Date: 28 Feb 2003

Graphs for Core Molecular Biology

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A graphic language—the graphic κ calculus—modeling protein interactions at the domain level is introduced. Complexation, activation and mixed forms of interaction are expressed as graph rewriting rules. A compilation in a low-level graph rewriting calculus, called mobile κ, is given and shown to be correct up to some suitable notion of observational equivalence. This intermediate language is of independent interest and can be easily implemented in π-like calculi.