Brownian dynamics Simulation for modeling ion permeation across bionanotubes

TitleBrownian dynamics Simulation for modeling ion permeation across bionanotubes
Publication TypeJournal Article
Year of Publication2005
AuthorsKrishnamurthy, V., and S. - H. Chung
JournalNanoBioscience, IEEE Transactions on
Pagination102 -111
Date Publishedmar.
Keywordsbioelectric potentials, Biological, biomembrane transport, bionanotubes, Brownian dynamics simulation, Brownian motion, cell membrane, Cell Membrane Permeability, Chemical, chlorine, Cl, ClC Cl/sup -/ channel, computer simulation, current flow, current-concentration curves, current-voltage curves, diffusion, Ion Channel Gating, ion channels, ion permeation modeling, Ions, K, KcsA K/sup +/ channel, Membrane Potentials, Models, nanotubes, permeation dynamics, physiological models, potassium, statistical consistency, Structure-Activity Relationship

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 ClC Cl- channel.


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