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Forward and Backward Bisimulations for Chemical Reaction Networks

Cardelli, Luca and Tribastone, Mirco and Tschaikowski, Max and Vandin, Andrea Forward and Backward Bisimulations for Chemical Reaction Networks. In: 26th International Conference on Concurrency Theory (CONCUR 2015), September 1–4, 2015, Madrid, Spain pp. 226-239. ISSN 1868-8969. ISBN 978-3-939897-91-0. (2015)

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We present two quantitative behavioral equivalences over species of a chemical reaction network(CRN) with semantics based on ordinary differential equations.Forward CRN bisimulationiden-tifies a partition where each equivalence class represents the exact sum of the concentrations ofthe species belonging to that class. Backward CRN bisimulationrelates species that have theidentical solutions at all time points when starting from the same initial conditions. Both notionscan be checked using only CRN syntactical information, i.e., by inspection of the set of reactions. We provide a unified algorithm that computes the coarsest refinement up to our bisimulationsin polynomial time. Further, we give algorithms to compute quotient CRNs induced by a bisim-ulation. As an application, we find significant reductions in a number of models of biologicalprocesses from the literature. In two cases we allow the analysis of benchmark models whichwould be otherwise intractable due to their memory requirements.

Item Type: Conference or Workshop Item (Paper)
Identification Number: 10.4230/LIPIcs.CONCUR.2015.226
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 09:23
Last Modified: 13 Apr 2016 09:23
URI: http://eprints.imtlucca.it/id/eprint/3441

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