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Modeling and Simulating Biological Processes with Stochastic Multiset Rewriting

Authors Matteo Cavaliere, Sean Sedwards



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DagSemProc.06161.7.pdf
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Matteo Cavaliere
Sean Sedwards

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Matteo Cavaliere and Sean Sedwards. Modeling and Simulating Biological Processes with Stochastic Multiset Rewriting. In Simulation and Verification of Dynamic Systems. Dagstuhl Seminar Proceedings, Volume 6161, pp. 1-8, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2006)
https://doi.org/10.4230/DagSemProc.06161.7

Abstract

Membrane systems were originally introduced as models of computation inspired by the structure and the functioning of living cells. More recently, membrane systems have been shown to be suitable also to model cellular processes. Inspired by brane calculi, a new model of membrane system with peripheral proteins has been recently introduced. Such model has compartments (enclosed by membranes), floating objects, and objects attached to the internal and external surfaces of the membranes. The objects can be processed/transported inside/across the compartments and the transport is regulated by opportune objects attached to the membranes surfaces. We present a stochastic simulator of this model, with a style of syntax based on chemical reactions. We show that the simulator can be particularly useful in modelling biological processes that involve compartments, surface and integral membrane proteins, transport and processing of chemical substances. As examples we present the simulation of circadian clock and the G-protein cycle in yeast.
Keywords
  • Systems biology
  • membrane systems
  • formal language
  • simulation

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