Physical Sciences and Mathematics Commons^™

Cellular Remains In A ~3.42-Billion-Year-Old Subseafloor Hydrothermal Environment, Barbara Cavalazzi, Laurence Lamelle, Alexandre Simionovici, Sherry L. Cady, Michael J. Russell, Elena Bailo, Roberto Canteri, Emanuele Enrico, Alain Manceau, Multiple Additional Authors

Geology Faculty Publications and Presentations

Subsurface habitats on Earth host an extensive extant biosphere and likely provided one of Earth’s earliest microbial habitats. Although the site of life’s emergence continues to be debated, evidence of early life provides insights into its early evolution and metabolic affinity. Here, we present the discovery of exceptionally well-preserved, ~3.42-billion-year-old putative filamentous microfossils that inhabited a paleo-subseafloor hydrothermal vein system of the Barberton greenstone belt in South Africa. The filaments colonized the walls of conduits created by low-temperature hydrothermal fluid. Combined with their morphological and chemical characteristics as investigated over a range of scales, they can be considered the oldest …

Stemloop-Finder: A Tool For The Detection Of Dna Hairpins With Conserved Motifs., Alyssa A. Pratt, Ellis L. Torrance, George W. Kasun, Kenneth M. Stedman, Ignacio De La Higuera

Center for Life in Extreme Environments Publications

Nucleic acid secondary structures play important roles in regulating biological processes. StemLoop-Finder is a computational tool to recognize and annotate conserved structural motifs in large data sets. The program is optimized for the detection of stem-loop structures that may serve as origins of replication in circular replication-associated protein (Rep)-encoding single-stranded (CRESS) DNA viruses.

Comparing Instruments For Measuring Runoff From Experimental Ecoroof Platforms: A Case Study On Test Plots At Portland State University, Chance F. Hodges

University Honors Theses

Stormwater management is a primary ecological benefit ecoroofs provide to ecosystems. Quantification of runoff from large scale ecoroofs is difficult to replicate, so researchers often utilize smaller experimental ecoroof platforms. This approach is becoming increasingly common, so it is useful to compare and contrast approaches for runoff measurement at the platform scale. This paper uses the four 17.86 m² ecoroof platforms located on the Science Research and Teaching Center (SRTC) at Portland State University (PSU) in Portland, OR as a case study. A unique condition of these platforms is that they are installed at grade on the roof with …

Application Of Topological Data Analysis To Multi-Resolution Matching Of Aerosol Optical Depth Maps, Dorcas Ofori-Boateng, Huikyo Lee, Krzysztof M. Gorski, Michael J. Garay, Yulia R. Gel

Mathematics and Statistics Faculty Publications and Presentations

Topological data analysis (TDA) combines concepts from algebraic topology, machine learning, statistics, and data science which allow us to study data in terms of their latent shape properties. Despite the use of TDA in a broad range of applications, from neuroscience to power systems to finance, the utility of TDA in Earth science applications is yet untapped. The current study aims to offer a new approach for analyzing multi-resolution Earth science datasets using the concept of data shape and associated intrinsic topological data characteristics. In particular, we develop a new topological approach to quantitatively compare two maps of geophysical variables …

Universal Biological Motions For Educational Robot Theatre And Games, Rajesh Venkatachalapathy, Martin Zwick, Adam Slowik, Kai Brooks, Mikhail Mayers, Roman Minko, Tyler Hull, Bliss Brass, Marek Perkowski

Complex Systems Faculty Publications and Presentations

Paper presents a concept that is new to robotics education and social robotics. It is based on theatrical games, in motions for social robots and animatronic robots. Presented here motion model is based on Drift Differential Model from biology and Fokker-Planck equations. This model is used in various areas of science to describe many types of motion. The model was successfully verified on various simulated mobile robots and a motion game of three robots called "Mouse and Cheese."

Self-Contained Photon Coincidence Counting With Ni Myrio Ecosystem, Georges Oates Larsen, Andres H. La Rosa

University Honors Theses

Digital coincidence counting units (CCU) have made experimental verification of fundamental quantum mechanical principles financially accessible to undergraduate level teaching programs. However, recent implementations of these systems are not easily ported to National Instruments (NI) FPGAs, making them unsuitable for physics departments that have heavily invested in the NI ecosystem. Therefore, there is clear need for a detailed implementation based on an NI FPGA. We present a formal description of one such implementation, based on the NI myRIO (NI's lower-cost, student-oriented offering) which achieves 6.9 ns minimum guaranteed-distinguishable delay and 32.2 MHz peak coincidence counting rate with four input channels …

Functional Role Of The N-Terminal Domain In Connexin 46/50 By In Silico Mutagenesis And Molecular Dynamics Simulation, Umair Khan

University Honors Theses

Connexins form intercellular channels known as gap junctions that facilitate diverse physiological roles, from long-range electrical and chemical coupling to nutrient exchange. Recent structural studies on Cx46 and Cx50 have defined a novel and stable open state and implicated the amino-terminal (NT) domain as a major contributor to functional differences between connexin isoforms. This thesis presents two studies which use molecular dynamics simulations with these new structures to provide mechanistic insight into the function and behavior of the NTH in Cx46 and Cx50. In the first, residues in the NTH that differ between Cx46 and Cx50 are swapped between the …

Case Study Of Scrum Methodology As Used By A Capstone Team, Lilly I. Yeaton

University Honors Theses

Scrum is widely used in the software industry to manage all kinds of projects. This case study examines the way in which a capstone team used the methodology and models the specific project management processes they used over the course of their project. These models and the process modifications therein are then compared to the team’s velocity at different points in the project. The results of this analysis suggest a correlation between asynchronous daily meetings and sprint reviews and improved velocity.

Automated Decision Making And Machine Learning: Regulatory Alternatives For Autonomous Settings, Alyssa Heminger

University Honors Theses

Given growing investment capital in research and development, accompanied by extensive literature on the subject by researchers in nearly every domain from civil engineering to legal studies, automated decision-support systems (ADM) are likely to see a place in the foreseeable future. Artificial intelligence (AI), as an automated system, can be defined as a broad range of computerized tasks designed to replicate human neural networks, store and organize large quantities of information, detect patterns, and make predictions with increasing accuracy and reliability. By itself, artificial intelligence is not quite science-fiction tropes (i.e. an uncontrollable existential threat to humanity) yet not without …

Do Secondary Cyclones Increase The Category Scale Of Atmospheric Rivers?, Edgar Sanchez Fausto

University Honors Theses

Atmospheric rivers (ARs) play a crucial role in delivering precipitation worldwide. This makes them an important phenomenon for water resource specialists to study. One such interest is to understand what mechanisms make ARs produce significant rainfall and associated hazards such as flooding. One possible mechanism is that AR duration or intensity may increase when it interacts with a secondary cyclone, either of which can increase the AR category scale. The purpose of this study is to determine whether AR and secondary cyclone interactions increase the category scale ARs. Out of 52 AR events analyzed, 32 events contained at least one …

Literature Review: Pollutant Removal Efficacy Of Floating Treatment Wetlands Across Water Bodies, Sophie Johnson

University Honors Theses

Wetland numbers are declining worldwide and there is a need to replace the water filtration services they provide. One emerging option is floating treatment wetlands (FTW). FTW are a floating mat that serves as a habitat for aquatic plants whose roots are suspended in the water and that remove both organic and inorganic pollutants like nutrients (nitrogen and phosphorus), potentially toxic metals, and suspended solids. A literature search was performed to examine the efficacy of FTW pollutant removal. Specifically, I inspected 1) how effective FTW are at removing a range of nutrients; 2) what types of plants are most effective …

A Study Of Stable Isotopes In Snow On Mt. Hood, Oregon, Maya Felix

University Honors Theses

Over the 2020-2021 Winter, event-based and end-of-season snow samples were collected on Mt. Hood near Government Camp, OR and analyzed for their stable isotopic compositions of ¹⁸O and ²H. It was found that surficial snow collected through the winter had higher variation in isotopic values than samples from a snow pit collected in spring. This suggests homogenization occurred in the snowpack over the season from snow metamorphism, sublimation, and/or melting. Homogenization of the snowpack will likely become more pronounced as temperatures increase and rain falls more often than snow due to climate change. Research that utilizes the snowpack …

Soft Lithographic Replication Of High Length-Scale Micropillars From Laser-Ablated Fused-Silica Templates, Jason Pitts

University Honors Theses

Soft lithography is a well-established route to wafer-scale reproduction of micro- and nanoscale features in a wide variety of materials. Nevertheless, micron length scales have yet to be explored, despite the potential utility of such structures. Here, polymer micropillars of 6-12 μm length, approximately 0.5-1.5 μm wide at 10 μm spacing are reproduced from a polydimethylsiloxane (PDMS) mold made from patterned cellulose acetate (CA). The patterned CA was cast from a rigid fused silica template machined by a pulsed femtosecond laser. Pore topographic features were successfully reproduced in Norland Optical Adhesive (NOA), polycaprolactone (PCL), Nafion, acrylonitrile butadiene styrene (ABS), and …

Understanding Ransomware Trajectory To Create An Informed Prediction, J. D. Klusnick

University Honors Theses

Ransomware is a form of extortion in which digital files are rendered inaccessible until a ransom payment is made. Modern ransomware emerged in 2006 and its destructive influence has been expanding ever since. In recent years cybercriminals have evolved who they target, what computer systems they target, and how they infect those systems. Meanwhile, cybersecurity experts have modelled ransomware methods allowing them to innovate their defense techniques across three paradigms: recovery, detection, and prevention. Ultimately either ransomware attackers or ransomware defenders will dominate this ongoing conflict. A review of the literature indicates that the ransomware crime wave will likely be …

Efficacy Of Ryr2 Inhibitor El20 In Induced Pluripotent Stem Cell-Derived Cardiomyocytes From A Patient With Catecholaminergic Polymorphic Ventricular Tachycardia., Tarah A. Word, Ann P. Quick, Christina Y. Miyake, Mayra K. Shak, Xiaolu Pan, Jean J. Kim, Hugh D. Allen, Martha Sibrian-Vazquez, Robert M. Strongin, Andrew P. Landstrom, Xander H T Wehrens

Chemistry Faculty Publications and Presentations

Catecholaminergic polymorphic ventricular tachycardia (CPVT) is an inherited cardiac arrhythmia syndrome that often leads to sudden cardiac death. The most common form of CPVT is caused by autosomal-dominant variants in the cardiac ryanodine receptor type-2 (RYR2) gene. Mutations in RYR2 promote calcium (Ca ) leak from the sarcoplasmic reticulum (SR), triggering lethal arrhythmias. Recently, it was demonstrated that tetracaine derivative EL20 specifically inhibits mutant RyR2, normalizes Ca handling and suppresses arrhythmias in a CPVT mouse model. The objective of this study was to determine whether EL20 normalizes SR Ca handling and arrhythmic events in induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) …

Total Synthesis And Antimalarial Activity Of 2-(-Hydroxybenzyl)-Prodigiosins, Isoheptylprodigiosin, And Geometric Isomers Of Tambjamine Myp1 Isolated From Marine Bacteria., Papireddy Kancharla, Yuexin Li, Monish Yeluguri, Rozalia A. Dodean, Kevin A. Reynolds, Jane X. Kelly

Chemistry Faculty Publications and Presentations

Highly efficient and straightforward synthetic routes toward the first total synthesis of 2-(-hydroxybenzyl)-prodigiosins (-), isoheptylprodigiosin (), and geometric isomers of tambjamine MYP1 ((/)-) have been developed. The crucial steps involved in these synthetic routes are the construction of methoxy-bipyrrole-carboxaldehydes (MBCs) and a 20-membered macrocyclic core and a regioselective demethylation of MBC analogues. These new synthetic routes enabled us to generate several natural prodiginines - in larger quantity. All of the synthesized natural products exhibited potent asexual blood-stage antiplasmodial activity at low nanomolar concentrations against a panel of parasites, with a great therapeutic index. Notably, prodiginines and - provided curative in …

Numerical Techniques And Simulations For Studying Various High Power Optical Fiber Amplifiers, Particularly For Ytterbium (Yb+3), And Thulium (Tm+3) Doped Fibers, Tathagata Goswami

Dissertations and Theses

In this dissertation we present a simplified scalar numerical model, derived from Maxwell's field equations, for the fiber laser amplifier simulations. Maxwell's equations are reduced using a technique called Coupled Mode Theory (CMT).

The reduced model is made more efficient through a new scale model, referred to as an equivalent short fiber, which captures some of the essential characteristics of a longer fiber. The equivalent short fiber can be viewed as a fiber made using artificial (nonphysical) material properties that in some sense compensates for its reduced length. The computations can be accelerated by a factor approximately equal to the …

A Method For Comparative Analysis Of Trusted Execution Environments, Stephano Cetola

Dissertations and Theses

The problem of secure remote computation has become a serious concern of hardware manufacturers and software developers alike. Trusted Execution Environments (TEEs) are a solution to the problem of secure remote computation in applications ranging from "chip and pin" financial transactions to intellectual property protection in modern gaming systems. While extensive literature has been published about many of these technologies, there exists no current model for comparing TEEs. This thesis provides hardware architects and designers with a set of tools for comparing TEEs. I do so by examining several properties of a TEE and comparing their implementations in several technologies. …

Tellurorhodamine Photocatalysts In Aerobic Oxidation Reactions: Development Of Synthetic Methods And Reaction Mechanisms, Irving D. Rettig

Dissertations and Theses

Aerobic oxidation photocatalysis involves the use of oxygen as an oxidant species, coupled to a light driven catalyst to achieve useful chemical transformations. Catalytic aerobic oxidation reactions can be defined as either oxidase-like, in which O₂ acts as an electron donor/acceptor but is not incorporated into the reaction products, or oxygenase-like where O₂ acts as an electron donor/acceptor and is incorporated into the reaction products. A multitude of inorganic catalysts have been developed that can achieve a wide scope of oxidase-like or oxygenase-like reactivity, however, it is rare for a catalyst to be capable of both. We report …

A Community Of Fear: Emotion And The Hydro-Social Cycle In East Porterville, Michael Egge

Geography Masters Research Papers

Broader governance challenges driving water insecurity globally are well documented in the literature, however the power-laden relationships and emotions that shape water access at the household and community levels are yet to be fully investigated, especially in the context of water consolidation projects. In this article, we examine the role of emotions in mediating access to water and in the production of resource struggles among marginalized communities existing outside of conventional regulatory frameworks. We bring together two relational approaches – the hydro-social cycle and emotional political ecology – to examine water insecurity and how it manifests in the historically disadvantaged …

Investigations Into Size And Surface Control Of Silicon Nanocrystals For Improved Optical Properties, James Donald Barnes

Dissertations and Theses

The discovery of visible photoluminescence (PL) from nanocrystalline porous silicon in 1990 led to extensive research into the mechanisms of the emergent properties, and optimization of these properties, for use in applications. The widespread use of silicon nanoparticles (Si NPs) in commercial applications is currently limited by three main factors: 1) poor radiative recombination efficiency of the interband transition, 2) instability of the interband photoluminescence, and 3) a lack of scalable methods for producing Si NPs that are both highly crystalline and size monodisperse.

To address these limitations, this dissertation correlates changes in the photoluminescence properties of hydrogen passivated silicon …

Understory Species Increase Project: Investigating The Revegetation Of Native Herbaceous Species From Seed In Urban Forest Fragments, Erin Mcelroy

Environmental Science and Management Professional Master's Project Reports

Management of urban forest fragments often aims to reduce invasive species and promote native species abundance and diversity. Often, these environments lack natural establishment of native forest species, including herbaceous species that are especially sensitive to site conditions. While herbaceous understory species may represent a small proportion of forest biomass, they perform important functions within forest environments, including nutrient cycling, erosion and runoff control, and providing habitat for wildlife, as well as hosting the greatest biodiversity among other forest strata. However, many restoration projects focus primarily on the revegetation of dominant woody forest species, such as hardwood trees and shrubs. …

Current Stormwater Practices And Future Implementation At Portland State University With The Uncertainty Of Climate Change, Evan Suemori, Alexandra Vargas Quiñones

Environmental Science and Management Professional Master's Project Reports

Stormwater runoff is one of the most critical environmental issues in urban areas and is only expected to worsen as climate change persists (EPA, 2016). When precipitation events occur, stormwater travels across impervious surfaces collecting soils and pollutants which can negatively impact water quality in receiving waters. Additionally, stormwater has human health impacts, specifically through flooding and the contamination of drinking water. According to the Intergovernmental Panel on Climate Change (IPCC), it has been determined that climate change will increase the frequency, intensity, and/or number of precipitation events in some regions, including the Pacific Northwest, and decrease in others (IPCC, …

Influence Of Climate Change On Forest Fire Occurrence And Distribution Of Sri Lanka And Modeling Of Forest Fire, Mohan Heenatigala

Environmental Science and Management Professional Master's Project Reports

Forest fire is one of the main causes for forest degradation and deforestation which affect ecosystem services provided by the given landscapes. Weather variables like temperature, wind speed and direction, rainfall, and relative humidity also govern the forest fire regime and vulnerability. On the other hand, forest fuel characteristics, human impacts, population density, forest canopy density, slope, elevation, road density, closeness to the human settlement areas are other factors that determine the forest fire impact and potential of damage. Annually, 100 to 2500 hectares of forest resources are damaged due to forest fires in Sri Lanka. From the past few …

Economic Valuation Of Ecosystem Services Provided By Forest Ecosystems In Sri Lanka: A Study Based On 2010 Forest Cover Classification And The Teeb Database, Isuru Jayantha Alawaththa Kankanamge

Environmental Science and Management Professional Master's Project Reports

Ecosystem service valuation is becoming popular among the economists, ecologists, scientists and policy makers. As a result, various research, publications and programs have arisen and content of literature is developed rapidly. Even though this field of study is developing rapidly, Sri Lankan ecosystems have not yet been valued or evaluated yet in terms of economic returns. Hence, the main purpose of this study is to calculate and define economic value for each forest polygon of 2010 forest cover data base by using the value transferring approach. This data base will be an effective tool to have a fair cost-benefits analyses …

The Spatial And Temporal Evolution Of The Portland And Tualatin Forearc Basins, Oregon, Usa, Darby P. Scanlon, John Bershaw, Ray E. Wells, Ashley R. Streig

Geology Faculty Publications and Presentations

The Portland and Tualatin basins are part of the Salish-Puget-Willamette Lowland, a 900-km-long, forearc depression lying between the volcanic arc and the Coast Ranges of the Cascadia convergent margin. Such inland seaways are characteristic of warm, young slab subduction. We analyzed the basins to better understand their evolution and relation to Coast Range history and to provide an improved tectonic framework for the Portland metropolitan area. We model three key horizons in the basins: (1) the top of the Columbia River Basalt Group (CRBG), (2) the bottom of the CRBG, and (3) the top of Eocene basement. Isochore maps constrain …

Multilevel Hierarchical Decomposition Of Finite Element White Noise With Application To Multilevel Markov Chain Monte Carlo, Hillary R. Fairbanks, Umberto E. Villa, Panayot S. Vassilevski

Mathematics and Statistics Faculty Publications and Presentations

In this work we develop a new hierarchical multilevel approach to generate Gaussian random field realizations in an algorithmically scalable manner that is well suited to incorporating into multilevel Markov chain Monte Carlo (MCMC) algorithms. This approach builds off of other partial differential equation (PDE) approaches for generating Gaussian random field realizations; in particular, a single field realization may be formed by solving a reaction-diffusion PDE with a spatial white noise source function as the right-hand side. While these approaches have been explored to accelerate forward uncertainty quantification tasks, e.g., multilevel Monte Carlo, the previous constructions are not directly applicable …

Agency, Sense Of Place, And Knowledge On The Zumwalt Prairie: A Social Study Of Place-Based Conservation And Resilience, Dana Elyse Hellman

Dissertations and Theses

Shifting and often diminishing environmental conditions, due to climate change, resource loss, and ecosystem degradation, pose a significant concern to both social and ecological systems. The field of conservation science has attempted to address environmental threats through varying approaches, transitioning from fortress conservation and complete human exclusion to community-based and co-managed models which incorporate human actors and social dimensions in the conservation process. The latest iteration of conservation scholarship, place-based conservation, is deeply rooted in interdisciplinary, social scientific thinking, and calls for significant practitioner engagement with local knowledge, practices, social constructions, and place meanings. It is an approach which emphasizes …

Photoemission Electron Microscopy For Direct Observation Of Photonic And Plasmonic Phenomena, Theodore Stenmark

Dissertations and Theses

Photoemission electron microscopy (PEEM) is a high-resolution microscopy technique that collects photoemitted electrons from the sample surface to form an image. PEEM offers a non-scanning imaging method with a spatial resolution in the range of 5-100nm by combining the advantages of light excitation and electron imaging. Our work looks at PEEM as an analysis tool for photonic and plasmonic phenomena. Photonic wave guiding structures exhibiting a strong dispersion relation have attracted considerable attention for applications in integrated optics, communications and sensing devices. Line defects in a photonic crystal (PC) slab offer a highly efficient way to create light with group …

Urban Lakes: Ecosystem Services And Management, Laura Costadone

Dissertations and Theses

Lakes provide a variety of ecosystem services and benefits that greatly contribute to urban sustainability. Despite the growing interest in integrating freshwater systems into management and policy decisions, urban lakes are often overlooked in land-use planning. Nutrient and pollutant runoff from the surrounding urbanized watershed result in water quality deterioration that negatively impact the lake ecological functions and related ecosystem services. The vulnerability and degradation of these urban ecosystems should be a matter of concern, especially considering that, in rapidly growing metropolitan areas, the demand for aesthetic and recreational services provided by urban lakes is increasing. The overall goal of …