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Comparing Chemical Reaction Networks:A Categorical and Algorithmic Perspective

Cardelli, Luca and Tribastone, Mirco and Tschaikowski, Max and Vandin, Andrea Comparing Chemical Reaction Networks:A Categorical and Algorithmic Perspective. In: Thirty-First Annual ACM/IEEE Symposium on LOGIC IN COMPUTER SCIENCE (LICS), July 5-8, 2016, New York, USA (In Press) (2016)

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We study chemical reaction networks (CRNs) as a kernel language for concurrency models with semantics based on ordinary differential equations. We investigate the problem of comparing two CRNs,i.e., to decide whether the trajectories of asource CRN can be matched by a target CRN under an appropriate choice of initial conditions. Using a categorical framework, we extend and relate model-comparison approaches based on structural (syntactic) and on dynamical (semantic) properties of a CRN, proving their equivalence. Then, we provide an algorithm to compare CRNs, running linearly in time with respect to the cardinality of all possible comparisons. Finally, we apply our results to biological models from the literature.

Item Type: Conference or Workshop Item (Paper)
Uncontrolled Keywords: chemical reaction networks, bisimulation, model com-parison, ordinary differential equations
Subjects: Q Science > QA Mathematics > QA75 Electronic computers. Computer science
Research Area: Computer Science and Applications
Depositing User: Caterina Tangheroni
Date Deposited: 13 Apr 2016 08:14
Last Modified: 13 Apr 2016 08:14
URI: http://eprints.imtlucca.it/id/eprint/3433

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