Grand Canonical Monte Carlo - Brownian Dynamics algorithm
A novel computational algorithm based on Grand Canonical Monte Carlo (GCMC) and Brownian Dynamics (BD) has been developed 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 illustrated with simulations of simple test systems and of the OmpF porin of E coli.
W. IM, S. SEEFELD and B. ROUX, "A grand canonical monte carlo-Brownian dynamics algorithm for simulating ion channels", Biophys. J. 79, 788-801 (2000). [ PubMed ] [ pdf ]
W. IM and B. ROUX, "Ion Permeation and Selectivity of OmpF Porin: A Theoretical Study Based on Molecular Dynamics, Brownian Dynamics, and Continuum Electrodiffusion Theory.", J. Mol. Biol. 322, 851-869 (2002). [ PubMed ] [ pdf ]