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Bulletin of Mathematical Biology

, Volume 81, Issue 5, pp 1613–1644 | Cite as

Computing Weakly Reversible Deficiency Zero Network Translations Using Elementary Flux Modes

  • Matthew D. JohnstonEmail author
  • Evan Burton
Article
  • 40 Downloads

Abstract

We present a computational method for performing structural translation, which has been studied recently in the context of analyzing the steady states and dynamical behavior of mass-action systems derived from biochemical reaction networks. Our procedure involves solving a binary linear programming problem where the decision variables correspond to interactions between the reactions of the original network. We call the resulting network a reaction-to-reaction graph and formalize how such a construction relates to the original reaction network and the structural translation. We demonstrate the efficacy and efficiency of the algorithm by running it on 508 networks from the European Bioinformatics Institutes’ BioModels database. We also summarize how this work can be incorporated into recently proposed algorithms for establishing mono- and multistationarity in biochemical reaction systems.

Keywords

Biochemical reactions Deficiency Multistationarity Binary programming 

Mathematics Subject Classification

92C42 90C10 

Notes

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Copyright information

© Society for Mathematical Biology 2019

Authors and Affiliations

  1. 1.Department of MathematicsSan José State UniversitySan JoseUSA

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