Multi-Scale Modeling of DNA-Templated Aggregates for Excitonic Applications

Quantum entanglement occupies a central role in the application of quantum mechanics towards emerging technologies of quantum information systems. Meanwhile, quantum entanglement is believed to be observed at room temperature in photosynthetic complexes in plants and algae through the energy transfer of dye molecules. The goal of this project is to engineer dye properties and their arrangement when dyes and aggregates are covalently attached to DNA so that the emergent property of exciton delocalization is as coherent, predictable, detectable and controllable. The creation of such a platform would enable the continued study of near room-temperature quantum entanglement and the more specific phenomenon of coherent exciton delocalization. DNA is focused on due to advances in the field of DNA nanotechnology that simplify the conditions necessary to promote exciton delocalization. We developed and implemented a multiscale modeling approach to provide detailed insight into dye- and dye aggregate-DNA interactions at different time and length scales, predict dye and aggregate properties and the factors controlling the properties, and derive basic design principles to inform and guide experiments. Specifically, this project focuses on the squaraine (SQ) dyes because of their strong and narrow absorption band. We used Density Functional Theory (DFT)-based methods to investigate the electronic and photophysical properties of dyes, and Molecular Dynamics (MD) to explore the positions and orientations of dyes and aggregates templated on DNA scaffolds, such as Holliday Junction (HJ). which contains four double-stranded DNA duplexes joined together at a single junction. Together, this multiscale approach advances our understanding of dye-DNA systems applied towards room-temperature molecular excitonic quantum computing and quantum entanglement.