Finite element simulation of 3D ion channel systems: continuum model, numerical method, and software platform
主 题: Finite element simulation of 3D ion channel systems: continuum model, numerical method, and software platform
报告人: 卢本卓研究员 (中国科学院计算数学与科学工程计算研究所)
时 间: 2013-10-14 16：00-17:00
地 点: 全斋29（主持人：张磊）
As it is hard to apply all-atomic model to simulate the whole process of ion permeation in ion channel, we use continuum electrodiffusion description for ion flow in the channel system. Electrodiffusion process exists in many apparently different physical objects such as electrolyte cell, nanofluidic device, charged porous media, and ion channel in biology. Real 3D ion channel is particularly difficult to simulate due to the multiscale nature of the transport process, the complex geometry/boundary of the channel protein system, and the singular charge distribution inside the channel protein(s). For those reasons, there are so far only a very few softwares publicly available in this important area of biology. We will show our recent relevant works and a complete tool chain that forms a software platform for molecular structure-based study of ion permeation in a channel. In the first part, we’ll talk about the continuum models and numerical works. They include the Poisson-Boltzmann equation, the Poisson-Nernst-Planck equations and their improved forms, and some efficient algorithms we developed for the solution of these equations. In the second part, we will describe the molecular meshing problem which is essential for finite/boundary element modelings. We recently developed a novel and robust mesh generation tool TMSmesh that can practically handle complex and arbitrarily large biomolecular system. In the third part, I will briefly introduce a visualization system, VCMM, which is under development and will facilitate researches in this area. Finally, we will show applications using our parallel finite element solver to compute properties such as current-voltage characteristics (I-V curves) and conductance to a few channel systems. The results agree well with those obtained with Brownian Dynamics simulations and experiments.