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BMC Systems Biology

, 6:143

Methods, software and technology

Abstract

BackgroundA heat shock response model of Escherichia coli developed by Srivastava, Peterson, and Bentley 2001 has multiscale nature due to its species numbers and reaction rate constants varying over wide ranges. Applying the method of separation of time-scales and model reduction for stochastic reaction networks extended by Kang and Kurtz 2012, we approximate the chemical network in the heat shock response model.

ResultsScaling the species numbers and the rate constants by powers of the scaling parameter, we embed the model into a one-parameter family of models, each of which is a continuous-time Markov chain. Choosing an appropriate set of scaling exponents for the species numbers and for the rate constants satisfying balance conditions, the behavior of the full network in the time scales of interest is approximated by limiting models in three time scales. Due to the subset of species whose numbers are either approximated as constants or are averaged in terms of other species numbers, the limiting models are located on lower dimensional spaces than the full model and have a simpler structure than the full model does.

ConclusionsThe goal of this paper is to illustrate how to apply the multiscale approximation method to the biological model with significant complexity. We applied the method to the heat shock response model involving 9 species and 18 reactions and derived simplified models in three time scales which capture the dynamics of the full model. Convergence of the scaled species numbers to their limit is obtained and errors between the scaled species numbers and their limit are estimated using the central limit theorem.

KeywordsMultiscale Markov chains Chemical reaction Reaction networks Heat shock Electronic supplementary materialThe online version of this article doi:10.1186-1752-0509-6-143 contains supplementary material, which is available to authorized users.

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Autor: Hye-Won Kang

Fuente: https://link.springer.com/



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