Spectral Rate Theory for Two-State Kinetics.
Spectral Rate Theory for Two-State Kinetics.
复制标题
二态动力学的谱率理论
DOI：
10.1103/physrevx.4.011020
复制
发表时间：
2014
期刊：
影响因子：
--
通讯作者：
Frank Noé
中科院分区：
文献类型：
--
作者：
Jan-Hendrik Prinz;John D. Chodera;Frank Noé
经典速率理论通常在以下情况下失败：所使用的可观察参数或序参数是不良反应坐标或所观察到的信号被噪声劣化，使得反应物和产物之间不可能有明确的分离。在这里，我们提出了一个一般的光谱两态率理论遍历动力系统的热平衡，明确考虑到如何观察系统。该理论允许标准利率理论所造成的系统估计误差被理解和量化。我们还阐明了连接的光谱速率理论与流行的马尔可夫状态建模方法的分子模拟研究。一个最佳的速率估计公式，即使反应坐标差，也能得到稳健和无偏的结果，并可应用于计算机模拟和单分子实验。不需要定义分割面。该理论的另一个结果是反应坐标质量的无模型定义。反应坐标质量可以由直接可计算的观察质量从下方界定，从而提供允许通过调整实验装置来优化反应坐标质量的措施。此外，相应的部分概率分布可以得到反应物和产物状态沿着观察到的序参数，即使当这些强烈重叠。过滤（平均）和不相关的噪声的影响也进行了检查。该方法被证明的数值例子和实验单分子力探针数据的p5ab RNA发夹和脱辅基肌红蛋白在低，这里集中在两个状态的动力学的情况下。
Classical rate theories often fail in cases where the observable(s) or order parameter(s) used is a poor reaction coordinate or the observed signal is deteriorated by noise, such that no clear separation between reactants and products is possible. Here, we present a general spectral two-state rate theory for ergodic dynamical systems in thermal equilibrium that explicitly takes into account how the system is observed. The theory allows the systematic estimation errors made by standard rate theories to be understood and quantified. We also elucidate the connection of spectral rate theory with the popular Markov state modeling approach for molecular simulation studies. An optimal rate estimator is formulated that gives robust and unbiased results even for poor reaction coordinates and can be applied to both computer simulations and single-molecule experiments. No definition of a dividing surface is required. Another result of the theory is a model-free definition of the reaction coordinate quality. The reaction coordinate quality can be bounded from below by the directly computable observation quality, thus providing a measure allowing the reaction coordinate quality to be optimized by tuning the experimental setup. Additionally, the respective partial probability distributions can be obtained for the reactant and product states along the observed order parameter, even when these strongly overlap. The effects of both filtering (averaging) and uncorrelated noise are also examined. The approach is demonstrated on numerical examples and experimental single-molecule force-probe data of the p5ab RNA hairpin and the apo-myoglobin protein at low, focusing here on the case of two-state kinetics.
登录
查看更多内容
非平衡系统中的详细平衡
DOI：
--
发表时间：
1997
期刊：
影响因子：
--
作者：
F. Barra;M. Clerc;E. Tirapegui
通讯作者：
E. Tirapegui
影响因子：
3.4
作者：
Elms, Phillip J.;Chodera, John D.;Marqusee, Susan
通讯作者：
Marqusee, Susan
影响因子：
4.4
作者：
Kube, Susanna;Weber, Marcus
通讯作者：
Weber, Marcus
影响因子：
16.6
作者：
Hoffmann, Armin;Woodside, Michael T.
通讯作者：
Woodside, Michael T.
凝聚相异构化动力学动力学理论的轨迹分析
影响因子：
4.4
作者：
J. Montgomery;D. Chandler;B. Berne
通讯作者：
B. Berne