In the last decades, experimental investigations have evidenced the role of biological noise in cellular processes, and several stochastic approaches have been proposed to modelling and simulation of biochemical networks. Here, we review the main stochastic procedures defined for single-volume biochemical systems (SSA, tau-leaping), and discuss their practical utility and limitations. Then, within the framework of membrane systems, we propose a multivolume generalization of the tau-leaping algorithm, called tau-DPP, feasible for the stochastic analysis of complex biochemical systems. Finally, we present a case-study application of tau-DPP to an intracellular genetic oscillator, coupled with an intercellular communication mechanism
Besozzi, D., Cazzaniga, P., Pescini, D., Mauri, G. (2009). A multivolume approach to stochastic modelling with membrane systems. In A. Condon, D. Harel, A. Salomaa, Winfree E (a cura di), Algorithmic Bioprocesses (pp. 519-542). Berlin : Springer-Verlag [10.1007/978-3-540-88869-7_26].
A multivolume approach to stochastic modelling with membrane systems
BESOZZI, DANIELA;PESCINI, DARIO;MAURI, GIANCARLO
2009
Abstract
In the last decades, experimental investigations have evidenced the role of biological noise in cellular processes, and several stochastic approaches have been proposed to modelling and simulation of biochemical networks. Here, we review the main stochastic procedures defined for single-volume biochemical systems (SSA, tau-leaping), and discuss their practical utility and limitations. Then, within the framework of membrane systems, we propose a multivolume generalization of the tau-leaping algorithm, called tau-DPP, feasible for the stochastic analysis of complex biochemical systems. Finally, we present a case-study application of tau-DPP to an intracellular genetic oscillator, coupled with an intercellular communication mechanism
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