Publication Date


Date of Final Oral Examination (Defense)


Type of Culminating Activity


Degree Title

Doctor of Philosophy in Materials Science and Engineering


Materials Science and Engineering

Major Advisor

William B. Knowlton, Ph.D.

Major Advisor

Bernard Yurke, Ph.D.


Paul H. Davis, Ph.D.


Paul W.K. Rothemund, Ph.D.


The concept of quantum computing was first developed in the early 1980’s. The attraction of quantum computers is their potential capacity to solve extremely complex problems, such as factorization, on a timescale far faster than that of classical computers. However, realization of quantum computation is currently in its infancy, and recent implementations possess serious drawbacks that reduce their appeal. Some challenges of current designs include the necessity to cool the systems using liquid helium to near absolute zero temperatures (15 mK) in order to maintain sufficiently long-lifetimes of the Qbits (i.e., unit of quantum information), difficulty with scaling up the processing systems, and prohibitively high manufacturing costs.

Fundamentally, the key physical effect that enables high processing speeds in quantum computers is quantum superposition, which allows a single qbit to have two (or more) definite states (e.g., 0 and 1) simultaneously. Maintaining a superposition of states at room temperature, however, has proven difficult with silicon-based technology. Coherent exciton delocalization, which involves the superposition of excitonic states characterized by the delocalization of excitons (i.e., electron-hole pairs) across spatially proximate but separated molecules, has been observed in biological photosynthetic systems at ambient temperatures (295 K). Natural photosynthetic systems are composed of protein scaffolds that encompass and elegantly arrange an aggregate of optically active dye molecules (i.e., cluster of chromophores) with nanometer-scale precision in a manner that promotes coherence despite the inherently warm and “noisy” (i.e., rapidly fluctuating) environment inside a plant. As a result, light energy absorbed from the sun is quickly and efficiently transferred through the dye aggregate in a wavelike manner that both optimizes the transfer pathway and minimizes energy loss. Thus, exploiting excitonic delocalization, as inspired by biology, offers a potential path forward towards realizing quantum computing at room temperature.

Here, we demonstrate coherent exciton delocalization in systems that utilize DNA, a biological material that affords atomically precise arrangement of dyes (e.g., Cy5) with nanometer proximity, as a scaffold. Leveraging the inherent programmability and functionality of DNA, which undergoes Watson-Crick base-pairing to enable simple structural control than the complex folding mechanisms involved with proteins, we have designed two dye-DNA complexes that are described in two journal manuscripts contained within this dissertation (Chapters 2 and 3). The first manuscript, which described the behavior and spectral properties of a relatively simple linear dye-DNA complex, achieved two milestones towards quantum information processing: (i) the identification of Cy5 dyes as promising candidates for the development of exciton-based devices and quantum gates due to the large Davydov splitting observed spectrally (i.e., a manifestation of dye-dye coupling and coherent exciton delocalization), and (ii) the data necessary to determine the physical parameters for a phenomenological theoretical model of exciton transport between Cy5 dyes within a DNA complex. The second manuscript, which encompassed a larger, more rigid, two-dimensional Holliday junction structure designed to form dye aggregates of a pre-determined size including dimers, trimers, and tetramers, validated the physical parameters used in the theoretical work for the first manuscript, showing that the same parameters can be used for other dye-DNA configurations. It also demonstrated that large Davydov splitting in dye aggregates can be achieved using a larger, more rigid two-dimensional Holliday junction structure. Taken together, the two manuscripts combined give confidence to the phenomenological theoretical model, which can be used as a predictive engineering tool for designing dye-DNA based excitonic devices and quantum gates, or as an analysis tool for determining dye configurations based on spectral data.