Reaction systems models for the heatshock response

Tutkimustuotos: Kirja/lehti/raporttiTutkimusraporttiAmmatillinen


Reaction systems are a formal framework for modeling processes driven by bio-
chemical reactions. They are based on the mechanisms of facilitation and inhi-
bition. 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 differ-
ent as a modeling framework than traditional frameworks such as ODEs or con-
tinuous time Markov chains. We construct in this paper a reaction systems 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 discuss
two different approaches for building the model. We conclude with a discussion
on the expressivity of reaction systems as compared to that of ODE-based models.
ISBN (elektroninen)978-952-12-2879-7
TilaJulkaistu - 2013
OKM-julkaisutyyppiD4 Julkaistut kehitykset tai tutkimusraportit tai tutkimukset


NimiTUCS Technical Reports
ISSN (painettu)1239-1891


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