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Title: Stochastic lumping analysis for linear kinetics and its application to the fluctuation relations between hierarchical kinetic networks

Abstract

Conventional studies of biomolecular behaviors rely largely on the construction of kinetic schemes. Since the selection of these networks is not unique, a concern is raised whether and under which conditions hierarchical schemes can reveal the same experimentally measured fluctuating behaviors and unique fluctuation related physical properties. To clarify these questions, we introduce stochasticity into the traditional lumping analysis, generalize it from rate equations to chemical master equations and stochastic differential equations, and extract the fluctuation relations between kinetically and thermodynamically equivalent networks under intrinsic and extrinsic noises. The results provide a theoretical basis for the legitimate use of low-dimensional models in the studies of macromolecular fluctuations and, more generally, for exploring stochastic features in different levels of contracted networks in chemical and biological kinetic systems.

Authors:
;  [1]
  1. Institute of Physics, National Chiao Tung University, Hsinchu 300, Taiwan (China)
Publication Date:
OSTI Identifier:
22415759
Resource Type:
Journal Article
Journal Name:
Journal of Chemical Physics
Additional Journal Information:
Journal Volume: 142; Journal Issue: 18; Other Information: (c) 2015 AIP Publishing LLC; Country of input: International Atomic Energy Agency (IAEA); Journal ID: ISSN 0021-9606
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL AND ANALYTICAL CHEMISTRY; BASES; BIOCHEMICAL REACTION KINETICS; DIFFERENTIAL EQUATIONS; FLUCTUATIONS; MATHEMATICAL MODELS; MOLECULES; PHYSICAL PROPERTIES; REACTION KINETICS; STOCHASTIC PROCESSES

Citation Formats

Deng, De-Ming, and Chang, Cheng-Hung. Stochastic lumping analysis for linear kinetics and its application to the fluctuation relations between hierarchical kinetic networks. United States: N. p., 2015. Web. doi:10.1063/1.4919952.
Deng, De-Ming, & Chang, Cheng-Hung. Stochastic lumping analysis for linear kinetics and its application to the fluctuation relations between hierarchical kinetic networks. United States. doi:10.1063/1.4919952.
Deng, De-Ming, and Chang, Cheng-Hung. Thu . "Stochastic lumping analysis for linear kinetics and its application to the fluctuation relations between hierarchical kinetic networks". United States. doi:10.1063/1.4919952.
@article{osti_22415759,
title = {Stochastic lumping analysis for linear kinetics and its application to the fluctuation relations between hierarchical kinetic networks},
author = {Deng, De-Ming and Chang, Cheng-Hung},
abstractNote = {Conventional studies of biomolecular behaviors rely largely on the construction of kinetic schemes. Since the selection of these networks is not unique, a concern is raised whether and under which conditions hierarchical schemes can reveal the same experimentally measured fluctuating behaviors and unique fluctuation related physical properties. To clarify these questions, we introduce stochasticity into the traditional lumping analysis, generalize it from rate equations to chemical master equations and stochastic differential equations, and extract the fluctuation relations between kinetically and thermodynamically equivalent networks under intrinsic and extrinsic noises. The results provide a theoretical basis for the legitimate use of low-dimensional models in the studies of macromolecular fluctuations and, more generally, for exploring stochastic features in different levels of contracted networks in chemical and biological kinetic systems.},
doi = {10.1063/1.4919952},
journal = {Journal of Chemical Physics},
issn = {0021-9606},
number = 18,
volume = 142,
place = {United States},
year = {2015},
month = {5}
}