Fast methods for simulation of biomolecule electrostatics

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.

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INDEX TERMS

Primary Classification:
  B. Hardware
  B.6 LOGIC DESIGN
      B.6.3 Design Aids
          Subjects: Simulation

Additional Classification:
  D. Software
  D.2 SOFTWARE ENGINEERING
      D.2.2 Design Tools and Techniques

          Nouns: Delphi

  G. Mathematics of Computing
  G.1 NUMERICAL ANALYSIS
      G.1.9 Integral Equations
          Subjects: Integro-differential equations

General Terms:
Experimentation, Measurement, Theory