Multi-resolution framework for the characterization of protein mechanisms

莱斯大学的塞西莉亚·克莱门蒂教授得到了化学系化学理论、模型和计算方法项目的支持， 开发多尺度蛋白质模型和新策略，探索复杂的自由能景观。该项目使用粗粒化作为开发多分辨率蛋白质模型的起点，该模型与理论上稳健的框架相结合，该框架涉及Fokker-Planck扩散方程的超对称推广，以及集体变量的数学严格定义。这些方法被应用于快速定位分子动力学景观中的稀有事件区域，并为复杂系统的基准测试和创建新模型提供了坚实的基础。所开发的方法用于表征蛋白质动力学的功能方面的时间尺度上达到传统的approaches.The更广泛的影响，这项研究是在生物科学。 Clementi教授参与了计算分子生物学课程的开发和一个包括向当地学校介绍的外展计划。该项目由分子和细胞生物学系的分子生物物理学项目共同资助。

Prof. Cecilia Clementi of Rice University is supported by an award from the Chemical Theory, Models and Computational Methods program in the Division of Chemistry to develop multiscale protein models and new strategies to explore complex free energy landscapes. This project uses coarse graining as the starting point to develop multi-resolution protein models, which are combined with a theoretically robust framework involving a supersymmetric generalization of the Fokker-Planck diffusion equation, and a mathematically rigorous definition of collective variables. These methods are applied to rapidly locate rare event regions in molecular dynamics landscapes, and give a robust foundation for benchmarking and creating new models of complex systems. The developed methodology is used to characterize the functional aspects of protein dynamics on timescales out of reach to conventional approaches.The broader impacts of this research are in the biological sciences. Prof. Clementi is involved with the development of courses in computational molecular biology and an outreach program involving presentations to local schools.This project is co-funded by the Molecular Biophysics program in Division of Molecular and Cellular Biology.