Nanotech 2005 Vol. 1
Nanotech 2005 Vol. 1
Technical Proceedings of the 2005 NSTI Nanotechnology Conference and Trade Show, Volume 1

Computational Biology Chapter 9

Application of Grid Focusing Methodology to Transport Monte Carlo Model for Ion Channel Simulations

Authors: G.A. Kathawala, T. van der Straaten and U. Ravaioli

Affilation: University of Illinois at Urbana-Champaign, United States

Pages: 544 - 547

Keywords: ion channel, Monte Carlo, focus grid, Poisson

Abstract:
Simulation of Ion Channels has long been an outstanding research problem in the biophysical community. Our transport Monte Carlo model BioMOCA is a particle based approach where we treat water implicitly. It has been used to perform simulations of Porin and Gramacidin channels for time scales of few hundered nanoseconds and more for calculation of current flowing throught the channels. Two of the most critical issues important for proper ion channel simulation in these approaches are fine grid resolution of the protein region and the presence of large ion baths on either side of the channel. The simultaneous realization of these two issues in a self-consistent manner requires the solution of Poisson equation on a fine grid with a large number of grid points which is computationally expensive. We here propose the use of grid focusing methodology to achieve this goal in a computationally efficient way. For typical Gramicidin simulations with a 28x28x76 Å simulation domain, focus grid scheme gives a speedup of over 100% as compared to a single grid solution with identical fine mesh resolution. The currents obtained from a 1.5 _s simulation using the two approaches lie within 10 % of each other, which is well within the statistical margins.

Application of Grid Focusing Methodology to Transport Monte Carlo Model for Ion Channel Simulations

ISBN: 0-9767985-0-6
Pages: 844
Hardcopy: $109.95