Quantifying the Hydrological Setting of Upper Flow Regime Channels of the Triassic Dockum Group of West Texas

Type: Graduate
Author(s): Samuel Walker Geological Sciences John Holbrook Geological Sciences
Advisor(s): John Holbrook Geological Sciences

The Triassic Dockum Group of the western Texas High Plains is studied in depth paleontologically, but until recently lacked a detailed sedimentological evaluation. Recent research of the Dockum Group in Palo Duro Canyon, Texas, provides new interpretations of the complex fluvial lacustrine strata of the comprising formations based on analysis of individual lithofacies. Identified within the lithofacies assemblages are numerous channel belts composed of upper flow regime bedforms. Observed upper flow regime bedforms in outcrop range from upper plane bed, antidunes, breaking antidunes, chutes and pools, and cyclic steps with increasing flow velocity respectively. These channel belts record extreme flow events from repeating massive storms that perpetuated throughout the Texas region of Triassic Pangea. These unique reservoir-quality channels are interpreted to be resultant of a megamonsoonal climate producing massive pulses of rapid flow allowing for the preservation of upper flow regime bedforms. While these channels are identified in outcrop they have not been quantified in distribution, variability in fill, connectivity and formative discharge.
This study aims to test the megamonsoonal hypothesis by quantifying the discharge of these channels and testing if the distribution density and paleodischarge of these channels is consistent with local dominance of megamonsoonal conditions. Upper flow regime structures are rarely preserved in the rock record and extremely difficult to observe directly during natural formation in modern rivers. Most of the equations used to quantify flow conditions for these structures are derived from flume tank experiments. These are applied to the upper flow regime bedforms found in outcrops of the Dockum Group to reconstruct paleohydrology. Current flume tank research reinforces Kennedy’s equations defining relationships between the wavelengths of stable antidune apexes (λ), mean flow depth (hm) and mean flow velocity (U). These equations are modified to account for different upper flow regime structures formed under increasing velocity and discharge identified in outcrop. Bedform distribution, size, and type are variables determined from outcrop measurement. Paleoflow velocities, Froude numbers and relative water depths are determined with an observed margin of error. Scaling relationships and field measurements provide constraints on channel cross sectional area and channel-belt density. This data along with grain size distribution provides tangible numbers for calculating formative discharge. Preliminary results align with data from flume tank experiments and are consistent with major floods produced by substantial storm events verifying the megamonsoonal hypothesis.

Campanian-Maastrichtian Ankylosaurs of West Texas

Type: Graduate
Author(s): Bryanna West Geological Sciences
Advisor(s): Arthur Busbey Geological Sciences

Deeper Exploration of the C*-Algebras Arising from Uniformly Recurrent Subgroups and their Relationship with Crossed Products

Type: Graduate
Author(s): Douglas Wagner Mathematics
Advisor(s): José Carrión Mathematics

A group is a mathematical construct that represents the symmetries of an object. These symmetries transform the object through what is called a group action. Graphs—Cayley graphs, in particular—provide a rich source of symmetries for forming groups. A graph and its group action can be modeled by a collection of infinite matrices known as a C*-algebra. In a paper in the Journal of Functional Analysis, Gábor Elek used dynamical systems called Uniformly Recurrent Subgroups (URS) to construct a new type of C*-algebra. We further develop understanding of these C*-algebras using tools from other areas of operator theory. In particular, comparisons with the well-known crossed-product construction have proven useful.

Graphene Quantum Dot Formulation for Cancer Imaging and Redox-Based Drug Delivery

Type: Graduate
Author(s): ELIZABETH CAMPBELL Physics & Astronomy Giridhar Akkaraju Biology Roberto Gonzalez-Rodriguez Chemistry & Biochemistry Kayla Green Chemistry & Biochemistry Tanvir Hasan Physics & Astronomy Bong Lee Physics & Astronomy Anton Naumov Physics & Astronomy Tate Truly Biology
Advisor(s): Anton Naumov Physics & Astronomy

Treatment of complex conditions, such as cancer, has been substantially advanced by a field of molecular therapeutics. However, many of these therapies are limited by the dose toxicity and lack the predictive power of tomography-guided approaches. Nanomaterial platforms can address these drawbacks, safely delivering therapeutics, concomitantly imaging their delivery pathways, and presenting sites for targeting agent attachment. Graphene quantum dots (GQDs) possess physical properties that are critical for biomedical applications, including small size (3-5 nm), high quantum yield, low cytotoxicity, and pH-dependent fluorescence emission. Nitrogen doped graphene quantum dots (N-GQDs) are now utilized as a platform for a targeted treatment formulation geared toward cancer therapeutic. Our work utilizes nitrogen-doped GQDs as an emissive platform for covalent attachment of a targeting agent (hyaluronic acid (HA) targeted to the CD44 receptors on several cancer cell types) and oxidative stress-based cancer therapeutic (ferrocene (Fc)). The synthesized multifunctional formulation is characterized and its efficacy evaluated in vitro. Elemental mapping indicates that the purified from reactants synthetic product has an average iron content of 0.64 atomic percent, suggesting the successful attachment of the therapeutic, while FFT analysis of TEM images confirms the crystalline structure of the GQDs. Although GQDs alone yield no cytotoxicity as quantified via the MTT assay up to the maximum imaging concentrations of 1 mg/mL, the Fc-HA-GQD formulation exhibits a higher cytotoxic response in the cancer cells (HeLa) targeted by the HA as opposed to healthy ones (HEK-293) that do not overexpress CD44, suggesting cancer-selective targeted efficacy. As Fc induces oxidative stress that is less mitigated in cancer cells, we expect it to also contribute to the observed cancer-selective treatment response. As a result, we propose Fc-HA-GQD formulation as a multifunctional targeted delivery, imaging, and cancer-specific treatment agent further to be studied in vivo.

Surface Plasmon Coupled Emission: a new super sensitive technique

Type: Graduate
Author(s): Luca Ceresa Physics & Astronomy
Advisor(s): Zygmunt Gryczynski Physics & Astronomy

Fluorescence has proved itself to be a useful tool in a wide variety of fields, ranging from environmental sensing to biomedical diagnostics. In this study, we propose to utilize a novel fluorescence-based technique called Surface Plasmon Coupled Emission (SPCE) to monitor molecular binding and to detect low concentrations of physiological markers (e.g. biomarkers present in the human body as a result of a disease). SPCE is characterized by directional emission that allows for a superior sensitivity and selectivity for detection. The development of an SPCE-based detection platform will allow for simple, fast and sensitive detection in a compact configuration that can be relatively easily implemented in the field or in primary care offices. Surface plasmon induced fluorescence at the interface of a thin metal layer (e.g. 50 nm of silver or gold) and a dielectric (e.g. glass) allows for highly enhanced excitation of fluorophores deposited on top of the metal film and very efficient detection due to the directional nature of this emission. As a result, we expect highly improved detection sensitivity compared to other fluorescence detection methods or other surface detection methods such as surface plasmon attenuated reflection (SPR).

Direct Excitation to the Triplet State: 5-Bromoindole

Type: Graduate
Author(s): Jose Chavez Physics & Astronomy Julian Borejdo Biology Luca Ceresa Physics & Astronomy Rafal Fudala Biology Ignacy Gryczynski Physics & Astronomy Joseph Kimball Physics & Astronomy Emma Kitchner Physics & Astronomy Tanya Shtoyko Chemistry & Biochemistry
Advisor(s): Zygmunt Gryczynski Physics & Astronomy

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.

Using an agent-based model to explore the impact of inoculum dose and transmission mode on viral infection

Type: Graduate
Author(s): Baylor Fain Physics & Astronomy
Advisor(s): Hana Dobrovolny Physics & Astronomy

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.

Utilizing Bogoliubov Transformations to Improve Accuracy in Computing Eigenvalues of Perturbed Harmonic Oscillators

Type: Graduate
Author(s): Carson Huey-You Physics & Astronomy
Advisor(s): Magnus Rittby Physics & Astronomy

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.

Multi-Swabbing the Deck

Type: Graduate
Author(s): Emma Kitchner Physics & Astronomy Luca Ceresa Physics & Astronomy Jose Chavez Physics & Astronomy
Advisor(s): Karol Gryczynski Physics & Astronomy

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.

Investigating Modulation of Graphene Oxide Fluorescence via External Electric Fields

Type: Graduate
Author(s): Bong Han Lee Physics & Astronomy Fabian Grote Physics & Astronomy Thomas Paz Physics & Astronomy Conor Ryan Physics & Astronomy Alina Valimukhametova Physics & Astronomy
Advisor(s): Anton V. Naumov Physics & Astronomy

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.