Publication Date

8-1-2023

Date of Final Oral Examination (Defense)

May 2023

Type of Culminating Activity

Dissertation

Degree Title

Doctor of Philosophy in Materials Science and Engineering

Department

Materials Science and Engineering

Major Advisor

William B. Knowlton, Ph.D.

Major Advisor

Bernard Yurke, Ph.D.

Advisor

Ryan D. Pensack, Ph.D.

Advisor

Joseph Melinger, Ph.D.

Advisor

Daniel B. Turner, Ph.D.

Abstract

The invention and widespread adoption of the digital computer in the last century has led to an era of rapid technological advancement that has continued to the present day. This advancement has been sustained to a large degree by continued miniaturization of the electronic components in microprocessors, which results in increased computing power and energy efficiency. In recent years, this strategy has produced diminishing returns because the cost for each incremental size reduction increases as engineers approach the fundamental scaling limits of silicon-based semiconductor devices. Meanwhile, breakthroughs in DNA nanotechnology hold great promise for a new generation of self-assembled nanodevices with applications in nanoscale computing and quantum computing.

DNA nanotechnology has emerged as a means to realize directed self-assembly of arbitrary nanostructures that can be functionalized with nanoparticles or dyes to create nanophotonic devices. Of particular interest for computing applications are DNA-templated nanophotonic devices in which dye molecules are assembled into designated spatial configurations in order to control the evolution of optically generated excited states. These excited states, known as molecular excitons, arise from electronic interactions between dyes and are sensitive to the proximity and orientation of dyes relative to one another. To date, a number of DNA-templated excitonic devices such as optical switches, sensors, and energy relays have been demonstrated.

The function of the above devices may be enhanced by using DNA to assemble closely-spaced assemblies of dyes, known as dye aggregates, that experience close-range coherent interactions that can drastically alter their properties with respect to the isolated dye. For example, coherent interactions can result in spectral shifts in absorption and fluorescence, modulation of absorption and fluorescence intensity, and facilitate lossless energy transfer. These properties are extremely sensitive to the mutual orientation and separation of the constituent dyes, and the structure-property relationships of DNA templated dye aggregates are an active area of research.

Here, we present three photophysical studies of cyanine dye aggregates assembled on DNA. In the first study, we use DNA to assemble heteroaggregate tetramers of the cyanine dyes Cy5 and Cy5.5. We observe that changing the ratio of Cy5 to Cy5.5 within the heteroaggregates produces incremental shifts in their optical absorption frequencies that are reminiscent of alloying. In the second study, the excited-state relaxation kinetics of a DNA templated Cy5 dimer and tetramer are compared to those of the monomer. A combination of steady-state and time-dependent absorption spectroscopies indicate that the relaxation kinetics of the aggregates are dominated by a rapid nonradiative relaxation pathway that is introduced upon aggregation. In the third study, a larger set of DNA-templated Cy5 aggregates are studied, including three dimers, a trimer, and a tetramer. We find that nonradiative quenching persists across these structures. We additionally model the aggregate spectra based on their steady-state absorption and circular dichroism spectra to infer a possible relationship between the relaxation kinetics and structural parameters such as intermolecular separation and the number of dyes comprising the aggregate.

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