Physical Sciences and Mathematics Commons^™

Analysis Of Ab Initio Protein Structure Prediction Methods, Maytha Alshammari, Jing He

College of Sciences Posters

Protein structure prediction produces atomic models of three-dimensional structure of a protein from its amino acid sequence. Understanding the function mechanism of proteins requires knowledge of three-dimensional structures. When developing new enzymes and drugs, it's essential to understand the structure of the target protein. In this study, we analyze models predicted using two ab initio protein structure prediction methods, trRosetta and Quark. A set of thirty protein chains was used to evaluate the effectiveness of the methods. The thirty chains were collected from Protein Data Bank (June – November, 2020). The length and the relative position of the predicted secondary …

A Bootstrap Test For Informative Intra-Cluster Group Sizes In Clustered Data, Hasika K. Wickrama Senevirathne, Sandipan Dutta

College of Sciences Posters

Clustered data are frequently observed in various domains of scientific and social studies. In a typical clustered data, units within a cluster are correlated while units between different clusters are independent. An example of such clustered data can be found in dental studies where individuals are treated as clusters and the teeth in an individual are the units within a cluster. While analyzing such clustered data, it has been observed that the number of units present in a cluster can be informative in terms of being associated with the outcome from that cluster. Specifically, when the aim is to compare …

Hydrodynamics And Sediment Transport In The Tidally Influenced James River, Ollie Gilchrest, Rip Hale

The Graduate School Posters

The tidally influenced James River is an important economic, ecologic, and cultural resource for VA residents. Tidal rivers have been historically understudied, however they are critical transition zones, the dynamics of which have implications for freshwater supply and sediment trapping. Globally, estimates suggest that >30% of fluvial sediment is trapped in the tidal zone, the location and dynamics of which are actively changing due to sea level rise and saltwater encroachment. In addition, analysis of historical water levels on the James River has shown a decrease in the tidal range since 1940. The present study combines >1-year’s worth of hydrographic …

Organic Matter Content And Grain Size Analysis In Seagrass Sediments, Adriana Amrhein, Rip Hale

College of Sciences Posters

Anthropogenic stresses including increased water temperatures, decreased water quality, sea level rise, ocean acidification and sediment biogeochemical processes have caused a significant loss in seagrass meadow acreage. Seagrass meadows provide coastal protection from storms and recently have been emphasized for their importance in sequestering and storing “Blue Carbon” from the atmosphere and ocean. Seagrass meadows can trap this blue carbon in their sediment as organic carbon, and it can be stored for hundreds to thousands of years. Restoration efforts of seagrass meadows in the Virginia coast started in the 1990s and effects of increasing seagrass density can be observed in …

Dust Deposition To The Bermuda Region: A Comparison Of Estimates Using Seasonally-Resolved Measurements Of Aluminum In Water-Column, Aerosol, And Rain Samples, Tara Williams, Peter Sedwick, Bettina Sohst, Joe Resing, Kristen Buck, Salvatore Caprara, Rod Johnson, Dan Ohnemus, Ben Twining, Alessandro Tagliabue

College of Sciences Posters

Dust deposition is a major source of bioactive trace elements to the surface ocean, yet this flux remains difficult to constrain. Previously, time-averaged dust flux has been estimated using surface ocean dissolved aluminum (DAl) concentrations, assumed values for aerosol aluminum solubility (%Al_S), and the residence time of DAl in the surface mixed layer (SML). We apply this method to estimate dust deposition in the Bermuda Atlantic Time-series Study (BATS) region using water-column DAl data from cruises in 2019, which is compared with direct flux estimates from contemporaneous measurements of aluminum in aerosols and rain collected on Bermuda. Seasonal …

Acceleration Of U.S. Southeast And Gulf Coast Sea-Level Rise Amplified By Internal Climate Variability, Sönke Dangendorf, Noah Hendricks, Qiang Sun, John Klinck, Tal Ezer, Thomas Frederikse, Francisco M. Calafat, Thomas Wahl, Torbjörn E. Törnqvist

CCPO Publications

While there is evidence for an acceleration in global mean sea level (MSL) since the 1960s, its detection at local levels has been hampered by the considerable influence of natural variability on the rate of MSL change. Here we report a MSL acceleration in tide gauge records along the U.S. Southeast and Gulf coasts that has led to rates (>10 mm yr⁻¹ since 2010) that are unprecedented in at least 120 years. We show that this acceleration is primarily induced by an ocean dynamic signal exceeding the externally forced response from historical climate model simulations. However, when the …

Towards A Holistic And Comparative Analysis Of The Free Content Web: Security, Privacy, And Performance, Abdulrahman Alabduljabbar

Electronic Theses and Dissertations, 2020-2023

Free content websites that provide free books, music, games, movies, etc., have existed on the Internet for many years. While it is a common belief that such websites might be different from premium websites providing the same content types in terms of their security, a rigorous analysis that supports this belief is lacking from the literature. In particular, it is unclear if those websites are as safe as their premium counterparts. In this dissertation, we set out to investigate the similarities and differences between free content and premium websites, including their risk profiles. Moreover, we analyze and quantify through measurements …

Analysis Of Polycyclic Aromatic Hydrocarbons In Tobacco Related Samples Via High Performance Liquid Chromatography And Laser Excited Time Resolved Shpol' Skii Spectroscopy, Ahmed Comas

Electronic Theses and Dissertations, 2020-2023

Human exposure to polycyclic aromatic hydrocarbons (PAHs) due to cigarette smoke is well known. It is also known that PAHs are not inherent components of tobacco. Their presence in cigarette smoke results from the curing process of tobacco leaves used for the fabrication of cigarettes and the incomplete combustion of tobacco during the smoking process. The two chromatographic versions of EPA method 610 are popular approaches for the analysis of PAHs in a wide variety of samples. This method, which is based either on High-Performance Liquid-Chromatography (HPLC) or Gas-Chromatography (GC) has shown the presence of Benzo[a]pyrene (B[a]P) in tobacco samples …

Analysis Of Multi-Drug Resistant Mycobacterium Tuberculosis Using Split Deoxyribozymes, Abryana Fergus

Electronic Theses and Dissertations, 2020-2023

Globally, tuberculosis, a disease caused by the species of Mycobacterium tuberculosis (Mtb) complex, stands as a leading cause of death from a single infectious agent. Even though antituberculous drugs are available, treatment is challenging due to antibiotic resistance associated with point mutations in the bacterial genome. Resistance to the first-line antibiotics – rifampin and isoniazid – results in multidrug-resistant tuberculosis (MDR) requiring a more complicated treatment regimen. Timely and accurate identification of drug-resistant TB cases can help prescribe the most effective treatment and prevent the spread of infection. This research aims to develop an assay to discern multi-drug resistant forms …

Mapping The Focal Points Of Wordpress: A Software And Critical Code Analysis, Bryce Jackson

Electronic Theses and Dissertations, 2020-2023

Programming languages or code can be examined through numerous analytical lenses. This project is a critical analysis of WordPress, a prevalent web content management system, applying four modes of inquiry. The project draws on theoretical perspectives and areas of study in media, software, platforms, code, language, and power structures. The applied research is based on Critical Code Studies, an interdisciplinary field of study that holds the potential as a theoretical lens and methodological toolkit to understand computational code beyond its function. The project begins with a critical code analysis of WordPress, examining its origins and source code and mapping selected …

Probing The Structure-Activity Relationships Of Electrocatalytic Nanomaterials Using Scanning Electrochemical Microscopy, Zackary Parsons

Electronic Theses and Dissertations, 2020-2023

Electrocatalysis plays a central role in the development of renewable energy technologies as it enables direct conversion between renewable electricity and chemical energy. To design efficient electrocatalysts, it is essential to understand the relationship between the structure and the activity of electrocatalytic materials. Scanning electrochemical microscopy (SECM) is a scanning probe technique capable of imaging local electrocatalytic activity under operating conditions, of which the spatial resolution depends on the size and shape of the probe. Compared to commercial SECM probes which have limited resolution capabilities, I have developed novel nanoelectrode probes by etching sharp platinum tips followed by electropolymerization coating …

Discovering Vulnerabilities And Designing Trustworthy Defenses In Iot Systems And Devices, Bryan Pearson

Electronic Theses and Dissertations, 2020-2023

Internet of Things (IoT) dominates many functions in the modern world, from sensing and reporting temperature, humidity, and air quality, to controlling and automating homes, commercial buildings, and equipment. However, IoT systems have received scrutiny in recent years due to countless security incidents, which can have physical and even deadly consequences. This research provides a comprehensive assessment of the security of IoT systems and devices, including low-cost microcontroller (MCU) based sensors, cloud services, and Building Automation Systems (BAS). We begin by exploring the current landscape of vulnerabilities and defenses in modern IoT applications. We show that many security needs can …

Evolution Of Density And Velocity Perturbations In A Slowly Contracting Universe, Olivia R. Bitcon

Honors Undergraduate Theses

One focus of research in cosmology regards the growth of structure in the universe: how we end up with stars, galaxies, galaxy clusters, and large scale structure in a universe that appears homogeneous and isotropic on large scales. Using cosmological perturbation theory, we investigate the evolution of density and velocity perturbations corresponding to a universe that is slowly contracting (Ijjas and Steinhardt), testing with and comparing different values for the equation-of-state parameter. This allows for the comparison of the growth of large scale structure in scenarios including a matter-dominated expanding universe, a dark energy-dominated expanding universe, and now, an ekpyrotic …

Clustering Of Diverse Multiplex Networks, Yaxuan Wang

Electronic Theses and Dissertations, 2020-2023

This dissertation introduces the DIverse MultiPLEx Generalized Dot Product Graph (DIMPLE-GDPG) network model where all layers of the network have the same collection of nodes and follow the Generalized Dot Product Graph (GDPG) model. In addition, all layers can be partitioned into groups such that the layers in the same group are embedded in the same ambient subspace but otherwise all matrices of connection probabilities can be different. In common particular cases, where layers of the network follow the Stochastic Block Model (SBM) and Degree Corrected Block Model (DCBM), this setting implies that the groups of layers have common community …

Machine Learning Algorithms For Molecular Signature Identification With High-Throughput Genome Sequencing Data, Jiao Sun

Electronic Theses and Dissertations, 2020-2023

Powered by the high-throughput genomic technologies, the RNA sequencing (RNA-Seq) method is capable of measuring transcriptome-wide mRNA expressions and molecular activities in cells. Elucidation of gene expressions at the isoform resolution enables the detection of better molecular signatures for phenotype prediction, and the identified biomarkers may provide insights into the functional consequences of disease. This dissertation research focuses on developing advanced machine learning algorithms for mining large-scale RNA-Seq data in cancer transcriptome analysis. A platform-integrated model for transcript quantification (IntMTQ) is developed to improve the performance of RNA-Seq on isoform expression estimation. IntMTQ provides more precise RNA-Seq-based isoform quantification, and …

Evolutionary History And Adaptation To Salinity In American Alligators, John Konvalina

Electronic Theses and Dissertations, 2020-2023

Stressful environments can commonly be found at the edge of a species range and may be a driver for adaption in suboptimal environments. Furthermore, the edge of a species' range can expand and contract over time, resulting in multiple independent invasions of the same stressful habitat. Elucidating population genetic structure and demographic history can aid in determining the which geologic factors impact range distributions and when climatic changes occurred driving genetic patterns observed in contemporary populations. Moreover, populations at the edge of the species range may adapt to the stressful environments that occur at the range edge and exhibit genetic …

2023 January - Tennessee Monthly Climate Report, Tennessee Climate Office, East Tennessee State University

Tennessee Climate Office Monthly Report

No abstract provided.

2022 - Tennessee Annual Climate Summary, Tennessee Climate Office, East Tennessee State University

Tennessee Climate Office Monthly Report

No abstract provided.

Crosshair Optimizer, Jason Torrence

All Master's Theses

Metaheuristic optimization algorithms are heuristics that are capable of creating a "good enough'' solution to a computationally complex problem. Algorithms in this area of study are focused on the process of exploration and exploitation: exploration of the solution space and exploitation of the results that have been found during that exploration, with most resources going toward the former half of the process. The novel Crosshair optimizer developed in this thesis seeks to take advantage of the latter, exploiting the best possible result as much as possible by directly searching the area around that best result with a stochastic approach. This …

Design, Evolution, And Evaluation Of A General Chemistry-Bridging Course, Scott A. Reid

Chemistry Faculty Research and Publications

General chemistry I/II courses are important gateway courses for a variety of STEM majors, as poor performance in these courses is often associated with lower rates of student success and retention. Much research has explored preparatory or remedial strategies to improve student outcomes. In this article, we report a different approach, which involved the development of a bridging or intervention course designed to capture students who are not or have not succeeded in general chemistry I and prepare them to retake the course in the following semester or summer. The course was initially developed as an eight-week module in the …

Using Superatomic Clusters And Charge Transfer Ligands To Control Electronic Characteristics Of Phosphorene Nanoribbons And Phosphorene Monolayer, Ryan Lambert

Theses and Dissertations

Phosphorene is a two-dimensional electron poor p-type semiconductor with high carrier mobility and great promise for applications in electronics and optoelectronics. As the main theme in this dissertation, the following work represents different investigations of various electronic properties associated with phosphorene. Most notable are the findings on charge transfer doping with metal-chalcogenide superatoms which displays novel control of the two most important properties of a semiconductor – the band gap energy and the nature of carriers. By tuning the width of the gap and p-/n-type character of conduction, we gain control over a material’s capacity to play a certain role …

Rainbow Turan Methods For Trees, Victoria Bednar

Theses and Dissertations

The rainbow Turan number, a natural extension of the well-studied traditional
Turan number, was introduced in 2007 by Keevash, Mubayi, Sudakov and Verstraete. The rainbow Tur ́an number of a graph F , ex*(n, F ), is the largest number of edges for an n vertex graph G that can be properly edge colored with no rainbow F subgraph. Chapter 1 of this dissertation gives relevant definitions and a brief history of extremal graph theory. Chapter 2 defines k-unique colorings and the related k-unique Turan number and provides preliminary results on this new variant. In Chapter 3, we explore the …

Innovations In Drop Shape Analysis Using Deep Learning And Solving The Young-Laplace Equation For An Axisymmetric Pendant Drop, Andres P. Hyer

Theses and Dissertations

Axisymmetric Drop Shape Analysis (ADSA) is a technique commonly used to determine surface or interfacial tension. Applications of traditional ASDA methods to process analytical technologies are limited by computational speed and image quality. Here, we address these limitations using a novel machine learning approach to analysis. With a convolutional neural network (CNN), we were able to achieve an experimental fit precision of (+/-) 0.122 mN/m in predicting the surface tension of drop images at a rate of 1.5 ms^-1 versus 7.7 s^-1, which is more than 5,000 times faster than the traditional method. The results are validated on real images …

On The Cohomology Of Solvable Leibniz Algebras, Jorg Feldvoss, Friedrich Wagemann

University Faculty and Staff Publications

This paper is a sequel to J. Feldvoss and F. Wagemann: On Leibniz cohomology, (2021), where we mainly consider semisimple Leibniz algebras. It turns out that the analogue of the Hochschild-Serre spectral sequence for Leibniz cohomology cannot be applied to many ideals, and therefore this spectral sequence seems not to be applicable for computing the cohomology of non-semi-simple Leibniz algebras. The main idea of the present paper is to use similar tools as developed by Farnsteiner for Hochschild cohomology (see R. Farnsteiner: On the cohomology of associative algebras and Lie algebras (1987) and R. Farnsteiner: On the vanishing of homology …

Face Anti-Spoofing And Deep Learning Based Unsupervised Image Recognition Systems, Enoch Solomon

Theses and Dissertations

One of the main problems of a supervised deep learning approach is that it requires large amounts of labeled training data, which are not always easily available. This PhD dissertation addresses the above-mentioned problem by using a novel unsupervised deep learning face verification system called UFace, that does not require labeled training data as it automatically, in an unsupervised way, generates training data from even a relatively small size of data. The method starts by selecting, in unsupervised way, k-most similar and k-most dissimilar images for a given face image. Moreover, this PhD dissertation proposes a new loss function to …

Minimal Sets, Union-Closed Families, And Frankl's Conjecture, Christopher S. Flippen

Theses and Dissertations

The most common statement of Frankl's conjecture is that for every finite family of sets closed under the union operation, there is some element which belongs to at least half of the sets in the family. Despite its apparent simplicity, Frankl's conjecture has remained open and highly researched since its first mention in 1979. In this paper, we begin by examining the history and previous attempts at solving the conjecture. Using these previous ideas, we introduce the concepts of minimal sets and minimally-generated families, some ideas related to viewing union-closed families as posets, and some constructions of families involving poset-defined …

Multimodal Emotion Analysis With Focused Attention, Siddhi Kiran Bajracharya

Dissertations and Theses

Emotion analysis, a subset of sentiment analysis, involves the study of a wide array of emotional indicators. In contrast to sentiment analysis, which restricts its focus to positive and negative sentiments, emotion analysis extends beyond these limitations to a diverse spectrum of emotional cues. Contemporary trends in emotion analysis lean toward multimodal approaches that leverage audiovisual and text modalities. However, implementing multimodal strategies introduces its own set of challenges, marked by a rise in model complexity and an expansion of parameters, thereby creating a need for a larger volume of data. This thesis responds to this challenge by proposing a …

Stability Properties Of A System Of Receptors In The Presence Of Attractive Domains, Basim Mohammed Al-Maliki

Graduate Theses, Dissertations, and Problem Reports

I use mathematical modeling to understand aspects of molecular processes in living cells. Specifically, we look at the first few steps in cell signaling. Signal initiation requires that receptors located on the cell membrane bind together to form dimers. Microscopic imaging of receptors on the cell membrane revealed that receptors tend to accumulate in small areas (clusters). Studies also show that the membrane has a complex landscape consisting of domains and barriers of various origin.

Here we study the way receptor dimerization is influenced by domains on the cell membrane. Our underlying hypothesis is that the physical and chemical properties …

Natural Fracture Evolution: Investigations Into The Middle Devonian Marcellus Shale, Appalachian Basin, Usa, Natalie Abigail Mitchell

Graduate Theses, Dissertations, and Problem Reports

Optimizing recovery from unconventional shale reservoirs has generated considerable research into optimal recovery methods through hydraulic fracturing design and shale reservoir characterization in the development of long-term hydrocarbon producers. Permeability at multiple scales from nanometer-scale pore sizes and nano-darcy permeability to completion-induced fractures defining a 100’s of meter stimulated reservoir volume plays a significant role in hydrocarbon flow during production in shale reservoirs. Preexisting cemented fractures in unconventional shale reservoirs are abundant and preferentially reactivate during induced hydraulic fracturing treatment to create necessary large-scale permeability. While previous investigations have significantly improved our knowledge of shale reservoirs, it has also highlighted …

Novel Technique In Production Of Pb (Ii)- Imprinted Polymers, Ehab Mohammed, Mostafa M. Elsheikh, Adham A. El-Zomrawy, Farag A. Ahmed

Al-Azhar Bulletin of Science

Ion imprinting techniques were used to produce ion imprinted polymer (IIP) particles for the selective removal of Pb2+ from aqueous environments. As the Templating monomers, acrylic acid, acrylic amine ligand, and Methylene Bisacrylamide crosslinker were chosen. The imprinted polymer was prepared by free radical polymerization. By leaching with 0.1 M HCl, the (Pb2+) ion was removed from the template. The polymer particles were characterized by IR spectroscopy, Thermal analysis and potentiometric analysis. The produced polymer was mechanically crushed into fine particles, assembled into a sensor probe, and linked to a bare HB graphite pencil electrode (GPE). The sensor has a …