Exhibit 10.1

SEPARATION AGREEMENT AND RELEASE

THIS SEPARATION AGREEMENT AND RELEASE (this “Agreement”) is made and entered
into as of January 6, 2009 (the “Execution Date”), by and between ACCELRYS,
INC., (the “Company”) and Mark J. Emkjer (the “Executive”).

RECITALS

WHEREAS, Executive wishes to resign as President and Chief Executive Officer of
the Company and to resign as a member of the Company’s Board of Directors
effective January 5, 2009 and to resign as an employee of the Company effective
February 1, 2009, and the Company wishes to accept such resignation;

WHEREAS, the parties hereto desire to set forth the terms and conditions upon
which Executive’s employment with the Company will terminate effective as of the
Execution Date.

NOW, THEREFORE, in consideration of the mutual covenants contained herein, and
for other good and valuable consideration, the receipt and sufficiency of which
are hereby acknowledged, the parties hereto agree as follows:

AGREEMENT

1. Termination of Employment. The parties acknowledge and agree that effective
as of the Execution Date: (i) Executive has resigned, and the Company has
accepted Executive’s resignation, as a member of the Company’s Board of
Directors and as the Company’s President and Chief Executive Officer; (ii) that
certain Employment Agreement, dated as of May 21, 2006, by and between the
Company and Executive (the “Employment Agreement”) shall be deemed terminated,
superseded and replaced in its entirety by this Agreement; and (iii) neither the
Company nor Executive shall have any rights, duties, obligations or liabilities
under the Employment Agreement, which shall be deemed null and void and of no
further force or effect. Notwithstanding the foregoing, Executive shall remain
as an employee “at will” with the Company through January 31, 2009, during which
time Executive shall continue to report to the Board of Directors of the Company
and shall provide such services and perform such tasks as are reasonably
requested by the Board of Directors of the Company or its designee; provided,
however, that effective February 1, 2009, Executive hereby resigns from the
Company as an employee of the Company.

2. SEPARATION PAYMENTS; TAX MATTERS.

2.1 Severance Payments.

(a) Subject to the terms of this Agreement, in consideration of Executive’s
release of claims against the Company pursuant to Section 3 of this Agreement
and Executive’s covenants set forth in Sections 4 and 5 of this Agreement, the
Company shall: (i) pay to Executive, on February 1, 2009, a lump-sum amount
equal to $315,000 (less applicable withholdings); (ii) pay to Executive, each
month for a period of twelve (12) months following February 1, 2009 (as defined
below), an amount equal to $140,000 (less applicable withholdings), the first
payment of which shall be made on February 15, 2009 and all payments of which
shall be made in accordance with the Company’s regular payroll practices; and
(iii) reimburse or otherwise pay Executive’s Consolidated Omnibus Budget
Reconciliation Act of 1985 (COBRA) payments for medical and dental insurance
under the Company’s applicable plans for the lesser of (x) twenty four
(24) months from January 31, 2009 or (y) the date upon which Executive becomes
eligible for medical coverage from a new employer, provided that Executive shall
notify the Company no later than fifteen (15) days after becoming eligible for
such coverage. The payments and benefits referenced in clauses “(i)” through
“(iii)” of the previous sentence are referred to herein as the “Severance
Payments”.

(b) Each of the parties expressly acknowledges and agrees that: (i) absent the
terms of this Agreement, Executive would not otherwise be entitled to receive
any of the Severance Payments in connection with Executive’s termination by way
of resignation; and (ii) in the event that Executive materially breaches any
provision of Sections 3, 4 or 5 of this Agreement, Executive’s rights to receive
any remaining Severance Payments pursuant to Section 2.1(a) shall immediately
terminate and Executive shall no longer be entitled to receive any such
remaining Severance Payments.

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2.2 Accrued Salary and Vacation; Equity. On January 31, 2009, the Company shall
pay to Executive all accrued but unpaid salary and all accrued but unused paid
time off and vacation benefits earned through January 31, 2009, if any
(collectively, the “Required Payment”). Each of the parties expressly
acknowledges and agrees that the Required Payment is being made to Executive in
accordance with applicable laws and regulations and that Executive would be
entitled to receive the Required Payment regardless of whether or not Executive
enters into this Agreement. Executive acknowledges and agrees that on
January 31, 2009 all vesting under stock options, restricted stock or any other
equity awards shall cease, and Executive shall only be entitled to exercise
vested equity awards and only in accordance with their terms.

2.3 Section 409A Compliance. Notwithstanding anything to the contrary contained
herein, no portion of the Severance Payments will be paid during the six
(6) month period following the date of separation from service unless the
Company reasonably determines that paying such portion immediately following the
termination of Executive’s employment would not result in the imposition of any
tax under Section 409A (“Section 409A”) of the Internal Revenue Code of 1986, as
amended (the “Code”), in which case such portion shall be paid in accordance
with Section 2.1(a). If any portion of the Severance Payments is not paid to
Executive in accordance with Section 2.1(a) as a result of the previous
sentence, on the first day following such six (6) month period, the Company will
pay to Executive a lump-sum amount equal to the cumulative portions of the
Severance Payments that were not, but would have otherwise been, paid to
Executive during such six-month period pursuant to Section 2.1(a). Thereafter,
Executive will receive the remaining Severance Payments in accordance with
Section 2.1(a).

2.4 Taxes. Executive will be responsible for the payment of any tax liability
incurred as a result of this Agreement. The Company may withhold tax on any
payments or benefits provided to Executive pursuant to this Agreement as
required by law or regulation. Executive is solely responsible and liable for
the satisfaction of all taxes and penalties that may arise under Section 409A of
the Code, and the Company shall not have any obligation to indemnify or
otherwise hold Executive harmless from any or all of such taxes. The Company
shall have the sole discretion to interpret the requirements of the Code,
including Section 409A, for purposes of this Section 2.4, but shall only act in
accordance with written advice from its accountants and attorneys.

3. RELEASE OF CLAIMS.

3.1 Release. Effective as of the date that is eight (8) days after the Execution
Date (the “Effective Date”), Executive irrevocably and unconditionally releases
any and all Released Claims (as defined below) that Executive may have against:
(i) the Company; (ii) each of the Company’s current and former parents,
subsidiaries, related companies, partnerships or joint ventures; (iii) with
respect to each of parties listed in the foregoing clauses “(i)” and “(ii)”,
such party’s predecessors and successors; or (iv) with respect to each of the
parties listed in the foregoing clauses “(i)”, “(ii)” and “(iii)”, all of such
party’s past, present, and future employees, officers, directors, stockholders,
owners, representatives, assigns, attorneys, agents, insurers, employee benefit
programs (and the trustees, administrators, fiduciaries and insurers of such
programs) and any other persons acting by, through, under or in concert with any
of such persons or entities and their successors (each, a “Company Released
Party” and, collectively, the “Company Released Parties”).

3.2 Released Claims. For purposes of this Agreement, the term “Released Claims”
shall include, to the fullest extent permitted by applicable law, all known and
unknown claims, promises, causes of action or similar rights of any type
(“Claims”) that Executive may have arising under the Employment Agreement, the
Company’s Fiscal Year 2009 Management Incentive Plan, any federal, state or
local laws (including statutes, regulations, other administrative guidance and
common law doctrines), including, without limitation, the following: the Age
Discrimination in Employment Act (the “ADEA”) and Executive Order 11,141; Title
VII of the Civil Rights Act of 1964, Sections 1981 and 1983 of the Civil Rights
Act of 1866, and Executive Order 11,246; the Equal Pay Act, the Americans With
Disabilities Act and Sections 503 and 504 of the Rehabilitation Act of 1973;
California state laws that prohibit discrimination in employment based on
disability, race, creed, color, national origin, ancestry, age, marital status,
affectional or sexual orientation, sex or military status; and any other
federal, state, or local laws that prohibit discrimination in employment; the
Employee Retirement Income Security Act of 1974; the Fair Labor Standards Act of
1938; the Family and Medical Leave Act of 1993; and any other federal laws
relating to employment. In connection with this Section 3, Executive expressly
acknowledges that some examples of

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Released Claims include, without limitation: (i) Claims that in any way relate
to or arose during Executive’s employment with the Company, or the termination
of such employment, such as Claims for compensation, bonuses, commissions, lost
wages or unused accrued vacation or sick pay; (ii) Claims that in any way relate
to the design or administration of any “employee welfare benefit plan”
maintained by the Company; and (iii) any Claims to attorneys’ fees or other
indemnities (such as under the Civil Rights Attorneys’ Fees Act), with respect
to the Released Claims, except as expressly provided in this Agreement.

3.3 Unknown Claims. Executive expressly acknowledges and agrees that:
(i) Executive has been advised and understands that the Released Claims may
include Claims that Executive does not currently know about (“Unknown Claims”);
(ii) Executive knowingly and voluntarily intends to grant the release of such
Unknown Claims as Released Claims although Executive recognizes that someday
Executive might regret having done so; and (iii) Executive desires to assume the
risk of releasing the Unknown Claims as Released Claims and acknowledges and
agrees that the release set forth in this Section 3 shall remain effective in
all respects in any such case. With full understanding of the potential
consequences of Executive’s actions, to the fullest extent permitted by law,
Executive expressly waives all rights Executive might have under any law that is
intended to protect Executive from waiving Claims such as the Unknown Claims,
including, without limitation, Section 1542 of the Civil Code of the State of
California which reads as follows: “A general release does not extend to claims
which the creditor does not know or suspect to exist in his favor at the time of
executing the release, which if known by him must have materially affected his
settlement with the debtor.” Notwithstanding the foregoing, nothing in the
release given by Executive under this Section 3 shall release any Claim
Executive may have for any breach by a Company Released Party of this Agreement.
Nothing herein releases the Company’s indemnification obligations to Executive
pursuant to its certificate of incorporation, bylaws or any indemnification
agreement with Executive.

3.4 ADEA Claims. Executive acknowledges and agrees that, prior to the Execution
Date, Executive was advised, as required by the ADEA, that: (i) the release of
the Released Claims pursuant to this Agreement does not apply to any Claims that
may arise after Executive signs this Agreement; (ii) Executive had the right to
consult, and should have consulted, with an attorney prior to executing this
Agreement; (iii) Executive was entitled to a period of twenty-one (21) days to
consider the release contained in this Agreement (although Executive may have
chosen to voluntarily execute this release earlier); (iv) Executive will have
seven (7) days following the execution of this Agreement to revoke such
Agreement, in which event the Effective Date shall not occur and the Company
shall have no obligation hereunder; and (v) this Agreement will not be deemed
effective until the Effective Date.

4. NON-COMPETITION; NON-SOLICITATION; NON-DISPARAGEMENT.

4.1 Restrictions. In consideration of the payments made to Executive under
Section 2.1(a), for a period commencing on February 1, 2009 and continuing for
twenty-four (24) months thereafter, Executive shall not, directly or indirectly:

(a) be employed by, engaged in or participate in the ownership, management,
operation or control of, or act in any advisory or other capacity (including as
an individual, principal, agent, executive, consultant or otherwise) for, any
Competing Entity which conducts its business within the Territory (as defined
below); provided, however, that notwithstanding the foregoing, Executive may
make solely passive investments in any Competing Entity, the common stock of
which is “publicly held” and of which Executive shall not own or control,
directly or indirectly, in the aggregate securities which constitute five
percent (5%) or more of the voting power of such Competing Entity;

(b) solicit or divert any business or any customer or known prospective customer
from the Company or assist any person or entity in doing so or attempting to do
so;

(c) cause or seek to cause any person or entity to refrain from dealing or doing
business with the Company or assist any person or entity in doing so;

(d) solicit for employment, or advise or recommend to any other person or entity
that he, she or it employ or solicit for employment or retention as an employee
or consultant, any person who is an employee of, or exclusive consultant to, the
Company; or

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(e) make any derogatory or disparaging statement(s) regarding the Company or its
affiliates, directors or employees.

4.2 Definitions. For purposes of this Section 4:

(a) “Competing Entity” means any entity which is presently or hereafter engaged
in any business of the type or character engaged in by the Company or any of its
subsidiaries including, without limitation: (i) the business of developing,
marketing or selling software programs which use molecular simulation or
analysis to predict chemical or biological activities; (ii) the business of
developing, marketing or selling software programs that store, manage or analyze
chemical or biological information; or (iii) any business which is otherwise
competitive with a business conducted by the Company or any of its subsidiaries.

(b) “Territory” means North America, Europe and Japan.

4.3 Exceptions. Notwithstanding anything to the contrary set forth in this
Section 4, Executive may engage in the activities set forth in Section 4.1 with
the prior written consent of the Company, which consent shall not be
unreasonably withheld. Further, in determining whether a specific activity by
Executive for a Competing Entity shall be permitted, the Company will consider,
among other things, the nature and scope of: (i) the duties to be performed by
Executive; and (ii) the business activities of the Competing Entity at the time
of Executive’s proposed engagement by such entity.

4.4 Acknowledgement. Executive acknowledges and agrees that the covenants set
forth in this Section 4 are reasonable and necessary in all respects for the
protection of the Company’s legitimate business interests (including, without
limitation, the Company’s confidential, proprietary information and trade
secrets and client goodwill, which represents a significant portion of the
Company’s net worth and in which the Company has a property interest).
Notwithstanding anything to the contrary set forth in this Agreement: (i) if any
provision set forth in this Section 4 is deemed invalid or unenforceable for any
reason, it is the parties’ intention that such provision be equitably reformed
or modified to the extent necessary (and only to such extent necessary) to
render it valid and enforceable in all respects; and (ii) in the event that the
time period and geographic scope referenced above is deemed unreasonable,
overbroad, or otherwise invalid, it is the parties’ intention that the enforcing
court shall reduce or modify the time period and/or geographic scope to the
extent necessary (and only to such extent necessary) to render them valid and
enforceable in all respects.

5. ADDITIONAL REPRESENTATIONS, WARRANTIES AND COVENANTS OF EXECUTIVE. In
connection with the transactions contemplated by this Agreement, Executive
hereby represents, warrants and covenants to and for the benefit of the Company
as follows:

5.1 Pursuit of Claims. (i) As of the Execution Date, Executive has not filed,
initiated or prosecuted (or caused to be filed, initiated or prosecuted);
(ii) as of the Effective Date, Executive shall not have filed, initiated or
prosecuted (or caused to be filed, initiated or prosecuted); and (iii) following
the Effective Date, Executive shall not file, initiate or prosecute (or cause to
be filed, initiated or prosecuted), in each case of clauses “(i)” through
“(iii)”, any lawsuit, complaint, charge, action, compliance review,
investigation or proceeding with respect to any Released Claim, whether as a
named plaintiff, class member or otherwise.

5.2 Ownership of Claims. As of the Execution Date, Executive has not assigned or
transferred (or attempted to assign or transfer), and as of the Effective Date,
Executive shall not have assigned or transferred (or have attempted to assign or
transfer), any of the Released Claims to any third party.

5.3 No Admission of Liability. Executive acknowledges that neither the Company
nor any of the other Company Released Parties believes, or has admitted, that it
has committed any wrongdoing with respect to Executive, and Executive agrees
that at no time following the Execution Date shall Executive assert that the
release of Released Claims contained in this Agreement constitutes an admission
of wrongdoing by the Company or any other Company Released Party.

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5.4 Company Property. On January 31, 2009, unless otherwise authorized in
writing by a member of the Board of Directors of the Company, Executive shall
return to the Company all files, memoranda, documents, records, copies of the
foregoing, keys, building passes, security passes, access or identification
cards and any other property of the Company or any other Company Released Party
that was in Executive’s control, provided that Executive may retain his
computer, subject to his confidentiality obligations hereunder.

5.5 Confidential Information. Executive acknowledges that, during the term of
Executive’s employment with the Company, Executive has gained knowledge of and
had access to certain confidential and proprietary information of and relating
to the Company and the other Company Released Parties (the “Confidential
Information”). From and after the Execution Date, Executive agrees to hold in
trust and confidence all such Confidential Information and Executive shall not
disclose such Confidential Information to any third parties without the prior
written consent of the applicable Company Released Party; provided, however,
that nothing in this Section 5.6 shall prohibit Executive from making any
disclosures to the extent legally required, provided that Executive notifies the
Company in advance of any such required disclosure and permits the Company to
take all steps it deems to be appropriate to prevent or limit such disclosure.
Without limiting the generality of the foregoing, Executive further acknowledges
and agrees that Executive shall remain bound by any agreement with the Company
or any other Company Released Party, relating to the Confidential Information
(or any portion thereof) or similar information, to which Executive is subject
as of the Execution Date.

5.6 Implementation. Executive agrees that, at all times following the Execution
Date, Executive shall sign any and all documents, certificates and other
instruments, and take any and all other actions reasonably requested by the
Company or any other Company Released Party, necessary to implement the terms of
this Agreement.

6. MISCELLANEOUS.

6.1 Notices. Any notices or other communications required or permitted hereunder
shall be given to the appropriate party at the address of such party specified
to the other party on the Execution Date or at such other address as such party
shall specify by ten (10) days advance written notice to the other party hereto.
Such notice shall be in writing and shall be deemed given: (i) upon personal
delivery; (ii) upon delivery by facsimile transmission with receipt confirmed if
sent during normal business hours; if not, then on the next business day;
(iii) if sent by certified or registered mail, postage prepaid, three (3) days
after the date of mailing; or (iv) one (1) day after deposit with a
nationally-recognized overnight courier, specifying next day delivery, with
verification of receipt.

6.2 Governing Law. This Agreement shall be construed in accordance with, and
governed in all respects by, the laws of the State of California as applied to
contracts to be performed entirely within such state between California
residents.

6.3 Injunctive Relief. The parties hereto acknowledge and agree that irreparable
harm would occur in the event of any breach of this Agreement and that there is
no adequate remedy at law for any breach of a party’s obligations hereunder
(including money damages). Accordingly, the parties expressly agree that, upon
any breach or threatened breach of this Agreement by any party, the other
parties hereto shall be entitled to obtain injunctive relief, including specific
performance, in addition to any available remedies at law, from any court of
competent jurisdiction, wherever located, without the requirement of posting a
bond.

6.4 Successors and Assigns. This Agreement shall bind the heirs, personal
representatives, successors, assigns, executors, and administrators of each
party, and inures to the benefit of each party, its agents, directors, officers,
employees, heirs, successors and assigns.

6.5 Amendments. No amendments or additions to this Agreement shall be binding
unless made in writing and signed by each of the parties hereto.

6.6 Severability. Except as expressly set forth in Section 4.4, if any provision
of this Agreement is held to be unenforceable under applicable law, each such
provision shall be excluded from this Agreement and the balance of the Agreement
shall be interpreted as if such provision were so excluded and shall be
enforceable in accordance with its terms.

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6.7 Entire Agreement. This Agreement constitutes the entire agreement among the
parties with respect to the subject matter hereof, and no party shall be liable
or bound to any other party in any manner by any warranties, representations or
covenants except as specifically set forth herein.

6.8 Counterparts. This Agreement may be executed in multiple counterparts, each
of which shall be deemed an original, but all of which together shall constitute
one and the same instrument. Delivery of an executed counterpart of this
Agreement by facsimile or electronic “.pdf” copies shall be equally as effective
as delivery of an original executed counterpart of this Agreement.

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IN WITNESS WHEREOF, the parties hereto have executed this SEPARATION AGREEMENT
AND RELEASE as of the Execution Date.

 

COMPANY: ACCELRYS, INC. /s/ Ken Coleman Ken Coleman Chairman, Board of Directors
EXECUTIVE: /s/ Mark J. Emkjer Mark J. Emkjer