Adaptive controlled Brownian dynamics approach for permeation in bio-nanotubes

TitleAdaptive controlled Brownian dynamics approach for permeation in bio-nanotubes
Publication TypeConference Paper
Year of Publication2005
AuthorsKrishnamurthy, V., and S. - H. Chung
Conference NameAcoustics, Speech, and Signal Processing, 2005. Proceedings. (ICASSP '05). IEEE International Conference on
Paginationv/929 - v/932 Vol. 5
Date Publishedmar.
Keywordsadaptive control, adaptive controlled Brownian dynamics, Angstrom unit spatial scale, bio-nanotubes, biological nanotubes, biomembrane transport, Brownian motion, femtosecond time scale, gradient methods, ion channel, ion channels, ion propagation, large protein molecules, nanotubes, permeation, proteins, simulated current, simulation, stochastic gradient algorithm, stochastic programming

Ion channels are biological nanotubes formed by large protein molecules. In this paper we address the permeation problem which deals with the propagation of individual ions in an ion channel at an Angstrom unit spatial scale and femtosecond time scale. We present an adaptive controlled Brownian dynamics simulation approach to predict the structure of an ion channel. The Brownian dynamics algorithm is coupled with a stochastic gradient algorithm to match the simulated current with experimentally determined currents.


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