Physical Sciences and Mathematics Commons^™

Workflow Critical Path: A Data-Oriented Critical Path Metric For Holistic Hpc Workflows, Daniel D. Nguyen, Karen L. Karavanic

Computer Science Faculty Publications and Presentations

Current trends in HPC, such as the push to exascale, convergence with Big Data, and growing complexity of HPC applications, have created gaps that traditional performance tools do not cover. One example is Holistic HPC Workflows — HPC workflows comprising multiple codes, paradigms, or platforms that are not developed using a workflow management system. To diagnose the performance of these applications, we define a new metric called Workflow Critical Path (WCP), a data-oriented metric for Holistic HPC Workflows. WCP constructs graphs that span across the workflow codes and platforms, using data states as vertices and data mutations as edges. …

Distribution And Characterization Of Rhyolites Of The Strawberry Volcanics -- Evolution Of A Major Rhyolite Field Associated With Columbia River Basalt Magmatism, Eastern Oregon, Usa, Chanel Leigh Dvorak

Dissertations and Theses

The Strawberry Rhyolites constitute a significant rhyolite field among the largest in Oregon. Aerial coverage of approximately 386 km² and an overall estimated volume of ~67 km³ using a median thickness for each unit. On the other hand, the total volume could be greater than 100 km³ if greater thicknesses apply. The Strawberry Rhyolites, a largely unknown mid-Miocene silicic volcanic rocks, crop out amongst voluminous flood basalt flows of the Columbia River Basalt Group (CRBG) in eastern Oregon. The eruptive activity of the Strawberry Rhyolites is currently constrained to span a period of about 2 million years, …

An Instructional Guide To Environmental Campaigns For K-12 Schools, Erin Mccarty

University Honors Theses

Evidence suggests environmental education can correlate with both short- and long-term behavioral changes, but existing research on the effectiveness of popular environmental education tactics show mixed results. Qualitative research was used in this study to assess student engagement and behavioral change within the context of environmental education campaigns. Ideally, students exposed to environmental campaigns become more informed on environmental issues and adjust their behavior to align with the campaign’s objectives. However, only a portion of environmental campaigns have these desired effects on their students. Based on a preliminary literature review, I anticipated the defining catalyst on post-campaign behavioral engagement would …

Characterization And Interpretation Of Feldspathic Chromite Assemblages (Fcas) In Four Ordinary Chondrites: An Electron Backscatter Diffraction (Ebsd) Study, Kimberly Louisa Maccini

Dissertations and Theses

Feldspathic Chromite Assemblages (FCAs) are chemically distinctive assemblages rich in Na, Al, and Cr that are found in a variety of chondrites. They consist of concentrations of chromite associated mainly with feldspathic material, either feldspar or the glassy material known as maskelynite. Professor Alan Rubin (2003) has proposed that some FCAs formed by shock melting, but the origin of different types of feldspathic chromite assemblages are unclear and have not been studied with more modern techniques such as Electron Backscatter Electron Diffraction (EBSD).

Here EBSD was used to study FCAs in four metamorphosed ordinary chondrites of different shock stages, including …

Ecological Exposure And Effects Of Microplastics In Crabs Along The Pacific Coast, Dorothy A. Horn

Dissertations and Theses

Microplastics have been documented across the global oceans as an ubiquitous pollutant. Found in the water column, sediment, shorelines, estuaries, freshwater streams and rivers along with terrestrial soils, flora and fauna. The continuous input of plastic waste into the marine environment doesn't seem to be slowing as the amount of plastic created each year increases globally.

This study investigated (1) the effects of microplastic ingestion in the indicator species, the Pacific mole crab (Emerita analoga), testing the predator avoidance behavior, reproductive output and parasitism effects when an adult female gravid crab had ingested microplastics (2) adult mortality, hatching …

Quantum Field Theories, Topological Materials, And Topological Quantum Computing, Muhammad Ilyas

Dissertations and Theses

A quantum computer can perform exponentially faster than its classical counterpart. It works on the principle of superposition. But due to the decoherence effect, the superposition of a quantum state gets destroyed by the interaction with the environment. It is a real challenge to completely isolate a quantum system to make it free of decoherence. This problem can be circumvented by the use of topological quantum phases of matter. These phases have quasiparticles excitations called anyons. The anyons are charge-flux composites and show exotic fractional statistics. When the order of exchange matters, then the anyons are called non-Abelian anyons. Majorana …

Modifying The Aspect Survey To Support The Validity Of Student Perception Data From Different Active Learning Environments, Nicole Naibert, Erin E. Shortlidge, Jack Barbera

Chemistry Faculty Publications and Presentations

Measuring students’ perceptions of active learning activities may provide valuable insight into their engagement and subsequent performance outcomes. A recently published measure, the Assessing Student Engagement in Class Tool (ASPECT), was developed to assess student perceptions of various active learning environments. As such, we sought to use this measure in our courses to assess the students’ perceptions of different active learning environments. Initial results analyzed with confirmatory factor analysis (CFA) indicated that the ASPECT did not function as expected in our active learning environments. Therefore, before administration within an introductory biology course that incorporated two types of active learning strategies, …

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 …

Conserved And Divergent Features Of Neuronal Camkii Holoenzyme Structure, Function, And Highorder Assembly, Olivia R. Buonarati, Adam P. Miller, Steven J. Coultrap, K. Ulrich Bayer, Steve L. Reichow

Chemistry Faculty Publications and Presentations

Neuronal CaMKII holoenzymes (^a and ^b isoforms) enable molecular signal computation underlying learning and memory but also mediate excitotoxic neuronal death. Here, we provide a comparative analysis of these signaling devices, using single-particle electron microscopy (EM) in combination with biochemical and live cell imaging studies. In the basal state, both isoforms assemble mainly as 12-mers (but also 14-mers and even 16-mers for the b isoform). CaMKIIa and ^b isoforms adopt an ensemble of extended activatable states (with average radius of 12.6 versus 16.8 nm, respectively), characterized by multiple transient intra- and interholoenzyme interactions associated with distinct functional properties. The …

Rapid Method For Consistency And Concentration Reporting Of Cannabidiol Using 1H-Nmr And Computer-Assisted Chemical Software, Michael A. Fernando

University Honors Theses

An integrated computational method was demonstrated with hemp-derived Cannabidiol for an assessment of its purity and concentration. The sample was structurally verified, high purity, and 2.98 mmol/L in dissolved DMSO. The method presented is a general approach to assessing purity and concentration for any small organic molecule in CMC-Assist.

2d Vs 3d Tracking In Bacterial Motility Analysis, Jacqueline Acres, Jay Nadeau

Physics Faculty Publications and Presentations

Digital holographic microscopy provides the ability to observe throughout a large volume without refocusing. This capability enables simultaneous observations of large numbers of microorganisms swimming in an essentially unconstrained fashion. However, computational tools for tracking large 4D datasets remain lacking. In this paper, we examine the errors introduced by tracking bacterial motion as 2D projections vs. 3D volumes under different circumstances: bacteria free in liquid media and bacteria near a glass surface. We find that while XYZ speeds are generally equal to or larger than XY speeds, they are still within empirical uncertainties. Additionally, when studying dynamic surface behavior, the …

Community College Geoscience Faculty Perspectives On Critical Thinking Instructional Tools, Mariela Salas Bao

Dissertations and Theses

Research has shown that modern courses and programs designed to foster critical thinking vary in both content and delivery, in turn leading to differences in their effectiveness. Few studies have investigated critical thinking among nontraditional students at community colleges taking STEM courses, especially within the geosciences. Furthermore, such research has focused primarily on the students with few if any studies involving faculty. This study examined the perceptions held by community college geoscience faculty regarding critical thinking and how such perceptions influenced their choice of instructional strategies. This study used a basic qualitative methodology and a maximum variation sampling to select …

Exploring The Potential Use Of Porous Silica Nanoparticles In Cest-Mri, Lydia Makotamo

Dissertations and Theses

Magnetic resonance imaging (MRI) is a widely used modality in diagnostics, treatment, and monitoring various conditions due to its ability to generate high-resolution images using non-ionizing radiation. The advent of contrast agents, which generally work by increasing the spin relaxation rate constants of water protons, has led to image enhancement. Despite the usefulness of this class of agents in diagnostic medicine, their inability to provide in-depth functional and anatomical information, coupled with their high detection limits, has led to new agents being explored.

Chemical exchange saturation transfer (CEST) presents an alternative route to generate signals via repetitive saturations transfers between …

Designing Environmentally Responsible And Highly Effective Bioorthogonally Functionalized Chiral Mri Contrast Agents, Karley Breann Maier

Dissertations and Theses

Magnetic resonance imaging (MRI) revolutionized diagnostic imaging and modernized the characterization of numerous diseases. The clinical success of MRI is in large part due to the employment of gadolinium-based contrast agents (GBCAs). Due to sensitivity limitations, GBCAs are indicated at markedly high dosages (~1 g Gd³⁺ per exam). The routine use of such large quantities of gadolinium poses significant health and environmental risks. There are growing concerns over the effects of dechelation of the metal in vivo and the possible effect of resulting gadolinium deposition. Concurrently, there is a rising awareness of gadolinium anomalies borne by GBCAs which undergo …

Situate: An Agent-Based System For Situation Recognition, Max Henry Quinn

Dissertations and Theses

Computer vision and machine learning systems have improved significantly in recent years, largely based on the development of deep learning systems, leading to impressive performance on object detection tasks. Understanding the content of images is considerably more difficult. Even simple situations, such as "a handshake", "walking the dog", "a game of ping-pong", or "people waiting for a bus", present significant challenges. Each consists of common objects, but are not reliably detectable as a single entity nor through the simple co-occurrence of their parts.

In this dissertation, toward the goal of developing machine learning systems that demonstrate properties associated with understanding, …

Geometric Characterization Of Continuously Defective Elastic Crystals, Marek Z. Elźanowski

Mathematics and Statistics Faculty Publications and Presentations

We show how some differential geometric structures associated with a concept of a homogeneous space appear naturally in a kinematic model of continuously distributed defects in an elastic crystal solid and discuss how one can use them to describe the defectiveness of such a continuum.

The Imperative For Climate Action At Portland State University, Stephen Percy

Office of the President Publications and Presentations

Portland State University President Stephen Percy announces the formation of the Climate Change Initiative.

Research Sites Get Closer To Field Camps Over Time: Informing Environmental Management Through A Geospatial Analysis Of Science In The Mcmurdo Dry Valleys, Antarctica, Stephen M. Chignell, Madeline E. Myers, Adrian Howkins, Andrew Fountain

Geology Faculty Publications and Presentations

As in many parts of the world, the management of environmental science research in Antarctica relies on cost-benefit analysis of negative environmental impact versus positive scientific gain. Several studies have examined the environmental impact of Antarctic field camps, but very little work looks at how the placement of these camps influences scientific research. In this study, we integrate bibliometrics, geospatial analysis, and historical research to understand the relationship between field camp placement and scientific production in the McMurdo Dry Valleys of East Antarctica. Our analysis of the scientific corpus from 1907–2016 shows that, on average, research sites have become less …

From Mdp To Alphazero, David Robert Sewell

Dissertations and Theses

In this paper I will explain the AlphaGo family of algorithms starting from first principles and requiring little previous knowledge from the reader. The focus will be upon one of the more recent versions AlphaZero but I hope to explain the core principles that allowed these algorithms to be so successful. I will generally refer to AlphaZero as theses [sic] core set of principles and will make it clear when I am referring to a specific algorithm of the AlphaGo family. AlphaZero in short combines Monte Carlo Tree Search (MCTS) with Deep learning and self-play. We will see how these …

Estimated Amounts And Rates Of Carbon Mobilized By Landsliding In Old-Growth Temperate Forests Of Se Alaska, Bryce A. Vascik, Adam M. Booth, Brian Buma, Matteo Berti

Geology Faculty Publications and Presentations

Landslides, a forest disturbance, mobilize carbon (C) sequestered in vegetation and soils. Mobilized C is deposited either onto hillslopes or into the water, sequestering C from and releasing C to the atmosphere at different time scales. The C-dense old-growth temperate forests of SE Alaska are a unique location to quantify C mobilization rate by frequent landslides that often evolve into saturated moving masses known as debris flows. In this study, the amount of C mobilized by debris flows over historic time scales was estimated by combining a landslide inventory with maps of modeled biomass and soil carbon. We analyzed SE …

Silica Sinter And The Evolution Of Hot Springs In The Alvord/Pueblo Valleys, Southeast Oregon, Usa, Leslie Allen Mowbray, Michael L. Cummings

Geology Faculty Publications and Presentations

Hot springs in the Alvord/Pueblo valleys in southeastern Oregon are analogous to Basinand- Range hydrothermal systems where heat source and permeable pathways are met through crustal thinning. Silica sinter deposition at Mickey Springs, Alvord Valley, predates the late Pleistocene high stand of pluvial Lake Alvord. At Borax Lake, Pueblo Valley, sinter deposition occurred during the Holocene. This study examines the evolution of springs at Mickey Springs, where three morphologies of sinter are present: (1) basalt clasts surrounded by sinter in interbedded conglomerate and sandstone, (2) pool-edge and aprons of sinter surrounding depressions (12–32 m diameter), and (3) quaquaversal sinter mounds …

Molecular Mechanisms Underlying Enhanced Hemichannel Function Of A Cataract-Associated Cx50 Mutant, Jun-Jie Tong, Umair Khan, Bassam George Haddad, Peter J. Minogue, Eric C. Beyer, Vivian M. Berthoud, Steve L. Reichow, Lisa Ebihra

Chemistry Faculty Publications and Presentations

Connexin-50 (Cx50) is among the most frequently mutated genes associated with congenital cataracts. Although most of these disease-linked variants cause loss of function because of misfolding or aberrant trafficking, others directly alter channel properties. The mechanistic bases for such functional defects are mostly unknown. We investigated the functional and structural properties of a cataract-linked mutant, Cx50T39R (T39R), in the Xenopus oocyte system. T39R exhibited greatly enhanced hemichannel currents with altered voltage-gating properties compared to Cx50 and induced cell death. Coexpression of mutant T39R with wild-type Cx50 (to mimic the heterozygous state) resulted in hemichannel currents whose properties were indistinguishable from …

Understanding Hyperporphyrin Spectra: Tddft Calculations On Diprotonated Tetrakis(-Aminophenyl)Porphyrin., Jeanet Conradie, Carl C. Wamser, Abhik Ghosh

Chemistry Faculty Publications and Presentations

A detailed TDDFT study (with all-electron STO-TZ2P basis sets and the COSMO solvation model) has been carried out on the effect of diprotonation on the UV-vis-NIR spectra of free-base tetraphenylporphyrin and tetrakis(-aminophenyl)porphyrin. The diprotonated forms have been modeled as their bis-formate complexes, i.e., as so-called porphyrin diacids. The dramatic redshift of the Q-band of the TAPP diacid has been explained in terms of an elevated "a" HOMO and lowered LUMOs, both reflecting infusion of aminophenyl character into the otherwise classic Gouterman-type frontier MOs. The exercise has also yielded valuable information on the performance of different exchange-correlation functionals. Thus, the hybrid …

Validation Of A Spatial Agent-Based Model For Taenia Solium Transmission (“Cystiagent”) Against A Large Prospective Trial Of Control Strategies In Northern Peru, Ian W. Pray, Francesco Pizzitutti, Gabrielle Bonnet, Eloy Gonzalez-Gustavson, Wayne Wakeland, William K. Pan, William E. Lambert, Armando E. Gonzalez, Hector H. Garcia, Seth E. O’Neal

Systems Science Faculty Publications and Presentations

Background: The pork tapeworm (Taenia solium) is a parasitic helminth that imposes a major health and economic burden on poor rural populations around the world. As recognized by the World Health Organization, a key barrier for achieving control of T. solium is the lack of an accurate and validated simulation model with which to study transmission and evaluate available control and elimination strategies. CystiAgent is a spatially-explicit agent based model for T. solium that is unique among T. solium models in its ability to represent key spatial and environmental features of transmission and simulate spatially targeted interventions, such as ring …

Effects Of Progesterone Concentrations And Follicular Wave During Growth Of The Ovulatory Follicle On Conceptus And Endometrial Transcriptome In Dairy Cows, R S. Bisinotto, E S. Ribeiro, L F. Greco, Daniel Taylor-Rodríguez, A D. Ealy, H Ayres, F S. Lima, N Martinez, W W. Thatcher, J E P Santos

Mathematics and Statistics Faculty Publications and Presentations

Objectives were to evaluate the effects of follicular wave and progesterone concentration on growth of the ovulatory follicle, conceptus elongation, uterine IFN-τ concentration, and transcriptome of conceptus and endometrium of pregnant cows on d 17 of gestation. Nonlactating nonpregnant Holstein cows were assigned randomly to one of 3 treatments: ovulation of a first-wave follicle (FW, n = 15); ovulation of a first-wave follicle and progesterone supplementation (FWP4, n = 12); and ovulation of a second-wave follicle (SW, n = 19). Ovulation of a first- or second-wave follicle was achieved by initiating the Ovsynch protocol (d -9 GnRH, d -2 and …

Predicting Human–Pathogen Protein–Protein Interactions Using Natural Language Processing Methods, Nikhil Mathews, Tuan Tran, Banafsheh Rekabdar, Chinwe Ekenna

Computer Science Faculty Publications and Presentations

In this paper, we predict the interaction of proteins between Humans and Yersinia pestis via amino acid sequences. We utilize multiple Natural Language Processing (NLP) methods available in deep learning in a unique format and produce promising results. Our developed model gives a cross-validation AUC score of 0.92 and is comparable with other work that utilizes extensive biochemical properties i.e, network and sequence in conjunction. We achieve this by combining advanced tools in neural machine translation into an integrated end-to-end deep learning framework as well as methods of preprocessing that are novel to the field of bioinformatics. We show that …

Project To Establish Growth & Mortality Rates Of Three Carex Species In Two Planting Types At Thomas Dairy Site, Tigard, Oregon, Ben Huffine

Environmental Science and Management Professional Master's Project Reports

Clean Water Services (CWS) currently increases the diversity of their wetland restoration projects using a plug planting method utilizing juvenile herbaceous plants. They have planted most of their projects using this method and plan to continue until a better one is discovered. According to the literature reviewed in this paper, juvenile plants are smaller and weaker than more mature plants and therefore have higher mortality rates. This paper is the culmination of work completed of phase 1 of this two-phase project. The objective of this project (both phases) was to design and establish a study that would test, in the …

Closed Canopies Crowd Out Bats: Planning Artificial Gap Creation, Alana Simmons

Environmental Science and Management Professional Master's Project Reports

Managed even-aged forest stands often lack small to medium-sized canopy gaps that help to increase habitat diversity and, in turn, wildlife diversity. A large body of literature suggests that this habitat diversity is especially important for bat communities and that bat activity and diversity can be depressed in closed canopy, even-aged stands. Open- and edge-adapted bats have evolved specific wing morphologies and echolocation call structures that make them reliant upon forest gaps as energy efficient foraging grounds in otherwise structurally cluttered forests. Artificial gap creation projects that increase habitat diversity have been implemented to benefit ungulates, and a similar approach …

Geodetic Constraints On A 25-Year Magmatic Inflation Episode Near Three Sisters, Central Oregon, Robert Mccaffrey, Michael Lisowsk, Charles W. Wicks, Daniel Dzurisin

Geology Faculty Publications and Presentations

Crustal inflation near the Three Sisters volcanic center documented since the mid-1990s has persisted for more than two decades. We update past analyses of the event through 2020 by simultaneously inverting InSAR interferograms, GPS time series, and leveling data for time-dependent volcanic deformation source parameters. We explore several source models to estimate how the deformation rate varied through time and to identify parameters that can reproduce measured deformation. Our preferred model is a Mogi source 4.1 km below sea level (5.9 km below the surface) about 5 km west of the summit of South Sister. Inflation started in late 1995 …

Expanding Temperature Sensing For The Orion Bms 2, Samuel J. Parker

University Honors Theses

Formula SAE (FSAE) is an annual collegiate design competition that takes place across the globe. Portland State University’s team, Viking Motorsports, was committed to designing an Electric Vehicle (EV) for the 2021 FSAE competition. The team designed a completely custom lithium-ion cell battery that is managed by an Orion BMS 2 battery management system. The FSAE rulebook requires a robust temperature monitoring system for any EV power supply. The Orion BMS 2 can only directly collect data from eight temperature sensors, which is not enough to meet FSAE regulation. However, the BMS can be configured to monitor many more sensors …