Fast methods for simulation of biomolecule electrostatics

  • Authors:

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

  • Affiliations:

  • Massachusetts Institute of Technology, Cambridge, MA;Massachusetts Institute of Technology, Cambridge, MA;Massachusetts Institute of Technology, Cambridge, MA;Massachusetts Institute of Technology, Cambridge, MA;Massachusetts Institute of Technology, Cambridge, MA

  • Venue:
  • Proceedings of the 2002 IEEE/ACM international conference on Computer-aided design
  • Year:
  • 2002

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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.