A method of `speed coefficients' for biochemical model reduction applied to the NF-B system
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Publication:2512949
DOI10.1007/S00285-014-0775-XzbMATH Open1306.92022arXiv1403.1610OpenAlexW2154200460WikidataQ41839205 ScholiaQ41839205MaRDI QIDQ2512949FDOQ2512949
Authors: Simon West, L. J. Bridge, Michael R. H. White, Pawel Paszek, V. N. Biktashev 
Publication date: 2 February 2015
Published in: Journal of Mathematical Biology (Search for Journal in Brave)
Abstract: The relationship between components of biochemical network and the resulting dynamics of the overall system is a key focus of computational biology. However, as these networks and resulting mathematical models are inherently complex and non-linear, the understanding of this relationship becomes challenging. Among many approaches, model reduction methods provide an avenue to extract components responsible for the key dynamical features of the system. Unfortunately, these approaches often require intuition to apply. In this manuscript we propose a practical algorithm for the reduction of biochemical reaction systems using fast-slow asymptotics. This method allows the ranking of system variables according to how quickly they approach their momentary steady state, thus selecting the fastest for a steady state approximation. We applied this method to derive models of the Nuclear Factor kappa B network, a key regulator of the immune response that exhibits oscillatory dynamics. Analyses with respect to two specific solutions, which corresponded to different experimental conditions identified different components of the system that were responsible for the respective dynamics. This is an important demonstration of how reduction methods that provide approximations around a specific steady state, could be utilised in order to gain a better understanding of network topology in a broader context.
Full work available at URL: https://arxiv.org/abs/1403.1610
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perturbation theorymodel reductionfast-slow systemscharacteristic timescalessignaling networksKrishna modelnuclear factor kappa Bparameter embedding
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Cited In (12)
- About bifurcational parametric simplification
- Transactions on Computational Systems Biology I
- Fast-slow asymptotics for a Markov chain model of fast sodium current
- Suitability and utility of computational analysis tools: characterization of erythrocyte parameter variation
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- Parameter inference to motivate asymptotic model reduction: an analysis of the gibberellin biosynthesis pathway
- Algorithmic asymptotic analysis of the NF-\(\kappa\mathrm B\) signaling system
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- Identification of microbiota dynamics using robust parameter estimation methods
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