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FBO DAILY - FEDBIZOPPS ISSUE OF MARCH 01, 2015 FBO #4845
SOLICITATION NOTICE

R -- Development, Testing, and Application of pH Simulation Methods for the Computational Biophysics Section (CBS)

Notice Date

2/27/2015
 

Notice Type

Presolicitation
 

NAICS

541712 — Research and Development in the Physical, Engineering, and Life Sciences (except Biotechnology)
 

Contracting Office

Department of Health and Human Services, National Institutes of Health, National Heart, Lung and Blood Institute, Rockledge Dr. Bethesda, MD, Office of Acquisitions, 6701 Rockledge Dr RKL2/6100 MSC 7902, Bethesda, Maryland, 20892-7902
 

ZIP Code

20892-7902
 

Solicitation Number

HHS-NIH-NHLBI-CSB-HI-2015-079-CDB
 

Archive Date

3/21/2015
 

Point of Contact

Chris Bocus, Phone: 3014027888
 

E-Mail Address

chris.bocus@nih.gov
(chris.bocus@nih.gov)
 

Small Business Set-Aside

N/A
 

Description

INTRODUCTION: THIS IS A PRE-SOLICITATION NON-COMPETITIVE (NOTICE OF INTENT) SYNOPSIS TO AWARD A PURCHASE ORDER WITHOUT PROVIDING FOR FULL OR OPEN COMPETITION (INCLUDING BRAND-NAME). The National Institutes of Health (NIH), National Heart, Lung, and Blood Institute (NHLBI), Office of Acquisitions (OA), on intends to negotiate and award a purchase order on a sole source noncompetitive basis to Johns Hopkins University, 3400 North Charles Street W400 Wyman Park Bldg., Baltimore, MD, 21218-2680 to provide research development, testing, and application services for pH simulation methods for the Computational Biophysics Section (CBS). PROCUREMENT: The contractor will provide technical assistance in the following projects: 1) Evaluating the accuracy of the newly developed constant pH algorithm based on enveloping distribution sampling and Hamiltonian replica exchange (EDS-HREX). The method has been recently developed and has only been applied to single amino acid residues, a small peptide and a small protein. The contractor will evaluate the accuracy of this method on calculation of pKa values on more challenging peptide and protein systems. 2) Develop and test new sampling methods based on the EDS-HREX, as it is anticipated that the EDS-HREX method will experience sampling problems. 3) Utilize EDS-HREX method for improving other simulation protocols, such as methods for calculations of binding free energies. 4) Study biologically and medically important systems with the newly developed simulation methods, or other relevant simulation methods. BACKGROUND: The mission of the NHLBI Division of Intramural Research (DIR) is to perform robust scientific and clinical research leading to a better understanding of biology and clinical pathology. To attain this goal, we have built a strong basic science foundation and coupled it closely with innovative technology development and outstanding clinical research both at the NIH Clinical Center and in partnership with local hospitals. The purview of our research is broad, encompassing investigations into the basic principles of molecular, cellular, and organ-level biology and their relationship to disease. Some current areas of fundamental interest include single molecule structure; protein assembly; molecular and cell biology; cell signaling and motility; membrane trafficking; physiology; systems biology; engineering and technology development. Insights into disease mechanisms derived from basic studies form the basis for translational research into new diagnostic and therapeutic approaches. DIR investigators also conduct concept-based clinical studies in the areas of interventional and surgical cardiology; pulmonary medicine; sickle cell anemia; bone marrow transplant; and hematologic disorders. The Computational Biophysics Section (CBS), National Heart, Lung and Blood Institute (NHLBI) of the National Institutes of Health (NIH) conducts a program to study problems of biological and medical significance using theoretical and computational techniques. The CBS is involved in development, maintenance and testing of new methods that will enable better description of such processes. These methods are implemented within the molecular modeling and simulation program CHARMM. This program is extensively used in the computational chemistry and computational biology communities, and has produced widely useful results. Development of new and improved methods for molecular dynamics (MD) simulations at constant pH has become an active area of research. Constant pH MD have a theoretical advantage over regular MD in that the protonation state of ionizable groups can change during the course of the trajectory. Constant pH simulations are also used for calculations of pKa values of ionizable groups. When it comes to calculations of pKa values, constant pH simulations directly sample protonation/deprotonation induced conformational changes, and thus have a theoretical advantage over more traditional continuum electrostatics calculations which are based on a single structure. Development of better methods for constant pH simulations will advance the field of molecular simulations and help in understanding of the pH driven processes in biology. Changes in intracellular pH regulate a number of normal and pathological cellular processes. For example, cytosolic and extracytosolic pH in cancerous tumors and in tissues under inflammatory response is different from normal cells and tissues. Furthermore, processes that involve transfer of protons are among the most fundamental energy transduction mechanisms in biological systems. They are essential for acid-base catalysis in enzymes, and for photosynthesis and respiration. PURPOSE AND OBJECTIVE: The purpose of this procurement is to work on development, testing and applications of better simulation methods that utilize the recently developed method for constant pH simulations in explicit solvent. ANTICIPATED PERIOD OF PERFORMANCE: Base: March 24, 2015 through March 23, 2016 Option Period 1: March 24, 2016 through March 23, 2017 Option Period 2: March 24, 2017 through March 23, 2018 JUSTIFICATION: The determination by the Government to award a contract without providing for full and open competition is based upon the market research conducted as prescribed in FAR Part 10-Market Research. The key personnel on Johns Hopkins has unique expertise that is critical to the success of the proposed work, involved in development and testing of novel methods for enhanced sampling in constant pH simulations in CHARMM. Additionally, the key personnel has extensive experience in the use of molecular dynamics simulations and program CHARMM, and authored 7 publications that utilize regular molecular dynamics, as well as enhanced sampling techniques in CHARMM. REGULATORY AUTHORITY: This acquisition is conducted under the authority of the Federal Acquisition Regulations (FAR) Subpart 13.106-1(b) Soliciting from a single source, only one responsible source and no other supplies or services will satisfy agency requirements. ADDITIONAL INFORMATION: Industry Classification (NAICS) Code is 541712, Research and Development in the Physical, Engineering, and Life Sciences (Except Biotechnology) and the Small Business Size Standard is 500 Employees. This acquisition is conducted under the procedures as prescribed in FAR subpart 13-Simplified Acquisition Procedures. The solicitation document, the incorporated provisions and clauses are those in the Federal Acquisition Circular 2005-78, effective December 26, 2014. The determination by the Government to award a purchase order on a sole source noncompetitive basis to provide research development, testing, and application services for pH simulation methods for the Computational Biophysics Section (CBS) to Johns Hopkins University, 3400 North Charles Street W400 Wyman Park Bldg., Baltimore, MD, 21218-2680, is based upon the market research conducted in accordance with one or more of the techniques specified in FAR Part 10-Market Research, Subpart 10.002(b)(2). This synopsis is not a request for competitive proposals. However, interested parties may identify their interest and capability to respond to this notice. Responses to this notice shall contain sufficient information to establish the interested parties' bona-fide capabilities for fulfilling the requirement and include: unit price, list price, shipping and handling costs, the delivery period after contract award, the prompt payment discount terms, the F.O.B. Point (Destination or Origin), the Dun & Bradstreet Number (DUNS), the Taxpayer Identification Number (TIN), and the certification of business size. All offerors must have an active registration in the System for Award Management (SAM) www.sam.gov." A determination by the Government not to compete this proposed contract based upon responses to this notice is solely within the discretion of the Government. The information received will normally be considered solely for the purposes of determining whether to proceed on a non-competitive basis or to conduct a competitive procurement. All responses must be received by March 6, 2015 at 12:00 p.m. EST. Responses must reference synopsis number HHS-NIH-NHLBI-CSB-HI-2015-079-CDB, may be submitted to the National, Heart, Lung and Blood Institute, Office of Acquisition, COAC Services Branch, 6701 Rockledge Drive, Rm 6207, Bethesda, Maryland 20892-7902, Attention: Chris Bocus. Response may be submitted electronically to chris.bocus@ nih.gov. Faxes will not be accepted. Responses will only be accepted if dated and signed by an authorized company representative. "All responsible sources may submit a bid, proposal, or quotation which shall be considered by the agency."
 

Web Link

FBO.gov Permalink
(https://www.fbo.gov/spg/HHS/NIH/NHLBI/HHS-NIH-NHLBI-CSB-HI-2015-079-CDB/listing.html)
 

Place of Performance

Address: Bethesda, Maryland, 20892, United States

Zip Code: 20892
 

Record

SN03655000-W 20150301/150228000725-c216ace55bfe2bd8de4254c90481912c (fbodaily.com)
 

Source

FedBizOpps Link to This Notice
(may not be valid after Archive Date)

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