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

University Of Delaware, Newark DE

Investigators

Abstract

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.