A multiscale approximation in a heat shock response model of E. coli

BMC Systems Biology

Hye-Won Kang¹ 

[1]Mathematical Biosciences Institute, Ohio State University, Columbus, OH, USA

关键词: Heat shock;    Reaction networks;    Chemical reaction;    Markov chains;    Multiscale;   

Others  :  1143458
DOI  :  10.1186/1752-0509-6-143

 received in 2011-11-17, accepted in 2012-11-07,  发布年份 2012

【 摘 要 】

Background

A 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.

Results

Scaling 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.

Conclusions

The 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.

【 授权许可】

   
2012 Kang; licensee BioMed Central Ltd.

【 图 表 】

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