Suppr超能文献

最大口径:一种应用于双态动力学的变分方法。

Maximum Caliber: a variational approach applied to two-state dynamics.

作者信息

Stock Gerhard, Ghosh Kingshuk, Dill Ken A

机构信息

Institute of Physical and Theoretical Chemistry, J W Goethe University, Max-von-Laue-Str. 7, D-60438 Frankfurt, Germany.

出版信息

J Chem Phys. 2008 May 21;128(19):194102. doi: 10.1063/1.2918345.

Abstract

We show how to apply a general theoretical approach to nonequilibrium statistical mechanics, called Maximum Caliber, originally suggested by E. T. Jaynes [Annu. Rev. Phys. Chem. 31, 579 (1980)], to a problem of two-state dynamics. Maximum Caliber is a variational principle for dynamics in the same spirit that Maximum Entropy is a variational principle for equilibrium statistical mechanics. The central idea is to compute a dynamical partition function, a sum of weights over all microscopic paths, rather than over microstates. We illustrate the method on the simple problem of two-state dynamics, A<-->B, first for a single particle, then for M particles. Maximum Caliber gives a unified framework for deriving all the relevant dynamical properties, including the microtrajectories and all the moments of the time-dependent probability density. While it can readily be used to derive the traditional master equation and the Langevin results, it goes beyond them in also giving trajectory information. For example, we derive the Langevin noise distribution rather than assuming it. As a general approach to solving nonequilibrium statistical mechanics dynamical problems, Maximum Caliber has some advantages: (1) It is partition-function-based, so we can draw insights from similarities to equilibrium statistical mechanics. (2) It is trajectory-based, so it gives more dynamical information than population-based approaches like master equations; this is particularly important for few-particle and single-molecule systems. (3) It gives an unambiguous way to relate flows to forces, which has traditionally posed challenges. (4) Like Maximum Entropy, it may be useful for data analysis, specifically for time-dependent phenomena.

摘要

我们展示了如何将一种应用于非平衡统计力学的通用理论方法——最大口径法,最初由E. T. 杰恩斯提出[《物理化学年度评论》31, 579 (1980)],应用于两态动力学问题。最大口径法是一种动力学变分原理,其精神与最大熵作为平衡统计力学的变分原理相同。核心思想是计算一个动力学配分函数,即对所有微观路径而非微观状态的权重求和。我们在两态动力学的简单问题A<-->B上阐述该方法,首先针对单个粒子,然后针对M个粒子。最大口径法为推导所有相关动力学性质提供了一个统一框架,包括微观轨迹和时间相关概率密度的所有矩。虽然它可以很容易地用于推导传统的主方程和朗之万结果,但它超越了这些,还给出了轨迹信息。例如,我们推导朗之万噪声分布而不是假设它。作为解决非平衡统计力学动力学问题的一种通用方法,最大口径法具有一些优点:(1) 它基于配分函数,因此我们可以从与平衡统计力学的相似性中获得见解。(2) 它基于轨迹,因此比像主方程这样基于总体的方法提供更多动力学信息;这对于少粒子和单分子系统尤为重要。(3) 它给出了一种明确的方法来关联流和力,这在传统上是一个挑战。(4) 与最大熵一样,它可能对数据分析有用,特别是对于时间相关现象。

相似文献

1
Maximum Caliber: a variational approach applied to two-state dynamics.
J Chem Phys. 2008 May 21;128(19):194102. doi: 10.1063/1.2918345.
2
Maximum caliber inference of nonequilibrium processes.
J Chem Phys. 2010 Jul 21;133(3):034119. doi: 10.1063/1.3455333.
4
Stochastic dynamics of complexation reaction in the limit of small numbers.
J Chem Phys. 2011 May 21;134(19):195101. doi: 10.1063/1.3590918.
5
The Maximum Caliber Variational Principle for Nonequilibria.
Annu Rev Phys Chem. 2020 Apr 20;71:213-238. doi: 10.1146/annurev-physchem-071119-040206. Epub 2020 Feb 19.
6
Teaching the principles of statistical dynamics.
Am J Phys. 2006 Feb 1;74(2):123-133. doi: 10.1119/1.2142789.
7
Perspective: Maximum caliber is a general variational principle for dynamical systems.
J Chem Phys. 2018 Jan 7;148(1):010901. doi: 10.1063/1.5012990.
8
Steepest entropy ascent model for far-nonequilibrium thermodynamics: unified implementation of the maximum entropy production principle.
Phys Rev E Stat Nonlin Soft Matter Phys. 2014 Oct;90(4):042113. doi: 10.1103/PhysRevE.90.042113. Epub 2014 Oct 7.
9
Rate processes with dynamical disorder: a direct variational approach.
J Chem Phys. 2006 May 28;124(20):204111. doi: 10.1063/1.2200695.
10
Microcanonical origin of the maximum entropy principle for open systems.
Phys Rev E Stat Nonlin Soft Matter Phys. 2012 Oct;86(4 Pt 1):041126. doi: 10.1103/PhysRevE.86.041126. Epub 2012 Oct 15.

引用本文的文献

1
An update on passive transport in and out of plant cells.
Plant Physiol. 2021 Dec 4;187(4):1973-1984. doi: 10.1093/plphys/kiab406.
3
Inferring a network from dynamical signals at its nodes.
PLoS Comput Biol. 2020 Nov 30;16(11):e1008435. doi: 10.1371/journal.pcbi.1008435. eCollection 2020 Nov.
4
The Maximum Caliber Variational Principle for Nonequilibria.
Annu Rev Phys Chem. 2020 Apr 20;71:213-238. doi: 10.1146/annurev-physchem-071119-040206. Epub 2020 Feb 19.
5
Conformational Free Energy Changes via an Alchemical Path without Reaction Coordinates.
J Phys Chem Lett. 2018 Aug 2;9(15):4428-4435. doi: 10.1021/acs.jpclett.8b01851. Epub 2018 Jul 24.
6
Inferring Microscopic Kinetic Rates from Stationary State Distributions.
J Chem Theory Comput. 2014 Aug 12;10(8):3002-3005. doi: 10.1021/ct5001389. Epub 2014 Jun 2.
7
Data-driven quantification of the robustness and sensitivity of cell signaling networks.
Phys Biol. 2013 Dec;10(6):066002. doi: 10.1088/1478-3975/10/6/066002. Epub 2013 Oct 29.
8
Probing the origins of two-state folding.
J Chem Phys. 2013 Oct 14;139(14):145104. doi: 10.1063/1.4823502.
10
A derivation of the master equation from path entropy maximization.
J Chem Phys. 2012 Aug 21;137(7):074103. doi: 10.1063/1.4743955.

本文引用的文献

1
Teaching the principles of statistical dynamics.
Am J Phys. 2006 Feb 1;74(2):123-133. doi: 10.1119/1.2142789.
2
Measuring flux distributions for diffusion in the small-numbers limit.
J Phys Chem B. 2007 Mar 8;111(9):2288-92. doi: 10.1021/jp067036j. Epub 2007 Feb 13.
3
Stochastic simulation of chemical kinetics.
Annu Rev Phys Chem. 2007;58:35-55. doi: 10.1146/annurev.physchem.58.032806.104637.
4
Probing the kinetics of single molecule protein folding.
Biophys J. 2004 Dec;87(6):3633-41. doi: 10.1529/biophysj.104.046243. Epub 2004 Oct 1.
5
Mechanics of DNA packaging in viruses.
Proc Natl Acad Sci U S A. 2003 Mar 18;100(6):3173-8. doi: 10.1073/pnas.0737893100. Epub 2003 Mar 10.
6
Experimental demonstration of violations of the second law of thermodynamics for small systems and short time scales.
Phys Rev Lett. 2002 Jul 29;89(5):050601. doi: 10.1103/PhysRevLett.89.050601. Epub 2002 Jul 15.
7
Probability of second law violations in shearing steady states.
Phys Rev Lett. 1993 Oct 11;71(15):2401-2404. doi: 10.1103/PhysRevLett.71.2401.

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