- Abstract:
- A language of formal proteins, the kappa-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 mkappa-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 pi-calculus, a standard foundational language for concurrency theory.
- Links To Paper
- No links available
- Bibtex format
- @Article{EDI-INF-RR-1169,
- author = {
Vincent Danos
and C Laneve
},
- title = {Formal Molecular Biology},
- journal = {Theorectical Computer Science},
- publisher = {Elsevier},
- year = 2004,
- volume = {325 (1)},
- pages = {69-110},
- doi = {10.1016/j.tcs.2004.03.065},
- }
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