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Real time dynamical properties of biomolecules from ab initio quantum dynamics

从头计算量子动力学的生物分子的实时动力学特性

基本信息

批准号：
238016737
负责人：
Dr. Mariana Rossi
金额：
--
依托单位：
Department of Chemistry
依托单位国家：
德国
项目类别：
Research Fellowships
财政年份：
2013
资助国家：
德国
起止时间：
2012-12-31 至 2014-12-31
项目状态：
已结题

来源：
https://gepris.dfg.de/gepris/projekt/238016737?language=en
关键词：
Real time dynamical properties biomolecules

项目摘要

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.

将核量子效应（NQE）纳入计算机模拟的实时动态观测值的评估是一个长期的挑战，特别是在现实材料和分子的从头计算电子结构计算领域。在这个项目中，我建议探索方法的解决方案和应用的挑战，包括核量子效应的自相关函数从第一性原理路径积分模拟评估。我将开发新的方法来降低成本，并加速收敛的环聚合物和质心从头算分子动力学（AIMD）。我还计划探索新的概念和技术，以获得量子自相关函数的虚假影响存在于上述两种方法。牛津大学Manolopoulos教授小组的专业知识对这些发展非常重要。我将应用开发的框架评估AIMD衍生的，NQE，非谐波红外光谱的中型到大型生物分子。我将计算气相光谱，包括溶剂化效应，通过逐步水合，直到完全水合，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见解。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，我希望在牛津大学的实验支持。