1-D Brownian Dynamics Simulation With Its Application in Study of Ion Channel
Tang, Yuzhou
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Permalink
https://hdl.handle.net/2142/85447
Description
Title
1-D Brownian Dynamics Simulation With Its Application in Study of Ion Channel
Author(s)
Tang, Yuzhou
Issue Date
2005
Doctoral Committee Chair(s)
Jakobsson, Eric
Department of Study
Biophysics and Computational Biology
Discipline
Biophysics and Computational Biology
Degree Granting Institution
University of Illinois at Urbana-Champaign
Degree Name
Ph.D.
Degree Level
Dissertation
Keyword(s)
Biophysics, General
Language
eng
Abstract
The ion permeation through cell membrane facilitated by ion channel system is essentially 1-D diffusion process. With faster computer and more advanced algorithm, this process could be investigated by Brownian Dynamics simulation, which is a more straightforward and accurate method than traditional permeation theory. The basic assumption is that the motion of ion in the solution consists of a random collision with surrounding media and a deterministic drifting caused by interaction with other molecules. The ongoing research is to implement a 1-D Brownian Dynamics simulation program on supercomputer which not only represents permeation process as realistic as possible but also runs fast enough to generate sufficient data within reasonable time so that we could retrieve statistically meaningful information. Through statistical analysis of simulation data, we could correlate the experimental observation with the underlying ion channel system, understand how significant each component of the system affects the permeation process, and furthermore figure out how to control and regulate this process. Then, this 1-D BD simulation is applied on the ion channel system based on the high-resolution structures of KcsA. By comparison between simulation results and experimental results, the effectiveness and accuracy of the simulation is approved. With some further modifications, this method could be applied in the study of more ion channel systems.
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