Comparing Chemical Reaction Networks: A Categorical and Algorithmic Perspective

Luca Cardelli, Mirco Tribastone, Max Tschaikowski, Andrea Vandin

Research output: Chapter in Book/Report/Conference proceedingArticle in proceedingsResearchpeer-review

Abstract

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 a source 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.

Original languageEnglish
Title of host publicationProceedings of the 31st Annual ACM-IEEE Symposium on Logic in Computer Science, LICS 2016
Number of pages10
Volume05-08-July-2016
PublisherInstitute of Electrical and Electronics Engineers Inc.
Publication date5 Jul 2016
Pages485-494
ISBN (Electronic)9781450343916
DOIs
Publication statusPublished - 5 Jul 2016
Externally publishedYes
Event31st Annual ACM/IEEE Symposium on Logic in Computer Science, LICS 2016 - New York, United States
Duration: 5 Jul 20168 Jul 2016

Conference

Conference31st Annual ACM/IEEE Symposium on Logic in Computer Science, LICS 2016
CountryUnited States
CityNew York
Period05/07/201608/07/2016
SponsorAssociation for Computing Machinery, Association for Computing Machinery, European Association for Computer Science Logic, IEEE, IEEE

Keywords

  • bisimulation
  • chemical reaction networks
  • model comparison
  • ordinary differential equations

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