Digital Commons Network^™

The Security Layer, Mark Thomas O'Neill

Theses and Dissertations

Transport Layer Security (TLS) is a vital component to the security ecosystem and the most popular security protocol used on the Internet today. Despite the strengths of the protocol, numerous vulnerabilities result from its improper use in practice. Some of these vulnerabilities arise from weaknesses in authentication, from the rigidity of the trusted authority system to the complexities of client certificates. Others result from the misuse of TLS by developers, who misuse complicated TLS libraries, improperly validate server certificates, employ outdated cipher suites, or deploy other features insecurely. To make matters worse, system administrators and users are powerless to fix …

Optimizing Gas Mixture Composition For The Rtpc Detector For Bonus 12 At Jefferson Lab., Joshua H. Lehman

Theses and Dissertations

The main objective of this thesis is to perform a study of and optimize the most direct and practical gas mixture composition inside the Radial Time Projection Chamber for the Barely-Offshell Nucleon Structure (BONuS 12) detector for use in the CLAS 12 detector in Experimental Hall B at Thomas Jefferson National Accelerator Facility (JLab). The optimization of these conditions will enhance the performance and resolution of the detector. The original BONuS 6 experiment utilized a gas composition of 80 % He and 20% Dimethyl Ether (DME). With the extensive 12 GeV energy upgrade constructed at JLab and the new BONuS …

The Structure And Stability Of Cationic Metal-Benzene Clusters, Daniel P. Rabayda

Theses and Dissertations

We have investigated the size-dependent stability and structure of benzene, aluminum-benzene, and vanadium-benzene clusters. Motivated by gas-phase experimental studies performed by an experimental collaborator, we have used first-principle electronic structure methods to identify the structure of Al⁺(Bz)_n, V⁺(Bz)_n, and Bz_n clusters. Our studies reveal that cationic aluminum-benzene clusters have a magic number of 13, and that its high stability may be understood by analyzing the structure of the cluster. We also investigate the structure of vanadium-benzene clusters which have a magic number of 2. Here I examine the benzene-cation and benzene-benzene …

Indirect Relatedness, Evaluation, And Visualization For Literature Based Discovery, Sam Henry

Theses and Dissertations

The exponential growth of scientific literature is creating an increased need for systems to process and assimilate knowledge contained within text. Literature Based Discovery (LBD) is a well established field that seeks to synthesize new knowledge from existing literature, but it has remained primarily in the theoretical realm rather than in real-world application. This lack of real-world adoption is due in part to the difficulty of LBD, but also due to several solvable problems present in LBD today. Of these problems, the ones in most critical need of improvement are: (1) the over-generation of knowledge by LBD systems, (2) a …

Electronic Structure Of Cathode Materials In Lithium Ion Batteries, John M. Swanlund

Theses and Dissertations

Lithium ion batteries are ubiquitous in modern life, from powering hand-held electronic devices to electric vehicles. And with the necessary drive toward renewable energy sources like solar and wind, electricity storage for the grid promises to drive up the demand for higher performing, less expensive, safer, and more environmentally friendly secondary batteries. Recent research has theorized that replacing halogens in batteries’ electrolytes with non-halogens can yield desirable performance characteristics while eliminating the most dangerous and problematic chemicals. This thesis explores the possibility that a similar approach can be taken with the cathodes of lithium ion batteries. The active material in …

Some Intuition Behind Large Cardinal Axioms, Their Characterization, And Related Results, Philip A. White

Theses and Dissertations

We aim to explain the intuition behind several large cardinal axioms, give characterization theorems for these axioms, and then discuss a few of their properties. As a capstone, we hope to introduce a new large cardinal notion and give a similar characterization theorem of this new notion. Our new notion of near strong compactness was inspired by the similar notion of near supercompactness, due to Jason Schanker.

Monitoring Software And Charged Particle Identification For The Clas12 Detector, William A. Oliver

Theses and Dissertations

The CEBAF Large Acceptance Spectrometer for the 12 GeV era, known as CLAS12, uses the time of flight (TOF) system to identify charged particles from scattering events between the beam and target. The TOF system is divided into two parts: The Forward time of flight system, and the Central time of flight system. These two sub-systems subtend different polar angles of the detector geometry for wide acceptance of scattered particles. Reconstruction is the service used to identify particles from the interactions between the beam and target, called as a vertex or the point where the interaction occurs. The vertex position …

Methods For Evaluating Dropout Attrition In Survey Data, Camille J. Hochheimer

Theses and Dissertations

As researchers increasingly use web-based surveys, the ease of dropping out in the online setting is a growing issue in ensuring data quality. One theory is that dropout or attrition occurs in phases that can be generalized to phases of high dropout and phases of stable use. In order to detect these phases, several methods are explored. First, existing methods and user-specified thresholds are applied to survey data where significant changes in the dropout rate between two questions is interpreted as the start or end of a high dropout phase. Next, survey dropout is considered as a time-to-event outcome and …

Searching For Clean Observables In $B -> D* /Tau- \Bar{\Nu}_{\Tau}$ Decays, Michael D. Williams Jr.

Theses and Dissertations

In this thesis, the clean angular observables in the $\bar{B} \to D^{*+} \ell^- \bar{\nu}_{\ell}$ angular distribution is studied. Similar angular observables are widely studied in $B \to K^* \mu^+ \mu^-$ decays. We believed that these angular observables may have different sensitivities to different new physics structures.

Expansion Of The Genetic Code To Include Acylated Lysine Derivatives And Photocaged Histidine, William D. Kinney

Theses and Dissertations

The genetic code of all known organisms is comprised of the 20 proteinogenic amino acids that serve as building blocks on a peptide chain to form a vast array of proteins. Proteins are responsible for virtually every biological process in all organisms; however, the 20 amino acids contain a limited number of functional groups that often leaves much to be desired. The lack of diversity addresses the need to increase the genetic repertoire of living cells to include a variety of amino acids with novel structural, chemical, and physical properties not found in the common 20 amino acids. In order …

Using Coherence To Improve The Calculation Of Active Acoustic Intensity With The Phase And Amplitude Gradient Estimator Method, Mylan Ray Cook

Theses and Dissertations

Coherence, which gives the similarity of signals received at two microphone locations, can be a powerful tool for calculating acoustic quantities, particularly active acoustic intensity. To calculate active acoustic intensity, a multi-microphone probe is often used, and therefore coherence between all microphone pairs on the probe can be obtained. The phase and amplitude gradient estimator (PAGE) method can be used to calculate intensity, and is well suited for many situations. There are limitations to this method—such as multiple sources or contaminating noise in the sound field—which can cause significant error. When there are multiple sources or contaminating noise present, the …

Evolution Of Object-Oriented Methods From The Reverse Engineering Of Programming Code, Pann Ajjimaporn

Theses and Dissertations

Many software development projects fail because of their inability to deliver the product in a timely and cost-effective manner, i.e. the software crisis. In a commercial airline company, a safety-critical system for preventing a “single-point of failure” needs to be developed and certified. To meet the project deadline an Agile approach was used in developing the first portion of the system. An appropriate software development methodology, i.e. reverse-engineering was then applied to the software system to develop method that would be used in system maintenance and evaluation.

The goals of this research study were to develop a segment of one …

Assessing The Quality Of Software Development Tutorials Available On The Web, Manziba A. Nishi

Theses and Dissertations

Both expert and novice software developers frequently access software development resources available on the Web in order to lookup or learn new APIs, tools and techniques. Software quality is affected negatively when developers fail to find high-quality information relevant to their problem. While there is a substantial amount of freely available resources that can be accessed online, some of the available resources contain information that suffers from error proneness, copyright infringement, security concerns, and incompatible versions. Use of such toxic information can have a strong negative effect on developer’s efficacy. This dissertation focuses specifically on software tutorials, aiming to automatically …

2nd Tier Assay For The Detection Of Congenital Adrenal Hyperplasia By Virginia’S Newborn Screening Laboratory: Steroid Profile By Hplc-Ms/Ms, Christopher E. Nixon

Theses and Dissertations

Congenital Adrenal Hyperplasia (CAH) encompasses several disorders related to disruptions in the adrenal steroid production pathway. These disruptions may cause virilization of the external female sex organs, incorrect gender assignment, precocious puberty, and in the most severe form, may cause life-threatening salt wasting and adrenal crisis if not detected and treated early in the newborn period.

17α-Hydroxyprogesterone (17-OHP) is the primary target for immunofluorescence detection of CAH from dried blood spots in newborn screening (NBS). Unfortunately, current immunoassay techniques for the detection of CAH suffer from high false positive rates. The primary factors contributing to false positive determinations can include …

Adhesion At Solid/Liquid Interfaces, Neda Ojaghlou

Theses and Dissertations

The adhesion at solid/liquid interface plays a fundamental role in diverse fields and helps explain the structure and physical properties of interfaces, at the atomic scale, for example in catalysis, crystal growth, lubrication, electrochemistry, colloidal system, and in many biological reactions. Unraveling the atomic structure at the solid/liquid interface is, therefore, one of the major challenges facing the surface science today to understand the physical processes in the phenomena such as surface coating, self-cleaning, and oil recovery applications. In this thesis, a variety of theory/computational methods in statistical physics and statistical mechanics are used to improve understanding of water adhesion …

Kings In The Direct Product Of Digraphs, Morgan Norge

Theses and Dissertations

A k-king in a digraph D is a vertex that can reach every other vertex in D by a directed path of length at most k. A king is a vertex that is a k-king for some k. We will look at kings in the direct product of digraphs and characterize a relationship between kings in the product and kings in the factors. This is a continuation of a project in which a similar characterization is found for the cartesian product of digraphs, the strong product of digraphs, and the lexicographic product of digraphs.

Statistical Designs For Network A/B Testing, Victoria V. Pokhilko

Theses and Dissertations

A/B testing refers to the statistical procedure of experimental design and analysis to compare two treatments, A and B, applied to different testing subjects. It is widely used by technology companies such as Facebook, LinkedIn, and Netflix, to compare different algorithms, web-designs, and other online products and services. The subjects participating in these online A/B testing experiments are users who are connected in different scales of social networks. Two connected subjects are similar in terms of their social behaviors, education and financial background, and other demographic aspects. Hence, it is only natural to assume that their reactions to online products …

Spectral Methods For The Detection And Characterization Of Topologically Associated Domains, Kellen Garrison Cresswell

Theses and Dissertations

The three-dimensional (3D) structure of the genome plays a crucial role in gene expression regulation. Chromatin conformation capture technologies (Hi-C) have revealed that the genome is organized in a hierarchy of topologically associated domains (TADs), sub-TADs, and chromatin loops which is relatively stable across cell-lines and even across species. These TADs dynamically reorganize during development of disease, and exhibit cell- and conditionspecific differences. Identifying such hierarchical structures and how they change between conditions is a critical step in understanding genome regulation and disease development. Despite their importance, there are relatively few tools for identification of TADs and even fewer for …

Nanostructured Materials For Photocatalysis, Water Treatment And Solar Desalination, Hiran D. Kiriarachchi

Theses and Dissertations

Maintaining a constant supply of clean drinking water is among the most pressing global challenges in our time. About one-third of the population is affected by the water scarcity and it can only get worse with climate change, rapid industrialization, and the population growth. Even though nearly 70 percent of the planet is covered by water, the consumable freshwater content is only 2.5 percent of it. Unfortunately, the accessible portion of it is only 1 percent. Even so, most of the freshwater bodies are choked with pollution. Considering the vast availability of saline water on the planet and the increasing …

Electronic And Geometric Structure Of Alnom And Alnom +, Albert R. Armstrong

Theses and Dissertations

Generally, the electronic stability of aluminum clusters is associated with either closed electronic shells of delocalized electrons, or aluminum in the +3 state. To explore alternative routes for electronic stability in aluminum oxide clusters, theoretical methods were used to examine the geometric and electronic structure of Al_nO_m (2≤n≤7; 1≤m≤10) clusters. Two types of electronically stable clusters with large HOMO-LUMO gaps were identified the first being Al_2nO_3m clusters with a +3 oxidation state on the aluminum, and the second being planar clusters such as Al₄O₄, Al₅O₃, Al …

Manufactured By Nature: Growing Generatively Designed Products, Mohammad Jawad

Theses and Dissertations

Mass production and assembly lines are yesterday’s manufacturing methods. They have exhausted Earth’s resources and limited the possibilities of design in terms of both form and material, prompting designers to search for new processes. A new generation of making includes biomimicry-inspired technologies such as 3D printing and parametric simulation, which have transformed the production paradigm. Utilizing nature as industry, this thesis explores the possibility of “growing” designed objects by employing nature’s own processes and resources. It integrates bio materials, generative design and additive manufacturing to produce objects for a post-industrial world. The project outcomes employ natural minerals, crystallization and 3D …

The Development Of Intrinsically Cell-Permeable Peptide Libraries Using Mrna Display, Nicolas A. Abrigo

Theses and Dissertations

Peptides are emerging as promising therapeutics due to their inhibitory affinity towards protein-protein interactions (PPI). However, peptides have been limited mainly by their poor bio-stability and lack of cell permeability. Efforts to generate drug-like peptides have led to the development of macrocyclic peptides, which exhibit improved stability. Yet, most macrocyclic peptides still require the assistance of a cell penetrating peptide (CPP) for cellular entry.

High throughput technologies have been exceptional tools for the discovery of peptides to interrupt PPIs. This work details the recent advancements we have made to improve our high throughput technique, mRNA display, to yield more therapeutically …

Assessing The Impact Of Incorporating Residential Histories Into The Spatial Analysis Of Cancer Risk, Anny-Claude Joseph

Theses and Dissertations

In many spatial epidemiologic studies, investigators use residential location at diagnosis as a surrogate for unknown environmental exposures or as a geographic basis for assigning measured exposures. Inherently, they make assumptions about the timing and location of pertinent exposures which may prove problematic when studying long latency diseases such as cancer.

In this work we explored how the association between environmental exposures and disease risk for long-latency health outcomes like cancer is affected by residential mobility. We used simulation studies conditioned on real data to evaluate the extent to which the commonly held assumption of no residential mobility 1) affected …

Evaluation Of Private Landowner Intention To Create Early Successional Habitat In Virginia's Appalachian Region, Hannah M. Coovert

Theses and Dissertations

As human land uses continue to expand rapidly across the landscape, the management practices of private landowners are an essential part of effective conservation of biodiversity. Conservation of early successional habitats (ESH) and the species that depend on them is a priority in the eastern United States, and efforts to create more ESH on private lands has primarily focused on forest landowners and the harvesting of timber. Private lands with significant pasture cover in a forested landscape present an additional opportunity to create and maintain ESH, yet our understanding of landowner values and attitudes about management strategies in pastures (i.e., …

Methods For Joint Normalization And Comparison Of Hi-C Data, John C. Stansfield

Theses and Dissertations

The development of chromatin conformation capture technology has opened new avenues of study into the 3D structure and function of the genome. Chromatin structure is known to influence gene regulation, and differences in structure are now emerging as a mechanism of regulation between, e.g., cell differentiation and disease vs. normal states. Hi-C sequencing technology now provides a way to study the 3D interactions of the chromatin over the whole genome. However, like all sequencing technologies, Hi-C suffers from several forms of bias stemming from both the technology and the DNA sequence itself. Several normalization methods have been developed for normalizing …

Straintronic Nanomagnetic Devices For Non-Boolean Computing, Md Ahsanul Abeed

Theses and Dissertations

Nanomagnetic devices have been projected as an alternative to transistor-based switching devices due to their non-volatility and potentially superior energy-efficiency. The energy efficiency is enhanced by the use of straintronics which involves the application of a voltage to a piezoelectric layer to generate a strain which is ultimately transferred to an elastically coupled magnetostrictive nanomaget, causing magnetization rotation. The low energy dissipation and non-volatility characteristics make straintronic nanomagnets very attractive for both Boolean and non-Boolean computing applications. There was relatively little research on straintronic switching in devices built with real nanomagnets that invariably have defects and imperfections, or their adaptation …

Genome-Wide Systems Genetics Of Alcohol Consumption And Dependence, Kristin Mignogna

Theses and Dissertations

Widely effective treatment for alcohol use disorder is not yet available, because the exact biological mechanisms that underlie this disorder are not completely understood. One way to gain a better understanding of these mechanisms is to examine the genetic frameworks that contribute to the risk for developing this disorder. This dissertation examines genetic association data in combination with gene expression networks in the brain to identify functional groups of genes associated with alcohol consumption and dependence.

The first study took advantage of the behavioral complexity of human samples, and experimental capabilities provided by mouse models, by co-analyzing gene expression networks …

Metallic Systems At The Nano And Micro Scale: Bimetallic Nanoparticles As Catalysts And Mcraly Bond Coats In Thermal Barrier Coatings, Kenneth Kane

Theses and Dissertations

The dissertation is split into two parts. The first part will be focused on changes in material properties found at the nanoscale, as miscibility and electronic structure can change significantly with size. The formation of classically-immiscible bimetallic nanoparticles (BNPs) becomes favorable at the nanoscale and novel catalytic properties can emerge from the bimetallic alloying. The formation of alloyed and non-alloyed BNPs is achieved through pulse laser ablation (PLA) and a significant increase in catalytic activity is observed for both. Recently discovered, the increased activity in the non-alloyed BNPs, deemed multicomponent photocatalysis, is examined and the proposed mechanism discussed. The second …

Bayesian Nonparametric Analysis Of Longitudinal Data With Non-Ignorable Non-Monotone Missingness, Yu Cao

Theses and Dissertations

In longitudinal studies, outcomes are measured repeatedly over time, but in reality clinical studies are full of missing data points of monotone and non-monotone nature. Often this missingness is related to the unobserved data so that it is non-ignorable. In such context, pattern-mixture model (PMM) is one popular tool to analyze the joint distribution of outcome and missingness patterns. Then the unobserved outcomes are imputed using the distribution of observed outcomes, conditioned on missing patterns. However, the existing methods suffer from model identification issues if data is sparse in specific missing patterns, which is very likely to happen with a …

Improving Student Achievement Through The Implementation Of A Classroom Performance System, Stacy Maria Artis

Theses and Dissertations

This applied dissertation was designed to implement and examine the impact of a classroom performance system (CPS) on student achievement for Grade 9 mathematics students. Seventy-five students in 4 Coordinate Algebra classes were observed during the regular school day for 9 weeks. The treatment group received CPS-based instruction, and the control group received traditional mathematics instruction without the use of a CPS. The teacher was the same for all classes.

Data from benchmark assessments as well as quarterly grade reports were compared for both groups. The findings of this study showed mixed results in relation to the impact of CPS-based …