Computation of transit times using the milestoning method with applications to polymer translocation
Computation of transit times using the milestoning method with applications to polymer translocation
复制标题
DOI：
10.1063/1.4817200
复制
发表时间：
2013-08-14
影响因子：
4.4
通讯作者：
Makarov, Dmitrii E.
中科院分区：
文献类型：
--
作者：
Hawk, Alexander T.;Konda, Sai Sriharsha M.;Makarov, Dmitrii E.
Milestoning是一种有效的近似计算长时间的大分子系统的动力学和热力学，这是无法实现的蛮力分子动力学模拟。里程碑的一个常见用途是计算感兴趣的构象转变的平均首次通过时间（MFPT）。然而，MFPT并不总是实验观察到的时间尺度。特别是，过渡路径的持续时间，或平均通过时间，可以在单分子实验中测量，如研究通过孔易位的聚合物和蛋白质折叠的荧光共振能量转移研究。在这里，我们展示了如何使用里程碑计算渡越时间，并说明我们的方法，通过将其应用到易位的聚合物通过一个狭窄的孔。(C)2013 AIP Publishing LLC.
Milestoning is an efficient approximation for computing long-time kinetics and thermodynamics of large molecular systems, which are inaccessible to brute-force molecular dynamics simulations. A common use of milestoning is to compute the mean first passage time (MFPT) for a conformational transition of interest. However, the MFPT is not always the experimentally observed timescale. In particular, the duration of the transition path, or the mean transit time, can be measured in single-molecule experiments, such as studies of polymers translocating through pores and fluorescence resonance energy transfer studies of protein folding. Here we show how to use milestoning to compute transit times and illustrate our approach by applying it to the translocation of a polymer through a narrow pore. (C) 2013 AIP Publishing LLC.