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Reaction Systems Models for the Heat Shock Response

Sepinoud Azimi, Bogdan Iancu, Ion Petre, Reaction Systems Models for the Heat Shock Response. TUCS Technical Reports 1075, TUCS, 2013.

Abstract:

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.

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BibTeX entry:

@TECHREPORT{tAzIaPe13a,
  title = {Reaction Systems Models for the Heat Shock Response},
  author = {Azimi, Sepinoud and Iancu, Bogdan and Petre, Ion},
  number = {1075},
  series = {TUCS Technical Reports},
  publisher = {TUCS},
  year = {2013},
}

Belongs to TUCS Research Unit(s): Computational Biomodeling Laboratory (Combio Lab)

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