Characterizing Solvent Density Fluctuations in Dynamical Observation Volumes
Characterizing Solvent Density Fluctuations in Dynamical Observation Volumes
复制标题
表征动态观察体积中的溶剂密度波动
DOI：
10.1021/acs.jpcb.8b11423
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发表时间：
2019
期刊：
影响因子：
--
通讯作者：
Patel, Amish J.
中科院分区：
文献类型：
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作者：
Jiang, Zhitong;Remsing, Richard C.;Rego, Nicholas B.;Patel, Amish J.
疏水效应驱动不同的水性组装体，例如胶束形成或蛋白质折叠，其中溶剂起重要作用。因此，表征溶剂密度波动的自由能可以导致对这些过程的重要见解。虽然技术，如间接伞形采样（INDUS）方法可以用来表征溶剂波动的静态观察体积的各种大小和形状，表征溶剂如何介导固有的动态过程，如自组装或构象变化，仍然是一个挑战。在这项工作中，我们推广的INDUS方法，以促进增强采样的溶剂波动的动态观测体积，其位置和形状可以演变。我们说明了这种概括的有用性，通过表征水密度波动的动态体积有关的灵活的溶质的水化，组装的小疏水体，和构象转变的模型肽。我们也用这种方法来探测硬球的动力学。
Hydrophobic effects drive diverse aqueous assemblies, such as micelle formation or protein folding, wherein the solvent plays an important role. Consequently, characterizing the free energetics of solvent density fluctuations can lead to important insights into these processes. Although techniques such as the indirect umbrella sampling (INDUS) method can be used to characterize solvent fluctuations in static observation volumes of various sizes and shapes, characterizing how the solvent mediates inherently dynamic processes, such as self-assembly or conformational change, remains a challenge. In this work, we generalize the INDUS method to facilitate the enhanced sampling of solvent fluctuations in dynamical observation volumes, whose positions and shapes can evolve. We illustrate the usefulness of this generalization by characterizing water density fluctuations in dynamical volumes pertaining to the hydration of flexible solutes, the assembly of small hydrophobes, and conformational transitions in a model peptide. We also use the method to probe the dynamics of hard spheres.