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Title: Predicting Function of Biological Macromolecules: A Summary of LDRD Activities: Project 10746

Abstract

This LDRD project has involved the development and application of Sandia's massively parallel materials modeling software to several significant biophysical systems. They have been successful in applying the molecular dynamics code LAMMPS to modeling DNA, unstructured proteins, and lipid membranes. They have developed and applied a coupled transport-molecular theory code (Tramonto) to study ion channel proteins with gramicidin A as a prototype. they have used the Towhee configurational bias Monte-Carlo code to perform rigorous tests of biological force fields. they have also applied the MP-Sala reacting-diffusion code to model cellular systems. Electroporation of cell membranes has also been studied, and detailed quantum mechanical studies of ion solvation have been performed. In addition, new molecular theory algorithms have been developed (in FasTram) that may ultimately make protein solvation calculations feasible on workstations. Finally, they have begun implementation of a combined molecular theory and configurational bias Monte-Carlo code. They note that this LDRD has provided a basis for several new internal (e.g. several new LDRD) and external (e.g. 4 NIH proposals and a DOE/Genomes to Life) proposals.

Authors:
; ; ; ; ; ; ;
Publication Date:
Research Org.:
Sandia National Labs., Albuquerque, NM (US); Sandia National Labs., Livermore, CA (US)
Sponsoring Org.:
US Department of Energy (US)
OSTI Identifier:
805869
Report Number(s):
SAND2002-3743
TRN: US200303%%346
DOE Contract Number:  
AC04-94AL85000
Resource Type:
Technical Report
Resource Relation:
Other Information: PBD: 1 Nov 2002
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; ALGORITHMS; CELL MEMBRANES; DNA; IMPLEMENTATION; LIPIDS; MEMBRANES; PROTEINS; SOLVATION

Citation Formats

FRINK, LAURA J. D., REMPE, SUSAN L, MEANS, SHAWN A, STEVENS, MARK J, CROZIER, PAUL S, MARTIN, MARCUS G, SEARS, MARK P, and HJALMARSON, HAROLD P. Predicting Function of Biological Macromolecules: A Summary of LDRD Activities: Project 10746. United States: N. p., 2002. Web. doi:10.2172/805869.
FRINK, LAURA J. D., REMPE, SUSAN L, MEANS, SHAWN A, STEVENS, MARK J, CROZIER, PAUL S, MARTIN, MARCUS G, SEARS, MARK P, & HJALMARSON, HAROLD P. Predicting Function of Biological Macromolecules: A Summary of LDRD Activities: Project 10746. United States. doi:10.2172/805869.
FRINK, LAURA J. D., REMPE, SUSAN L, MEANS, SHAWN A, STEVENS, MARK J, CROZIER, PAUL S, MARTIN, MARCUS G, SEARS, MARK P, and HJALMARSON, HAROLD P. Fri . "Predicting Function of Biological Macromolecules: A Summary of LDRD Activities: Project 10746". United States. doi:10.2172/805869. https://www.osti.gov/servlets/purl/805869.
@article{osti_805869,
title = {Predicting Function of Biological Macromolecules: A Summary of LDRD Activities: Project 10746},
author = {FRINK, LAURA J. D. and REMPE, SUSAN L and MEANS, SHAWN A and STEVENS, MARK J and CROZIER, PAUL S and MARTIN, MARCUS G and SEARS, MARK P and HJALMARSON, HAROLD P},
abstractNote = {This LDRD project has involved the development and application of Sandia's massively parallel materials modeling software to several significant biophysical systems. They have been successful in applying the molecular dynamics code LAMMPS to modeling DNA, unstructured proteins, and lipid membranes. They have developed and applied a coupled transport-molecular theory code (Tramonto) to study ion channel proteins with gramicidin A as a prototype. they have used the Towhee configurational bias Monte-Carlo code to perform rigorous tests of biological force fields. they have also applied the MP-Sala reacting-diffusion code to model cellular systems. Electroporation of cell membranes has also been studied, and detailed quantum mechanical studies of ion solvation have been performed. In addition, new molecular theory algorithms have been developed (in FasTram) that may ultimately make protein solvation calculations feasible on workstations. Finally, they have begun implementation of a combined molecular theory and configurational bias Monte-Carlo code. They note that this LDRD has provided a basis for several new internal (e.g. several new LDRD) and external (e.g. 4 NIH proposals and a DOE/Genomes to Life) proposals.},
doi = {10.2172/805869},
journal = {},
number = ,
volume = ,
place = {United States},
year = {2002},
month = {11}
}

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