Computer Simulation of Protein Structure and Dynamics

这是一个用计算机模拟研究生物分子动力学的两部分项目。在第一部分中，将使用多时间步长的朗之万动力学算法来模拟蛋白质在多纳秒范围内的分子运动的时间依赖性，以模拟测量蛋白质如何在从几纳秒到几十纳秒的时间尺度上运动的实验。核磁共振测量和快速光学光谱测量后的激光脉冲，给蛋白质一个冲击将被考虑。在项目的第二部分，将通过固定开始(未折叠)和结束(折叠)构象以及检查从未折叠到折叠构象的各种反应路径来检查蛋白质折叠。这项研究的目的是研究随着展开和折叠状态之间允许的时间步数增加而发生的折叠轨迹的类型。

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.