Tryptophan is one of the few amino acids that is intrinsically photoluminescent. This is because its side chain consists of indole. Indole’s photoluminescence has both fluorescence (emits for nanoseconds) and phosphorescence (emits for microseconds). Fluorescence emission comes from a singlet to singlet transition, while phosphorescence from a forbidden triplet to singlet transition. Taking advantage of tryptophan’s intrinsic emission, we can use it as a label-free probe for protein dynamics. For some of these dynamics, such as myosin binding to actin, the fluorescence lifetime of nanoseconds is too fast to monitor changes. The phosphorescence lifetime is much better suited to monitor these changes of large biomolecule interactions. Before any binding studies are developed, we have characterized the basic properties of indole’s phosphorescent properties. We began by embedding indole (as well as 5 – bromoindole) in a polymer matrix (PVA) to immobilize and thus increase the phosphorescence at room temperature. We discovered that using a longer wavelength of excitation (405 nm instead of 290 nm) we excite directly from the singlet state to the triplet state of indole, a typically forbidden process. This populates the triplet state without any transitions to the singlet state. This allows the polarization of phosphorescence emission to be preserved, and anisotropy measurements can be used to monitor biomolecular processes.

In a virus study, the inoculum dose is the initial amount of virus used. It is correlated to the initial
amount of cells that become infected at the start of the study and thereby also correlated with the
amount of virus that will be produced by infected cells at the beginning of that study. Those virus spread
through a body in two known ways: cell free transmission and cell to cell transmission. While previous
research has investigated viruses based on free cell transmission, few models have incorporated cell to
cell transmission leading to unclear results and bias to certain variables. This research accounts for both
modes of transmission, using an agent-based framework, and varies the initial amount of virus, to
understand how inoculum dose affects the two transmission modes. Utilizing parallel processing, the
model represents virus infection and spread in a two-dimensional layer of cells in order to generate total
virus over time graphs for corresponding initial amount of virus. This project demonstrates how a
combination of agent-based models and parallel processing can allow researchers to perform the rapid
and large simulations necessary for viral dynamics research efficiently and affordably.

In order to calculate the ground and excited states of a perturbed harmonic oscillator, we use computer codes developed from the results of coupled cluster techniques. More specifically, we have implemented a diagrammatic approach in order to efficiently derive cluster amplitude and energy equations, along with iterative Bogoliubov transformations in order to improve the accuracy of computed energies. Such Bogoliubov transformations improve the zeroth order Hamiltonian, which is shown for a quadratic and quartic perturbation. These results are then compared to exact results obtained from numerical integration of the Schrödinger equation, though we note that numerical integration cannot be performed for more complex systems of coupled harmonic oscillators under perturbation. Explicit coupled cluster equations are also presented for such coupled systems subjected to similar perturbations.

DNA biomarkers are of growing significance for the personalized medicine, with applications including diagnosis, prognosis, and determination of targeted therapies. However, even unicellular organisms can represent a heterogenous system on a molecular level. Improving the detection limits for low DNA concentrations will allow for better decision making, e.g., in clinical medicine, research endeavors, and human identification in forensic investigations where frequently only a minute amount of evidence material is available.
The first step for DNA collection is typically collecting specimen by specialized medical swabs. Medical swabs come in all different materials, shapes and sizes. They are not the same, but they are often used interchangeably. For DNA testing swabs can be used in buccal and surface swabbing for DNA. Then the swab with DNA on it is sent for analysis. A common analysis technique is using fluorescence. But what if the swab itself has some fluorescence? Do different types of swabs have different fluorescence? We want to test the inherent fluorescence of a variety of different types and brands of medical swabs to determine the kind with the best properties for highly sensitive DNA detection. If the swab’s fluorescence is short-lived, we expect that we will be able to separate out the swab’s signal from the DNA’s signal by using long-lived dyes and our novel multipulse excitation scheme.

With the advent of graphene, there has been an interest in utilizing this material and its derivative, graphene oxide (GO) for novel applications in nanodevices such as bio and gas sensors, solid state supercapacitors and solar cells. Although GO exhibits lower conductivity and structural stability, it possesses an energy band gap that enables fluorescence emission in the visible/near infrared leading to a plethora of optoelectronic applications. In order to allow fine-tuning of its optical properties in the device geometry, new physical techniques are required that unlike existing chemical approaches yield substantial alteration of GO structure. Such desired new technique is one that is electronically-controlled and lead to reversible changes in GO optoelectronic properties. In this work, we for the first time investigate the methods to controllably alter the optical response of GO with the electric field and provide theoretical modelling of the electric field-induced changes. Field-dependent GO emission is studied in bulk GO/PVP films with up to 6% reversible decrease under 1.6 V/µm electric fields. On an individual flake level, a more substantial over 50% quenching is achieved for select GO flakes in polymeric matrix between interdigitated microelectrodes subject to two orders of magnitude higher fields. This effect is modelled on a single exciton level by utilizing WKB approximation for electron escape form the exciton potential well. In an aqueous suspension at low fields GO flakes exhibit electrophoretic migration indicating a degree of charge separation and a possibility of manipulating GO materials on a single-flake level to assemble electric field-controlled microelectronics. As a result of this work, we suggest the potential of varying the optical and electronic properties of GO via the electric field for the advancement and control over its optoelectronic device applications.