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BioMOCA: A Transport Monte Carlo Approach to Ion Channel Simulation

T.A. van der Straaten, G. Kathawala and U. Ravaioli
Beckman Institute, University of Illinois, US

Keywords: ion channels, Monte-Carlo simulation, nanodevices

Abstract:
Ion channels are highly charged proteins found in the cell membrane, which regulate ion transport to the cell. Most channels switch between conducting and non-conducting states and many can selectively transmit or block a particular ion species. Some perform specialized functions similar to complex electronic systems. The possibility of embedding ion channels in electronic circuits may therefore have broad technological impact. Simulation of conduction in ion channels in atomic detail is difficult because ion traversal through the channel is a rare event. Transport must be resolved on a femtosecond scale, while macroscopic conduction occurs over microseconds. Molecular Dynamics is the most popular tool for studying ion channels but the computational requirements limit simulations to nanosecond timescales. Drift-diffusion models can compute macroscopic current quickly but sacrifice molecular detail. We describe a 3-D ion channel simulator, BioMOCA, based on the transport Monte Carlo methodology. Water, protein and membrane are treated as dielectric media, drastically reducing computational load. Ion trajectories are traced as sequences of free flights interrupted by scattering events. Ion size is included using a Lennard-Jones potential. Simulation results are reported for two different channels, gramicidin and ompF porin.

Nanotech 2004 Conference Technical Program Abstract

 
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