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Articles 1 - 30 of 1827
Full-Text Articles in Physical Sciences and Mathematics
Minimal Specialization: The Coevolution Of Network Structure And Dynamics, Annika King
Minimal Specialization: The Coevolution Of Network Structure And Dynamics, Annika King
Theses and Dissertations
The changing topology of a network is driven by the need to maintain or optimize network function. As this function is often related to moving quantities such as traffic, information, etc., efficiently through the network, the structure of the network and the dynamics on the network directly depend on the other. To model this interplay of network structure and dynamics we use the dynamics on the network, or the dynamical processes the network models, to influence the dynamics of the network structure, i.e., to determine where and when to modify the network structure. We model the dynamics on the network …
Dna-Templated Nanofabrication Of Metal-Semiconductor Heterojunctions And Their Electrical Characterization, Chao Pang
Theses and Dissertations
Bottom-up nanofabrication, although still in its early stages with formidable challenges, is considered a potential alternative method to address the limitations of traditional top-down techniques by offering benefits including process simplification, cost reduction, and environmental friendliness. DNA-templated nanofabrication, one of the most powerful bottom-up methods, presents an innovative way to create advanced nanoelectronics. In this approach, nanomaterials with specific electronic, photonic, or other functions are precisely and programmably positioned on DNA nanostructures from a disordered collection of smaller parts. These self-assembled structures offer significant potential for improving many fields such as biosensing, drug delivery and electronic device manufacturing. This dissertation …
A Bilevel Approach To Resource Allocation For Utility-Based Request-Response Systems, Tanner Jack Sundwall
A Bilevel Approach To Resource Allocation For Utility-Based Request-Response Systems, Tanner Jack Sundwall
Theses and Dissertations
We present a novel bilevel programming formulation that aims to solve a resource allocation problem for request-response systems. Our formulation is motivated by potential inefficiencies in the allocation of computational resources to incoming user requests in such systems. In our experience, systems often operate with a surplus of resources despite potentially incurring unjustifiable cost. Our work attempts to optimize the tradeoff between the financial cost of resources and the opportunity cost of unfulfilled user demand. Our bilevel formulation consists of an \textit{upper} problem which has a constraint value appearing in the \textit{lower} problem. We derive efficient methods for finding global …
Dissecting Trypanosome Metabolism By Discovering Glycolytic Inhibitors, Drug Targets, And Glycosomal Ph Regulation, Daniel Hale Call
Dissecting Trypanosome Metabolism By Discovering Glycolytic Inhibitors, Drug Targets, And Glycosomal Ph Regulation, Daniel Hale Call
Theses and Dissertations
Trypanosoma brucei, the causative agent of African trypanosomiasis, and its relatives Trypanosoma cruzi and several Leishmania species belong to a class of protozoa called kinetoplastids that cause a significant health burden in tropical and semitropical countries across the world. While an improved therapy was recently approved for African trypanosomiasis, the therapies available to treat infections caused by T. cruzi and Leishmania spp. remain relatively poor. Improving our understanding of T. brucei metabolism can inform on metabolism of its relatives. The purpose of the research presented in this dissertation was to develop novel tools and methods to study metabolism in T. …
An Investigation Of The Interactions Of Gradient Coherence And Network Pruning In Neural Networks, Zachary Yauney
An Investigation Of The Interactions Of Gradient Coherence And Network Pruning In Neural Networks, Zachary Yauney
Theses and Dissertations
We investigate the coherent gradient hypothesis and show that the coherence measurements are different on real and random data regardless of the network's initialization. We introduce "diffs," an attempt at an element-wise approximation at coherence, and investigate their properties. We study how coherence is affected by increasing the width of simple fully-connected networks. We then prune those fully-connected networks and find that sparse networks outperform dense networks with the same number of nonzero parameters. In addition, we show that it is possible to increase the performance of a sparse network by scaling the size of the dense parent network it …
Trip - Transformer Interatomic Potential Predicts Realistic Energy Surface Using Physical Bias, Bryce Eric Hedelius
Trip - Transformer Interatomic Potential Predicts Realistic Energy Surface Using Physical Bias, Bryce Eric Hedelius
Theses and Dissertations
Accurate interatomic energies and forces enable high-quality molecular dynamics simulations, torsion scans, potential energy surface mapping, and geometry optimization. Machine learning algorithms have enabled rapid estimates of energies and forces with high accuracy. Further development of machine learning algorithms holds promise for producing general potentials that support dozens of atomic species. I present my own Transformer Interatomic Potential (TrIP): a chemically sound potential based on the SE(3)-Transformer. TrIP's species-agnostic architecture--using continuous atomic representation and homogenous graph convolutions--encourages parameter sharing between atomic species for more general representations of chemical environments, keeps a reasonable number of parameters, serves as a form of …
Head Tail Open: Open Tailed Classification Of Imbalanced Document Data, Chetan Joshi
Head Tail Open: Open Tailed Classification Of Imbalanced Document Data, Chetan Joshi
Theses and Dissertations
Deep learning models for scanned document image classification and form understand- ing have made significant progress in the last few years. High accuracy can be achieved by a model with the help of copious amounts of labelled training data for closed-world classification. However, very little work has been done in the domain of fine-grained and head-tailed(class imbalance with some classes having high numbers of data points and some having a low number of data points) open-world classification for documents. Our proposed method achieves a better classification results than the baseline of the head-tail-novel/open dataset. Our techniques include separating the head-tail …
Unique K3 Surfaces With Purely Non-Symplectic Automorphism: Insights From Weighted Projective Spaceunique K3 Surfaces With Purely Non-Symplectic Automorphism:\\Insights From Weighted Projective Space, Elizabeth Melville
Theses and Dissertations
K3 surfaces have garnered attention across various fields, from optics and dynamics to high energy physics, making them a subject of extensive study for many decades. Recent work by mathematicians, including Brandhorst [1], has focused on non-symplectic automorphisms, aiming to categorize K3 surfaces that admit such automorphisms. Brandhorst made a list of unique K3 surfaces with purely non-symplectic automorphisms and established specific criteria for a K3 surface to be isomorphic to one on his list. This thesis aims to provide an alternative representation of select K3 surfaces from Brandhorst's list. While Brandhorst predominantly characterizes these surfaces as elliptic K3 surfaces, …
The Generation Of Terahertz Light And Its Applications In The Study Of Vibrational Motion, Aldair Alejandro
The Generation Of Terahertz Light And Its Applications In The Study Of Vibrational Motion, Aldair Alejandro
Theses and Dissertations
Terahertz (THz) spectroscopy is a powerful tool that uses ultrashort pulses of light to study the properties of materials on picosecond time scales. THz light can be generated through a variety of methods. In our lab, we generate THz through the process of optical rectification in nonlinear optical (NLO) organic crystals. THz light can be used to study several phenomena in materials, such as spin precession, electron acceleration, vibrational and rotational motion. The work presented in this dissertation is divided into two parts: (1) the generation of THz light and (2) applications of THz light. The first portion of this …
Multifunctional And Moisture Tolerant Zinc-Based Mono- And Bi-Metallic Metal-Organic Framework (Mof) Thin Films, Emmanuel Agbata
Multifunctional And Moisture Tolerant Zinc-Based Mono- And Bi-Metallic Metal-Organic Framework (Mof) Thin Films, Emmanuel Agbata
Theses and Dissertations
Many applications of metal-organic frameworks (MOFs) are highly dependent on their structures. The type and consistency of structure inform their properties. Zinc-based MOFs are applicable in different fields because of the low toxicity of zinc materials and are therefore also useful for catalysis. While MOF-5, a zinc-based MOF with carboxylate linkers is moisture intolerant, a variant of this is moisture tolerant. The introduction of a nitrogen-based linker in the zinc MOF which renders the structure moisture-tolerant. This material has not been explored as much, despite its multifunctional properties. Furthermore, the growth of Zn-based bimetallics of this MOF has not yet …
Applying Mathematical Modeling To The Study Of Family Systems, Dahlia Maxwell
Applying Mathematical Modeling To The Study Of Family Systems, Dahlia Maxwell
Theses and Dissertations
Mathematical modeling provides a powerful framework for insight into current scientific theories as well as hypothesis generation for further research. Despite its undeniable potential to enrich scientific advancement, the application of mathematical modeling remains conspicuously scarce in the field of family science. The complexity inherent in family dynamics, coupled with the intricate interplay of emotions in the individual, underscores the necessity of a robust analytical approach. Addressing this critical gap in the literature, this thesis introduces a sophisticated mathematical model of family dynamics integrating essential elements from family systems theory, emotion dynamics, and appraisal theory. The model is implemented as …
Advancing Single-Cell Proteomics Through Innovations In Liquid Chromatography And Mass Spectrometry, Kei Grant Isaac Webber
Advancing Single-Cell Proteomics Through Innovations In Liquid Chromatography And Mass Spectrometry, Kei Grant Isaac Webber
Theses and Dissertations
Traditional proteomics studies can measure many protein biomarkers simultaneously from a single patient-derived sample, promising the possibility of syndromic diagnoses of multiple diseases sharing common symptoms. However, precious cellular-level information is lost in conventional bulk-scale studies that measure tissues comprising many types of cells. As single cells are the building blocks of organisms and are easier to biopsy than traditional bulk samples, performing proteomics on a single-cell level would benefit clinicians and patients. Single-cell proteomics, combined with mass spectrometry imaging, can be used to analyze cells in their microenvironment, preserving spatial information. We have previously used laser-capture microdissection to isolate …
Robot Proficiency Self-Assessment Using Assumption-Alignment Tracking, Xuan Cao
Robot Proficiency Self-Assessment Using Assumption-Alignment Tracking, Xuan Cao
Theses and Dissertations
A robot is proficient if its performance for its task(s) satisfies a specific standard. While the design of autonomous robots often emphasizes such proficiency, another important attribute of autonomous robot systems is their ability to evaluate their own proficiency. A robot should be able to conduct proficiency self-assessment (PSA), i.e. assess how well it can perform a task before, during, and after it has attempted the task. We propose the assumption-alignment tracking (AAT) method, which provides time-indexed assessments of the veracity of robot generators' assumptions, for designing autonomous robots that can effectively evaluate their own performance. AAT can be considered …
N-H Nhc Palladium Catalysts Derived From Unique 2-Phosphinoimidazole Precursors For C-C Cross Coupling Reactions And Application Of Slow Releasing Polymers Impregnated With Gibberellic Acid To Overcome Seed Dormancy For Land Reclamation, Alexandra Jean Setelin Larson
N-H Nhc Palladium Catalysts Derived From Unique 2-Phosphinoimidazole Precursors For C-C Cross Coupling Reactions And Application Of Slow Releasing Polymers Impregnated With Gibberellic Acid To Overcome Seed Dormancy For Land Reclamation, Alexandra Jean Setelin Larson
Theses and Dissertations
Organometallic chemistry is highly dependent upon the ligands which are employed on a metal's surface. These ligands control steric bulk and electronics of the metal center which can change the reactivity of the organometallic complex. Ligands that are standard in organometallic chemistry include phosphine ligands. These phosphine ligands have been utilized in the field since the 1960's and have shaped the development of many key organometallic catalysts. Phosphine ligands are easily functionalized and highly reactive. This increased reactivity, however, causes severe limitations as phosphine ligands are often unstable under standard benchtop conditions and must be handled both air and moisture …
Gt-Ches And Dycon: Improved Classification For Human Evolutionary Systems, Joseph S. Johnson
Gt-Ches And Dycon: Improved Classification For Human Evolutionary Systems, Joseph S. Johnson
Theses and Dissertations
The purpose of this work is to rethink the process of learning in human evolutionary systems. We take a sober look at how game theory, network theory, and chaos theory pertain specifically to the modeling, data, and training components of generalization in human systems. The value of our research is three-fold. First, our work is a direct approach to align machine learning generalization with core behavioral theories. We made our best effort to directly reconcile the axioms of these heretofore incompatible disciplines -- rather than moving from AI/ML towards the behavioral theories while building exclusively on AI/ML intuition. Second, this …
Development Of Bifunctional Peptides As Scaffolds For Bifunctional Catalysis And A Novel Method Of Peptide Stapling Using Squaric Esters, Adam X. Wayment
Development Of Bifunctional Peptides As Scaffolds For Bifunctional Catalysis And A Novel Method Of Peptide Stapling Using Squaric Esters, Adam X. Wayment
Theses and Dissertations
Enzymes are some of nature's most powerful tools in chemical processes. However, their molecular complexity makes them difficult to synthesize and complicates their application in traditional organic synthesis. Peptides, a building block of enzymes, can be rapidly synthesized and have been used as a possible alternative in achieving enzyme-like catalysis. However, most peptide-based catalysts are limited in reaction-scope and are unable to incorporate traditional organic catalysts. We have designed a helical peptide scaffold capable of being functionalized with a wide variety of organocatalysts as well as transition-metal based catalysts. In order to understand how the peptide structure effects reactivity and …
New Mathematics Teachers' Goals, Orientations, And Resources That Influence Implementation Of Principles Learned In Brigham Young University's Teacher Preparation Program, Caroline S. Gneiting
New Mathematics Teachers' Goals, Orientations, And Resources That Influence Implementation Of Principles Learned In Brigham Young University's Teacher Preparation Program, Caroline S. Gneiting
Theses and Dissertations
Research in mathematics education shows that new mathematics teachers struggle to implement reform teaching practices that they learned in their teacher preparation programs. In this study, the researcher observed and interviewed three new mathematics teachers (within five years of graduation) to further explore the question of why new teachers use or do not use what they learned in their teacher preparation program. The study uses an expanded version of Schoenfeld's decision-making theory of Orientations, Goals, and Resources. This theory proved useful in the analysis of the research data, providing a framework to incorporate and organize the numerous reasons suggested by …
Usability-Driven Security Enhancements In Person-To-Person Communication, Tarun Kumar Yadav
Usability-Driven Security Enhancements In Person-To-Person Communication, Tarun Kumar Yadav
Theses and Dissertations
In the contemporary digital landscape, ensuring secure communication amid widespread data exchange is imperative. This dissertation focuses on enhancing the security and privacy of end-to-end encryption (E2EE) applications while maintaining or improving usability. The dissertation first investigates and proposes improvements in two areas of existing E2EE applications: countering man-in-the-middle and impersonation attacks through automated key verification and studying user perceptions of cryptographic deniability. Insights from privacy-conscious users reveal concerns about the lack of E2EE support, app siloing, and data accessibility by client apps. To address these issues, we propose an innovative user-controlled encryption system, enabling encryption before data reaches the …
Open System Neural Networks, Bradley Hatch
Open System Neural Networks, Bradley Hatch
Theses and Dissertations
Recent advances in self-supervised learning have made it possible to reuse information-rich models that have been generally pre-trained on massive amounts of data for other downstream tasks. But the pre-training process can be drastically different from the fine-tuning training process, which can lead to inefficient learning. We address this disconnect in training dynamics by structuring the learning process like an open system in thermodynamics. Open systems can achieve a steady state when low-entropy inputs are converted to high-entropy outputs. We modify the the model and the learning process to mimic this behavior, and attend more to elements of the input …
Understanding The Origin, Evolution, And Dynamics Of Transneptunian Binaries, Benjamin C N Proudfoot
Understanding The Origin, Evolution, And Dynamics Of Transneptunian Binaries, Benjamin C N Proudfoot
Theses and Dissertations
This dissertation discusses research that focuses on understanding transneptunian objects (TNOs) using a variety of techniques and approaches. In Chapter 1, I introduce the main concepts used throughout this dissertation and discuss the current understanding of the transneptunian region. In Chapter 2, I discuss my efforts to understand how Neptune's late stages of migration affect the Haumea family, the only known collisional family in the transneptunian region. Using advanced simulations of Neptune migration, I find that the Haumea family can plausibly form before the termination of giant planet migration and show that this extensively mixes the family. The simplest explanation …
Simulating Government Institutions In Networked Societies, Michael Richards
Simulating Government Institutions In Networked Societies, Michael Richards
Theses and Dissertations
Modern human societies give rise to the expression of complex group dynamics between the members of said society due to the abundance of continued interactions. Of particular interest are how institutions affect these interactions between societal members, alter the resulting group dynamics, and impact society as a whole through their rules. Simulating these dynamics allows for greater insight into how these institutions function and allows researchers to pose interesting questions and test hypotheses within a laboratory setting. We present a novel approach to simulating institutions, particularly governments, within a networked society. This approach builds upon the Junior High Game, which …
Local Atomic And Magnetic Structure Of Multiferroic (Sr,Ba)(Mn,Ti)O3, Braedon Jones
Local Atomic And Magnetic Structure Of Multiferroic (Sr,Ba)(Mn,Ti)O3, Braedon Jones
Theses and Dissertations
We present a detailed study of the local atomic and magnetic structure of the type-I multiferroic perovskite system (Sr,Ba)(Mn,Ti)O3 using x-ray and neutron pair distribution function (PDF) analysis, polarized neutron scattering, and muon spin relaxation (μSR) techniques. The atomic PDF analysis reveals widespread nanoscale tetragonal distortions of the crystal structure even in the paraelectric phase with average cubic symmetry, corresponding to incipient ferroelectricity in the local structure. Magnetic PDF analysis, polarized neutron scattering, and μSR likewise confirm the presence of short-range antiferromagnetic correlations in the paramagnetic state, which grow in magnitude as the temperature approaches the magnetic transition. We show …
Progress Towards The Development Of Asymmetric Conditions For Intramolecular Heteroatom/Dehydro-Diels-Alder Reactions For Synthesizing Furo[3,4-C] Pyranones And Anticancer Podophyllotoxins, Peter Mpaata
Theses and Dissertations
Furo[3,4-c] pyranone is a unique bicyclic molecular structure found in bioactive sesquiterpene isobolivianine and in artificial cytotoxic stilbene derivatives. The structure of furo[3,4-c] pyranone is analogous to cyclopenta[c] pyran structure found in potent cytotoxic iridoids like catapol. Chiral substrates for intramolecular hetero-Diels-Alder (IHDA) reaction have been synthesized in yields ranging from 39% to 81%. These compounds undergo [4+2] cycloaddition via ambimodal/ bispericyclic process to give a mixture of furo[3,4-c] pyranone in yields ranging 40-70% and aryl tetralin lactone derivatives. Density functional theory (DFT) calculations have been performed to gain insight into the mechanism leading to the formation of these compounds. …
In-Depth Geochemical Analysis Of Turbidite-Associated Shales Of The Pindos Basin, Greece, Jonathon Michael Sevy
In-Depth Geochemical Analysis Of Turbidite-Associated Shales Of The Pindos Basin, Greece, Jonathon Michael Sevy
Theses and Dissertations
Detailed geochemical analysis of the turbidite-associated shales of the Cretaceous Katafito Formation, Greece, reveals important details regarding the paleoenvironment, paleoproductivity, and regional tectonics of the Pindos Basin. The Katafito Formation was deposited along an active margin at the early onset of closure of the Tethys Sea in the Pindos sub-basin. While careful studies of the coarse clastic component of turbidites are common, this study consisted of a detailed geochemical characterization of the fine-grained portions, which helped reveal paleoenvironmental information about the basin. This study combined organic and inorganic geochemistry utilizing elemental, mineralogical, and organic chemical signatures from fine-grained turbidite-associated sediments …
Synthesis Of Yaku'amide A Analogues And Progress Toward Synthesis Of Virosine A, Alexander S. Ramos
Synthesis Of Yaku'amide A Analogues And Progress Toward Synthesis Of Virosine A, Alexander S. Ramos
Theses and Dissertations
The first project in this dissertation endeavors to outline the total synthesis of yaku'amide A and its analogs. Yaku'amide A is a natural product comprised of dehydroamino acids, including E-dehydro isoleucine, and unprecedented Z-dehydro isoleucine. These amino acids present a significant challenge to their synthesis owing to their unsymmetrical nature. To simplify the synthesis process, we synthesized analogs by substituting the E and Z dehydroamino acids with symmetrical subunits. This substitution facilitated the synthesis process and enabled us to obtain a similar three-dimensional structure to that of the natural product. Furthermore, biological testing of the simplified analogs revealed potency similar …
Interfacial Properties Of Hybrid Lipid-Polymer Bilayers: Applications In Drug Delivery And Biosensors, Keith L. Willes
Interfacial Properties Of Hybrid Lipid-Polymer Bilayers: Applications In Drug Delivery And Biosensors, Keith L. Willes
Theses and Dissertations
Amphiphilic block copolymers are unique macro-molecules capable of self-assembling into bilayers analogous to naturally occurring lipid membranes. When combined with lipids, these copolymers form hybrid membranes with unique and sometimes unpredictable properties, including increased chemical and mechanical stability. These synthetically enhanced biological structures represent a versatile platform suitable for a wide range of applications, from advanced biosensing devices to drug delivery systems. The realization of these advancements necessitates a deep understanding of material properties, including the ability to predict and control interfacial behaviors. It has been shown that in the case of pure lipid membranes, interfacial behaviors are dominated by …
Using Quantitative And Kinetic Proteomics To Explore Proteostasis, Nathan Raul Zuniga Pina
Using Quantitative And Kinetic Proteomics To Explore Proteostasis, Nathan Raul Zuniga Pina
Theses and Dissertations
Every cell consists of carefully orchestrated biomolecules such as lipids, carbohydrates, and proteins. To maintain internal stability (homeostasis), cells maintain the right amount of these molecules at the right time and at the right place. This process is especially true for proteins since they are the foundation functional units within the cell. Proteins form structures and perform chemistry that bestows cells overarching functional roles. Cells maintain protein homeostasis (proteostasis) by modulating synthesis, folding, and degradation processes (turnover) to maintain the abundance levels for all proteins. This is the foundational kinetic model of proteostasis that is covered in this work, and …
Stability, Longevity, And Regulatory Bionetworks, Christian N. K. Anderson
Stability, Longevity, And Regulatory Bionetworks, Christian N. K. Anderson
Theses and Dissertations
Genome-wide studies of diseases and chronic conditions frequently fail to uncover marked or consistent differences in RNA or protein concentrations. However, the developing field of kinetic proteomics has made promising discoveries in differences in the turnover rate of these same proteins, even when concentrations were not necessarily different. The situation can theoretically be modeled mathematically using bifurcation equations, but uncovering the proper form of these is difficult. To this end, we developed TWIG, a method for characterizing bifurcations that leverages information geometry to identify drivers of complex systems. Using this, we characterized the bifurcation and stability properties of all 132 …
Monitoring Brain Region-Specific Control Of Protein Turnover And Concentration Using Proteomics, Rebecca Suzanne Burlett
Monitoring Brain Region-Specific Control Of Protein Turnover And Concentration Using Proteomics, Rebecca Suzanne Burlett
Theses and Dissertations
Regulation of metabolism is vital to health and lies at the core of many different diseases. The breakdown of metabolisms' regulation within the brain can lead to neurological disease like Alzheimer's Disease (AD). AD is known to affect brain regions responsible for memory and memory processing like the hippocampus and entorhinal cortex. The regulation of these regions' protein quality, synthesis, and degradation deviate from 'normal' or 'healthy' levels when AD is happening. It is known there is a breakdown of regulation in those regions; however, little is known about the specifics of regulation in healthy brains regions or how it …
Dispensing With Humans In Human-Computer Interaction Research, Courtni L. Byun
Dispensing With Humans In Human-Computer Interaction Research, Courtni L. Byun
Theses and Dissertations
Machine Learning models have become more advanced than could have been supposed even a few years ago, often surpassing human performance on many tasks. Large language models (LLM) can produce text indistinguishable from human-produced text. This begs the question, how necessary are humans - even for tasks where humans appear indispensable? Qualitative Analysis (QA) is integral to human-computer interaction research, requiring both human-produced data and human analysis of that data to illuminate human opinions about and experiences with technology. We use GPT-3 and ChatGPT to replace human analysis and then to dispense with human-produced text altogether. We find GPT-3 is …