Development of algorithms combining molecular dynamics with time-dependent quantum statistical mechanics for environment-assisted electronic transport through biomolecules

在这个由化学系的化学理论、模型和计算方法计划和材料研究部的凝聚态物质和材料理论计划共同资助的项目中，特拉华大学的布拉尼斯拉夫·尼科利奇教授正在开发一个新的理论模型，并向公众开放支持计算机程序。这个模型将允许研究人员模拟带电的小分子或中性分子通过具有生物学意义的较大分子的传输。这些生物分子可以连接到微小的微型设备上。开发模拟生物分子与这些设备结合的理论模型对于开发快速、低成本的DNA和蛋白质测序至关重要。这种研究可以扩展到个性化医学的开发，以及直接从阳光产生燃料的系统的开发。这项研究集中在化学、物理、生物和工程领域，培养学生和博士后在基础研究、工业应用和高性能科学计算方面追求职业生涯。这项研究通过结合经典分子动力学、多终端分子电子学的非平衡格林函数+密度泛函理论和降低计算复杂性的含时量子输运算法(按时间步长线性缩放)，开发了包含非常多原子的系统的多尺度理论和计算工具。这些工具被用来模拟和设计由二维材料(如石墨烯、氮化硼和过渡金属二卤化物)组成的纳米结构，这些材料拥有用于超快DNA和蛋白质测序的纳米孔，或者用于研究蛋白质复合体中光合作用能量转移的依赖于时间的运输。除了对量子相干性、传输效率、波动环境引起的退相以及非平衡电子对原子运动的反馈之间的相互作用这一基本兴趣之外，该项目进行的高性能计算模拟还可以显著缩短在生物传感和人工光合作用光收集应用中走向功能设备的道路。

In this project, co-funded by the Chemical Theory, Models and Computational Methods program in the Division of Chemistry and the Condensed Matter and Materials Theory program in the Division of Materials Research, Professor Branislav Nikolic of the University of Delaware is developing a new theoretical model with supporting computer programs open to the public. This model will allow researchers to simulate the transport of small charged or neutral molecules through larger molecules of biological interest. These biomolecules can be coupled to small, microscopic devices. The development of the theoretical models to simulate the combination of biological molecules to these devices is critical to develop fast and low-cost DNA and protein sequencing. Such research could be extended to the development of personalized medicine, as well as for the development of systems that generate fuels directly from sunlight. This research at the intersection of chemistry, physics, biology and engineering trains students and postdoctoral fellows to pursue careers in basic research, industrial applications and high performance scientific computing. This research develops multiscale theoretical and computational tools for systems containing very large number of atoms by combining classical molecular dynamics, nonequilibrium Green functions + density functional theory for multiterminal molecular electronics, and time-dependent quantum transport algorithms of reduced computational complexity (scaling linearly in the number of time steps). The tools are employed to model and design nanostructures made of two-dimensional materials (like graphene, boron nitride and transition metal dichalcogenide) hosting nanopores for ultrafast DNA and protein sequencing, or to investigate time-dependent transport in protein complexes for photosynthetic energy transfer. Besides fundamental interest in the interplay between quantum coherence, transfer efficiency, fluctuating environment-induced dephasing, and feedback of nonequilibrium electrons on the motion of atoms, the high performance computing simulations conducted on this project can significantly shorten the path toward functional devices for applications in biosensing and artificial photosynthetic light harvesting.