Literature DB >> 12779453

Invariant manifold methods for metabolic model reduction.

Marc R. Roussel1, Simon J. Fraser.   

Abstract

After the decay of transients, the behavior of a set of differential equations modeling a chemical or biochemical system generally rests on a low-dimensional surface which is an invariant manifold of the flow. If an equation for such a manifold can be obtained, the model has effectively been reduced to a smaller system of differential equations. Using perturbation methods, we show that the distinction between rapidly decaying and long-lived (slow) modes has a rigorous basis. We show how equations for attracting invariant (slow) manifolds can be constructed by a geometric approach based on functional equations derived directly from the differential equations. We apply these methods to two simple metabolic models. (c) 2001 American Institute of Physics.

Year:  2001        PMID: 12779453     DOI: 10.1063/1.1349891

Source DB:  PubMed          Journal:  Chaos        ISSN: 1054-1500            Impact factor:   3.642


  8 in total

1.  Automated refinement and inference of analytical models for metabolic networks.

Authors:  Michael D Schmidt; Ravishankar R Vallabhajosyula; Jerry W Jenkins; Jonathan E Hood; Abhishek S Soni; John P Wikswo; Hod Lipson
Journal:  Phys Biol       Date:  2011-08-10       Impact factor: 2.583

2.  A multi-time-scale analysis of chemical reaction networks: I. Deterministic systems.

Authors:  Chang Hyeong Lee; Hans G Othmer
Journal:  J Math Biol       Date:  2009-04-07       Impact factor: 2.259

Review 3.  Time-scale separation--Michaelis and Menten's old idea, still bearing fruit.

Authors:  Jeremy Gunawardena
Journal:  FEBS J       Date:  2013-10-17       Impact factor: 5.542

4.  New time-scale criteria for model simplification of bio-reaction systems.

Authors:  Junwon Choi; Kyung-won Yang; Tai-yong Lee; Sang Yup Lee
Journal:  BMC Bioinformatics       Date:  2008-08-12       Impact factor: 3.169

5.  Identifying optimal models to represent biochemical systems.

Authors:  Mochamad Apri; Maarten de Gee; Simon van Mourik; Jaap Molenaar
Journal:  PLoS One       Date:  2014-01-08       Impact factor: 3.240

6.  Driving the Model to Its Limit: Profile Likelihood Based Model Reduction.

Authors:  Tim Maiwald; Helge Hass; Bernhard Steiert; Joep Vanlier; Raphael Engesser; Andreas Raue; Friederike Kipkeew; Hans H Bock; Daniel Kaschek; Clemens Kreutz; Jens Timmer
Journal:  PLoS One       Date:  2016-09-02       Impact factor: 3.240

7.  Some Aspects of Time-Reversal in Chemical Kinetics.

Authors:  Ulrich Maas
Journal:  Entropy (Basel)       Date:  2020-12-07       Impact factor: 2.524

8.  A model reduction method for biochemical reaction networks.

Authors:  Shodhan Rao; Arjan van der Schaft; Karen van Eunen; Barbara M Bakker; Bayu Jayawardhana
Journal:  BMC Syst Biol       Date:  2014-05-03
  8 in total

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