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Mathias John, Cédric Lhoussaine, and Joachim Niehren (2009)

Dynamic Compartments in the Imperative Pi-Calculus

In: CMSB 2009 - Computational Methods in Systems Biology, ed. by Pierpaolo Degano and Roberto Gorrieri, vol. 5688/2009, pp. 235-250, Springer Verlag. LNCS.

Dynamic compartments with mutable configurations and variable volumes are of basic interest for the stochastic modeling of biochemistry in cells. We propose a new language to express dynamic compartments that we call the Imperative Pi-Calculus. It is obtained from the Attributed Pi-Calculus by adding imperative assignment operations to a global store. Previous approaches to dynamic compartments are improved in flexibility or efficiency. This is illustrated by an appropriate model of osmosis and a correct encoding of BioAmbients.

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