TY - JOUR
T1 - Simulation of ion conduction in the ompF porin channel using BioMOCA
AU - Lee, Kyu Il
AU - Park, Young June
AU - van der Straaten, Trudy
AU - Kathawala, Gulzar
AU - Ravaioli, Umberto
N1 - Funding Information:
This work has been supported by the NSF Network for Computational Nanotechnology, Brain Korea 21 Project, and Nano Systems Institute—National Core Research Center (NSI-NCRC) program of KOSEF, Korea.
Copyright:
Copyright 2005 Elsevier B.V., All rights reserved.
PY - 2005/4
Y1 - 2005/4
N2 - 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.
AB - 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.
KW - Ion channel
KW - Monte Carlo simulation
KW - ompF porin channel
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U2 - 10.1007/s10825-005-7129-2
DO - 10.1007/s10825-005-7129-2
M3 - Article
AN - SCOPUS:25144454514
VL - 4
SP - 157
EP - 160
JO - Journal of Computational Electronics
JF - Journal of Computational Electronics
SN - 1569-8025
IS - 1-2
ER -