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Reservoir Boundaries in Brownian Dynamics Simulations of Ion Channels

Corry, Ben; Hoyles, Matthew; Allen, Toby; Walker, M; Kuyucak, Serdar; Chung, Shin-Ho

Description

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...[Show more]

dc.contributor.authorCorry, Ben
dc.contributor.authorHoyles, Matthew
dc.contributor.authorAllen, Toby
dc.contributor.authorWalker, M
dc.contributor.authorKuyucak, Serdar
dc.contributor.authorChung, Shin-Ho
dc.date.accessioned2015-12-13T23:24:20Z
dc.identifier.issn0006-3495
dc.identifier.urihttp://hdl.handle.net/1885/92180
dc.description.abstractBrownian 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.
dc.publisherBiophysical Society
dc.sourceBiophysical Journal
dc.subjectKeywords: ion channel; article; diffusion coefficient; ion conductance; membrane potential; Monte Carlo method; Biophysics; Cations; Cell Membrane; Computer Simulation; Dose-Response Relationship, Drug; Ions; Membrane Potentials; Models, Statistical; Monte Carlo Me
dc.titleReservoir Boundaries in Brownian Dynamics Simulations of Ion Channels
dc.typeJournal article
local.description.notesImported from ARIES
local.description.refereedYes
local.identifier.citationvolume82
dc.date.issued2002
local.identifier.absfor029901 - Biological Physics
local.identifier.ariespublicationMigratedxPub23186
local.type.statusPublished Version
local.contributor.affiliationCorry, Ben, College of Physical and Mathematical Sciences, ANU
local.contributor.affiliationHoyles, Matthew, College of Physical and Mathematical Sciences, ANU
local.contributor.affiliationAllen, Toby, College of Physical and Mathematical Sciences, ANU
local.contributor.affiliationWalker, M, College of Physical and Mathematical Sciences, ANU
local.contributor.affiliationKuyucak, Serdar, College of Physical and Mathematical Sciences, ANU
local.contributor.affiliationChung, Shin-Ho, College of Physical and Mathematical Sciences, ANU
local.description.embargo2037-12-31
local.bibliographicCitation.startpage1975
local.bibliographicCitation.lastpage1984
dc.date.updated2015-12-12T09:20:05Z
local.identifier.scopusID2-s2.0-0036213027
CollectionsANU Research Publications

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