Journal of Computational Electronics

, Volume 4, Issue 1, pp 171–174

A Simulative Model for the Analysis of Conduction Properties of Ion Channels Based on First-Principle Approaches

  • Fabio Affinito
  • Rossella Brunetti
  • Carlo Jacoboni
  • Enrico Piccinini
  • Massimo Rudan
  • Albertino Bigiani
  • Paolo Carloni
Article

DOI: 10.1007/s10825-005-7132-7

Cite this article as:
Affinito, F., Brunetti, R., Jacoboni, C. et al. J Comput Electron (2005) 4: 171. doi:10.1007/s10825-005-7132-7

Abstract

A physical model and a simulation framework are proposed for the analysis of conduction properties of ion channels. The permeation path of ions along the channel is defined through the simultaneous occupancy of a set of individual ion binding sites within the pore identified from structural X-ray data and Molecular Dynamics (MD) simulations. All permitted elementary transitions between different channel configurations and their rate constants can be evaluated from the atomistic structure and MD data and are implemented into a statistical model which is then coded in a Monte Carlo simulator. Results for K ions permeating the KcsA channel are shown.

Keywords

ion channelsKcsAmolecular dynamicsstatistical modelsMonte Carlo simulator

Copyright information

© Springer Science + Business Media, Inc. 2005

Authors and Affiliations

  • Fabio Affinito
    • 1
  • Rossella Brunetti
    • 1
  • Carlo Jacoboni
    • 1
  • Enrico Piccinini
    • 2
  • Massimo Rudan
    • 2
  • Albertino Bigiani
    • 3
  • Paolo Carloni
    • 4
  1. 1.INFM-S3 Research Center and Dipartimento di FisicaUniversità di Modena e Reggio EmiliaItaly
  2. 2.Dipartimento di Ingegneria Elettronica, Informatica e SistemisticaUniversità di BolognaItaly
  3. 3.INFM and Dipartimento di Scienze BiomedicheUniversità di Modena e Reggio EmiliaItaly
  4. 4.INFM and Scuola Internazionale Superiore di Studi AvanzatiTriesteItaly