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Title:Formal Molecular Biology
Authors: Vincent Danos ; C Laneve
Date: 2004
Publication Title:Theorectical Computer Science
Publication Type:Journal Article Publication Status:Published
Volume No:325 (1) Page Nos:69-110
DOI:10.1016/j.tcs.2004.03.065 ISBN/ISSN:0304-3975
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.
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Bibtex format
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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