Fast methods for simulation of biomolecule electrostatics

Author

Kuo, Shihhsien S. ; Altman, Michael D. ; Bardhan, Jaydeep P. ; Tidor, Bruce ; White, Jacob K.

Author_Institution

Dept. of Electr. Eng. & Comput. Sci., MIT, Cambridge, MA, USA

fYear

2002

fDate

10-14 Nov. 2002

Firstpage

466

Lastpage

473

Abstract

Computer simulation is an important tool for improving our understanding of biomolecule electrostatics, in part to aid in drug design. However, the numerical techniques used in these simulation tools do not exploit fast solver approaches widely used in analyzing integrated circuit interconnects. In this paper we describe one popular formulation used to analyze biomolecule electrostatics, present an integral formulation of the problem, and apply the precorrected-FFT method to accelerate the solution of the integral equations.

Keywords

electrostatics; fast Fourier transforms; integral equations; medical computing; molecular biophysics; numerical analysis; biomolecule electrostatics simulation methods; computer simulation; drug design; fast solver approaches; integral equations; integrated circuit interconnects; numerical techniques; precorrected-FFT method; simulation tools; Analytical models; Circuit analysis; Circuit simulation; Computational modeling; Computer simulation; Drugs; Electrostatics; Integral equations; Integrated circuit interconnections; Molecular biophysics;

fLanguage

English

Publisher

ieee

Conference_Titel

Computer Aided Design, 2002. ICCAD 2002. IEEE/ACM International Conference on

ISSN

1092-3152

Print_ISBN

0-7803-7607-2

Type

conf

DOI

10.1109/ICCAD.2002.1167573

Filename

1167573