AN AUTOMATIC 3-DIMENSIONAL FINITE-ELEMENT MESH GENERATION SYSTEM FOR THE POISSON-BOLTZMANN EQUATION

We present an automatic three-dimensional mesh generation system for t he solution of the Poisson-Boltzmann equation using a finite element d iscretization. The different algorithms presented allow the constructi on 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 algor ithm, is used to construct the tetrahedral elements incrementally and embed the Richards surface of the molecule into the mesh as a set of t riangular faces. A direct mesh construction algorithm is then used to refine the existing mesh in the neighborhood of the dielectric interfa ce. This will allow an accurate calculation of the induced polarizatio n charge to be carried out while maintaining a sparse grid structure i n the rest of the computational space. The inclusion of an ionic bound ary at some finite distance from the dielectric interface can be autom atically achieved as the grid point distribution outside the solute mo lecule is constructed using a set of surfaces topologically equivalent to this boundary. The meshes obtained by applying the algorithm to re al molecular geometries are described. (C) 1997 John Wiley & Sons, Inc .