Synchronous Balanced Analysis

Conference paper

DOI: 10.1007/978-3-319-47151-8_6

Part of the Lecture Notes in Computer Science book series (LNCS, volume 9957)
Cite this paper as:
Beica A., Danos V. (2016) Synchronous Balanced Analysis. In: Cinquemani E., Donzé A. (eds) Hybrid Systems Biology. HSB 2016. Lecture Notes in Computer Science, vol 9957. Springer, Cham

Abstract

When modeling Chemical Reaction Networks, a commonly used mathematical formalism is that of Petri Nets, with the usual interleaving execution semantics. We aim to substitute to a Chemical Reaction Network, especially a “growth” one (i.e., for which an exponential stationary phase exists), a piecewise synchronous approximation of the dynamics: a resource-allocation-centered Petri Net with maximal-step execution semantics. In the case of unimolecular chemical reactions, we prove the correctness of our method and show that it can be used either as an approximation of the dynamics, or as a method of constraining the reaction rate constants (an alternative to flux balance analysis, using an emergent formally defined notion of “growth rate” as the objective function), or a technique of refuting models.

Keywords

Chemical Reaction Networks Approximation Resource allocation Max-parallel execution of Petri Nets Flux balance analysis 

Copyright information

© Springer International Publishing AG 2016

Authors and Affiliations

  1. 1.École Normale SupérieureParisFrance

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