Using FPGA Devices to Accelerate Biomolecular Simulations

Author

Alam, Sadaf R. ; Agarwal, Pratul K. ; Smith, Melissa C. ; Vetter, Jeffrey S. ; Caliga, David

Author_Institution

Oak Ridge Nat. Lab., TN

Volume

40

Issue

3

fYear

2007

fDate

3/1/2007 12:00:00 AM

Firstpage

66

Lastpage

73

Abstract

A field-programmable gate array implementation of a molecular dynamics simulation method reduces the microprocessor time-to-solution by a factor of three while using only high-level languages. The application speedup on FPGA devices increases with the problem size. The authors use a performance model to analyze the potential of simulating large-scale biological systems faster than many cluster-based supercomputing platforms

Keywords

biology computing; field programmable gate arrays; high level languages; microprocessor chips; molecular biophysics; FPGA device; biomolecular simulation; cluster-based supercomputing platform; field-programmable gate array; high-level language; large-scale biological system; microprocessor chip; molecular dynamics simulation method; Acceleration; Application software; Atomic measurements; Computational modeling; Electrostatics; Field programmable gate arrays; Microprocessors; Potential energy; Predictive models; Random access memory; Biomolecular simulations; FPGAs; reconfigurable computing;

fLanguage

English

Journal_Title

Computer

Publisher

ieee

ISSN

0018-9162

Type

jour

DOI

10.1109/MC.2007.108

Filename

4133999