A simple calculus for proteins and cells

AbstractThe 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