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，由化学系的化学理论，模型和计算方法项目以及材料研究系的凝聚态物质和材料理论项目共同资助，特拉华州大学的Branislav Nikolic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。该模型将允许研究人员模拟小的带电或中性分子通过生物学感兴趣的大分子的运输。这些生物分子可以耦合到小的，微观的设备。开发理论模型来模拟生物分子与这些设备的结合对于开发快速和低成本的DNA和蛋白质测序至关重要。这种研究可以扩展到个性化医疗的开发，以及直接从阳光中产生燃料的系统的开发。这项研究在化学，物理，生物和工程的交叉点培养学生和博士后研究员从事基础研究，工业应用和高性能科学计算的职业。本研究通过结合经典分子动力学，非平衡绿色函数+密度泛函理论的多端分子电子学，和时间相关的量子输运算法的计算复杂性降低（线性缩放的时间步长的数量），包含非常大量的原子的系统开发多尺度的理论和计算工具。这些工具用于建模和设计由二维材料（如石墨烯，氮化硼和过渡金属二硫属化物）制成的纳米结构，这些材料具有用于超快DNA和蛋白质测序的纳米孔，或者用于研究蛋白质复合物中的时间依赖性运输以进行光合能量转移。除了对量子相干性，传输效率，波动环境引起的退相和非平衡电子对原子运动的反馈之间的相互作用的基本兴趣外，该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捕获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.