Exact and Approximate Stochastic Simulation of Intracellular Calcium Dynamics

[摘要] In simulations of chemical systems, the main task is to find an exact or approximate solution of thechemical master equation(CME) that satisfies certain constraints with respect to computation time and accuracy. WhileBrownian motionsimulations of single molecules are often too time consuming to represent the mesoscopic level, the classicalGillespie algorithmis a stochastically exact algorithm that provides satisfying results in the representation of calcium microdomains.Gillespie's algorithmcan be approximated viathetau-leapmethod and thechemical Langevin equation(CLE). Both methods lead to a substantial acceleration in computation time and a relatively small decrease in accuracy. Elimination of the noise terms leads to the classical, deterministic reaction rate equations (RRE). For complex multiscale systems, hybrid simulations are increasinglyproposed to combine the advantages of stochastic and deterministic algorithms. An often used exemplary cell type in this context are striated muscle cells (e.g., cardiac and skeletal muscle cells). The properties of these cells are well described and they express many common calcium-dependent signalingpathways. The purpose of the present paper is to provide an overview of the aforementioned simulation approaches and their mutual relationships in the spectrum ranging from stochastic to deterministic algorithms.

[学科分类] 基础医学