Formal molecular biology

AbstractA language of formal proteins, the κ-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 mκ-calculus, is considered, where interactions have to be at most binary. We show how to embed the coarser-grained language in the latter, a property 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