The European Physical Journal B

, Volume 84, Issue 4, pp 673–684 | Cite as

Simulating feedback and reversibility in substrate-enzyme reactions

  • D. A. J. van Zwieten
  • J. E. Rooda
  • D. Armbruster
  • J. D. Nagy
Open Access
Regular Article Focus Section on Frontiers in Network Science: Advances and Applications

Abstract

We extend discrete event models (DEM) of substrate-enzyme reactions to include regulatory feedback and reversible reactions. Steady state as well as transient systems are modeled and validated against ordinary differential equation (ODE) models. The approach is exemplified in a model of the first steps of glycolysis with the most common regulatory mechanisms. We find that in glycolysis, feedback and reversibility together act as a significant damper on the stochastic variations of the intermediate products as well as for the stochastic variation of the transit times. This suggests that these feedbacks have evolved to control both the overall rate of, as well as stochastic fluctuations in, glycolysis.

Keywords

Discrete Event Search Time Stochastic Variation Discrete Event Simulation Substrate Molecule 

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Copyright information

© The Author(s) 2011

Open Access This article is distributed under the terms of the Creative Commons Attribution License which permits any use, distribution and reproduction in any medium, provided the original author(s) and source are credited.

Authors and Affiliations

  • D. A. J. van Zwieten
    • 1
  • J. E. Rooda
    • 1
  • D. Armbruster
    • 1
    • 2
  • J. D. Nagy
    • 3
  1. 1.Department of Mechanical EngineeringEindhoven University of TechnologyEindhovenThe Netherlands
  2. 2.School of Mathematical and Statistical SciencesArizona State UniversityTempeUSA
  3. 3.Department of Life SciencesScottsdale Community CollegeScottsdaleUSA

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