Bulletin of Mathematical Biology

, Volume 77, Issue 12, pp 2180–2211 | Cite as

A Geometric Method for Model Reduction of Biochemical Networks with Polynomial Rate Functions

  • Satya Swarup Samal
  • Dima Grigoriev
  • Holger Fröhlich
  • Andreas Weber
  • Ovidiu Radulescu
Original Article

Abstract

Model reduction of biochemical networks relies on the knowledge of slow and fast variables. We provide a geometric method, based on the Newton polytope, to identify slow variables of a biochemical network with polynomial rate functions. The gist of the method is the notion of tropical equilibration that provides approximate descriptions of slow invariant manifolds. Compared to extant numerical algorithms such as the intrinsic low-dimensional manifold method, our approach is symbolic and utilizes orders of magnitude instead of precise values of the model parameters. Application of this method to a large collection of biochemical network models supports the idea that the number of dynamical variables in minimal models of cell physiology can be small, in spite of the large number of molecular regulatory actors.

Keywords

Model reduction Algebraic systems biology Complexity 

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Copyright information

© Society for Mathematical Biology 2015

Authors and Affiliations

  • Satya Swarup Samal
    • 1
  • Dima Grigoriev
    • 2
  • Holger Fröhlich
    • 1
  • Andreas Weber
    • 3
  • Ovidiu Radulescu
    • 4
  1. 1.Algorithmic BioinformaticsBonn-Aachen International Center for ITBonnGermany
  2. 2.CNRS, Mathématiques, Université de LilleVilleneuve d’AscqFrance
  3. 3.Institut für Informatik IIUniversity of BonnBonnGermany
  4. 4.DIMNP UMR CNRS 5235University of MontpellierMontpellierFrance

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