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Article Dans Une Revue Theoretical Computer Science Année : 2008

Computational self-assembly

Vincent Danos
Min Zhang
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Résumé

The object of this paper is to appreciate the computational limits inherent in the combinatorics of an applied concurrent (aka agent-based) language kappa. That language is primarily meant as a visual and concise notation for biological signalling pathways. Descriptions in kappa, when enriched with suitable kinetic information, generate simulations as continuous time Markov chains. However, kappa can be studied independently of the intended application, in a purely computational fashion, and this is what we are doing here. Specifically, we define a compilation of kappa into a language where interactions can involve at most two agents at a time. That compilation is generic, the blow up in the number of rules is linear in the total rule set size, and the methodology used in deriving the compilation relies on an implicit causality analysis. The correctness proof is given in details, and correctness is spelt out in terms of the existence of a specific weak bisimulation. To compensate for the binary restriction, one allows components to create unique identifiers (aka names). An interesting by-product of the analysis is that when using acyclic rules, one sees that name creation is not needed, and can be fully reduced to binary form.
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Dates et versions

hal-00155297 , version 1 (18-06-2007)

Identifiants

  • HAL Id : hal-00155297 , version 1

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Pierre-Louis Curien, Vincent Danos, Jean Krivine, Min Zhang. Computational self-assembly. Theoretical Computer Science, 2008, 404 ((1-2)), pp.61-75. ⟨hal-00155297⟩
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