An Adaptive,Finite Difference Solver for the Nonlinear Poisson-Boltzmann Equation with Applications to Biomolecular Computations  

作　　者：Mohammad Mirzadeh Maxime Theillard Asdis Helgadottir David Boy Frederic Gibou 

机构地区：[1]Department of Mechanical Engineering,University of California,Santa Barbara,CA 93106,USA [2]Department of Computer Science,University of California,Santa Barbara,CA 93106,USA

出　　处：《Communications in Computational Physics》2013年第1期150-173,共24页计算物理通讯（英文）

基　　金：supported in part by the W.M.Keck Foundation,by the Institute for Collaborative Biotechnologies through contract no.W911NF-09-D-0001 from the U.S.Army Research Office;by ONR under grant agreement N00014-11-1-0027;by the National Science Foundation under grant agreement CHE 1027817;by the Department of Energy under grant agreement DE-FG02-08ER15991.

摘　　要：We present a solver for the Poisson-Boltzmann equation and demonstrate its applicability for biomolecular electrostatics computation.The solver uses a level set framework to represent sharp,complex interfaces in a simple and robust manner.It also uses non-graded,adaptive octree grids which,in comparison to uniform grids,drastically decrease memory usage and runtime without sacrificing accuracy.The basic solver was introduced in earlier works[16,27],and here is extended to address biomolecular systems.First,a novel approach of calculating the solvent excluded and the solvent accessible surfaces is explained;this allows to accurately represent the location of the molecule’s surface.Next,a hybrid finite difference/finite volume approach is presented for discretizing the nonlinear Poisson-Boltzmann equation and enforcing the jump boundary conditions at the interface.Since the interface is implicitly represented by a level set function,imposing the jump boundary conditions is straightforward and efficient.

关 键 词：POISSON-BOLTZMANN non-graded adaptive grid octree data structure level set irregular domain hybrid finite volume/finite difference 

分 类 号：O17[理学—数学]