高分子稀有跃迁自由能分布和跃迁时间的微观计算
Microscopically Computing Free-energy Profiles and Transition Path Time of Rare Macromolecular Transitions
摘要：
我们引入了一个严格的方法来微观计算的可观的特征的热力学和动力学罕见的大分子过渡，它是可能的，以确定一个先验的慢反应坐标。为了采样统计上显着的反应途径的合奏，我们定义了一个有偏见的分子动力学（MD），其中跨越障碍的过渡加速，而不引入任何非物理外力。与其他有偏MD方法相比，在本方法中，为了加速过渡而产生的系统误差可以解析计算，因此可以进行校正。这允许作为反应坐标的函数的自由能分布的计算上有效的重建，并且允许计算相应的扩散系数。然后可以在主导反应途径（DRP）方法内容易地评估过渡路径时间。我们说明和测试这种方法通过表征热激活过渡的二维能量表面和一个小的蛋白质片段内的粗粒度模型的折叠。
英文摘要：
We introduce a rigorous method to microscopically compute the observables which characterize the thermodynamics and kinetics of rare macromolecular transitions for which it is possible to identify a priori a slow reaction coordinate. In order to sample the ensemble of statistically significant reaction pathways, we define a biased molecular dynamics (MD) in which barrier-crossing transitions are accelerated without introducing any unphysical external force. In contrast to other biased MD methods, in the present approach the systematic errors which are generated in order to accelerate the transition can be analytically calculated and therefore can be corrected for. This allows for a computationally efficient reconstruction of the free-energy profile as a function of the reaction coordinate and for the calculation of the corresponding diffusion coefficient. The transition path time can then be readily evaluated within the Dominant Reaction Pathways (DRP) approach. We illustrate and test this method by characterizing a thermally activated transition on a two-dimensional energy surface and the folding of a small protein fragment within a coarse-grained model.
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