Formal molecular biology

TLDR: A finer-grained concurrent model, the mK-calculus, is considered, where interactions have to be at most binary, and it is shown how to embed the coarser- grained language in the latter, a properly which the authors call self-assembly.

Abstract: A language of formal proteins, the K-calculus, is introduced. Interactions are modeled at the domain level, bonds are represented by means of shared names, and reactions are required to satisfy a causality requirement of monotonicity.An example of a simplified signalling pathway is introduced to illustrate how standard biological events can be expressed in our protein language. A more comprehensive example, the lactose operon, is also developed, bringing some confidence in the formalism considered as a modeling language.Then a finer-grained concurrent model, the mK-calculus, is considered, where interactions have to be at most binary. We show how to embed the coarser-grained language in the latter, a properly which we call self-assembly.Finally we show how the finer-grained language can itself be encoded in π-calculus, a standard foundational language for concurrency theory.