an automatic three-dimensional finite element mesh generation system for the poisson-boltzmann equation文档.pdf

— — An Automatic Three-Dimensional Finite Element Mesh Generation System for the Poisson Boltzmann Equation 1 2 CHRISTIAN M. CORTIS, * RICHARD A. FRIESNER 1Department of Applied Physics and Center for Biomolecular Simulation, Columbia University, New York, New York 10027 2 Department of Chemistry and Center for Biomolecular Simulation, Columbia University, New York, New York 10027 Received 3 September 1996; accepted 12 March 1997 ABSTRACT: We present an automatic three-dimensional mesh generation system for the solution of the Poisson Boltzmann equation using a finite element discretization. The different algorithms presented allow the construction of a tetrahedral mesh using a predetermined spatial distribution of vertices adapted to the geometry of the dielectric continuum solvent model. A constrained mesh generation strategy, based on Bowyer’s algorithm, is used to construct the tetrahedral elements incrementally and embed the Richards surface of the molecule into the mesh as a set of triangular faces. A direct mesh construction algorithm is then used to refine the existing mesh in the neighborhood of the dielectric interface. This will allow an accurate calculation of the induced polarization charge to be carried out while maintaining a sparse