A Simple Calculus for Proteins and Cells

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, analyze 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.

• Type: Journal
• Year: 2007
• Where: ENTCS
• Authors: Cosimo Laneve, Fabien Tarissan
• Keywords: Biological Systems, Brane Calculi, ENTCS 2007, Process Calculi