文章基本信息

标题：A computationally efficient algorithm for fitting ion channel parameters
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作者：Zachary R. Teed ; Jonathan R. Silva
期刊名称：MethodsX
印刷版ISSN：2215-0161
电子版ISSN：2215-0161
出版年度：2016
卷号：3
页码：577-588
DOI：10.1016/j.mex.2016.11.001
语种：English
出版社：Elsevier
摘要：Graphical abstract Display Omitted Abstract Continuous time Markov models have been widely used to describe ion channel kinetics, providing explicit representation of channel states and transitions. Fitting models to experimental data remains a computationally demanding task largely due to the high cost of model evaluation. Here, we propose a method to efficiently optimize model parameters and structure. Voltage clamp channel protocols can be decomposed into a series of fixed steps of constant voltage resulting in a set of linear systems of differential equations. Given the linear systems, ODE integration can be swapped for the faster matrix exponential routine. With our parallelized implementation, optimized models are able to reproduce a wide range of experimentally collected data within one minute, a 50 times speedup over ODE integration. • The cost of the objective function is reduced by employing the matrix exponential • The likelihood of convergence is improved by applying synchronous start simulated annealing • The approach was tested by optimizing parameters for a model of the cardiac voltage-gated Na+ channel, NaV1.5, and the KCNQ1 K+ channel.
关键词：Cardiac action potential;Ion channels;Computer modeling