A simple calculus for proteins and cells

The use of process calculi to represent biological systems has led to the design of different calculi such as brane calculi [1] and κ-calculus [3]. Both have proved to be useful to model different types of biological systems. As an attempt to unify the two directions, 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. Proteinprotein interactions have to be at most binary and cell interactions have to fit with sort constraints. We define the semantics of bioκ-calculus, analyse its properties, and discuss its expressiveness by modelling two significant examples: a signalling pathway and a virus infection.