Fast Method for DNA Simulations on Parallel Computers

Award Information
Agency:
Department of Health and Human Services
Branch
n/a
Amount:
$484,590.00
Award Year:
1995
Program:
SBIR
Phase:
Phase II
Contract:
n/a
Award Id:
22295
Agency Tracking Number:
22295
Solicitation Year:
n/a
Solicitation Topic Code:
n/a
Solicitation Number:
n/a
Small Business Information
Continuum Dynamics, Inc. (Currently CONTINUUM DYNAMICS INC)
P. O. Box 3073, Building 9A, Princeton, NJ, 08543
Hubzone Owned:
N
Minority Owned:
N
Woman Owned:
N
Duns:
n/a
Principal Investigator:
Kiat Chua
(310) 312-0085
Business Contact:
() -
Research Institution:
n/a
Abstract
TELEPHONE NUMBER: (609) 734-9282 AWARDEE NUMBER: 1 R43 GM50132-01 The ultimate goal is to develop advanced computational tools, based on finite element and fast hierarchical multipole methods, for the realistic, large-scale numerical simulation of polyelectrolyte DNA supercoils using high-performance parallel-processing supercomputers. DNA supercoiling is an important facet of biological processes that entail local helical unwinding or denaturation. Recent computer simulations have demonstrated the potential for clarifying the biological role of local structures and ligand binding on DNA super-coiling. The polyelectrolyte character of the DNA has not been included because of computational constraint. The present effort aims to develop a fast O(NlogN) method for the robust treatment of the polyelectrolyte effect in prototypical Monte Carlo and finite element computations. The method will be implemented on advanced parallel- processing platforms using a novel low-overhead communication strategy. The new strategy exploits the multi-level near-field/far-field structure of the fast hierarchical method to eliminate the globality of the electrostatic problem. The resulting computational tools will be designed to take full advantage of the computing power put forth by high-performance parallel-processing supercomputers and will serve to showcase a Grand Challenge application of High Performance Computing in large scale biological systems.

* information listed above is at the time of submission.

Agency Micro-sites


SBA logo

Department of Agriculture logo

Department of Commerce logo

Department of Defense logo

Department of Education logo

Department of Energy logo

Department of Health and Human Services logo

Department of Homeland Security logo

Department of Transportation logo

Enviromental Protection Agency logo

National Aeronautics and Space Administration logo

National Science Foundation logo
US Flag An Official Website of the United States Government