Computer Simulation of Protein Structure and Dynamics

这是一个由两部分组成的项目，用于使用计算机模拟研究生物分子动力学。在第一部分中，蛋白质分子运动在多纳秒范围内的时间依赖性将使用多时间步长朗格万动力学算法来模拟实验，这些实验测量蛋白质如何在从几纳秒到几十纳秒不等的时间尺度上运动。将考虑在激光脉冲后进行核磁共振测量和快速光谱学测量，从而使蛋白质受到冲击。在项目的第二部分，将通过固定起始（未展开）和结束（折叠）构象以及检查从未展开构象到折叠构象的各种反应路径来检查蛋白质折叠。本研究的目的是研究随着折叠态和展开态之间的时间步长增加而出现的折叠轨迹。

This is a two-part project for the study of biomolecular dynamics using computer simulation. In the first part the time-dependence of the molecular motion of a protein in the multi-nanosecond range will be simulated using a multiple time step Langevin dynamics alogorithm to model experiments which measure how proteins move on time scales varying from a few nanoseconds to many tens of nanoseconds. NMR measurements and fast optical spectroscopy measurements following a laser pulse which gives the protein a shock will be considered. In the second part of the project, protein folding will be examined by fixing the beginning (unfolded) and ending (folded) conformations and examining various reaction paths leading from the unfolded to the folded conformation. The aim of the research is to study the kinds of folding trajectories which occur as the number of time steps allowed between the unfolded and folded states is increased.