Formal molecular biology

• Published in: Theoretical computer science 2004-09, Vol.325 (1), p.69-110
• Main Authors: Danos, Vincent, Laneve, Cosimo
• Format: Article
• Language: English
• Subjects: Algorithmics. Computability. Computer arithmetics; Applied sciences; Automata. Abstract machines. Turing machines; Biological and medical sciences; Computer science; control theory; systems; Exact sciences and technology; Fundamental and applied biological sciences. Psychology; General aspects; Language theory and syntactical analysis; Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects); Theoretical computing
• ISSN: 0304-3975; 1879-2294
• DOI: 10.1016/j.tcs.2004.03.065

A 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.