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

Krishnamurthy, Vikram; Hoyles, Matthew; Saab, Rayan; Chung, Shin-Ho


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...[Show more]

CollectionsANU Research Publications
Date published: 2006
Type: Journal article
Source: Journal of Computational and Theoretical Nanoscience
DOI: 10.1166/jctn.2006.010


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