Tropical geometries and dynamics of biochemical networks application to hybrid cell cycle models
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Publication:5404097
DOI10.1016/J.ENTCS.2012.05.016zbMATH Open1283.92043arXiv1109.4085OpenAlexW2138389139WikidataQ113318109 ScholiaQ113318109MaRDI QIDQ5404097FDOQ5404097
Authors: Vincent Noël, S. A. Vakulenko, Ovidiu Radulescu, Dima Grigoriev 
Publication date: 21 March 2014
Published in: Electronic Notes in Theoretical Computer Science (Search for Journal in Brave)
Abstract: We use the Litvinov-Maslov correspondence principle to reduce and hybridize networks of biochemical reactions. We apply this method to a cell cycle oscillator model. The reduced and hybridized model can be used as a hybrid model for the cell cycle. We also propose a practical recipe for detecting quasi-equilibrium QE reactions and quasi-steady state QSS species in biochemical models with rational rate functions and use this recipe for model reduction. Interestingly, the QE/QSS invariant manifold of the smooth model and the reduced dynamics along this manifold can be put into correspondence to the tropical variety of the hybridization and to sliding modes along this variety, respectively
Full work available at URL: https://arxiv.org/abs/1109.4085
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- Methods of model reduction for large-scale biological systems: a survey of current methods and trends
- Qualitative dynamics of chemical reaction networks: an investigation using partial tropical equilibrations
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- Model reduction of biochemical reactions networks by tropical analysis methods
- New algorithms for solving tropical linear systems
- Response to stress via underlying deep gene regulation networks
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