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Milestoning: An Efficient Approach for Atomically Detailed Simulations of Kinetics in Biophysics.
Annual Review of Biophysics ( IF 12.4 ) Pub Date : 2020-05-06 , DOI: 10.1146/annurev-biophys-121219-081528
Ron Elber 1
Affiliation  

Recent advances in theory and algorithms for atomically detailed simulations open the way to the study of the kinetics of a wide range of molecular processes in biophysics. The theories propose a shift from the traditionally very long molecular dynamic trajectories, which are exact but may not be efficient in the study of kinetics, to the use of a large number of short trajectories. The short trajectories exploit a mapping to a mesh in coarse space and allow for efficient calculations of kinetics and thermodynamics. In this review, I focus on one theory: Milestoning is a theory and an algorithm that offers a hierarchical calculation of properties of interest, such as the free energy profile and the mean first passage time. Approximations to the true long-time dynamics can be computed efficiently and assessed at different steps of the investigation. The theory is discussed and illustrated using two biophysical examples: ion permeation through a phospholipid membrane and protein translocation through a channel.

中文翻译:

里程碑:生物物理动力学动力学详细模拟的有效方法。

原子详细模拟的理论和算法方面的最新进展为生物物理学中广泛的分子过程动力学的研究开辟了道路。这些理论提出了从传统的非常长的分子动力学轨迹转变为使用大量短轨迹的转变,传统的分子动力学轨迹是精确的,但在动力学研究中可能并不有效。短轨迹利用在粗糙空间中到网格的映射,并允许有效地计算动力学和热力学。在这篇综述中,我将重点关注一个理论:Milestoning是一种理论和算法,可以对感兴趣的特性(例如自由能分布和平均首次通过时间)进行分层计算。可以真实地计算出真实的长期动态的近似值,并可以在调查的不同步骤对其进行评估。
更新日期:2020-05-06
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