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Molecular Signaling - Model Decomposition and Stochastic Fragments


Tatjana Petrov, A. Ganguly, H. Koeppl

Second International Workshop on Static Analysis and Systems Biology (SASB 2011)

In this paper, we discuss a method for decomposition, abstraction and reconstruction of the stochastic semantics of rule-based systems with conserved number of agents. Abstraction is induced by counting fragments instead of the species, which are the standard entities of information in molecular signaling. The rule-set can be decomposed to smaller rule-sets, so that the fragment-based dynamics of the whole rule-set is exactly a composition of species-based dynamics of smaller rule-sets. The reconstruction of the transient species-based dynamics is possible for certain initial distributions. We show that, if all the rules in a rule set are reversible, the reconstruction of the species-based dynamics is always possible at the stationary distribution. We use a case study of colloidal aggregation to demonstrate that the method can reduce the state space exponentially with respect to the standard species-based description.


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% Autogenerated BibTeX entry
@InProceedings { PetGan:2011:IFA_3993,
    author={Tatjana Petrov and A. Ganguly and H. Koeppl},
    title={{Molecular Signaling - Model Decomposition and Stochastic
    booktitle={Second International Workshop on Static Analysis and
	  Systems Biology (SASB 2011)},
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