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Stochastic multi-particle Brownian Dynamics simulation of biological ion channels: A Finite Element approach

Biological ion channels are protein tubes that span the cell membrane. They provide a conduction pathway and regulate the flow of ions though the low dielectric membrane. Modeling the dynamics of these channels is crucial in understanding their functionality. This paper proposes a novel simulation framework for modeling ion channels that is based on Finite Element Method (FEM). By using FEM, this is the first framework to allow the use of multiple dielectric constants inside the channel thus providing a more realistic model of the channel. Due to the run-time complexity of the problem, lookup tables must be constructed in memory to store pre-calculated electric potential information. Because of the large number of elements involved in FEM and channel resolution requirements there is the potential for very large lookup tables leading to a performance “bottleneck”. This paper discusses strategies for minimizing table size and shows that currently available personal computers are sufficient for attaining reasonable levels of accuracy. For the framework proposed, results show diminishing returns in accuracy with tables sized greater than 2.2 GB.