Reservoir boundaries in Brownian dynamics simulations of ion channels

Biophysical Journal
Ben CorryShin-Ho Chung

Abstract

Brownian dynamics (BD) simulations provide a practical method for the calculation of ion channel conductance from a given structure. There has been much debate about the implementation of reservoir boundaries in BD simulations in recent years, with claims that the use of improper boundaries could have large effects on the calculated conductance values. Here we compare the simple stochastic boundary that we have been using in our BD simulations with the recently proposed grand canonical Monte Carlo method. We also compare different methods of creating transmembrane potentials. Our results confirm that the treatment of the reservoir boundaries is mostly irrelevant to the conductance properties of an ion channel as long as the reservoirs are large enough.

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Citations

Nov 13, 2004·European Biophysics Journal : EBJ·Ben Corry, Shin-Ho Chung
Jul 3, 2008·European Biophysics Journal : EBJ·Taira VoraShin-Ho Chung
Dec 1, 2003·Journal of Biological Physics·Serdar Kuyucak, Turgut Bastug
Sep 30, 2010·The Journal of General Physiology·Ben CorryBoris Martinac
Aug 10, 2013·The Journal of Chemical Physics·Dezső BodaDirk Gillespie
Aug 31, 2002·Biophysical Journal·Scott EdwardsShin-Ho Chung
Apr 9, 2005·IEEE Transactions on Nanobioscience·Vikram Krishnamurthy, Shin-Ho Chung
May 21, 2005·Biochimica Et Biophysica Acta·Ben CorryShin-Ho Chung
Sep 8, 2009·Drug Discovery Today·Yalini ArinaminpathyMark B Gerstein
Jan 18, 2008·Biophysical Journal·Dezso BodaDirk Gillespie
Apr 29, 2009·Biochimica Et Biophysica Acta·Chen Song, Ben Corry
Apr 19, 2016·Journal of Chemical Theory and Computation·Carlos J F SolanoUlrich Kleinekathöfer
Mar 24, 2005·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·A Singer, Z Schuss
Dec 1, 2012·Nanoscale·Niraj ModiUlrich Kleinekathöfer
Nov 13, 2008·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Sisir RoyRodolfo Llinas
Feb 9, 2005·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·A SingerR S Eisenberg
Aug 11, 2005·Physical Review Letters·B NadlerA Singer
Aug 12, 2014·Journal of Chemical Theory and Computation·Claudio BertiClaudio Fiegna
Nov 20, 2012·The Journal of Physical Chemistry. B·Dan Gordon, Shin-Ho Chung
Nov 9, 2018·Journal of Chemical Theory and Computation·Carlos J F SolanoUlrich Kleinekathöfer
Mar 31, 2006·The Journal of Physical Chemistry. B·Hyonseok HwangMark A Ratner

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