FFTSVD: A Fast Multiscale Boundary-Element Method Solver Suitable for Bio-MEMS and Biomolecule Simulation

Authors:
M. D. Altman;J. P. Bardhan;B. Tidor;J. K. White
Affiliations:
-;-;-;-
Venue:
IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems
Year:
2006

Citing 0
Cited 4

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Fast Analytical Methods for Macroscopic Electrostatic Models in Biomolecular Simulations

SIAM Review

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Abstract

This paper presents a fast boundary-element method (BEM) algorithm that is well suited for solving electrostatics problems that arise in traditional and bio-microelectromechanical systems (bio-MEMS) design. The algorithm, FFTSVD, is Green's-function-independent for low-frequency kernels and efficient for inhomogeneous problems. FFTSVD is a multiscale algorithm that decomposes the problem domain using an octree and uses sampling to calculate low-rank approximations to dominant source distributions and responses. Long-range interactions at each length scale are computed using the FFT. Computational results illustrate that the FFTSVD algorithm performs better than precorrected-FFT (pFFT)-style algorithms or the multipole-style algorithms in FastCap.