Hybrid Calculus of Wrapped Compartments

Mario Coppo
(Dipartimento di Informatica, Università di Torino)
Ferruccio Damiani
(Dipartimento di Informatica, Università di Torino)
Maurizio Drocco
(Dipartimento di Informatica, Università di Torino)
Elena Grassi
(Dipartimento di Informatica, Università di Torino)
Eva Sciacca
(Dipartimento di Informatica, Università di Torino)
Salvatore Spinella
(Dipartimento di Informatica, Università di Torino)
Angelo Troina
(Dipartimento di Informatica, Università di Torino)

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 analyze 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 CWC, a calculus on which we can express the compartmentalisation of a biological system whose evolution is defined by a set of rewrite rules.

In Gabriel Ciobanu and Maciej Koutny: Proceedings Fourth Workshop on Membrane Computing and Biologically Inspired Process Calculi 2010 (MeCBIC 2010), Jena, Germany, 23 August 2010, Electronic Proceedings in Theoretical Computer Science 40, pp. 102–120.
Published: 30th October 2010.

ArXived at: https://dx.doi.org/10.4204/EPTCS.40.8 bibtex PDF

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