沿反应坐标动力学马尔可夫性的单分子测试
Single-Molecule Test for Markovianity of the Dynamics along a Reaction Coordinate.
作者信息
Berezhkovskii Alexander M, Makarov Dmitrii E
机构信息
Mathematical and Statistical Computing Laboratory, Office of Intramural Research, Center for Information Technology , National Institutes of Health , Bethesda , Maryland 20892 , United States.
Department of Chemistry , University of Texas at Austin , Austin , Texas 78712 , United States.
出版信息
J Phys Chem Lett. 2018 May 3;9(9):2190-2195. doi: 10.1021/acs.jpclett.8b00956. Epub 2018 Apr 16.
Abstract
In an effort to answer the much-debated question of whether the time evolution of common experimental observables can be described as one-dimensional diffusion in the potential of mean force, we propose a simple criterion that allows one to test whether the Markov assumption is applicable to a single-molecule trajectory x( t). This test does not involve fitting of the data to any presupposed model and can be applied to experimental data with relatively low temporal resolution.
摘要
为了回答一个备受争议的问题，即常见实验可观测量的时间演化是否可以描述为在平均力势中的一维扩散，我们提出了一个简单的标准，该标准可以用来检验马尔可夫假设是否适用于单分子轨迹x(t)。这个检验不涉及将数据拟合到任何预先设定的模型，并且可以应用于时间分辨率相对较低的实验数据。
相似文献
1
Single-Molecule Test for Markovianity of the Dynamics along a Reaction Coordinate.沿反应坐标动力学马尔可夫性的单分子测试
J Phys Chem Lett. 2018 May 3;9(9):2190-2195. doi: 10.1021/acs.jpclett.8b00956. Epub 2018 Apr 16.
2
Communication: Coordinate-dependent diffusivity from single molecule trajectories.通讯：单分子轨迹的坐标相关扩散系数。
J Chem Phys. 2017 Nov 28;147(20):201102. doi: 10.1063/1.5006456.
3
Projected metastable Markov processes and their estimation with observable operator models.投影亚稳态马尔可夫过程及其可观算子模型估计
J Chem Phys. 2015 Oct 14;143(14):144101. doi: 10.1063/1.4932406.
4
Transition path dynamics in the binding of intrinsically disordered proteins: A simulation study.固有无序蛋白质结合中的转变路径动力学：模拟研究。
J Chem Phys. 2019 Dec 21;151(23):235101. doi: 10.1063/1.5129150.
5
Projected and hidden Markov models for calculating kinetics and metastable states of complex molecules.用于计算复杂分子动力学和亚稳态的预测和隐马尔可夫模型。
J Chem Phys. 2013 Nov 14;139(18):184114. doi: 10.1063/1.4828816.
6
Limitations of a Fokker-Planck description of nucleation.福克-普朗克成核描述的局限性。
Phys Rev E Stat Nonlin Soft Matter Phys. 2010 Jul;82(1 Pt 1):011128. doi: 10.1103/PhysRevE.82.011128. Epub 2010 Jul 20.
7
Non-Markov bond model for dynamic force spectroscopy.用于动态力谱学的非马尔可夫键模型
J Chem Phys. 2020 Feb 14;152(6):064104. doi: 10.1063/1.5134742.
8
Transition Path Times in Non-Markovian Activated Rate Processes.非马尔可夫激活率过程中的转变路径时间。
J Phys Chem B. 2018 Dec 13;122(49):11400-11413. doi: 10.1021/acs.jpcb.8b07361. Epub 2018 Sep 17.
9
Meaningful interpretation of subdiffusive measurements in living cells (crowded environment) by fluorescence fluctuation microscopy.荧光波动显微镜对活细胞（拥挤环境）中的亚扩散测量进行有意义的解释。
Curr Pharm Biotechnol. 2010 Aug;11(5):527-43. doi: 10.2174/138920110791591454.
10
Dynamical coring of Markov state models.马尔可夫状态模型的动力学核化。
J Chem Phys. 2019 Mar 7;150(9):094111. doi: 10.1063/1.5081767.
引用本文的文献
1
High-order Michaelis-Menten equations allow inference of hidden kinetic parameters in enzyme catalysis.高阶米氏方程可用于推断酶催化中隐藏的动力学参数。
Nat Commun. 2025 Mar 20;16(1):2739. doi: 10.1038/s41467-025-57327-2.
2
Spectral Map for Slow Collective Variables, Markovian Dynamics, and Transition State Ensembles.慢集体变量、马尔可夫动力学和过渡态系综的光谱图
J Chem Theory Comput. 2024 Sep 12;20(18):7775-84. doi: 10.1021/acs.jctc.4c00428.
3
General theory for localizing the where and when of entropy production meets single-molecule experiments.用于定位熵产生的位置和时间的一般理论与单分子实验相结合。
Proc Natl Acad Sci U S A. 2024 Aug 13;121(33):e2405371121. doi: 10.1073/pnas.2405371121. Epub 2024 Aug 9.
4
Milestoning estimators of dissipation in systems observed at a coarse resolution.粗分辨率下观测系统中耗散的里程碑式估计量。
Proc Natl Acad Sci U S A. 2024 Apr 23;121(17):e2318333121. doi: 10.1073/pnas.2318333121. Epub 2024 Apr 16.
5
Fast protein folding is governed by memory-dependent friction.快速蛋白质折叠由依赖记忆的摩擦力控制。
Proc Natl Acad Sci U S A. 2023 Aug;120(31):e2220068120. doi: 10.1073/pnas.2220068120. Epub 2023 Jul 25.
6
A universal description of stochastic oscillators.随机振荡器的通用描述。
Proc Natl Acad Sci U S A. 2023 Jul 18;120(29):e2303222120. doi: 10.1073/pnas.2303222120. Epub 2023 Jul 11.
7
Microcanonical coarse-graining of the kinetic Ising model.动力学伊辛模型的微正则粗粒化
J Chem Phys. 2020 Feb 28;152(8):084104. doi: 10.1063/1.5139228.
8
Measuring the average shape of transition paths during the folding of a single biological molecule.测量单个生物分子折叠过程中过渡路径的平均形状。
Proc Natl Acad Sci U S A. 2019 Apr 23;116(17):8125-8130. doi: 10.1073/pnas.1816602116. Epub 2019 Apr 5.
9
Communication: Transition-path velocity as an experimental measure of barrier crossing dynamics.通讯：作为实验测量势垒穿越动力学的渡越速度。
J Chem Phys. 2018 May 28;148(20):201102. doi: 10.1063/1.5030427.
本文引用的文献
1
Slow domain reconfiguration causes power-law kinetics in a two-state enzyme.慢的结构域重排导致两态酶的幂律动力学。
Proc Natl Acad Sci U S A. 2018 Jan 16;115(3):513-518. doi: 10.1073/pnas.1714401115. Epub 2018 Jan 3.
2
Transition path times reveal memory effects and anomalous diffusion in the dynamics of protein folding.转变路径时间揭示了蛋白质折叠动力学中的记忆效应和异常扩散。
J Chem Phys. 2017 Oct 21;147(15):152707. doi: 10.1063/1.4993228.
3
Nonexponential Kinetics of Loop Formation in Proteins and Peptides: A Signature of Rugged Free Energy Landscapes?蛋白质和肽中环形成的非指数动力学：崎岖自由能景观的特征？
J Phys Chem B. 2017 Oct 19;121(41):9518-9525. doi: 10.1021/acs.jpcb.7b07075. Epub 2017 Oct 6.
4
Theoretical and computational validation of the Kuhn barrier friction mechanism in unfolded proteins.对展开蛋白质中库恩障碍摩擦机制的理论和计算验证。
Sci Rep. 2017 Mar 21;7(1):269. doi: 10.1038/s41598-017-00287-5.
5
Reconciling transition path time and rate measurements in reactions with large entropic barriers.在具有较大熵垒的反应中协调过渡路径时间和速率测量。
J Chem Phys. 2017 Feb 21;146(7):071101. doi: 10.1063/1.4977177.
6
Direct observation of transition paths during the folding of proteins and nucleic acids.直接观察蛋白质和核酸折叠过程中的转变路径。
Science. 2016 Apr 8;352(6282):239-42. doi: 10.1126/science.aad0637.
7
Perspective: Computer simulations of long time dynamics.视角：长时间动力学的计算机模拟
J Chem Phys. 2016 Feb 14;144(6):060901. doi: 10.1063/1.4940794.
8
Transition-Path Probability as a Test of Reaction-Coordinate Quality Reveals DNA Hairpin Folding Is a One-Dimensional Diffusive Process.作为反应坐标质量检验的跃迁路径概率揭示DNA发夹折叠是一个一维扩散过程。
J Phys Chem Lett. 2015 Mar 19;6(6):1005-10. doi: 10.1021/acs.jpclett.5b00176. Epub 2015 Mar 5.
9
Extracting the diffusion tensor from molecular dynamics simulation with Milestoning.使用里程碑法从分子动力学模拟中提取扩散张量。
J Chem Phys. 2015 Jan 7;142(1):014105. doi: 10.1063/1.4904882.
10
The roughness of the protein energy landscape results in anomalous diffusion of the polypeptide backbone.蛋白质能量景观的粗糙度导致多肽主链的反常扩散。
Phys Chem Chem Phys. 2015 Jan 14;17(2):762-82. doi: 10.1039/c4cp03058c. Epub 2014 Nov 20.
Zotero 插件