Nano Science and Technology InstituteNano Science and Technology Institute
Nano Science and Technology Institute 2004 NSTI Nanotechnology Conference & Trade Show
Nanotech 2004
BioNano 2004
Program
Topics & Tracks
Sunday
Monday
Tuesday
Wednesday
Thursday
Index of Authors
Keynotes
Awards
Tutorials
Business & Investment
2004 Sub Sections
Sponsors
Exhibitors
Venue 2004
Proceedings
Organization
Press Room
Purchase CD/Proceedings
NSTI Events
Subscribe
Site Map
 
Nanotech Proceedings
Nanotechnology Proceedings
Supporting Organizations
Nanotech Supporting Organizations
Media Sponsors
Nanotech Media Sponsors
Event Contact
696 San Ramon Valley Blvd., Ste. 423
Danville, CA 94526
Ph: (925) 353-5004
Fx: (925) 886-8461
E-mail:
 
 

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
NCSA, US

Keywords: ion channels, electrostatics, brownian dynamics, multiscale, semiconductors,nanotubes,CAD

Abstract:
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

 
Sponsors
Nanotech Sponsors
News Headlines
NSTI Online Community
 
 

© Nano Science and Technology Institute, all rights reserved.
Terms of use | Privacy policy | Contact