Ion permeation in ion channel is a typical multiscale and multi-physics process. Continuum models are commonly used to combine with molecular model in order to bridge different scales and to take into account the average influence of solvent environment on biomolecules. We treat the ionic flow in a channel as a continuum electrodiffusion process. Electrodiffusion also exists in many physical objects such as semiconductor, electrolyte cell, nanofluidic device, charged porous media. Ion flow in a 3D 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). I will talk about our finite element simulation framework for this research project. In the first part, I'll briefly introduce the Poisson-Nernst-Planck model, some improved forms, and the numerical strategies we have developed/implemented. The second part describes the issue of molecular surface/volume mesh generation and our meshing tool which is essential for finite/boundary element simulations. In the third part, I will show a visualization system, VCMM, which specifically designed to facilitate researches in this area, especially using finite/boundary element methods. Finally, illustrations will be given to compute properties such as molecular electrostatics, ionic size effects, and current-voltage characteristics of some ion channel systems. Some results are also compared with those from experimental data and Brownian dynamic simulations.

Finite element simulation of ion transport in ion channel: Model, numerics, and software platform

248th National Meeting (2014)

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