Biophysical Journal 73: 1830-1841 (1997)
© 1997 the Biophysical Society

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Computation of molecular electrostatics with boundary element methods.

National Center for Supercomputing Applications, Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, Urbana 61801, USA.

ABSTRACT

In continuum approaches to molecular electrostatics, the boundary element method (BEM) can provide accurate solutions to the Poisson-Boltzmann equation. However, the numerical aspects of this method pose significant problems. We describe our approach, applying an alpha shape-based method to generate a high-quality mesh, which represents the shape and topology of the molecule precisely. We also describe an analytical method for mapping points from the planar mesh to their exact locations on the surface of the molecule. We demonstrate that derivative boundary integral formulation has numerical advantages over the nonderivative formulation: the well-conditioned influence matrix can be maintained without deterioration of the condition number when the number of the mesh elements scales up. Singular integrand kernels are characteristics of the BEM. Their accurate integration is an important issue. We describe variable transformations that allow accurate numerical integration. The latter is the only plausible integral evaluation method when using curve-shaped boundary elements.