Communication Dans Un Congrès Année : 2020

Rewriting Theory for the Life Sciences

Résumé

The Kappa biochemistry and the MØD organo-chemistry frameworks are amongst the most intensely developed applications of rewriting theoretical methods in the life sciences to date. A typical feature of these types of rewriting theories is the necessity to implement certain structural constraints on the objects to be rewritten (a protein is empirically found to have a certain signature of sites, a carbon atom can form at most four bonds,. . .). In this paper, we contribute to the theoretical foundations of these types of rewriting theory a number of conceptual and technical developments that permit to implement a universal theory of continuous-time Markov chains (CTMCs) for stochastic rewriting systems. Our core mathematical concepts are a novel rule algebra construction for the relevant setting of rewriting rules with conditions, both in Double-and in Sesqui-Pushout semantics, augmented by a suitable stochastic mechanics formalism extension that permits to derive dynamical evolution equations for pattern-counting statistics.

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hal-02920023 , version 1 (18-12-2020)

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Nicolas Behr, Jean Krivine. Rewriting Theory for the Life Sciences. International Conference on Graph Transformation 2020, Jun 2020, Bergen, Norway. pp.185-202, ⟨10.1007/978-3-030-51372-6_11⟩. ⟨hal-02920023⟩
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