Computer simulation of ion conductance in membrane channels

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Abstract
We present a method for calculation of electric forces in biological channels, which facilitates microscopic modeling of ion transport in channels using computer simulation. The method is based on solving Poisson’s equation on a grid and storing the electric potential and field for various configurations in a table. During simulations, the potential and field at any point are calculated by interpolating between table entries rather than solving Poisson’s equation. This speeds up computer simulations by orders of magnitude with minimal loss in accuracy. With this method, one can run simulations long enough to determine the channel conductance, which can be compared directly with experimental data. Since conductance is the most important observable quantity in description of membrane channels, this method will be very useful in future simulation studies of channels.