Toward an Integrated Computational Environment for Multiscale Computational Design of Nanoscale Ion Channel Semiconductors
S. Natarajan, S. Varma, Y. Tang, S. Parker, J. Mashl and E. Jakobsson
Keywords: ion channels, electrostatics, brownian dynamics, multiscale, semiconductors,nanotubes,CAD
This paper describes the design and operation of an integrated multiscale computational environment for design of nanoscale ion channel semiconductors, the Ion Channel Workbench. The present work builds on an earlier multiscale calculation from our lab in which we showed that this approach could provide a close correspondence to experimental electrophysiological data on potassium channels. The current paper advances the previous work by incorporation of multiscale into a single integrated computation, in which the results of calculation at one stage automatically feed as input to calculations at other stages. The accuracy of the electrostatics calculations for protonation has been improved by a protocol that systematically considers possible protonation states for interactions between possibly charged residues. The Brownian dynamics simulation has been improved by an algorithm that is valid over a wide range of time step sizes ranging from the inertial to the Markovian domains. The improved Brownian dynamics simulations retain the efficiency of the one-dimensional approximation but capture the three-dimensional character of the physical situation by channel radius-dependence of the ion-ion interactions. These improvements result in a distribution of permeant ions in the channel that is much closer to the crystallographic results than is the case with our previous results.
Nanotech 2004 Conference Technical Program Abstract