Dependency Graphs and Mass Conservation in Reaction Systems

D4 Publicerad utvecklings- eller forskningsrapport eller studie

Interna författare/redaktörer

Publikationens författare: Sepinoud Azimi, Cristian Gratie, Sergiu Ivanov, Ion Petre
Förläggare: Turku Centre for Computer Science (TUCS)
Publiceringsår: 2014
ISBN: 978-952-12-3123-0


Reaction systems is a new mathematical formalism inspired by the biological cell, which focuses on an abstract set-based representation of chemical reactions via facilitation and inhibition. In this article we focus on the property of mass conservation for reaction systems. We show that conservation of sets gives rise to a relation between the species, which we capture in the concept of the conservation dependency graph. We then describe an application of this relation to the problem of listing all conserved sets. We further give a sufficient negative polynomial criterion which can be used in proving that a set is not conserved. Finally, we present a simulator of reaction systems, which also includes an implementation of the algorithm for listing the conserved sets of a given reaction system.


conservation dependency graph, conserved set, mass conservation, model checking, reaction system, Simulator

Senast uppdaterad 2020-05-04 vid 08:26