摘要
本文介绍一个面向生物分子模拟的并行有限元解法器,该解法器基于三维并行自适应有限元软件平台PHG^([1]),计算并模拟在生物溶液系统在静电场下的扩散过程.该解法器的最新版本在已有算法的基础上^([2]),添加了整体求解、含时求解等一些新算法,规范并扩展了边界条件的选取,并整合多项辅助功能,现提供对于Poisson-Nernst-Planck(PNP)方程的两个含时算法和四个稳态算法,以及对于Smoluchowski-Poisson-Boltzmann(SPB)方程的一个稳态算法.解法器可模拟生物分子,离子通道和纳米管等模型,通过有限元方法计算静电场和离子浓度分布,并计算电流强度、反应速率等物理量,可研究离子通道的选择机理,酶的催化反应过程及反应速率等问题.相关软件、工具和进展见www.continuummodel.org.
In this paper a parallel finite element solver for biomolecular simulations is introduced. This solver is based on the three dimensional parallel finite element toolbox PHG and able to simulate the diffusion process influenced by electrostatic field in biological solution. The solver is developed from our previous work with new algorithms added, now offering two time-dependent algorithms and four steady-state algorithms for the Poisson-Nernst-Planck equations, while one steady-state algorithm is provided for Smoluchowski-Poisson-Boltzmann equations. The solver is able to simulate the biomolecular models, including ion channel and nanopore, and solve electrostatic field and concentration distributions for all species. Furthermore, current and reaction rate is calculated to study the functions of ion channel and enzyme.
出处
《数值计算与计算机应用》
CSCD
2016年第1期67-82,共16页
Journal on Numerical Methods and Computer Applications
关键词
解法器
PHG
生物溶液
静电场
扩散
算法
solver
PHG
biological solution
electrostatic field
diffusion
algorithm
