The modelling and analysis of biological systems has deep roots in Mathematics, specifically in the field of Ordinary Differential Equations (ODEs). Alternative approaches based on formal calculi, often derived from process algebras or term rewriting systems, provide a quite complementary way to analyse the behaviour of biological systems. These calculi allow to cope in a natural way with notions like compartments and membranes, which are not easy (sometimes impossible) to handle with purely numerical approaches, and are often based on stochastic simulation methods. Recently, it has also become evident that stochastic effects in regulatory networks play a crucial role in the analysis of such systems. Actually, in many situations it is necessary to use stochastic models. For example when the system to be described is based on the interaction of few molecules, when we are at the presence of a chemical instability, or when we want to simulate the functioning of a pool of entities whose compartmentalised structure evolves dynamically. In contrast, stable metabolic networks, involving a large number of reagents, for which the computational cost of a stochastic simulation becomes an insurmountable obstacle, are efficiently modelled with ODEs. In this paper we define a hybrid simulation method, combining the stochastic approach with ODEs, for systems described in the Calculus of Wrapped Compartments (CWC), a calculus on which we can express the compartmentalisation of a biological system whose evolution is defined by a set of rewrite rules.

Simulation techniques for the calculus of wrapped compartments

COPPO, Mario;DAMIANI, Ferruccio;DROCCO, MAURIZIO;GRASSI, ELENA;SCIACCA, EVA;SPINELLA, SALVATORE;TROINA, ANGELO
2012-01-01

Abstract

The modelling and analysis of biological systems has deep roots in Mathematics, specifically in the field of Ordinary Differential Equations (ODEs). Alternative approaches based on formal calculi, often derived from process algebras or term rewriting systems, provide a quite complementary way to analyse the behaviour of biological systems. These calculi allow to cope in a natural way with notions like compartments and membranes, which are not easy (sometimes impossible) to handle with purely numerical approaches, and are often based on stochastic simulation methods. Recently, it has also become evident that stochastic effects in regulatory networks play a crucial role in the analysis of such systems. Actually, in many situations it is necessary to use stochastic models. For example when the system to be described is based on the interaction of few molecules, when we are at the presence of a chemical instability, or when we want to simulate the functioning of a pool of entities whose compartmentalised structure evolves dynamically. In contrast, stable metabolic networks, involving a large number of reagents, for which the computational cost of a stochastic simulation becomes an insurmountable obstacle, are efficiently modelled with ODEs. In this paper we define a hybrid simulation method, combining the stochastic approach with ODEs, for systems described in the Calculus of Wrapped Compartments (CWC), a calculus on which we can express the compartmentalisation of a biological system whose evolution is defined by a set of rewrite rules.
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http://dx.doi.org/10.1016/j.tcs.2011.12.063
Term rewriting systems; Stochastic/deterministic simulation methods; Hybrid simulation; Biochemical systems
Mario Coppo; Ferruccio Damiani; Maurizio Drocco; Elena Grassi; Eva Sciacca; Salvatore Spinella; Angelo Troina
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/2318/92784
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