Formal molecular biology

  • Authors:

  • Vincent Danos;Cosimo Laneve

  • Affiliations:

  • Équipe PPS, CNRS & Universitéé Paris 7, Paris, Cedex 75251, France;Department of Computer Science, University of Bologna, France

  • Venue:
  • Theoretical Computer Science - Special issue: Computational systems biology
  • Year:
  • 2004

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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.