Title :
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
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;
Conference_Titel :
Computer Aided Design, 2002. ICCAD 2002. IEEE/ACM International Conference on
Print_ISBN :
0-7803-7607-2
DOI :
10.1109/ICCAD.2002.1167573
