Physical Sciences and Mathematics Commons^™

A Computational Study On A Globular Protein And An Intrinsically Disordered Protein, Cecilia Chavez Garcia

Electronic Thesis and Dissertation Repository

We present molecular dynamics (MD) simulations of two protein targets for drug design: Triosephosphate isomerase (TIM) and Methyl CpG binding protein 2 (MeCP2). First, we studied three TIM proteins: TcTIM, TbTIM and a chimeric protein (Mut1). The first two are homologous enzymes with high sequence similarity, albeit different biophysical parameters. The chimeric protein has TbTIM’s sequence and 13 single point mutations, which are sufficient to obtain TcTIM-like behaviour in reactivation experiments. We analyzed the residue interaction networks observed in the all-atom MD simulations, as well as their electrostatic interactions and the impact of simulation length on them. A conserved salt …

Some Optical And Electrical Properties Of Cadmium Sulfide And Lead Sulfide Thin Films Prepared By Electron Beam Deposition, Achiri Celestine Tange

Archived Theses and Dissertations

No abstract provided.

Resource Optimization Property Manager For Autonomic Computing, Hazem A. M. Sharaf El Din

Archived Theses and Dissertations

No abstract provided.

Moment-Preserving Piecewise Approximation For 1-D And 2-D Signals, Soha M. A. A. Seif

Archived Theses and Dissertations

No abstract provided.

For Children’S Sake, Gerry Boyle

Colby Magazine

For three decades, Steve Nicholas has worked to create more sustainable cities. He tells videographer Reggie Huang why we must make progress on this urgent problem before it’s turned over to the next generation.

Fighting Climate Change Is A Capital Idea: Graham Macmillan Sees Market Incentives As Powerful Tools, Gerry Boyle

Colby Magazine

In coming years, action on climate may come from what some would consider the least likely direction—capital markets. Where some people might consider the demands of capital markets to be at the root of social and environmental problems, Graham Macmillan ’97 sees market incentive as wielding powerful leverage to help bring about solutions to the world’s most vexing challenges.

Spatio-Temporal Relation Modeling For Few-Shot Action Recognition, Anirudh Thatipelli, Sanath Narayan, Salman Hameed Khan, Rao Muhammad Anwer, Fahad Shahbaz Khan, Bernard Ghanem

Computer Vision Faculty Publications

We propose a novel few-shot action recognition framework, STRM, which enhances class-specific feature discriminability while simultaneously learning higher-order temporal representations. The focus of our approach is a novel spatio-temporal enrichment module that aggregates spatial and temporal contexts with dedicated local patch-level and global frame-level feature enrichment sub-modules. Local patch-level enrichment captures the appearance-based characteristics of actions. On the other hand, global framelevel enrichment explicitly encodes the broad temporal context, thereby capturing the relevant object features over time. The resulting spatio-temporally enriched representations are then utilized to learn the relational matching between query and support action sub-sequences. We further introduce a …

Ten Simple Rules For Creating A Scientific Web Application, Jessica L. Burnett, Renee Dale, Chung-Yi Hou, Gabriela Palomo-Muoz, Kaitlin Stack Whitney, Steve Aulenbach, Robert Sky Bristol, Denis Valle, Tristan P. Wellman

School of Natural Resources: Faculty Publications

The use of scientific web applications (SWApps) across biological and environmental sciences has grown exponentially over the past decades or so. Although quantitative evidence for such increased use in practice is scant, collectively, we have observed that these tools become more commonplace in teaching, outreach, and in science coproduction (e.g., as decision support tools). Despite the increased popularity of SWApps, researchers often receive little or no training in creating such tools. Although rolling out SWApps can be a relatively simple and quick process using modern, popular platforms like R shiny apps or Tableau dashboards, making them useful, usable, and sustainable …

Newgrange Skyscape In Stellarium, Frank Prendergast

Articles

Newgrange Skyscape in Stellarium is a new customised landscape planetarium model giving the user the unique ability to interrogate the dynamic sky above the Boyne Valley on any date of interest during the hours of daylight or darkness. Archaeological, astronomical and topographical points of interest are labelled in the model and visible even during the hours of darkness. These are summarily described in a short gazetteer appended at the end of the instruction document to encourage further exploration of the wonderful heritage found in the Boyne Valley and beyond.

Watch on Youtube: https://www.youtube.com/watch?app=desktop&v=aGPsVGBXkY4

Watch on Vimeo: https://vimeo.com/493351576

Exploring The Impact Of Social Influence Mechanisms And Network Density On Societal Polarization, Justin Mittereder

Student Research Submissions

I present an agent-based model, inspired by the opinion dynamics
(OD) literature, to explore the underlying behaviors that may induce
societal polarization. My agents interact on a social network, in which
adjacent nodes can influence each other, and each agent holds an array
of continuous opinion values (on a 0-1 scale) on a number of separate
issues. I use three measures as a proxy for the virtual society’s “po-
larization:” the average assortativity of the graph with respect to the
agents’ opinions, the number of non-uniform issues, and the number
of distinct opinion buckets in which agents have the same …

Machine Learning And Radiomic Features To Predict Overall Survival Time For Glioblastoma Patients, Lina Chato, Shahram Latifi

Electrical & Computer Engineering Faculty Research

Glioblastoma is an aggressive brain tumor with a low survival rate. Understanding tumor behavior by predicting prognosis outcomes is a crucial factor in deciding a proper treatment plan. In this paper, an automatic overall survival time prediction system (OST) for glioblastoma patients is developed on the basis of radiomic features and machine learning (ML). This system is designed to predict prognosis outcomes by classifying a glioblastoma patient into one of three survival groups: short-term, mid-term, and long-term. To develop the prediction system, a medical dataset based on imaging information from magnetic resonance imaging (MRI) and non-imaging information is used. A …

Determining The Biochemical Mechanisms And Binding Activities Of A Type Iv-A Crispr-Cas Ding Helicase, Matt Armbrust

Fall Student Research Symposium 2021

CRISPR-Cas systems are adaptive prokaryotic immune systems that enable host cells to defend against attack from foreign nucleic acids such as phage infections or plasmids. CRISPR-Cas systems are diverse and encompass 2 classes, 6 types, and 33 subtypes. The Type IV-A CRISPR-Cas system from Pseudomonas aeruginosa strain 83 is composed of five different genes (csf1, csf2, csf3, cas6, and dinG). Type IV-A systems are poorly understood, and currently there is little research detailing their biological and biochemical mechanism of immunity. CasDinG, an ancillary protein within the Type IV-A system, is required for an immune response in vivo. However, the role …

Measuring Irregularity Via Approximate Entropy: How Does Perceived Human Instability Affect One's Own Stability?, Madi Braunersrither

Fall Student Research Symposium 2021

In a study performed at Utah State University, participants were prompted to evaluate the stability of pictured human postures while standing on a force plate. The force plate was used to collect the center of pressure of the subjects by recording measurements in the vertical and horizontal directions. The way these factors fluctuate over time and the irregularity in this fluctuation, specifically, can give insight into the subject’s postural stability. Rather than working with summary statistics such as means and variances of fitting parameters of a distribution as commonly done in statistics, we want to measure irregularity through analyzing the …

Climate Change Impacts On Atmospheric Ammonia And Implications For Human Health, Casey Olson, Connor Snow, Bridger Jorgensen

Fall Student Research Symposium 2021

According to national data Cache Valley has the highest concentrations of atmospheric ammonia in the nation. This study aims to answer the questions of whether climate variables and events such as precipitation, averaged winds, geopotential height, and teleconnections can be used to predict the behavior of pollutants and how human biology is potentially affected. Data from the Utah Climate Center shows that the 3rd yearly quartile has the highest levels of airborne ammonia due to the high levels of fertilizer use and livestock emissions in the farming industry in Cache Valley. After data analysis, there seems to be a connection …

Explicit Synchronized Solitary Waves For Some Models For The Interaction Of Long And Short Waves In Dispersive Media., Bruce Brewer

Fall Student Research Symposium 2021

Four systems have recently been proposed for the study of the interaction of long and short waves in dispersive media. This poster establishes the synchronized solitary wave solutions for one of these systems.

Creating Transparent And Accessible Methods For Approximating The Composite Strength Of Concrete Sandwich Wall Panels, Ruth Taylor

Fall Student Research Symposium 2021

Background: The method of designing partially composite sandwich wall panels (SWPs) relies strongly on the use of percent of composite action. Calculating these values proves to be a complex and virtually inaccessible process for practicing engineers, resulting in the reliance on proprietary software or connector-system manufacturers for the necessary values. We simulated percent composite action data, including several relevant variables, to examine the relationship and determine if simple and accessible methods of calculation could be created. Methods: Code from collaborating engineers used to calculate percent composite action with the Iterative Sandwich Beam Theory (ISBT) method was translated into R, a …

Art As An Educator, Kylie Hansen

Fall Student Research Symposium 2021

When looking at art, eyes are often drawn to the foreground of the canvas, which can leave out many details and not tell the whole story a painting has to offer. The process of analyzing and looking deeper into works of art would be common in a perfect world; its lessons can be universal. Everyone should study art because it increases skills that can be used for many things. Art can reframe views of the world as well as condition the mind to look past quick judgments. Art teaches one to slow down and analyze situations before acting and may …

Understanding How Changes In Precipitation Intensity Will Affect Vegetation In The Western U.S., Cristina Chirvasa

Fall Student Research Symposium 2021

Precipitation events are becoming more intense as the atmosphere warms, but it remains unclear how precipitation intensification will affect plant growth in arid and semiarid ecosystems. There is conflicting evidence suggesting that larger precipitation events may either increase or decrease plant growth. Here, we report the growth responses of herbaceous and woody plants to experimental manipulations of precipitation intensity in a cold, semi-arid ecosystem in Utah, USA. In this experiment, precipitation was collected and redeposited as fewer, larger events with total annual precipitation kept constant across treatments. Results from the first two growing seasons revealed that more intense events ‘pushed’ …

Scattering Of Light From Periodic Conducting Nanostructures, Wesley Mills

Fall Student Research Symposium 2021

Light scattered from periodic structures generates numerous fascinating phenomena, from diffraction patterns to the black patches on some butterfly wings. The simple scalar wave formulation based on Huygens principle can account for many diffraction and radiation patterns in the far field. However, when the structure dimensions are smaller than the wavelength, light polarization and structure details become important, and the vector formulation based on Maxwell's equations is necessary. I will present an analytic calculation and a numerical simulation on light scattering from two-dimensional conducting grids to model the reflectance from butterfly wings and broadband absorption structures made from carbon nanotube …

Source Apportionment And Health Risk Assessment Of Nitrate In Foothill Aquifers Of Western Ghats, South India, Banajarani Panda, S. Chidambaram, Daniel D. Snow, Arindam Malakar, Dhiraj Kr Singh, L. Ramanathan

Nebraska Water Center: Faculty Publications

The present research reports the level of nitrate (NO₃^-), associated health risks and possible sources of contamination in groundwater from south India. Many samples (32%) are above or approaching the recommended level of NO₃^- for safe drinking water. The correlation analysis indicates different sources of NO₃^- contamination in different regions rather than a common origin. The isotopic measurements provide information about potential nitrogen sources contributing NO₃^- to the groundwater. Based on isotope analysis, the sources of NO₃^- in the groundwater of this region are likely to be from (a) …

Element Contamination In Port Everglades – Preparing For Ecological Impacts, Laura White

All HCAS Student Capstones, Theses, and Dissertations

Port dredging is of economic importance worldwide but its impacts to the marine environment through the remobilization of elemental contaminants are not well understood. A massive deepening and widening of Port Everglades, Florida, will begin in 2023. Contaminated sediment disturbed during the dredging process could be released and prove to be harmful to three coral reef tracks located beginning 1.5 miles away from the port. This study focused on identifying and quantifying 14 different trace elements: arsenic (As), cadmium (Cd), cobalt (Co), chromium (Cr), copper (Cu), mercury (Hg), lead (Pb), manganese (Mn), molybdenum (Mo), nickel (Ni), selenium (Se), tin (Sn), …

Proquest Tdm Studio: A Text And Data Mining Solution, Anamika Megwalu, Anne Marie Engelsen

Faculty Research, Scholarly, and Creative Activity

TDM Studio is an integrated platform offered by ProQuest for data and text mining. TDM stands for text and data mining. This cloud-based, all-in-one innovative product is designed to offer researchers a clean interface with rights-cleared content, Jupyter notebook, and data visualization tools. As a result, researchers can now search Pro-Quest databases, create large datasets, import data to Jupyter notebook for analysis, and download results within a day.

Teacher Education Programs Of Top Pisa Scoring Countries, Stephanie Kafer

Honors Projects

This research paper aims to investigate the teacher education programs of four different countries that have consistently scored high on the international Programme for International Student Assessment (PISA) test. This project intends to answer two questions: What locations consistently perform high on the Programme for International Student Assessment (PISA) test? What do the teacher training programs look like for these locations and are there commonalities between programs of different locations? The first question is answered using statistics of PISA scores from the past twenty years and from those statistics, the top four countries that this paper focuses on are Finland, …

Nutrient Intake And Dietary Inflammatory Potential In Current And Recovered Anorexia Nervosa, Olivia Patsalos, Bethan Dalton, Christia Kyprianou, Joseph Firth, Nitin Shivappa Mbbs, Mph, Ph.D., James Hébert Scd, Ulrike Schmidt, Hubertus Himmerich

Faculty Publications

Anorexia nervosa (AN) is characterised by disrupted and restrictive eating patterns. Recent investigations and meta-analyses have found altered concentrations of inflammatory markers in people with current AN. We aimed to assess nutrient intake in participants with current or recovered AN, as compared to healthy individuals, and explore group differences in dietary inflammatory potential as a possible explanation for the observed alterations in inflammatory markers. We recruited participants with current AN (n = 51), those recovered from AN (n = 23), and healthy controls (n = 49). We used the Food Frequency Questionnaire (FFQ), to calculate a Dietary …

Responses Of Benthic Calcifying Algae To Ocean Acidification Differ Between Laboratory And Field Settings, Heather N. Page, Keisha D. Bahr, Tyler Cyronak, Elizabeth B. Jewett, Maggie D. Johnson, Sophie J. Mccoy

Marine & Environmental Sciences Faculty Articles

Accurately predicting the effects of ocean and coastal acidification on marine ecosystems requires understanding how responses scale from laboratory experiments to the natural world. Using benthic calcifying macroalgae as a model system, we performed a semi-quantitative synthesis to compare directional responses between laboratory experiments and field studies. Variability in ecological, spatial, and temporal scales across studies, and the disparity in the number of responses documented in laboratory and field settings, make direct comparisons difficult. Despite these differences, some responses, including community-level measurements, were consistent across laboratory and field studies. However, there were also mismatches in the directionality of many responses …

Error Propagation And Algorithmic Design Of Contour Integral Eigensolvers With Applications To Fiber Optics, Benjamin Quanah Parker

Dissertations and Theses

In this work, the finite element method and the FEAST eigensolver are used to explore applications in fiber optics. The present interest is in computing eigenfunctions u and propagation constants β satisfing [sic] the Helmholtz equation Δu + k²n²u = β²u. Here, k is the freespace wavenumber and n is a spatially varying coefficient function representing the refractive index of the underlying medium. Such a problem arises when attempting to compute confinement losses in optical fibers that guide laser light. In practice, this requires the computation of functions u referred to as …

Analyzing And Detecting Android Malware And Deepfake, Md Shohel Rana

Dissertations

Rapid advances in artificial intelligence (AI), machine learning (ML), and deep learning (DL) over the past several decades have produced a variety of technologies and tools that, among numerous cybersecurity issues, have enticed cybercriminals and hackers to design malware for the Android operating systems and/or manipulate multimedia. For example, high-quality and realistic fake videos, images, or audios have been created to spread misinformation and propaganda, foment political discord and hate, or even harass and blackmail people; these manipulated, high-quality and realistic videos became known recently as Deepfake. There has been much work done in recent years on malware analysis and …

Non-Linear Optical Characterization Of Stressed Materials, Kaylee N. Rellaford

Theses and Dissertations

Interactions between materials, their surfaces, and applied stresses are involved in every man-made construction in the world. Therefore, finding ways to interact without altering inherent properties of materials is of great interest. Surface spectroscopies, including second harmonic generation (SHG) and sum frequency generation (SFG), are inherently noninvasive testing methods. Both SHG and SFG are well-developed techniques that can be used in various applications including the characterization of material state. Both of these techniques allow for a noninvasive analysis of various materials, such as metals and polymers. We have used SHG as a method to characterize the change in signal strength …

Late Cretaceous Paleoceanographic Evolution And The Onset Of Cooling In The Santonian At Southern High Latitudes (Iodp Site U1513, Se Indian Ocean), Maria Rose Petrizzo, Kenneth G. Macleod, David K. Watkins, Erik Wolfgring, Brian T. Huber

Department of Earth and Atmospheric Sciences: Faculty Publications

The latest Cenomanian to Santonian sedimentary record recovered at IODP Expedition 369 Site U1513 in the Mentelle Basin (SE Indian Ocean, paleolatitude 60°S at 85 Ma) is studied to interpret the paleoceanographic evolution in the Southern Hemisphere. The planktonic foraminiferal assemblage changes, the depth ecology preferences of different species, and the surface and seafloor temperature inferred from the stable isotopic values measured on foraminiferal tests provide meaningful information to the understanding of the Late Cretaceous climate. The hothouse climate during the Turonian-Santonian, characterized by weak latitudinal temperature gradients and high atmospheric CO₂ concentrations, is followed by a progressive cooling …

Violation Of Magnetic Flux Conservation By Superconducting Nanorings, Iris Mowgood, Gurgen Melkonyan, Rajendra Dulal, Serafim Teknowijoyo, Sara Chahid, Armen Gulian

Mathematics, Physics, and Computer Science Faculty Articles and Research

The behavior of magnetic flux in the ring-shaped finite-gap superconductors is explored from the view-point of the flux-conservation theorem which states that under the variation of external magnetic field "the magnetic flux through the ring remains constant" (see, e.g., [L.D. Landau and E.M. Lifshitz, Electrodynamics of Continuos Media, vol. 8 (New York, Pergamon Press, 1960), Section 42]). Our results, based on the time-dependent Ginzburg-Landau equations and COMSOL modeling, made it clear that in the general case, this theorem is incorrect. While for rings of macroscopic sizes the corrections are small, for micro and nanorings they become rather substantial. The physical …