Suppr超能文献

用于研究催化反应网络中少数效应的分析框架:化学主方程的概率生成函数方法

An Analytical Framework for Studying Small-Number Effects in Catalytic Reaction Networks: A Probability Generating Function Approach to Chemical Master Equations.

作者信息

Nakagawa Masaki, Togashi Yuichi

机构信息

Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University Higashi-Hiroshima, Japan.

Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima UniversityHigashi-Hiroshima, Japan; Research Center for the Mathematics on Chromatin Live Dynamics, Hiroshima UniversityHigashi-Hiroshima, Japan.

出版信息

Front Physiol. 2016 Mar 24;7:89. doi: 10.3389/fphys.2016.00089. eCollection 2016.

Abstract

Cell activities primarily depend on chemical reactions, especially those mediated by enzymes, and this has led to these activities being modeled as catalytic reaction networks. Although deterministic ordinary differential equations of concentrations (rate equations) have been widely used for modeling purposes in the field of systems biology, it has been pointed out that these catalytic reaction networks may behave in a way that is qualitatively different from such deterministic representation when the number of molecules for certain chemical species in the system is small. Apart from this, representing these phenomena by simple binary (on/off) systems that omit the quantities would also not be feasible. As recent experiments have revealed the existence of rare chemical species in cells, the importance of being able to model potential small-number phenomena is being recognized. However, most preceding studies were based on numerical simulations, and theoretical frameworks to analyze these phenomena have not been sufficiently developed. Motivated by the small-number issue, this work aimed to develop an analytical framework for the chemical master equation describing the distributional behavior of catalytic reaction networks. For simplicity, we considered networks consisting of two-body catalytic reactions. We used the probability generating function method to obtain the steady-state solutions of the chemical master equation without specifying the parameters. We obtained the time evolution equations of the first- and second-order moments of concentrations, and the steady-state analytical solution of the chemical master equation under certain conditions. These results led to the rank conservation law, the connecting state to the winner-takes-all state, and analysis of 2-molecules M-species systems. A possible interpretation of the theoretical conclusion for actual biochemical pathways is also discussed.

摘要

细胞活动主要依赖于化学反应,尤其是那些由酶介导的反应,这使得这些活动被建模为催化反应网络。尽管浓度的确定性常微分方程(速率方程)在系统生物学领域已被广泛用于建模目的,但有人指出,当系统中某些化学物种的分子数量较少时,这些催化反应网络的行为方式可能与这种确定性表示在性质上有所不同。除此之外,用省略数量的简单二元(开/关)系统来表示这些现象也是不可行的。由于最近的实验揭示了细胞中存在稀有化学物种,能够对潜在的少数分子现象进行建模的重要性正在得到认可。然而,大多数先前的研究都是基于数值模拟,用于分析这些现象的理论框架尚未得到充分发展。受少数分子问题的推动,这项工作旨在为描述催化反应网络分布行为的化学主方程开发一个分析框架。为了简单起见,我们考虑了由双体催化反应组成的网络。我们使用概率生成函数方法在不指定参数的情况下获得化学主方程的稳态解。我们得到了浓度的一阶和二阶矩的时间演化方程,以及在某些条件下化学主方程的稳态解析解。这些结果引出了秩守恒定律、从连接状态到胜者全得状态的转变,以及对双分子M物种系统的分析。我们还讨论了该理论结论对实际生化途径的一种可能解释。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6cef/4805594/4bed5195eb5f/fphys-07-00089-g0001.jpg

相似文献

2
A closure scheme for chemical master equations.
Proc Natl Acad Sci U S A. 2013 Aug 27;110(35):14261-5. doi: 10.1073/pnas.1306481110. Epub 2013 Aug 12.
4
Validity conditions for moment closure approximations in stochastic chemical kinetics.
J Chem Phys. 2014 Aug 28;141(8):084103. doi: 10.1063/1.4892838.
5
DeepCME: A deep learning framework for computing solution statistics of the chemical master equation.
PLoS Comput Biol. 2021 Dec 8;17(12):e1009623. doi: 10.1371/journal.pcbi.1009623. eCollection 2021 Dec.
6
Master equations and the theory of stochastic path integrals.
Rep Prog Phys. 2017 Apr;80(4):046601. doi: 10.1088/1361-6633/aa5ae2.
9
Stochastic analysis of complex reaction networks using binomial moment equations.
Phys Rev E Stat Nonlin Soft Matter Phys. 2012 Sep;86(3 Pt 1):031126. doi: 10.1103/PhysRevE.86.031126. Epub 2012 Sep 20.
10
Analytical Derivation of Moment Equations in Stochastic Chemical Kinetics.
Chem Eng Sci. 2011 Feb 1;66(3):268-277. doi: 10.1016/j.ces.2010.10.024.

本文引用的文献

1
Distinguishing between discreteness effects in stochastic reaction processes.
Phys Rev E Stat Nonlin Soft Matter Phys. 2015 May;91(5):052814. doi: 10.1103/PhysRevE.91.052814. Epub 2015 May 26.
2
Theoretical analysis of discreteness-induced transition in autocatalytic reaction dynamics.
Phys Rev E Stat Nonlin Soft Matter Phys. 2015 Feb;91(2):022707. doi: 10.1103/PhysRevE.91.022707. Epub 2015 Feb 13.
3
Exact results for a noise-induced bistable system.
Phys Rev E Stat Nonlin Soft Matter Phys. 2015 Feb;91(2):022115. doi: 10.1103/PhysRevE.91.022115. Epub 2015 Feb 11.
5
Noise-induced bistable states and their mean switching time in foraging colonies.
Phys Rev Lett. 2014 Jan 24;112(3):038101. doi: 10.1103/PhysRevLett.112.038101. Epub 2014 Jan 22.
6
Small-number effects: a third stable state in a genetic bistable toggle switch.
Phys Rev Lett. 2012 Dec 14;109(24):248107. doi: 10.1103/PhysRevLett.109.248107. Epub 2012 Dec 13.
7
A design principle for a posttranslational biochemical oscillator.
Cell Rep. 2012 Oct 25;2(4):938-50. doi: 10.1016/j.celrep.2012.09.006. Epub 2012 Oct 19.
8
Noise-induced metastability in biochemical networks.
Phys Rev E Stat Nonlin Soft Matter Phys. 2012 Jul;86(1 Pt 1):010106. doi: 10.1103/PhysRevE.86.010106. Epub 2012 Jul 30.
9
A probability generating function method for stochastic reaction networks.
J Chem Phys. 2012 Jun 21;136(23):234108. doi: 10.1063/1.4729374.
10
Wnt signalling pathway parameters for mammalian cells.
PLoS One. 2012;7(2):e31882. doi: 10.1371/journal.pone.0031882. Epub 2012 Feb 21.

文献AI研究员

20分钟写一篇综述,助力文献阅读效率提升50倍。

立即体验

用中文搜PubMed

大模型驱动的PubMed中文搜索引擎

马上搜索

文档翻译

学术文献翻译模型,支持多种主流文档格式。

立即体验