Dynamics in Condensed Molecular Systems

为了了解凝聚分子体系中的化学反应动力学，本文进行了以下几个方面的研究：(1)序列选择模拟。蛋白质序列以特定的方式设计，以实现相互作用之间的一致性，以促进从未折叠的伸展链到折叠的天然构象的快速折叠。一种可能的情况是，在进化史上，通过达尔文式的选择过程选择了满足一致性条件的序列。使用新开发的经验势进行了计算机模拟，在计算机上验证了功能选择情景的有效性。(2)蛋白质折叠晶格模型中的动力学分配分析。当存在天然构象以外的竞争能量极小值时，折叠动力学应该表现出最简单的漏斗势中没有的动力学分配行为。建立了晶格模型来分析分配现象，并与溶菌酶的观测数据进行了比较。(3)液态水中偶极场的介观结构和动力学及其在水化过程中的作用。对液态水的MD模拟分析不是取每个分子的平均值，而是取多个分子经过的每个空间位置的平均值。在每个空间位置上平均的偶极场中发现了意想不到的介观结构。研究了它的动力学及其在生物分子水化中的意义。

In order to understand chemical reaction dynamics in condensed molecular systems, following topics were studied.(1) Sequence selection simulation. Protein sequence is designed in a specific way to realize consistency among interactions in order to facilitate the rapid folding from the unfolded stretched chain to the folded native conformation. A possible scenario is that sequences were selected to satisfy the consistency conditions through the Darwinian selection process in the evolutionary history. A computer simulation was conducted using the newly developed empirical potential to show the validity of the functional selection scenario in computer.(2) Analyses of kinetic partitioning in a lattice model of protein folding. When there are competing energy minima other than the native conformation, the folding dynamics should show kinetic partitioning behaviors which are not found in the simplest funnel potential. A lattice model was developed to analyze the partitioning phenomena and compared to the observed data of lysozyme.(3) Mesoscopic structure and dynamics of the dipole field in liquid water and its role in hydration. MD simulation of liquid water is analyzed by taking average not on each molecule but on each spatial position through which many molecules pass by. Unexpected mesoscopic structures are found in the dipole field averaged on each spatial position. Its dynamics and implications in hydration of biomolecules were studied.