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Dynamic Compartments in the Imperative Pi Calculus

Mathias John 1 Cédric Lhoussaine 2 Joachim Niehren 3, 4, * 
* Corresponding author
3 MOSTRARE - Modeling Tree Structures, Machine Learning, and Information Extraction
LIFL - Laboratoire d'Informatique Fondamentale de Lille, Inria Lille - Nord Europe
4 BioComputing - Programming Languages for Biological Modeling and Simulation
LIFL - Laboratoire d'Informatique Fondamentale de Lille
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 BioAmbients.
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Submitted on : Thursday, October 8, 2009 - 9:21:46 PM
Last modification on : Friday, February 4, 2022 - 3:11:47 AM
Long-term archiving on: : Tuesday, June 15, 2010 - 9:06:35 PM


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Mathias John, Cédric Lhoussaine, Joachim Niehren. Dynamic Compartments in the Imperative Pi Calculus. Computational Methods in Systems Biology, 7th International Conference, Aug 2009, Bologna, Italy. pp.235-250, ⟨10.1007/978-3-642-03845-7⟩. ⟨inria-00422970⟩



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