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.
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Groupe de Recherche en Transport Membranaire (GRTM), Départements de Physique et de Chimie, Université de Montréal, Montreal, Quebec H3C 3J7, Canada.
Seefeld
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Roux
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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