title: Stochastic representations of ion channel kinetics and exact stochastic simulation of neuronal dynamics.
abstract: In this paper we provide two representations for stochastic ion channel kinetics, and compare the performance of exact simulation with a commonly used numerical approximation strategy. The first representation we present is a random time change representation, popularized by Thomas Kurtz, with the second being analogous to a "Gillespie" representation. Exact stochastic algorithms are provided for the different representations, which are preferable to either (a) fixed time step or (b) piecewise constant propensity algorithms, which still appear in the literature. As examples, we provide versions of the exact algorithms for the Morris-Lecar conductance based model, and detail the error induced, both in a weak and a strong sense, by the use of approximate algorithms on this model. We include ready-to-use implementations of the random time change algorithm in both XPP and Matlab. Finally, through the consideration of parametric sensitivity analysis, we show how the representations presented here are useful in the development of further computational methods. The general representations and simulation strategies provided here are known in other parts of the sciences, but less so in the present setting.
authors.affiliation: Department of Mathematics, University of Wisconsin, Madison, WI, USA, anderson@math.wisc.edu.
authors.forename: David F
authors.initials: DF
authors.lastname: Anderson
authors.forename: Bard
authors.initials: B
authors.lastname: Ermentrout
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Thomas
mesh_terms: D000818:Animals; D001696:Biomechanical Phenomena; D003198:Computer Simulation; D007473:Ion Channels / Q000502:physiology*; D008959:Models, Neurological; D009474:Neurons / Q000502:physiology*; D017711:Nonlinear Dynamics; D013269:Stochastic Processes
chemical_list: D007473:Ion Channels