14th IFAC Symposium on System Identification, SYSID 2006

SYSID-2006 Paper Abstract

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Paper FrA6.5

Krishnamurthy, Vikram (Univ. of British Columbia), Vora, Taira (ANU), Chung, Shin-Ho (ANU)

Shape Estimation of Biological Nanotubes Using Controlled Brownian Dynamics Simulation Algorithm

Scheduled for presentation during the Regular Session "Identification in Biological Systems" (FrA6), Friday, March 31, 2006, 11:50−12:10, Newcastle Room

14th IFAC Symposium on System Identification, March 29 - 31, 2006, Newcastle, Australia

This information is tentative and subject to change. Compiled on July 16, 2018

Keywords Biological Systems, Recursive Identification

Abstract

Ion channels are protein macromolecules that form biological nanotubes in the cell membrane of living cells. In this paper we use a parameterized molecular structure to formulate the ion channel shape estimation as a discrete stochastic optimization problem. We use Brownian dynamics simulations controlled with discrete stochastic optimization algorithms to estimate the shape of Sodium ion channels. The Brownian dynamics simulation emulates the propagation of individual ions through the Sodium ion channel nanotube at a femto time second time scale and Angstrom unit ($10^{-10}$ meter) spatial scale. The algorithms presented in this paper are provably convergent. In numerical studies that use experimental measurements of an actual Sodium ion channel, we show that the proposed algorithms efficiently learn the shape of Sodium ion channels.