Physical Sciences and Mathematics Commons^™

Applying Machine Learning Algorithms For The Analysis Of Biological Sequences And Medical Records, Shaopeng Gu

Electronic Theses and Dissertations

The modern sequencing technology revolutionizes the genomic research and triggers explosive growth of DNA, RNA, and protein sequences. How to infer the structure and function from biological sequences is a fundamentally important task in genomics and proteomics fields. With the development of statistical and machine learning methods, an integrated and user-friendly tool containing the state-of-the-art data mining methods are needed. Here, we propose SeqFea-Learn, a comprehensive Python pipeline that integrating multiple steps: feature extraction, dimensionality reduction, feature selection, predicting model constructions based on machine learning and deep learning approaches to analyze sequences. We used enhancers, RNA N6- methyladenosine sites and …

X-Ray Fluorescence Analysis Of Tuscaloosa Marine Shale Cuttings From Horizontally Drilled Wells, Xiaotian Wang

Electronic Theses and Dissertations

The Upper Cretaceous Tuscaloosa Marine Shale (TMS) is a gray to black fissile marine shale deposited at depth of between 10,000 and 20,000 ft near the ancient Gulf of Mexico. The TMS has been gradually developed as a hydrocarbon reservoir in the past several decades. But there are rare researches evaluating geochemical properties based on chemostratigraphy of the TMS. The objective of this research is to spatially evaluate geophysical properties and chemostratigraphy of the TMS, to characterize elemental changes along well paths and to evaluate the effect of basic sample clean on XRF results. The data available for this study …

Optimizing The Performance Of Complex Engineering Systems Aided By Artificial Neural Networks, Khalil Qatu

Electronic Theses and Dissertations

In the first problem Polyetherimide graphene nanoplatelets papers (PEIGNP) were tested with different graphene loadings varying from 0-97 weight percent (WT%). The resulting stress-strain curves were utilized to develop two ANN models. Stress-controlled and strain-controlled models. Both models shoan excellent correlation to the experimental. Several Mechanical properties were calculated from the predicted stress-strain curves namely; toughness maximum strength maximum strain and maximum tangent modulus. Both models captured the same overall behavior of the PEIGNP composite. However the strain-controlled model was found to predict lower stress than the stress-controlled model. Finally a Graphical User Interface (GUI) was developed to aid in …

Geographic Variations Of Sound Channel Axis In The Global Ocean, Mukunda Kumar Acharya

Electronic Theses and Dissertations

Sound signals are used for imaging and communication in the ocean. Underwater sound speed has a minimum at a certain depth that forms a sound channel for long-range underwater sound propagation. The geographic variation of sound channel is crucial in uses of underwater sound in various environments including ocean acoustic tomography and monitoring of global warming. In this work, sound speed and depth of the channel axis in the global ocean are characterized for their variation with the latitude, longitude, and depth.

X-Ray Crystal Structure Of Au36(Sph-Pch3)24 Nanomolecules, Vigneshraja Ganeshraj

Electronic Theses and Dissertations

Au36(SR)24 is one of the most comNanomolecules (NM) in gold NM field and crystal structures of Au36(SR)24 with different thiolate protecting ligand such as tert-butylbenzene thiol, thiophenol and cyclopentane thiol have been reported. It has been predicted that aromatic thiol protected Au36(SR)24 NM have same core structures like the other reported Au36(SR)24 NMs. Due to the steric and electronic conjugation effects the staples on the gold core exhibit minor changes in the bond length without affecting the gold core. By varying the Gold:Thiol ratio the NM size can be controlled. Herein, we report the synthesis, isolation and characterization of two …

Development Of Cobalt And Iron Catalysts Bearing Rigid Polydentate Ligands For Proton Reduction And C-H Bond Oxidation, Lizhu Chen

Electronic Theses and Dissertations

The demand for energy consumption has increased exponentially since the Industrial Revolution. The major source of this energy has been and continues to be fossil fuels. The depletion of fossil fuels and environmental concerns associated with their combustion has motivated us to develop a renewable energy alternative to meet future energy demands. Hydrogen is a clean energy alternative to fossil fuels, which can be generated from solar-driven water splitting. However, more efficient and inexpensive catalysts for the hydrogen evolution reaction (HER) are needed. In this context, hydrogen production has been investigated with a stable and highly reactive cobalt-based catalyst. While …

Structural Controls And Depositional Environments Of The Glen Rose Subgroup In Pelahatchie Field In Rankin County, Mississippi, Chesney Petkovsek

Electronic Theses and Dissertations

Following Lion Oil’s drilling of the Sowell #1, Lower Cretaceous step-out drilling in Pelahatchie Field has led to the establishment of Mooringsport, Paluxy, Rodessa, Sligo, and Hosston oil and gas condensate production along the flanks and crest of a salt feature within Rankin County, Mississippi. Exploration of salt features has been intermittent throughout Mississippi, but has shifted from targeting pay zones along the crests of domal and piercement salt features in the 1940s, to targeting reserves along the flanks of these features in the 1970s. The dominant structural feature in Pelahatchie Field is an elongate north-south-trending salt ridge. Results of …

Scheduling Irregular Workloads On Gpus, David Arthur Troendle

Electronic Theses and Dissertations

This doctoral research aims at understanding the nature of the overhead for data irregular GPU workloads, proposing a solution, and examining the consequences of the result. We propose a novel, retry-free GPU workload scheduler for irregular workloads. When used in a Breadth First Search (BFS) algorithm, the proposed simple, monolithic concurrent queue scales to within 10% of ideal scalability on AMD’s Fiji GPU with 14,336 active threads. The dissertation presents an important finding that the retry overhead associated with Compare and Swap (CAS) operations is the principle reason why concurrent queues do not scale well as the number of clients …

A Computational Approach To Predicting And Understanding New Psychoactive Substances (Nps) For Developing A Database For State And Federal Crime Laboratories, Caroline Amelia Spencer

Electronic Theses and Dissertations

The object of this dissertation was to use a computational approach to predict and understand new psychoactive substances (NPS) to develop a database for state and federal crime. The primary scope of the dissertation was to better understand the interactions that take place between new psychoactive substances and their corresponding receptors. Through analysis of the interactions between the amino acids within the receptors and the NPS an understanding into the pharmacology and toxicology of these drugs can be gained. NPS such as synthetic cannabinoids fentanyl and its analogs and kratom have become more problematic for both state and federal crime …

Investigation Of Narrow Bipolar Events In Mississippi Thunderstorms, Sampath Asiri Bandara

Electronic Theses and Dissertations

In the first part of the study FA and Log-RF data were used to examine low-altitude (<8.0 km) negative NBEs (NNBEs) to see how many -CG flashes were initiated by NNBEs. Out of 686 -CG flashes only 33 (5%) flashes were initiated by an NNBE. These NNBEs occurred at an average altitude of 6.2 km had average amplitude (range-normalized amplitude to 100 km) of 0.4 V/m and had average VHF (Log-RF) power of 130 W. Since the low-altitude NNBEs were substantially weaker than positive NBEs that initiate intracloud (IC) flashes it is hypothesized that -CG flashes are easier to initiate than IC flashes. The second part of the study investigated the properties of 201 positive NBEs (+NBEs). The +NBEs were classified in two ways: into Types A-D [Karunarathne et al. 2015] and into three different groups: Isolated Not-isolated and IC flash-initiator or INBE [Wu et al. 2014]. The average VHF (Log-RF) power of NBEs within the A-D categories were 1.9 4 9.8 and 13.2 kW respectively while the powers for the Isolated Not-isolated and INBE categories were 10.1 4 and 10.1 kW respectively. The third study considered 34 NBEs that occurred close in space and time to each other: 13 pairs of NBEs one group of three +NBEs and one group of five +NBEs. The NBEs were overlaid on radar data of the parent thunderstorms. The data indicate that the individual NBEs in each group initiated in separate intense electric field regions of small extent rather than in a single large-scale electric field region. This dissertation investigates Narrow Bipolar Events (NBEs) which are a type of short-duration (10- 30 µs) lightning discharge. The study primarily used data from NBEs collected in 2016 at seven sensor sites within 50 km of Oxford Mississippi USA. Each sensor site had three electromagnetic antennas called Fast Antenna (FA) dE⁄dt and Log-RF with bandwidths of 0-2.5 MHz 0-1.0 MHz and 186-192 MHz respectively. NBEs are often isolated from other lightning events in thunderclouds but they sometimes initiate negative cloud-to-ground (-CG) and intracloud (IC) lightning flashes or they can occur during these flashes.

Effects Of Halogen Bonding And Nir Tuning Of Dyes For Dye-Sensitized Solar Cells, Alexandra Baumann

Electronic Theses and Dissertations

With current energy demands being met through the utilization of energy sources such as petroleum, natural gas, and coal, the non-renewable nature of these sources will eventually approach depletion as world wide energy consumption increases yearly. As a result the need for a renewable energy alternative has become imminent. One appealing alternative that has gained considerable attention since its development due to a low cost and a high solar to electric conversion efficiency are dye-sensitized solar cells (DSCs). This dissertation describes efforts to design and synthesize improved organic dyes utilizing three analogous methods: first, through decreasing non-productive pathways such as …

Broadband Mid-Infrared Frequency Combs Generated Via Frequency Division, Qitian Ru

Electronic Theses and Dissertations

Frequency combs have revolutionized metrology and demonstrated numerous applications in science and technology. Combs operating in the mid-infrared region could be beneficial for molecular spectroscopy for several reasons. First, numerous molecules have their spectroscopic signatures in this region. Furthermore, the atmospheric window (3-5μm and 8-14μm) is located here. Additionally, a mid-infrared frequency comb could be employed as a diagnostic tool for the many components of human breath, as well as for detection of harmful gases and contaminants in the atmosphere. In this thesis, I used synchronously pumped subharmonic optical parametric oscillators (OPOs) operating at degeneracy to produce ultra-broadband outputs near …

Artificial Magnetism And Topological Phenomena In Optics, Midya Parto

Electronic Theses and Dissertations

Recent years have witnessed intense research activities to effectively control the flow of photons using various classes of optical structures such as photonic crystals and metamaterials. In this regard, optics has benefited from concepts in condensed matter and solid-state physics, where similar problems concerning electronic wavefunctions arise. An important example of such correspondence is associated with the photon dynamics under the effect of an artificial magnetic field. This is especially important since photons, as neutral bosons, do not inherently interact with magnetic fields. One way to mitigate this issue is to exploit magneto-optical materials. However, as is well known, using …

A Comparison Of Bayesian Estimation Techniques In A Multidimensional Two-Parameter Partial Credit Item Response Model, Peiyan Liu

Electronic Theses and Dissertations

Bayesian estimation methods have shown better performance than the traditional Marginal Maximum Likelihood (MML) estimation method for parameter estimation in relatively simple item response models. However, extant literature is lacking on the investigation of Bayesian parameter estimation approaches for a multidimensional two parameter partial credit (M2PPC) model, therefore this simulation study investigated the performance of two Bayesian Markov Chain Monte Carlo (MCMC) algorithms: Gibbs Sampler and Hamiltonian Monte Carlo-No-U-Turn-Sampler (HMC-NUTS) for M2PPC models' parameter estimation. It compared the estimation accuracy and computing speed in different combinations of situations, including prior choices, test lengths, and the relationships between dimensions.

The datasets …

Non-Hermitian And Space-Time Mode Management, Nicholas Nye

Electronic Theses and Dissertations

In the last few years, optics has witnessed the emergence of two fields namely metasurfaces and parity-time (PT) symmetry. Optical metasurfaces are engineered structures that provide unique responses to electromagnetic waves, absent in natural materials. On the other hand, PT symmetry has emerged from quantum mechanics, when a new class of non-Hermitian Hamiltonian quantum systems was shown to have real eigenvalues. In this work, we demonstrate how PT-symmetric diffractive structures are capable of eliminating diffraction orders in specific directions, while maintaining/enhancing the remaining orders. In the second part of this work, we emphasize on supersymmetry (SUSY) and its applications in …

Metastable-State Photoacids: Synthesis, Properties, And Applications, Parth Patel

Electronic Theses and Dissertations

Reversible photochromic compounds have the ability to reversibly change its color when it absorbs photons of a particular wavelength. This process of color change is a consequence of structural changes within the compound, such as cis-trans photo-isomerization. Some examples of photochromic compounds are spiropyrans, spirooxazines, diarylethenes and azobenzenes. These compounds have been extensively studied for decades, and are used in various applications such as biomedicine, chemical sensors and harvesting solar energy. However, majority of photochromic compounds are initially activated by ultraviolet (UV) light. The use of UV light is harmful for biological applications and photo-degrade the compound over repeated use. …

Computational Imaging Systems For High-Speed, Adaptive Sensing Applications, Yangyang Sun

Electronic Theses and Dissertations

Driven by the advances in signal processing and ubiquitous availability of high-speed low-cost computing resources over the past decade, computational imaging has seen the growing interest. Improvements on spatial, temporal, and spectral resolutions have been made with novel designs of imaging systems and optimization methods. However, there are two limitations in computational imaging. 1), Computational imaging requires full knowledge and representation of the imaging system called the forward model to reconstruct the object of interest. This limits the applications in the systems with a parameterized unknown forward model such as range imaging systems. 2), the regularization in the optimization process …

The Characterization Of Condom Lubricants And Personal Hygiene Products Using Dart-Tofms And Gc- Ms And The Investigation Of Gold Nanoparticle Behavior In Water And The Interaction With Blood Serum Proteins, Yasmine Moustafa

Electronic Theses and Dissertations

This dissertation is divided into two independent research projects. First, condom lubricants, sexual lubricants, and personal hygiene products (PHPs) were studied using direct analysis in real time-time-of-flight-mass spectrometry (DART-TOFMS) and gas chromatography-mass spectrometry (GC-MS). The purpose addressed the concern of perpetrators resorting to new tactics, i.e. using condoms to remove seminal fluid that could provide a DNA link to a suspect, leading to the need of the consideration of condom lubricants as pieces of sexual assault evidence. Due to condom lubricants having a chemical composition resembling PHPs, the investigation of both sample groups was analyzed to prevent false positives. Although …

Cryogenic Performance Projections For Ultra-Small Oxide-Free Vertical-Cavity Surface-Emitting Lasers, Mina Bayat

Electronic Theses and Dissertations

Small-sized vertical-cavity surface-emitting laser (VCSEL) may offer very low power consumption along with high reliability for cryogenic data transfer. Cryogenic data transfer has application in supercomputers and superconducting for efficient computing and also focal plane array cameras operating at 77 K, and at the lower temperature of 4 K for data extraction from superconducting circuits. A theoretical analysis is presented for 77 K and 4 K operation based on small cavity, oxide-free VCSEL sizes of 2 to 6 µm, that have been shown to operate efficiently at room temperature. Temperature dependent operation for optimally-designed VCSELs are studied by calculating the …

Design And Fabrication Of Scalable Multifunctional Multimaterial Fibers And Textiles, Felix Tan

Electronic Theses and Dissertations

Multimaterial fibers eschew the traditional mono-material structures typical of traditional optical fibers for novel internal architectures that combine disparate materials with distinct optical, mechanical, and electronic properties, thereby enabling novel optoelectronic functionalities delivered in the form factor of an extended fiber. This new class of fibers developed over the past two decades is attracting interest from researchers in such different fields as optics, textiles, and biomedicine. The juxtaposition of multiple materials integrated at micro- and nanoscales in complex geometries while ensuring intimate smooth interfaces extending continuously for kilometers facilitates unique applications such as non-invasive laser surgery, self-monitoring fibers, e-textiles, and …

Stable, Highly Luminescent Perovskite-Polymer Composites For Photonics Applications, Juan He

Electronic Theses and Dissertations

Metal halide perovskites (simplified as perovskites as below), particularly those in nanocrystal forms, have recently emerged as highly efficient, bandgap tunable photonics materials that can be easily solution processed at low cost for display, lighting or other energy conversion applications. However, the quick degradation of perovskite nanocrystals under external stresses or upon colloidal aggregations has been a major challenge for most applications where high reliability is normally required. In this thesis, we have explored a polymer swelling-deswelling microencapsulation (SDM) process that enables the dispersion, in-situ crystallization and subsequent surface passivation of perovskite nanocrystals in polymer matrices, and leads to ultrastable …

Computational Imaging With Limited Photon Budget, Zheyuan Zhu

Electronic Theses and Dissertations

The capability of retrieving the image/signal of interest from extremely low photon flux is attractive in scientific, industrial, and medical imaging applications. Conventional imaging modalities and reconstruction algorithms rely on hundreds to thousands of photons per pixel (or per measurement) to ensure enough signal-to-noise (SNR) ratio for extracting the image/signal of interest. Unfortunately, the potential of radiation or photon damage prohibits high SNR measurements in dose-sensitive diagnosis scenarios. In addition, imaging systems utilizing inherently weak signals as contrast mechanism, such as X-ray scattering-based tomography, or attosecond pulse retrieval from the streaking trace, entail prolonged integration time to acquire hundreds of …

Optical Sensing Of Structural Dynamics In Complex Media, Jose Rafael Guzman Sepulveda

Electronic Theses and Dissertations

Quantifying the structural dynamics of complex media is challenging because of the multiple temporal and spatial scales involved. Thanks to the ability to retrieve collective dynamics noninvasively, light scattering-based approaches are often the methods of choice. This dissertation discusses specific features of dynamic light scattering that utilizes spatio-temporal coherence gating. It is demonstrated that this optical fiber-based approach can operate over a large range of optical regimes and it has a number of unique capabilities such as an effective isolation of single scattering, a large sensitivity, and a high collection efficiency. Moreover, the approach also provides means for proper ensemble …

Tumor-Targeted Conjugated Polymer Nanoparticles With Encapsulated Iron And Its Biomedical Application For In Vitro Killing Of Melanoma Cell Lines Through Ferroptosis Assisted Chemodynamic Therapy (Cdt), Khalaf Jasim

Electronic Theses and Dissertations

Melanoma represents one of the most aggressive and lethal forms of skin cancer, with annually rising incidences throughout the world. Although chemotherapy modalities remain the mainstay of treatment, the therapeutic potential of chemotherapy typically is hampered by multidrug resistance (MDR) and nonspecific drug distribution that causes side-effects. To surmount such limitations, novel nanoformulations of low band-gap poly ({4,8-bis [(2-ethylhexyl) oxy] benzo [1,2-b:4,5-b?] dithiophene-2,6-diyl}{3-fluoro-2-[(2-ethylhexyl) carbonyl] thieno [3,4-b] thiophenediyl}) (PTB7) and poly [2,1,3-benzothiadiazole- 4,7- diyl [4,4-bis (2-ethylhexyl)- 4H-cyclopenta [2,1-b:3,4-b'] dithiophene-2,6-diyl]] (PCPDTBT) were fabricated by a reprecipitation method. These conjugated polymer nanoparticles were functionalized with the polypeptide endothelin-3 (EDN3-CPNPs) to target melanoma. The …

Structure Of Reflectin Protein Probed By Solid-State Nuclear Magnetic Resonance, Tommy Boykin

Electronic Theses and Dissertations

An unusual protein found in squids, termed reflectin, possesses the unique ability for optical reflectivity and proton conductivity. Reflectin has the potential to become optically and electronically tunable, however, the molecular structure of reflectin has yet to be determined. Previous literature has considered using reflectin proteins as diffraction gratings, protonic transistors, and substrates for neural stem cell growth. Applying recombinant protein techniques, we purified the reflectin 4Ax4 protein. We determined the leucine, tryptophan, and threonine amino acids are in an ordered state by solid-state nuclear magnetic resonance (NMR). Knowing these ordered amino acids is possibly the key to understanding reflectin's …

Spectral Properties Of The Finite Hilbert Transform On Two Adjacent Intervals Via The Method Of Riemann-Hilbert Problem, Elliot Blackstone

Electronic Theses and Dissertations

In this dissertation, we study a self-adjoint integral operator $\hat{K}$ which is defined in terms of finite Hilbert transforms on two adjacent intervals. These types of transforms arise when one studies the interior problem of tomography. The operator $\hat{K}$ possesses a so-called "integrable kernel'' and it is known that the spectral properties of $\hat{K}$ are intimately related to a $2\times2$ matrix function $\Gamma(z;\lambda)$ which is the solution to a particular Riemann-Hilbert problem (in the $z$ plane). We express $\Gamma(z;\lambda)$ explicitly in terms of hypergeometric functions and find the small $\lambda$ asymptotics of $\Gamma(z;\lambda)$. This asymptotic analysis is necessary for the …

Hybrid Integration Of Second- And Third-Order Highly Nonlinear Waveguides On Silicon Substrates, Guillermo Fernando Camacho Gonzalez

Electronic Theses and Dissertations

In order to extend the capabilities and applications of silicon photonics, other materials and compatible technologies have been developed and integrated on silicon substrates. A particular class of integrable materials are those with high second- and third-order nonlinear optical properties. This work presents contributions made to nonlinear integrated photonics on silicon substrates, including chalcogenide waveguides for over an octave supercontinuum generation, and rib-loaded thin-film lithium niobate waveguides for highly efficient second-harmonic generation. Through the pursuit of hybrid integration of the two types of waveguides for applications such as on-chip self-referenced optical frequency combs, we have experimentally demonstrated fabrication integrability of …

Semi-Analytical Solutions Of Non-Linear Differential Equations Arising In Science And Engineering, Mangalagama Dewasurendra

Electronic Theses and Dissertations

Systems of coupled non-linear differential equations arise in science and engineering are inherently nonlinear and difficult to find exact solutions. However, in the late nineties, Liao introduced Optimal Homotopy Analysis Method (OHAM), and it allows us to construct accurate approximations to the systems of coupled nonlinear differential equations. The drawback of OHAM is, we must first choose the proper auxiliary linear operator and then solve the linear higher-order deformation equation by spending lots of CPU time. However, in the latest innovation of Liao's "Method of Directly Defining inverse Mapping (MDDiM)" which he introduced to solve a single nonlinear ordinary differential …

Mathematical Investigation Of The Spatial Spread Of An Infectious Disease In A Heterogeneous Environment, Arielle Gaudiello

Electronic Theses and Dissertations

Outbreaks of infectious diseases can devastate a population. Researchers thus study the spread of an infection in a habitat to learn methods of control. In mathematical epidemiology, disease transmission is often assumed to adhere to the law of mass action, yet there are numerous other incidence terms existing in the literature. With recent global outbreaks and epidemics, spatial heterogeneity has been at the forefront of these epidemiological models. We formulate and analyze a model for humans in a homogeneous population with a nonlinear incidence function and demographics of birth and death. We allow for the combination of host immunity after …

Frames And Phase Retrieval, Ted Juste

Electronic Theses and Dissertations

Phase retrieval tackles the problem of recovering a signal after loss of phase. The phase problem shows up in many different settings such as X-ray crystallography, speech recognition, quantum information theory, and coherent diffraction imaging. In this dissertation we present some results relating to three topics on phase retrieval. Chapters 1 and 2 contain the relevant background materials. In chapter 3, we introduce the notion of exact phase-retrievable frames as a way of measuring a frame's redundancy with respect to its phase retrieval property. We show that, in the d-dimensional real Hilbert space case, exact phase-retrievable frames can be of …