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Articles 211 - 240 of 2906

Full-Text Articles in Physical Sciences and Mathematics

Quantifying Protein Quality To Understand Protein Homeostasis (Supplemental Data), Hsien-Jung Lavender Lin Jul 2022

Quantifying Protein Quality To Understand Protein Homeostasis (Supplemental Data), Hsien-Jung Lavender Lin

ScholarsArchive Data

This data set includes the supplementary data for chpaters 3 and 4 in the dissertation Quantifying Protein Quality to Understand Protein Homeostasis. It includes various excel worksheets that were used to generate the data reported in the dissertation. We make this data available to the public so anyone who wants to reproduce the results has the resources and access to other perspectives that weren't discussed in depth in the dissertation. Chapter 3 used mass-spectrometry to quantify the surface accessibility differences in human serum albumin (HSA)between patients with and without rheumatoid arthritis (RA). We found certain residues are less reactive …

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The Telsam Protein Polymer Significantly Improves The Speed And Propensity Of Crystallization Of Target Proteins, Seyedeh Sara Soleimani Jun 2022

The Telsam Protein Polymer Significantly Improves The Speed And Propensity Of Crystallization Of Target Proteins, Seyedeh Sara Soleimani

Theses and Dissertations

While conducting pilot studies into the usefulness of fusion to TELSAM polymers as a potential protein crystallization strategy, we observed novel properties in crystals of two TELSAM–target protein fusions, as follows. (i) A TELSAM–target protein fusion can crystallize more rapidly and with greater propensity than the same target protein alone. (ii) TELSAM–target protein fusions can be crystallized at low protein concentrations. This unprecedented observation suggests a route to crystallize proteins that can only be produced in microgram amounts. (iii) The TELSAM polymers themselves need not directly contact one another in the crystal lattice in order to form well-diffracting crystals. This …

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Efficient And Adaptive Decentralized Sparse Gaussian Process Regression For Environmental Sampling Using Autonomous Vehicles, Tanner A. Norton Jun 2022

Efficient And Adaptive Decentralized Sparse Gaussian Process Regression For Environmental Sampling Using Autonomous Vehicles, Tanner A. Norton

Theses and Dissertations

In this thesis, I present a decentralized sparse Gaussian process regression (DSGPR) model with event-triggered, adaptive inducing points. This DSGPR model brings the advantages of sparse Gaussian process regression to a decentralized implementation. Being decentralized and sparse provides advantages that are ideal for multi-agent systems (MASs) performing environmental modeling. In this case, MASs need to model large amounts of information while having potential intermittent communication connections. Additionally, the model needs to correctly perform uncertainty propagation between autonomous agents and ensure high accuracy on the prediction. For the model to meet these requirements, a bounded and efficient real-time sparse Gaussian process …

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Understanding College Students' Use Of Written Feedback In Mathematics, Erin Loraine Carroll Jun 2022

Understanding College Students' Use Of Written Feedback In Mathematics, Erin Loraine Carroll

Theses and Dissertations

Many teachers want to help their students develop a growth mindset about their ability to do mathematics. Research has shown, however, that teachers simply do not know how to promote growth mindsets in their classrooms. Existing research suggests that one way teachers can support students' development of a growth mindset is through the written feedback they provide students. This study combines the research done on students' mindsets and written feedback to examine the interaction between student mindset and written feedback by analyzing written feedback provided to students in a College Algebra class and how students used that feedback based on …

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Patterned And Infiltrated Vertically Aligned Carbon Nanotube Ultra-Black Materials, Kevin Laughlin Jun 2022

Patterned And Infiltrated Vertically Aligned Carbon Nanotube Ultra-Black Materials, Kevin Laughlin

Theses and Dissertations

Ultra-black materials reflect less than 1% of incident light, and are used in a wide variety of applications from low signal detector systems, to jewelry. The darkest ultra-black materials are made with vertically aligned carbon nanotubes (VACNTs). One downside to these VACNT based ultra-black material, is they are extremely fragile, and the types of surfaces they can be grown on is limited. Here I created a strengthened ultra-black material that can withstand light handling and drying from water exposure, and can be transferred to other substrates while remaining ultra-black. I also present theoretical models with supporting data on how to …

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Quantum Decoherence In Time-Dependent Anharmonic Systems, Ty Beus Jun 2022

Quantum Decoherence In Time-Dependent Anharmonic Systems, Ty Beus

Theses and Dissertations

This dissertation studies quantum decoherence in anharmonic oscillator systems to monitor and understand the way the systems evolve. It also explores methods to control the systems' evolution, and the effects of decoherence when applicable. We primarily do this by finding the time evolution of the systems using their Lie algebraic structures. We solve for a generalized Caldirola-Kanai Hamiltonian, and propose a general way to produce a desired evolution of the system. We apply the analysis to the effects of Dirac delta fluctuations in mass and frequency, both separately and simultaneously. We also numerically demonstrate control of the generalized Caldirola-Kanai system …

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Towards Color-Based Two-Hand 3d Global Pose Estimation, Fanqing Lin Jun 2022

Towards Color-Based Two-Hand 3d Global Pose Estimation, Fanqing Lin

Theses and Dissertations

Pose estimation and tracking is essential for applications involving human controls. Specifically, as the primary operating tool for human activities, hand pose estimation plays a significant role in applications such as hand tracking, gesture recognition, human-computer interaction and VR/AR. As the field develops, there has been a trend to utilize deep learning to estimate the 2D/3D hand poses using color-based information without depth data. Within the depth-based as well as color-based approaches, the research community has primarily focused on single-hand scenarios in a localized/normalized coordinate system. Due to the fact that both hands are utilized in most applications, we propose …

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Synthesis And Applications Of Α,Β-Dehydroamino Acid-Containing Peptides, Diego A. Moya Jun 2022

Synthesis And Applications Of Α,Β-Dehydroamino Acid-Containing Peptides, Diego A. Moya

Theses and Dissertations

Yaku’amide A (YA) is a linear anticancer peptide that is rich in bulky dehydroamino acids (ΔAAs) and β-hydroxyamino acids (β-OHAAs). In our recent total synthesis of YA, we featured a one-pot anti dehydration–azide reduction–O→N acyl transfer process for the stereospecific construction of Z- and E- ∆Ile residues. Despite previous total syntheses and our efforts, the synthesis of YA remains lengthy. Via computational studies, we identified two analogue peptides that closely resemble the conformation of YA. The use of simpler and symmetrical bulky ΔAAs such as dehydrovaline (ΔVal) and dehydroethylnorvaline (ΔEnv) as surrogates of ∆Ile, along with azlactone chemistry for their …

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The Regulation Of Atg9a-Mediated Aggrephagy By An Ulk1-Independent Atg13-Atg101 Complex, Joshua Youngs Jun 2022

The Regulation Of Atg9a-Mediated Aggrephagy By An Ulk1-Independent Atg13-Atg101 Complex, Joshua Youngs

Undergraduate Honors Theses

Aggrephagy, a type of autophagy, is an essential cellular process by which protein aggregates are collected and broken down in the lysosome. Protein aggregates are implicated in several diseases including Alzheimer’s disease, diabetes, and cancer. Here, we investigate the ATG13-ATG101 protein complex, a sub-complex of the canonical ULK1 complex whose regulatory role in aggrephagy is not completely understood. We also develop a protein fragment complementation (PFC) assay using the biotin ligase TurboID to study the functions of the ATG13-ATG101 complex with increased specificity. We demonstrate that ATG13 is required for optimal degradation of p62-ubiquitin condensates. We also show that a …

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Synthesis Of Yaku’Amide A Analogues And Impact Of Dehydroamino Acids On The Structure And Stability Of Incipient 310 Helical Peptides, Daniel Joaquin Jun 2022

Synthesis Of Yaku’Amide A Analogues And Impact Of Dehydroamino Acids On The Structure And Stability Of Incipient 310 Helical Peptides, Daniel Joaquin

Theses and Dissertations

The first project in this dissertation describes the total synthesis of yaku’amide A analogues. Natural product yaku’amide A possesses potent anticancer activity and exhibits a novel mode of action. However, due to its complex asymmetrical isoleucine dehydroamino acids, the synthesis of this polypeptide poses a unique challenge. Despite the efficient synthesis developed in our lab, the total synthesis of this natural product remains lengthy. In order to simplify the overall synthesis, symmetrical dehydroamino acids were incorporated to replace the dehydroisoleucine residues yielding two analogues of yaku’amide A that closely resembles the conformation of the natural product. Biological testing of the …

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Finding Patterns In The Inertia Of The Distance Squared Matrix Of Unicyclic Graphs, Kellon Sandall, Mark Kempton, Christian Howell Jun 2022

Finding Patterns In The Inertia Of The Distance Squared Matrix Of Unicyclic Graphs, Kellon Sandall, Mark Kempton, Christian Howell

Undergraduate Honors Theses

We analyze the spectrum of the distance squared matrix of a tree and give a relation between the inertia of the distance squared matrix and the structure of the tree. We take the result one step further and consider the addition of exactly one cycle in the tree. We obtain an expression for the inertia of the distance squared matrix of a cycle graph. We obtain a bound on the inertia of the distance squared matrix of an arbitrary unicyclic graph.

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Gas Phase Techniques For The Study Of Biomolecular And Supramolecular Structures And Chemistry, Andrew J. Arslanian Jun 2022

Gas Phase Techniques For The Study Of Biomolecular And Supramolecular Structures And Chemistry, Andrew J. Arslanian

Theses and Dissertations

This dissertation expounds on the investigations of the structure and chemistry of peptides and supramolecular host-guest systems in the gas phase. These investigations used two different kinds of analytical instrument: Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) and ion mobility mass spectrometry (IM-MS, IMS). These investigations were complemented by chemical modeling. The FTICR was used to radially trap ions with its 4.7 T magnet, which allowed the ions to undergo sustained off-resonance irradiation collision-induced dissociation (SORI-CID). A subsequent event then measured the collision cross sections (σ) of the targeted precursor ion and one of the selected product ions. These …

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Development Of Cooperative Catalytic Systems And Bimetallic Catalysts For Organic Synthesis, Kelton Guy Forson Jun 2022

Development Of Cooperative Catalytic Systems And Bimetallic Catalysts For Organic Synthesis, Kelton Guy Forson

Theses and Dissertations

The development of new catalysts for organic synthesis is an important pursuit that enables the discovery of new and more efficient reactions and the identification of new reaction mechanisms. Cooperative catalytic systems and bimetallic catalysts represent unique approaches to catalyst development that achieve reactivity that cannot be obtained with a single catalyst or metal. These types of catalysts can activate substrates in unique ways, facilitate reactions under mild conditions, increase substrate scope, and provide access to completely new transformations. The first part of this work describes the development of a cooperative nickel-titanium-catalyzed amination of allylic alcohols. The cooperative effects of …

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Modeling Inter-Particle Magnetic Correlations In Magnetite Nanoparticle Assemblies Using X-Ray Magnetic Scattering Data, Johnathon Michael Rackham Jun 2022

Modeling Inter-Particle Magnetic Correlations In Magnetite Nanoparticle Assemblies Using X-Ray Magnetic Scattering Data, Johnathon Michael Rackham

Theses and Dissertations

Magnetic nanoparticles are used in nanotechnologies and biomedical applications, such as drug targeting, hyperthermia, MRI contrasting agents, and bio-separation of compound solutions. Magnetite (Fe3O4) nanoparticles stand to be effective in these roles due to the non-toxic nature of magnetite and its ease of manufacture. To this end, a greater understanding of the magnetic behavior of the individual magnetite nanoparticles is needed when a collection of them is used. This research seeks to discover the local magnetic ordering of ensembles of magnetite nanoparticles at various stages of the magnetization process, temperatures above and below their blocking temperature, and for various particle …

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An Iterative Numerical Method For Multiple Scattering Using High Order Local Absorbing Boundary Conditions, Jonathan Harriman Hale May 2022

An Iterative Numerical Method For Multiple Scattering Using High Order Local Absorbing Boundary Conditions, Jonathan Harriman Hale

Theses and Dissertations

This thesis outlines an iterative approach for determining the scattered wave for two dimensional multiple acoustic scattering problems using high order local absorbing boundary conditions and second order finite difference. We seek to approximate the total wave as it is scattered off of multiple arbitrarily shaped obstacles. This is done by decomposing the scattered wave into the superposition of single scattered waves. We then repeatedly solve the single scattering system for each obstacle, while updating the boundary conditions based off the incident wave and the scattered wave off the other obstacles. We solve each single scattering by enclosing the obstacle …

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Language Learning Using Models Of Intentionality In Repeated Games With Cheap Talk, Jonathan Berry Skaggs May 2022

Language Learning Using Models Of Intentionality In Repeated Games With Cheap Talk, Jonathan Berry Skaggs

Theses and Dissertations

Language is critical to establishing long-term cooperative relationships among intelligent agents (including people), particularly when the agents' preferences are in conflict. In such scenarios, an agent uses speech to coordinate and negotiate behavior with its partner(s). While recent work has shown that neural language modeling can produce effective speech agents, such algorithms typically only accept previous text as input. However, in relationships among intelligent agents, not all relevant context is expressed in conversation. Thus, in this paper, we propose and analyze an algorithm, called Llumi, that incorporates other forms of context to learn to speak in long-term relationships modeled as …

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A Visual Focus On Form Understanding, Brian Lafayette Davis May 2022

A Visual Focus On Form Understanding, Brian Lafayette Davis

Theses and Dissertations

Paper forms are a commonly used format for collecting information, including information that ultimately will be added to a digital database. This work focuses on the automatic extraction of information from form images. It examines what can be achieved at parsing forms without any textual information. The resulting model, FUDGE, shows that computer vision alone is reasonably successful at the problem. Drawing from the strengths and weaknesses of FUDGE, this work also introduces a novel model, Dessurt, for end-to-end document understanding. Dessurt performs text recognition implicitly and is capable of outputting arbitrary text, making it a more flexible document processing …

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Tabletop Extreme-Ultraviolet Source Using High Harmonic Generation For Polarization Sensitive Imaging, Taylor Jordan Buckway May 2022

Tabletop Extreme-Ultraviolet Source Using High Harmonic Generation For Polarization Sensitive Imaging, Taylor Jordan Buckway

Theses and Dissertations

We are developing a tabletop extreme-ultraviolet source using high harmonic generation at Brigham Young University. The thesis goes over the theory of high harmonic generation using the three-step model. This tabletop source was designed for probing magnetic domains of iron nanoparticles. We present optimization of the 42 eV and 52 eV harmonics through phase matching. Phase matching consists of tuning the intensity of the IR beam and pressure of the gas medium. The target gas medium used for this thesis is argon. The 42 eV harmonic was optimized to 8.2 billion photons per second. This was used with a 1500 …

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Network Specialization: A Topological Mechanism For The Emergence Of Cluster Synchronization, Ethan Walker May 2022

Network Specialization: A Topological Mechanism For The Emergence Of Cluster Synchronization, Ethan Walker

Theses and Dissertations

Real-world networks are dynamic in that both the state of the network components and the structure of the network (topology) change over time. Most studies regarding network evolution consider either one or the other of these types of network processes. Here we consider the interplay of the two, specifically, we consider how changes in network structure effect the dynamics of the network components. To model the growth of a network we use the specialization model known to produce many of the well-known features observed in real-world networks. We show that specialization results in a nontrivial equitable partition of the network …

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Characterizing Equivalence And Correctness Properties Of Dynamic Mode Decomposition And Subspace Identification Algorithms, Samuel Gregory Neff Apr 2022

Characterizing Equivalence And Correctness Properties Of Dynamic Mode Decomposition And Subspace Identification Algorithms, Samuel Gregory Neff

Theses and Dissertations

We examine the related nature of two identification algorithms, subspace identification (SID) and Dynamic Mode Decomposition (DMD), and their correctness properties over a broad range of problems. This investigation begins by noting the strong relationship between the two algorithms, both drawing significantly on the pseudoinverse calculation using singular value decomposition, and ultimately revealing that DMD can be viewed as a substep of SID. We then perform extensive computational studies, characterizing the performance of SID on problems of various model orders and noise levels. Specifically, we generate 10,000 random systems for each model order and noise level, calculating the average identification …

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How Failures Cascade In Software Systems, Barbara W. Chamberlin Apr 2022

How Failures Cascade In Software Systems, Barbara W. Chamberlin

Theses and Dissertations

Cascading failures involve a failure in one system component that triggers failures in successive system components, potentially leading to system wide failures. While frequently used fault tolerant techniques can reduce the severity and the frequency of such failures, they continue to occur in practice. To better understand how failures cascade, we have conducted a qualitative analysis of 55 cascading failures, described in 26 publicly available incident reports. Through this analysis we have identified 16 types of cascading mechanisms (organized into eight categories) that capture the nature of the system interactions that contribute to cascading failures. We also discuss three themes …

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A Permutation-Based Confidence Distribution For Rare-Event Meta-Analysis, Travis Andersen Apr 2022

A Permutation-Based Confidence Distribution For Rare-Event Meta-Analysis, Travis Andersen

Theses and Dissertations

Confidence distributions (CDs), which provide evidence across all levels of significance, are receiving increasing attention, especially in meta-analysis. Meta-analyses allow independent study results to be combined to produce one overall conclusion and are particularly useful in public health and medicine. For studies with binary outcomes that are rare, many traditional meta-analysis methods often fail (Sutton et al. 2002; Efthimiou 2018; Liu et al. 2018; Liu 2019; Hunter and Schmidt 2000; Kontopantelis et al. 2013). Zabriskie et al. (2021b) develop a permutation-based method to analyze such data when study treatment effects vary beyond what is expected by chance. In this work, …

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The Perception Of At-Risk Students On Caring Student-Teacher Relationships And Its Impact On Their Productive Disposition, Brittany Hopper Apr 2022

The Perception Of At-Risk Students On Caring Student-Teacher Relationships And Its Impact On Their Productive Disposition, Brittany Hopper

Theses and Dissertations

The importance of a positive, caring relationship with students in the classroom is under-researched in mathematics education. Research shows that a positive student-teacher relationship can have many long-term positive results for the student. Many of these results directly impact a student's productive disposition towards mathematics. At-risk students are in greater need of positive relationships and an increase in productive disposition. Using Joan Tronto's (1993) elements of care, I examine the student perspective of these kinds of relationships and how the student sees development of their own productive disposition.

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Accurate Band Energies Of Metals With Quadratic Integration, Jeremy John Jorgensen Apr 2022

Accurate Band Energies Of Metals With Quadratic Integration, Jeremy John Jorgensen

Theses and Dissertations

Materials play an important role in society. Historically, and even at present, materials have been discovered by trial and error, and many of the most useful materials have been discovered by chance. The high-throughput approach aims to remove (as much as possible) chance and guesswork at the experimental level by filtering out materials candidates that are not predicted to exist. Many successes have been recorded. In the high-throughput approach to materials discovery, machined-learned models of materials are created from databases of theoretical materials. These databases are the result of millions of density-functional-theory (DFT) simulations. The size and accuracy of the …

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A Multidimensional Convolutional Bootstrapping Method For The Analysis Of Degradation Data, Jared M. Clark Apr 2022

A Multidimensional Convolutional Bootstrapping Method For The Analysis Of Degradation Data, Jared M. Clark

Theses and Dissertations

While Monte Carlo methods for bootstrapping are typically easy to implement, they can be quite time intensive. This work aims to extend an established convolutional method of bootstrapping to work when convolutions in two or more dimensions are required. The convolutional method relies on efficient computational tools rather than Monte Carlo simulation which can greatly reduce the computation time. The proposed method is particularly well suited for the analysis of degradation data when the data are not collected on time intervals of equal length. The convolutional bootstrapping method is typically much faster than the Monte Carlo bootstrap and can be …

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Inhibition Of Cell Adhesion And Actin Localization During Migration Upon Protective Antigen Mutant Ligand Binding To The Capillary Morphogenesis Gene 2, Sai Lun Lee Apr 2022

Inhibition Of Cell Adhesion And Actin Localization During Migration Upon Protective Antigen Mutant Ligand Binding To The Capillary Morphogenesis Gene 2, Sai Lun Lee

Theses and Dissertations

Capillary Morphogenesis Gene 2 protein (CMG2) is a type 1 transmembrane receptor known as the anthrax toxin receptor 2 (ANTXR2). While it is documented that the cell surface receptor CMG2 mediates anthrax toxin entry into the cell via endocytosis, the physiological role of CMG2 is not well understood. Others have suggested that CMG2 may have a role in mediating ECM homeostasis and angiogenesis. Additionally, both anthrax protective antigen (PA) and a furin protease-resistant mutant, PASSSR, inhibit corneal neovascularization in a mouse model, and interestingly PASSSR has a greater affinity to CMG2 receptor. PASSSRalso has a more potent antiangiogenic effect than …

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Physics-Guided Machine Learning In Ocean Acoustics Using Fisher Information, Michael Craig Mortenson Apr 2022

Physics-Guided Machine Learning In Ocean Acoustics Using Fisher Information, Michael Craig Mortenson

Theses and Dissertations

Waterborne acoustic signals carry information about the ocean environment. Ocean geoacoustic inversion is the task of estimating environmental parameters from received acoustic signals by matching the measured sound with the predictions of a physics-based model. A lower bound on the uncertainty associated with environmental parameter estimates, the Cramér-Rao bound, can be calculated from the Fisher information, which is dependent on derivatives of a physics-based model. Physics-based preconditioners circumvent the need for variable step sizes when computing numerical derivatives. This work explores the feasibility of using a neural network to perform geoacoustic inversion for environmental parameters and their associated uncertainties from …

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The Novel Protein Crystallization Chaperone Telsam Stabilizes Weak Crystal Contacts, Accelerates Crystallization Of Fused Target Proteins, And Solves The Crystallographic Phase Problem, Supeshala Dilrukshi Sarath Nawarathnage Apr 2022

The Novel Protein Crystallization Chaperone Telsam Stabilizes Weak Crystal Contacts, Accelerates Crystallization Of Fused Target Proteins, And Solves The Crystallographic Phase Problem, Supeshala Dilrukshi Sarath Nawarathnage

Theses and Dissertations

We studied the usefulness of genetic fusion to TELSAM polymers as an effective protein crystallization strategy. We observed novel properties in crystals of two TELSAM-target protein fusions. TELSAM as a crystallization chaperone shows rapid crystallization when it's fused to target proteins and possibly with a greater propensity. Some TELSAM-target fusions crystallized more rapidly than the same target protein alone. TELSAM-target proteins can be crystallized at relatively low protein concentrations such as 0.1 mg/mL. TELSAM requires no TELSAM polymers touching one another in the crystal lattice in order to form well-diffracting crystals. This lack of crystal contacts has not been observed …

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“If I Could Do This, I Feel Anyone Could:” The Design And Evaluation Of A Two-Factor Authentication Manager, Garrett D. Smith Apr 2022

“If I Could Do This, I Feel Anyone Could:” The Design And Evaluation Of A Two-Factor Authentication Manager, Garrett D. Smith

Theses and Dissertations

Two-factor authentication (2FA) is a strong defense against account compromise. However, usability studies reveal challenges with 2FA setup. The process to manually setup and remove 2FA methods differs across websites. We present a system design for a 2FA manager to automatically setup and remove 2FA methods. Potential benefits are reduced time, fewer mistakes, consistent terminology, a single workflow for users to learn, and the ability to rapidly transition to a new 2FA method—e.g., when replacing a lost 2FA method. We create two proof-of-concept implementations of our design, one as a browser extension and one integrated as a feature in an …

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Using Connections To Make Predictions On Dynamic Networks, Rebecca Dorff Jones Apr 2022

Using Connections To Make Predictions On Dynamic Networks, Rebecca Dorff Jones

Theses and Dissertations

Networks are sets of objects that are connected in some way and appear abundantly in nature, sociology, and technology. For many centuries, network theory focused on static networks, which are networks that do not change. However, since all networks transform over time, static networks have limited applications. By comparison, dynamic networks model how connections between objects change over time. In this work, we will explore how connections in dynamic networks change and how we can leverage these changes to make predictions about future iterations of networks. We will do this by first considering the link prediction problem, using either Katz …

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