Formal molecular biology

Vincent Danos, Cosimo Laneve

Research output: Contribution to journalArticlepeer-review

Abstract

A language of formal proteins, theκ-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.
Original languageEnglish
Pages (from-to)69 - 110
Number of pages42
JournalTheoretical Computer Science
Volume325
Issue number1
DOIs
Publication statusPublished - Sep 2004

Fingerprint Dive into the research topics of 'Formal molecular biology'. Together they form a unique fingerprint.

Cite this