Physical Sciences and Mathematics Commons^™

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 …

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 …

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 …

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

Complex Systems 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 …

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 …

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 …

The Return To Anisotropy Across A Jet In Crossflow, Gregory P. Sakradse

Dissertations and Theses

With data from experiments on a jet of air emitting from an orifice flush with the floor of a wind tunnel providing a transverse flow, analysis is conducted to extract information about the state of anisotropy in the Reynolds stress tensor. Inflow velocities are modulated across two distinct turbulence intensity regimes while holding jet exit conditions constant, providing an opportunity to isolate effects of both jet to crossflow velocity ratio, r and the effects of the turbulence carried by the crossflow. Anisotropy in the Reynolds stress tensor is examined through anisotropy invariant maps and evolution of the function F, …

Major Controls On Diagenesis In The Martin Bridge Formation: Wallowa Mountains, Oregon, Jane Lyra Eisenberg

Dissertations and Theses

Diagenetic alteration in carbonates has long frustrated scientists who wish to use their chemistry and/or texture to understand conditions at the time of deposition. Though indicators of diagenesis are well documented, their interpretation is not always straightforward. Despite the large volume of research on the subject, the positive identification and interpretation of diagenesis is a source of ongoing debate in the scientific community.

The goal of this study is to better understand the timing of, and controls on, diagenetic alteration in the Martin Bridge Formation (MBF), a Triassic-aged limestone that was altered following deposition. Thirty-nine samples of MBF with differing …

Mid-Miocene Icelandites Of Eastern Oregon: Petrogenesis And Magmatic Lineage To Main-Phase Crbg With Constraints On Storage Sites, Melissa Aileen Carley

Dissertations and Theses

The La-Grande Owyhee eruptive axis is a mid-Miocene to Pliocene ~300 km long volcanic belt located at the eastern margin of the Columbia River Basalt Group (CRBG) in Oregon. Within this volcanic belt there are numerous vents that have produced a large volume of petrologically diverse rocks ranging from the tholeiitic flood basalts of the CRBG to rhyolitic tuffs of caldera complexes such as the Lake Owyhee Volcanic field. Icelandites, which are iron rich andesites, are known to occur in association with silica saturated to oversaturated tholeiitic basalts as a minor part of continental flood basalt volcanism. This study investigates …

Convergence Analysis Of Some Tent-Based Schemes For Linear Hyperbolic Systems, Dow Drake, Jay Gopalakrishnan, Joachim Schöberl, Christoph Wintersteiger

Mathematics and Statistics Faculty Publications and Presentations

Finite element methods for symmetric linear hyperbolic systems using unstructured advancing fronts (satisfying a causality condition) are considered in this work. Convergence results and error bounds are obtained for mapped tent pitching schemes made with standard discontinuous Galerkin discretizations for spatial approximation on mapped tents. Techniques to study semidiscretization on mapped tents, design fully discrete schemes, prove local error bounds, prove stability on spacetime fronts, and bound error propagated through unstructured layers are developed.

Selenium Probes For The Detection Of Thioredoxin Reductase Activity, Tendai Joseph Mafireyi

Dissertations and Theses

The identification and quantification of proteins and enzymatic activity in living tissues frequently requires the use of invasive procedures such as biopsy. These techniques can inhibit measurements of protein levels in real-time, and the disruption of tissue can lead to the loss of important information concerning the spatial distribution and differential activities in various cell types. The use of small organic fluorescent probes that rely on activation or accumulation within a tissue embody robust methods of detection that address these issues. This dissertation describes the design, synthesis and evaluation of fluorescent probes that can detect the enzyme thioredoxin reductase (TrxR). …

Forest Fire Effects On The Temporal Variability Of Landscape Snow Albedo Relative To Burn Severity, Max Gersh

Dissertations and Theses

Snow-water storage is decreasing, while forest fires are increasing in duration, size, frequency, and intensity, due to climate change. Most forest fires occur in the seasonal snow zone, altering snow mass and energy balance for many years following fire. Following forest fires, Surface snow albedo (SSA) decreases, as light absorbing particles (LAP), particularly black carbon (BC) produced in forest fires get deposited throughout the snowpack, altering snowpack energy balance driving earlier snowmelt in burned forests. While SSA decreases, landscape snow albedo (LSA) increases following fire, as more of the snow-covered surface becomes visible beneath the burned forest canopy, brightening the …

Efficient Neuromorphic Algorithms For Gamma-Ray Spectrum Denoising And Radionuclide Identification, Merlin Phillip Carson

Dissertations and Theses

Radionuclide detection and identification are important tasks for deterring a potentially catastrophic nuclear event. Due to high levels of background radiation from both terrestrial and extraterrestrial sources, some form of noise reduction pre-processing is required for a gamma-ray spectrum prior to being analyzed by an identification algorithm so as to determine the identity of anomalous sources. This research focuses on the use of neuromorphic algorithms for the purpose of developing low power, accurate radionuclide identification devices that can filter out non-anomalous background radiation and other artifacts created by gamma-ray detector measurement equipment, along with identifying clandestine, radioactive material.

A sparse …

Catastrophic Beach Sand Losses Due To Erosion From Predicted Future Sea Level Rise (0.5–1.0 M), Based On Increasing Submarine Accommodation Spaces In The High-Wave-Energy Coast Of The Pacific Northwest, Washington, Oregon, And Northern California, Usa, Curt D. Peterson, Don Joseph Pettit, Kara E. P. Kingen, Sandy Vanderburgh, Chuck Rosenfeld

Geology Faculty Publications and Presentations

The U.S. Pacific Northwest (PNW) coastline (1000 km) has been analyzed for conditions that could impact beach erosion from potential near-future (100 year) sea level rise (SLR). Heavy mineral analysis of river, beach, and shelf samples (n = 105) establish the sources of the beach deposits. River bedload discharge and intervening estuarine sinks for river sand supplies (n = 31) were normalized to the one century time interval. Twenty-six subcell beaches (657 km in combined length) were surveyed (153 profiles) for beach sand widths (20–412 m) and sand cross-sectional areas (20–1810 m2 ) above wave-cut platforms and/or 0 m tidal …

Rotten Green Tests In Java, Pharo And Python, Vincent Aranega, Julien Delplanque, Matias Martinez, Andrew P. Black, Stéphane Ducasse, Anne Etien, Christopher Fuhrman, Guillermo Polito

Computer Science Faculty Publications and Presentations

Rotten Green Tests are tests that pass, but not because the assertions they contain are true: a rotten test passes because some or all of its assertions are not actually executed. The presence of a rotten green test is a test smell, and a bad one, because the existence of a test gives us false confidence that the code under test is valid, when in fact that code may not have been tested at all. This article reports on an empirical evaluation of the tests in a corpus of projects found in the wild. We selected approximately one hundred mature …

Rhyolite Stratigraphy Along Succor Creek: Insights Into The Eruptive History Of The Three Fingers And Mahogany Mountain Volcanic Field, Cassandra Caryl Black

Dissertations and Theses

The Mahogany Mountain and Three Fingers calderas with their associated tuffs, the tuff of Leslie Gulch and tuff of Spring Creek, respectively, were the centerpiece of a larger rhyolite center that developed in response to Columbia River Basalt volcanism as numerous other mid Miocene rhyolite centers in a corridor from Baker City in the north to northern Nevada. Previous studies suggest a two caldera model, while others advocated for a single large caldera producing solely the tuff of Leslie Gulch. This study refines the eruptive stratigraphy along the northeastern margin of this rhyolite field with important implications for the entire …

Investigation Of Environmental-Friendly, Membraneless Hydrogen Peroxide Fuel Cells, Bao Nguyen

Dissertations and Theses

Human-induced climate change is one of the biggest threats to humanity in the 21^st century. This is caused by the increase in greenhouse gas concentrations in the Earth's atmosphere. The burning of fossil fuels is the primary cause of climate change. This problem can be addressed by replacing fossil fuels with fuel sources that have clean by-products and are cost-effective. For the last few decades, hydrogen (H₂) has been extensively studied as an alternative to carbon-based fossil fuels. Currently, H₂ still has many shortcomings for commercial applications. The photocatalytic production of H₂ still suffers from …

Balanced Polymorphism Fuels Rapid Selection In An Invasive Crab Despite High Gene Flow And Low Genetic Diversity., C K. Tepolt, E D. Grosholz, Catherine E. De Rivera, G M. Ruiz

Environmental Science and Management Faculty Publications and Presentations

Adaptation across environmental gradients has been demonstrated in numerous systems with extensive dispersal, despite high gene flow and consequently low genetic structure. The speed and mechanisms by which such adaptation occurs remain poorly resolved, but are critical to understanding species spread and persistence in a changing world. Here, we investigate these mechanisms in the European green crab Carcinus maenas, a globally distributed invader. We focus on a northwestern Pacific population that spread across >12 degrees of latitude in 10 years from a single source, following its introduction 1,500 km, we examine genetic structure using 9,376 Single Nucleotide Polymorphisms (SNPs). We …

Simulating Dislocation Densities With Finite Element Analysis, Ja'nya Breeden, Dow Drake, Saurabh Puri

REU Final Reports

A one-dimensional set of nonlinear time-dependent partial differential equations developed by Acharya (2010) is studied to observe how differing levels of applied strain affect dislocation walls. The framework of this model consists of a convective and diffusive term which is used to develop a linear system of equations to test two methods of the finite element method. The linear system of partial differential equations is used to determine whether the standard or Discontinuous Galerkin method will be used. The Discontinuous Galerkin method is implemented to discretize the continuum model and the results of simulations involving zero and non-zero applied strain …

Digitally Reporting Trail Obstructions In Forest Park, Colton S. Maybee

REU Final Reports

The inclusion of technology on the trail can lead to better experiences for everyone involved in the hobby. Hikers can play a more prominent role in the maintenance of the trails by being able to provide better reports of obstructions while directly on the trail. This paper goes into the project of revamping the obstruction report system applied at Forest Park in Portland, Oregon. Most of my contributions to the project focus on mobile app development with some research into path planning algorithms related to the continuations of this project.

Forest Park Trail Monitoring, Adan Robles, Colton S. Maybee, Erin Dougherty

REU Final Reports

Forest Park, one of the largest public parks in the United States with over 40 trails to pick from when planning a hiking trip. One of the main problems this park has is that there are too many trails, and a lot of the trails extend over 3 miles. Due to these circumstances’ trails are not checked frequently and hikers are forced to hike trails in the area with no warnings of potential hazards they can encounter. In this paper I researched how Forest Park currently monitors its trails and then set up a goal to solve the problem. We …

Spatial Analysis Of Landscape Characteristics, Anthropogenic Factors, And Seasonality Effects On Water Quality In Portland, Oregon, Katherine Gelsey, Daniel Ramirez

REU Final Reports

Urban areas often struggle with deteriorated water quality as a result of complex interactions between landscape factors such as land cover, use, and management as well as climatic variables such as weather, precipitation, and atmospheric conditions. Green stormwater infrastructure (GSI) has been introduced as a strategy to reintroduce pre-development hydrological conditions in cities, but questions remain as to how GSI interacts with other landscape factors to affect water quality. We conducted a statistical analysis of six relevant water quality indicators in 131 water quality stations in four watersheds around Portland, Oregon using data from 2015 to 2021. Indiscriminate of station …