Document:

exv10w1

 

Exhibit 10.1

Master Security Agreement No. 6081110

MASTER SECURITY AGREEMENT

No. 6081110

Dated as of March 31, 2006 (“Agreement”)

     THIS AGREEMENT 
is between Oxford Finance Corporation (together
with its successors and assigns,
if any, “Secured Party”)
and Alnylam Pharmaceuticals, Inc.
(“Debtor”). Secured Party has an office at 133 N. Fairfax Street,
Alexandria, VA 22314. Debtor is a corporation
organized and existing under the laws of the state of Delaware. Debtor’s mailing address and chief
place of business is 300 Third Street, 3rd and 4th Floor,
Cambridge, MA 02142.

1. CREATION OF SECURITY INTEREST.

     Debtor grants to Secured Party, its successors and assigns, a security interest in and against
all property financed by the Secured Party and listed on
any collateral schedule now or in the future annexed to or made a part of this Agreement
(“Collateral Schedule”), and in and against all additions,
attachments, accessories and accessions to such property, all substitutions, replacements or
exchanges therefore, and all insurance and/or other proceeds
thereof (all such property is individually and collectively called
the “Collateral”). This security
interest is given to secure the payment and performance of
all debts, obligations and liabilities of any kind whatsoever of Debtor to Secured Party, now
existing or arising in the future, including but not limited to the
payment and performance of certain Promissory Notes from time to time identified on any Collateral
Schedule (collectively “Notes”
and each a “Note”),
and any renewals, extensions and modifications of such debts, obligations and liabilities (such
Notes, debts, obligations and liabilities are called the
“Indebtedness”). Debtor acknowledges that, notwithstanding that the Note(s) may be paid in full,
this Security Agreement shall continue to secure the
payment and performance of all such Indebtedness, now existing or arising in the future, and that
Secured Party shall be under no obligation to release the
Collateral unless and until all Indebtedness of Debtor to Secured Party has been paid and
satisfied; provided, however, Secured Party, in its sole and
exclusive discretion, may elect to release some of the Collateral without prejudice to Secured
Party’s security interest in the remaining Collateral.

2. REPRESENTATIONS, WARRANTIES AND COVENANTS OF DEBTOR.

     Debtor represents, warrants and covenants as of the date of this Agreement and as of the date
of each Collateral Schedule that:

	 	(a)	 	Due Organization. Debtor’s exact legal name is as set forth in the preamble of this Agreement
and Debtor is, and will remain, duly organized,
existing and in good standing under the laws of the State of Delaware set forth in the preamble of
this Agreement, has its chief executive
offices at the location specified in the preamble, and is, and will remain duly qualified and
licensed in every jurisdiction wherever necessary to
carry on its business and operations;
	 
	 	(b)	 	Power and Capacity to Enter Into and Perform Obligations. Debtor has adequate power and
capacity to enter into, and to perform its
obligations under this Agreement, each Collateral Schedule, each Note and any other documents
executed in connection with each Collateral
Schedule and the Indebtedness (all of the foregoing are called the
”Debt Documents”);
	 
	 	(c)	 	Due Authorization. This Agreement and the other Debt Documents have been duly authorized,
executed and delivered by Debtor and
constitute legal, valid and binding agreements enforceable in accordance with their terms, except
to the extent that the enforcement of
remedies may be limited under applicable bankruptcy and insolvency laws;
	 
	 	(d)	 	 Approvals and Consents. No approval, consent or withholding of objections is required from any
governmental authority or instrumentality
with respect to the entry into, or performance by Debtor of any of the Debt Documents, except any
already obtained;
	 
	 	(e)	 	No Violations or Defaults. The entry into, and performance by, Debtor of the Debt Documents
will not (i) violate any of the organizational
documents of Debtor or any material judgment, order, law or regulation applicable to Debtor, or
(ii) result in any breach of or constitute a
default under any material contract to which Debtor is a party, or result in the creation of any
lien, claim or encumbrance on any of Debtor’s
property (except for liens in favor of Secured Party) pursuant to any indenture, mortgage, deed of
trust, bank loan, credit agreement, or other
agreement or instrument to which Debtor is a party;
	 
	 	(f)	 	Litigation. There are no suits or proceedings pending in court or before any commission, board
or other administrative agency against or
affecting Debtor which could reasonably be expected to, in the aggregate, have a material adverse
effect on Debtor, its business or operations,
or its ability to perform its obligations under the Debt Documents, nor does Debtor have reason to
believe that any such suits or proceedings
are threatened;

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	 	(g)	 	Solvency. The fair salable value of Debtor’s assets (including goodwill minus disposition
costs) exceeds the fair value of its liabilities; the
Debtor is not left with unreasonably small capital after the transactions in this Agreement or any
Collateral Schedule and Debtor is able to pay
its debts (including trade debts) as they mature.
	 
	 	(h)	 	Financial Statements Prepared In Accordance with GAAP. All financial statements delivered to
Secured Party in connection with the
Indebtedness have been prepared in accordance with generally accepted accounting principles, and
since the date of the most recent financial
statement, there has been no material adverse change in Debtor’s financial condition;
	 
	 	(i)	 	Use of Collateral. The Collateral is not, and will not be, used by Debtor for personal, family
or household purposes;
	 
	 	(j)	 	Collateral in Good Condition and Repair. The Collateral is, and will remain, in good condition
and repair (ordinary wear and tear excepted);
	 
	 	(k)	 	Location of Collateral. All of the tangible Collateral is located at the locations set forth on
each Collateral Schedule, or such other location as
the Debtor shall have given notice to the Secured Party as provided in the next sentence. Debtor
shall give the Secured Party twenty (20) days
prior written notice of any relocation of any Collateral;
	 
	 	(l)	 	 Ownership of Collateral. Debtor is, and will remain, the sole and lawful owner, and in
possession of, the Collateral, and has the sole right and
lawful authority to grant the security interest described in this Agreement;
	 
	 	(m)	 	 Encumbrances. Except to the extent the Collateral is comprised of or constitutes leasehold
improvements, the Collateral is, and will remain,
free and clear of all liens, claims and encumbrances of any kind whatsoever, except for Permitted
Liens;
	 
	 	(n)	 	[Omitted]
	 
	 	(o)	 	Taxes. All federal, state and local tax returns required to be filed by Debtor have been filed
with the appropriate governmental agencies and
all taxes due and payable by Debtor have been timely paid except as contested in good faith and by
appropriate proceedings and for which
adequate reserves have been established. Debtor will pay when due all taxes, assessments and other
liabilities except as contested in good faith
and by appropriate proceedings and for which adequate reserves have been established;
	 
	 	(p)	 	No Defaults. No event or condition exists under any material agreement, instrument or document
to which Debtor is a party or may be
subject, or by which Debtor or any of its properties are bound, which constitutes a default or an
event of default thereunder, or will, with the
giving of notice, passage of time, or both, would constitute a default or event of default
thereunder;
	 
	 	(q)	 	Certification of Financial Information. All reports, certificates, schedules, notices and
financial information submitted by Debtor to the
Secured Party pursuant to this Agreement shall be certified as true and correct in all material
respects as of the date thereof by the president,
chief financial officer, or vice president of finance of Debtor or other person designated by any
of the foregoing; and
	 
	 	(r)	 	Notice of Material Adverse Change. Debtor shall give the Secured Party prompt written notice of
any event, occurrence or other matter which
(a) has resulted or may reasonably be expected to result in a material adverse change in its
financial condition or business operations, or (b)
which would impair in a material manner the ability of Debtor to perform its obligations hereunder
or under any of the Debt Documents, or (c)
which would impair in a material manner the ability of Secured Party to enforce the Indebtedness or
realize upon the Collateral.
	 
	 	(s)	 	Change in Management. Debtor shall provide Secured Party with written notice within thirty (30)
days (unless notice has been filed with the
Securities and Exchange Commission and is publicly available, in which case no written notice need
be given) after any change in the persons
holding the offices of Chief Executive Officer or Chief Financial Officer.
	 
	 	(t)	 	Transactions with Affiliates. Debtor shall not, without the prior written consent of Secured
Party, directly or indirectly enter into or permit to
exist any material transaction with any Affiliate of Debtor except for transactions that are upon
fair and reasonable terms that are no less
favorable to Debtor than would be obtained in an arm’s length transaction with a nonaffiliated
Person.
	 
	 	(u)	 	Audits. Debtor shall allow Secured Party during normal business hours and upon reasonable prior
written notice to audit Debtor’s Collateral
at Debtor’s expense; provided that such audits will be conducted no more often than every twelve
(12) months unless an Event of Default has
occurred and is continuing.
	 
	 	(v)	 	 Perfection Certificate. Debtor has previously delivered to the Secured Party a certificate
signed by the Debtor and entitled “Perfection

Certificate” (the “Perfection Certificate”). The Debtor represents and warrants to the Secured
Party that as of the date thereof , there has been

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	 	 	 	no change in any information provided in the Perfection Certificate since the date on which it was
executed by the Debtor which would make such information misleading in any material respect.
	 
	 	(w)	 	 Primary Account and Wire Transfer Instructions. Debtor maintains its Primary Account (the
“Primary Operating Account”) and the Wire
Transfer Instructions for the Primary Operating Account are as follows:

Silicon Valley Bank

3003 Tassman Drive

Santa Clara, CA 95054

ABA No.: 121140399

Account No.: 3300339977

Account Name: Alnylam US Inc.

Swift Code: SVBKUS6S

	 	 	 	Debtor hereby agrees that Loans will be advanced to the account specified above (unless Secured
Party is otherwise notified in writing fifteen (15) days prior to any due date) and regularly scheduled payments will be automatically debited
from the same account.

3. COLLATERAL.

	 	 	The Debtor covenants and agrees that, so long as any of the Debt Documents shall remain in
effect, or unless the Secured Party shall otherwise consent in writing:

	 	(a)	 	 Possession of Collateral; Inspection of Collateral. Until the declaration of any Event of
Default, Debtor shall remain in possession of the Collateral. Secured Party may inspect any of the Collateral during normal business hours after
giving Debtor reasonable prior notice.
	 
	 	(b)	 	 Maintenance of Collateral. Debtor shall (i) use the Collateral only in its trade or business,
(ii) maintain all of the Collateral in good operating
order and repair, normal wear and tear excepted, and (iii) except to the extent the Collateral is
comprised of or constitutes leasehold
improvements, keep all of the Collateral free and clear of all liens, claims and encumbrances
(except for Permitted Liens).
	 
	 	(c)	 	 Disposition of Collateral. Secured Party does not authorize and Debtor agrees it shall not (i)
part with possession of any of the Collateral
(except to Secured Party or for maintenance and repair), (ii) remove any of the Collateral from the
continental United States, or (iii) sell, rent,
lease, mortgage, license, grant a security interest in or otherwise transfer or encumber (except
for Permitted Liens) any of the Collateral, except
to the extent that (i) all obligations of Debtor to Secured Party have been satisfied or (ii) with
the prior written agreement of Secured Party,
such Collateral is promptly replaced with assets of equal or greater value.
	 
	 	(d)	 	 Taxes. Debtor shall pay promptly when due all taxes, license fees, assessments and public and
private charges owing by the Debtor levied or
assessed on any of the Collateral, on its use, or on this Agreement or any of the other Debt
Documents, except to the extent such taxes, license
fees, assessments or public and private charges are being contested in good faith and by
appropriate proceedings and for which adequate
reserves have been established. At its option, and after reasonable prior written notice to the
Debtor, Secured Party may discharge taxes, liens,
security interests or other encumbrances at any time levied or placed on the Collateral (except to
the extent being contested in good faith) and
may pay for the reasonable maintenance, insurance and preservation of the Collateral and effect
compliance with the terms of this Agreement
or any of the other Debt Documents. Debtor agrees to reimburse Secured Party, on demand, all
reasonable costs and expenses incurred by
Secured Party in connection with such payment or performance and agrees that such reimbursement
obligation shall constitute Indebtedness.
	 
	 	(e)	 	Books and Records. Debtor shall, at all times, keep accurate and complete records of the
Collateral, and Secured Party shall have the right,
subject to the restrictions in Section 3(a) hereof, to inspect and make copies of all of Debtor’s
books and records relating to the Collateral
during normal business hours, after giving Debtor reasonable prior notice.
	 
	 	(f)	 	Third Party Possession of Collateral. Debtor agrees and acknowledges that any third person who
may at any time possess all or any portion of
the Collateral shall be deemed to hold, and shall hold, the Collateral as the agent of, and as
pledge holder for, Secured Party. Secured Party
may at any time give notice to any third person described in the preceding sentence that such third
person is holding the Collateral as the agent
of, and as pledge holder for, the Secured Party.
	 
	 	(g)	 	Change of Address, Name or Jurisdiction. The Debtor has not at any time within the past four
(4) months either changed its name or changed
the state of jurisdiction in which it is organized and existing, nor has it maintained its chief
executive office or any of the Collateral at any
other location, except as set forth above, and shall not do so hereafter except upon prior written
notice to the Secured Party. The Secured Party
shall be entitled to rely upon the foregoing unless it receives twelve (12) days’ advance written
notice of a change in the Debtor’s name, state
of jurisdiction, address of the Debtor’s chief executive offices or location of the Collateral.

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	 	(h)	 	Fixtures. Except to the extent the Collateral is comprised of or constitutes leasehold
improvements, (i) not permit any item of the Collateral to
become a fixture to real estate or an accession to other property without the prior written consent
of the Secured Party, (ii) the Collateral is
now and shall at all times remain personal property except with the Secured Party’s prior written
consent and (iii)if any of the Collateral is or
will be attached to real estate in such a manner as to become a fixture under applicable state law
and if such real estate is encumbered, the
Debtor will use reasonable efforts to seek from the holder of each Lien or encumbrance a written
consent and subordination to the security
interest hereby granted, or a written disclaimer of any interest in the Collateral, in a form
reasonably acceptable to the Secured Party.
	 
	 	(i)	 	Distributions. Debtor shall not pay any dividends or make any distributions on its equity
securities (except in equity securities of the Debtor).
	 
	 	(j)	 	Indebtedness Payments. Debtor shall not:

(i) prepay, redeem, purchase, defease or otherwise satisfy in any manner prior to the scheduled
repayment thereof any Subordinated Indebtedness
for borrowed money or lease obligations without the consent of the Secured Party, such consent not
to be unreasonably withheld;

(ii) prepay, redeem, purchase, defease or otherwise satisfy in any manner prior to the scheduled
repayment thereof any Additional Indebtedness
(exclusive of Subordinated Indebtedness which is governed by clause (i) above) for borrowed money
or lease obligations in an amount in excess
of One Million Dollars ($1,000,000) within any six (6) month period without also prepaying a
Ratable Portion (as defined below) to the Secured
Party;

(iii) amend, modify or otherwise change the terms of any Additional Indebtedness for borrowed money
or lease obligations so as to accelerate
the scheduled repayment thereof in violation of clauses (i) and
(ii) above.

For the avoidance of doubt, Debtor shall be permitted to make regularly scheduled or regularly
required payment, repayment or redemptions of
Permitted Indebtedness.

For purposes of this Section 3(j), “Ratable Portion” means an amount equal to the product of (A)
the amount of Indebtedness owed to the
Secured Party at the time multiplied by (B) a fraction, the numerator of which is the dollar amount
of all prepayments within that six (6) month
period in excess of $1,000,000 and the denominator of which is the sum of (i) all outstanding
Additional Indebtedness (other than Subordinated
Indebtedness) and (ii) the Indebtedness owed to the Secured Party.

	 	(k)	 	[Omitted]

4. INSURANCE.

	 	(a)	 	Risk of Loss. Debtor shall at all times bear the entire risk of any loss, theft, damage to,
or destruction of, any of the Collateral from any cause
whatsoever.
	 
	 	(b)	 	Insurance Requirements. Debtor agrees to keep the Collateral insured against loss or damage by
fire and extended coverage perils, theft,
burglary, and for any or all Collateral, which are vehicles, for risk of loss by collision, and if
requested by Secured Party, against such other
risks as Secured Party may reasonably require but in any event in no greater amount or coverage
than maintained by similar businesses in a
similar geographic area. The insurance coverage shall be in an amount no less than the [full
replacement value] of the Collateral, and
deductible amounts, insurers and policies shall be reasonably acceptable to Secured Party (provided
that the deductible amounts, insurers and
policies in effect as of the date hereof shall be deemed to satisfy this requirement). Debtor shall
deliver to Secured Party policies or certificates
of insurance evidencing such coverage. Each policy shall name Secured Party as a loss payee, shall
provide for coverage to Secured Party
regardless of the breach by Debtor of any warranty or representation made therein, shall not be
subject to co-insurance, and shall provide that
coverage may not be canceled or altered by the insurer except upon thirty (30) days prior written
notice to Secured Party, except for failure to
pay which shall require no more that ten (10) days prior notice to Secured Party. Debtor appoints
Secured Party as its attorney-in-fact to make
proof of loss, claim for insurance and adjustments with insurers in each case with respect to the
Collateral, and to receive payment of and
execute or endorse all documents, checks or drafts in connection with insurance payments made with
respect to Collateral. Secured Party shall
not act as Debtor’s attorney-in-fact unless an event of default shall have occurred and be
continuing. Proceeds of insurance shall be applied, at
the option of Secured Party, to repair or replace the Collateral or to reduce any of the
Indebtedness.

5. REPORTS.

	 	(a)	 	Notice of Events. Debtor shall promptly notify Secured Party of (i) any change in the name
of Debtor, (ii) any change in the state of its
incorporation or registration, (iii) any relocation of its chief executive offices, (iv) any of the
Collateral being lost, stolen, missing, destroyed,

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	 	 	 	materially damaged or worn out, (v) any lien, claim or encumbrance other than Permitted Liens
attaching to or being made against any of the
Collateral, or (vi) any occurrence of any Event of Default
pursuant to Section 7 herein.
	 
	 	(b)	 	Financial Statements, Reports and Certificates. Debtor will deliver to Secured Party within
ninety (90) days of the close of each fiscal year of
Debtor, Debtor’s complete financial statements including a balance sheet, income statement,
statement of shareholders’ equity and statement of
cash flows, each prepared in accordance with generally accepted accounting principles consistently
applied, certified by a recognized firm of
certified public accountants reasonably satisfactory to Secured Party. Debtor will deliver to
Secured Party copies of Debtor’s quarterly
financial statements including a balance sheet, income statement and statement of cash flows, each
prepared by Debtor in accordance with
generally accepted accounting principles consistently applied by Debtor and certified by Debtor’s
chief financial officer, vice president of
finance or other person designated by either of them, within forty-five (45) days after the close
of each of Debtor’s fiscal quarter. So long as
the Debtor is required to make filings of its annual and quarterly financial information with the
Securities Exchange Commission, the Debtor
shall not be required to actually deliver copies of the foregoing reports to the Secured Party who
may access them via a publicly available
website. Debtor will deliver to Secured Party promptly upon request of Secured Party, in form
reasonably satisfactory to Secured Party, such
other and additional information as Secured Party may reasonably request from time to time.

6. FURTHER ASSURANCES.

	 	(a)	 	Further Assurances Regarding Security Interests. Debtor shall, upon request of Secured
Party, furnish to Secured Party such further
information, execute and deliver to Secured Party such documents and instruments (including,
without limitation, Uniform Commercial Code
financing statements) and shall do such other acts and things as Secured Party may at any time
reasonably request relating to the perfection or
protection of the security interest created by this Agreement or for the purpose of carrying out
the intent of this Agreement. Without limiting
the foregoing, Debtor shall cooperate and do all acts necessary to continue in Secured Party a
perfected first security interest in the Collateral
(subject to Permitted Liens and the fact that certain Collateral may be comprised of or constitute
leasehold improvements), and shall use
reasonable efforts to obtain and furnish to Secured Party any subordinations, releases, landlord
waivers, lessor waivers, mortgagee waivers, or
control agreements, and similar documents as may be from time to time reasonably requested by, and
in form and substance satisfactory to,
Secured Party in each case with respect to the Collateral only.
	 
	 	(b)	 	Authorization To File Financing Statements. Debtor shall perform any and all acts requested by
the Secured Party to establish, maintain and
continue the Secured Party’s security interest and liens in the Collateral, including but not
limited to, executing or authenticating financing
statements and such other instruments and documents when and as reasonably requested by the Secured
Party. Debtor hereby authorizes
Secured Party through any of Secured Party’s employees, agents or attorneys to file any and all
financing statements, including, without
limitation, any original filings, continuations, transfers or amendments thereof required to
perfect Secured Party’s security interest and liens in
the Collateral under the UCC without authentication or execution by Debtor, but which items shall
be consistent with the terms and limitations
set forth herein. Debtor hereby irrevocably authorizes the Secured Party at any time and from time
to time to file in any filing office in any
Uniform Commercial Code jurisdiction any initial financing statement(s) and amendments thereto that
(a) indicate the Collateral (i) is subject
to Secured Party’s security interest, regardless of whether any particular asset comprised in the
Collateral falls within the scope of Article 9 of
the Uniform Commercial Code of the State or such jurisdiction, or (ii) as being of an equal or
lesser scope or with greater detail, and (b)
provide any other information required by part 5 of Article 9 of the Uniform Commercial Code of the
State or such other jurisdiction for the
sufficiency or filing office acceptance of any financing statement or amendment, including (i)
whether the Debtor is an organization, the type
of organization and any organization identification number issued to the Debtor, and (ii) in the
case of a financing statement filed as a fixture
filing, a sufficient description of real property to which the Collateral relates. The Debtor
agrees to furnish any such information to the
Secured Party promptly upon the Secured Party’s request.
	 
	 	(c)	 	Indemnification. Debtor shall indemnify and defend the Secured Party, its successors and
assigns, and their respective directors, officers and
employees, from and against all claims, actions and suits (including, without limitation, related
attorneys’ fees) of any kind whatsoever arising,
directly or indirectly, in connection with any of the Collateral or the Debt Documents, except any
of the foregoing arising out of or caused by
the gross negligence, willful misconduct or bad faith of any indemnified party, or from the Secured
Party’s breach of any Debt Document.

7. DEFAULT AND REMEDIES.

	 	(a)	 	Defaults. Debtor shall be in default under this Agreement and each of the other Debt
Documents if any one of the following should occur
(each an “Event of Default”):

	 	(i)	 	Debtor breaches its obligation to pay when due any installment or other amount due or coming
due under any of the Debt Documents,
and such breach continues for a period of 5 days after written notice from Secured Party;

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	 	(ii)	 	Debtor, without the prior written consent of Secured Party, does sell, rent, lease, license,
mortgage, grant a security interest in, or
otherwise transfer or encumber, or allow Liens (except for Permitted Liens or leasehold
improvements) upon, any of the Collateral,
except as otherwise permitted herein;
	 
	 	(iii)	 	Debtor breaches any of its insurance obligations under
Section 4;
	 
	 	(iv)	 	Debtor breaches any of its obligations under Sections 2(m)
or 3(j);
	 
	 	(v)	 	Debtor breaches any of its other non-payment obligations under any of the Debt Documents and
fails to cure that breach within thirty
(30) days after notice from Secured Party;
	 
	 	(vi)	 	Any warranty, representation or statement made by Debtor in any of the Debt Documents or
otherwise in connection with any of the
Indebtedness shall be false or misleading in any material respect at the time when made;
	 
	 	(vii)	 	Any material portion of the Collateral is subjected to attachment, execution, levy, seizure
or confiscation in any legal proceeding or
otherwise, or if any legal or administrative proceeding is commenced against Debtor or any of the
Collateral, which subjects any
material portion of the Collateral to a material risk of attachment, execution, levy, seizure or
confiscation and no bond is posted or
protective order obtained to negate such risk, and the foregoing is not removed, released,
discharged or terminated within 30 days after
notice;
	 
	 	(viii)	 	Debtor breaches or is in default under any other written agreement between Debtor and
Secured Party that is not remedied within any
applicable cure period;
	 
	 	(ix)	 	Debtor dissolves, terminates its existence, becomes insolvent or ceases to do business as a
going concern;
	 
	 	(x)	 	[Omitted];
	 
	 	(xi)	 	A receiver is appointed for all or of any material part of the property of Debtor, or Debtor
makes any assignment for the benefit of
creditors;
	 
	 	(xii)	 	Debtor files a petition under any bankruptcy, insolvency or similar law, or any such petition
is filed against Debtor and is not dismissed
within forty-five (45) days;
	 
	 	(xiii)	 	Debtor’s improper filing of an amendment or termination statement relating to a filed
financing statement describing the Collateral;
	 
	 	(xiv)	 	Debtor shall merge with or consolidate into any other entity or sell all or substantially all
of its assets or in any manner terminate its
existence, unless such (1) merger, consolidation, sale or termination is approved by Secured Party,
which approval shall be in Secured
Party’s sole discretion, but shall not be unreasonably withheld or delayed; provided, however, if
Secured Party does not consent, then
Debtor can prepay the Indebtedness without premium or penalty, or (2) such persons or entities
which control the right to vote Debtor’s
voting stock immediately prior to such merger, consolidation, sale or termination, control the
right to vote more than 50% of the voting
stock of the successor entity or entity which owns the sold assets;
	 
	 	(xv)	 	[Omitted]
	 
	 	(xvi)	 	If Debtor is a publicly held corporation, there shall be a change in the ownership of
Debtor’s stock such that Debtor is no longer subject
to the reporting requirements of Section 13 of the Securities Exchange Act of 1934 or no longer has
a class of equity securities registered
under Section 12 of the Securities Exchange Act of 1934, unless such change in ownership is
approved by Secured Party, which
approval shall be in Secured Party’s sole discretion; provided, however, if Secured Party does not
consent, then Debtor can prepay the
Indebtedness without premium or penalty;
	 
	 	(xvii)	 	Debtor defaults, after giving effect to any grace or cure periods, under any other financing
arrangement between Debtor and a third party
resulting in a right by such third party or parties, whether or not exercised, to accelerate the
maturity of any indebtedness thereunder in
an amount in excess of Five Hundred Thousand Dollars ($500,000);
	 
	 	(xviii)	 	Secured Party shall have determined in its sole and good faith judgment that there is a
material impairment in the perfection or priority
of the Secured Party’s security interest in the Collateral; or

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	 	(xix)	 	Secured Party shall have determined in its sole and good faith judgment, which judgment shall
not be unreasonable, that there has been a
material adverse change in the financial condition, or business operations of Debtor from the date
hereof, or a change or event shall have
occurred which would reasonably be expected to materially impair the ability of Debtor to perform
its obligations hereunder or under
any of the other Debt Documents to which it is a party or of Secured Party to enforce the
Indebtedness or realize upon the Collateral.

	 	(b)	 	 Acceleration. If an Event of Default has occurred and is continuing, the Secured Party, at its
option, may declare any or all of the Indebtedness
to be immediately due and payable, without demand or notice to Debtor or any Guarantor (provided
that if there is a default as a result of a
bankruptcy or insolvency all Indebtedness shall become immediately due and payable without any
action by Secured Party). The accelerated
obligations and liabilities shall bear interest (both before and after any judgment) until paid in
full at the Default Rate.
	 
	 	(c)	 	Rights and Remedies. Secured Party shall have all of the rights and remedies of a Secured
Party under the Uniform Commercial Code, and
under any other applicable law. Without limiting the foregoing, Secured Party shall have the right
to (i) notify any account debtor of Debtor
or any obligor on any instrument which constitutes part of the Collateral to make payment to the
Secured Party, (ii) with or without legal
process, enter any premises where the Collateral may be and take possession of and remove the
Collateral from the premises or store it on the
premises, (iii) sell the Collateral at public or private sale, in whole or in part, and have the
right to bid and purchase at said sale, or (iv) lease
or otherwise dispose of all or part of the Collateral, applying proceeds from such disposition to
the obligations then in default. If requested by
Secured Party, Debtor shall promptly assemble the Collateral and make it available to Secured Party
at a place to be designated by Secured
Party, which is reasonably convenient to both parties. Secured Party may also render any or all of
the Collateral unusable at the Debtor’s
premises and may dispose of such Collateral on such premises without liability for rent or costs.
Any notice that Secured Party is required to
give to Debtor under the Uniform Commercial Code of the time and place of any public sale or the
time after which any private sale or other
intended disposition of the Collateral is to be made shall be deemed to constitute reasonable
notice if such notice is given to the last known
address of Debtor at least ten (10) days prior to such action. Upon the occurrence and during the
continuation of a default, Debtor hereby
appoints Secured Party as Debtor’s attorney-in-fact, with full authority in Debtor’s place and
stead and in Debtor’s name or otherwise, from
time to time in Secured Party’s sole and arbitrary discretion, to take any action and to execute
any instrument which Secured Party may be
deemed necessary or advisable to accomplish the purpose of this Agreement. To the extent it would
not result in or cause a breach, default or
other violation under any applicable license or agreement, Secured Party is granted a non-exclusive
royalty free license to use Debtor’s
Intellectual Property exclusively for the limited purpose of Secured Party’s remarketing and
disposition of Collateral in the exercise of Secured
Party’s rights or remedies hereunder. For the avoidance of doubt, this non-exclusive royalty free
license shall terminate concurrently with
Secured Party’s disposition of Collateral.
	 
	 	(d)	 	Application of Proceeds. The proceeds and/or avails of the Collateral, or any part thereof, and
the proceeds and the avails of any remedy
hereunder (as well as any other amounts of any kind held by Secured Party, at the time of or
received by Secured Party after the occurrence of
an Event of Default hereunder) shall be paid to and applied as follows:

	 	a.	 	First, to the payment of reasonable out-of-pocket costs and expenses, including all reasonable
amounts expended to preserve the value of
the Collateral, all reasonable costs of repossession, storage, and disposition including without
limitation attorneys’, appraisers’, and
auctioneers’ fees, of foreclosure or suit, if any, and of such sale and the exercise of any other
rights or remedies, and of all proper fees,
and reasonable expenses, liability and advances, including reasonable legal expenses and attorneys’
fees, incurred or made hereunder by
Secured Party;
	 
	 	b.	 	Second, to the payment to Secured Party of the amount then owing or unpaid on the Loans for
scheduled payments, any accrued and
unpaid interest, and all other Indebtedness (provided,
however, if such proceeds shall be
insufficient to pay in full the whole amount so
due, owing or unpaid upon the Loans, then to the unpaid interest thereon, then to the outstanding
principal amount of the Loans, and then
to the payment of other amounts then payable to Secured Party under any of the Debt Documents );
and
	 
	 	c.	 	Third, to the payment of the surplus, if any, to Debtor, its successors and assigns, or to
whomsoever may be lawfully entitled to receive
the same.

	 	(e)	 	Fees and Costs. Debtor agrees to pay all reasonable attorneys’ fees and other costs incurred by
Secured Party in connection with the
enforcement, assertion, defense or preservation of Secured Party’s rights and remedies under this
Agreement, or if prohibited by law, such
lesser sum as may be permitted. Debtor further agrees that such fees and costs shall constitute
Indebtedness.
	 
	 	(b)	 	Remedies Cumulative. Secured Party’s rights and remedies under this Agreement or otherwise
arising are cumulative and may be exercised
singularly or concurrently. Neither the failure nor any delay on the part of the Secured Party to
exercise any right, power or privilege under
this Agreement shall operate as a waiver, nor shall any single or partial exercise of any right,
power or privilege preclude any other or further
exercise of that or any other right, power or privilege. SECURED PARTY SHALL NOT BE DEEMED TO HAVE
WAIVED ANY OF ITS
RIGHTS UNDER THIS AGREEMENT OR UNDER ANY OTHER AGREEMENT, INSTRUMENT OR PAPER SIGNED BY DEBTOR

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Master Security Agreement No. 6081110

	 	 	 	UNLESS SUCH WAIVER IS EXPRESSED IN WRITING AND SIGNED BY SECURED PARTY. A waiver on any one
occasion shall not
be construed as a bar to or waiver of any right or remedy on any future occasion.
	 
	 	(g)	 	WAIVER OF JURY TRIAL. DEBTOR AND SECURED PARTY UNCONDITIONALLY WAIVE THEIR RIGHTS TO A JURY
TRIAL
OF ANY CLAIM OR CAUSE OF ACTION BASED UPON OR ARISING OUT OF THIS AGREEMENT, ANY OF THE OTHER DEBT
DOCUMENTS, ANY OF THE INDEBTEDNESS SECURED HEREBY, ANY DEALINGS BETWEEN DEBTOR AND SECURED PARTY
RELATING TO THE SUBJECT MATTER OF THIS TRANSACTION OR ANY RELATED TRANSACTIONS, AND/OR THE
RELATIONSHIP THAT IS BEING ESTABLISHED BETWEEN DEBTOR AND SECURED PARTY. THE SCOPE OF THIS WAIVER
IS
INTENDED TO BE ALL ENCOMPASSING OF ANY AND ALL DISPUTES THAT MAY BE FILED IN ANY COURT. THIS WAIVER
IS IRREVOCABLE. THIS WAIVER MAY NOT BE MODIFIED EITHER ORALLY OR IN WRITING. THE WAIVER ALSO SHALL
APPLY TO ANY SUBSEQUENT AMENDMENTS, RENEWALS, SUPPLEMENTS OR MODIFICATIONS TO THIS AGREEMENT,
ANY OTHER DEBT DOCUMENTS, OR TO ANY OTHER DOCUMENTS OR AGREEMENTS RELATING TO THIS TRANSACTION
OR ANY RELATED TRANSACTION. THIS AGREEMENT MAY BE FILED AS A WRITTEN CONSENT TO A TRIAL BY THE
COURT.

8. MISCELLANEOUS.

	 	(a)	 	 Assignment. This Agreement and/or any of the other Debt Documents may be assigned, in whole
or in part, by Secured Party without notice
to Debtor (provided that no such assignment shall be made to any competitor of Debtor), and Debtor
agrees not to assert against any such
assignee, or assignee’s assigns, any defense, set-off, recoupment claim or counterclaim which
Debtor has or may at any time have against
Secured Party for any reason whatsoever (all such defenses, set-offs, recoupment claims or
counterclaims being expressly preserved). Debtor
agrees that if Debtor receives written notice of an assignment from Secured Party, Debtor will pay
all amounts payable under any assigned
Debt Documents to such assignee or as instructed by Secured Party. Debtor also agrees to confirm in
writing receipt of the notice of
assignment as may be reasonably requested by Secured Party or assignee.
	 
	 	(b)	 	 Notices. All notices to be given in connection with this Agreement shall be in writing, shall
be addressed to the parties at their respective
addresses set forth in this Agreement (unless and until a different address may be specified in a
written notice to the other party), and shall be
deemed given (i) on the date of receipt if delivered in hand or by facsimile transmission, (ii) on
the next business day after being sent by
overnight mail, and (iii) on the fourth business day after being sent by regular, registered or
certified mail. As used herein, the term “business
day” shall mean and include any day other than Saturdays, Sundays, or other days on which
commercial banks in New York, New York are
required or authorized to be closed.
	 
	 	(c)	 	 Correction of Errors. Secured Party may correct manifest errors and fill in all blanks in this
Agreement, any Collateral Schedule or in any
Note consistent with the agreement of the parties;
	 
	 	(d)	 	Time is of the Essence. Time is of the essence of this Agreement. This Agreement shall be
binding, jointly and severally, upon all parties
described as the “Debtor” and their respective heirs, executors, representatives, successors and
assigns, and shall inure to the benefit of
Secured Party, its successors and assigns.
	 
	 	(e)	 	 Entire Agreement. This Agreement and the Debt Documents constitute the entire agreement between
the parties with respect to the subject
matter of this Agreement and supersede all prior understandings (whether written, verbal or
implied) with respect to such subject matter.
NEITHER THIS AGREEMENT NOR ANY OF THE DEBT DOCUMENTS SHALL BE CHANGED OR TERMINATED ORALLY OR BY
COURSE OF CONDUCT, BUT ONLY BY A WRITING SIGNED BY BOTH PARTIES. Section headings contained in this
Agreement have
been included for convenience only, and shall not affect the construction or interpretation of this
Agreement. This Agreement is the result of
negotiations between and has been reviewed by each of Debtor and Secured Party executing this
Agreement as of the date hereof and their
respective counsel; accordingly, this Agreement shall be deemed to be the product of the parties
hereto, and no ambiguity shall be construed in
favor of or against Debtor or Secured Party.
	 
	 	(f)	 	 Termination of Agreement. This Agreement shall continue in full force and effect until all of
the Indebtedness has been paid in full to Secured
Party or its assignee; provided, that Debtor’s indemnity obligations set forth in Section 6(c)
shall survive until all applicable statute of
limitations periods with respect to actions that may be brought against Secured Party have run. The
surrender, upon payment or otherwise, of
any Note or any of the other documents evidencing any of the Indebtedness shall not affect the
right of Secured Party to retain the Collateral
for such other Indebtedness as may then exist or as it may be reasonably contemplated will exist in
the future. This Agreement shall
automatically be reinstated if Secured Party is ever required to return or restore the payment of
all or any portion of the Indebtedness (all as
though such payment had never been made). Secured Party shall, at Debtor’s sole cost and expense,
execute such further documents and take
such further actions as may be reasonably necessary to effect the release of its security interests
contemplated by this paragraph, including duly
executing and delivering termination statements for filing in all relevant jurisdictions under the
Code.

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Master Security Agreement No. 6081110

	 	(g)	 	CHOICE OF LAW. DEBTOR AGREES THAT SECURED PARTY AND/OR ITS SUCCESSORS AND ASSIGNS SHALL HAVE
THE
OPTION BY WHICH STATE LAWS THIS AGREEMENT SHALL BE GOVERNED AND CONSTRUED: (A) THE LAWS OF THE
COMMONWEALTH OF VIRGINIA; OR (B) IF COLLATERAL HAS BEEN PLEDGED TO SECURE THE LIABILITIES, THEN BY
THE
LAWS OF THE STATE OR STATES WHERE THE COLLATERAL IS LOCATED, AT SECURED PARTY’S OPTION. THIS CHOICE
OF STATE LAWS IS EXCLUSIVE TO THE SECURED PARTY. DEBTOR SHALL NOT HAVE ANY OPTION TO CHOOSE THE
LAWS BY WHICH THIS AGREEMENT SHALL BE GOVERNED. DEBTOR ACKNOWLEDGES THAT THIS AGREEMENT IS
BEING SIGNED BY THE SECURED PARTY IN PARTIAL CONSIDERATION OF SECURED PARTY’S RIGHT TO ENFORCE IN
THE
JURISDICTION STATED ABOVE. DEBTOR CONSENTS TO JURISDICTION IN THE COMMONWEALTH OF VIRGINIA OR THE
STATE IN WHICH ANY COLLATERAL IS LOCATED AND VENUE IN ANY FEDERAL OR STATE COURT IN THE
COMMONWEALTH OF VIRGINIA OR THE STATE IN WHICH COLLATERAL IS LOCATED FOR SUCH PURPOSES AND WAIVES
ANY AND ALL RIGHTS TO CONTEST SAID JURISDICTION AND VENUE AND ANY OBJECTION THAT SAID COUNTY IS NOT
CONVENIENT. DEBTOR WAIVES ANY RIGHTS TO COMMENCE ANY ACTION AGAINST SECURED PARTY IN ANY
JURISDICTION EXCEPT VIRGINIA, OR IF SECURED PARTY CHOOSES TO LITIGATE IN A STATE WHERE COLLATERAL
IS
LOCATED THEN IN SUCH COUNTY AND STATE.
	 
	 	(h)	 	Power of Attorney. To facilitate direct collection, the Debtor hereby appoints the Secured
Party and any officer or employee of the Secured
Party, as the Secured Party may from time to time designate, as attorney-in-fact for the Debtor,
effective while any event of default has
occurred and is continuing, to (a) endorse the name of the Debtor in favor of the Secured Party
upon any and all checks, drafts, money orders,
notes, acceptances or other evidences of payment of Collateral that may come into the Secured
Party’s possession; and (b) do all acts and
things necessary to carry out this Agreement and the transactions contemplated hereby, including
signing the name of the Debtor on any
instruments required by law in connection with the transactions contemplated hereby and on
financing statements as permitted by the Virginia
Uniform Commercial Code. This power, being coupled with an interest, is irrevocable so long as the
Loan remains unsatisfied, or any Debt
Document remains effective.
	 
	 	(i)	 	Loss, Depreciation or Other Damage. The Secured Party shall not be liable for or prejudiced by
any loss, depreciation or other damage to
Collateral unless caused by the Secured Party’s willful and malicious act, its gross negligence or
bad faith, and the Secured Party shall have no
duty to take any action to preserve or collect any Collateral.
	 
	 	(j)	 	Demand; Protest. Debtor waives demand, protest, notice of protest, notice of default or
dishonor, notice of payment and nonpayment, notice
of any default, nonpayment at maturity, release, compromise, settlement, extension, or renewal of
accounts, documents, instruments, and
guarantees at any time held by Secured Party on which Debtor may in any way be liable.

9. DEFINITIONS.

     As used herein, the following terms, when initial capital letters are used, shall have the
respective meanings set forth below. In addition, all terms
defined in the Code shall have the meanings given therein unless otherwise defined herein.

Defined Terms. As used in this Agreement, the following terms shall have the following meanings,
unless the context otherwise requires:

“Additional Indebtedness” means, with respect to Debtor or any of its subsidiaries, the aggregate
amount of, without duplication, (a) all
obligations of such Person for borrowed money, (b) all obligations of such Person evidenced by
bonds, debentures, notes or other similar
instruments, (c) all obligations of such Person to pay the deferred purchase price of property or
services (excluding trade payables aged less
than one hundred eighty (180) days), (d) all capital lease obligations of such Person, (e) all
obligations or liabilities of others secured by a Lien
on any asset of such Person, whether or not such obligation or liability is assumed, (f) all
obligations or liabilities of others guaranteed by such
Person, and (g) any other obligations or liabilities which are required by GAAP to be shown as debt
on the balance sheet of such Person,
exclusive of trade debt. Unless otherwise indicated, the term “Additional Indebtedness” shall
include all Indebtedness of Debtor and all of its
subsidiaries.

“Affiliate” of a Person is a Person that owns or controls directly or indirectly the Person, any
Person that controls or is controlled by or is
under common control with the Person, and each of that Person’s senior executive officers,
directors, partners and, for any Person that is a
limited liability company, that Person’s managers and members.

“Code” means the Virginia Uniform Commercial Code (including revised Article 9 thereof).

“Collateral”
has the meaning given such capitalized term in Section 1.

“Collateral
Schedule” has the meaning given such capitalized term in Section 1.

“Debt
Documents” has the meaning given such capitalized term in Section 2(b).

“Default Rate” is the lower of eighteen percent (18%) per annum or the maximum rate not prohibited
by applicable law.

 Page 9 of 11

 

Master Security Agreement No. 6081110

“Indebtedness”
has the meaning given such capitalized term in Section 1.

“Intellectual Property” shall mean (a) all of the Debtor’s right, title and interest, whether now
owned or existing or hereafter acquired or
arising, in and to all domestic and foreign copyrights, copyright registrations and copyright
applications, whether or not registered or filed with
any governmental authority, together with (i) all renewals thereof, (ii) all present and future
rights of the Debtor under all present and future
license agreements relating thereto, whether the Debtor is licensee or licensor thereunder, (iii)
all income, royalties, damages and payments
now or hereafter due and/or payable to the Debtor thereunder or with respect thereto, including,
without limitation, damages and payments for
past, present or future infringements thereof, (iv) all of the Debtor’s present and future claims,
causes of action and rights to sue for past,
present or future infringements thereof, and (v) all rights corresponding thereto throughout the
world (collectively “Copyright Rights”); (b) all
of the Debtor’s right, title and interest, whether now owned or existing or hereafter acquired or
arising, in and to all United States and foreign
patents, and pending and abandoned United States and foreign patent applications, including,
without limitation, the inventions and
improvements described or claimed therein, together with(i) any reissues, divisions, continuations,
certificates of re-examination, extensions
and continuations-in-part thereof, (ii) all present and future rights of the Debtor under all
present and future license agreements relating thereto,
whether the Debtor is licensee or licensor thereunder, (iii) all income, royalties, damages and
payments now or hereafter due and/or payable to
the Debtor thereunder or with respect thereto, including, without limitation, damages and payments
for past, present or future infringements
thereof, (iv) all of the Debtor’s present and future claims, causes of action and rights to sue for
past, present or future infringements thereof,
and (v) all rights corresponding thereto throughout the world (collectively “Patent Rights”); (c)
all of the Debtor’s right, title and interest,
whether now owned or existing or hereafter acquired or arising, in and to all domestic and foreign
trademarks, trademark registrations,
trademark applications and trade names, whether or not registered or filed with any governmental
authority, together with (i) all renewals
thereof, (ii) all present and future rights of the Debtor under all present and future license
agreements relating thereto, whether the Debtor is
licensee or licensor thereunder, (iii) all income, royalties, damages and payments now or hereafter
due and/or payable to the Debtor thereunder
or with respect thereto, including, without limitation, damages and payments for past, present or
future infringements thereof, (iv) all of the
Debtor’s present and future claims, causes of action and rights to sue for past, present or future
infringements thereof, and (v) all rights
corresponding thereto throughout the world (collectively “Trademark Rights”); (d) all present and
future licenses and license agreements of
the Debtor, and all rights of the Debtor under or in connection therewith, whether the Debtor is
licensee or licensor thereunder, including,
without limitation, any present or future franchise agreements under which the Debtor is franchisee
or franchisor, together with (i) all renewals
thereof, (ii) all income, royalties, damages and payments now or hereafter due and/or payable to
the Debtor thereunder or with respect thereto,
including, without limitation, damages and payments for past, present or future infringements
thereof, (iii) all claims, causes of action and
rights to sue for past, present or future infringements thereof, and (iv) all rights corresponding
thereto throughout the world (collectively
“License Rights”); (e) all present and future trade secrets of the Debtor; and (f) all other
present and future intellectual property of the Debtor.

“Lien(s)” shall mean any voluntary or involuntary mortgage, pledge, deed of trust, assignment,
security interest, encumbrance, hypothecation,
lien, or charge of any kind (including any conditional sale or other title retention agreement, any
financing lease having substantially the same
economic effect as any of the foregoing, and the filing of, or agreement to give, any financing
statement under the Uniform Commercial Code
or comparable law of any jurisdiction).

“Loan” means an advance of credit by Secured Party to Debtor.

“Note”
has the meaning given such capitalized term in Section 1.

“Permitted Indebtedness” means and includes: (i) Indebtedness of Debtor to Secured Party, (ii)
Additional Indebtedness arising from the
endorsement of instruments in the ordinary course of business, and (iii) Subordinated Indebtedness.

“Permitted Liens” means: (i) liens in favor of Secured Party, (ii) liens for taxes not yet due or
for taxes being contested in good faith and
which do not involve, in the reasonable judgment of Secured Party, any imminent risk of the sale,
forfeiture or loss of any of the Collateral,
(iii) inchoate material men’s, mechanic’s, repairmen’s and similar liens arising by operation of
law in the normal course of business for
amounts which are not delinquent, and (iv) Liens existing on the date hereof and set forth in
Schedule A, and any refinancings, amendments
and modifications thereof.

“Person” is any individual, sole proprietorship, partnership, limited liability company, joint
venture, company association, trust,
unincorporated organization, association, corporation, institution, public benefit corporation,
firm, joint stock company, estate, entity or
government agency.

“Primary
Operating Account” has the meaning given such capitalized term in Section 2(w).

“Secured Party’s Expenses” means all reasonable costs or expenses (including reasonable attorneys’
fees and expenses) incurred in
connection with the preparation, negotiation, documentation, administration and funding of the Debt
Documents; and Secured Party’s
reasonable attorneys’ fees, costs and expenses incurred in amending, modifying, enforcing or
defending the Debt Documents (including fees
and expenses of appeal or review), including the exercise of any rights or remedies afforded
hereunder or under applicable law, whether or not
suit is brought, whether before or after bankruptcy or insolvency, including without limitation all
fees and costs incurred by Secured Party in
connection with Secured Party’s enforcement of its rights in a bankruptcy or insolvency proceeding
filed by or against Debtor or its property.

“Subordinated Indebtedness” means Additional Indebtedness subordinated to the Indebtedness of
Debtor to Secured Party on terms and
conditions acceptable to Secured Party in its sole discretion.

 Page 10 of 11

 

Master Security Agreement No. 6081110

     IN WITNESS WHEREOF, Debtor and Secured Party, intending to be legally bound hereby, have
duly executed this Agreement in
one or more counterparts, each of which shall be deemed to be an original, as of the day and year first aforesaid.

	 	 	 	 	 	 	 	 	 
	SECURED PARTY:	 	DEBTOR:	 	 
	 
	 	 	 	 	 	 	 	 
	Oxford Finance Corporation
	 	Alnylam Pharmaceuticals, Inc.	 	 
	 
	 	 	 	 	 	 	 	 
	By:

	 	/s/ Michael J. Altenburger	 	By:	 	/s/ Patricia L. Allen	 	 
	 

	 	 

	 	 	 	 

	 	 
	 
	 	 	 	 	 	 	 	 
	Name:

	 	Michael J. Altenburger	 	Name:	 	Patricia L. Allen	 	 
	 

	 	 

	 	 	 	 

	 	 
	 
	 	 	 	 	 	 	 	 
	Title:

	 	Chief Financial Officer	 	Title:	 	VP, Finance and Treasurer	 	 
	 

	 	 

	 	 	 	 

	 	 

 Page 11 of 11

 

	 	 	 
	Promissory Note

	 	Master Security Agreement No.6081110

Schedule No. 01

PROMISSORY NOTE

To Master Security Agreement No. 6081110

March 31, 2006

(Date)

FOR VALUE RECEIVED, Alnylam Pharmaceuticals, Inc., a Delaware corporation, located at the address
stated below (“Maker”) promises to pay to the order
of Oxford Finance Corporation or any subsequent holder hereof (each, a “Payee”) at its office
located at 133 N. Fairfax Street, Alexandria, VA 22314 or at such
other place as Payee or the holder hereof may designate, the principal sum of Two Hundred Forty
Thousand, Four Hundred Ninety-Eight and Twenty One-Hundredths Dollars ($240,498.20), with interest on the unpaid principal balance, from the date
hereof through and including the dates of payment, at a fixed
interest rate of ten and seven one-hundredths percent (10.07%) per annum, in forty-eight (48)
consecutive monthly installments of principal and interest as
follows:

	 	 	 	 	 
	Periodic	 	 
	Installment	 	Amount
	 
	1— 48

	 	$	6056.92	 

each
(“Periodic Installment”) and a final installment which shall be in the amount of the total
outstanding principal and interest, if any. The first Periodic
Installment shall be due and payable on or about March 31, 2006, and the following Periodic
Installments and the final installment shall be due and payable on
the first day of each succeeding month (each, a “Payment
Date”) beginning May 1, 2006. Such
installments have been calculated on the basis of a 360-day
year of twelve 30-day months. Each payment may, at the option of the Payee, be calculated and
applied on an assumption that such payment would be made on
its due date. If Maker receives the proceeds for which this Note is given to secure payment thereof
on any date other than the first day of a month, Maker agrees
to pay any initial partial month interest payment from the date of this Note to the first day of
the following month at the same rate set forth above (“Interim
Interest”).

The acceptance by Payee of any payment which is less than payment in full of all amounts due and
owing at such time shall not constitute a waiver of Payee’s
right to receive payment in full at such time or at any prior or subsequent time.

The Maker hereby expressly authorizes the Payee to insert the date value is actually given in the
blank space on the face hereof and on all related documents
pertaining hereto.

This Note may be secured by a security agreement (“Security Agreement” and any Security Agreement,
this Note and any other document evidencing or
securing this loan is hereinafter called a “Debt Document”).

Time is of the essence hereof. If any installment or any other sum due under this Note or any
Security Agreement is not received when due, or within five (5)
days thereafter the Maker agrees to pay, in addition to the amount of each such installment or
other sum, a late payment charge of five percent (5%) of the
amount of said installment or other sum, but not exceeding any lawful maximum. If (i) Maker fails
to make payment of any amount due hereunder (other than
due to the fault of Oxford Finance Corporation); or (ii) an event of default has occurred under any
Security Agreement, then the entire principal sum remaining
unpaid, together with all accrued interest thereon and any other sum payable under this Note or any
Security Agreement, at the election of Payee, shall
immediately become due and payable, with interest thereon at the lesser of (x) four percent (4%)
per annum above the otherwise applicable rate or (y) the highest
rate not prohibited by applicable law from the date of such accelerated maturity until paid (both
before and after any judgment).

Notwithstanding anything to the contrary contained herein or in the Security Agreement, Maker may
prepay in full, but not in part, its entire Indebtedness
hereunder by payment of the entire outstanding Indebtedness plus an additional sum as a premium
equal to the following percentages of the remaining principal
balance for the indicated period:

     From the date of this Note until the first annual anniversary date of this Note: five percent (5%)

     From the first annual anniversary date of this Note until the second annual anniversary date of
this Note: three percent (3%)

     From the second annual anniversary date of this Note until the third annual anniversary date of
this Note: two percent (2%)

     From the third annual anniversary date of this Note until the fourth annual anniversary date of
this Note: one percent (1%)

 Page 1 of 3 

 

The Maker and all sureties, endorsers, guarantors or any others (each such person, other than the
Maker, an “Obligor”) who may at any time become liable for
the payment hereof jointly and severally consent hereby to any and all extensions of time,
renewals, waivers or modifications of, and all substitutions or releases
of, security or of any party primarily or secondarily liable on this Note or any Security Agreement
or any term and provision of either, which may be made,
granted or consented to by Payee, and agree that suit may be brought and maintained against any one
or more of them, at the election of Payee without joinder of
any other as a party thereto, and that Payee shall not be required first to foreclose, proceed
against, or exhaust any security hereof in order to enforce payment of
this Note. The Maker and each Obligor hereby waives presentment, demand for payment, notice of
nonpayment, protest, notice of protest, notice of dishonor,
and all other notices in connection herewith, as well as filing of suit (if permitted by law) and
diligence in collecting this Note or enforcing any of the security
hereof, and agrees to pay (if and to the extent permitted by law) all reasonable out of pocket and
documented expenses incurred in collection, including Payee’s
actual and reasonable attorneys’ fees.

Maker and Payee intend to comply with all applicable federal and Virginia laws, including
applicable usury laws (or the usury laws of any jurisdiction whose
usury laws are deemed to apply to the Note or any other Debt Document despite the intention and
desire of the parties to apply the usury laws of the
Commonwealth of Virginia). Accordingly, the provisions of this paragraph shall govern and control
over every other provision of this Note or any other Debt
Document which conflicts or is inconsistent with this Section, even if such provision declares that
it controls. As used in this paragraph, the term “interest”
includes the aggregate of all charges, fees, benefits or other compensation which constitute
interest under applicable law, provided that, to the maximum extent
permitted by applicable law, (a) any non-principal payment shall be characterized as an expense or
as compensation for something other than the use,
forbearance or detention of money and not as interest, and (b) all interest at any time contracted
for, reserved, charged or received shall be amortized, prorated,
allocated and spread, in equal parts during the full term of the obligations. In no event shall
Maker or any other person be obligated to pay, or Payee have any
right or privilege to reserve, receive or retain, (a) any interest in excess of the maximum amount
of non-usurious interest permitted under the laws of the
Commonwealth of Virginia or the applicable laws (if any) of the United States or of any other
state, or (b) total interest in excess of the amount which Payee
could lawfully have contracted for, reserved, received, retained or charged had the interest been
calculated for the full term of the obligations. On each day, if
any, that the interest rate (the “Stated Rate”) called for under this Note or any other Debt
Document exceeds the maximum non-usurious rate, the rate at which
interest shall accrue shall automatically be fixed by operation of this sentence at the maximum
non-usurious rate for that day. Thereafter, interest shall accrue at
the Stated Rate unless and until the Stated Rate again exceeds the maximum non-usurious rate, in
which case, the provisions of the immediately preceding
sentence shall again automatically operate to limit the interest accrual rate to the maximum
non-usurious rate. The daily interest rates to be used in calculating
interest at the maximum non-usurious rate shall be determined by dividing the applicable maximum
non-usurious rate by the number of days in the calendar year
for which such calculation is being made. None of the terms and provisions contained in this Note
or in any other Debt Document which directly or indirectly
relate to interest shall ever be construed without reference to this paragraph, or be construed to
create a contract to pay for the use, forbearance or detention of
money at an interest rate in excess of the maximum non-usurious rate. If the term of any obligation
is shortened by reason of acceleration of maturity as a result
of any Event of Default or by any other cause, or by reason of any required or permitted
prepayment, and if for that (or any other) reason Payee at any time,
including but not limited to, the stated maturity, is owed or receives (and/or has received)
interest in excess of interest calculated at the maximum non-usurious
rate, then and in any such event all of any such excess interest shall be canceled automatically as
of the date of such acceleration, prepayment or other event
which produces the excess, and, if such excess interest has been paid to Payee, it shall be
credited pro tanto against the then-outstanding principal balance of
Maker’s obligations to Payee, effective as of the date or dates when the event occurs which causes
it to be excess interest, until such excess is exhausted or all of
such principal has been fully paid and satisfied, whichever occurs first, and any remaining balance
of such excess shall be promptly refunded to its payor.

THE MAKER HEREBY UNCONDITIONALLY WAIVES ITS RIGHTS TO A JURY TRIAL OF ANY CLAIM OR CAUSE OF ACTION
BASED
UPON OR ARISING OUT OF, DIRECTLY OR INDIRECTLY, THIS NOTE, ANY OF THE RELATED DOCUMENTS, ANY
DEALINGS
BETWEEN MAKER AND PAYEE RELATING TO THE SUBJECT MATTER OF THIS TRANSACTION OR ANY RELATED
TRANSACTIONS,
AND/OR THE RELATIONSHIP THAT IS BEING ESTABLISHED BETWEEN MAKER AND PAYEE. THE SCOPE OF THIS WAIVER
IS
INTENDED TO BE ALL ENCOMPASSING OF ANY AND ALL DISPUTES THAT MAY BE FILED IN ANY COURT (INCLUDING,
WITHOUT
LIMITATION, CONTRACT CLAIMS, TORT CLAIMS, BREACH OF DUTY CLAIMS, AND ALL OTHER COMMON LAW AND
STATUTORY
CLAIMS.) THIS WAIVER IS IRREVOCABLE, MEANING THAT IT MAY NOT BE MODIFIED EITHER ORALLY OR IN
WRITING, AND THE
WAIVER SHALL APPLY TO ANY SUBSEQUENT AMENDMENTS, RENEWALS, SUPPLEMENTS OR MODIFICATIONS TO THIS
NOTE,
ANY RELATED DOCUMENTS, OR TO ANY OTHER DOCUMENTS OR AGREEMENTS RELATING TO THIS TRANSACTION OR ANY
RELATED TRANSACTION. IN THE EVENT OF LITIGATION, THIS NOTE MAY BE FILED AS A WRITTEN CONSENT TO A
TRIAL BY
THE COURT.

This Note and any Security Agreement constitute the entire agreement of the Maker and Payee with
respect to the subject matter hereof and supercedes all prior
understandings, agreements and representations, express or implied.

No variation or modification of this Note, or any waiver of any of its provisions or conditions,
shall be valid unless in writing and signed by an authorized
representative of Maker and Payee. Any such waiver, consent, modification or change shall be
effective only in the specific instance and for the specific purpose
given.

 Page 2 of 3 

 

Any provision in this Note or any Security Agreement which is in conflict with any statute, law or
applicable rule shall be deemed omitted, modified or altered to
conform thereto.

Upon receipt of an affidavit (and appropriate indemnity if requested by the Maker) of an officer of
Payee as to the loss, theft, destruction or mutilation of this
Note or any Debt Document which is not of public record, and, in the case of any such loss, theft,
destruction or mutilation, upon surrender and cancellation of
such Note or other Debt Document, Maker will issue, in lieu thereof, a replacement Note or other
Debt Document in the same principal amount thereof and
otherwise of like tenor.

It is understood and agreed that this Note and all of the Debt Documents were negotiated and have
been or will be delivered to Payee in the Commonwealth of
Virginia, which State the parties agree has a substantial relationship to the parties and to the
underlying transactions embodied by this Note and the Debt
Documents. Maker agrees to furnish to Payee at Payee’s office in Alexandria, VA, all further
instruments, certifications and documents to be furnished
hereunder. The parties also agree that if collateral is pledged to secure the debt evidenced by
this Note, that the state or states in which such collateral is located
each have a substantial relationship to the parties and to the underlying transaction embodied by
this Note and the Debt Documents.

MAKER AGREES THAT THE PAYEE OF THIS NOTE SHALL HAVE THE OPTION BY WHICH STATE LAWS THIS NOTE SHALL
BE GOVERNED
AND CONSTRUED: (A) THE LAWS OF THE COMMONWEALTH OF VIRGINIA; OR (B) IF COLLATERAL HAS BEEN PLEDGED
TO SECURE THE
DEBT EVIDENCED BY THIS NOTE, THEN BY THE LAWS OF THE STATE OR STATES WHERE THE COLLATERAL IS
LOCATED, AT PAYEE’S
OPTION. THIS CHOICE OF STATE LAWS IS EXCLUSIVE TO THE PAYEE OF THIS NOTE. MAKER SHALL NOT HAVE ANY
OPTION TO
CHOOSE THE LAWS BY WHICH THIS NOTE SHALL BE GOVERNED. MAKER AND GUARANTORS HEREBY CONSENT TO THE
EXERCISE OF
JURISDICTION OVER IT BY ANY FEDERAL COURT SITTING IN VIRGINIA OR ANY VIRGINIA COURT SELECTED BY
PAYEE, FOR THE
PURPOSES OF ANY AND ALL LEGAL PROCEEDINGS ARISING OUT OF OR RELATING TO THE NOTE, THE LOAN
AGREEMENT AND ALL
OTHER DOCUMENTS. MAKER AND GUARANTORS IRREVOCABLY WAIVE, TO THE FULLEST EXTENT PERMITTED BY LAW,
ANY
OBJECTION WHICH IT MAY NOW OR HEREAFTER HAVE TO THE LAYING OF VENUE OF ANY SUCH PROCEEDING BROUGHT
IN ANY SUCH
COURT, ANY CLAIM BASED ON THE CONSOLIDATION OF PROCEEDINGS IN SUCH COURTS IN WHICH PROPER VENUE MAY
LIE IN
DIVERGENT JURISDICTIONS, AND ANY CLAIM THAT ANY SUCH PROCEEDING BROUGHT IN ANY SUCH COURT HAS BEEN
BROUGHT IN
AN INCONVENIENT FORUM. MAKER AND GUARANTORS HEREBY IRREVOCABLY WAIVE, TO THE FULLEST EXTENT
PERMITTED BY
LAW, ANY AND ALL RIGHT TO TRIAL BY JURY IN ANY LEGAL PROCEEDING ARISING OUT OF OR RELATING TO THIS
NOTE, THE OTHER
DOCUMENTS OR THE TRANSACTIONS CONTEMPLATED THEREBY.

	 	 	 	 	 	 	 
	 	 	Alnylam Pharmaceuticals, Inc.	 	 
	 
	 	 	 	 	 	 
	/s/ Michael
Mason

	 	By:	 	/s/ Patricia L. Allen	 	 
	 

(Witness)

	 	 	 	 

	 	 
	Michael
Mason

	 	Name:	 	Patricia L. Allen	 	 
	 

(Print name)

	 	 	 	 

	 	 
	300 Third St.,
Cambridge, MA 02142

	 	Title:	 	VP, Finance and Treasurer	 	 
	 

(Address)

	 	 	 	 

	 	 
	 
	 	 	 	 	 	 
	 	 	Federal Tax ID #: 77-0602661
	 	 
	 
	 	 	 	 	 	 
	 	 	Address: 300 Third Street, 3rd and 4th Floor
	 	 
	 	 	 	        Cambridge, MA 02142	 	 

 Page 3 of 3 

 

	 	 	 
	Promissory Note

	 	Master Security Agreement No.6081110
	 

	 	Schedule No. 02

PROMISSORY NOTE

To Master Security Agreement No. 6081110

March 31, 2006

(Date)

FOR VALUE RECEIVED, Alnylam Pharmaceuticals, Inc., a Delaware corporation, located at the address
stated below (“Maker”) promises to pay to the order
of Oxford Finance Corporation or any subsequent holder hereof (each, a “Payee”) at its office
located at 133 N. Fairfax Street, Alexandria, VA 22314 or at such
other place as Payee or the holder hereof may designate, the principal sum of One Hundred
Forty-Seven Thousand, One Hundred Seventy-Four and Eighty-Five
One-Hundredths Dollars ($147,174.85), with interest on the unpaid principal balance, from the date
hereof through and including the dates of payment, at a fixed
interest rate of ten and nine one-hundredths percent (10.09%) per annum, in thirty-six (36)
consecutive monthly installments of principal and interest as follows:

	 	 	 	 	 
	Periodic	 	 
	Installment	 	Amount
	1- 36

	 	$	4,715.49	 

each
(“Periodic Installment”) and a final installment which shall be in the amount of the total
outstanding principal and interest, if any. The first Periodic
Installment shall be due and payable on or about March 31, 2006, and the following Periodic
Installments and the final installment shall be due and payable on
the first day of each succeeding month (each, a “Payment
Date”) beginning May 1, 2006. Such
installments have been calculated on the basis of a 360-day
year of twelve 30-day months. Each payment may, at the option of the Payee, be calculated and
applied on an assumption that such payment would be made on
its due date. If Maker receives the proceeds for which this Note is given to secure payment thereof
on any date other than the first day of a month, Maker agrees
to pay any initial partial month interest payment from the date of this Note to the first day of
the following month at the same rate set forth above (“Interim
Interest”).

The acceptance by Payee of any payment which is less than payment in full of all amounts due and
owing at such time shall not constitute a waiver of Payee’s
right to receive payment in full at such time or at any prior or subsequent time.

The Maker hereby expressly authorizes the Payee to insert the date value is actually given in the
blank space on the face hereof and on all related documents
pertaining hereto.

This Note may be secured by a security agreement (“Security Agreement” and any Security Agreement,
this Note and any other document evidencing or
securing this loan is hereinafter called a “Debt Document”).

Time is of the essence hereof. If any installment or any other sum due under this Note or any
Security Agreement is not received when due, or within five (5)
days thereafter the Maker agrees to pay, in addition to the amount of each such installment or
other sum, a late payment charge of five percent (5%) of the
amount of said installment or other sum, but not exceeding any lawful maximum. If (i) Maker fails
to make payment of any amount due hereunder (other than
due to the fault of Oxford Finance Corporation); or (ii) an event of default has occurred under any
Security Agreement, then the entire principal sum remaining
unpaid, together with all accrued interest thereon and any other sum payable under this Note or any
Security Agreement, at the election of Payee, shall
immediately become due and payable, with interest thereon at the lesser of (x) four percent (4%)
per annum above the otherwise applicable rate or (y) the highest
rate not prohibited by applicable law from the date of such accelerated maturity until paid (both
before and after any judgment).

Notwithstanding anything to the contrary contained herein or in the Security Agreement, Maker may
prepay in full, but not in part, its entire Indebtedness
hereunder by payment of the entire outstanding Indebtedness plus an additional sum as a premium
equal to the following percentages of the remaining principal
balance for the indicated period:

     From the date of this Note until the first annual anniversary date of this Note: five percent (5%)

     From the first annual anniversary date of this Note until the second annual anniversary date of
this Note: three percent (3%)

     From the second annual anniversary date of this Note until the third annual anniversary date of
this Note: two percent (2%)

The Maker and all sureties, endorsers, guarantors or any others (each such person, other than the
Maker, an “Obligor”) who may at any time become liable for
the payment hereof jointly and severally consent hereby to any and all extensions of time,
renewals, waivers or modifications of, and all substitutions or releases
of, security or of any party primarily or secondarily liable on this Note or any Security Agreement
or any term and provision of either, which may be made,
granted or consented to by Payee, and agree that suit may be brought and maintained against any one
or more of them, at the election of Payee without joinder of

 Page 1 of 3 

 

any other as a party thereto, and that Payee shall not be required first to foreclose, proceed
against, or exhaust any security hereof in order to enforce payment of
this Note. The Maker and each Obligor hereby waives presentment, demand for payment, notice of
nonpayment, protest, notice of protest, notice of dishonor,
and all other notices in connection herewith, as well as filing of suit (if permitted by law) and
diligence in collecting this Note or enforcing any of the security
hereof, and agrees to pay (if and to the extent permitted by law) all reasonable out of pocket and
documented expenses incurred in collection, including Payee’s
actual and reasonable attorneys’ fees.

Maker and Payee intend to comply with all applicable federal and Virginia laws, including
applicable usury laws (or the usury laws of any jurisdiction whose
usury laws are deemed to apply to the Note or any other Debt Document despite the intention and
desire of the parties to apply the usury laws of the
Commonwealth of Virginia). Accordingly, the provisions of this paragraph shall govern and control
over every other provision of this Note or any other Debt
Document which conflicts or is inconsistent with this Section, even if such provision declares that
it controls. As used in this paragraph, the term “interest”
includes the aggregate of all charges, fees, benefits or other compensation which constitute
interest under applicable law, provided that, to the maximum extent
permitted by applicable law, (a) any non-principal payment shall be characterized as an expense or
as compensation for something other than the use,
forbearance or detention of money and not as interest, and (b) all interest at any time contracted
for, reserved, charged or received shall be amortized, prorated,
allocated and spread, in equal parts during the full term of the obligations. In no event shall
Maker or any other person be obligated to pay, or Payee have any
right or privilege to reserve, receive or retain, (a) any interest in excess of the maximum amount
of non-usurious interest permitted under the laws of the
Commonwealth of Virginia or the applicable laws (if any) of the United States or of any other
state, or (b) total interest in excess of the amount which Payee
could lawfully have contracted for, reserved, received, retained or charged had the interest been
calculated for the full term of the obligations. On each day, if
any, that the interest rate (the “Stated Rate”) called for under this Note or any other Debt
Document exceeds the maximum non-usurious rate, the rate at which
interest shall accrue shall automatically be fixed by operation of this sentence at the maximum
non-usurious rate for that day. Thereafter, interest shall accrue at
the Stated Rate unless and until the Stated Rate again exceeds the maximum non-usurious rate, in
which case, the provisions of the immediately preceding
sentence shall again automatically operate to limit the interest accrual rate to the maximum
non-usurious rate. The daily interest rates to be used in calculating
interest at the maximum non-usurious rate shall be determined by dividing the applicable maximum
non-usurious rate by the number of days in the calendar year
for which such calculation is being made. None of the terms and provisions contained in this Note
or in any other Debt Document which directly or indirectly
relate to interest shall ever be construed without reference to this paragraph, or be construed to
create a contract to pay for the use, forbearance or detention of
money at an interest rate in excess of the maximum non-usurious rate. If the term of any obligation
is shortened by reason of acceleration of maturity as a result
of any Event of Default or by any other cause, or by reason of any required or permitted
prepayment, and if for that (or any other) reason Payee at any time,
including but not limited to, the stated maturity, is owed or receives (and/or has received)
interest in excess of interest calculated at the maximum non-usurious
rate, then and in any such event all of any such excess interest shall be canceled automatically as
of the date of such acceleration, prepayment or other event
which produces the excess, and, if such excess interest has been paid to Payee, it shall be
credited pro tanto against the then-outstanding principal balance of
Maker’s obligations to Payee, effective as of the date or dates when the event occurs which causes
it to be excess interest, until such excess is exhausted or all of
such principal has been fully paid and satisfied, whichever occurs first, and any remaining balance
of such excess shall be promptly refunded to its payor.

THE MAKER HEREBY UNCONDITIONALLY WAIVES ITS RIGHTS TO A JURY TRIAL OF ANY CLAIM OR CAUSE OF ACTION
BASED
UPON OR ARISING OUT OF, DIRECTLY OR INDIRECTLY, THIS NOTE, ANY OF THE RELATED DOCUMENTS, ANY
DEALINGS
BETWEEN MAKER AND PAYEE RELATING TO THE SUBJECT MATTER OF THIS TRANSACTION OR ANY RELATED
TRANSACTIONS,
AND/OR THE RELATIONSHIP THAT IS BEING ESTABLISHED BETWEEN MAKER AND PAYEE. THE SCOPE OF THIS WAIVER
IS
INTENDED TO BE ALL ENCOMPASSING OF ANY AND ALL DISPUTES THAT MAY BE FILED IN ANY COURT (INCLUDING,
WITHOUT
LIMITATION, CONTRACT CLAIMS, TORT CLAIMS, BREACH OF DUTY CLAIMS, AND ALL OTHER COMMON LAW AND
STATUTORY
CLAIMS.) THIS WAIVER IS IRREVOCABLE, MEANING THAT IT MAY NOT BE MODIFIED EITHER ORALLY OR IN
WRITING, AND THE
WAIVER SHALL APPLY TO ANY SUBSEQUENT AMENDMENTS, RENEWALS, SUPPLEMENTS OR MODIFICATIONS TO THIS
NOTE,
ANY RELATED DOCUMENTS, OR TO ANY OTHER DOCUMENTS OR AGREEMENTS RELATING TO THIS TRANSACTION OR ANY
RELATED TRANSACTION. IN THE EVENT OF LITIGATION, THIS NOTE MAY BE FILED AS A WRITTEN CONSENT TO A
TRIAL BY
THE COURT.

This Note and any Security Agreement constitute the entire agreement of the Maker and Payee with
respect to the subject matter hereof and supercedes all prior
understandings, agreements and representations, express or implied.

No variation or modification of this Note, or any waiver of any of its provisions or conditions,
shall be valid unless in writing and signed by an authorized
representative of Maker and Payee. Any such waiver, consent, modification or change shall be
effective only in the specific instance and for the specific purpose
given.

Any provision in this Note or any Security Agreement which is in conflict with any statute, law or
applicable rule shall be deemed omitted, modified or altered to
conform thereto.

 Page 2 of 3 

 

Upon receipt of an affidavit (and appropriate indemnity if requested by the Maker) of an officer of
Payee as to the loss, theft, destruction or mutilation of this
Note or any Debt Document which is not of public record, and, in the case of any such loss, theft,
destruction or mutilation, upon surrender and cancellation of
such Note or other Debt Document, Maker will issue, in lieu thereof, a replacement Note or other
Debt Document in the same principal amount thereof and
otherwise of like tenor.

It is understood and agreed that this Note and all of the Debt Documents were negotiated and have
been or will be delivered to Payee in the Commonwealth of
Virginia, which State the parties agree has a substantial relationship to the parties and to the
underlying transactions embodied by this Note and the Debt
Documents. Maker agrees to furnish to Payee at Payee’s office in Alexandria, VA, all further
instruments, certifications and documents to be furnished
hereunder. The parties also agree that if collateral is pledged to secure the debt evidenced by
this Note, that the state or states in which such collateral is located
each have a substantial relationship to the parties and to the underlying transaction embodied by
this Note and the Debt Documents.

MAKER AGREES THAT THE PAYEE OF THIS NOTE SHALL HAVE THE OPTION BY WHICH STATE LAWS THIS NOTE SHALL
BE GOVERNED
AND CONSTRUED: (A) THE LAWS OF THE COMMONWEALTH OF VIRGINIA; OR (B) IF COLLATERAL HAS BEEN PLEDGED
TO SECURE THE
DEBT EVIDENCED BY THIS NOTE, THEN BY THE LAWS OF THE STATE OR STATES WHERE THE COLLATERAL IS
LOCATED, AT PAYEE’S
OPTION. THIS CHOICE OF STATE LAWS IS EXCLUSIVE TO THE PAYEE OF THIS NOTE. MAKER SHALL NOT HAVE ANY
OPTION TO
CHOOSE THE LAWS BY WHICH THIS NOTE SHALL BE GOVERNED. MAKER AND GUARANTORS HEREBY CONSENT TO THE
EXERCISE OF
JURISDICTION OVER IT BY ANY FEDERAL COURT SITTING IN VIRGINIA OR ANY VIRGINIA COURT SELECTED BY
PAYEE, FOR THE
PURPOSES OF ANY AND ALL LEGAL PROCEEDINGS ARISING OUT OF OR RELATING TO THE NOTE, THE LOAN
AGREEMENT AND ALL
OTHER DOCUMENTS. MAKER AND GUARANTORS IRREVOCABLY WAIVE, TO THE FULLEST EXTENT PERMITTED BY LAW,
ANY
OBJECTION WHICH IT MAY NOW OR HEREAFTER HAVE TO THE LAYING OF VENUE OF ANY SUCH PROCEEDING BROUGHT
IN ANY SUCH
COURT, ANY CLAIM BASED ON THE CONSOLIDATION OF PROCEEDINGS IN SUCH COURTS IN WHICH PROPER VENUE MAY
LIE IN
DIVERGENT JURISDICTIONS, AND ANY CLAIM THAT ANY SUCH PROCEEDING BROUGHT IN ANY SUCH COURT HAS BEEN
BROUGHT IN
AN INCONVENIENT FORUM. MAKER AND GUARANTORS HEREBY IRREVOCABLY WAIVE, TO THE FULLEST EXTENT
PERMITTED BY
LAW, ANY AND ALL RIGHT TO TRIAL BY JURY IN ANY LEGAL PROCEEDING ARISING OUT OF OR RELATING TO THIS
NOTE, THE OTHER
DOCUMENTS OR THE TRANSACTIONS CONTEMPLATED THEREBY.

	 	 	 	 	 	 	 
	 	 	Alnylam Pharmaceuticals, Inc.	 	 
	 
	 	 	 	 	 	 
	/s/ Michael
Mason

	 	By:	 	/s/ Patricia L. Allen	 	 
	 

(Witness)

	 	 	 	 

	 	 
	Michael
Mason 

	 	Name:	 	Patricia L. Allen	 	 
	 

(Print name)

	 	 	 	 

	 	 
	300 Third St.,
Cambridge, MA 02142

	 	Title:	 	VP, Finance and Treasurer	 	 
	 

(Address)

	 	 	 	 

	 	 
	 
	 	 	 	 	 	 
	 	 	Federal Tax ID #: 77-0602661
	 	 
	 
	 	 	 	 	 	 
	 	 	Address: 300 Third Street, 3rd and 4th Floor
	 	 
	 	 	 	       Cambridge, MA 02142	 	 

 Page 3 of 3exv10w1

 

Exhibit 10.1

COST REIMBURSEMENT

SUBCONTRACT AGREEMENT

BETWEEN

CASE WESTERN RESERVE UNIVERSITY

AND

CYBERKINETICS NEUROTECHNOLOGY SYSTEMS, INC.

UNDER CONTRACT HHSN275200503403C

THIS AGREEMENT, by and between Case Western Reserve University, hereinafter referred to as “CWRU”
and Cyberkinetics Neurotechnology Systems, Inc. whose principal place of business is 100 Foxborough
Boulevard, Suite 240, Foxborough, Massachusetts 02045 hereinafter referred to as “SUBCONTRACTOR”,
is for the purpose as hereinafter set forth.

WHEREAS, CWRU is the recipient of the following award (hereinafter referred to as “PRIME AWARD” and
attached hereto as Exhibit A ) which is incorporated herein. All terms and conditions and
applicable clauses of the PRIME AWARD are carried forth and shall apply to this AGREEMENT:

	 	 	 
	Award Number:

	 	HHSN275200503403C
	Project Sponsor:

	 	NIH — NICHD
	Project Title:

	 	Controller Development for Upper Limb Movement
	CWRU Principal Investigator:

	 	Robert F. Kirsch
	SUBCONTRACTOR Principal Investigator:

	 	John Donoghue

And WHEREAS, said PRIME AWARD involves an approved collaborative effort between CWRU and
SUBCONTRACTOR where SUBCONTRACTOR has agreed to use its personnel, facilities, and reasonable
efforts in the performance of the work, THEREFORE, the parties mutually agree as follows:

ARTICLE I. STATEMENT OF WORK

SUBCONTRACTOR shall provide the necessary personnel, facilities, data and materials to perform the
services specified in the attached statement of work, marked Exhibit B, which by this reference is
incorporated herein.

ARTICLE II. SCHEDULE FOR DELIVERABLE ITEMS OR REPORTS OR BOTH

In connection with and as part of the work to be performed, SUBCONTRACTOR shall submit reports as
specified in the Statement of Work attached hereto and as otherwise required by CASE under the
terms of the PRIME AWARD.

ARTICLE III. PERIOD OF PERFORMANCE

Performance of this AGREEMENT shall begin September 2, 2005 and continue through * * * as the
initial period of performance. A final completion date is anticipated by * * *. Subsequent periods
of performance shall be extended, by amendment of this AGREEMENT, which shall be in writing and
signed by all parties to this AGREEMENT.

ARTICLE IV. ESTIMATED COST AND PAYMENT

The
estimated cost of this Agreement is USD * * *  for the initial period of
the contract. Total funds currently available for payment and
allotted to this agreement are  * * *. CWRU shall not, in the absence
of a modification

 

*** Information redacted pursuant to a confidential treatment request. An unredacted version of
this exhibit has been filed separately with the Commission.

1

 

hereto, be obligated to reimburse the Subcontractor for costs which
are in excess of the currently allotted amount specified in this article. Subcontractor shall
expend funds in strict accordance with the budget contained in Exhibit C, which is attached hereto
and made a part hereof.

It is estimated that the amount currently allotted will cover performance of the Agreement through
* * *.

CWRU may allot additional funds to the Agreement without the concurrence of the Subcontractor.

Negotiated increments for future periods are:

	 	 	 
	PERIOD	 	AMOUNT
	* * *

	 	* * *
	* * *

	 	* * *
	* * *

	 	* * *
	* * *

	 	* * *

The total amount shall not exceed * * * without the prior written approval of CWRU.

The funding for this Agreement is subject to and contingent upon the continuing availability of
Federal funds for the purpose hereof.

SUBCONTRACTOR shall submit itemized invoices to CWRU not more frequently than monthly. The final
invoice must be submitted no later than 60 days after the completion date. Said invoices must
represent actual expenses paid and be certified by an appropriate institutional official.
Subcontractor shall use NIH Invoice/Financing Request Form, NIH Form (RC-1), contained in
Attachment 1 to the Prime Award (Exhibit A) and shall reference the CWRU number RES501126.

Submit an original and one copy to:

	 	 	 
	Robert F. Kirsch

	 	Tel: (216) 368-3158
	Case Western Reserve University

	 	Fax: (216) 368-4969
	Department of Biomedical Engineering

	 	E-mail address: rfk3@case.edu
	10900 Euclid Avenue
	 	 
	Cleveland, OH 44106-7207
	 	 

For the purpose of determining the amount payable to SUBCONTRACTOR under this AGREEMENT, the
allowability of costs shall be determined in accordance with the Federal Acquisition Regulation
(FAR) and the Health and Human Services Acquisition Regulations (HHSAR), and the terms of this
AGREEMENT.

ARTICLE V. FEDERAL AGENCY AUDIT

Acceptance of AGREEMENT obligates the parties to comply with audit provisions applicable to Federal
agency grantees. SUBCONTRACTOR agrees to permit independent auditors to have access to any other
records and financial statements as necessary for CWRU to comply with regulations applicable to the
AGREEMENT and make available to CWRU such information and records as CWRU may reasonably request to
facilitate CWRU compliance with said requirements.

ARTICLE VI. PROJECT DIRECTOR (CWRU)

The project director representing CWRU for the purpose of technical direction of the contracts
performance shall be Dr. Robert F. Kirsch. Any changes to the scope of work by the Subcontractor
must be approved in writing by Dr. Kirsch.

ARTICLE VII. PROJECT DIRECTOR (SUBCONTRACTOR)

 

*** Information redacted pursuant to a confidential treatment request. An unredacted version of
this exhibit has been filed separately with the Commission.

2

 

The project director representing SUBCONTRACTOR for the purpose of technical direction in
accordance with Article I, shall be:

John Donoghue, PhD.

Cyberkinetics Neurotechnology Systems, Inc.,

100 Foxborough Blvd., Suite 240

Foxborough, MA 02035

Phone: (508) 549-9981, ext. 102

Fax: (508) 549-9985

jdonoghue@cyberkineticsinc.com

A change in the designated project director shall require the prior written approval of CWRU.

ARTICLE VIII. SPECIAL PROVISIONS.

	 	1.	 	The performance of SUBCONTRACTOR under this AGREEMENT shall conform to the requirements
of the PRIME AWARD, the Federal Acquisition Regulations and the Health and Human Services
Acquisition Regulations, as applicable. If the SUBCONTRACTOR is a non-US Institution, U.S.
Government regulations included herein apply only as specified by the Federal Acquisition
Regulations and the Health and Human Services Acquisition Regulations, as applicable.
	 
	 	2.	 	SUBCONTRACTOR agrees to maintain books, records, and documents and other evidence
pertaining to all costs and expenses incurred and revenues acquired under this AGREEMENT to
the extent and in such detail as will properly reflect all costs and expenses of whatever
nature for which reimbursement is claimed. The books of account and other records which are
applicable to this AGREEMENT shall at all times be available for inspection, review, and
audit by CWRU to determine proper application and use of all funds paid to or for the
account of benefit of SUBCONTRACTOR.
	 
	 	3.	 	This AGREEMENT may not be assigned in whole or in part without the prior written
consent of CWRU .
	 
	 	4.	 	SUBCONTRACTOR assumes sole responsibility for reimbursement to CWRU of a sum of money
equivalent to the amount of any expenditures disallowed should DHHS rule through audit
exception or other
appropriate means that expenditures from funds allocated to SUBCONTRACTOR were not made in
compliance with the regulations of DHHS or the provisions of the AGREEMENT.
	 
	 	5.	 	CWRU, through its authorized representative, has the right, upon reasonable advance
notice, at all reasonable times, to inspect or otherwise evaluate the work performed or
being performed by SUBCONTRACTOR.

ARTICLE IX. HEALTH AND SAFETY

The SUBCONTRACTOR is responsible for meeting Federal, State, and local health and safety standards
and for establishing and implementing necessary measures to minimize their employees’ risk of
injury or illness in activities related to NIH contracts.

ARTICLE X. HUMAN SUBJECTS

The internal practices of each Participating Institution shall apply to its portion of the project;
these practices shall be in compliance with applicable Federal Regulations as found in the PRIME
AWARD, Section H – Special Contract Requirements, Articles H.1, H.2, and H.15, and in HHSAR
352.270-8 “Protection of Human Subjects,” that can be found in full text at
http://ecfr.gpoaccess.gov/cgi/t/text/text-idx?c=ecfr&%3C?SID%3E&rgn=div8&view=text&node=48:4
 .0.1.8.25.1.1.21&idno=48

The question of whether human subjects involved in the work undertaken by one
Participating Institution will be

 

*** Information redacted pursuant to a confidential treatment request. An unredacted version of
this exhibit has been filed separately with the Commission.

3

 

placed at risk by the work planned at the other Participating
Institution shall be a matter for decision by both institution’s Institutional Review Board (IRB);
these Boards shall communicate directly when either judges it appropriate, with a record of the
final disposition provided to both. IRB review and approvals shall be completed before any
procedures can be initiated on human subjects.

By execution of this AGREEMENT, SUBCONTRACTOR also assures CWRU that all locations at which
portions of the project that involve the use of human subjects are carried out and have on file a
current Federal Wide Assurance through the Office of Human Research Protection (OHRP).
Cyberkinetics number is * * *.

ARTICLE XI. VERTEBRATE ANIMALS

Should warm-blooded animals be used in this project, SUBCONTRACTOR will comply with the applicable
portions of the Animal Welfare Act (P.L. 99-158) and will follow the guidelines prescribed in the
Public Health Services Policy on Humane Care and Use of Laboratory Animals.

ARTICLE XII. RECOMBINANT DNA

For all research involving recombinant DNA techniques, the SUBCONTRACTOR agrees to meet the
requirements of the NIH Guidelines for Research Involving Recombinant DNA Molecules (the
Guidelines) (59 FR 34496, July 5, 1994 or latest revision).

ARTICLE XIII. PATENTS AND INVENTIONS

Patent and invention rights will be in accordance with Government regulations as set forth in 37
CFR 401, as noted in the Federal Acquisition Regulations and the Health and Human Services
Acquisition Regulations.

	 	1.	 	Invention means any invention or discovery which is or may be patentable or otherwise
protectable under Title 35 of the United States Code, or any novel variety of plant which
is or may be protected under the Plant Variety Protection Act (7 U.S.C. 2321 et seq.).
	 
	 	2.	 	Subject Invention means any Invention of CWRU or SUBCONTRACTOR conceived or first
actually reduced to practice in the performance of work under this contract, provided
that in the case of a variety of plant, the date of determination [as defined in section
41 (d) of the Plant Variety Protection Act, 7 U.S.C. 2401 (d) ] must also occur during
the period of contract performance.
	 
	 	3.	 	Each party may retain the entire right, title, and interest throughout the world to
each Subject Invention subject to the provisions of 37 CFR 401.14 and 35 U.S.C. 203.
With respect to any Subject Invention in which that party retains title, the Federal
Government shall have a nonexclusive, nontransferable, irrevocable, paid-up license to
practice or have practiced for or on behalf of the United States the Subject Invention
throughout the world.
	 
	 	4.	 	If any Subject Invention is developed jointly by employees or agents of both parties,
both parties shall jointly own (without any duty to account to the other for profits) all
right, title and interest (including patents, copyrights, mask work rights, trade
secrets, and other intellectual property rights) therein. Both parties will engage in
good faith efforts to mutually agree on whether and how to pursue patent, copyright or
mask work protection of the invention in the U.S. and elsewhere. There shall be
appointed a technical advisory board consisting of an equal number of representatives
from each party. Upon the generation of
a Subject Invention that a party believes to be jointly developed with the other party,
such party shall so advise the other party, and the technical advisory board shall
determine which party made the greater contribution to the Subject Invention in question.
If the technical advisory board cannot reach a decision upon the matter, it shall be
referred to arbitration under Article XV hereof. The party that is determined to have
made the greater contribution shall take the lead in obtaining intellectual property
protection regarding the Subject Invention in question (the “Lead Party”). In the event
that it is determined that both parties made equal contributions, then for the first such
situation of a determination of equal
contributions the Lead Party shall be determined by
a toss of the coin. For subsequent determination of equal

 

*** Information redacted pursuant to a confidential treatment request. An unredacted version of
this exhibit has been filed separately with the Commission.

4

 

	 	 	 	contributions the parties shall
alternate in taking the role as Lead Party. The Lead Party shall keep the other party
fully advised of the steps being taken in regard to obtaining intellectual property
protection. If the other party disagrees with an action(s) of the Lead Party the matter
shall be submitted to arbitration, under Article XV hereof upon a request made by the
objecting party, if the request is made within thirty days of the objecting party learning
of the action in question. If either party fails to pay one-half of the expenses of
obtaining particular intellectual property protection within sixty days of being presented
with the bill for such, that party shall thereby forfeit all rights to practice under that
intellectual property protection in the country where such protection is being obtained.
	 
	 	5.	 	Each party shall have licensing and commercialization rights and options as will be
defined in an agreement which shall be made an addendum hereto which is currently being
negotiated in good faith by the parties. A copy of said agreement will be provided to
the National Institute of Child Health and Human Development (NICHD).
	 
	 	6.	 	If and when a Subject Invention is created that may be amenable to patenting and/or
licensing, the CWRU Principal Investigator will disclose the Subject Invention to the CWRU
Technology Transfer Office (“TTO”) and/or the SUBCONTRACTOR Principal Investigator will
disclose the Subject Invention to the SUBCONTRACTOR’s intellectual property office, each in
accordance with their respective policies and practices, thereby creating a “Disclosure.”
Each party will promptly notify the other party in writing of receipt of any Disclosure,
normally within four weeks (“Notification”). In no event shall the Notification be
delivered to a party with an insufficient period of time for that party to meet its
reporting requirements to the Federal Government.
	 
	 	7.	 	Regarding its sole Subject Inventions, each party may, at its discretion and consistent
with the requirements of 37 CFR 401.14(c)(3), file an application for, and take steps to
obtain and maintain the validity of a patent(s) related to a Disclosure, in the United
States and/or any other country, and/or may take any other action (such as Copyright
registration) to obtain other protection in any country.
	 
	 	8.	 	Each party agrees that it will advise their respective employees that it is necessary
to hold in confidence all technical information and know-how received from the other party
(the “Confidential Information”) in connection with this Agreement and that it will not
disclose any Confidential Information of the other party and will allow the review of any
proposed patent applications or other protective measures containing joint Subject
Inventions to ensure that no Confidential Information is included. The obligation of
nondisclosure will not apply to the extent Confidential Information (i) was known to the
receiving party at the time it was disclosed, other than by previous disclosure by the
disclosing party, as evidenced by the receiving party’s written records at the time of
disclosure; (ii) is at the time of disclosure or later becomes publicly known under
circumstances involving no breach of this Agreement; (iii) is lawfully and in good faith
made available to the receiving party by a third party who did not derive it, directly or
indirectly, from the disclosing party; or (iv) is independently developed by a receiving
party without the use of the disclosing party’s Confidential Information.

ARTICLE XIV. INTANGIBLE PROPERTY RIGHTS AND PUBLICATION

The Subcontractor agrees to acknowledge the support of CWRU and the NIH awarding unit whenever
activities funded in whole or in part by this subcontract are published in any news media. Any
survey, questionnaire or publication arising from and supported by this subcontract will include a
positive statement clearly setting forth that the contents are in no way the responsibility of the
NIH awarding unit. Rights in intangible property will be in accordance with Government regulations
as set forth 45 CFR 74.36, and the terms of the PRIME AWARD
regarding the NIH rights in copyrightable material and the disposition of royalties and other
income earned from a Copyrighted work as noted in the Federal Acquisition Regulations and the
Health and Human Services Acquisition Regulations.

The rights in data developed jointly will be jointly owned by the parties, and if developed solely
by one party, will be owned solely by that party; the data, itself, is the property of the U.S.
Government. Each party grants to the other party a non-exclusive, royalty-free license to use the
data developed solely by each other provided that each party uses such data only for its own
internal research and educational purposes. The parties agree to negotiate in good

 

*** Information redacted pursuant to a confidential treatment request. An unredacted version of
this exhibit has been filed separately with the Commission.

5

 

faith
in the
event that either requests a license for commercial purposes. In the event that there is any
discrepancy between this Article XIV and the Federal Acquisition Regulations (FAR) Clause No.
52.227-17 entitled “Rights in Data – Special Works,” the FAR Clause shall apply.

Publication of data and/or discoveries arising from the performance of the research investigation
described in the Statement of Work will be governed by scientific custom with respect to authorship
and may be subject to restriction based upon the need to protect confidential information and/or to
seek patent protection. CWRU and SUBCONTRACTOR acknowledge and agree that, to the extent a
proposed disclosure or publication includes data and/or discoveries from clinical trials conducted
at third party sites, such data and/or discoveries may not be disclosed or published prior to the
publication of the results of such clinical trials or confirmation with the third party site(s).
To this end, the Project Director, (CWRU) and the Project Director (SUBCONTRACTOR), in
collaboration with the NICHD Project Officer, will jointly review all proposed publications prior
to submission. Subject to publication of the results of the clinical trials described above, any
delay will not exceed * * * for the purpose of filing patents.

ARTICLE XV DISPUTE RESOLUTION

Any controversy or dispute arising under this Agreement (including, but not limited to, the
validity, scope and enforceability of this arbitration clause) shall be referred to and finally
settled by arbitration in the City of Cleveland, Ohio, under the auspices of, and conducted in
accordance with, the rules of the American Arbitration Association. All arbitration proceedings
shall be before a board of three (3) arbitrators, for each of which each party shall select one (1)
arbitrator and the selected arbitrators shall select the third arbitrator. The costs of the third
arbitrator shall be divided equally between the parties, and each party shall pay the costs of the
arbitrator selected by it. Any award of the arbitrators shall be final and conclusive on the
parties to this Agreement, and judgment upon such award may be entered in any court having
jurisdiction thereof.

Either party may seek injunctive relief for enforcement of this Dispute Resolution Article.

SUBCONTRACTOR hereby irrevocably and unconditionally:

	 	1.	 	Agrees that any legal action, suit or proceeding contemplated by this Section entitled
“Dispute Resolution” hereof (collectively, “Related Litigation”) may be brought in any
state or federal court of competent jurisdiction sitting in Cuyahoga County, Ohio, submits
to the jurisdiction of such courts, and to the fullest extent permitted by law agrees that
it will not bring any Related Litigation in any other forum (but nothing herein shall
affect the right of CWRU to bring any action, suit or proceeding in any other forum);
	 
	 	2.	 	Waives any objection which it may have at any time to the laying of venue of any
Related Litigation brought in any such court located in Cuyahoga County, Ohio, waives any
claim that any such Related Litigation has been brought in an inconvenient forum, and
waives any right to object, with respect to any Related Litigation brought in any such
court, that such court does not have jurisdiction over Licensee; and
	 
	 	3.	 	Consents and agrees to service of any summons, complaint or other legal process in any
Related Litigation by registered or certified mail, postage prepaid, to Licensee at the
address for notices described in the Section entitled “Notices” hereof, and consents and
agrees that such service shall constitute in every respect valid and effective service (but
nothing herein shall affect the validity or effectiveness of process served in any other
manner permitted by law).

ARTICLE XVI TERMINATION

In the event of termination of the PRIME AWARD, this AGREEMENT shall be automatically terminated as
of the termination date of the PRIME AWARD. SUBCONTRACTOR will be reimbursed for any noncancelable
obligations properly incurred up to the date of notice of termination.

ARTICLE XVII. INCORPORATION OF APPLICABLE PROVISIONS OF THE PRIME AWARD

 

*** Information redacted pursuant to a confidential treatment request. An unredacted version of
this exhibit has been filed separately with the Commission.

6

 

All applicable provisions of the PRIME AWARD between CWRU and NIH, shall be binding upon
SUBCONTRACTOR as noted in the Federal Acquisition Regulations and the Health and Human Services
Acquisition Regulations and as listed in EXHIBIT A1.

ARTICLE XVIII. PUBLICITY

No publicity matter having or containing any reference to the other party to this Agreement, or in
which the name of the other party is mentioned, shall be made use of until written approval has
first been obtained by the party making use of the other party’s name.

ARTICLE XIX. CIVIL RIGHTS, AGE DISCRIMINATION AND EQUAL EMPLOYMENT OPPORTUNITY

SUBCONTRACTOR will comply with TITLE VI of the Civil Rights Act of 1964, Executive Order 11246, and
the Age Discrimination Act of 1975. SUBCONTRACTOR assures CWRU that it has valid Assurances of
Compliance with the DHHS for compliance with the Civil Rights Act of 1964 (Form HHS 441) and
section 504 of the Rehabilitation Act of 1973, as amended (Form HHS 641).

ARTICLE XX. SCIENTIFIC MISCONDUCT

Subcontractor hereby certifies that it has established procedures for dealing with and reporting
possible misconduct in science as set forth in 42 CFR Part 50, Subpart A. The term “Scientific
Misconduct” means, the fabrication, falsification, plagiarism, or other practices that seriously
deviate from those that are commonly accepted within the scientific community for proposing,
conducting, or reporting research.

ARTICLE XXI. CONFLICT OF INTEREST

In accordance with DHHS rule entitled, “Responsibility of Applicants for Promoting Objectivity in
Research for which PHS Funding is Sought” (42 CFR Part 50, Subpart F), SUBCONTRACTOR certifies that
it has established Conflict of Interest Policy that complies with all requirements, rules,
procedures, and principles of 42 CFR Part 50, Subpart F, incorporated herein by reference. If
Subcontractor does not have a Conflict of Interest Policy, it agrees to abide by and comply with
all rules, regulations, and procedures of CWRU’s Conflict of Interest Policy
(http://ora.ra.cwru.edu/main_research_compliance_page.htm). Upon written request by CWRU,
Subcontractor also agrees to furnish a copy of its Conflict of Interest Policy to CWRU within 30
days of receipt of request.

ARTICLE XXII. DEBARMENT AND SUSPENSION

SUBCONTRACTOR certifies to the best of its knowledge and belief that it is not presently debarred,
suspended, or proposed for debarment or declared ineligible for the awards of consortia, by any
Federal Agency, in accordance with the OMB Guidelines (53 FR19161-19211).

ARTICLE XXIII. CERTIFICATION OF NON-DELINQUENCY ON FEDERAL DEBT

SUBCONTRACTOR certifies that it is in compliance with the Non-Delinquency on Federal Debt criteria,
in accordance with OMB circular A-129.

ARTICLE XXIV. CERTIFICATION OF DRUG-FREE WORKPLACE

SUBCONTRACTOR certifies that it has implemented an appropriate policy in accordance with the
Drug-Free Workplace Act of 1988, 45 CFR Part 76, Subpart F.

ARTICLE XXV. CERTIFICATION REGARDING LOBBYING

SUBCONTRACTOR certifies to the best of its knowledge and belief that no Federal appropriated funds
have been paid or will be paid, by or on the behalf of the SUBCONTRACTOR, to any person for
influencing or attempting to influence a Federal
officer or Federal employee of any agency in
connection with the awarding of any federal award

 

*** Information redacted pursuant to a confidential treatment request. An unredacted version of
this exhibit has been filed separately with the Commission.

7

 

(Section 1352, Title 31, 4.5 Code).

ARTICLE XXVI. CLEAN AIR AND WATER

(Applicable only if the award exceeds $100,000 or a facility to be used has been the subject of a
conviction under the Clean Air Act or the Federal Water Pollution Control Act, and is listed by
EPA, or if the award is not otherwise exempt.)

The recipient agrees as follows:

1) To comply with applicable standards, orders or regulations issued pursuant to the Clean Air Act,
as amended (42 USC 7401, et seq.) and of the Federal Water Pollution Control Act (33 USC 1251 et
seq.), 2) That no portion of the work under this award will be performed in a facility listed on
the Environmental Protection Agency (EPA) List of Violating Facilities on the date that this award
was effective unless and until the EPA eliminates the name of the facility or facilities from such
listings, 3) To use its best efforts to comply with clean air standards and clean water standards
at the facility in which the award is being performed.

ARTICLE XXVII. LIABILITY

Each party shall be responsible for its negligent acts or omissions and the negligent acts or
omissions of its employees, officers, and directors.

ARTICLE XXVIII. INDEPENDENT CONTRACTOR

SUBCONTRACTOR is and will be acting as an independent contractor in the performance of this work.
Neither the SUBCONTRACTOR nor its employees or agents shall be deemed employees of CWRU while
performing under this agreement.

ARTICLE XXIX. REPRESENTATION

Representatives of the Parties to this Consortium are as follows:

A. For CWRU

	I.  	 	Research Issues — Dr. Robert F. Kirsch — Tel:
(216) 368-3158 — Email: rfk3@case.edu
	 
	II. 	 	Fiscal Issues —  Paul Frey, Grants Accounting —
Tel. (216) 368-5930 — Email:
pbf@case.edu
	 
	III.	 	Contract Issues — Tricia Mehosky, Sponsored Projects
Administration — (216) 368-5307 —
Email:pam17@case.edu

B. For SUBCONTRACTOR

	I.  	 	Research Issues — Dr. John Donoghue, Chief
Scientific Officer — Tel: (508) 549-9981, ext.
102 — email: jdonoghue@cyberkineticsinc.com 
	 
	II. 	 	Fiscal Issues — David Keene, Controller — Tel:
(508) 549-9981, ext. 113 — email:
dkeene@cyberkineticsinc.com
	 
	III.	 	Contract Issues — J. Christopher Flaherty, Executive Vice President Intellectual Property
and Technology — Tel: (508) 549-9981, ext. 106 — email: 
jcflaherty@cyberkineticsinc.com; and Jessica Duda, Director of
Corporate Development —
Tel: (508) 549-9981, ext. 112 — email: jduda@cyberkineticsinc.com

ARTICLE XXX. ENTIRE AGREEMENT

This AGREEMENT constitutes the entire agreement between CWRU and SUBCONTRACTOR with respect to the
subject matter hereof. No waiver, modification or amendment of any of the terms or conditions
hereof shall be effective unless set forth in writing and duly signed by CWRU and SUBCONTRACTOR.

In WITNESS THEREOF, the parties have executed this agreement by their duly authorized officers on
the date first

 

*** Information redacted pursuant to a confidential treatment request. An unredacted version of
this exhibit has been filed separately with the Commission.

8

 

herein set out:

	 	 	 	 	 	 	 	 	 	 	 
	CASE WESTERN RESERVE UNIVERSITY	 	CYBERKINETICS NEUROTECHNOLOGY SYSTEMS, INC.
	 	 	 	 	 	 	 	 	 	 	 
	By:

	 	/s/ Eric M. Cottington 	 	 	 	By:	 	/s/ Kimi Iguchi 	 	 
	 

	 	 
	 	 	 	 	 	 	 	 
	 

	 	Signature
	 	 	 	 	 	Signature	 	 
	Date:

	 	      3/31/06 	 	 	 	Date:	 	      3/31/06 	 	 
	 

	 	 
	 	 	 	 	 	 	 	 
	 	 	 	 
	Eric M. Cottington, Ph.D.

Associate Vice President for Research

Office of Research Administration

10900 Euclid Avenue

Cleveland, Ohio 44106-7015 
	 	 	 	 	VP Finance 	 	 

 

*** Information redacted pursuant to a confidential treatment request. An unredacted version of
this exhibit has been filed separately with the Commission.

9

 

EXHIBIT
A — Prime Award

Intentionally omitted.

 

*** Information redacted pursuant to a confidential treatment request. An unredacted version of
this exhibit has been filed separately with the Commission.

 

 

EXHIBIT
A1 — Clauses Incorporated by Reference

This contract incorporates the following clauses by reference, with the same force and effect,
as if they were given in full text. The full text of the clauses may be access electronically at
http://www.arnet.gov/far.

	 	 	 	 	 	 	 
	Reg	 	Clause	 	Date	 	Clause Title
	FAR

	 	52.202-1
	 	Jul-04
	 	Definitions (Over $100,000)
	FAR

	 	52.203-3
	 	Apr-84
	 	Gratuities (Over $100,000)
	FAR

	 	52.203-5
	 	Apr-84
	 	Covenant Against Contingent Fees (Over $100,000)
	FAR

	 	52.203-6
	 	Jul-95
	 	Restrictions on Subcontractor Sales to the Government (Over $100,000)
	FAR

	 	52.203-7
	 	Jul-95
	 	Anti-Kickback Procedures (Over $100,000)
	FAR

	 	52.203-8
	 	Jan-97
	 	Cancellation, Rescission, and Recovery of Funds for Illegal or Improper Activity (Over $100,000)
	FAR

	 	52.203-10
	 	Jan-97
	 	Price or Fee Adjustment for Illegal or Improper Activity (Over $100,000)
	FAR

	 	52.203-12
	 	Sep-05
	 	Limitation on Payments to Influence Certain Federal Transactions (Over $100,000)
	FAR

	 	52.204-4
	 	Aug-00
	 	Printed or Copied Double-Sided on Recycled Paper (Over $100,000)
	FAR

	 	52.204-7
	 	Oct-03
	 	Central Contractor Registration
	FAR

	 	52.209-6
	 	Jan-05
	 	Protecting the Government’s Interests When Subcontracting With Contractors Debarred, Suspended, or
Proposed for Debarment (Over $25,000)
	FAR

	 	52.215-2
	 	Jun-99
	 	Audit and Records – Negotiation (Over $100,000)
	FAR

	 	52.215-8
	 	Oct-97
	 	Order of Precedence – Uniform Contract Format
	FAR

	 	52.215-10
	 	Oct-97
	 	Price Reduction for Defective Cost or Pricing Data
	FAR

	 	52.215-12
	 	Oct-97
	 	Subcontractor Cost or Pricing Data (Over $500,000)
	FAR

	 	52.215-14
	 	Oct-97
	 	Integrity of Unit Prices (Over $100,000)
	FAR

	 	52.215-15
	 	Oct-04
	 	Pension Adjustments and Asset Reversions
	FAR

	 	52.215-18
	 	Jul-05
	 	Reversion or Adjustment of Plans for Post-Retirement Benefits (PRB) other than Pensions
	FAR

	 	52.215-19
	 	Oct-97
	 	Notification of Ownership Changes
	FAR

	 	52.215-21
	 	Oct-97
	 	Requirements for Cost or Pricing Data or Information Other Than Cost or Pricing Data – Modifications
	FAR

	 	52.216-7
	 	Dec-02
	 	Allowable Cost and Payment
	FAR

	 	52.216-11
	 	Apr-84
	 	Cost Contract – No Fee
	FAR

	 	52.219-8
	 	May-04
	 	Utilization of Small Business Concerns (Over $100,000)

							
	FAR

	 	52.219-9
	 	Jul-05
	 	Small Business Subcontracting Plan (Over $500,000)
	FAR

	 	52.219-16
	 	Jan-99
	 	Liquidated Damages – Subcontracting Plan (Over $500,000)
	FAR

	 	52.222-2
	 	Jul-90
	 	Payment for Overtime Premium (Over $100,000) (Note: The dollar amount in paragraph (a) of this clause is
$0 unless otherwise specified in the contract.)
	FAR

	 	52.222-3
	 	Jun-03
	 	Convict Labor
	FAR

	 	52.222-21
	 	Feb-99
	 	Prohibition of Segregated Facilities
	FAR

	 	52.222-26
	 	Apr-02
	 	Equal Opportunity
	FAR

	 	52.222-35
	 	Dec-01
	 	Equal Opportunity for Special Disabled Veterans, Veterans of the Vietnam Era, and Other Eligible Veterans
	FAR

	 	52.222-36
	 	Jun-98
	 	Affirmative Action for Workers with Disabilities
	FAR

	 	52.222-37
	 	Dec-01
	 	Employment Reports on Special Disabled Veterans, Veterans of the Vietnam Era, and Other Eligible Veterans
	FAR

	 	52.223-6
	 	May-01
	 	Drug-Free Workplace
	FAR

	 	52.223-14
	 	Aug-03
	 	Toxic Chemical Release Reporting (Over $100,000)
	FAR

	 	52.225-1
	 	Jun-03
	 	Buy American Act – Supplies
	FAR

	 	52.225-13
	 	Feb-06
	 	Restrictions on Certain Foreign Purchases
	FAR

	 	52.227-1
	 	Jul-95
	 	Authorization and Consent, Alternate I (Apr 1984)
	FAR

	 	52.227-2
	 	Aug-96
	 	Notice and Assistance Regarding Patent and Copyright Infringement (Over $100,000)
	FAR

	 	52.227-11
	 	Jun-97
	 	Patent Rights – Retention by the Contractor (Short Form) (Note: In accordance with FAR 27.303(a)(2),
paragraph (f) is modified to include the requirements in FAR 27.303(a)(2)(i) through (iv). The frequency
of reporting in (i) is annual.
	FAR

	 	52.227-17
	 	Jun-87
	 	Rights in Data – Special Works
	FAR

	 	52.232-9
	 	Apr-84
	 	Limitation on Withholding of Payments
	FAR

	 	52.232-17
	 	Jun-96
	 	Interest (Over $100,000)
	FAR

	 	52.232-20
	 	Apr-84
	 	Limitation of Cost
	FAR

	 	52.232-23
	 	Jan-86
	 	Assignment of Claims
	FAR

	 	52.232-25
	 	Oct-03
	 	Prompt Payment, Alternate I (Feb 2002)
	FAR

	 	52.233-1
	 	Jul-02
	 	Disputes
	FAR

	 	52.233-3
	 	Aug-96
	 	Protest After Award, Alternate I (Jun 1985)
	FAR

	 	52.233-4
	 	Oct-04
	 	Applicable Law for Breach of Contract Claim
	FAR

	 	52.242-1
	 	Apr-84
	 	Notice of Intent to Disallow Costs
	FAR

	 	52.242-3
	 	May-01
	 	Penalties for Unallowable Costs (Over $500,000)
	FAR

	 	52.242-4
	 	Jan-97
	 	Certification of Final Indirect Costs

							
	FAR

	 	52.242-13
	 	Jul-95
	 	Bankruptcy (Over $100,000)
	FAR

	 	52.243-2
	 	Aug-87
	 	Changes – Cost Reimbursement, Alternate V (Apr 1984)
	FAR

	 	52.244-2
	 	Aug-98
	 	Subcontracts, Alternate I (January 2006)
	FAR

	 	52.244-5
	 	Dec-96
	 	Competition in Subcontracting (Over $100,000)
	FAR

	 	52.244-6
	 	Feb-06
	 	Subcontracts for Commercial Items
	FAR

	 	52.245-5
	 	May-04
	 	Government Property (Cost-Reimbursement, Time and Material, or Labor-Hour Contract)
	FAR

	 	52.246-23
	 	Feb-97
	 	Limitation of Liability (Over $100,000)
	FAR

	 	52.249-6
	 	Sep-96
	 	Termination (Cost-Reimbursement)
	FAR

	 	52.249-14
	 	Apr-84
	 	Excusable Delays
	FAR

	 	52.253-1
	 	Jan-91
	 	Computer Generated Forms
	HHSAR

	 	352.202-1
	 	Jan-01
	 	Definitions – with Alternate paragraph (h) (Jan 2001)
	HHSAR

	 	352.216-72
	 	Oct-90
	 	Additional Cost Principles
	HHSAR

	 	352.228-7
	 	Dec-91
	 	Insurance – Liability to Third Persons
	HHSAR

	 	352.232-9
	 	Apr-84
	 	Withholding of Contract Payments
	HHSAR

	 	352.233-70
	 	Apr-84
	 	Litigation and Claims
	HHSAR

	 	352.242-71
	 	Apr-84
	 	Final Decisions on Audit Findings
	HHSAR

	 	352.270-5
	 	Apr-84
	 	Key Personnel
	HHSAR

	 	352.270-6
	 	Jul-91
	 	Publications and Publicity
	HHSAR

	 	352.270-7
	 	Jan-01
	 	Paperwork Reduction Act

 

*** Information redacted pursuant to a confidential treatment request. An unredacted version of
this exhibit has been filed separately with the Commission.

 

 

EXHIBIT
B — Statement of Work

***

 

*** Information redacted pursuant to a confidential treatment request. An unredacted version of
this exhibit has been filed separately with the Commission.

 

 

EXHIBIT
C — Summary of Proposed Costs

***

 

*** Information redacted pursuant to a confidential treatment request. An unredacted version of
this exhibit has been filed separately with the Commission.

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