.74 per share on each such trading day, the holders, in addition to the shares deliverable upon conversion, will be entitled to receive a cash payment equal to the present value of the remaining scheduled payments of interest that would have been made on the 144A Notes being converted from the conversion date to the earlier of the date that is three years after the date the Company receive such notice of conversion and maturity (May 15, 2019). In the event of a fundamental change, as defined in the Indenture, holders of the 144A Notes may require the Company to purchase all or a portion of the 144A Notes at a price equal to 100% of the principal amount of the 144A Notes, plus any accrued and unpaid interest to, but excluding, the fundamental change repurchase date. Holders of the 144A Notes who convert their 144A Notes in connection with a make-whole fundamental change will receive additional shares representing the present value of the remaining interest payments which will be computed using a discount rate of 0.75%. If a holder of 144A Notes elects to convert their 144A Notes prior to the effective date of any make-whole fundamental change, such holder will not be entitled to an increased conversion rate in connection with such conversion.

Related Party Convertible Notes

Total R&D Convertible Notes

In July 2012, the Company entered into an agreement with Total that expanded Total's investment in the Biofene collaboration with the Company, provided new structure for a joint venture (referred to as the "Fuels JV") to commercialize the products encompassed by the diesel and jet fuel research and development program (or, the "Program"), and established a convertible debt structure for the collaboration funding from Total (referred to as the "July 2012 Agreements").

The purchase agreement for the notes related to the funding from Total (referred to as the "Total Purchase Agreement") provides for the sale of an aggregate of $105.0 million in notes as follows:

• As part of an initial closing under the purchase agreement (which initial closing was completed in two installments), (i) on July 30, 2012, the Company sold a 1.5% Senior Unsecured Convertible Note due March 2017 to Total in the face amount of $38.3 million, including $15.0 million in new funds and $23.3 million in previously-provided diesel research and development funding by Total, and (ii) on September 14, 2012, the Company sold another note (in the same form) for $15.0 million in new funds from Total.

• At a second closing under the Total Purchase Agreement (also completed in two installments) the Company sold additional notes for an aggregate of $30.0 million in new funds from Total ($10.0 million in June 2013 and $20.0 million in July 2013).

• The Total Purchase Agreement provides that additional notes may be sold in subsequent closings in July 2014 (for cash proceeds to the Company of $21.7 million, which would be settled in an initial installment of $10.85 million payable at such closing and a second installment of $10.85 million payable in January 2015).

The notes issued to Total pursuant to the Total Purchase Agreement have a maturity date of March 1, 2017, an initial conversion price equal to $7.0682 per share for the notes issued under the initial closing, an initial conversion price equal $3.08 per share for the notes issued under the second closing and an initial conversion price equal to $4.11 per share for the notes issued (and that remain to be issued) under the third closing. The notes bear interest of 1.5% per annum (with a default rate of 2.5%), accruing from the date of funding and payable at maturity or on conversion or a change of control where Total exercises the right to require the Company to repay the notes. Accrued interest is cancelled if the notes are cancelled based on a “Go” decision (see Note 8, "Significant Agreements"). The agreements contemplate that the research and development efforts under the Program may extend through 2016, with a series of “Go/No Go” decisions by Total through such date tied to funding by Total. The notes issuable under the third closing will be senior secured promissory notes, pursuant to the exchange agreed to by Total and the Company in December 2013.

The notes become convertible into the Company's common stock (i) within 10 trading days prior to maturity (if they are not cancelled as described above prior to their maturity date), (ii) on a change of control of the Company, (iii) if Total is no longer the largest stockholder of the Company following a “No-Go” decision (subject to a six-month lock-up with respect to any shares of common stock issued upon conversion), and (iv) on a default by the Company. If Total makes a final “Go” decision, then the notes will be exchanged by Total for equity interests in the Fuels JV, after which the notes will not be convertible and any obligation to pay principal or interest on the notes will be extinguished. In case of a “Go” decision only with respect to jet fuel, the parties would form an operational joint venture only for jet fuel (and the rights associated with diesel would terminate), 70% of the outstanding notes would remain outstanding and become payable by the Company, and 30% of the outstanding notes would be cancelled. If Total makes a “No-Go” decision, outstanding notes will remain outstanding and become payable at maturity.

In connection with a December 2012 private placement of the Company’s common stock involving certain existing stockholders of the Company, Total elected to participate in the private placement by exchanging approximately $5.0 million of its $53.3 million in senior unsecured convertible promissory notes into 1,677,852 shares of the Company's common stock at a price of $2.98 per share. As such, $5.0 million of Total's outstanding $53.3 million in senior unsecured convertible promissory notes was cancelled. The cancellation of the debt was treated as an extinguishment of debt in accordance with the guidance outlined in ASC 470-50. As a result of the exchange and cancellation of the $5.0 million debt the Company recorded a loss from extinguishment of debt of $0.9 million.

In March 2013, the Company entered into a letter agreement with Total (referred to as the "March 2013 Letter Agreement") under which Total agreed to waive its right to cease its participation in the parties' fuels collaboration at the July 2013 decision point and committed to proceed with the July 2013 funding tranche of $30.0 million (subject to the Company's satisfaction of the relevant closing conditions for such funding in the Total Purchase Agreement). As consideration for this waiver and commitment, the Company agreed to:

• reduce the conversion price for the senior unsecured convertible promissory notes to be issued in connection with such funding from $7.0682 per share to a price per share equal to the greater of (i) the consolidated closing bid price of the Company's common stock on the date of the March 2013 Letter Agreement, plus $0.01, and (ii) $3.08 per share, provided that the conversion price would not be reduced by more than the maximum possible amount permitted under the rules of NASDAQ such that the new conversion price would require the Company to obtain stockholder consent; and

• grant Total a senior security interest in the Company's intellectual property, subject to certain exclusions and subject to release by Total when the Company and Total enter into final documentation regarding the establishment of the Fuels JV.

In addition to the waiver by Total described above, Total also agreed that, at the Company's request and contingent upon the Company meeting its obligations described above, it would pay advance installments of the amounts otherwise payable at the July 2013 closing. Specifically, if the Company requested such advance installments, subject to certain closing conditions and delivery of certifications regarding the Company's cash levels, Total was obligated to fund $10.0 million no later than May 15, 2013, and an additional $10.0 million no later than June 15, 2013, with the remainder to be funded on the original July 2013 closing date.

In June 2013, the Company sold and issued a 1.5% Senior Unsecured Convertible Note to Total in the face amount of $10.0 million with a March 1, 2017 maturity date pursuant to the Total Purchase Agreement as discussed above. In accordance with the March 2013 Letter Agreement, this convertible note has an initial conversion price equal to $3.08 per share of the Company's common stock. The Company did not request the May advance of $10.0 million, but did request the June advance (as described above), under which this convertible note was issued.

In July 2013, the Company sold and issued a 1.5% Senior Unsecured Convertible Note to Total in the face amount of $20.0 million with a March 1, 2017 maturity date pursuant to the Total Purchase Agreement as discussed above. This purchase and sale completed Total's commitment to purchase $30.0 million of such notes by July 2013. In accordance with the March 2013 Letter Agreement, this convertible note has an initial conversion price equal to $3.08 per share of the Company's common stock.

The conversion prices of the notes issued under the Total Purchase Agreement are subject to adjustment for proportional adjustments to outstanding common stock and under anti-dilution provisions in case of certain dividends and distributions. Total has a right to require repayment of 101% of the principal amount of the notes in the event of a change of control of the Company and the notes provide for payment of unpaid interest on conversion following such a change of control if Total does not require such repayment. The Total Purchase Agreement and notes include covenants regarding payment of interest, maintenance of the Company's listing status, limitations on debt, maintenance of corporate existence, and filing of SEC reports. The notes include standard events of default resulting in acceleration of indebtedness, including failure to pay, bankruptcy and insolvency, cross-defaults, and breaches of the covenants in the purchase agreement and notes, with added default interest rates and associated cure periods applicable to the covenant regarding SEC reporting. Furthermore, the notes include restrictions on the amount of debt the Company is permitted to incur. With exceptions for certain existing debt, refinancing of such debt and certain other exclusions and waivers, the notes provide that the Company's total outstanding debt at any time cannot exceed the greater of $200.0 million or 50% of its consolidated total assets and its secured debt cannot exceed the greater of $125.0 million or 30% of its consolidated total assets. In connection with the Company’s closing of a short-term bridge loan for $35.0 million provided by Temasek in October 2013, Total waived compliance with the debt limitations outlined above as to the $35.0 million bridge loan and the August 2013 Financing.

In April 2014, the Company and Total entered into a letter agreement dated as of March 29, 2014 (referred to as the "March 2014 Letter Agreement") to amend the Amended and Restated Master Framework Agreement entered into as of December 2, 2013 (included as part of JV Documents, as defined below) and the Total Purchase Agreement. Under the March 2014 Letter Agreement, the Company agreed to, (i) amend the conversion price of the convertible notes to be issued in the third closing under the Total Purchase Agreement from $7.0682 to $4.11 subject to stockholder approval at the Company's 2014 annual meeting (which was attained in May 2014), (ii) extend the period during which Total may exchange for other Company securities certain outstanding convertible promissory notes issued under the July 2012 Agreements from June 30, 2014 to the later of December 31, 2014 and the date on which the Company shall have raised $75.0 million of equity and/or convertible debt financing (excluding any convertible promissory notes issued pursuant to the Total Purchase Agreement), (iii) eliminate the Company’s ability to qualify, in a disclosure letter to Total, certain of the representations and warranties that the Company must make at the closing of any third closing sale, and (iv) beginning on March 31, 2014, provide Total with monthly reporting on the Company’s cash, cash equivalents and short-term investments. In consideration of these agreements, Total agreed to waive its right not to consummate the closing of the issuance of the third closing notes if it decides not to proceed with the collaboration and makes a "No-Go" decision with respect thereto.

JVCO Convertible Notes

In December 2013, in connection with the Company's entry into a Shareholders Agreement and License Agreement and related documents (collectively, referred to as the "JV Documents") with Total and Total Amyris BioSolutions B.V. (or "JVCO") relating to the establishment of JVCO (see Note 7, "Joint Venture and Noncontrolling Interest"), Amyris (i) exchanged the $69.0 million of the outstanding Total unsecured convertible notes issued pursuant to the Total Purchase Agreement and issued replacement 1.5% senior secured convertible notes, in principal amounts equal to the principal amount of each cancelled note (the “Replacement Notes”), (ii) granted to Total a security interest in and lien on all Amyris’s rights, title and interest in and to Amyris’s shares in the capital of JVCO and (iii) agreed that any securities to be purchased and sold at the third closing under the Total Purchase Agreement by Total will be 1.5%, senior secured convertible notes instead of senior unsecured convertible notes. As a consequence of executing the JV Documents and forming JVCO, the security interests in all of the Company’s intellectual property, granted by Amyris in favor of Total, Temasek, and certain Fidelity Entities pursuant the Restated Intellectual Property Security Agreement dated as of October 16, 2013, were automatically terminated effective as of December 2, 2013 upon Total’s and the Company’s joint written notice to Temasek.

As of June 30, 2014 and December 31, 2013, $40.3 million and $51.5 million, respectively, of Replacement Notes were outstanding, net of debt discount of $13.1 million and $17.6 million, respectively.

August 2013 Financing Convertible Notes and 2013 Bridge Loans

In connection with the August 2013 Financing, the Company entered into the August 2013 SPA with Total and Temasek to sell up to $73.0 million in convertible promissory notes in private placements, with such notes to be sold and issued over a period of up to 24 months from the date of signing. The August 2013 SPA provided for the August 2013 Financing to be divided into two tranches (the first tranche for $42.6 million and the second tranche for $30.4 million), each with differing closing conditions. Of the total possible purchase price in the financing, $60.0 million to be paid in the form of cash by Temasek ($35.0 million in the first tranche and up to $25.0 million in the second tranche) and $13.0 million to be paid by the exchange and cancellation of outstanding convertible promissory notes held by Total in connection with its exercise of pro rata rights ($7.6 million in the first tranche and $5.4 million in the second tranche). The August 2013 SPA included requirements that the Company meet certain production milestones before the second tranche would become available, obtain stockholder approval prior to completing any closing of the transaction, and issue a warrant to Temasek to purchase 1,000,000 shares of the Company's common stock at an exercise price of $0.01 per share, exercisable only if Total converts notes previously issued to Total in the second closing under the Total Purchase Agreement. In September 2013, prior to the initial closing of the August 2013 Financing, the Company's stockholders approved the issuance in the private placement of up to $110.0 million aggregate principal amount of senior convertible promissory notes, the issuance of a warrant to purchase 1,000,000 shares of the Company's common stock and the issuance of the common stock issuable upon conversion or exercise of such notes and warrant, which approval included the transactions contemplated by the August 2013 Financing.

In September 2013, the Company entered into a bridge loan agreement with an existing investor to provide additional cash availability of up to $5.0 million. As of June 30, 2014, the Company had not drawn any funds from the agreement and the facility expired in October 2013 in accordance with its terms.

In October 2013, the Company sold and issued a bridge note to Temasek (referred to as the “Temasek Bridge Note”) in exchange for a bridge loan of $35.0 million. The Temasek Bridge Note was due on February 2, 2014 and accrued interest at a rate of 5.5% quarterly from the October 4, 2013 date of issuance. The Temasek Bridge Note was cancelled on October 16, 2013 as payment for Temasek’s purchase of Tranche I Notes in the first tranche of the August 2013 Financing as further described below.

In October 2013, the Company amended the August 2013 SPA to include the Fidelity Entities in the first tranche of the August 2013 Financing with an investment amount of $7.6 million, and to proportionally increase the amount acquired by exchange and cancellation of outstanding convertible promissory notes held by Total in connection with its exercise of pro rata rights to $14.6 million ($9.2 million in the first tranche and up to $5.4 million in the second tranche). Also in October 2013, the Company completed the closing of the first tranche of the August 2013 Financing, issuing a total of $51.8 million in Tranche I Notes for cash proceeds of $7.6 million and cancellation of outstanding convertible promissory notes of $44.2 million, of which $35.0 million resulted from cancellation of the Temasek Bridge Note and the remaining $9.2 million from the exchange and cancellation of an outstanding convertible note held by Total. As a result of the exchange and cancellation of the $35.0 million Temasek Bridge Note and the $9.2 million Total convertible note for the Tranche I Notes, the Company recorded a loss from extinguishment of debt of $19.9 million. The Tranche I Notes are due sixty months from the date of issuance and will be convertible into the Company’s common stock at a conversion price equal to $2.44, which represents a 15% discount to a trailing 60-day weighted-average closing price of the common stock on NASDAQ through August 7, 2013, subject to adjustment as described below. The Tranche I Notes are convertible at the option of the holder: (i) at any time after 18 months from the date of the August 2013 SPA, (ii) on a change of control of the Company and (iii) upon the occurrence of an event of default. The conversion price of the Tranche I Notes would be reduced to $2.15 if (a)(i) a specified Company manufacturing plant had failed to achieve a total production of 1.0 million liters within a run period of 45 days prior to June 30, 2014, or (ii) the Company fails to achieve gross margins from product sales of at least 5% prior to June 30, 2014, or (b) the Company reduces the conversion price of certain existing promissory notes held by Total prior to the repayment or conversion of the Tranche I Notes. In 2013, the Company achieved a total production of 1.0 million liters within a run period of 45 days in satisfaction of clause (a)(i) of the preceding sentence and the Company is currently evaluating the achievement of clause (a)(ii) of the preceding sentence. If either of the production and margin milestones in clause (a) above were to occur, and the Company also reduces the conversion price of certain existing promissory notes held by Total prior to the repayment or conversion of the Tranche I Notes as set forth in clause (b) above, the conversion price of the Tranche I Notes will be reduced to $1.87. Each Tranche I Note accrues interest from the date of issuance until the earlier of the date that such Tranche I Note is converted into the Company’s common stock or is repaid in full. Interest accrues at a rate of 5% per six months, compounded semiannually (with graduated interest rates of 6.5% applicable to the first 180 days and 8% applicable thereafter as the sole remedy should the Company fail to maintain NASDAQ listing status or at 6.5% for all other defaults). Interest for the first 30 months is payable in kind and added to the principal every six-months and thereafter, the Company may continue to pay interest in kind by adding to the principal every six-months or may elect to pay interest in cash. The Tranche I Notes may be prepaid by the Company after 30 months from the issuance date and initial interest payment; thereafter the Company has the option to prepay the Tranche I Notes every six months at the date of payment of the semi-annual coupon.

In January 2014, the Company sold and issued, for face value, approximately $34.0 million of convertible promissory notes in the second tranche of the August 2013 Financing (referred to as the “Tranche II Notes”). At the closing, Temasek purchased $25.0 million of the Tranche II Notes and Wolverine Asset Management, LLC (referred to as “Wolverine”) purchased $3.0 million of the Tranche II Notes, each for cash. Total purchased approximately $6.0 million of the Tranche II Notes through cancellation of the same amount of principal of previously outstanding convertible promissory notes held by Total. As a result of the exchange and cancellation of the $6.0 million Total convertible note for the Tranche II Notes, the Company recorded a loss from extinguishment of debt of $9.4 million. The Tranche II Notes will be due sixty months from the date of issuance and will be convertible into shares of common stock at a conversion price equal to $2.87, which represents a trailing 60-day weighted-average closing price of the common stock on NASDAQ through August 7, 2013, subject to adjustment as described below. Specifically, the Tranche II Notes are convertible at the option of the holder (i) at any time 12 months after issuance, (ii) on a change of control of the Company, and (iii) upon the occurrence of an event of default. Each Tranche II Note will accrue interest from the date of issuance until the earlier of the date that such Tranche II Note is converted into common stock or repaid in full. Interest will accrue at a rate per annum equal to 10%, compounded annually (with graduated interest rates of 13% applicable to the first 180 days and 16% applicable thereafter as the sole remedy should the Company fail to maintain NASDAQ listing status or at 12% for all other defaults). Interest for the first 36 months shall be payable in kind and added to principal every year following the issue date and thereafter, the Company may continue to pay interest in kind by adding to principal on every year anniversary of the issue date or may elect to pay interest in cash.

In addition to the conversion price adjustments set forth above, the conversion prices of the Tranche I Notes and Tranche II Notes are subject to further adjustment (i) according to proportional adjustments to outstanding common stock of the Company in case of certain dividends and distributions, (ii) according to anti-dilution provisions, and (iii) with respect to notes held by any purchaser other than Total, in the event that Total exchanges existing convertible notes for new securities of the Company in connection with future financing transactions in excess of its pro rata amount. Notwithstanding the foregoing, holders of a majority of the principal amount of the notes outstanding at the time of conversion may waive any anti-dilution adjustments to the conversion price. The purchasers have a right to require repayment of 101% of the principal amount of the notes in the event of a change of control of the Company and the notes provide for payment of unpaid interest on conversion following such a change of control if the purchasers do not require such repayment. The August 2013 SPA, Tranche I Notes and Tranche II Notes include covenants regarding payment of interest, maintenance of the Company’s listing status, limitations on debt and on certain liens, maintenance of corporate existence, and filing of SEC reports. The notes include standard events of default resulting in acceleration of indebtedness, including failure to pay, bankruptcy and insolvency, cross-defaults, and breaches of the covenants in the August 2013 SPA, Tranche I Notes and Tranche II Notes, with default interest rates and associated cure periods applicable to the covenant.

As of June 30, 2014 and December 31, 2013, the related party convertible notes outstanding under the Tranche I and Tranche II Notes were $46.2 million and $37.9 million, respectively, net of debt discount of $31.6 million and $6.3 million, respectively. The debt discount is the result of the bifurcation of the conversion options that contain "make-whole" provisions or down round conversion price adjustment provisions associated with the outstanding debt.

Rule 144A Convertible Notes Sold to Related Parties

As discussed above under “Rule 144A Convertible Note Offering”, the Company sold and issued $75.0 million aggregate principal amount of 144A Notes pursuant to Rule 144A of the Securities Act. In connection with obtaining a waiver from one of its existing investors, Total, of its preexisting contractual right to exchange certain senior secured convertible notes previously issued by Amyris pursuant to the Total Purchase Agreement for 144A Notes issued in the transaction, Amyris used approximately $9.7 million of the net proceeds to repay such amount of previously issued notes held by Total, which represented the amount of notes purchased by Total from the Initial Purchaser under the Rule 144A Convertible Note Offering. As a result of the settlement of the $9.7 million Total convertible notes, the Company recorded a loss from extinguishment of debt of $1.1 million.

Additionally, Foris Ventures, LLC (a fund affiliated with John Doerr) and Temasek each participated in the Rule 144A Convertible Note Offering and purchased $5.0 million and $10.0 million, respectively, of the convertible promissory notes sold thereunder.

As of June 30, 2014 the related party convertible notes outstanding under the 144A Notes were $14.0 million, net of discount of $10.7 million.

As of June 30, 2014 and December 31, 2013 the total related party convertible notes outstanding were $100.5 million and $89.5 million, respectively, net of discount of $55.3 million and $23.9 million, respectively. The Company recorded a loss from extinguishment of debt from the settlement, exchange and cancellation of related party convertible notes for the three months ended June 30, 2014 and 2013, of $1.1 million and zero, respectively, and $10.5 million and zero for the six months ended June 30, 2014 and 2013, respectively.

Loans Payable

In December 2009, the Company entered into a loans payable agreement with the lessor of its Emeryville, California pilot plant under which it borrowed a total of $0.3 million, bearing an interest rate of 10.0% per annum and to be repaid over a period of 96 months. As of June 30, 2014 and December 31, 2013, there was no amount outstanding under the loan. In June 2013, as part of the April 30, 2013 amendment entered into regarding the Company's operating lease for its headquarters, the Company recorded the elimination of this loan payable as a lease incentive and recorded approximately $0.2 million to deferred rent liability in the condensed consolidated balance sheet. The deferred rent liability is being amortized to expense over the remaining lease term.

In July 2012, the Company entered into a Note of Bank Credit and a Fiduciary Conveyance of Movable Goods Agreement (together, referred to as the "July 2012 Bank Agreements") with each of Nossa Caixa Desenvolvimento (or “Nossa Caixa”) and Banco Pine S.A. (or “Banco Pine”). Under the July 2012 Bank Agreements, the Company pledged certain farnesene production assets as collateral for the loans of R$52.0 million. The Company's total acquisition cost for such pledged assets was approximately R$68.0 million (approximately US$30.9 million based on the exchange rate as of June 30, 2014). The Company is also a parent guarantor for the payment of the outstanding balance under these loan agreements. Under the July 2012 Bank Agreements, the Company could borrow an aggregate of R$52.0 million (approximately US$23.6 million based on the exchange rate as of June 30, 2014) as financing for capital expenditures relating to the Company's manufacturing facility located in Brotas, Brazil. Specifically, Banco Pine, agreed to lend R$22.0 million and Nossa Caixa agreed to lend R$30.0 million. The funds for the loans are provided by BNDES, but are guaranteed by the lenders. The loans have a final maturity date of July 15, 2022 and bear a fixed interest rate of 5.5% per year. The loans are also subject to early maturity and delinquency charges upon occurrence of certain events including interruption of manufacturing activities at the Company's manufacturing facility in Brotas, Brazil for more than 30 days, except during sugarcane off-season. For the first two years that the loans are outstanding, the Company is required to pay interest only on a quarterly basis. After August 15, 2014, the Company is required to pay equal monthly installments of both principal and interest for the remainder of the term of the loans. As of June 30, 2014 and December 31, 2013, a principal amount of $23.6 million and $22.2 million, respectively, was outstanding under these loan agreements.

In October 2013, the Company borrowed $0.6 million from a third party lender to pay for the Company's current insurance premiums. The loan is payable in nine monthly installments of principal and interest. Interest accrues at a rate of 3.24% per annum. As of June 30, 2014 and December 31, 2013, the outstanding unpaid loan balance was zero and $0.4 million, respectively.

In February 2014, the Company borrowed $0.2 million from a third party lender to pay for the Company's consolidated VIE's current insurance premiums. The loan is payable in ten monthly installments of principal and interest. Interest accrues at a rate of 5.95% per annum. As of June 30, 2014 and December 31, 2013, the outstanding unpaid loan balance was $0.1 million and zero, respectively.

In March 2013, the Company entered into a one-year-term export financing agreement with ABC for approximately $2.5 million to fund exports through March 2014. This loan is collateralized by future exports from the Company's subsidiary in Brazil. As of June 30, 2014, the loan was fully paid.

In March 2014, the Company entered into an additional one-year-term export financing agreement with ABC for approximately $2.2 million to fund exports through March 2015. This loan is collateralized by future exports from the Company's subsidiary in Brazil. As of June 30, 2014, the principal amount outstanding under this agreement was $2.2 million.The Company is also a parent guarantor for the payment of the outstanding balance under these loan agreements. 

Letters of Credit

In June 2012, the Company entered into a letter of credit agreement for $1.0 million under which it provided a letter of credit to the landlord of its headquarters in Emeryville, California, in order to cover the security deposit on the lease. This letter of credit is secured by a certificate of deposit. Accordingly, the Company has $1.7 million and $0.9 million as restricted cash as of June 30, 2014 and December 31, 2013.

Future minimum payments under the debt agreements as of June 30, 2014 are as follows (in thousands):

Years ending December 31:	Related Party Convertible Debt			Convertible Debt			Loans Payable			Credit Facility
2014 (remaining six months)	$	744		$	1,891		$	4,080		$	2,539
2015	1,606			4,020			4,114			15,426
2016	1,606			4,020			3,935			20,301
2017	58,849			28,715			3,772			7,822
2018	74,485			15,685			3,612			472
Thereafter	75,825			56,798			11,751			131
Total future minimum payments	213,115			111,129			31,264			46,691
Less: amount representing interest(1)	(112,635		)	(53,225		)	(5,265		)	(8,719		)
Present value of minimum debt payments	100,480			57,904			25,999			37,972
Less: current portion	—			—			(5,218		)	(4,705		)
Noncurrent portion of debt	$	100,480		$	57,904		$	20,781		$	33,267

______________ 

⁽¹⁾ Including debt discount of $83.9 million related to the embedded derivative associated with the related party and non-related party convertible debt which will be accreted to interest expense under the effective interest method over the term of the convertible debt.

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Balance Sheet Components

6 Months Ended

Jun. 30, 2014

Organization, Consolidation and Presentation of Financial Statements [Abstract]

Balance Sheet Components

Balance Sheet Components

Inventories, net

Inventories are stated at the lower of cost or market and consist of the following (in thousands):

	June 30, 2014		December 31, 2013
Raw materials	$	2,468	$	1,796
Work-in-process	6,536		7,292
Finished goods	5,749		1,800
Inventories, net	$	14,753	$	10,888

Prepaid Expenses and Other Current Assets

Prepaid expenses and other current assets is comprised of the following (in thousands):

	June 30, 2014		December 31, 2013
Maintenance (1)	$	393	$	258
Prepaid insurance(1)	603		894
Manufacturing catalysts	1,715		1,536
Recoverable VAT and other taxes	2,776		5,125
Other (1)	1,651		1,705
Prepaid expenses and other current assets	$	7,138	$	9,518

______________ 

⁽¹⁾  Certain classifications of prior period amounts have been made to conform to the current period presentation. Such reclassifications did not materially change previously reported consolidated financial statements.

Property, Plant and Equipment, net

Property, plant and equipment, net is comprised of the following (in thousands):

	June 30, 2014			December 31, 2013
Leasehold improvements	$	39,208		$	39,034
Machinery and equipment	101,383			96,585
Computers and software	8,946			8,509
Furniture and office equipment	2,584			2,535
Buildings	7,606			7,148
Vehicles	436			488
Construction in progress	44,635			41,387
	204,798			195,686
Less: accumulated depreciation and amortization	(64,142		)	(55,095		)
Property, plant and equipment, net	$	140,656		$	140,591

The Company's first, purpose-built, large-scale Biofene production plant in southeastern Brazil commenced operations in December 2012. This plant is located at Brotas in the state of São Paulo, Brazil and is adjacent to an existing sugar and ethanol mill, Paraíso Bioenergia. The Company's construction in progress consists primarily of the upfront plant design and the initial construction of a second large-scale production plant in Brazil, located at the Sao Martinho S.A. (or "SMSA") (formerly Usina São Martinho S.A.) sugar and ethanol mill (also in the state of São Paulo, Brazil).

Property, plant and equipment, net includes $3.8 million and $3.4 million of machinery and equipment under capital leases as of June 30, 2014 and December 31, 2013, respectively. Accumulated amortization of assets under capital leases totaled $1.8 million and $1.5 million as of June 30, 2014 and December 31, 2013, respectively.

Depreciation and amortization expense, including amortization of assets under capital leases was $3.7 million and $4.1 million for the three months ended June 30, 2014 and 2013, respectively, and was $7.5 million and $8.5 million for the six months ended June 30, 2014 and 2013, respectively.

The Company capitalizes interest costs incurred to construct plant and equipment. The capitalized interest is recorded as part of the depreciable cost of the asset to which it relates to and is amortized over the asset's estimated useful life. Interest cost capitalized as of June 30, 2014 and December 31, 2013 was $0.5 million and $0.5 million, respectively.

Other Assets

Other assets are comprised of the following (in thousands):

	June 30, 2014		December 31, 2013
Deposits on property and equipment, including taxes	$	2,095	$	1,970
Recoverable taxes from Brazilian government entities	9,064		6,599
Debt issuance cost (2)	978		454
Investments in joint venture (1)	2,170		68
Other (2)	1,519		1,494
Total other assets	$	15,826	$	10,585

______________ 

⁽¹⁾  The investments in joint venture represents the Company's investments in the joint venture with Novvi LLC and Total Amyris Biosolutions B.V. of $2.1 million and $0.1 million as of June 30, 2014, respectively, and zero and $0.1 million as of December 31, 2013, respectively.

⁽²⁾  Certain classifications of prior period amounts have been made to conform to the current period presentation. Such reclassifications did not materially change previously reported consolidated financial statements.

Accrued and Other Current Liabilities

Accrued and other current liabilities are comprised of the following (in thousands):

	June 30, 2014		December 31, 2013
Professional services	$	2,093	$	2,279
Accrued vacation	2,516		2,274
Payroll and related expenses	3,939		5,066
Tax-related liabilities	157		825
Deferred rent, current portion	1,111		1,111
Accrued interest	1,246		3,176
Contractual obligations to contract manufacturers	853		4,241
Other	846		2,249
Total accrued and other current liabilities	$	12,761	$	21,221

Derivative Liability

Derivative liability is comprised of the following (in thousands):

	June 30, 2014		December 31, 2013
Fair market value of swap obligation	$	2,808	$	3,600
Fair value of compound embedded derivative liability(1)	145,032		131,117
Total derivative liability	$	147,840	$	134,717

______________ 

⁽¹⁾  The compound embedded derivative liability represents the fair value of the bifurcated conversion options that contain "make-whole" provisions or down round conversion price adjustment provisions included in the outstanding Total Notes, Tranche I Notes, Tranche II Notes and the Rule 144A Convertible Note Offering (see Note 3, "Fair value of financial instruments" and Note 5, "Debt").

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Comprehensive Income (Loss)

6 Months Ended

Jun. 30, 2014

Equity [Abstract]

Comprehensive Income (Loss)

Comprehensive Income (Loss)

Comprehensive income (loss) represents all changes in stockholders’ equity (deficit) except those resulting from investments or contributions by stockholders. The Company’s foreign currency translation adjustments represent the components of comprehensive income (loss) excluded from the Company’s net loss and have been disclosed in the condensed consolidated statements of comprehensive loss for all periods presented.

The components of accumulated other comprehensive loss are as follows (in thousands):

	June 30, 2014			December 31, 2013
Foreign currency translation adjustment, net of tax	$	(15,634	)	$	(20,087	)
Total accumulated other comprehensive loss	$	(15,634	)	$	(20,087	)

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Employee Benefit Plan

6 Months Ended

Jun. 30, 2014

Compensation and Retirement Disclosure [Abstract]

Employee Benefit Plan

Employee Benefit Plan

The Company established a 401(k) Plan to provide tax deferred salary deductions for all eligible employees. Participants may make voluntary contributions to the 401(k) Plan up to 90% of their eligible compensation, limited by certain Internal Revenue Service (referred to as the "IRS") restrictions. Effective January 2014, the Company implemented a discretionary employer match plan whereby the Company will match employee contributions up to the IRS limit or 90% of compensation, with a minimum one year of service required for vesting. The total matching amount for the three and six months ended June 30, 2014 was $0.1 million and $0.2 million, respectively.

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Significant Agreements

6 Months Ended

Jun. 30, 2014

Significant Agreements [Abstract]

Significant Agreements

Significant Agreements

Collaboration Agreement with Michelin and Braskem

In September 2011, the Company entered into a collaboration agreement with Manufacture Francaise des Pneumatiques Michelin (or “Michelin”). Under the terms of the September 2011 collaboration agreement, the Company and Michelin agreed to collaborate on the development, production and worldwide commercialization of isoprene or isoprenol, generally for tire applications, using the Company's technology. Under the agreement, Michelin agreed to pay an upfront payment to the Company of $5.0 million.

In June 2014, the Company entered into a collaboration agreement with Braskem S.A. and Braskem America, Inc. (or “Braskem”) and Michelin to collaborate to develop the technology to produce and possibly commercialize renewable isoprene. The term of the collaboration agreement commenced on June 30, 2014 and will continue, unless earlier terminated in accordance with the agreement, until the first to occur of (i) the date that is three (3) years following the actual date on which a Work Plan is completed, which date is estimated to occur on or about December 30, 2020 or (ii) the date of the commencement of commissioning of a production plant for the production of renewable isoprene. The June 2014 collaboration agreement terminated and supersedes the September 2011 collaboration agreement with Michelin, and as a result of the signing of the June 2014 collaboration agreement, the upfront payment by Michelin of $5.0 million is being rolled into the new collaboration agreement between Michelin, Braskem and the Company as Michelin's collaboration funding towards the research and development activities to be performed. As of June 30, 2014, the $5.0 million from Michelin is still recorded as "Deferred Revenue" in the condensed consolidated balance sheet .

Collaboration Partner Joint Development and License Agreement

In April 2013, the Company entered into a joint development and license agreement with a collaboration partner. Under the terms of the multi-year agreement, the collaboration partner and the Company will jointly develop certain fragrance ingredients. The collaboration partner will have exclusive rights to these fragrance ingredients for applications in the flavors and fragrances field, and the Company will have exclusive rights in other fields. The collaboration partner and the Company will share in the economic value derived from these ingredients. The joint development and license agreement provided for up to $6.0 million in funding based upon the achievement of certain technical milestones which are considered substantive by the Company during the first phase of the collaboration.

In February 2014, the Company entered into an amendment to the joint development and license agreement with the collaboration partner noted in the preceding paragraph to proceed with the second phase of the collaboration and the development of a certain fragrance ingredient. The Company recognized revenue for the three and six months ended June 30, 2014 of $0.8 million and $1.0 million, respectively, and zero for the three and six months ended June 30, 2013, respectively, under this agreement.

Collaboration Partner Master Collaboration and Joint Development Agreement

In March 2013, the Company entered into a Master Collaboration Agreement with the collaboration partner to establish a collaboration for the development and commercialization of multiple renewable flavors and fragrances (referred to as "F&F") compounds. Under this agreement, except for rights granted under preexisting collaboration relationships, the Company granted the collaboration partner exclusive access for such compounds to specified Company intellectual property for the development and commercialization of F&F products in exchange for research and development funding and a profit sharing arrangement. The agreement superseded and expanded the prior collaboration agreement between the Company and the collaboration partner.

The agreement provides annual, up-front funding to the Company by the collaboration partner of $10.0 million for each of the first three years of the collaboration. The initial payment of $10.0 million was received by the Company in March 2013 and the second payment was received in March 2014. The Company recognized revenue under this agreement for the three months ended June 30, 2014 and 2013, of $2.5 million and $2.8 million, respectively, and for the six months ended June 30, 2014 and 2013, of $5.0 million and $3.2 million, respectively. The agreement contemplates additional funding by the collaboration partner of up to $5.0 million under three potential milestone payments, as well as additional funding by the collaboration partner on a discretionary basis.

Kuraray Collaboration Agreement and Securities Purchase Agreement

In March 2014, the Company entered into the Second Amended and Restated Collaboration Agreement with Kuraray Co., Ltd. (or “Kuraray”) in order to extend the term of the original agreement dated July 21, 2011 for an additional two years and add additional fields and products to the scope of development. In consideration for the Company’s agreement to extend the term of the original collaboration agreement and add additional fields and products, Kuraray will pay the Company $4.0 million in two (2) equal installments of $2.0 million. The first installment was paid on April 30, 2014 and the second installment is due on April 30, 2015. In connection with the collaboration agreement Kuraray signed a Securities Purchase Agreement in March 2014 to purchase 943,396 shares of the Company's common stock at a price per share of $4.24 per share. The Company issued 943,396 shares of its common stock at a price per share of $4.24 in April 2014 for aggregate cash proceeds of $4.0 million.

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Joint Ventures and Noncontrolling Interest - Narrative (Details)			1 Months Ended			0 Months Ended	6 Months Ended	1 Months Ended
	Mar. 31, 2014 EUR (€)	Mar. 26, 2013 Joint Venture with Cosan [Member] USD ($)	Mar. 31, 2013 Joint Venture with Cosan [Member] Corporate Joint Venture [Member]	Jun. 30, 2011 Joint Venture with Cosan [Member] Corporate Joint Venture [Member]	Mar. 26, 2013 Joint Venture with Cosan [Member] Corporate Joint Venture [Member]	Mar. 26, 2013 Joint Venture with Cosan [Member] Amyris Brasil S.A. Subsidiary [Member] BRL	Jun. 30, 2014 Joint Venture with Cosan [Member] Amyris Brasil S.A. Subsidiary [Member] BRL	Apr. 30, 2010 SMA Industria Quimica S.A. [Member] Corporate Joint Venture [Member]	Apr. 14, 2010 SMA Industria Quimica S.A. [Member] Corporate Joint Venture [Member] member Y	Jun. 30, 2014 Maximum [Member] SMA Industria Quimica S.A. [Member] Corporate Joint Venture [Member] USD ($)	Mar. 31, 2014 Maximum [Member] SMA Industria Quimica S.A. [Member] Corporate Joint Venture [Member] BRL
Redeemable Noncontrolling Interest [Line Items]
Initial Term of Joint Venture			20 years	20 years				20 years
Initial Term Shareholders Agreement				10 years
Equity Method Investment Number of Members of Executive Committee									3
Equity Method Investment Number of Company Appointed Members of Executive Committee									2
Equity Method Investment Number of Members of Board of Directors									4
Equity Method Investment Number of Members of Board of Directors Appointed by Each Venture									2
Due from Joint Ventures										$ 28,100,000	61,800,000
Equity Method Investment Period Company is required to Purchase Output of SMA									4
Equity Method Investment, Ownership Percentage				50.00%	50.00%				50.00%
Obligation to Fund Agreement, Cash Portion		10,000,000
Equity Method Investment Ownership Percentage Required				10.00%
Agreement to Sell Equity Ownership						22,000	9,989
Capitalization, Long-term Debt and Equity	€ 100,000

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Commitments and Contingencies

6 Months Ended

Jun. 30, 2014

Commitments and Contingencies Disclosure [Abstract]

Commitments and Contingencies

Commitments and Contingencies

Lease Obligations

The Company leases certain facilities and finances certain equipment under operating and capital leases, respectively. Operating leases include leased facilities and capital leases include leased equipment (see Note 4, "Balance Sheet Components"). The Company recognizes rent expense on a straight-line basis over the non-cancellable lease term and records the difference between rent payments and the recognition of rent expense as a deferred rent liability. Where leases contain escalation clauses, rent abatements, and/or concessions, such as rent holidays and landlord or tenant incentives or allowances, the Company applies them as a straight-line rent expense over the lease term. The Company has non-cancellable operating lease agreements for office, research and development, and manufacturing space that expire at various dates, with the latest expiration in February 2031. Rent expense under operating leases was $1.3 million and $1.4 million for the three months ended June 30, 2014 and 2013, respectively, and was $2.7 million and $2.1 million for the six months ended June 30, 2014 and 2013, respectively.

Future minimum payments under the Company's lease obligations as of June 30, 2014, are as follows (in thousands):

Years ending December 31:	Capital Leases			Operating Leases		Total Lease Obligations
2014 (remaining six months)	$	557		$	3,182	$	3,739
2015	462			6,606		7,068
2016	159			6,614		6,773
2017	—			6,588		6,588
2018	—			6,675		6,675
Thereafter	—			32,320		32,320
Total future minimum lease payments	1,178			$	61,985	$	63,163
Less: amount representing interest	(68		)
Present value of minimum lease payments	1,110
Less: current portion	(882		)
Long-term portion	$	228

GuarantorArrangements

The Company has agreements to indemnify its officers and directors for certain events or occurrences while the officers or directors are serving in their official capacities. The indemnification period remains enforceable for the officer's or director’s lifetime. The maximum potential amount of future payments the Company could be required to make under these indemnification agreements is unlimited; however, the Company has a director and officer insurance policy that limits its exposure and enables the Company to recover a portion of any future payments. As a result of its insurance policy coverage, the Company believes the estimated fair value of these indemnification agreements is minimal. Accordingly, the Company had no liabilities recorded for these agreements as of June 30, 2014 and December 31, 2013.

The Company entered into the FINEP Credit Facility to finance a research and development project on sugarcane-based biodiesel (see Note 5, "Debt"). The FINEP Credit Facility is guaranteed by a chattel mortgage on certain equipment of the Company. The Company's total acquisition cost for the equipment under this guarantee is approximately R$6.0 million (approximately US$2.7 million based on the exchange rate as of June 30, 2014).

The Company entered into the BNDES Credit Facility to finance a production site in Brazil (see Note 5, "Debt").The BNDES Credit Facility is collateralized by a first priority security interest in certain of the Company's equipment and other tangible assets with a total acquisition cost of R$24.9 million (approximately US$11.3 million based on the exchange rate as of June 30, 2014). The Company is a parent guarantor for the payment of the outstanding balance under the BNDES Credit Facility. Additionally, the Company is required to provide certain bank guarantees under the BNDES Credit Facility. Accordingly, the Company has a $0.8 million and $0.7 million as restricted cash as of June 30, 2014 and December 31, 2013, respectively.

The Company entered into loan agreements and security agreement where the Company pledged certain farnesene production assets as collateral (the fiduciary conveyance of movable goods) with each of Nossa Caixa and Banco Pine (see Note 5, "Debt"). The Company's total acquisition cost for the farnesene production assets pledged as collateral under these agreements is approximately R$68.0 million (approximately US$30.9 million based on the exchange rate as of June 30, 2014). The Company is also a parent guarantor for the payment of the outstanding balance under these loan agreements. 

The Company had an export financing agreement with ABC for approximately $2.5 million for a one year term to fund exports through March 2014. As of June 30, 2014, the loan was fully paid. The Company has entered into another export financing agreement with the same bank for approximately $2.2 million for a one year term to fund exports through March 2015. This loan is collateralized by future exports from Amyris Brasil. The Company is also a parent guarantor for the payment of the outstanding balance under these loan agreements. 

Under an operating lease agreement for its office facilities in Brazil, which commenced on November 15, 2011, the Company is required to maintain restricted cash or letters of credit equal to 3 months of rent of approximately R$0.2 million (approximately US$0.1 million based on the exchange rate as of June 30, 2014) in the aggregate as a guarantee that the Company will meet its performance obligations under such operating lease agreement.

In October 2013, the Company entered into a letter agreement with Total relating to the Temasek Bridge Note and to the closing of the August 2013 Financing (referred to as the "Amendment Agreement") (see Note 5, "Debt"). In the August 2013 Financing, the Company was required to provide the purchasers under the August 2013 SPA with a security interest in the Company’s intellectual property if Total still held such security interest as of the initial closing of the August 2013 Financing. Under the terms of a previous Intellectual Property Security Agreement by and between the Company and Total (referred to as the "Security Agreement"), the Company had previously granted a security interest in favor of Total to secure the obligations of the Company under certain convertible promissory notes issued and issuable to Total under the Total Purchase Agreement. The Security Agreement provided that such security interest would terminate if Total and the Company entered into certain agreements relating to the formation of the Fuels JV. In connection with Total’s agreement to (i) permit the Company to grant the security interest under the Temasek Bridge Note and the August 2013 Financing and (ii) waive a secured debt limitation contained in the outstanding convertible promissory notes issued pursuant to the Total Purchase Agreement and held by Total (referred to as the “Total Securities”), the Company entered into the Amendment Agreement. Under the Amendment Agreement, the Company agreed to reduce, effective December 2, 2013, the conversion price for the Total Securities issued in 2012 (approximately $48.3 million of which are outstanding as of the date hereof) from $7.0682 per share to $2.20, the market price per share of the Company’s common stock as of the signing of the Amendment Agreement, as determined in accordance with applicable NASDAQ rules, unless the Company and Total entered into the JV Documents on or prior to December 2, 2013. The Company and Total entered into the JV agreements on December 2, 2013 and the Amendment Agreement and all security interests thereunder were automatically terminated and the conversion price of the Total Securities remained at $7.0682 per share.

In December 2013, in connection with the execution of JV Documents entered into by and among Amyris, Total and JVCO relating to the establishment of the JVCO (see Note 5, "Debt" and Note 7, "Joint Venture and Noncontrolling Interest"), Amyris agreed to exchange the $69.0 million outstanding Total unsecured convertible notes issued pursuant to the Total Purchase Agreement and issue replacement 1.5% senior secured convertible notes, in principal amounts equal to the principal amount of each Replacement Notes and grant a security interest to Total in and lien on all Amyris’s rights, title and interest in and to Amyris’s shares in the capital of the JVCO. Following execution of the JV Documents, all notes that have been issued and that remain to be issued in connection with the third closing under the Total Purchase Agreement (up to $21.7 million in the aggregate; with $10.85 million in principal amount of such remaining notes issued on July 31, 2014, and an additional $10.85 million in principal amount of such remaining notes to be issued by January 31, 2015) are senior secured convertible notes instead of senior unsecured convertible notes.

In March 2014, the Company and Hercules Technology Growth Capital, Inc. entered into a loan and security agreement to make available to the Company a loan in the aggregate principal amount of up to $25.0 million (see Note5 "Debt"). Loans under the facility are secured by various liens, including a lien on certain Company intellectual property. In connection with the Hercules loan, the Company agreed to certain customary representations and warranties and covenants, as well as certain covenants with respect to obtaining additional financing as described above and performance covenants related to revenues and cash flows starting with the third quarter of 2014. If the Company had not satisfied the equity financing covenant, a forbearance fee of $10.0 million would have become due and payable at the end of the initial term of the loan. The Company borrowed the full amount available under the facility and received the funds on March 31, 2014. In June 2014, the Company and Hercules entered into the Hercules Amendment of the Loan and Security Agreement entered into on March 29, 2014. Pursuant to the Hercules Amendment, the parties agreed to remove (i) a requirement for the Company to pay a forbearance fee of $10.0 million in the event certain covenants were not satisfied, (ii) a covenant that the Company maintain positive cash flow commencing with the fiscal quarter beginning October 1, 2014, (iii) a covenant that, beginning with the fiscal quarter beginning July 1, 2014, the Company and its subsidiaries achieve certain projected cash product revenues and projected cash product gross profits, and (iv) an obligation for the Company to file a registration statement on Form S-3 with the SEC by no later than June 30, 2014 and complete an equity financing of more than $50.0 million by no later than September 30, 2014. Under the Hercules Amendment, in connection with the amendments and modification or removal of the covenants described above, the Company agreed to include a new covenant requiring the Company to maintain unrestricted, unencumbered cash in an amount equal to at least 50% of the remaining principal amount then outstanding under the Hercules Loan Facility and borrow an additional tranche of $5.0 million, subject to obtaining specified third party consents under outstanding convertible promissory notes. The Hercules Loan Facility is collateralized by liens on the Company's assets, including on certain Company intellectual property.

Purchase Obligations

As of June 30, 2014, the Company had $6.8 million in purchase obligations which included $5.9 million in non-cancellable contractual obligations and construction commitments, of which $2.4 million have been accrued as loss on purchase commitments.

Other Matters

Certain conditions may exist as of the date the financial statements are issued, which may result in a loss to the Company but will only be recorded when one or more future events occur or fail to occur. The Company's management assesses such contingent liabilities, and such assessment inherently involves an exercise of judgment. In assessing loss contingencies related to legal proceedings that are pending against and by the Company or unasserted claims that may result in such proceedings, the Company's management evaluates the perceived merits of any legal proceedings or unasserted claims as well as the perceived merits of the amount of relief sought or expected to be sought.

If the assessment of a contingency indicates that it is probable that a material loss has been incurred and the amount of the liability can be estimated, then the estimated liability would be accrued in the Company's financial statements. If the assessment indicates that a potential material loss contingency is not probable but is reasonably possible, or is probable but cannot be estimated, then the nature of the contingent liability, together with an estimate of the range of possible loss if determinable and material would be disclosed. Loss contingencies considered to be remote by management are generally not disclosed unless they involve guarantees, in which case the guarantee would be disclosed.

In May 2013, a securities class action complaint was filed against the Company and its CEO, John G. Melo, in the U.S. District Court for the Northern District of California. In October 2013, the lead plaintiffs filed a consolidated amended complaint. The complaint, as amended, sought unspecified damages on behalf of a purported class that would comprise all individuals who acquired the Company's common stock between April 29, 2011 and February 8, 2012. The complaint alleged securities law violations based on the Company's commercial projections during that period. In December 2013, the Company filed a motion to dismiss the complaint. In March 2014, the court issued an order granting the Company's motion to dismiss with leave to amend the complaint. The plaintiffs declined to amend their complaint further and, on June 12, 2014, the court issued an order (based on stipulation of the parties) dismissing the action with prejudice.

In August 2013, a complaint entitled Steve Shannon, derivatively on behalf of Amyris, Inc. v. John G. Melo et al and Amyris, Inc., was filed against the Company as nominal defendant in the United States District Court for the Northern District of California. The lawsuit sought unspecified damages on behalf of the Company from certain of its current and former officers, directors and employees and alleges these defendants breached their fiduciary duties to the Company and unjustly enriched themselves by making allegedly false and misleading statements and omitting certain material facts in the Company's securities filings. Because this purported stockholder derivative action is based on substantially the same facts as the securities class action described above, the two actions were related and were heard by the same judge. On June 23, 2014, following the dismissal of the related class action (discussed above), the court issued an order (based on stipulation of the parties) dismissing the action with prejudice.

The Company is subject to disputes and claims that arise or have arisen in the ordinary course of business and that have not resulted in legal proceedings or have not been fully adjudicated. Such matters that may arise in the ordinary course of business are subject to many uncertainties and outcomes are not predictable with assurance. Therefore, if one or more of these legal disputes or claims resulted in settlements or legal proceedings that were resolved against the Company for amounts in excess of management’s expectations, the Company’s consolidated financial statements for the relevant reporting period could be materially adversely affected.

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Joint Ventures and Noncontrolling Interest

6 Months Ended

Jun. 30, 2014

Joint Ventures and Noncontrolling Interest [Abstract]

Joint Ventures and Noncontrolling Interest

Joint Ventures and Noncontrolling Interest

Novvi S.A.

In June 2011, the Company entered into joint venture agreements with Cosan Combustíveis e Lubrificantes S.A. and Cosan S.A. Industria e Comércio (such Cosan entities, collectively or individually, “Cosan”), related to the formation of a joint venture to focus on the worldwide development, production and commercialization of base oils made from Biofene for the automotive, commercial and industrial lubricants markets (referred to as the "Original JV Agreement"). The parties originally envisioned operating their joint venture through Novvi S.A., a Brazilian entity jointly owned by Cosan and Amyris Brasil.

Under the Original JV Agreement and related agreements, the Company and Cosan each owned 50% of the Novvi S.A. and each party would share equally in any costs and any profits ultimately realized by Novvi S.A. The joint venture agreement had an initial term of 20 years from the date of the Original JV Agreement, subject to earlier termination by mutual written consent or by a non-defaulting party in the event of specified defaults by the other party. The shareholders' agreement had an initial term of 10 years from the date of the agreement, subject to earlier termination if either the Company or Cosan ceases to own at least 10% of the voting stock of Novvi S.A. Since its formation, Novvi S.A. had minimal operating activities while the Company and Cosan continued to determine and finalize the strategy and operating activities for the joint venture. Upon determination by the Company and Cosan that the joint venture should be operated out of a U.S. entity, the operating activities of Novvi S.A. ceased. The Company has identified that Novvi S.A. is a VIE and determined that the power to direct activities, which most significantly impact the economic success of the joint venture, is equally shared between the Company and Cosan. Accordingly, the Company is not the primary beneficiary and therefore accounts for its investment in Novvi S.A. under the equity method of accounting.

In March 2013, the Company, Amyris Brasil and Cosan entered into a termination agreement to terminate the Original JV Agreement. In addition, Amyris Brasil agreed to sell, its 50% ownership in Novvi S.A. to Cosan for approximately R$22,000 (approximately US$9,989 based on the exchange rate as of June 30, 2014), which represented the current value of its 50% equity ownership in Novvi S.A., a now-dormant company. Upon the consummation of the transaction with the shares transferring from Amyris Brasil to Cosan, the Novvi S.A. shareholders agreement automatically terminated.

Novvi LLC

In September 2011, the Company and Cosan US, Inc. (or "Cosan U.S.") formed Novvi LLC, a U.S. entity that is jointly owned by the Company and Cosan U.S. (or "Novvi"). In March 2013, the Company and Cosan U.S. entered into agreements to (i) expand their base oils joint venture to also include additives and lubricants and (ii) operate their joint venture exclusively through Novvi. Specifically, the parties entered into an Amended and Restated Operating Agreement for Novvi (referred to as the "Operating Agreement"), which sets forth the governance procedures for Novvi and the joint venture and the parties' initial contribution. The Company also entered into an IP License Agreement with Novvi (referred to as the "IP License Agreement") under which the Company granted Novvi (i) an exclusive (subject to certain limited exceptions for the Company), worldwide, royalty-free license to develop, produce and commercialize base oils, additives, and lubricants derived from Biofene for use in automotive and industrial lubricants markets and (ii) a non-exclusive, royalty-free license, subject to certain conditions, to manufacture Biofene solely for its own products. In addition, both the Company and Cosan U.S. granted Novvi certain rights of first refusal with respect to alternative base oil and additive technologies that may be acquired by the Company or Cosan U.S. during the term of the IP License Agreement. Under these agreements, the Company and Cosan U.S. will each own 50% of Novvi and each party will share equally in any costs and any profits ultimately realized by the joint venture. Novvi is governed by a six member Board of Managers (or the "Board Managers"), with three managers represented by each investor. The Board of Managers appoints the officers of Novvi, who are responsible for carrying out the daily operating activities of Novvi as directed by the Board of Managers. The IP License Agreement has an initial term of 20 years from the date of the agreement, subject to standard early termination provisions such as uncured material breach or a party's insolvency. Under the terms of the Operating Agreement, Cosan U.S. is obligated to fund its 50% ownership share of Novvi in cash in the amount of $10.0 million and the Company is obligated to fund its 50% ownership share of Novvi through the granting of an IP License to develop, produce and commercialize base oils, additives, and lubricants derived from Biofene for use in the automotive, commercial and industrial lubricants markets which has been agreed upon by Cosan U.S. and Amyris valued at $10.0 million. In March 2013, the Company measured its initial contribution of intellectual property to Novvi at the Company's carrying value of the licenses granted under the IP License Agreement, which was zero. Additional funding requirements to finance the ongoing operations of Novvi are expected to happen through revolving credit or other loan facilities provided by unrelated parties (i.e. such as financial institutions); cash advances or other credit or loan facilities provided by the Company and Cosan U.S. or their affiliates; or additional capital contributions by the Company and Cosan U.S.

In April 2014, the Company subscribed and purchased Membership Units of Novvi for an aggregate purchase price of $0.2 million. Also in April 2014, the Company contributed $2.1 million in cash in exchange of receiving additional Membership Units in Novvi. Each member owns 50% of Novvi's issued and outstanding Membership Units. The Company recorded its investment in Novvi of $2.1 million under "Other Assets" in the condensed consolidated balance sheet.

The Company has identified Novvi as a VIE and determined that the power to direct activities, which most significantly impact the economic success of the joint venture (i.e. continuing research and development, marketing, sales, distribution and manufacturing of Novvi products), is equally shared between the Company and Cosan U.S. Accordingly, the Company is not the primary beneficiary and therefore accounts for its investment in Novvi under the equity method of accounting. The Company will continue to reassess its primary beneficiary analysis of Novvi if there are changes in events and circumstances impacting the power to direct activities that most significantly affect Novvi's economic success. Under the equity method, the Company's share of profits and losses are included in “Other income (expense), net” in the condensed consolidated statements of operations. For the three and six months ended June 30, 2014, the Company recorded $0.2 million of its share of Novvi's net loss. The Company recorded collaboration revenue of zero and $0.3 million for the three months ended June 30, 2014 and 2013, respectively, and zero and $2.8 million for the six months ended June 30, 2014 and 2013, respectively, from the research and development activities that it has performed on behalf of Novvi.

Total Amyris BioSolutions B.V.

In November 2013, the Company and Total formed JVCO. The common equity of JVCO is jointly owned (50%/50%) by the Company and Total, and the preferred equity of JVCO is 100% owned by the Company. The Parties have agreed that JVCO’s purpose is limited to executing the License Agreement and maintaining such licenses under it, unless and until either (i) Total elects to go forward with either the full (diesel and jet fuel) JVCO commercialization program or the jet fuel component of the JVCO commercialization program (referred to as a “Go Decision”), (ii) Total elects to not continue its participation in the R&D Program and JVCO (referred to as a “No-Go Decision”), or (iii) Total exercises any of its rights to buy out the Company’s interest in JVCO. Following a Go Decision, the articles and shareholders’ agreement would be amended and restated to be consistent with the shareholders’ agreement contemplated by the July 2012 Agreements (see Note 5, "Debt" and Note 8, "Significant Agreements").

The JVCO has an initial capitalization of €0.1 million (approximately US$0.1 million based on the exchange rate as of June 30, 2014). The Company has identified JVCO as a VIE and determined that the Company is not the primary beneficiary and therefore accounts for its investment in JVCO under the equity method of accounting. Under the equity method, the Company's share of profits and losses are included in "Other income (expense), net" in the condensed consolidated statements of operations. No later than six months prior to July 31, 2016, the Company and Total shall amend the July 2012 Agreements to reflect the corporate structure of JVCO, amend and restate the articles of association of JVCO, finalize and agree on a five-year plan and an initial budget, maximize economic viability and value of JVCO and enter into the Total license agreement. The Company will reevaluate its assessment in 2016 based on the specific terms of the final shareholders' agreement.

SMA Indústria Química S.A.

In April 2010, the Company established SMA Indústria Química (or "SMA"), a joint venture with Sao Martinho S.A. (or "SMSA") (formerly Usina São Martinho S.A.), to build a production facility in Brazil. SMA is located at the SMSA mill in Pradópolis, São Paulo state. The joint venture agreements establishing SMA have a 20 year initial term.

 SMA is managed by a three member executive committee, of which the Company appoints two members, one of whom is the plant manager who is the most senior executive responsible for managing the construction and operation of the facility. SMA is governed by a four member board of directors, of which the Company and SMSA each appoint two members. The board of directors has certain protective rights which include final approval of the engineering designs and project work plan developed and recommended by the executive committee.

The joint venture agreements require the Company would fund the construction costs of the new facility and SMSA would reimburse the Company up to R$61.8 million (approximately US$28.1 million based on the exchange rate as of June 30, 2014) of the construction costs after SMA commences production. After commercialization, the Company would market and distribute Amyris renewable products produced by SMA and SMSA would sell feedstock and provide certain other services to SMA. The cost of the feedstock to SMA would be a price that is based on the average return that SMSA could receive from the production of its current products, sugar and ethanol. The Company would be required to purchase the output of SMA for the first four years at a price that guarantees the return of SMSA’s investment plus a fixed interest rate. After this four year period, the price would be set to guarantee a break-even price to SMA plus an agreed upon return.

Under the terms of the joint venture agreements, if the Company becomes controlled, directly or indirectly, by a competitor of SMSA, then SMSA has the right to acquire the Company’s interest in SMA. If SMSA becomes controlled, directly or indirectly, by a competitor of the Company, then the Company has the right to sell its interest in SMA to SMSA. In either case, the purchase price shall be determined in accordance with the joint venture agreements, and the Company would continue to have the obligation to acquire products produced by SMA for the remainder of the term of the supply agreement then in effect even though the Company would no longer be involved in SMA’s management.

The Company has a 50% ownership interest in SMA. The Company has identified SMA as a variable interest entity (or "VIE") pursuant to the accounting guidance for consolidating VIEs because the amount of total equity investment at risk is not sufficient to permit SMA to finance its activities without additional subordinated financial support, as well as because the related commercialization agreement provides a substantive minimum price guarantee. Under the terms of the joint venture agreement, the Company directs the design and construction activities, as well as production and distribution. In addition, the Company has the obligation to fund the design and construction activities until commercialization is achieved. Subsequent to the construction phase, both parties equally fund SMA for the term of the joint venture. Based on those factors, the Company was determined to have the power to direct the activities that most significantly impact SMA’s economic performance and the obligation to absorb losses and the right to receive benefits. Accordingly, the financial results of SMA are included in the Company’s consolidated financial statements and amounts pertaining to SMSA’s interest in SMA are reported as noncontrolling interests in subsidiaries.

The Company completed a significant portion of the construction of the new facility in 2012. The Company suspended construction of the facility in order to focus on completing and operating the Company's smaller production facility in Brotas, Brazil. In February 2014, the Company entered into an amendment to the joint venture agreement with SMSA which updated and documented certain preexisting business plan requirements related to the start-up of construction at the joint venture operated plant and set forth, among other things, (i) the extension of the deadline for the commencement of operations at the joint venture operated plant to no later than 18 months following the construction of the plant, which shall occur no later than March 31, 2017, and (ii) the extension of an option held by SMSA to build a second large-scale farnesene production facility to no later than December 31, 2018 with the commencement of operations at such second facility to occur no later than April 1, 2019.

Glycotech

In January 2011, the Company entered into a production service agreement (referred to as the "Glycotech Agreement") with Glycotech, Inc. (or "Glycotech"), under which Glycotech provides process development and production services for the manufacturing of various Company products at its leased facility in Leland, North Carolina. The Company products manufactured by Glycotech are owned and distributed by the Company. Pursuant to the terms of the Glycotech Agreement, the Company is required to pay the manufacturing and operating costs of the Glycotech facility, which is dedicated solely to the manufacture of Amyris products. The initial term of the Glycotech Agreement was for a two year period commencing on February 1, 2011 and the Glycotech Agreement renews automatically for successive one-year terms, unless terminated by the Company. Concurrent with the Glycotech Agreement, the Company also entered into a Right of First Refusal Agreement with the lessor of the facility and site leased by Glycotech (referred to as the "ROFR Agreement"). Per conditions of the ROFR Agreement, the lessor agreed not to sell the facility and site leased by Glycotech during the term of the Glycotech Agreement. In the event that the lessor is presented with an offer to sell or decides to sell an adjacent parcel, the Company has the right of first refusal to acquire it.

The Company has determined that the arrangement with Glycotech qualifies as a VIE. The Company determined that it is the primary beneficiary of this arrangement since it has the power through the management committee over which it has majority control to direct the activities that most significantly impact Glycotech's economic performance. In addition, the Company is required to fund 100% of Glycotech's actual operating costs for providing services each month while the facility is in operation under the Glycotech Agreement. Accordingly, the Company consolidates the financial results of Glycotech. As of June 30, 2014, the carrying amounts of the consolidated VIE's assets and liabilities were not material to the Company's condensed consolidated financial statements.

The table below reflects the carrying amount of the assets and liabilities of the two consolidated VIEs for which the Company is the primary beneficiary. As of June 30, 2014, the assets include $22.9 million in property, plant and equipment, $4.1 million in other assets and $0.5 million in current assets. The liabilities include $0.2 million in accounts payable and accrued current liabilities and $0.1 million in loan obligations by Glycotech to its shareholders that are non-recourse to the Company. The creditors of each consolidated VIE have recourse only to the assets of that VIE.

	June 30,		December 31,
(In thousands)	2014		2013
Assets	$	27,509	$	25,730
Liabilities	$	421	$	229

The change in noncontrolling interest for the six months ended June 30, 2014 and 2013, is summarized below (in thousands):

	2014			2013
Balance at January 1	$	(584	)	$	(877	)
Foreign currency translation adjustment	(42		)	54
Gain (loss) attributable to noncontrolling interest	(60		)	261
Balance at June 30	$	(686	)	$	(562	)

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Goodwill and Intangible Assets

6 Months Ended

Jun. 30, 2014

Goodwill and Intangible Assets Disclosure [Abstract]

Goodwill and Intangible Assets

Goodwill and Intangible Assets

The following table presents the components of the Company's intangible assets (in thousands):

		June 30, 2014							December 31, 2013
	Useful Life in Years	Gross Carrying Amount		Accumulated Amortization			Net Carrying Value		Gross Carrying Amount		Accumulated Amortization			Net Carrying Value
In-process research and development	Indefinite	$	8,560	$	—		$	8,560	$	8,560	$	—		$	8,560
Acquired licenses and permits	2	772		(772		)	—		772		(772		)	—
Goodwill	Indefinite	560		—			560		560		—			560
		$	9,892	$	(772	)	$	9,120	$	9,892	$	(772	)	$	9,120

The following table presents the activity of intangible assets for the six months ended June 30, 2014 (in thousands):

	December 31, 2013								June 30, 2014
	Net Carrying Value		Additions		Adjustments		Amortization		Net Carrying Value
In-process research and development	$	8,560	$	—	$	—	$	—	$	8,560
Acquired licenses and permits	—		—		—		—		—
Goodwill	560		—		—		—		560
	$	9,120	$	—	$	—	$	—	$	9,120

The intangible assets acquired through the Draths Corporation acquisition in October 2011 of in-process research and development of $8.6 million and goodwill of $0.6 million are treated as indefinite lived intangible assets until completion or abandonment of the projects, at which time the assets will be amortized over the remaining useful life or written-off, as appropriate. If the carrying amount of the assets is greater than the measures of fair value, impairment is considered to have occurred and a write-down of the asset is recorded. Any finding that the value of its intangible assets has been impaired would require the Company to write-down the impaired portion, which could reduce the value of its assets and reduce (increase) its net income (loss) for the year in which the related impairment charges occur. As of June 30, 2014 and December 31, 2013, no impairment of the goodwill and intangible assets was recorded.    

Acquired licenses and permits are amortized using a straight-line method over its estimated useful life. Amortization expense for this intangible was zero and $32,000 for the six months ended June 30, 2014 and 2013, respectively. As of June 30, 2014, acquired licenses and permits were fully amortized.

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Goodwill and Intangible Assets (Details) (USD $)			6 Months Ended
	Jun. 30, 2014	Dec. 31, 2013	Jun. 30, 2014 Acquired Licenses and Permits [Member]	Jun. 30, 2013 Acquired Licenses and Permits [Member]	Dec. 31, 2013 Acquired Licenses and Permits [Member]	Jun. 30, 2014 In Process Research and Development [Member]	Dec. 31, 2013 In Process Research and Development [Member]	Oct. 31, 2011 Draths Corporation [Member]
Schedule of Finite-Lived and Indefinite-Lived Intangible Assets [Line Items]
Indefinite-Lived Intangible Assets (Excluding Goodwill)						$ 8,560,000	$ 8,560,000
Finite-Lived Intangible Asset, Useful Life			2 years
Finite-Lived Intangible Assets, Gross			772,000		772,000
Finite-Lived Intangible Assets, Accumulated Amortization	(772,000)	(772,000)	(772,000)		(772,000)
Finite-Lived Intangible Assets, Net	9,120,000	9,120,000	0		0
Goodwill	560,000	560,000
Goodwill and Intangible Assets, Gross	9,892,000	9,892,000
Goodwill and Intangible Assets, Net	9,120,000	9,120,000
Business Acquisition, Purchase Price Allocation, In-Process Research and Development								8,600,000
Business Acquisition, Purchase Price Allocation, Goodwill and Other Intangible Assets, Amount								600,000
Amortization of Intangible Assets			$ 0	$ (32,000)

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Stockholders' Deficit - Common Stock Warrants (Details) (Common Stock [Member], USD $) In Millions, except Share data, unless otherwise specified	3 Months Ended	12 Months Ended		3 Months Ended
	Mar. 31, 2014 Warrants In Connection With Capital Lease Arrangement [Member]	Dec. 31, 2013 Warrants In Connection With Capital Lease Arrangement [Member]	Dec. 31, 2012 Warrants In Connection With Capital Lease Arrangement [Member]	Mar. 31, 2014 Warrants In Connection With Issuance of Tranche I Convertible Promissory Notes [Member]	Oct. 31, 2013 Warrants In Connection With Issuance of Tranche I Convertible Promissory Notes [Member]
Class of Warrant or Right [Line Items]
Class of Warrant or Right, Outstanding			21,087		1,000,000
Class of Warrant or Right, Exercise Price of Warrants or Rights			10.67		0.01
Warrants and Rights Outstanding			$ 0.2		$ 1.3
Contractual term (in years)		10 years		3 years 5 months
Risk-free interest rate	2.00%			0.77%
Expected volatility	86.00%			45.00%
Expected dividend yield	0.00%			0.00%

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Significant Agreements - Narrative (Details) (USD $)	6 Months Ended			0 Months Ended		3 Months Ended			6 Months Ended		3 Months Ended		6 Months Ended
	Jun. 30, 2014	Jun. 30, 2013	Apr. 04, 2014	Apr. 23, 2013 International Flavors & Fragrances Inc Agreement [Member]	Mar. 13, 2013 Firmenich SA Agreement [Member]	Jun. 30, 2014 Firmenich SA Agreement [Member]	Jun. 30, 2013 Firmenich SA Agreement [Member]	Mar. 31, 2013 Firmenich SA Agreement [Member]	Jun. 30, 2014 Firmenich SA Agreement [Member]	Jun. 30, 2013 Firmenich SA Agreement [Member]	Mar. 31, 2014 Kuraray Securities Purchase Agreement [Member] Common Stock [Member]	Mar. 31, 2014 Kuraray Securities Purchase Agreement, Equal Installment Amount [Member] Common Stock [Member]	Jun. 30, 2014 Common Stock [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration Agreement, Range of Funding, First Phase of Collaberation				$ 6,000,000
Collaboration Agreement, Annual Funding								10,000,000
Collaboration Agreement, Period								3 years
Revenue Reognized, Including Portion Related to Milestone Method						2,500,000	2,800,000		5,000,000	3,200,000
Revenue Recognition, Milestone Method, Potential Revenue to be Recognized					5,000,000
Proceeds from issuance of common stock in private placements, net of issuance costs	4,000,000	19,980,000									4,000,000	2,000,000
Stock Issued During Period, Shares, New Issues													943,396
Stock Issued During Period, Price Per Share, New Issues											$ 4.24
Pilot plant service agreement			900,000
Sublease agreement			100,000
Accrued Liabilities	$ 300,000

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Reporting Segments (Tables)

6 Months Ended

Jun. 30, 2014

Segment Reporting [Abstract]

Schedule of Revenue from External Customers and Long-Lived Assets, by Geographical Areas

Revenues by geography are based on the location of the customer. The following tables set forth revenue and long-lived assets by geographic area (in thousands):

Revenues

	Three Months Ended June 30,				Six Months Ended June 30,
	2014		2013		2014		2013
United States	$	2,815	$	4,458	$	4,788	$	10,022
Brazil	1,402		1,259		2,050		2,077
Europe	2,985		4,005		6,338		4,230
Asia	2,105		1,127		2,172		2,389
Total	$	9,307	$	10,849	$	15,348	$	18,718

Long-Lived Assets

	June 30, 2014		December 31, 2013
United States	$	49,628	$	54,015
Brazil	90,375		85,891
Europe	653		685
Total	$	140,656	$	140,591

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Debt - BNDES Credit Facility (Details) (BNDES Credit Facility [Member], BNDES [Member]) In Millions, unless otherwise specified	1 Months Ended						1 Months Ended
	Dec. 31, 2011 BRL Monthly_installment	Jun. 30, 2014 USD ($)	Jun. 30, 2014 BRL	Mar. 31, 2014 BRL	Dec. 31, 2013 USD ($)	Dec. 31, 2013 BRL	Dec. 31, 2011 Maximum [Member] BRL
Line of Credit Facility [Line Items]
Line of Credit Facility, Maximum Borrowing Capacity		$ 10.2					22.4
Line of Credit Facility, Initial Tranche	19.1
Line of Credit Facility, Additional Tranche, Available Upon Delivery of Additional Guarantees	3.3
Period Credit Line Is Available							12 months
Line of Credit Facility Number of Monthly Payments (in monthly installment)	60
Debt Instrument, Interest Rate, Stated Percentage	7.00%
Line of Credit Facility, Unused Capacity, Commitment Fee Percentage	0.10%
Collateral Provided By Company, Certain Equipment and Other Tangible Assets, Amount		11.3		24.9
Line of Credit Facility, Bank Guarantee, Percentage	10.00%
Line of Credit Facility, Bank Guarantee, Percentage, Second Tranche	90.00%
Guarantor Obligations, Liquidation Proceeds, Percentage	130.00%
Line of Credit Facility, Amount Outstanding		$ 6.1	13.4		$ 6.5	15.3

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Income Taxes

6 Months Ended

Jun. 30, 2014

Income Tax Disclosure [Abstract]

Income Taxes

Income Taxes

For the three months ended June 30, 2014 and 2013, the Company recorded a provision for income taxes of $0.1 million and $0.2 million, respectively, and $0.2 million and $0.5 million for the six months ended June 30, 2014 and 2013, respectively. The provision for income taxes for the six months ended June 30, 2014 and 2013 consisted of an accrual of Brazilian withholding tax on intercompany interest liability. Other than the above mentioned provision for income tax, no additional provision for income taxes has been made, net of the valuation allowance, due to cumulative losses since the commencement of operations.

As of June 30, 2014, the US Internal Revenue Service (the "IRS") has completed its audit of the Company for tax year 2008 which concluded that there were no adjustments resulting from the audit. While the statutes are closed for tax year 2008, the US federal tax carryforwards (net operating losses and tax credits) may be adjusted by the IRS in the year in which the carryforward is utilized.

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Summary of Significant Accounting Policies (Policies)

6 Months Ended

Jun. 30, 2014

Accounting Policies [Abstract]

Basis of Presentation

Basis of Presentation

The accompanying interim condensed consolidated financial statements have been prepared in accordance with the accounting principles generally accepted in the United States of America (“GAAP”) and with the instructions for Form 10-Q and Regulation S-X. Accordingly, they do not include all of the information and notes required for complete financial statements. These interim condensed consolidated financial statements should be read in conjunction with the consolidated financial statements and notes thereto contained in the Company’s Form 10-K filed with the Securities and Exchange Commission (“SEC”) on April 2, 2014. The unaudited condensed consolidated financial statements include the accounts of the Company and its consolidated subsidiaries. All intercompany accounts and transactions have been eliminated in consolidation.

Principles of Consolidations

Principles of Consolidation

The Company has interests in joint venture entities that are variable interest entities (“VIEs”). Determining whether to consolidate a variable interest entity requires judgment in assessing (i) whether an entity is a VIE and (ii) if the Company is the entity’s primary beneficiary and thus required to consolidate the entity. To determine if the Company is the primary beneficiary of a VIE, the Company evaluates whether it has (i) the power to direct the activities that most significantly impact the VIE’s economic performance and (ii) the obligation to absorb losses or the right to receive benefits of the VIE that could potentially be significant to the VIE. The Company’s evaluation includes identification of significant activities and an assessment of its ability to direct those activities based on governance provisions and arrangements to provide or receive product and process technology, product supply, operations services, equity funding and financing and other applicable agreements and circumstances. The Company’s assessment of whether it is the primary beneficiary of its VIEs requires significant assumptions and judgment.

The condensed consolidated financial statements of the Company include the accounts of Amyris, Inc., its subsidiaries and two consolidated VIEs with respect to which the Company is considered the primary beneficiary, after elimination of intercompany accounts and transactions. Disclosure regarding the Company’s participation in the VIEs is included in Note 7, "Joint Ventures and Noncontrolling Interest."

Use of Estimates

Use of Estimates

In preparing the unaudited condensed consolidated financial statements, management must make estimates and assumptions that affect the reported amounts of assets and liabilities and disclosure of contingent assets and liabilities as of the date of the unaudited condensed consolidated financial statements and the reported amounts of revenue and expenses during the reporting period. Actual results could differ from those estimates.

Recent Accounting Pronouncements

Recent Accounting Pronouncements

In July 2013, the Financial Accounting Standards Board ("FASB") issued an amended accounting standard update on the financial statement presentation of unrecognized tax benefits. The amended guidance provides that a liability related to an unrecognized tax benefit would be presented as a reduction of a deferred tax asset for a net operating loss carryforward, a similar tax loss or a tax credit carryforward if such settlement is required or expected in the event the uncertain tax position is disallowed. The new guidance became effective for the Company on January 1, 2014 and will be applied prospectively to unrecognized tax benefits that exist at the effective date with retrospective applications permitted. The Company's current presentation of unrecognized tax benefits conforms with the amended guidance. Accordingly, there was no significant impact to the Company resulting from the guidance.

In May 2014, the FASB issued a new guidance related to revenue recognition. This new standard will replace all current GAAP guidance on this topic and eliminate all industry-specific guidance. The new revenue recognition standard provides a unified model to determine how revenue is recognized. The core principle of the guidance is that an entity should recognize revenue to depict the transfer of promised goods or services to customers in an amount that reflects the consideration to which the entity expects to be entitled in exchange for those goods or services. This guidance will be effective for the Company beginning January 1, 2017 and can be applied either retrospectively to each period presented or as a cumulative-effect adjustment as of the date of adoption. The Company is currently assessing the impact of adopting this new accounting standard on its financial statements.

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Debt (Details) (USD $) In Thousands, unless otherwise specified	Jun. 30, 2014	Dec. 31, 2013	Dec. 02, 2013
Debt Instrument [Line Items]
Long-term Debt	$ 222,355	$ 152,062
Less: current portion	(9,923)	(6,391)
Long-term debt	212,432	145,671
Credit Facility [Member]
Debt Instrument [Line Items]
Long-term Debt	37,972	8,767
Years ending December 31: [Abstract]
2014	2,539
2015	15,426
2016	20,301
2017	7,822
2018	472
Thereafter	131
Total future minimum payments	46,691
Less: amount representing interest	(8,719)
Present value of minimum debt payments	37,972
Less: current portion	(4,705)
Noncurrent portion of debt	33,267
Convertible Debt [Member]
Debt Instrument [Line Items]
Long-term Debt	57,904	28,537
Years ending December 31: [Abstract]
2014	1,891
2015	4,020
2016	4,020
2017	28,715
2018	15,685
Thereafter	56,798
Total future minimum payments	111,129
Less: amount representing interest	(53,225)
Present value of minimum debt payments	57,904
Less: current portion	0
Noncurrent portion of debt	57,904
Related Party Convertible Notes [Member]
Debt Instrument [Line Items]
Long-term Debt	100,480	89,499	25,000
Years ending December 31: [Abstract]
2014	744
2015	1,606
2016	1,606
2017	58,849
2018	74,485
Thereafter	75,825
Total future minimum payments	213,115
Less: amount representing interest	(112,635)
Present value of minimum debt payments	100,480
Less: current portion	0
Noncurrent portion of debt	100,480
Loans Payable [Member]
Debt Instrument [Line Items]
Long-term Debt	25,999	25,259
Years ending December 31: [Abstract]
2014	4,080
2015	4,114
2016	3,935
2017	3,772
2018	3,612
Thereafter	11,751
Total future minimum payments	31,264
Less: amount representing interest	(5,265)
Present value of minimum debt payments	25,999
Less: current portion	(5,218)
Noncurrent portion of debt	$ 20,781

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Fair Value of Financial Instruments - Banco Pine Textuals (Details) (Banco Pine July 2012 Loan Agreement [Member]) In Millions, unless otherwise specified	Jul. 30, 2012 BRL	Jun. 30, 2014 Interest Rate Swap [Member] USD ($)	Jun. 30, 2014 Interest Rate Swap [Member] BRL
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Notional Amount of Interest Rate Derivatives		$ 10.0	22.0
Debt Instrument, Face Amount	22.0
Derivative, Fixed Interest Rate		3.94%	3.94%

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Condensed Consolidated Statements of Comprehensive Loss (USD $) In Thousands, unless otherwise specified	3 Months Ended		6 Months Ended
	Jun. 30, 2014	Jun. 30, 2013	Jun. 30, 2014	Jun. 30, 2013
Comprehensive income (loss):
Net loss	$ 35,510	$ 38,914	$ 19,154	$ 71,229
Foreign currency translation adjustment, net of tax	1,578	(4,742)	4,411	(4,031)
Total comprehensive loss	(33,932)	(43,656)	(14,743)	(75,260)
Income (loss) attributable to noncontrolling interest	31	38	60	(261)
Foreign currency translation adjustment attributable to noncontrolling interest	19	(62)	42	(54)
Comprehensive loss attributable to Amyris, Inc.	$ (33,882)	$ (43,680)	$ (14,641)	$ (75,575)

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Fair Value of Financial Instruments

6 Months Ended

Jun. 30, 2014

Fair Value Disclosures [Abstract]

Fair Value of Financial Instruments

Fair Value of Financial Instruments

The inputs to the valuation techniques used to measure fair value are classified into the following categories:

Level 1: Quoted market prices in active markets for identical assets or liabilities.

Level 2: Observable market-based inputs or unobservable inputs that are corroborated by market data.

Level 3: Unobservable inputs that are not corroborated by market data.

As of June 30, 2014, the Company’s financial assets and financial liabilities are presented below at fair value and were classified within the fair value hierarchy as follows (in thousands):

	Level 1		Level 2		Level 3		Balance as of June 30, 2014
Financial Assets
Money market funds	$	74,765	$	—	$	—	$	74,765
Certificates of deposit	1,453		—		—		1,453
Total financial assets	$	76,218	$	—	$	—	$	76,218
Financial Liabilities
Loans payable (1)	$	—	$	20,360	$	—	$	20,360
Credit facilities  (1)	—		39,864		—		39,864
Convertible notes (1)	—		—		227,638		227,638
Compound embedded derivative liability	—		—		145,032		145,032
Currency interest rate swap derivative liability	—		2,808		—		2,808
Total financial liabilities	$	—	$	63,032	$	372,670	$	435,702

________

⁽¹⁾ These liabilities are carried on the condensed consolidated balance sheet on a historical basis.

The Company’s assessment of the significance of a particular input to the fair value measurement in its entirety requires management to make judgments and consider factors specific to the asset or liability. The fair values of money market funds are based on fair values of identical assets. The fair values of the loans payable, convertible notes, credit facilities and currency interest rate swaps are based on the present value of expected future cash flows and assumptions about current interest rates and the creditworthiness of the Company. Market risk associated with the fixed and variable rate long-term debt relates to the potential reduction in fair value and negative impact to future earnings, respectively, from an increase in interest rates.

The carrying amounts of certain financial instruments, such as cash equivalents, short term investments, accounts receivable, accounts payable and accrued liabilities, approximate fair value due to their relatively short maturities and low market interest rates, if applicable. The fair values of the loans payable, convertible notes and credit facilities are based on the present value of expected future cash flows and assumptions about current interest rates and the creditworthiness of the Company.

The following table provides a reconciliation of the beginning and ending balances for the convertible notes measured at fair value using significant unobservable inputs (Level 3) (in thousands):

	2014
Balance at January 1	$	131,952
Additions to convertible notes	93,295
Change in fair value of convertible notes	2,391
Balance at June 30	$	227,638

The Company’s financial assets and financial liabilities as of December 31, 2013 are presented below at fair value and were classified within the fair value hierarchy as follows (in thousands):

	Level 1		Level 2		Level 3		Balance as of December 31, 2013
Financial Assets
Money market funds	$	398	$	—	$	—	$	398
Certificates of deposit	1,428		—		—		1,428
Total financial assets	$	1,826	$	—	$	—	$	1,826
Financial Liabilities
Loans payable	$	—	$	18,491	$	—	$	18,491
Credit facilities	—		7,571		—		7,571
Convertible notes	—		—		131,952		131,952
Compound embedded derivative liability	—		—		131,117		131,117
Currency interest rate swap derivative liability	—		3,600		—		3,600
Total financial liabilities	$	—	$	29,662	$	263,069	$	292,731

Derivative Instruments

The following table provides a reconciliation of the beginning and ending balances for the compound embedded derivative liability measured at fair value using significant unobservable inputs (Level 3) (in thousands):

	2014
Balance at January 1	$	131,117
Transfers in to Level 3 net of cancellation (1)	86,551
Total (income) loss from change in fair value of derivative liability	(72,636		)
Balance at June 30	$	145,032

________

⁽¹⁾ Includes $1.1 million removal of derivative liability related to debt extinguishment.

The compound embedded derivative liability represents the fair value of the bifurcated conversion options that contain "make-whole" provisions or down round conversion price adjustment provisions of outstanding convertible promissory notes issued to Total Energies Nouvelles Activités USA (formerly known as Total Gas & Power USA, SAS, or “Total”), as well as Tranche I Notes, Tranche II Notes and notes issued under the Rule 144A Convertible Note Offering (see Note 5, "Debt"). There is no current observable market for this type of derivative and, as such, the Company determined the fair value of the embedded derivative using a Monte Carlo simulation valuation model for the Total Notes and the binomial lattice model for the Tranche I Notes, Tranche II Notes and the Rule 144A Convertible Note Offering. A Monte Carlo simulation valuation model combines expected cash outflows with market-based assumptions regarding risk-adjusted yields, stock price volatility, probability of a change of control and the trading information of the Company's common stock into which the notes are convertible. A binomial lattice model generates two probable outcomes - one up and another down - arising at each point in time, starting from the date of valuation until the maturity date. A lattice model was initially used to determine if the convertible notes would be converted, called or held at each decision point. Within the lattice model, the following assumptions are made: (i) the convertible notes will be converted early if the conversion value is greater than the holding value or (ii) the convertible notes will be called if the holding value is greater than both (a) redemption price and (b) the conversion value at the time. If the convertible notes are called, then the holder will maximize their value by finding the optimal decision between (1) redeeming at the redemption price and (2) converting the convertible notes. Using this lattice method, the Company valued the embedded derivative using the "with-and-without method", where the fair value of the convertible notes including the embedded derivative is defined as the "with", and the fair value of the convertible notes excluding the embedded derivative is defined as the "without". This method estimates the fair value of the embedded derivative by looking at the difference in the values between the convertible notes with the embedded derivative and the fair value of the convertible notes without the embedded derivative. The lattice model uses the stock price, conversion price, maturity date, risk-free interest rate, estimated stock volatility and estimated credit spread. The Company marks the compound embedded derivative to market due to the conversion price not being indexed to the Company's own stock. Except for the "make-whole interest" provision included in the conversion option, which is only required to be settled in cash upon a change of control at the noteholder's option, the compound embedded derivative will be settled in either cash or shares. As of June 30, 2014, the Company has sufficient common stock available to settle the conversion option in shares. As of June 30, 2014 and December 31, 2013, included in "Derivative Liability" on the condensed consolidated balance sheet is the Company's compound embedded derivative liability of $145.0 million and $131.1 million, respectively, which represents the fair value of the equity conversion option or a "make-whole" provision relating to the outstanding senior secured convertible promissory notes issued to Total, Tranche I Notes, Tranche II Notes and notes issued under the Rule 144A Convertible Note Offering as described above.

In June 2012, the Company entered into a loan agreement with Banco Pine S.A. (or "Banco Pine") under which Banco Pine provided the Company with a short term loan (referred to as the "Banco Pine Bridge Loan") (see Note 5, "Debt"). At the time of the Banco Pine Bridge Loan, the Company also entered into a currency interest rate swap arrangement with Banco Pine with respect to the repayment of R$22.0 million (approximately US$10.0 million based on the exchange rate as of June 30, 2014). The swap arrangement exchanges the principal and interest payments under the Banco Pine Bridge Loan of R$22.0 million entered into in July 2012 for alternative principal and interest payments that are subject to adjustment based on fluctuations in the foreign exchange rate between the U.S. dollar and Brazilian real. The swap has a fixed interest rate of 3.94%. Changes in the fair value of the swap are recognized in “Gain (loss) from change in fair value of derivative instruments" in the condensed consolidated statements of operations.

Derivative instruments measured at fair value as of June 30, 2014 and December 31, 2013, and their classification on the condensed consolidated balance sheets and condensed consolidated statements of operations, are presented in the following tables (in thousands except contract amounts):

	Liability as of
	June 30, 2014			December 31, 2013
Type of Derivative Contract	Quantity of Short Contracts	Fair Value		Quantity of Short Contracts	Fair Value
Currency interest rate swap, included as net liability in derivative liability	1	$	2,808	1	$	3,600

	Income Statement Classification	Three Months Ended June 30,					Six Months Ended June 30,
Type of Derivative Contract		2014		2013			2014	2013
		Gain (Loss) Recognized					Gain (Loss) Recognized
Currency interest rate swap (1)	Gain (loss) from change in fair value of derivative instruments	$	722	$	(1,639	)	$1,056	$	(1,651	)

___________ 

⁽¹⁾  Certain classifications of prior period amounts have been made to conform to the current period presentation. Such reclassifications did not materially change previously reported consolidated financial statements.

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Commitments and Contingencies (Details) (USD $)	3 Months Ended		6 Months Ended
	Jun. 30, 2014	Jun. 30, 2013	Jun. 30, 2014	Jun. 30, 2013	Dec. 31, 2013
Commitments and Contingencies Disclosure [Abstract]
Operating Leases, Rent Expense	$ 1,300,000	$ 2,100,000	$ 2,700,000	$ 1,400,000
Capital Leases, Future Minimum Payments Due [Abstract]
2014	557,000		557,000
2015	462,000		462,000
2016	159,000		159,000
2017	0		0
2018	0		0
Thereafter	0		0
Total future minimum lease payments	1,178,000		1,178,000
Less: amount representing interest	(68,000)		(68,000)
Present value of minimum lease payments	1,110,000		1,110,000
Less: current portion	(882,000)		(882,000)		(956,000)
Long-term portion	228,000		228,000		287,000
Operating Leases, Future Minimum Payments Due, Fiscal Year Maturity [Abstract]
2014	3,182,000		3,182,000
2015	6,606,000		6,606,000
2016	6,614,000		6,614,000
2017	6,588,000		6,588,000
2018	6,675,000		6,675,000
Thereafter	32,320,000		32,320,000
Total future minimum lease payments	61,985,000		61,985,000
Capital Leases And Operating Leases, Future Minimum Payments Due, Next Twelve Months	3,739,000		3,739,000
Capital Leases And Operating Leases, Future Minimum Payments Due, Due in Two Years	7,068,000		7,068,000
Capital Leases And Operating Leases, Future Minimum Payments Due, Due in Three Years	6,773,000		6,773,000
Capital Leases And Operating Leases, Future Minimum Payments Due, Due in Four Years	6,588,000		6,588,000
Capital Leases And Operating Leases, Future Minimum Payments Due, Due in Five Years	6,675,000		6,675,000
Capital Leases And Operating Leases, Future Minimum Payments Due, Due Thereafter	32,320,000		32,320,000
Capital Leases And Operating Leases, Future Minimum Payments Due	$ 63,163,000		$ 63,163,000

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Stock-Based Compensation - Stock-Based Compensation Expense (Details) (USD $)	3 Months Ended		6 Months Ended
	Jun. 30, 2014	Jun. 30, 2013	Jun. 30, 2014	Jun. 30, 2013
Employee Service Share-based Compensation, Allocation of Recognized Period Costs [Line Items]
Allocated Share-based Compensation Expense	$ 3,683,000	$ 4,985,000	$ 7,197,000	$ 9,178,000
Employee Share Based Compensation [Member]
Employee Service Share-based Compensation, Allocation of Recognized Period Costs [Line Items]
Weighted average period expense is to be recognized			2 years 0 months 26 days
Expected dividend yield	0.00%	0.00%	0.00%	0.00%
Risk-free interest rate	2.00%	1.00%	2.00%	1.00%
Expected term (in years)	6 years 1 month 2 days	6 years 1 month 6 days	6 years 1 month 6 days	6 years 1 month 6 days
Expected volatility	75.00%	82.00%	75.00%	82.00%
Employee Share Based Compensation [Member] | Common Stock [Member]
Employee Service Share-based Compensation, Allocation of Recognized Period Costs [Line Items]
Unrecognized compensation expense	15,000,000		15,000,000
Weighted average period expense is to be recognized			2 years 11 months 5 days
Employee Share Based Compensation [Member] | Restricted Stock Units (RSUs) [Member]
Employee Service Share-based Compensation, Allocation of Recognized Period Costs [Line Items]
Unrecognized compensation expense	4,900,000		4,900,000
Research and Development [Member]
Employee Service Share-based Compensation, Allocation of Recognized Period Costs [Line Items]
Allocated Share-based Compensation Expense	909,000	1,049,000	1,707,000	2,296,000
Sales General and Administrative [Member]
Employee Service Share-based Compensation, Allocation of Recognized Period Costs [Line Items]
Allocated Share-based Compensation Expense	$ 2,774,000	$ 3,936,000	$ 5,490,000	$ 6,882,000

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Fair Value of Financial Instruments (Tables)

6 Months Ended

Jun. 30, 2014

Fair Value Disclosures [Abstract]

Schedule of Fair Value, Assets and Liabilities Measured on Recurring Basis

The Company’s financial assets and financial liabilities as of December 31, 2013 are presented below at fair value and were classified within the fair value hierarchy as follows (in thousands):

	Level 1		Level 2		Level 3		Balance as of December 31, 2013
Financial Assets
Money market funds	$	398	$	—	$	—	$	398
Certificates of deposit	1,428		—		—		1,428
Total financial assets	$	1,826	$	—	$	—	$	1,826
Financial Liabilities
Loans payable	$	—	$	18,491	$	—	$	18,491
Credit facilities	—		7,571		—		7,571
Convertible notes	—		—		131,952		131,952
Compound embedded derivative liability	—		—		131,117		131,117
Currency interest rate swap derivative liability	—		3,600		—		3,600
Total financial liabilities	$	—	$	29,662	$	263,069	$	292,731

As of June 30, 2014, the Company’s financial assets and financial liabilities are presented below at fair value and were classified within the fair value hierarchy as follows (in thousands):

	Level 1		Level 2		Level 3		Balance as of June 30, 2014
Financial Assets
Money market funds	$	74,765	$	—	$	—	$	74,765
Certificates of deposit	1,453		—		—		1,453
Total financial assets	$	76,218	$	—	$	—	$	76,218
Financial Liabilities
Loans payable (1)	$	—	$	20,360	$	—	$	20,360
Credit facilities  (1)	—		39,864		—		39,864
Convertible notes (1)	—		—		227,638		227,638
Compound embedded derivative liability	—		—		145,032		145,032
Currency interest rate swap derivative liability	—		2,808		—		2,808
Total financial liabilities	$	—	$	63,032	$	372,670	$	435,702

________

⁽¹⁾ These liabilities are carried on the condensed consolidated balance sheet on a historical basis.

Fair Value, Liabilities Measured on Recurring Basis, Unobservable Input Reconciliation

The following table provides a reconciliation of the beginning and ending balances for the convertible notes measured at fair value using significant unobservable inputs (Level 3) (in thousands):

	2014
Balance at January 1	$	131,952
Additions to convertible notes	93,295
Change in fair value of convertible notes	2,391
Balance at June 30	$	227,638

Schedule of Derivative Instruments in Statement of Financial Position, Fair Value

The following table provides a reconciliation of the beginning and ending balances for the compound embedded derivative liability measured at fair value using significant unobservable inputs (Level 3) (in thousands):

	2014
Balance at January 1	$	131,117
Transfers in to Level 3 net of cancellation (1)	86,551
Total (income) loss from change in fair value of derivative liability	(72,636		)
Balance at June 30	$	145,032

________

⁽¹⁾ Includes $1.1 million removal of derivative liability related to debt extinguishment.

Derivative instruments measured at fair value as of June 30, 2014 and December 31, 2013, and their classification on the condensed consolidated balance sheets and condensed consolidated statements of operations, are presented in the following tables (in thousands except contract amounts):

	Liability as of
	June 30, 2014			December 31, 2013
Type of Derivative Contract	Quantity of Short Contracts	Fair Value		Quantity of Short Contracts	Fair Value
Currency interest rate swap, included as net liability in derivative liability	1	$	2,808	1	$	3,600

Schedule of Derivative Instruments, Gain (Loss) in Statement of Financial Performance

	Income Statement Classification	Three Months Ended June 30,					Six Months Ended June 30,
Type of Derivative Contract		2014		2013			2014	2013
		Gain (Loss) Recognized					Gain (Loss) Recognized
Currency interest rate swap (1)	Gain (loss) from change in fair value of derivative instruments	$	722	$	(1,639	)	$1,056	$	(1,651	)

___________ 

⁽¹⁾  Certain classifications of prior period amounts have been made to conform to the current period presentation. Such reclassifications did not materially change previously reported consolidated financial statements.

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Reporting Segments (Details) (USD $) In Thousands, unless otherwise specified	3 Months Ended		6 Months Ended
	Jun. 30, 2014	Jun. 30, 2013	Jun. 30, 2014	Jun. 30, 2013	Mar. 31, 2014 businessactivities segmentmanagers	Dec. 31, 2013
Revenues from External Customers and Long-Lived Assets [Line Items]
Segment Reporting, Number of Business Activities					1
Segment Reporting, Number of Segment Managers Held Accountable					0
Revenues	$ 9,307	$ 10,849	$ 15,348	$ 18,718
Long-Lived Assets	140,656		140,656			140,591
United States [Member]
Revenues from External Customers and Long-Lived Assets [Line Items]
Revenues	2,815	4,458	4,788	10,022
Long-Lived Assets	49,628		49,628			54,015
Brazil [Member]
Revenues from External Customers and Long-Lived Assets [Line Items]
Revenues	1,402	1,259	2,050	2,077
Long-Lived Assets	90,375		90,375			85,891
Europe [Member]
Revenues from External Customers and Long-Lived Assets [Line Items]
Revenues	2,985	4,005	6,338	4,230
Long-Lived Assets	653		653			685
Asia [Member]
Revenues from External Customers and Long-Lived Assets [Line Items]
Revenues	$ 2,105	$ 1,127	$ 2,172	$ 2,389

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Summary of Significant Accounting Policies - Principles of Consolidations (Details)	6 Months Ended
	Jun. 30, 2014 consolidated_VIE
Accounting Policies [Abstract]
Variable Interest Entity Number of Entities (in VIEs)	2

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Related Party Transactions

6 Months Ended

Jun. 30, 2014

Related Party Transactions [Abstract]

Related Party Transactions

Related Party Transactions

Letter Agreements with Total

In March 2013 and March 2014, respectively, the Company entered into letter agreements with Total that reduced the respective conversion prices of certain convertible promissory notes issuable under the Total Purchase Agreement, as described under “Related Party Convertible Notes” in Note 5, "Debt."

Related Party Financings

In March 2013, the Company completed a private placement of 1,533,742 shares of its common stock to an existing stockholder, Biolding Investment SA ("Biolding"), at a price of $3.26 per share for aggregate proceeds of $5.0 million. This private placement represented the final tranche of Biolding's preexisting contractual obligation to fund $15.0 million upon satisfaction by the Company of certain criteria associated with the commissioning of the Company's production plant in Brotas, Brazil.

In June 2013, the Company sold and issued a 1.5% Senior Unsecured Convertible Note to Total in the face amount of $10.0 million with a March 1, 2017 maturity date pursuant to the Total Purchase Agreement as discussed above under “Related Party Convertible Notes” in Note 5, “Debt."

In July 2013, the Company sold and issued a 1.5% Senior Unsecured Convertible Note to Total in the face amount of $20.0 million with a March 1, 2017 maturity date pursuant to the Total Purchase Agreement as discussed above under “Related Party Convertible Notes” in Note 5, “Debt."

In August 2013, the Company entered into a securities purchase agreement by and among the Company, Total and Temasek, each a beneficial owner of more than 5% of the Company's existing common stock at the time of the transaction, for a private placement of convertible promissory notes in an aggregate principal amount of $73.0 million. The initial closing of the August 2013 Financing was completed in October 2013 for the sale of approximately$42.6 million of these Tranche I Notes and the second closing of the August 2013 Financing for the sale of approximately $30.4 million of these Tranche II Notes was completed in January 2014.

In September 2013, the Company entered into a bridge loan agreement with an existing investor to provide additional cash availability of up to $5.0 million as needed before the initial closing of the August 2013 Financing. The Company did not use this facility and it expired in October 2013 in accordance with its terms.

In October 2013, the Company sold and issued a senior secured promissory note to Temasek for a bridge loan of $35.0 million. The note was due on February 2, 2014 and accrued interest at a rate of 5.5% each four months from October 4, 2013 (with a rate of 2% per month if a default occurred). The note was cancelled as payment for the investor’s purchase of Tranche I Notes in the August 2013 Financing.

In December 2013, the Company agreed to issue to Temasek $25.0 million of Tranche II Notes for cash. Total purchased approximately $6.0 million of Tranche II Notes through cancellation of the same amount of principal of previously outstanding convertible promissory notes held by Total (in respect of Total’s preexisting contractual right to maintain its pro rata ownership position through such cancellation). Such financing transactions closed in January 2014 (see Note 5, "Debt").

In December 2013, the Company agreed (i) to exchange the $69.0 million outstanding Total unsecured convertible notes and issue a replacement 1.5% senior secured convertible notes, in principal amounts equal to the principal amount of each cancelled note (see Note 5, "Debt") and (ii) that all notes issued in connection with a third closing under the Total Purchase Agreement will be senior secured convertible notes instead of senior unsecured convertible notes (see Note 5, "Debt").

In May 2014, the Company sold and issued 144A Notes pursuant to the Rule 144A Convertible Note Offering. In connection with obtaining a waiver from one of its existing investors, Total, of its preexisting contractual right to exchange certain senior secured convertible notes previously issued by Amyris for new notes issued in the Rule 144A Convertible Note Offering, Amyris used approximately $9.7 million of the net proceeds of the Rule 144A Convertible Note Offering to repay such amount of previously issued notes (representing the amount of notes purchased by Total from the Initial Purchaser under the Rule 144A Convertible Note Offering). Additionally, Foris Ventures, LLC (a fund affiliated with John Doerr) and Temasek each participated in the Rule 144A Convertible Note Offering and purchased $5.0 million and $10.0 million, respectively, of the convertible promissory notes sold thereunder (see Note 5, “Debt").

As of June 30, 2014 and December 31, 2013, convertible notes with related parties were outstanding in aggregate principal of $100.5 million and $89.5 million, respectively, net of debt discount of $55.3 million and $23.9 million, respectively. The Company recorded a loss from extinguishment of debt from the settlement, exchange and cancellation of related party convertible notes for the three months ended June 30, 2014 and 2013, of $1.1 million and zero, respectively, and $10.5 million and zero for the six months ended June 30, 2014 and 2013, respectively (see Note 5, "Debt").

The fair value of the derivative liability related to the related party convertible notes as of June 30, 2014 and December 31, 2013 is $107.2 million and $116.8 million, respectively. The Company recognized for the three months ended June 30, 2014 and 2013, a $4.0 million loss from change in fair value of the derivative instruments and $1.4 million gain from change in fair value of the derivative instruments, respectively, and $53.1 million and $2.5 million gain from change in fair value of the derivative instruments for the six months ended June 30, 2014 and 2013, respectively, related to these derivative liabilities (see Note 3, "Fair Value of Financial Instruments").

Related Party Revenue

The Company recognized related party revenue from Novvi of zero and $0.3 million for the three months ended June 30, 2014 and 2013, respectively, and zero and $2.8 million for the six months ended June 30, 2014 and 2013, respectively, from the research and development activities that it has performed on behalf of Novvi. The related party accounts receivables from Novvi as of June 30, 2014 and December 31, 2013, was $20,604 and $0.3 million, respectively.

The Company recognized related party revenue from Total of $30,625 and $32,441 for the three months ended June 30, 2014 and 2013, respectively, and $33,250 and $35,294 for the six months ended June 30, 2014 and 2013, respectively, from product sales. The related party accounts receivables from Total as of June 30, 2014 and December 31, 2013, was $30,625 and $0.2 million, respectively.

Joint Venture

In November 2013, the Company and Total formed JVCO as discussed above under “Joint Venture and Noncontrolling Interest” in Note 7.

Pilot Plant Agreements

In May 2014, the Company received the final consents necessary for the Pilot Plant Services Agreement ("Pilot Plant Services Agreement") and a Sublease Agreement (the "Sublease Agreement"), each dated as of April 4, 2014 (collectively the “Pilot Plant Agreements”), between the Company and Total for a term of 5 years. Under the terms of the Pilot Plant Services Agreement, the Company will provide certain fermentation and downstream separations scale-up services and training to Total and will receive an aggregate annual fee payable by Total for all services in the amount of up to approximately $0.9 million. Under the Sublease Agreement, the Company will receive an annual base rent payable by Total of approximately $0.1 million. As of June 30, 2014, the Company received $0.3 million in cash under the Pilot Plant Agreements from Total which was recorded as "Other Current Liability" on the condensed consolidated balance sheet.