The Study Of Hydrophobic Biomolecules With Matrix Assisted Laser Desorption Ionization Mass Spectrometry And Atomic Force Microscopy, Brandy L. Perkins

LSU Doctoral Dissertations

Abstract

Matrix assisted laser desorption ionization (MALDI) mass spectrometry (MS) can be used to obtain localization and chemical information of hydrophobic biomolecules on tissue samples.  A technique has been developed to modify a standard MALDI matrix that improves the selectivity for hydrophobic biomolecules on the tissue sample. The modification involves the use of a Group of Uniform Materials Based on Organic Salts (GUMBOS). GUMBOS are ionic liquids (IL) that are bulky organic ions with a counter ion that can be changed for tuning.  They are more stable than traditional matrices under vacuum.  Unlike traditional IL’s, the GUMBOS melting point ranges …

A Data-Driven Framework For Mitigating Breast Cancer Overdiagnosis: From Estimation To Risk-Adjusted Computer-Aided Diagnosis, William M. Brown Jr.

LSU Doctoral Dissertations

In Computer-Aided Diagnosis (CAD) of cancer, standard cost metrics (false-positives and false-negatives) fundamentally fail to account for overdiagnosis. Overdiagnosis is a critical scenario where a disease is correctly detected (true-positive) but is biologically indolent and would never have caused the patient harm or symptoms. While widely recognized in the medical community as a major healthcare crisis driving stressful and invasive overtreatment, overdiagnosis remains severely under-researched within computer science and engineering. This dissertation addresses this interdisciplinary gap by defining the three key computational challenges of overdiagnosis: (i) accurate estimation, (ii) harm quantification, and (iii) algorithmic mitigation. To overcome the estimation challenge, …

Scattered Light Noise At Ligo Livingston Observatory Induced By Microseismic Ground Motion, Debasmita Nandi

LSU Doctoral Dissertations

Gravitational waves are “ripples” in the fabric of spacetime and create a minuscule change in the distance between two points. After publishing his theory of general relativity in 1915, Albert Einstein predicted the existence of gravitational waves as a consequence of the theory. Almost 100 years after the theoretical prediction, gravitational waves were detected for the first time in 2015 by the Advanced LIGO detectors in Livingston, Louisiana, and Hanford, Washington. Gravitational waves have a very small amplitude, making it very challenging to detect them. Different types of noise sources either of instrumental or environmental origin can reduce the astrophysical …

Unraveling The Nanoscopic Characteristics Of The Heterogeneous Deep Eutectic Solvent Formed By Lauric Acid And N-Methylacetamide: An Experimental And Computational Approach, Laura X. Sepulveda

LSU Doctoral Dissertations

Deep eutectic solvents (DESs) are attractive systems for extraction and separation of compounds. One example of this is the DES formed by the combination of lauric acid (LA) and N-methylacetamide (NMA), system that has been shown to efficiently separate oil/water mixtures through gel formation between LA and oil molecules. Structural characterization of this system using small-angle X-ray scattering (SAXS) and vibrational spectroscopy revealed the existence of nanometer-scale LA domains embedded in a continuous polar NMA phase, where LA and NMA interact through hydrogen bonding. These LA domains are responsible for the separation efficiency of linear organic molecules. However, this DES …

Evaluating Soil Health And Crop Yield In Louisiana Agricultural Systems: Impacts Of Best Management Practices And Prediction Models, Hector J. Mendoza Lagos

LSU Doctoral Dissertations

The adoption of conservation management practices is critical for improving soil health, enhancing nutrient use efficiency, and sustaining crop productivity in row crop systems in Louisiana. This study evaluated the role of conservation agronomic practices, soil biochemical indicators, and machine learning predictive models to improve soil nutrient dynamics, soil health indicators, microbial communities (MC), and crop productivity on a corn (Zea mays L.) research plot scale and in a commercial forty-hectare cotton (Gassypium hirsutum L.)-corn-soybean (Glycine max L.) rotation system in northeast Louisiana. The objectives of the study were to evaluate soil nutrient dynamics and MCs under …

Momentum Space Algorithm For Electronic Structure Of Double-Incommensurate Trilayer Graphene, Kenneth Silver Beard

LSU Doctoral Dissertations

Numerical algorithms for computing the electronic structure of incommensurate 2D-materials using ab initio models are critical for predicting material properties and guiding experiments. For bilayers, momentum space and continuum models have been introduced to approximate observables of ab initio tight-binding models using a momentum description, despite the lack of periodicity in the tight-binding model required for Bloch theory. A similar structure has been introduced for double-incommensurate trilayers using a continuum model, where the three lattices are mutually incommensurate. However, this description leads to a four-dimensional lattice space, and numerical convergence of the density of states has been observed to be …

Machine Learning Based Models For Simulation And Analysis Of Bulk Earth Melt System, Abin Shakya

LSU Doctoral Dissertations

Understanding the segregation of bulk Earth melt systems into metallic (core) and silicate (mantle) phases under high-pressure and high-temperature conditions is central to modeling Earth’s interior, yet relevant experimental and computational studies remain limited. This work develops a machine learning–based simulation pipeline that iteratively couples first-principles (quantum mechanical) calculations with neural network training to generate high-fidelity force fields. Using major-element Fe–Mg–Si–O melt systems, with and without H and N, as testbeds, we demonstrate that this framework enables large-scale molecular dynamics simulations at near first-principles accuracy. We further introduce a sequence of phase identification methods, progressing from statistical binning of elemental …

Extremal Connectivity In Graphs And Matroids, Yiwei Ge

LSU Doctoral Dissertations

Connectivity is a central theme in both graph theory and matroid theory. This dissertation investigates extremal connectivity in graphs and matroids, with emphasis on unavoidable structures and minimal connectivity phenomena.

Chapter 2 introduces cycle-contraction minors of graphs and investigates their structural properties. We establish a connection between cc-minors and induced subgraphs via graph duality. The main result gives an unavoidable-families characterization for cc-minors of sufficiently large loopless $2$-connected graphs.

Chapter 3 studies super-minimally $3$-connected graphs, namely $3$-connected graphs that have no proper $3$-connected subgraphs. We establish extremal bounds on structural parameters of these graphs, including the minimum number of degree-$3$ …

Circuits And Enumeration Problems For Matroids, Christine H. Cho

LSU Doctoral Dissertations

This dissertation is a collection of work concerning the structure and enumeration of circuits and other distinguished sets in a matroid. The Tutte polynomial, recognized as the universal deletion-contraction invariant in matroid and graph theory, is a natural starting point when considering enumeration problems for matroids. The main result in Chapter 2 generalizes a theorem of Dean Lucas concerning the Tutte polynomial and its behavior under rank-preserving weak maps. This generalization provides an avenue for comparing the numbers of circuits, bases, rank-k flats, and hyperplanes of a matroid containing an element given two distinct, yet related, elements.

Chapter 3 addresses …

Forbidden Induced Restrictions And Unavoidable Minors In Matroids, Matthew P. Mizell

LSU Doctoral Dissertations

Targets are matroids that arise from a nested sequence of flats in a projective geometry. This class of matroids was introduced by Nelson and Nomoto, who found the forbidden induced restrictions for binary targets. In this dissertation, their result is generalized to targets arising from projective geometries over $GF(q)$. In addition, targets arising from nested sequences of affine flats are introduced and the forbidden induced restrictions for these affine targets are determined.

In 1963, Halin and Jung proved that every simple graph with minimum degree at least four has $K_5$ or $K_{2,2,2}$ as a minor. Mills and Turner proved an …

Biogeochemical Controls On Phosphorus Transport And Legacy Storage Across A Coastal Watershed, Lee Potter

LSU Doctoral Dissertations

Excess phosphorus (P) loading is a key driver of eutrophication and harmful algal blooms (HABs) in aquatic systems worldwide. This relationship is of increasing concern in coastal Louisiana, where climate variability, altered hydrology, and land-use change converge, resulting in increased hydrologic and nutrient loading into coastal systems. This dissertation examines controls on P cycling in the Lake Pontchartrain Basin through a multi-scale framework linking estuarine processes, watershed loading, climate and weather patterns, and sediment dynamics. The dissertation begins with an overview of the study region, P dynamics, and changes in hydrology and nutrient loading patterns. Chapter 2 presents a spatial …

Improving Stem Assessments: Strategies For Increasing The Accessibility And Adoption Of Two-Stage Exams, Kristina Callaghan

LSU Doctoral Dissertations

Over three decades of research have shown that students taught using active learning strategies achieve better learning outcomes compared to those taught using traditional methods. Two-stage exams, which pair a traditional exam with a group component, are an increasingly popular method for incorporating active learning within the assessment component of a course. Previous studies have shown this assessment strategy provides a variety of benefits for students, including increased engagement and collaboration, immediate feedback, and potentially increased content retention. However, the unique circumstances of each instructor can pose a non-trivial barrier to the implementation of two-stage exams. In this thesis, we …

Applications For The Quasi-Atomic Orbital And Constrained Density Functional Theory Methods On Catalytic Reactions, Alvaro David Loaiza Orduz

LSU Doctoral Dissertations

Selective activation of C–O, C–H, and C–C bonds underpins biomass upgrading, alkane functionalization, and CO₂ conversion. Despite their importance, the electronic factors governing catalytic performance remain incompletely understood, and many industrial processes still rely on empirical trends or material-specific observations. This dissertation addresses this gap by applying density functional theory (DFT), thermodynamic decomposition, and electronic-structure analysis to identify unifying principles of reactivity across transition-metal phosphides, vanadate oxides, copper-based electrocatalysts, and mixed IrO₂–RuO₂ layers. This work examines how charge transfer, orbital localization, and ligand-induced perturbations control reaction pathways in diverse catalytic systems. C–O bond scission in 2-methyltetrahydrofuran (MTHF) and methanol was …

Measurement Of 18f(Alpha,P)21ne With The Array For Nuclear Astrophysics And Structure With Exotic Nuclei (Anasen), Keilah S. Davis

LSU Doctoral Dissertations

Certain (α,p) reactions on proton-rich nuclei are among the most important nuclear reactions occurring during Type I X-ray bursts, as well as being impactful in stellar explosions during the Asymptotic Giant Branch (AGB) phase and on accreting white dwarfs (WD). However, large uncertainties remain for reaction rates on some radioactive nuclei due to the lack of direct measurements. The Array for Nuclear Astrophysics and Structure with Exotic Nuclei (ANASEN) is a gas target and charged-particle detector designed for direct measurements of (α,p) reactions. ANASEN was redesigned with two hexagonal barrels of 100-µm-thick silicon strip surrounding the beam axis over a …

Metacommunity Coupled Epidemiological And Biophysical Modeling Of An Emergent Coral Disease, Benjamin Holmes Farmer

LSU Doctoral Dissertations

Emerging infectious diseases pose imminent risk to the marine realm and coral reefs in particular. Since its emergence in 2014, stony coral tissue loss disease (SCTLD) has dramatically reduced living coral cover in Florida and charted a similar course in the Caribbean. SCTLD is by far the most severe coral disease in history and has driven highly susceptible species to local extinction, yet the mechanisms driving the regional epizootic are not well understood. Here, we developed reef-scale parameterizations of disease spread using model sites in the lower Florida Keys, developed extensive metacommunity habitat maps for the US Caribbean, and then …

Quantifying Uncertainty In Landscape Evolution And Provenance Analysis: Insights From Statistical And Numerical Modelling, Vivian Carmello Grom

LSU Doctoral Dissertations

Landscape evolution models (LEMs) and detrital zircon provenance are widely used to investigate Earth surface processes, yet both face challenges related to quantifying model behavior and interpreting sedimentary signals under realistic, heterogeneous conditions. This thesis addresses these challenges through analysis and case studies that develop and apply new approaches for analyzing landscape dynamics and assessing uncertainties in sediment provenance.

Chapter 1 introduces a quantitative framework for evaluating LEM outputs using Shannon Entropy, Moran’s I, and Geary’s C. Applied to simulations with steady uplift, periodic uplift, spatially variable uplift, and a timeseries of DEMs, these metrics capture spatial organization and information …

Satellite-Mediated Quantum Clock Synchronization: Towards Precise Timing At A Global Scale, Sage B. Ducoing

LSU Doctoral Dissertations

Accurate timekeeping is essential for scientific and technological advancements, particularly in areas of communication, networking, navigation, and high precision measurements. While many methods of time resolution are already established using classical resources, they fail to combine high precision outcomes with large-scale implementations. Additionally, numerous quantum networking architectures using satellite-assisted methods have demonstrated quantum communication on scales exceeding ground-based methods. For these reasons, we propose the use of a time synchronization method by which pairs of highly time-correlated photons are exchanged between clocks on satellites and clocks on Earth, al- lowing users to reconstruct the time offsets between their clocks. This …

Practical Real-Time Permanent Magnet Energy Spectrometer Using A Diode Array For Therapeutic Electron Beam Tuning And Quality Assurance, Mason W. Heath

LSU Doctoral Dissertations

Purpose: Develop a practical, real-time permanent magnet electron energy spectrometer and evaluate it for beam tuning and quality assurance (QA) of therapeutic electron beams.

Methods: Aim 1: A 0.55 T permanent magnet was coupled to Sun Nuclear SRS MapCHECK® PC boards, providing two interlaced diode arrays. Detector response, R_meas(z_diode) versus diode position z_diode, was extracted from raw diode array readings, correcting for diode sensitivity and other factors. Using Monte Carlo (MC) computed, monoenergetic detector response functions, a curve-fitting algorithm extracted the energy spectrum, from R_meas(z_diode). The energy spectra for 7-20 …

Determining The 17f(Α,P)20ne Reaction Rate For Application In Type I X-Ray Bursts, William Braverman

LSU Doctoral Dissertations

The ¹⁷F(α, p)²⁰Ne reaction has been identified as an alternate pathway for breakout from the hot-CNO cycle that can be important in some X-ray burst scenarios. The ¹⁷F(α, p)²⁰Ne reaction rate was previously determined through a parameterized exponential S-factor with a large enhancement from thermally-excited states based on statistical models with large uncertainties. We have measured the time-inverse ²⁰Ne(p,α)¹⁷F cross section at center-of-mass energies ranging from 5.50 to 7.10 MeV using an activation method with a proton beam on a neon gas cell. Coincident detections of 511-keV γ-rays, resulting from electron-positron …

How The Inter-Nucleon Force Shapes Emergent Collectivity And Imparts Uncertainties In Ab Initio Nuclear Observables, Kevin Becker

LSU Doctoral Dissertations

The importance of collective motion in atomic nuclei has been well-established for many decades. Even before the advent of the nuclear shell model and its much-needed answers to surprising empirical phenomena, collectivity and surface deformation have played a vital role in broadening our knowledge. Reconciling the collective and single-particle camps into a unified description required tremendous strides in the application of group theory and advances in high-performance supercomputing, and thanks to these efforts the symmetry-adapted no-core shell model, or SA-NCSM, has developed into a reliable model for the study of deformed light and medium-mass nuclei. State-of-the-art calculations reveal remarkably simple …

Compound-Specific Isotope Records Of Dust Provenance And Hydroclimate In The North Pacific And Marginal Seas Of East Asia: Integrating N-Alkane Δ13c And Δd With Standardized Analytical Frameworks, Julian W. Traphagan

LSU Doctoral Dissertations

This dissertation presents advancements in compound-specific isotope analysis (CSIA) through methodological innovation and paleoclimate reconstruction in Central and East Asia. Utilizing plant wax n-alkanes from International Ocean Discovery Program (IODP) and Ocean Drilling Program (ODP) sediment cores, this research reconstructs atmospheric circulation shifts responding to tectonic evolution and climate transitions since the Late Miocene.

Chapter 1 investigates hydrogen isotope compositions (δD_wax) from IODP U1430 (Sea of Japan), ODP 886, and ODP 1208 (North Pacific) to trace dust provenance and hydroclimate changes since ~13 Ma. Results reveal persistently segmented source-to-sink systems: the Sea of Japan dominated by westerly …

Investigation Of Co-Current And Counter-Current Multiphase Flow In Upstream Drilling And Production Applications, Hazem Fleifel

LSU Doctoral Dissertations

In the domain of upstream Petroleum Engineering, the dynamics of co-current and counter-current multiphase flows present huge challenges, significantly impacting the efficiency of associated processes. This study investigates two specific applications concerning these flow behaviors, involving both laboratory experiments and transient computer simulations. This work investigates two distinct well control and production enhancement processes, involving multiphase flow dynamics: the bullheading kill procedure and liquid-assisted gas lift (LAGL).

The first topic (Topic 1) explores the bullheading process, a type of well control methods, by challenging the traditional understanding that gas removal efficiency increases monotonically with injection pump flow rate. Through 1D …

Patterns And Processes Behind Secretive Marshbird Movement, Abundance, And Distribution Across Southeastern Louisiana, Leah Moran

LSU Doctoral Dissertations

Restoration and conservation of coastal Louisiana hinges on understanding the patterns and processes underlying habitat heterogeneity on the landscape and therefore the species that inhabits this region, including secretive marshbirds. Elusive in nature, this guild of birds has evolved under dynamic hydroperiods, and myriad plant communities present within wetlands. Only recently, however, has research focused on the role of hydrologic dynamics and vegetative structure and distribution on abundance, movement and detection of marshbirds, specifically within southeastern Louisiana. This study aimed to quantify the ecological patterns and processes, particularly hydrologic processes and landscape structure, driving breeding secretive marshbird movement, abundance and …

Quasistatic Peridynamics, Existence Of Unique Solution In The Presence Of Damage, Nuwanthi N. Samarawickrama

LSU Doctoral Dissertations

A mathematical model for damage propagation based on nonlocal potentials is developed within the framework of peridynamics. This model is applied to simulate damage evolution in cyclically loaded structures. By neglecting inertial effects, a well-posed quasistatic formulation for cyclic loading is obtained.\\ The resulting equation is expressed as a nonlocal and nonlinear integral operator that couples damage evolution to the deformation field.\\ This coupling occurs through the product of a damage factor and the derivative of a force potential. The damage factor ranges between zero and one, where one represents undamaged material and zero indicates complete damage.\\ It serves to …

Towards Leveraging Social Media Data For Fostering Collaborations Among Non-Profits, Monazil Chowdhury

LSU Doctoral Dissertations

Nonprofit organizations serve a crucial role in tackling a wide range of significant social, environmental, and economic issues. But it is often hard to get a clear picture of their work because their information is spread out and it is difficult to see how they are collaborating. To address this issue we developed a web-based tool to collect scattered data—from a variety of sources, such as the IRS, social media, and the Census, into one easy-to-use resource. The tool begins by taking IRS records and geocoding each nonprofit’s physical address With its coordinates. It then retrieves census tract information from …

Digital Forensics And Ai: Artifact Analysis And Using Ai In The Forensics Domain, Clinton Joel Walker

LSU Doctoral Dissertations

Digital Forensics (DF) is a field of forensic science focusing on the acquisition, authentication, and analysis of digital evidence while maintaining integrity of that data. DF analysts use forensic tools to parse large volumes of data for investigations and depend on them for identification of pertinent digital evidence in vast amounts of data. Keeping up with innovations and ever-expanding data volumes is a constant challenge for these investigators. The prevalence of Artificial Intelligence (AI) in everyday computing is rapidly expanding, with the use of Machine Learning (ML) and Large Language Models (LLM)s becoming increasingly commonplace. Innovations in technology bring new …

Gain Threshold Optimization Using Fano Resonance, Alina Oktiabrskaia

LSU Doctoral Dissertations

The study of resonances in electromagnetics plays a critical role in the design of optical systems. This dissertation investigates the interaction between resonance and gain in optical structures to establish a universal principle for achieving ultra-low-threshold lasing. Through the analysis of geometric symmetries, material properties, and coupling mechanisms, this research develops prototype structures applicable to a wide range of optical and electromagnetic systems. A range of models is considered, starting from a simple onedimensional string-resonator system (based on the model of H. Lamb), then advancing to two- and three-dimensional waveguide models, and culminating with a realistic high-contrast model in open …

Quantitative Boundary Doubling Estimates For Elliptic Equations, Jack Dalberg

LSU Doctoral Dissertations

We present an approach for obtaining quantitative boundary doubling inequalities for elliptic equations with Neumann boundary conditions. Carleman estimates are used to prove three-ball inequalities, which are then used to prove quantitative doubling inequalities, with bootstrapping from the interior to the boundary. This approach is illustrated by its application to the Laplace eigenvalue problem with homogeneous Neumann boundary conditions, where sharp doubling inequalities are recovered.

When then consider a equation with non homogeneous Neumann boundary conditions. By following the approach, we are able to obtain potentially sharp results. Finally, we are able to get an improvement on previously obtained results …

The Search For Magnetar Giant Flares In Archival Gamma-Ray Burst Data To Constrain Their Rates And Energetics, Aaron Trigg

LSU Doctoral Dissertations

Magnetar giant flares are rare, extremely bright bursts of gamma-rays from highly magnetized neutron stars. These events are difficult to identify because, at extragalactic distances, they can appear similar to other astrophysical phenomena. Only a handful have been confidently identified to date, limiting our understanding of their origin and physical properties. This dissertation focuses on expanding the sample of known events and enabling a more detailed characterization of their observational features. We report on two newly identified examples, GRB 180128A and GRB 231115A, that are consistent with a magnetar origin based on their spectral properties and association with nearby star-forming …

Investigation Of Subcellular Damage And Long-Term Non-Cancerous Cardiovascular Effects Following Whole-Body Photon Irradiation, Nousha Afshari

LSU Doctoral Dissertations

Current radiobiological models focus primarily on nuclear DNA damage and fail to fully explain radiation-induced noncancerous health effects. This dissertation investigates whether non-nuclear subcellular structures contribute to radiation-induced biological damage through experimental biomarker analysis and computational microdosimetry. The central hypothesis posits that whole-body photon irradiation results in subcellular non-nuclear damage, specifically increased circulating mitochondrial DNA concentrations, that correlates with radiation dose and long-term noncancerous effects such as cardiovascular disease.

Specific Aim 1 measured mitochondrial and nuclear DNA concentrations in banked blood samples from 72 Chinese rhesus macaques that previously received whole-body photon irradiation ($0-10$ Gy) from Cobalt-60 or LINAC sources. …