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Article Dans Une Revue Theoretical Computer Science Année : 2008

A simple calculus for proteins and cells

Résumé

The use of process calculi to represent biological systems has led to the design of different formalisms such as brane calculi and κ-calculus. Both have proved to be useful to model different types of biological systems. As an attempt to unify the formalisms, we introduce the bioκ-calculus , a simple calculus for describing proteins and cells, in which bonds are represented by means of shared names and interactions are modelled at the domain level. In bioκ-calculus, protein-protein interactions have to be at most binary and cell interactions have to fit with sort constraints. In this contribution we define the semantics of bioκ-calculus, analyse its properties , discuss the expressivity of the calculus by modelling two significant examples – a signalling pathway and a virus infection –, and study an implementation in Milner's π-calculus.
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Dates et versions

hal-01217855 , version 1 (20-10-2015)

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Cosimo Laneve, Fabien Tarissan. A simple calculus for proteins and cells. Theoretical Computer Science, 2008, Membrane Computing and Biologically Inspired Process Calculi, 404 (1-2), pp.127-141. ⟨10.1016/j.tcs.2008.04.011⟩. ⟨hal-01217855⟩

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