A Fast and Robust Poisson-Boltzmann Solver Based on Adaptive Cartesian Grids.

ABSTRACT: An adaptive Cartesian grid (ACG) concept is presented for the fast and robust numerical solution of the 3D Poisson-Boltzmann Equation (PBE) governing the electrostatic interactions of large-scale biomolecules and highly charged multi-biomolecular assemblies such as ribosomes and viruses. The ACG offers numerous advantages over competing grid topologies such as regular 3D lattices and unstructured grids. For very large biological molecules and multi-biomolecule assemblies, the total number of grid-points is several orders of magnitude less than that required in a conventional lattice grid used in the current PBE solvers thus allowing the end user to obtain accurate and stable nonlinear PBE solutions on a desktop computer. Compared to tetrahedral-based unstructured grids, ACG offers a simple

SUBMITTER: Boschitsch AH 

PROVIDER: S-EPMC3188438 | biostudies-literature | 2011 May

REPOSITORIES: biostudies-literature