An asymmetric approach to modeling ion channels using finite element analysis

Biological ion channels are water filled pores in the cell membrane. They regulate the flow of ions in and out of the cell. Modeling the dynamics of these channels and relating their structure to functionality is crucial in understanding the mechanisms by which they conduct. This paper proposes a novel Finite Element Method (FEM) based simulation framework for modeling of ion channels that does not assume channel symmetry. This is the first framework that allows the use of multiple dielectric constants inside such channels without assuming geometrical symmetry 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. The large number of elements involved in FEM and channel resolution requirements can potentially result in very large lookup tables leading to a performance ldquobottleneckrdquo. This paper answers the following question: Does the accuracy introduced by using an asymmetric model outweigh the inaccuracy caused by having to reduce the size and resolution of electric-field look-up tables? This paper compares the memory footprint of an ion channel simulator that assumes a symmetric channel model versus an asymmetric model. We show that currently available personal computers are sufficient for attaining reasonable levels of accuracy for both. Our results show diminishing returns in accuracy with tables sized greater than 8.5 GB for the asymmetric model.