A Grand Canonical Monte Carlo-Brownian dynamics algorithm for simulating ion channels.
A computational algorithm based on Grand Canonical Monte Carlo (GCMC) and Brownian Dynamics (BD) is described to simulate the movement of ions in membrane channels. The proposed algorithm, GCMC/BD, allows the simulation of ion channels with a realistic implementation of boundary conditions of concentration and transmembrane potential. The method is consistent with a statistical mechanical formulation of the equilibrium properties of ion channels (; Biophys. J. 77:139-153). The GCMC/BD algorithm is illustrated with simulations of simple test systems and of the OmpF porin of Escherichia coli. The approach provides a framework for simulating ion permeation in the context of detailed microscopic models.
Groupe de Recherche en Transport Membranaire (GRTM), Départements de Physique et de Chimie, Université de Montréal, Montreal, Quebec H3C 3J7, Canada.
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Im
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Seefeld
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Roux
D000465:Algorithms; D002462:Cell Membrane / Q000502:physiology*; D003196:Computer Graphics; D003198:Computer Simulation; D004926:Escherichia coli / Q000502:physiology; D007473:Ion Channels / Q000737:chemistry* / Q000502:physiology*; D007700:Kinetics; D008564:Membrane Potentials / Q000502:physiology; D008954:Models, Biological; D008958:Models, Molecular; D009010:Monte Carlo Method; D018272:Porins / Q000502:physiology*; D011487:Protein Conformation
D007473:Ion Channels; C109237:OmpF protein; D018272:Porins