SOLICITATION NOTICE
R -- Functional mechanisms of biomedically relevant membrane proteins
- Notice Date
- 12/13/2016
- Notice Type
- Combined Synopsis/Solicitation
- 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
- NHLBI-CSB-HL-2017-050-KEW
- Archive Date
- 1/3/2017
- Point of Contact
- Kyle Wisor, Phone: 3014023670, Jonathan M. Lear,
- E-Mail Address
-
Kyle.Wisor@nih.gov, john.lear@nih.gov
(Kyle.Wisor@nih.gov, john.lear@nih.gov)
- Small Business Set-Aside
- N/A
- Description
- (1) Action Code: Combined Synopsis/Solicitation (2) Date: December 13 (3) Year: 2016 (4) Contracting Office Zip Code: 20892 (5) Classification Code: R499 (6) Contracting Office Address: 6701 Rockledge Drive Rockledge II Bethesda, MD 20892 (7) Subject/Title: Functional mechanisms of biomedically relevant membrane proteins (8) Proposed Solicitation Number: NHLBI-CSB-HL-2017-050-KEW (9) Closing Response Date: 12/19/16 (10) Contact Point: Kyle Wisor, Contract Specialist (11) Contract Award and Solicitation Number: TBD (12) Contract Award Dollar Amount: TBD (13) Contract Line Item Number(s): TBD (14) Contractor Award Date: TBD (15) Contractor Name: TBD (16) Background: The National Institute of Health (NIH) is the nation's leading medical research agency and the primary Federal agency conducting, supporting and making medical discoveries that improve people's health and save lives. The National Heart, Lung, and Blood Institute (NHLBI) provides global leadership for a research, training, and education program to promote the prevention and treatment of heart, lung, and blood diseases and enhance the health of all individuals so that they can live longer and more fulfilling lives. The research program of the Theoretical Molecular Biophysics (TMB) section, NHLBI, is focused on elucidating the structural mechanisms of biomedically important molecular systems associated with cellular membranes, primarily using computationally-intensive, physics-based molecular simulations. To this end, a substantial effort is devoted to the development of novel quantitative approaches to characterize the structural dynamics and energetics of the molecular systems studied at the molecular level. New methodologies are implemented and disseminated in popular software tool-kits for advanced molecular simulation such as PLUMED (http://www.plumed.org/) and the Collective Variables Module [1, 2] (https://colvars.github.io/), both of which are publicly available and can be plugged-in into multiple software platforms usable on supercomputers, such as, LAMMPS (http://lammps.sandia.gov/), GROMACS (http://www.gromacs.org/), and NAMD (http://www.ks.uiuc.edu/Research/namd/) The proposed technical advances will greatly facilitate our ability to assess and rationalize the nature and controlling factors of the structural mechanisms underlying the biological function of proteins embedded and/or associated with cellular membranes. Furthermore, the dissemination of these methodologies through open-source software platforms will enable the community at large to benefit from this work. (i) "This is a combined synopsis/solicitation for commercial items prepared in accordance with the format in Subpart 12.6 as supplemented with additional information included in this notice. This announcement constitutes the only solicitation; quotes are being requested and a written solicitation will not be issued." (ii) The solicitation number is NHLBI-CSB-HL-2017-050-KEW and the solicitation is issued as a request for quote (RFQ). (iii) The solicitation document, the incorporated provisions and clauses are those in effect through Federal Acquisition Circular 2005-92 effective 18 NOV 2016. (iv) The associated NAICS code is 541712, Research and Development in the Physical, Engineering, and Life Sciences, and the small business size standard is 1,000 Employees. The acquisition is being conducted in accordance with the procedures of FAR Part 12 and 13. (v) The Contractor Requirements are listed below: Scope of Work: The contractor will provide technical assistance in the following projects: 1. Development of a local molecular-density descriptor. A new reaction coordinate will be designed following the general scheme proposed in a previous study [1]. The contractor will assist on identifying a suitable theoretical formulation of the aforementioned descriptor leading to a rigorous and more efficient implementation within the Collective Variables Module. In this regard, the contractor will help to devise a specific formulation of the descriptor in internal molecular coordinates, which will be particularly useful for applications to membrane proteins. 2. Implementation of the molecular density descriptor in the Collective Variables Module. Density-based descriptors are functions of the atomic coordinates of selected molecular species. In the case of a descriptor of the water/lipids density, the reaction coordinate is a function of a large number of atoms (tens of thousands) and hence the calculation of the descriptor at each time step in the course of a simulation is computationally demanding. The contractor will therefore also assist in the efficient implementation of the descriptor with a specific focus in selecting strategies to reduce the number atoms affecting the reaction coordinate at each time step, and in effective code parallelization. 3. Design and implementation of a reaction coordinate to accelerate lipid reorganization at the membrane/protein interface. Lipid exchange transitions usually occur on a time scale of hundreds of nanoseconds that is close to the limit of typical simulation times. A specific approach to accelerate lipid dynamics while preserving the correct structural properties of the membrane is currently lacking. Building upon the expertise of the contractor, he/she will help identify a suitable reaction coordinate for accelerating lipid exchange dynamics, coupling the lipid density descriptors with lipid order/disorder parameters. In this part of the project the contractor will also assist on the particular choice of the acceleration factor in order to minimally alter the membrane thermodynamics. 4. Validation and application using simplified models of membrane transporters and cellular membranes. The new tools will be initially tested on simplified protein and membrane models to assess the usefulness, efficiency and scalability of the techniques. The contractor will help to perform the initial tests and to set-up subsequent applications to simplified models. References 1. T. F. Miller III, E. Vanden-Eijnden, and D. Chandler. Solvent coarse-graining and the string method applied to the hydrophobic collapse of a hydrated chain. PNAS, 2007, 104: 14559-14564. Reporting Requirements While the contractor is on-site, weekly meetings will be held for review of the progress and possible reassignment of priorities to specific tasks to be accomplished. The contractor, in consultation with the TMB Principal Investigator and/or the designated project supervisor, must present a plan of work for the coming month and must prioritize the tasks to be accomplished in that period. The contractor must provide TMB 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, description of problems encountered, list of critical problems which might prevent successful completion of future tasks, tasks planned for the next month. Contractor Requirements 1. Knowledge of a wide range of numerical and computational techniques is required, including C and C++ programming languages. Knowledge and ability to utilize scripting languages is required. 2. General experience in the development, implementation and application of enhanced-sampling methods is required, as is specific knowledge of the program design of the Collective Variables Module (https://colvars.github.io/) and experience in implementing newly developed software into this module. Previous expertise in molecular-simulation studies of membrane protein systems is also required. A Ph.D. in Chemistry, Physics, Computer Science or similar is desired. (vi) Period of Performance Base Year: January 1, 2017 - September 30, 2017 Place of Performance: Most of the work on this contract shall take place in Building 50 of the NIH main campus (50 South Drive, Bethesda, MD 20892). The contractor will also be provided remote access to the computer system of the TMB section, for off-site work. (viii) The provision at FAR clause 52.212-1, Instructions to Offerors - Commercial Items, applies to this acquisition. (ix) The provision at FAR clause 52.212-2, Evaluation - Commercial Items, is applicable. Award will be made to the contractor providing the most advantageous quote to the Government, technical factors considered. Technical Factors: 1. Experience in the study of membrane protein systems and lipid membranes through advanced and/or enhanced-sampling molecular-simulation methods; 2. Experience in development and application of novel enhanced-sampling molecular-simulation methods; 3. Experience in the utilization and development of the Collective Variables Module; 4. Experience in the utilization and customization of molecular simulation software such as NAMD or GROMACS; 5. Experience in the development and implementation of high-level scientific software applications specific for molecular biophysics and structural biology. (x) FAR clause 52.212-3, Offeror Representations and Certifications - Commercial Items, is applicable. An offeror shall complete only paragraphs (b) of this provision if the offeror has completed the annual representations and certificates electronically via http://www.acquisition.gov. If an offeror has not completed the annual representations and certifications electronically at the System for Award Management (SAM) website, the offeror shall complete only paragraphs (c) through (p) of this provision. (xi) FAR clause at 52.212-4, Contract Terms and Conditions - Commercial Items, applies to this acquisition. (xii) FAR clause at 52.212-5, Contract Terms and Conditions Required to Implement Statutes or Executive Orders - Commercial Items, applies to this acquisition. Including the following clauses and Prohibitions:  52.219-28, Post Award Small Business Program Representation  52.222-3, Convict Labor  52.222-21, Prohibition of Segregated Facilities  52.222-26, Equal Opportunity  52.222-36, Equal Opportunity for Workers with Disabilities  52.222-50 Combating Trafficking in Persons  52.223-18, Encouraging Contractor Policies to Ban Text Messaging while Driving  52.225-13, Restrictions on Certain Foreign Purchases  52.222-53, Exemption from Application of the Service Contract Labor Standards to Contracts for Certain Services--Requirements (xiii) Additional Clauses:  52.232-39, Unenforceability of Unauthorized Obligations. (xiv) The Defense Priorities and Allocations System (DPAS) and assigned rating are not applicable. (xv) All responses must be received by December 19, 2016 at 9:00 AM EST and must reference number NHLBI-CSB-HL-2017-050-KEW. Responses may be submitted electronically to Kyle.Wisor@nih.gov or by U.S. mail to the National Heart, Lung, and Blood Institute, Office of Acquisitions, COAC Services Branch, 6701 Rockledge Drive, Suite 6150B, Bethesda, MD 20892-7902, Attention: Kyle Wisor. Phone: 301-827-7736; Fax responses will not be accepted (17) Place of Contract Performance: National Institutes of Health, NHLBI 50 South Drive Bethesda, MD 20892 (18) Set-aside Status: None
- Web Link
-
FBO.gov Permalink
(https://www.fbo.gov/spg/HHS/NIH/NHLBI/NHLBI-CSB-HL-2017-050-KEW/listing.html)
- Place of Performance
- Address: National Institutes of Health, NHLBI, 50 South Drive, Bethesda, Maryland, 20892, United States
- Zip Code: 20892
- Zip Code: 20892
- Record
- SN04350204-W 20161215/161213234452-b22ac17cc51e5801d3d420f19c6e0074 (fbodaily.com)
- Source
-
FedBizOpps Link to This Notice
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