Reaction System Models for the Heat Shock Response

A1 Journal article (refereed)

Internal Authors/Editors

Publication Details

List of Authors: Sepinoud Azimi, Bogdan Iancu, Ion Petre
Publisher: IOS Press
Publication year: 2014
Journal: Fundamenta Informaticae
Volume number: 131
Issue number: 3-4
Start page: 299
End page: 312
eISSN: 1875-8681


Reaction systems are a formal framework for modeling processes driven by biochemical reactions. They are based on the mechanisms of facilitation and inhibition. A main assumption is that if a resource is available, then it is present in sufficient amounts and as such, several reactions using the same resource will not compete concurrently against each other; this makes reaction systems very different as a modeling framework than traditional frameworks such as ODEs or continuous time Markov chains. We demonstrate in this paper that reaction systems are rich enough to capture the essential characteristics of ODE-based models. We construct a reaction system model for the heat shock response in such a way that its qualitative behavior correlates well with the quantitative behavior of the corresponding ODE model. We construct our reaction system model based on a novel concept of dominance graph that captures the competition on resources in the ODE model.
We conclude with a discussion on the expressivity of reaction systems as compared to that of ODE based models.

Last updated on 2020-15-07 at 07:37