BioMOCA: A transport Monte Carlo approach to ion channel simulation

T. A. Van Der Straaten, G. Kathawala, Umberto Ravaioli

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Ion channels are highly charged proteins that reside in the membrane of all living cells to regulate charge transport to the cell. Most channels have device-like behaviors that are interesting to the electronics community for their possible application in bio-device design. Simulating ion channels over time-scales relevant to conduction present a difficult time and space multi-scale problem that is beyond the scope of the Molecular Dynamics approach. To address this problem we have developed BioMOCA, a 3-D reduced particle ion channel simulator based on the transport Monte Carlo methodology. BioMOCA has been described elsewhere; here we use it to study the link between the electrostatic properties of the protein and selectivity in the gramicidin channel. We also present representative simulations of Na+ transport in gramicidin.

Original languageEnglish (US)
Title of host publication2004 NSTI Nanotechnology Conference and Trade Show - NSTI Nanotech 2004
EditorsM. Laudon, B. Romanowicz
Pages139-142
Number of pages4
StatePublished - Nov 3 2004
Event2004 NSTI Nanotechnology Conference and Trade Show - NSTI Nanotech 2004 - Boston, MA, United States
Duration: Mar 7 2004Mar 11 2004

Publication series

Name2004 NSTI Nanotechnology Conference and Trade Show - NSTI Nanotech 2004
Volume1

Other

Other2004 NSTI Nanotechnology Conference and Trade Show - NSTI Nanotech 2004
CountryUnited States
CityBoston, MA
Period3/7/043/11/04

Keywords

  • Gramicidin
  • Ion channels
  • Monte Carlo simulations
  • Nanodevices

ASJC Scopus subject areas

  • Engineering(all)

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