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BioMOCA

By Reza Toghraee1, Umberto Ravaioli1

1. University of Illinois at Urbana-Champaign

Ion channel simulator

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Version 1 - published on 02 May 2006

doi:10.4231/D3804XJ5W cite this

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Abstract

With the recent availability of high-resolution structure information for several key ion channel proteins and large-scale computational resources, Molecular Dynamics has become an increasingly popular tool for ion channel simulation. However, the CPU requirements for simulating ion transport on time scales relevant to conduction still exceed the resources presently available. To address the problem, we have developed Biology Monte Carlo (BioMOCA), a three-dimensional coarse-grained particle ion channel simulator based on the Boltzmann Transport Monte Carlo (BTMC) methodology.

screencapture

The BioMOCA code has progressed steadily to become a flexible tool for investigation of ionic transport that can be used as a complement of more expensive Molecular Dynamics simulations. The picture shown here on the left contains results from a simulation of ompf porin ionic channel. The volumes occupied by traversal trajectories followed by a K+ ion (green) and a Cl− ion (grey) show how cation and anion occupy different portion of the pore, reflecting the highly charge nature of the protein forming the channel. Available Molecular Dynamics simulations can only give a hint of such behavior, since time-resolution is restricted by computational cost. The information is very valuable for the analysis of pioneering devices that incorporate membranes with porin channels. A prototype device has been realized recently, for instance, at Arizona State University.

Credits

Computational Electronics Group, University of Illinois at Urbanca-Champign. This work funded by NSF.

Cite this work

Researchers should cite this work as follows:

  • T.A. Vad Der Straaten, G. Kathawala, A. Trellakis, R.S. Eisenberg, and U. Ravaioli, "BioMOCA - a Boltzmann transport Monte Carlo model for ion channel simulations," Molecular Simulatin, Vol. 31, No. 2-3, pp 151-171 (2005).
  • Reza Toghraee; Umberto Ravaioli (2006), "BioMOCA," https://nanohub.org/resources/biomoca. (DOI: 10.4231/D3804XJ5W).

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