Semi-Markov models for brownian dynamics permeation in biological ion channels.
Constructing accurate computational models that explain how ions permeate through a biological ion channel is an important problem in biophysics and drug design. Brownian dynamics simulations are large-scale interacting particle computer simulations for modeling ion channel permeation but can be computationally prohibitive. In this paper, we show the somewhat surprising result that a small-dimensional semi-Markov model can generate events (such as conduction events and dwell times at binding sites in the protein) that are statistically indistinguishable from brownian dynamics computer simulation. This approach enables the use of extrapolation techniques to predict channel conduction when performing the actual brownian dynamics simulation that is computationally intractable. Numerical studies on the simulation of gramicidin A ion channels are presented.
Department of Electrical and Computer Engineering, University of British Columbia, Vancouver V6T 1Z4, Canada. vikramk@ece.ubc.ca
Vikram
V
Krishnamurthy
Kai Yiu
KY
Luk
D001407:Bacillus / Q000737:chemistry / Q000378:metabolism / Q000502:physiology; D001665:Binding Sites; D002463:Cell Membrane Permeability; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D006096:Gramicidin / Q000378:metabolism*; D007473:Ion Channels / Q000737:chemistry* / Q000378:metabolism*; D007700:Kinetics; D008390:Markov Chains; D008954:Models, Biological; D056004:Molecular Dynamics Simulation; D016012:Poisson Distribution; D015203:Reproducibility of Results; D013269:Stochastic Processes; D013816:Thermodynamics
D007473:Ion Channels; D006096:Gramicidin