Conference paper
Comparing Chemical Reaction Networks : A Categorical and Algorithmic Perspective
Microsoft Research & University of Oxford, UK1
600268512
IMT Institute for Advanced Studies Lucca, Italy3
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.
| Language: | English |
|---|---|
| Publisher: | ACM |
| Year: | 2016 |
| Pages: | 485-494 |
| Proceedings: | 2016 31st Annual ACM/IEEE Symposium on Logic in Computer Science (LICS) |
| ISBN: | 1450343910 and 9781450343916 |
| ISSN: | 10436871 and 25755528 |
| Types: | Conference paper |
| DOI: | 10.1145/2933575.2935318 |
Biological system modeling Chemicals Computational modeling Emulation Logic Mathematical model Models of computation Partitioning algorithms Theory of computation Trajectory biological models bisimulation categorical framework chemical reaction networks chemical reactions concurrency models differential equations dynamical properties kernel language model comparison model-comparison approaches ordinary differential equations source CRN target CRN
