Application of grid focusing methodology to transport Monte Carlo model for ion channel simulations

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

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

Abstract

Reduced order particle based models have become popular recently for the study of ion channels. One of the key computational challenge for these methods is the fast and accurate calculation of electrostatic forces acting on the mobile ions. We have applied the electrostatic focusing method to address this issue. We have validated our method using bulk simulations and comparing the pair correlation functions with single grid setup. Full channel simulations were performed for ompF porin channel and important channel behavior like asymmetry of the channel and loss of selectivity at high bath concentrations were observed. We also observed the separation of pathways for anions and cations as they traverse the channel. Using focus grid method, we obtained an overall speedup of more than 50% for our channel simulations.

Original languageEnglish (US)
Title of host publication2005 NSTI Nanotechnology Conference and Trade Show - NSTI Nanotech 2005 Technical Proceedings
EditorsM. Laudon, B. Romanowicz
Pages544-547
Number of pages4
StatePublished - Dec 1 2005
Event2005 NSTI Nanotechnology Conference and Trade Show - NSTI Nanotech 2005 - Anaheim, CA, United States
Duration: May 8 2005May 12 2005

Publication series

Name2005 NSTI Nanotechnology Conference and Trade Show - NSTI Nanotech 2005 Technical Proceedings

Other

Other2005 NSTI Nanotechnology Conference and Trade Show - NSTI Nanotech 2005
CountryUnited States
CityAnaheim, CA
Period5/8/055/12/05

Keywords

  • Focus Grid
  • Ion Channels
  • Monte Carlo
  • Porin
  • Simulation

ASJC Scopus subject areas

  • Engineering(all)

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