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Fast Method for DNA Simulations on Parallel Computers

Award Information

Department of Health and Human Services
Award ID:
Program Year/Program:
1995 / SBIR
Agency Tracking Number:
Solicitation Year:
Solicitation Topic Code:
Solicitation Number:
Small Business Information
Continuum Dynamics, Inc.
34 Lexington Avenue Ewing, NJ 08618-2302
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Woman-Owned: No
Minority-Owned: No
HUBZone-Owned: No
Phase 2
Fiscal Year: 1995
Title: Fast Method for DNA Simulations on Parallel Computers
Agency: HHS
Contract: N/A
Award Amount: $484,590.00


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.

Principal Investigator:

Kiat Chua

Business Contact:

Small Business Information at Submission:

Continuum Dynamics, Inc.
P. O. Box 3073, Building 9A Princeton, NJ 08543

Number of Employees: N/A
Woman-Owned: No
Minority-Owned: No
HUBZone-Owned: No