Theory of Biomolecular Structure and Dynamics

这个项目将开发和应用使用计算机来了解生物分子活动的方法。特别是，分子动力学方法(使用计算机追踪这些分子中的原子运动)将得到进一步发展。下一阶段将出现的计算工具将包括模拟生物分子周围的水溶剂的更准确的模型，以及更强大的采样生物分子的形状和能量性质的方法。具有挑战性的新应用包括探索蛋白激酶和RAS蛋白的生物物理，以及细胞色素P450和蛋白辅助膜融合的新研究。青年科学家的培训将继续是该项目的中心重点。在之前的项目期间，十几名小组成员转而担任终身教职。同样数量的本科生在进入研究生院之前参与了研究；这些学生中的许多人是根据他们的工作撰写的期刊文章的第一作者，还有几个人来自科学界代表性较低的群体。所有这些招聘活动都将继续进行。小组成员还将继续有机会在加州大学圣迭戈分校的常规课程和NSF理论生物物理中心提供的暑期学校任教。这有助于该小组成功地培训青年科学家从事学术和研究工作，也是科学界的一项宝贵的外联活动。预计这项研究将带来的其他社会效益包括研究分子识别的实用新方法，这将有助于设计有用的分子和设备。在这个项目中开发的所有计算工具将尽可能自由地分发。

This project will develop and apply methods for using computers to understand the activity of biological molecules. In particular, the molecular dynamics method (which uses computers to trace out the atomic motion within such molecules) will be further developed. Computational tools that will emerge during the next period will include more accurate models for the watery solvent around the simulated biological molecules, and more powerful methods for sampling the shapes and energetic properties of the biological molecules. Challenging new applications include exploration of the biophysics of protein kinases and Ras proteins, and new studies of cytochrome P450s and protein-assisted membrane fusion. The training of young scientists will continue to be a central focus of the project. More than a dozen group members moved on to tenure-track faculty positions in the preceding project period. A similar number of undergraduates participated in research prior to going on to graduate school; many of these students are first authors of journal articles based on their work, and several are from underrepresented groups in science. All of these recruitment activities will continue. Group members will also continue to have the opportunity to teach in regular courses at UCSD and in summer schools offered by the NSF Center for Theoretical Biological Physics. This contributes to the success of the group in training young scientists for academic and research careers, and also represents a valuable outreach activity to the scientific community. Additional societal benefits expected to emerge from the research include practical new methods for the study of molecular recognition, which will be helpful in the design of useful molecules and devices. All the computational tools developed in this project will be distributed as freely as possible.