Physical Sciences and Mathematics Commons^™

Biophysical Factors Affecting Habitat Suitability For Crassostrea Virginica, Jason D. Tilley

Dissertations

Oyster reefs provide a variety of important ecosystem services. However, the mortality rate of eastern oyster, Crassostrea virginica, the dominant species that produces oyster reefs in the northern Gulf of Mexico, is increasing at an alarming rate due to a variety of abiotic and biological factors. I examined how biophysical factors, including the less-studied fatty acid profiles of the suspended particulate matter on which oysters feed, influenced morphometric condition of C. virginica.

I sampled suspended particulate matter (SPM) and oysters in-situ in the western Mississippi Sound, which historically supported the majority of oyster production in Mississippi waters. Sampling …

A Computational Kinetics Model To Quantify Radiation Induced Chemical Products Of Atmospheric Gas Mixtures, Patrick Ables

Dissertations

This research is focused on the development of a computational model which will calculate the effects of radiation on the chemical composition of the atmosphere. The approach utilizes the open-source chemical kinetics toolkit Cantera to model the creation of radiation-induced reactant species within irradiated air mixtures. Chemical solutions are iteratively stepped toward chemical equilibrium within a ‘constantly stirred’ (homogeneous) reactor of fixed volume. Three different radiation chemistry models are implemented in several different pulsed and continuous radiation schemes. The first model includes the mechanisms and rates of a pulse radiation model from the literature to test the validity of the …

Structural And Kinematic Investigation Of The Dadeville Complex-Brevard Zone Contact (Southern Appalachians): Polyphase Emplacement Of An Allochthonous Terrane On The Laurentian Margin, Andrew Williams

Master's Theses

The Dadeville Complex (DC) lies in the Inner Piedmont of eastern Alabama and western Georgia. The DC formed as a volcanic island arc during the Taconic orogeny (Ordovician Period) and was accreted onto Laurentia during the Acadian orogeny (Devonian-Mississippian Periods); however, the mechanism and role of accretion during the Acadian orogeny is not well constrained. Three proposed emplacement mechanisms for the DC include: (1) orogen-perpendicular translation; (2) orogen-parallel translation; (3) orogenic channel flow.

Today, the DC is a major (over 100 kilometers long) allochthonous terrane composed mostly of meta-igneous rocks. This study investigated structural fabrics and kinematic indicators in the …

Annotation Of Non-Model Species’ Genomes, Taiya Jarva

Master's Theses

The innovations in high throughput sequencing technologies in recent decades has allowed unprecedented examination and characterization of the genetic make-up of both model and non-model species, which has led to a surge in the use of genomics in fields which were previously considered unfeasible. These advances have greatly expanded the realm of possibilities in the fields of ecology and conservation. It is now possible to the identification of large cohorts of genetic markers, including single nucleotide polymorphisms (SNPs) and larger structural variants, as well as signatures of selection and local adaptation. Markers can be used to identify species, define population …

Solving The Cable Equation, A Second-Order Time Dependent Pde For Non-Ideal Cables With Action Potentials In The Mammalian Brain Using Kss Methods, Nirmohi Charbe

Master's Theses

In this thesis we shall perform the comparisons of a Krylov Subspace Spectral method with Forward Euler, Backward Euler and Crank-Nicolson to solve the Cable Equation. The Cable Equation measures action potentials in axons in a mammalian brain treated as an ideal cable in the first part of the study. We shall subject this problem to the further assumption of a non-ideal cable. Assume a non-uniform cross section area along the longitudinal axis. At the present time, the effects of torsion, curvature and material capacitance are ignored. There is particular interest to generalize the application of the PDEs including and …

Understanding The Flow Dynamics Of The Pearl River, Ms, Through Hydrodynamic Modeling, Nahruma Mehzabeen Pieu

Master's Theses

The Pearl River brings fresh water and nutrients into Lake Borgne regulating conditions for oyster growth in estuarine waters. However, there are no flow measurement stations installed on East Pearl or West Pearl either at the river outlets or after the upstream bifurcation of the Pearl. This study aims to model the Lower Pearl River to understand the flow dynamics in the major branches, and to determine the final outflow distribution into the Mississippi Sound, aiming to improve river forcing for ocean models studying estuarine dynamics of the Mississippi Sound.

Synthetic meandering bathymetry with updated banks is developed and applied …

The Mobility Of Long-Lived Radioisotopes And Their Burial In The Marine Environment, Neil Redmond

Dissertations

Marine sediments record chemical signals that reflect past environmental conditions. It is important to establish how these signals are created and whether they may be altered over time so that they can be useful for reconstructing ocean history. Measurements of uranium isotopes are used as a novel proxy for sedimentary diagenetic processes (Chapter 2). Because ²³⁴U can be ejected from mineral lattice during the decay of ²³⁸U, it creates a pool of U in porewater that is potentially mobilized and then deposited elsewhere in the core. We found that alpha-recoiled ²³⁴U is sensitive to differences in sediment …

Understanding The Impacts Of Topobathymetric Data On Storm Surge Model Predictions, Sydni Crain

Master's Theses

The topobathymetric characteristics of a region are regularly altered by natural and anthropogenic causes. This directly impacts the resulting storm surge during a hurricane. The primary goal of this research was to gain a better understanding of the impact that topography and bathymetry have on storm surge models, particularly the Advanced Circulation (ADCIRC) Model. Hurricane Zeta (2020) and Hurricane Ida (2021) were chosen as case studies; therefore, the Gulf of Mexico (GOM) was chosen as the study site. This research was completed by comparing ADCIRC storm surge results which were based on older, lower-resolution data with results derived from more …

Connecting Social And Ecological Systems In Small-Scale Fisheries In The Philippines, Sara Eisler Marriott

Dissertations

Nearly 50% of all marine fish capture in the Philippines is from artisanal fisheries, most of which is un- or under-reported. As in many emerging nations around the world, the Philippines cannot fully address overfishing by managing only half of the catch that comes from commercial fisheries. Marine reserves are a popular governance strategy for conservation and of growing interest for fisheries management. Many marine reserves in the Philippines, however, are not considered effective. In 2014, Rare, an international NGO, implemented a community-based management program to increase the effectiveness of the marine reserves, and while it found biomass increased, there …

Origin And Structure Of The First Sharp Diffraction Peak Of Amorphous Solids, Devilal Dahal

Dissertations

Several explanations have been reported in the literature about the origin of extended-range oscillations (EROs) in the atomic pair-correlation function of amorphous materials. Although the radial ordering beyond the short-range order of about 5 Å has been extensively studied in amorphous materials, the exact nature of the radial ordering beyond a nanometer is still not resolved. This dissertation address this problem and explains the nature of the EROs by using high-quality models of amorphous silicon (a-Si) obtained from Monte Carlo and Molecular Dynamics simulations. The extended-range ordering in a-Si is examined through radial oscillations on the length …

Determining The Refractive Index Of Phytoplankton Via Direct Measurement Of Cellular Structures, Michael Kamowski

Master's Theses

The refractive index of phytoplankton has never been directly measured before despite its importance towards studying the optical characteristics of marine particles. Previous attempts to measure it have been done through indirect methods. While these methods have proven useful, they contain assumptions about the particles morphology and composition that cause for uncertainty with the measurements. Through the use of the 3D Cell Explorer, a high precision holotomographic microscope, the RI of phytoplankton can be directly measured for the first time. With volume measurements, the phytoplankton were found to not display a single bulk RI, instead the bulk RI was different …

New Insights Into The Paleovegetation Of The Ancient Underwater Forest Located In The Northern Gulf Of Mexico, Karla Lizarraga Garcia

Master's Theses

A well-preserved remnant of an ancient bald cypress forest (hereafter, Underwater Forest) constitutes the only known archive of a glacial refuge on the once exposed continental shelf of the Northern Gulf of Mexico. This forest existed around 41-72 yBP (MIS 3-5) according to the existing dating methods applied on previous studies. As the climate conditions and sea levels changed, the vegetation of this glacial refuge shifted from bald cypress forests to open marshes, altering the vegetation dynamics. The present research analyzed four new cores (21DF-5A, 21DF-5B, 15DF-6, and 16DF-3A), which provided additional insights into the vegetation that once existed in …

Separating The R Vs. S Enantiomers Of A Quinoline Aimed At Inhibiting The Allosteric Binding Pocket Of Hiv-1 Integrase, Madison Canfield

Honors Theses

HIV-1 is a retroviral disease that infects CD4+ T cells in the body. Once inside the body, HIV-1 uses human cell machinery to replicate and reproduce using several enzymes to reverse transcribe viral RNA to DNA and integrate the viral DNA into the human genome to reproduce. Several drugs, such as NRTIs, INSTIs, NNRTIs, and PIs, have been created to inhibit specific parts of the viral life cycle and are used in combination to fight HIV-1. However, these medications face challenges of viral mutation and resistance, which increases the importance of creating more potent and effective drugs. Recently, a new …

Dissolved Copper Distributions In The Western Mississippi Sound: Characterizing An Unrecognized Endmember, Megan Hansen

Honors Theses

This study examined the distribution of dissolved copper (Cu) in the western Mississippi Sound, as the element can be beneficial or harmful to organisms depending on its concentration and its chemical form. A mixing experiment eliminated flocculation as a control on Cu distributions during estuarine mixing in both dissolved and colloidal fractions. Field sampling of the western Mississippi Sound occurred during a low river discharge period, and distributions of Cu indicated conservative mixing between fresh ([Cu] ≈ 17 nM) and saline ([Cu] ≈ 2 nM) sources in mid-to-high salinities. Storm outfalls were sampled after rain events to evaluate the impact …

Separating The R Vs. S Enantiomers Of A Quinoline Aimed At Inhibiting The Allosteric Binding Pocket Of Hiv-1 Integrase, Madison Canfield

Honors Theses

HIV-1 is a retroviral disease that infects CD4+ T cells in the body. Once inside the body, HIV-1 uses human cell machinery to replicate and reproduce using several enzymes to reverse transcribe viral RNA to DNA and integrate the viral DNA into the human genome to reproduce. Several drugs, such as NRTIs, INSTIs, NNRTIs, and PIs, have been created to inhibit specific parts of the viral life cycle and are used in combination to fight HIV-1. However, these medications face challenges of viral mutation and resistance, which increases the importance of creating more potent and effective drugs. Recently, a new …

Hydrothermal Fluid Transport Pathways Along Fractures And Veins At Brothers Volcano, Southern Kermadec Arc, Robert Atnip

Master's Theses

Hydrothermal fluid flow in fractures and veins is a key component in the mineralization of economic metals within calderas. But there are several methods by which fractures can form. Regional extension, episodic caldera collapse, and fluid overpressure all have the potential to create brittle features. Current studies focus on the formation of fractures and veins by these methods, but do not focus on the preferred movement of hydrothermal fluids through brittle features, nor which features are more dominant in active hydrothermal systems. This thesis introduces multiple studies to better understand which method of fracture creation dominates Brothers volcano. Data from …

Benthic Habitat Mapping Of Mountain Top Bank Within The Northern Gulf Of Mexico Through Integrated Geophysical And Visual Data Analysis, Bethany Pertain

Master's Theses

Mesophotic coral ecosystems (MCEs) are among the seafloor ecosystems that have been poorly studied throughout the world’s oceans, but they are a vital and diverse ecosystem that should be prioritized for future mapping and ecological studies. Priority should be given to them because they possess natural, social, and economic values, and face a variety of threats, all of which, if not better understood will result in the loss of this unique ecosystem. Insights into these ecosystems, among other deep-sea environments, are lacking due to difficulty accessing them, inherent lag between data collection by an autonomous system and observation by a …