Skip to main content
padlock icon - secure page this page is secure

Permeation in Gramicidin Ion Channels by Directly Estimating the Potential of Mean Force Using Brownian Dynamics Simulations

Buy Article:

$106.39 + tax (Refund Policy)

We present a method for estimating the 'best-fit' potential of mean force encountered by an ion permeating across the gramicidin-A ion channel. The proposed method does not require explicit use of a dielectric constant and can be applied to other ion channels. The potential of mean force is parameterized and its parameters are estimated using a stochastic optimization algorithm that controls Brownian dynamics simulations. A loss function measuring the differences between currents simulated using Brownian dynamics and currents observed at various applied potentials and ionic concentrations is calculated to compare between possible candidate parameters of the potential of mean force. The results obtained indicate that several possible potentials of mean force with barrier-heights and well-depths in the vicinity of 6 kT and 4.5 kT provide optimal fits to the observed currents. Using both "brute-force" search and stochastic optimization, a sensitivity analysis is conducted to show the effect of potential of mean force (PMF) parameter variations on the simulated currents fit to the observables. We illustrate the methods using the gramicidin channel as a test case and show that the results closely match the profiles of potential of mean force reported in the literature.
No Reference information available - sign in for access.
No Citation information available - sign in for access.
No Supplementary Data.
No Article Media
No Metrics


Document Type: Research Article

Publication date: October 1, 2006

More about this publication?
  • Journal of Computational and Theoretical Nanoscience is an international peer-reviewed journal with a wide-ranging coverage, consolidates research activities in all aspects of computational and theoretical nanoscience into a single reference source. This journal offers scientists and engineers peer-reviewed research papers in all aspects of computational and theoretical nanoscience and nanotechnology in chemistry, physics, materials science, engineering and biology to publish original full papers and timely state-of-the-art reviews and short communications encompassing the fundamental and applied research.
  • Editorial Board
  • Information for Authors
  • Submit a Paper
  • Subscribe to this Title
  • Terms & Conditions
  • Ingenta Connect is not responsible for the content or availability of external websites
  • Access Key
  • Free content
  • Partial Free content
  • New content
  • Open access content
  • Partial Open access content
  • Subscribed content
  • Partial Subscribed content
  • Free trial content
Cookie Policy
Cookie Policy
Ingenta Connect website makes use of cookies so as to keep track of data that you have filled in. I am Happy with this Find out more