Scientific Support Services

Added: Mar 16, 2017 4:36 pm INTRODUCTION

THIS IS A PRE-SOLICITATION NON-COMPETITIVE (NOTICE OF INTENT) SYNOPSIS TO AWARD A PURCHASE ORDER WITHOUT PROVIDING FOR FULL OR OPEN COMPETITION.

The National Heart, Lung, and Blood Institute (NHLBI), Office of Acquisitions (OA), intends to negotiate and award a purchase order on a noncompetitive sole source basis to the University of Maryland, Office of Sponsored Programs, 620 West Lexington Street, 4th Floor, Baltimore, MD 21201 to provide scientific support services to the NHLBI Division of Intramural Research (DIR) in accordance with the following information.

BACKGROUND

The National Institutes of Health (NIH), National Heart, Lung, and Blood Institute (NHLBI), Computational Biophysics Section (CBS) 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, including the explicit treatment of electronic polarization, represent the next generation of empirical force fields. In addition, combining explicit polarization with a multipole representation of the underlying charge distribution is anticipated to lead to additional accuracy in the model. Such advances are anticipated to yield improved models of the structure and dynamics of macromolecules including protein and nucleic acids. In addition, such models have the potential to significantly improve computer-aided drug design, thereby leading to more rapid development of improved therapeutic agents.

PURPOSE

From a theoretical perspective, the explicit treatment of electronic polarizability in combination with a multipole model of the underlying electron distribution clearly present an improvement over the empirical force fields used in traditional MD simulations and will thus have an impact on the entire field of molecular simulations. In practice, however, implementation of a new force field is a significant task requiring studies initially on small model compounds ultimately leading to models suitable for proteins. Furthermore, new methods for empirical force field optimization are needed. The purpose of this work is to develop and test a novel empirical force field that includes a multipole representation of the static charge distribution in combination with the explicit treatment of electronic polarizability using either the induced dipole or classical Drude oscillator models. The work will be presented in form of a publication in a scientific journal.

TASKS TO BE PERFORMED

The contractor shall provide technical assistance in the following projects:

1) Optimization of an empirical force field that contains a multipole representation of the static charge distribution in combination with the explicit treatment of electronic polarizability for water and small molecules representative of biological macromolecules. This will subsequently be extended to proteins and nucleic acids.

2) Evaluating the accuracy of the newly developed empirical force field against both quantum mechanical and experimental data. This will include thermodynamics properties as well as the structure and dynamics of proteins, DNA and RNA.

3) Application of the empirical force field to study the cooperativity of peptide and protein folding, in calculation of the pKa of protein residues and on the melting of DNA and RNA.

REPORTING REQUIREMENTS AND DELIVERABLES

The contractor, in consultation with CBS chief, must present a plan of work for the first month and must prioritize the tasks to be accomplished in that time. The contractor must provide CBS/LBC officials with a written, monthly status report, detailing the activity and progress made on tasks during the previous month. These reports will describe major accomplishments, descriptions of problems encountered, lists of critical problems which might prevent successful completion of future tasks, and tasks for the future month.

All the work on this contract shall take place on-site at Building 5635FL, 5635 Fishers Ln, in Rockville, MD. Once a week meetings will be required on site for review of the progress and possible re-assignment of priorities to specific tasks accomplished.

PERIOD OF PERFORMANCE

The period of performance will be one (1) year from the date of contract award.

JUSTIFICATION

The technical and scientific goals and deliverables required under this contract require an individual who is highly experienced with empirical force field development and optimization, enhanced sampling techniques, the program CHARMM, and molecular dynamics simulations.

Dr. Jing Huang at the University of Maryland has unique expertise that is critical to the success of the proposed work - he was involved in the validation the CHARMM36 force field against NMR data and was part of the team that developed the classical Drude oscillator polarizable force field. He then applied this model to investigate the cooperative folding of peptides, including the use of explicit solvent simulations. These studies have been published in the Journal of Computational Chemistry, Journal of Chemical Theory, and Computation and the Biophysical Journal. In addition, he has an extensive experience in the use of molecular dynamics simulations and the program CHARMM including the development and use of 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. (1) For purchases not exceeding the simplified acquisition threshold, contracting officers may solicit from one source if the contracting officer determines that the circumstances of the contract action deem only one source reasonably available (e.g., urgency, exclusive licensing agreements, or industrial mobilization).

ADDITIONAL INFORMATION

The North American Industry Classification System (NAICS) Code is 541990, All Other Professional, Scientific, and Technical Services, and the Small Business Size Standard is $15.0M. This acquisition is being conducted under FAR Part 13, Simplified Acquisition Procedures, therefore the requirements of FAR Part 6, Competitive Requirements, are not applicable and the resultant award will include all applicable provisions and clauses in effect through the Federal Acquisition Circular (FAC) 05-95 (January 19, 2017).

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 24, 2017 at 12:00pm EST and must reference synopsis number NHLBI-CSB-HL-2017-073-JML. Responses shall be submitted to the National Heart, Lung, and Blood Institute, Office of Acquisitions, COAC Services Branch, 6701 Rockledge Drive, Room 6151, Bethesda, Maryland 20892-7902, Attention: Jonathan M. Lear. Responses may be submitted electronically to john.lear@nih.gov. 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.