Physical Sciences and Mathematics Commons^™

New Methods For Stereoselective Glycosylation In Application To Significant Biomedical Targets, Melanie L. Shadrick

Dissertations

Glycosyl halides have been utilized for glycosylation reactions since the early studies by Arthur Michael, nearing the end of the 19^th century. Koenigs and Knorr then utilized silver salts to activate glycosyl bromides and chlorides to create synthetic glycosides. Many efforts to improve the outcome of reactions with glycosyl halides have emerged. The key emphasis has traditionally been placed on reaction rates, product yields, and stereocontrol. Recently, our lab reported that silver(I) oxide-mediated Koenigs-Knorr glycosylation reaction can be dramatically accelerated in the presence of catalytic acid additives. Methods to improve glycosylation was explored using mannosyl and glucosyl bromides. However, …

Binding Interactions Of Biologically Relevant Molecules Studied Using Surface-Modified And Nanostructured Surfaces, Palak Sondhi

Dissertations

This research focuses on the field of surface nanobioscience, wherein different nanosurfaces that will be used as working electrodes in the electrochemical cell are manufactured and surface modified to understand the critical binding interactions between biologically significant molecules like proteins, carbohydrates, small drug molecules, and glycoproteins. This research is essential if we are to determine whether a synthetic molecule can serve as a therapeutic candidate or diagnose a disease in its early stages. In order to fully understand the binding interactions, the study begins with defining some of the fundamental concepts, principles, and analytical tools for biosensing.

Afterwards, we addressed …

Topological Data Analysis Of Convolutional Neural Networks Using Depthwise Separable Convolutions, Eliot Courtois

Dissertations

In this dissertation, we present our contribution to a growing body of work combining the fields of Topological Data Analysis (TDA) and machine learning. The object of our analysis is the Convolutional Neural Network, or CNN, a predictive model with a large number of parameters organized using a grid-like geometry. This geometry is engineered to resemble patches of pixels in an image, and thus CNNs are a conventional choice for an image-classifying model.

CNNs belong to a larger class of neural network models, which, starting at a random initialization state, undergo a gradual fitting (or training) process, often a …

High Resolution Intracavity Laser Absorption Spectroscopy Of Transition Metal-Containing Diatomic Molecules, Kristin Bales

Dissertations

Three transition metal-containing diatomic molecules have been studied using intracavity laser spectroscopy. Many of the transitions were recorded using a Fourier-transform spectrometer for detection, allowing collection at Doppler-limited resolution for the gas phase molecules. Several vibrational bands in two electronic transition systems of tantalum fluoride (TaF) have been analyzed, and new molecular constants provided. Transitions involving six electronic states of tungsten sulfide (WS) have been analyzed, with new and updated constants provided, including a deperturbation analysis of three vibrational bands in two of the states. Finally, a fresh perspective on two electronic states of tungsten oxide (WO) included a deperturbation …

Near-Ir Spectroscopic Analysis Of The Primary Volatile Composition Of Long And Short-Period Comets, Younas Khan

Dissertations

Comets are among the most well-preserved objects that formed in the protosolar nebula ∼4.5 Gyr ago. Hence, they are important for understanding various aspects of the formation, evolution, and habitability of the solar system. Multiple primary volatiles (molecules directly sublimating into the coma from the nucleus) emit via rovibrational transitions in the near-IR, providing opportunities to calculate their abundances. To date, only ∼50 comets have been characterized for their primary volatiles, with the short-period Jupiter-family comets (JFCs) being significantly underrepresented. In contrast, hundreds of comets have been sampled at optical/UV wavelengths, primarily for the composition of daughter species, leading to …

Loss Scaling And Step Size In Deep Learning Optimizatio, Nora Alosily

Dissertations

Deep learning training consumes ever-increasing time and resources, and that is
due to the complexity of the model, the number of updates taken to reach good
results, and both the amount and dimensionality of the data. In this dissertation,
we will focus on making the process of training more efficient by focusing on the
step size to reduce the number of computations for parameters in each update.
We achieved our objective in two new ways: we use loss scaling as a proxy for
the learning rate, and we use learnable layer-wise optimizers. Although our work
is perhaps not the first …

Topological Data Analysis Of Weight Spaces In Convolutional Neural Networks, Adam Wagenknecht

Dissertations

Convolutional Neural Networks (CNNs) have become one of the most commonly used tools for performing image classification. Unfortunately, as with most machine learning algorithms, CNNs suffer from a lack of interpretability. CNNs are trained by using a training data set and a loss function to tune a set of parameters known as the layer weights. This tuning process is based on the classical method of gradient descent, but it relies on a strong stochastic component, which makes the weight behavior during training difficult to understand. However, since CNNs are governed largely by the weights that make up each of the …

Synthetic Amphiphiles As Antibiotic Potentiators, Helena Spikes

Dissertations

Antibiotic resistance has become a massive threat to modern medicine. Bacteria acquire resistance either through genetic mutations or mobile genetic elements, such as plasmids. The growing resistance crisis is exacerbated by over-prescription of antibiotics and improper use. As antimicrobial resistance becomes more widespread, superbugs (bacteria resistant to more than one class of drug) have evolved. Since few new drugs reach clinical trials and even fewer are approved by the FDA, we must find a way to make existing drugs more potent. One technique to accomplish this is by using combination therapy. By administering two or more drugs at a time, …

Ferrocenium Salt Aided Substitution Reactions And Synthesis Of Glycosylated Curcumin Derivatives, Deva Saroja Talasila

Dissertations

Organic synthesis has been significantly advanced with the employment of transition metal complexes. The discovery of transition metal catalysts provided the synthetic community with powerful tools for accelerating reactions and making them more selective and efficient. Many chemical reactions do not happen without a catalyst.

Iron-based catalysts have several advantages for the chemical industry because it is a non-toxic and ecologically friendly metal. Our group previously found that ferrocenium cations with a 3+ oxidation state of iron-catalyzed propargylic substitution reactions at low temperatures. The sandwich structure of ferrocenes allows substituents to be introduced on the cyclopentadienyl rings, which allows for …

Novel Thioglycosides As Versatile Glycosyl Donors For Oligosaccharide Synthesis, Ganesh Shrestha

Dissertations

This thesis is dedicated to the development of new methodologies for efficient synthesis of carbohydrate building blocks and their application to chemical glycosylation. S-Indolyl (SIn) anomeric moiety was investigated as a new leaving group. Understanding of the reaction pathways for the SIn moiety activation was achieved via the extended mechanistic study. The activation profile of indolylthio glycosides required large excess of activators. This drawback was partially addressed by the development of N-alkylated SInR derivatives. The activation process was studied by NMR and the increased understanding of the mechanism led to a discovery of different activation pathways taking place with …

Mechanism Of Sila- And Germafluorenes For Biological Applications, Shelby Jarrett

Dissertations

2,7-disubstituted silafluorenes and germafluorenes, originally designed for OLED applications, are a class of fluorescent dyes that have gained recent interest as probes for bioimaging and as biosensors to monitor cellular dynamics and interactions. Desirable biological probes absorb in the visible region, have high extinction coefficients, high quantum yield and excellent photostability. Here, their spectral properties are investigated under aqueous conditions for relevant biological applications. These molecules display intense blue fluorescence in the solid state and in solution, have high extinction coefficients, and exhibit appreciable solubility in aqueous solution. To better understand potential applications, the mechanism of fluorescence was investigated. It …

Bis(Tryptophan) Amphiphiles: Design, Synthesis And Efficacy As Antimicrobial Agents, Michael Mckeever

Dissertations

Amphiphiles play important roles in nature. These molecules contain both hydrophilic and hydrophobic regions, leading to some astonishing properties. The lipid bilayer of the cell membrane is a fascinating organization of amphiphilic phospholipids. Natural and synthetic amphiphiles, such as antimicrobial peptides, interact with the cell membrane. Such interactions can impact transport of molecules across the cell membrane, disrupting cell functions. In this work, a library of tryptophan-containing amphiphiles was synthesized and their antimicrobial properties were explored.

First, a library of bis(tryptophan) amphiphiles was synthesized. Preparation included a coupling reaction of a diamine with tryptophan residues, via their carboxy-termini, at …

The Global Rise Of Online Devices, Cyber Crime And Cyber Defense: Enhancing Ethical Actions, Counter Measures, Cyber Strategy, And Approaches, Naresh Kshetri

Dissertations

The rise of online devices, online users, online shopping, online gaming, and online teaching has ultimately given rise to online attacks and online crimes. As cases of COVID-19 seem to increase day by day, so do online crimes and attacks (as many sectors and organizations went 100% online). Technological advancements and cyber warfare already generated many ethical issues, as internet users increasingly need ethical cyber defense strategies.

Individual internet users have challenges on their end; and on the other end, nation states (some secretly, some openly), are investing in robot weapons and autonomous weapons systems (AWS). New technologies have combined …

New Methods For The Synthesis, Activation, And Application Of Thioglycosides, Samira Escopy

Dissertations

From their ubiquitous presence in Nature to their vital roles in biology and medicine, carbohydrates (sugars or glycans) are essential molecules of life, which are made and/or utilized by every living organism. Our cells are coated with sugars that are involved in almost every biological process and defensive mechanism in our body. To mention some of their crucial biological functions, carbohydrates are essential source of energy, they participate in blood coagulation, immune defense, cell growth, cell-cell interaction, and anti-inflammatory processes. Understanding of glycan functions and structure is crucial for the development of vaccines and therapeutics. Producing complex carbohydrates in sufficient …

Semi-Empirical Modeling Of Liquid Carbon's Containerless Solidification, Philip Chrostoski

Dissertations

Elemental carbon has important structural diversity, ranging from nanotubes through graphite to diamond. Previous studies of micron-size core/rim carbon spheres extracted from primitive meteorites suggest they formed around such stars via the solidification of condensed carbon-vapor droplets, followed by gas-to-solid carbon coating to form the graphite rims. Similar core/rim particles result from the slow cooling of carbon vapor in the lab. The long-range carbon bond-order potential was used to computationally study liquid-like carbon in (1.8 g/𝐜𝐦𝟑) periodic boundary (tiled-cube supercell) and containerless (isolated cluster) settings. Relaxations via conjugate-gradient and simulatedannealing nucleation and growth simulations using molecular dynamics were done to …

Critical Behavior In Evolutionary And Population Dynamics, Stephen Ordway

Dissertations

This study is an exploration of phase transition behavior in evolutionary and population dynamics, and techniques for predicting population changes, across the disciplines of physics, biology, and computer science. Under the looming threat of climate change, it is imperative to understand the dynamics of populations under environmental stress and to identify early warning signals of population decline. These issues are explored here in (1) a computational model of evolutionary dynamics, (2) an experimental system of decaying populations under environmental stress, and (3) a machine learning approach to predict population changes based on environmental factors. Through the lens of critical phase …

Computational Studies Of Carbon Nanocluster Solidification, Chathuri C. Silva

Dissertations

A subset of micron-size meteoritic carbon particles formed in red giant atmospheres show a core-rim structure, likely condensed from a vapor phase into super-cooled carbon droplets that nucleated graphene sheets (~40Å) on randomly oriented 5-atom loops during solidification, followed by coating with a graphite rim. Similar particles form during slow cooling of carbon vapor in the lab.

Here we investigate the nucleation and growth of carbon rings and graphene sheets using density functional theory (DFT). Our objectives: (1). explore different computational techniques in DFT-VASP for various carbon structures and compare the results with literature, (2). investigate the nucleation and growth …

Stereocontrolled Mannosylation By Hydrogen-Bond-Mediated Aglycone Delivery, Catherine Alex

Dissertations

Stereocontrolled Mannosylation by Hydrogen-Bond-Mediated Aglycone Delivery

Carbohydrates are the essential bio-molecules of life as they form the forefront of interactions with receptors, proteins, pathogens, or neighboring cells. On cell-surfaces, carbohydrates are mostly found as linear or branched glycoconjugates, and a majority of them are linked via either 1,2-cis or 1,2-trans O-glycosidic linkages. There is no template-driven pathway for achieving the synthesis of glycans unlike other biomolecules like proteins and nucleic acids. The synthesis of 1,2-trans glycosides can be reliably achieved via the neighboring group assistance. The synthesis of 1,2-cis glycosides is difficult because, beyond weak anomeric effects, there are …

Analysis Of The Primary Volatile Compositions In The Oort Cloud And Jupiter-Family Comets Towards The Goal Of Understanding Their Origin And Diversity, Mohammad Saki

Dissertations

Knowledge of the initial conditions present in the early solar nebula is required to understand the evolution and its current volatile content. Comets were some of the first objects to accrete in the solar nebula. They are among the most pristine (primitive) remnants of the solar system formation, and their present-day volatile composition likely reflects the composition and conditions where (and when) they formed. Therefore, they are fossils of the solar system formation. High-resolution near-infrared spectroscopy is a valuable tool for sampling the parent volatile (i.e., ices subliming directly from the nucleus) composition of comets via analysis of fluorescence emission …

Construct Linear Quasi-Interpolants On Infinite Intervals, Johara Farah Albaliwi

Dissertations

In solving the data interpolation problem, which is fundamental in data analysis, we typically deal with the data samples spread in a finite interval [a, b], which results in the operations involving finite-dimensional matrices. There are many interesting results developed under this framework. However, when the data samples are given from an infinite interval [a, ∞) (for certain special types of real-world applications), many existing results would not work anymore due to the special properties of the infinite data samples. A new framework should be established to support the infinite data samples.

In this dissertation, we develop a special tool …

Matrix Product Structure Of A Permuted Quasi Cyclic Code And Its Dual, Perian Perdhiku

Dissertations

In my Dissertation I will work mostly with Permuted Quasi Cyclic Codes. They are a generalization of Cyclic Codes, one of the most important families of Linear Codes in Coding Theory. Linear Codes are very useful in error detection and correction. Error Detection and Correction is a technique that first detects the corrupted data sent from some transmitter over unreliable communication channels and then corrects the errors and reconstructs the original data. Unlike linear codes, cyclic codes are used to correct errors where the pattern is not clear and the error occurs in a short segment of …

Ready To Engage? Urban Middle School Teachers’ Responsiveness To Targeted Engagement Interventions On Their Virtual Instructional Practices: An Action Research Study, Svetlana Nikic

Dissertations

Teachers’ effectiveness is associated with their instructional practices and is ultimately linked to students’ learning outcomes. In order to impact teachers’ effectiveness, schools focus substantial effort and resources on professional development led by an assumption that teachers’ classroom practices can be improved through targeted interventions. Even if this premise is correct, little information is available about how much a teacher’s practice may change through interventions, or which aspects of instructional practice are more receptive to improving teacher effectiveness (Garret et al., 2019).

This study took place at an urban middle school and examined teachers’ responsiveness to targeted engagement intervention in …

Instantaneous Frequency Estimation And Signal Separation Using Fractional Continuous Wavelet Transform, Abdelbaset R. Zeyani

Dissertations

In the signal processing field, time-frequency representations (TFR's) have intensively been improved to provide effective and powerful tools for reliable signal analysis. One of the most valuable and frequently used tools is Fourier transform (FT) which has been used to study the frequency content of stationary signals in the Fourier domain (FD). However, FT is not sufficient to study the frequency of non-stationary signals. For this particular type of signals to be best analyzed, some transforms such as the short time Fourier transform (STFT) and the continuous wavelet transform (CWT) have been introduced to provide us with a signal representation …

A Spectroscopic And Photometric Survey Of The W4 Hii Region And Its Young Stellar Population, Matt Wentzel-Long

Dissertations

The W4 HII region is home to a large number of O and B-type stars as well as the young open cluster IC 1805. OB-type produce intense photoionizing radiation and stellar winds that can induce star formation in surrounding molecular clouds and sometimes carve out large regions of decreased particle density called superbubbles. During the star formation process, young stellar objects (YSOs) are initially surrounded by circumstellar disks made of gas and dust which naturally dissipate after several million years. The dissipation of the disk is thought to occur for a variety of reasons, including photoevaporation by the encompassed protostar …

Synthesis Of Biologically Active Phosphorus Heterocycles, Giri Gnawali

Dissertations

This dissertation work is divided into two parts. The first part is focused in the development of methodology for the synthesis of phostones and phosphonosugars and advancement thereof. The second part is focused in the development of affinity probes based on analogs of natural products cyclophostin and the cyclipostins.

Phostone (3) and phosphonosugars are cyclic phosphonates. The anomeric carbon of sugar is replaced by a phosphorus atom. The synthesis of phostones has been achieved starting form the key intermediate, γ,δ-epoxy vinyl phosphonate (1). The palladium catalyzed ring opening of γ,δ-epoxy vinyl phosphonates by a nucleophile results …

Construct Local Quasi-Interpolation Operators Using Linear B-Splines, Abeer Alzahrani

Dissertations

The data interpolating problem is a fundamental problem in data analysis, and B-splines are frequently used as the basis functions for data interpolation. In the real-world applications, the real-time processing is very important. To achieve that, we cannot use any matrix inversion for large amount of data, and we also need to avoid using any global operator. To solve this problem, we develop a new method based on a local quasi-interpolation operator. To construct the local quasi-interpolation operator, we need to factorize the Shoenberg-Whitney matri- ces for the given data samples. Furthermore, our local quasi-interpolation operator should correspond to a …

New Catalytic Reactions In Carbohydrate Chemistry, Scott Geringer

Dissertations

Carbohydrates or sugars are some of the most diverse and abundant biological molecules. They are involved in a multitude of processes in the body such as fertilization, cell-cell communication, and cancer metathesis. Because of these vital functions, the study of sugars is rapidly growing field. The field however is limited due to the complex nature of sugars which results in difficulties in obtaining large quantities for study.

Protecting group manipulation is a large emphasis area in carbohydrate chemistry due to the need to selectively protect different functional groups of each molecule during synthesis. Catalytic and selective cleavage of protecting groups …

High-Order Adaptive Synchrosqueezing Transform, Jawaher Alzahrani

Dissertations

The prevalence of the separation of multicomponent non-stationary signals across many elds of research makes this concept an important subject of study. The synchrosqueezing transform (SST) is a particular type of reassignment method. It aims to separate and recover the components of a multicomponent non-stationary signal. The short time Fourier transform (STFT)-based SST (FSST) and the continuous wavelet transform (CWT)based SST (WSST) have been used in engineering and medical data analysis applications. The current study introduces the dierent versions of FSST and WSST to estimate instantaneous frequency (IF) and to recover components. It has a good concentration and reconstruction for …

Towards Completely Automated Glycan Synthesis, Matteo Panza

Dissertations

Carbohydrates are ubiquitous both in nature as biologically active compounds and in medicine as pharmaceuticals. Although there has been continued interest in the synthesis of carbohydrates, chemical methods require specialized knowledge and hence remain cumbersome. The need for development of rapid, efficient and operationally simple procedures has come to the fore. This dissertation focuses on the development of a fully automated platform that will enable both experts and non-specialists to perform the synthesis of glycans. Existing automated methods for the synthesis of oligosaccharides are highly sophisticated, operationally complex, and require significant user know-how. By contrast, high performance liquid chromatography (HPLC) …

Recover Data In Sparse Expansion Forms Modeled By Special Basis Functions, Abdulmtalb Mohamed Hussen

Dissertations

In data analysis and signal processing, the recovery of structured functions (in terms of frequencies and coefficients) with respect to certain basis functions from the given sampling values is a fundamental problem. The original Prony method is the main tool to solve this problem, which requires the equispaced sampling values.

In this dissertation, we use the equispaced sampling values in the frequency domain after the short time Fourier transform in order to reconstruct some signal expansions, such as the exponential expansions and the cosine expansions. In particular, we consider the case that the phase of the cosine expansion is quadratic. …