Real time dynamical properties of biomolecules from ab initio quantum dynamics

将核量子效应(NQE)纳入计算机模拟的实时动态观测的评估中是一个长期的挑战，特别是在现实材料和分子的从头计算电子结构领域。在这个项目中，我建议探索将核量子效应包括在自相关函数中的方法学解决方案和应用挑战，这些自关联函数是从第一原理路径积分模拟得到的。我将开发新的方法来降低成本并加速环聚合物和质心从头算分子动力学(AIMD)的收敛。我还计划探索新的概念和技术，以获得没有上述两种方法中已知的虚假效应的量子自相关函数。牛津大学马诺洛普洛斯教授团队的专业知识将对这些发展非常重要。我将应用开发的框架来评估中到大生物分子的AIMD派生的、含有NQE的非谐红外光谱。我将计算气相光谱，并包括逐步水化的溶剂化效应，直到完全水化，总是包括NQE。这些光谱将具有无与伦比的准确性，从而极大地帮助解释实验数据，并为多肽和蛋白质结构的表征带来宝贵的洞察力。作为最后的应用挑战，我计划描述质子泵通道的结构和动力学，我希望在那里得到牛津大学研究小组的实验支持。

The inclusion of nuclear quantum effects (NQE) in the evaluation of real-time dynamical observables from computer simulations is a standing challenge, especially in the realm of ab initio electronic structure calculations of realistic materials and molecules. In this project, I propose to explore methodological solutions and application challenges for the inclusion of nuclear quantum effects in auto-correlation functions evaluated from first-principles path integral simulations. I will develop new ways to reduce the cost and accelerate the convergence of ring-polymer and centroid ab initio molecular dynamics (AIMD). I also plan to explore new concepts and techniques of obtaining quantum auto-correlation functions free of the spurious effects known to exist in the two above mentioned methods. The expertise in Prof. Manolopoulos group in Oxford will be very important for these developments. I will apply the developed framework for the evaluation of AIMD-derived, NQE-containing, anharmonic IR spectra of medium to large biomolecules. I will calculate gas-phase spectra and include solvation effects through stepwise hydration, up to full hydration, always including NQE. These spectra will have unparalleled accuracy, thus helping enormously the interpretation of experimental data and bringing precious insight for the characterization of polypeptide and protein structure. As a final application challenge, I plan to describe the structure and dynamics of proton-pump channels, where I hope to have experimental support of Oxford-based groups.