Simulation of ion conduction in the ompF porin channel using BioMOCA

Kyu Il Lee, Young June Park, Trudy van der Straaten, Gulzar Kathawala, Umberto Ravaioli

Research output: Contribution to journalArticlepeer-review

Abstract

In this paper, we present a full three-dimensional simulation of the ompF porin channel using BioMOCA, a self-consistent particle-based ion channel simulation tool, based on the Boltzmann Transport Monte Carlo methodology widely used to simulate conduction in the solid-state device. Significant computational speed-up over atomistic Molecular Dynamics simulations is achieved by treating protein, membrane and water as continuum dielectric background media and computing only the trajectories of mobile ions in solution. A realistic channel structure with permanent fixed charges is mapped onto a finite mesh using the Cloud-in-Cell scheme. Electrostatic forces, computed by solving Poisson equation at regular intervals, are added to a pair-wise ion-ion interaction, which is necessary to prevent the unphysical coalescence of finite-sized ions. The interaction between ions and water is modeled as a random scattering process that thermalizes the ion. Using this tool we computed the complete current-voltage characteristic of the porin channel in approximately one week using ten IBM p690 processors. We also present steady-state ion channel occupancies and compare them with results obtained from recent drift-diffusion based simulations.

Original languageEnglish (US)
Pages (from-to)157-160
Number of pages4
JournalJournal of Computational Electronics
Volume4
Issue number1-2
DOIs
StatePublished - Apr 2005

Keywords

  • Ion channel
  • Monte Carlo simulation
  • ompF porin channel

ASJC Scopus subject areas

  • Electronic, Optical and Magnetic Materials
  • Atomic and Molecular Physics, and Optics
  • Modeling and Simulation
  • Electrical and Electronic Engineering

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