Graduate Defense: Austin Biaggne

Dissertation Information

Title: Data-Driven Multiscale Modeling Of Dye Aggregates In Dna For Excitonic Applications

Program: Doctor of Philosophy in Materials Science and Engineering

Advisor: Dr. Lan Li, Materials Science and Engineering

Committee Members: Dr. Bernard Yurke, Materials Science and Engineering, Dr. Jeunghoon Lee, Chemistry and Biochemistry, and Dr. Youngchan Kim, Materials Science and Engineering

Abstract

In this dissertation, a data-driven, multi-scale approach was implemented to study the structural, electronic, and dynamical behavior of dye monomers and aggregates for excitonic applications. The excitonic behavior of dye aggregates depends on both the constituent monomer properties as well as the relative dye orientations that make up the aggregate. Dye monomer properties can be augmented with substituents, but with a wide range of substituent types, ideal dye derivatives should be identified. To control the aggregation of dyes, DNA can be used as a scaffold, however, the ways in which dyes interact with each other and with DNA is not well understood.

Density functional theory (DFT) and time-dependent (TD) DFT calculations were performed to understand the structural and electronic properties of numerous dye molecules, with a focus on dyes in the cyanine family (e.g., Cy5). To determine the effects of substituents on Cy5, which are hypothesized to enhance the excitonic properties of dyes, Cy5 derivatives were screened using a combination of DFT and TD-DFT, the latter of which was used to calculate the excited state properties of the dyes. Trends among the electronic properties and substituent electron donating and withdrawing strengths were identified.

Molecular dynamics (MD) simulations were conducted to study the orientations of cyanine monomers and dimers attached to an array of DNA scaffolds, including DNA duplexes and Holliday junctions. Using MD, it was shown that both a Cy5 and Cy5.5 dimer bound bi-covalently to a DNA duplex form a dimer by intercalating into the DNA base-region. Cy5 and Cy5.5 homo- and heterodimers attached to DNA Holliday junctions were found to exhibit dimer orientations that depended strongly on the dye attachment locations and DNA conformers, which agreed with experimental studies. Results from this work can be used to guide the development of dye-DNA systems for applications that utilize dye aggregates and exciton dynamics.