Physical Sciences and Mathematics Commons^™

Advances In Differentially Methylated Region Detection And Cure Survival Models, Daniel Ahmed Alhassan

Doctoral Dissertations

"This dissertation focuses on two areas of statistics: DNA methylation and survival analysis. The first part of the dissertation pertains to the detection of differentially methylated regions in the human genome. The varying distribution of gaps between succeeding genomic locations, which are represented on the microarray used to quantify methylation, makes it challenging to identify regions that have differential methylation. This emphasizes the need to properly account for the correlation in methylation shared by nearby locations within a specific genomic distance. In this work, a normalized kernel-weighted statistic is proposed to obtain an optimal amount of "information" from neighboring locations …

Essays On Conditional Heteroscedastic Time Series Models With Asymmetry, Long Memory, And Structural Changes, K C M R Anjana Bandara Yatawara

Doctoral Dissertations

"The volatility of asset returns is usually time-varying, necessitating the introduction of models with a conditional heteroskedastic variance structure. In this dissertation, several existing formulations, motivated by the Generalized Autoregressive Conditional Heteroskedastic (GARCH) type models, are further generalized to accommodate more dynamic features of asset returns such as asymmetry, long memory, and structural breaks. First, we introduce a hybrid structure that combines short-memory asymmetric Glosten, Jagannathan, and Runkle (GJR) formulation and the long-memory fractionally integrated GARCH (FIGARCH) process for modeling financial volatility. This formulation not only can model volatility clusters and capture asymmetry but also considers the characteristic of long …

Recurrent Event Data Analysis With Mismeasured Covariates, Ravinath Alahakoon Mudiyanselage

Doctoral Dissertations

"Consider a study with n units wherein every unit is monitored for the occurrence of an event that can recur with random end of monitoring. At each recurrence, p concomitant variables associated to the event recurrence are recorded with q (q ≤ p) collected with errors. Of interest in this dissertation is the estimation of the regression parameters of event time regression models accounting for the covariates. To circumvent the problem of bias and consistency associated with model's parameter estimation in the presence of measurement errors, we propose inference for corrected estimating functions with well-behaved roots under additive measurement errors …

We Are Still Playing: A Meta-Analysis Of Game-Based Learning In Mathematics Education, Thomas Conmy

Doctoral Dissertations

The purpose of this meta-analysis was to investigate the effectiveness of the use of games as part of mathematics instruction on academic achievement in grades Kindergarten to 12 in the United States. There were 17 studies selected for investigation published from 2010 to 2023 that focused on game-based learning and mathematics. This meta-analysis fills the gap in the knowledge by examining classes that are using game based learning across three platforms of instruction: nondigital games, digital on computers, and mobile devices. The findings from this meta-analysis suggest that the usage of game-based learning in a classroom has a positive effect …

Efficient High Order Ensemble For Fluid Flow, John Carter

Doctoral Dissertations

"This thesis proposes efficient ensemble-based algorithms for solving the full and reduced Magnetohydrodynamics (MHD) equations. The proposed ensemble methods require solving only one linear system with multiple right-hand sides for different realizations, reducing computational cost and simulation time. Four algorithms utilize a Generalized Positive Auxiliary Variable (GPAV) approach and are demonstrated to be second-order accurate and unconditionally stable with respect to the system energy through comprehensive stability analyses and error tests. Two algorithms make use of Artificial Compressibility (AC) to update pressure and a solenoidal constraint for the magnetic field. Numerical simulations are provided to illustrate theoretical results and demonstrate …

Scanning Probe Microscopy Studies Of Petroleum Chemistry: Substrate-Dependent Catalytic Properties Of Mos2 And Automating Scanning Probe Microscopy With Machine Learning, Steven Arias

Doctoral Dissertations

With the growth of the population, society’s energy demands are mostly reliant on petroleum products that come from the refining of crude oil. Most of these refining reactions have been developed through averaging spectroscopic techniques, but scientists do not know exactly what is happening in these processes at the nano and atomic levels. This information is crucial when designing an efficient refining process that produces petroleum products that emit fewer harmful gases when combusting. Scanning probe microscopy techniques have become a powerful tool to look into the chemical structures found in petroleum products, to understand catalytic reactions in refining processes, …

Novel Quantum Materials For Spintronic And Opto-Electronic Applications, Ali Sarikhani

Doctoral Dissertations

"Multi-functional quantum materials play a crucial role in the development of spintronics and opto-electronics, as their properties can greatly influence device performance. For instance, in spintronics, materials such as ferromagnetic half-metals, Giant Magnetoresistants (GMR), and magnetic semiconductors have been extensively studied due to their ability to manipulate the spin of electrons for applications in magnetic storage. In opto-electronics, materials such as Diluted Magnetic Semiconductors (DMS) and non-oxide Transparent Conductors (TC) offer advantages such as tunable bandgap and high absorption coefficients, which enable improved device performance.

For this purpose, we have experimentally investigated the compounds that have shown theoretically interesting physical …

Core-Collapse Supernova Simulations With Spectral Two-Moment Neutrino Transport, Ran Chu

Doctoral Dissertations

The primary focus of this dissertation is to develop a next-generation, state-of-the-art neutrino kinetics capability that will be used in the context of the next-generation, state-of-the-art core-collapse supernova (CCSN) simulation frameworks \thornado\ and \FLASH.\index{CCSN} \thornado\ is a \textbf{t}oolkit for \textbf{h}igh-\textbf{or}der \textbf{n}eutrino-r\textbf{ad}iation hydr\textbf{o}dynamics, which is a collection of modules that can be incorporated into a simulation code/framework, such as \FLASH, together with a nuclear equation of state (EOS)\index{EOS} library, such as the \WeakLib\ EOS tables. The first part of this work extends the \WeakLib\ code to compute neutrino interaction rates from~\cite{Bruenn_1985} and produce corresponding opacity tables.\index{Bruenn 1985} The processes of emission, …

Constrained Collective Movement In Human-Robot Teams, Joshua Fagan

Doctoral Dissertations

This research focuses on improving human-robot co-navigation for teams of robots and humans navigating together as a unit while accomplishing a desired task. Frequently, the team’s co-navigation is strongly influenced by a predefined Standard Operating Procedure (SOP), which acts as a high-level guide for where agents should go and what they should do. In this work, I introduce the concept of Constrained Collective Movement (CCM) of a team to describe how members of the team perform inter-team and intra-team navigation to execute a joint task while balancing environmental and application-specific constraints. This work advances robots’ abilities to participate along side …

Controlling Polymer Molecular Structure And Morphology: From Illumination Of Conjugated Polymers To Polymer Chain Depolymerization, Josh Moncada

Doctoral Dissertations

Polymers remain a prominent component of our lives, and finding methods to control their structure or morphology are needed to tune material properties. This dissertation reports methods to alter the conformation, morphology, or structure of polymeric materials. Chapter two describes the impact of exposure to white light during annealing of conjugated polymer blends on their morphology and optoelectronic performance. The observed changes in the morphology correlate strongly to the variation in photoluminescence (PL) with illumination, including that the PL varies less with illumination at higher Poly[2-methoxy-5-(2-ethylhexyloxy)-1,4-phenylenevinylene] loadings, offering foundational understanding to guide the structure and optoelectronic performance of conjugated polymer …

Light Matter Interactions: A Study Of Soft Materials Using Linear And Nonlinear Spectroscopy, Muhammad Redwan Hassan

Doctoral Dissertations

The adoption of complex fluids for various industrial applications is becoming normal. Complex fluids offer tunability, wide range solubility, and chemical and thermal stability which are the factors that conventional polar and non-polar solvents often lack. However, fundamental studies of these fluid systems are still lacking which is limiting the appropriate use of these complex fluids in many applications. The goal of this dissertation was to study and characterize complex fluids for application in electrolytes for redox flow batteries. Chapter 3 and chapter 4 feature the study of microemulsions and deep eutectic solvents (DES) by fluorescence techniques. Fluorescence studies of …

Geochemical And Climatic Controls On The Sulfur Cycle In Volcanic Settings: Implications For The Origin Of Sulfur-Rich Deposits Investigated By The Spirit And Opportunity Rovers On Mars, Rhianna D. Moore

Doctoral Dissertations

On Earth, volcanic activity with elevated sulfur (S) degassing in the presence of water leads to the formation of hydrothermal deposits enriched in S-bearing minerals. Similar processes may have been an important source of S on Mars. The landing sites of Gusev crater and Meridiani Planum investigated by the Spirit and Opportunity rovers, respectively, showed elevated SO₄^2- [sulfate] concentrations, suggesting high- and low-temperature aqueous processes. However, the SO₄^2- contribution from subsequent aqueous weathering of hydrothermal S deposits has been poorly constrained, thus its importance to regional S cycling in the landing sites is unclear. In this …

Enhancing The Performance Of The Mtcnn For The Classification Of Cancer Pathology Reports: From Data Annotation To Model Deployment, Kevin De Angeli

Doctoral Dissertations

Information contained in electronic health records (EHR) combined with the latest advances in machine learning (ML) have the potential to revolutionize the medical sciences. In particular, information contained in cancer pathology reports is essential to investigate cancer trends across the country. Unfortunately, large parts of information in EHRs are stored in the form of unstructured, free-text which limit their usability and research potential. To overcome this accessibility barrier, cancer registries depend on expert personnel who read, interpret, and extract relevant information. Naturally, as the number of stored pathology reports increases every day, depending on human experts presents scalability challenges. Recently, …

Transition Metal Computational Catalysis: Mechanistic Approaches And Development Of Novel Performance Metrics, Brett Anthony Smith

Doctoral Dissertations

Computational catalysis is an ever-growing field, thanks in part to the incredible progression of computational power and the efficiency offered by our current methodologies. Additionally, the accuracy of computation and the emergence of new methods that can decompose energetics and sterics into quantitative descriptors has allowed for researchers to begin to identify important structure-function relationships that predict the properties of unexplored subspaces within the overall chemical space. Catalytic descriptors have been used frequently in data driven high-throughput computational screenings. With the use of machine learning, a large portion of the chemical space an be predicted in matter of minutes or …

Development Of A New High-Resolution Neutron Detector And Beta-Delayed Neutron Spectroscopy Of 24o., Shree K. Neupane

Doctoral Dissertations

An efficient neutron detection system with good energy resolution is needed to correctly characterize the decays of neutron-rich nuclei where beta-delayed neutron emission is a dominant decay mode. Precision neutron spectroscopy probes nuclear structure effects in neutron-rich nuclei and is essential to exploit the opportunities in new-generation radioactive beam facilities. A new high-resolution neutron detector, Neutron dEtector with Xn Tracking (NEXT), has been constructed, characterized, and tested in decay and reaction experiments. Its essential capability is the neutron interaction position localization, which enables improvement in energy resolution without compromising detection efficiency in the time-of-flight measurements. Neutron-gamma discrimination capability of NEXT …

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Constraining The 30p(P,Γ)31s Reaction Using 30p(D,Pγ)31p With Goddess, Rajesh Ghimire

Doctoral Dissertations

The ³⁰P(p,γ)³¹S reaction acts as a bottleneck for classical nova nucleosynthesis beyond A=30 in ONe novae, due in part to the long lifetime of ³⁰P (∼2.5 minutes) with respect to the timescale of a nova outburst. Also, the ³⁰P(p,γ)³¹S reaction rate directly affects the isotopic ratio of ³⁰Si/²⁸Si, which is an important nova identifier in the analysis of pre-solar grains. O/S, S/Al, O/P, and P/Al elemental abundance ratios can be used as nuclear thermometers for classical novae by constraining the ³⁰P(p,γ)³¹S reaction rate.

However, direct measurement of …

Development Of Raman Spectroscopic Methods For Detection Of Molecules Indicating Life In Extraterrestrial Environments, Grace Sarabia

Doctoral Dissertations

Mineral analysis is of great importance to the understanding of the world around us and worlds beyond. Geology, chemistry, and environmental studies all benefit from characterization of the structure and properties of minerals. While various techniques have been applied towards the study of minerals, we propose that Raman spectroscopy is specifically suited for the detection and study of minerals under various conditions, including for terrestrial and space applications.

In our terrestrial studies, we explored the polymorphs of calcium carbonate within freshwater mollusk shell matrices with Raman spectroscopy. We found that aragonite was the main calcium carbonate polymorph present in the …

The Impact Of A Nuclear Disturbance On A Space-Based Quantum Network, Alexander Miloshevsky

Doctoral Dissertations

Quantum communications tap into the potential of quantum mechanics to go beyond the limitations of classical communications. Currently, the greatest challenge facing quantum networks is the limited transmission range of encoded quantum information. Space-based quantum networks offer a means to overcome this limitation, however the performance of such a network operating in harsh conditions is unknown. This dissertation analyzes the capabilities of a space-based quantum network operating in a nuclear disturbed environment. First, performance during normal operating conditions is presented using Gaussian beam modeling and atmospheric modeling to establish a baseline to compare against a perturbed environment. Then, the DEfense …

Intra-Skeletal Variation In Stable Isotopes Through Non-Destructive Approaches: Applications Of The Patterns Of Skeletal Remodeling To Biological Anthropology, Armando Anzellini

Doctoral Dissertations

Stable isotope analysis is a well-established method in biological anthropology used to deliver data on residence, diet, and life history. Samples for these analyses are often collected from the diaphyses of long bones with an assumption of an expected rate of turnover between five and ten years, depending on the skeletal element. However, the biological foundations of this assumption are still uncertain, especially concerning the intra-skeletal and intra-element variation of isotopic signatures that may relate to patterns of remodeling. Exploring these gaps in intra-element isotopic variation requires fine-grained work using multiple bones from multiple individuals, but such work is limited …

Evaluation Of Distributed Programming Models And Extensions To Task-Based Runtime Systems, Yu Pei

Doctoral Dissertations

High Performance Computing (HPC) has always been a key foundation for scientific simulation and discovery. And more recently, deep learning models' training have further accelerated the demand of computational power and lower precision arithmetic. In this era following the end of Dennard's Scaling and when Moore's Law seemingly still holds true to a lesser extent, it is not a coincidence that HPC systems are equipped with multi-cores CPUs and a variety of hardware accelerators that are all massively parallel. Coupling this with interconnect networks' speed improvements lagging behind those of computational power increases, the current state of HPC systems is …

On Interpreting Eddy Covariance In Small Area Agricultural Situations With Contrasting Site Management., Joel Oetting

Doctoral Dissertations

This dissertation examined the carbon sequestration potential of a low C:N soil amendment and its incorporation into the soil over a rolling agricultural field. A segmented planar fit was developed to assess and correct the systematic errors the topography introduces on the carbon dioxide fluxes. The carbon dioxide fluxes were then be partitioned into gross primary productivity and soil respiration to understand the influence of the contrasting management practices, using flux variance partitioning. Concomitant with the partitioning, high resolution temporal and spatial scale remote sensing images were interpolated and standardized to conduct hypothesis testing for treatment effects.

Natural, Experimental, And Educational Explorations Of The Interiors Of Terrestrial Planetary Bodies, Nadine L. Grambling

Doctoral Dissertations

Planetary interiors are enigmatic, inaccessible, and vital to the processes that have formed the rocks we see on the surface of bodies in the inner Solar System today. Based on geophysical explorations of the Moon and Earth, along with information gleaned from rocks at the surface today, there is understanding of the basic structure and processes at depth. Using a combination of natural samples and experimental studies, we attempt to learn more about the physical conditions beneath the surface, and their effect on material properties and tectonics processes in the mantle.

On Earth, mid-ocean ridge processes have long been debated, …

Towards Reduced-Order Model Accelerated Optimization For Aerodynamic Design, Andrew L. Kaminsky

Doctoral Dissertations

The adoption of mathematically formal simulation-based optimization approaches within aerodynamic design depends upon a delicate balance of affordability and accessibility. Techniques are needed to accelerate the simulation-based optimization process, but they must remain approachable enough for the implementation time to not eliminate the cost savings or act as a barrier to adoption.

This dissertation introduces a reduced-order model technique for accelerating fixed-point iterative solvers (e.g. such as those employed to solve primal equations, sensitivity equations, design equations, and their combination). The reduced-order model-based acceleration technique collects snapshots of early iteration (pre-convergent) solutions and residuals and then uses them to project …

Analytical Techniques For The Analysis Of Uranium Bearing Materials, Nathaniel D. Fletcher

Doctoral Dissertations

The interest in the use of nuclear power has increased drastically in recent years. This is due to significantly increased efficiency at producing energy when compared to fossil fuels. With the increased use of nuclear power comes an increased need to for monitor for uranium bearing materials outside of regulatory control. This dissertation covers four projects aimed at improving the analysis of these materials. The first projects aims to develop a method that allows for the analysis of elements that exist in nature as anions by triple quadrupole ICP – MS. This would allow for the ability to measure more …

Tethered Axial Coordination As A Control Modality In Rhodium(Ii)-Catalyzed Carbene Transfer Reactions, Anthony Dean Abshire

Doctoral Dissertations

Rhodium(II) paddlewheels are versatile carbene transfer catalyst that are broadly applied in insertion reactions, cycloadditions, and ylide transformations. The effects of axial coordination in rhodium(II)-catalyzed carbene transfer reactions are still little understood due to compounding factors that are difficult to isolate. Traditionally, researchers study axial coordination by addition of Lewis base additives. To ensure interaction between the Lewis base and catalyst, high molar equivalents are used. This can also have the undesired effect of hampering the activity of the catalyst and suppressing the yield of the reaction. We have developed ligands with a tethered Lewis base to overcome these issues. …

Experimental Approaches To Evaluating Silicate Melt Properties And Trace Element Fractionation During Crystallization At High Pressures And High Temperatures, Megan D. Mouser

Doctoral Dissertations

Current understanding of the evolution and behavior of silicate materials that form in planetary interiors at high-pressures and high-temperatures largely come from experimental work as natural samples are either rare, or physically inaccessible. Laboratory experiments provide a comprehensive way to constrain the crystallization history, elemental partitioning, and viscosity of different silicate materials at planetary mantle pressure and temperature conditions. This work utilizes two high-pressure experimental techniques, the Paris-Edinburgh apparatus, and the piston cylinder apparatus, to measure physical and chemical properties of silicate materials. The viscosity of reduced, Fe-free silicate liquids, with and without sulfur (S-free and S-bearing), were measured to …

Imaging Normal Fluid Flow In He Ii With Neutrons And Lasers — A New Application Of Neutron Beams For Studies Of Turbulence, Xin Wen

Doctoral Dissertations

Turbulence is ubiquitous in life —from biology to astrophysics. The best direct numeric simulations (DNS) have only been benchmarked against low resolution, time-averaged experimental configurations—partly because of limitations in computing power. With time, computing power has greatly increased, so there is need for higher quality data of turbulent flow. In this dissertation, we explore a solution that enables quantitative visualization measurement of the velocity field in liquid helium, which has the potential of breaking new ground for high Reynolds number turbulence research and model testing.

Our technique involves creation of clouds of molecular tracers using 3He-neutron absorption reaction in liquid …

Elucidating The Importance Of Structure, Surfaces, And Interfaces In Polymer Nanoparticles And Nanocomposites, Jacob E. Fischer

Doctoral Dissertations

This dissertation details research conducted to elucidate the importance of structure, surfaces, and interfaces in both polymeric nanoparticles and polymer nanocomposites. The fundamental understanding that is garnered in these studies provides a foundation to rationally develop nanocomposites tailored for unique functionalities, performance and applications.

Soft polymeric nanoparticles, have shown to imbue non-traditional diffusive properties, the strength of which decreases with crosslinking density of the nanoparticle. The crosslinking dependent morphology of these nanoparticles is first characterized in a dilute solution of good solvent (Chapter 2). The scattering results revealed that the structure ranges from a swollen polymer in good solvent (0% …

The Structure Of 71ni Via Beta-Delayed Neutron Spectroscopy Of 71co, Andrew Keeler

Doctoral Dissertations

Studies of beta decays can give insights into the underlying structure of the nucleus. In particular, decays of closed-shell and near-closed-shell nuclei can provide important benchmarks for structure models, which are used in simulations of r-process nucleosynthesis. This work reports on a study of beta decays of ⁷¹Co produced in an experiment that was carried out in October 2016 at MSU’s National Superconducting Cyclotron Laboratory (NSCL) using the Versatile Array of Neutron Detectors at Low Energy (VANDLE). In order to carry out this experiment, a novel position-sensitive scintillating detector was developed to enable the sub-nanosecond timing response that VANDLE …

Understanding Liquid Dynamics Using The Van Hove Function From Inelastic Neutron Scattering Measurements, Yadu Krishnan Sarathchandran

Doctoral Dissertations

Liquid state physics remains relatively unexplored compared to solid-state physics, which achieved massive progress over the last century. The theoretical and experimental methodologies used in solid-state physics are not suitable to study the liquid state due to the latter's strong time dependence and the lack of periodicity in structure. The approaches based on phonon dynamics break down when phonons are over-damped and localized in liquids. The microscopic nature of atomic dynamics and many-body interactions leading to liquid state properties such as viscosity and dielectric loss in liquids remain unclear. Inelastic neutron scattering measurements were done to study the microscopic origins …