title: Brownian dynamics simulation for modeling ion permeation across bionanotubes.
abstract: The principles underlying Brownian dynamics (BD), its statistical consistency, and algorithms for practical implementation are outlined here. The ability to compute current flow across ion channels confers a distinct advantage to BD simulations compared to other simulation techniques. Thus, two obvious applications of BD ion channels are in calculation of the current-voltage and current-concentration curves, which can be directly compared to the physiological measurements to assess the reliability of the model and predictive power of the method. We illustrate how BD simulations are used to unravel the permeation dynamics in two biological ion channels-the KcsA K+ channel and CIC Cl- channel.
authors.affiliation: Department of Electrical and Computer Engineering, University of British Columbia, Vancouver, BC V6T 1Z4, Canada. vikramk@ece.ubc.ca
authors.forename: Vikram
authors.initials: V
authors.lastname: Krishnamurthy
authors.forename: Shin-Ho
authors.initials: SH
authors.lastname: Chung
mesh_terms: D002462:Cell Membrane / Q000737:chemistry* / Q000502:physiology*; D002463:Cell Membrane Permeability / Q000502:physiology*; D003198:Computer Simulation; D004058:Diffusion; D015640:Ion Channel Gating / Q000502:physiology*; D007473:Ion Channels / Q000737:chemistry / Q000502:physiology*; D007477:Ions; D008564:Membrane Potentials / Q000502:physiology; D008954:Models, Biological; D008956:Models, Chemical; D043942:Nanotubes / Q000737:chemistry* / Q000648:ultrastructure; D013329:Structure-Activity Relationship
chemical_list: D007473:Ion Channels; D007477:Ions