Dynamic Compartments in the Imperative Π-Calculus

Authors:
Mathias John;Cédric Lhoussaine;Joachim Niehren
Affiliations:
Computer Science, Modeling and Simulation Group, University of Rostock,;University of Lille 1, and BioComputing, LIFL (CNRS UMR8022) and IRI (CNRS USR3078),;INRIA, Lille and BioComputing, LIFL (CNRS UMR8022) and IRI (CNRS USR3078),
Venue:
CMSB '09 Proceedings of the 7th International Conference on Computational Methods in Systems Biology
Year:
2009

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Abstract

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 Π -calculus . It is obtained from the attributed Π -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 bioambBioAmbients.