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

在这个项目中，特拉华大学的Branislav Nikolic教授正在开发一个新的理论模型，并支持向公众开放的计算机程序，该项目由化学系的化学理论、模型和计算方法项目和材料研究部的凝聚态物质和材料理论项目共同资助。这个模型将允许研究人员模拟小带电分子或中性分子通过生物感兴趣的大分子的运输。这些生物分子可以耦合到微小的设备上。模拟生物分子与这些设备结合的理论模型的发展对于开发快速、低成本的DNA和蛋白质测序至关重要。这样的研究可以扩展到个性化医疗的发展，以及直接从阳光中产生燃料的系统的发展。该研究将化学、物理、生物和工程相结合，培养学生和博士后从事基础研究、工业应用和高性能科学计算方面的工作。本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时变量子输运算法（时间步长线性缩放），为包含大量原子的系统开发了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硫代化物）制成的纳米结构，这些材料承载着纳米孔，用于超快速DNA和蛋白质测序，或者用于研究光合能量转移的蛋白质复合物的时间依赖性运输。除了对量子相干性、转移效率、波动环境诱导的脱相和非平衡电子对原子运动的反馈之间的相互作用产生基本兴趣外，本项目进行的高性能计算模拟可以显着缩短生物传感和人工光合光收集应用的功能器件的路径。

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.