Commitments and Contingencies
12 Months Ended
Dec. 31, 2013
Commitments and Contingencies Disclosure [Abstract]  
Commitments and Contingencies
Commitments and Contingencies
Leases
The Company entered into an operating lease agreement in May 2010 that was set to expire in May 2015. Rent expense was being recognized on a straight-line basis over the lease term. In October 2013, the Company and SBC&D Co. (the “Lessor”) entered into a first amendment (the "First Amendment") to the Original Lease Agreement (as defined below) for the Company's facility at 3011 N. First Street, San Jose, California.
The First Amendment amended the original lease agreement dated May 2010 (“Original Lease Agreement”) between the Company and Novellus Systems, Inc. (the "Landlord"), contingent upon the Lessor acquiring title to the facility from Landlord (such date, the “Effective Date”), which occurred in November 2013 pursuant to a purchase agreement dated October 2013 between Lessor and Landlord.
The amendment provides for (i) extension of the term of the lease for a period of approximately one hundred thirty-nine (139) months from the Effective Date, (ii) elimination of the early termination option contained within the Original Lease Agreement and (iii) elimination of the cap with respect to the payments the Company makes for the operating costs of the facility or Lessor’s obligation to provide certain other utilities to the facility. The First Amendment will maintain the rental rate of the Original Lease Agreement through February 2016 and will increase the monthly basic rent to $196,000 effective March 2016 and automatically increase 2.5% each year thereafter through the end of the extended term of the lease. In addition, the First Amendment provides the Company with four months of free rent and a tenant improvement allowance of $1.0 million in the aggregate to be paid to the Company in equal installments over the course of the ten months after the Effective Date to be used for the modification, refurbishment, construction or installation of improvements to the facility.
The following table presents rent expense included in the Consolidated Statement of Operations (in thousands):
 
Years Ended December 31,
 
2013
 
2012
 
2011
Rent expense
$
1,377

 
$
1,297

 
$
1,961



Future commitments and obligations under this operating lease to be satisfied as they become due over the term are as follows (in thousands):
As of December 31:
 
The years ending December 31,
 
2014
$
1,286

2015
1,758

2016
2,253

2017
2,399

2018
2,459

Thereafter
17,557

Total
$
27,712



During 2013, the Company made payments in the amount of $1.5 million related to this operating lease. The first month of free rent was December 2013.
Symyx Asset Purchase and Note Payable
On July 28, 2011, the Company entered into an agreement with Symyx Technologies, Inc., a related party at the time of the agreement ("Symyx"), pursuant to which the Company agreed to use commercially reasonable efforts to allow Symyx to sell in the Company's initial public offering a total of 3,968,204 shares of common stock held by them, and Symyx agreed to sell such shares in the offering, transfer to the Company all patents held by them that relate to combinatorial processing and terminate future royalty obligations under the Symyx agreements to the extent they would have accrued after December 31, 2011. The Company completed this asset purchase in connection with the closing of its initial public offering in November 2011. In addition, the Company reimbursed Symyx for 50% of the underwriting discounts and commissions payable by them in connection with the sale of their common stock in the offering, which amount was equal to approximately $1.4 million.
In connection with entering into the agreement the Company recorded a derivative liability representing the value of the guaranteed return to Symyx and reimbursement of 50% of the underwriting discounts and commissions payable in connection with the offering. The Company recorded the liability at inception because it had effectively issued a written option that requires the Company to settle with a cash payment to Symyx. The initial fair value of the contract as of the date of the agreement was determined using a hybrid model utilizing a probability-weighted expected return model and a Monte Carlo Simulation model to be $2.8 million, which incorporates parameters such as the volatility of the Company's stock price, the time value of the feature, the strike price on the guarantee, the likelihood of an initial public offering, and the obligation to pay a portion of Symyx's selling costs. Between July 28, 2011 and the date of the offering, the Company adjusted the fair value of the derivative liability to market value, with changes in the market value recorded in other income (expense), net, in the Company's Consolidated Statement of Operations. On July 28, 2011, the Company recorded an intangible asset in the amount of $2.8 million that represents the value of the intangible assets that was transferred by Symyx to the Company upon the completion of the offering.
During 2011 and until the completion of the Company's initial public offering on November 23, 2011, the Company recorded charges to other income (expense), net in the amount of $25.9 million that represents the change in value of the derivative liability. The following table sets forth a summary of the changes in the fair value of the Company's derivative liability related to the Symyx asset purchase transaction (in thousands):
Minimum return to Symyx
$
67,000

Proceeds to Symyx from offering
(39,682
)
Initial fair value of derivative liability
(2,842
)
Reimbursement of offering related expenses
1,389

Mark-to-market adjustment
$
25,865



In connection with the consummation of the Symyx asset purchase transaction in November 2011, the Company issued Symyx a secured promissory note in a principal amount equal to $27.3 million with a term of 24 months and an interest rate equal to 4%. The note was payable in quarterly installments, each in an amount equal to the greater of $0.5 million that quarter or the amount of accrued interest, with a balloon payment at maturity, if applicable. The note was also pre-payable by the Company at any time without penalty or premium, and was secured by tangible personal property, excluding intellectual property. On May 31, 2013, the Company used $25.0 million of the net proceeds from a revolving line with SVB and $1.5 million of cash to retire and repay all remaining principal and accrued interest due on the note. Over the life of the Symyx note the Company paid a total of $29.0 million, of which approximately $1.6 million related to interest.
The following table presents payments made during the years ended December 31, 2013 and 2012 in connection with the note payable to Symyx (in thousands):
 
Years Ended December 31, 2013
 
Principal
 
Interest
 
Total
Symyx payments
$
26,516

 
$
437

 
$
26,953

 
Year Ended December 31, 2012
 
Principal
 
Interest
 
Total
Symyx payments
$
804

 
$
1,196

 
$
2,000



Silicon Valley Bank Loan Agreement
On May 31, 2013, the Company entered into a loan and security agreement (“Loan Agreement”) with SVB pursuant to which SVB made available to the Company loans under a revolving line to refinance existing indebtedness (including the repayment of the Symyx note) and for working capital and general business purposes, in a principal amount of up to $26.5 million. Under the Loan Agreement, SVB funded an initial credit extension in the principal amount of $25 million on May 31, 2013 and agreed to fund, subject to customary conditions, additional credit extensions under the revolving line on or prior to November 30, 2013. The Loan Agreement has a financial covenant that requires the Company to maintain a certain level of liquidity, and as of December 31, 2013, the Company was compliant with the terms of that loan covenant. Prior to November 30, 2013, the Company had the option to convert all or any part of the outstanding advances under the revolving line into a term loan, which could only be used once. The revolving line advances bear interest at a floating rate equal to the greater of 2.75% or the prime rate (customarily defined) minus 0.50%. On November 29, 2013 the Company converted the revolving line into a term loan for $25 million with SVB that bears interest at a fixed rate equal to 3.25%. The Company is obligated to pay interest at the applicable rate and $0.5 million of principal on a quarterly basis. The term loan matures on November 30, 2016 and the Company is obligated to pay all outstanding principal and accrued and unpaid interest on that date. At the Company's option, the Company may prepay the outstanding principal balance of the term loan in full or in part, subject to a pre-payment fee of 0.25% of the outstanding principal balance of the term loan if the term loan is outstanding for less than one year.

The following table presents payments made during the year ended December 31, 2013 for interest owed under the terms of the Loan Agreement (in thousands):
 
Years Ended December 31, 2013
 
Principal
 
Interest
 
Total
SVB payments
$

 
$
350

 
$
350



Estimated principal payments related to the SVB term loan are as follows (in thousands):
As of December 31:
 
2014
$
2,000

2015
2,000

2016
21,000

Total
$
25,000


Litigation
On August 23, 2013, the Company received a copy of a complaint from the California Division of Labor Standards and Enforcement ("DLSE") filed by an employee in the Company’s research and development group claiming that the employee is owed back pay due to an incorrect classification as an exempt employee for overtime purposes. The Company commenced a review of the employee's claim as well as a review of the Company’s policies regarding classification of employees for overtime purposes. The Company also agreed to enter mediation with the attorney who represents the employee that filed the claim with the DLSE as well as fourteen other current and former employees who are similarly situated. This mediation did not result in a settlement of the subject claims, and on February 18, 2014, the claimants filed a lawsuit against the Company in the United States District Court for the Northern District of California. The Company believes it has meritorious defenses to the claims and intends to vigorously defend against any of them in this regard. Nevertheless, as of December 31, 2013, the Company accrued its best estimate of the amount of probable loss associated with the matter and classified the resulting expense as research and development in its Consolidated Statements of Operations. While the Company cannot predict the outcome of this matter, or of any legal or administrative proceedings related to this matter that have commenced or may be commenced in the future, the Company believes the matter will not have a material adverse effect on its business, operating results, financial condition or cash flows.