Reduction of multiscale stochastic biochemical reaction networks using exact moment derivation

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Biochemical reaction networks (BRNs) in a cell frequently consist of reactions with disparate timescales. The stochastic simulations of such multiscale BRNs are prohibitively slow due to high computational cost for the simulations of fast reactions. One way to resolve this problem uses the fact that fast species regulated by fast reactions quickly equilibrate to their stationary distribution while slow species are unlikely to be changed. Thus, on a slow timescale, fast species can be replaced by their quasi-steady state (QSS): their stationary conditional expectation values for given slow species. As the QSS are determined solely by the state of slow species, such replacement leads to a reduced model, where fast species are eliminated. However, it is challenging to derive the QSS in the presence of nonlinear reactions. While various approximation schemes for the QSS have been developed, they often lead to considerable errors. Here, we propose two classes of multiscale BRNs which can be reduced by deriving an exact QSS rather than approximations. Specifically, if fast species constitute either a feedforward network or a complex balanced network, the reduced model based on the exact QSS can be derived. Such BRNs are frequently observed in a cell as the feedforward network is one of fundamental motifs of gene or protein regulatory networks. Furthermore, complex balanced networks also include various types of fast reversible bindings such as bindings between transcriptional factors and gene regulatory sites. The reduced models based on exact QSS, which can be calculated by the computational packages provided in this work, accurately approximate the slow scale dynamics of the original full model with much lower computational cost.
Publisher
PUBLIC LIBRARY SCIENCE
Issue Date
2017-06
Language
English
Article Type
Article
Keywords

CHEMICAL-REACTION NETWORKS; STEADY-STATE APPROXIMATIONS; GENE REGULATORY NETWORKS; HEAT-SHOCK RESPONSE; CIRCADIAN CLOCK; DEFICIENCY-ZERO; KINETICS; MODELS; NOISE; SIMULATION

Citation

PLOS COMPUTATIONAL BIOLOGY, v.13, no.6

ISSN
1553-734X
DOI
10.1371/journal.pcbi.1005571
URI
http://hdl.handle.net/10203/226675
Appears in Collection
MA-Journal Papers(저널논문)
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