Physical Sciences and Mathematics Commons^™

Application Of Numerical Modeling To Study River Dynamics: Hydro-Geomorphological Evolution Due To Extreme Events In The Sandy River, Oregon, Sarkawt Hamarahim Muhammad

Dissertations and Theses

The Sandy River (OR) is a coastal tributary of the Columbia River and has a steep hydroshed 1316 square kilometers which is located on the western side of Mount Hood (elevation range 3 m to 1800 m). The system exhibits highly variable flow: Its average discharge is ~40 m³/s, and the highest recorded discharge was 1739 m³/s in 1964. In this study I model the geomorphic sensitivity of an 1800m reach located the downstream of the former Marmot Dam, which was removed in 2007. The hydro-geomorphic response to major flood has implications for system management and …

Root-Enhanced Infiltration In Stormwater Bioretention Facilities In Portland, Oregon, Ted David Hart

Dissertations and Theses

I evaluated the effectiveness of plant roots to increase infiltration rates within stormwater bioretention facilities (SBFs), roadside planter compartments that filter stormwater. SBFs attenuate harmful effects of stormwater by reducing peak flow and retaining pollutants, with increased infiltration that improves both these functions. Researchers have shown that roots can increase infiltration within greenhouse, lab, field, and test SBF settings. However, no researchers have yet measured either the extent to which different root characteristics can increase infiltration or the variation in root characteristics and their effect on infiltration rates among plant assemblages within currently functioning SBFs.

To determine if root-enhanced infiltration …

Synthesis And Characterization Of The 2-Dimensional Transition Metal Dichalcogenides, Robert Browning

Dissertations and Theses

In the last 50 years, the semiconductor industry has been scaling the silicon transistor to achieve faster devices, lower power consumption, and improve device performance. Transistor gate dimensions have become so small that short channel effects and gate leakage have become a significant problem. To address these issues, performance enhancement techniques such as strained silicon are used to improve mobility, while new high-k gate dielectric materials replace silicon oxide to reduce gate leakage. At some point the fundamental limit of silicon will be reached and the semiconductor industry will need to find an alternate solution. The advent of graphene led …

Power-Aware Datacenter Networking And Optimization, Qing Yi

Dissertations and Theses

Present-day datacenter networks (DCNs) are designed to achieve full bisection bandwidth in order to provide high network throughput and server agility. However, the average utilization of typical DCN infrastructure is below 10% for significant time intervals. As a result, energy is wasted during these periods. In this thesis we analyze traffic behavior of datacenter networks using traces as well as simulated models. Based on the insight developed, we present techniques to reduce energy waste by making energy use scale linearly with load. The solutions developed are analyzed via simulations, formal analysis, and prototyping. The impact of our work is significant …

Mass Exchange Dynamics Of Surface And Subsurface Oil In Shallow-Water Transport, Saeed Moghimi, Jorge Ramirez, Juan M. Restrepo, Shankar Venkataramani

Civil and Environmental Engineering Faculty Publications and Presentations

We formulate a model for the mass exchange between oil at and below the sea surface. This is a particularly important aspect of modeling oil spills. Surface and subsurface oil have different chemical and transport characteristics and lumping them together would compromise the accuracy of the resulting model. Without observational or computational constraints, it is thus not possible to quantitatively predict oil spills based upon partial field observations of surface and/or sub-surface oil. The primary challenge in capturing the mass exchange is that the principal mechanisms are on the microscale. This is a serious barrier to developing practical models for …

Benzene Formation In Electronic Cigarettes, James F. Pankow, Kilsun Kim, Kevin J. Mcwhirter, Wentai Luo, Jorge O. Escobedo, Robert M. Strongin, Anna K. Duell, David H. Peyton

Chemistry Faculty Publications and Presentations

The heating of the fluids used in electronic cigarettes (“e-cigarettes”) used to create “vaping” aerosols is capable of causing a wide range of degradation reaction products. We investigated formation of benzene (an important human carcinogen) from e-cigarette fluids containing propylene glycol (PG), glycerol (GL), benzoic acid, the flavor chemical benzaldehyde, and nicotine.

Mechanism And Catalytic Strategy Of The Prokaryotic Specific Gtp Cyclohydrolase Ib, Naduni Paranagama, Shilah A. Bonnett, Jonathan Alvarez, Amit Luthra, Boguslaw Stec, Andrew Gustafson, Dirk Iwata-Reuyl, Manal A. Swairjo

Chemistry Faculty Publications and Presentations

GTP cyclohydrolase I catalyzes the first step in folic acid biosynthesis in bacteria and plants, biopterin biosynthesis in mammals, and the biosynthesis of 7-deazaguanosine modified tRNA nucleosides in bacteria and archaea. The type IB GTP cyclohydrolase (GCYH-IB) is a prokaryotic-specific enzyme found in a number of pathogens. GCYH-IB is structurally distinct from the canonical type IA GTP cyclohydrolase involved in biopterin biosynthesis in humans and animals, and thus is of interest as a potential antibacterial drug target. We report kinetic and inhibition data of Neisseria gonorrhoeae GCYH-IB, and two high-resolution crystal structures of the enzyme; one in complex with the …

Protection Of The Queuosine Biosynthesis Enzyme Quef From Irreversible Oxidation By A Conserved Intramolecular Disulfide, Adeba Mohammad, Adriana Bon Ramos, Bobby W.K. Lee, Spencer William Cohen, Maryam K. Kiani, Dirk Iwata-Reuyl, Boguslaw Stec, Manal A. Swairjo

Chemistry Faculty Publications and Presentations

QueF enzymes catalyze the nicotinamide adenine dinucleotide phosphate (NADPH)-dependent reduction of the nitrile group of 7-cyano-7-deazaguanine (preQ0) to 7-aminomethyl-7-deazaguanine (preQ1) in the biosynthetic pathway to the tRNA modified nucleoside queuosine. The QueF-catalyzed reaction includes formation of a covalent thioimide intermediate with a conserved active site cysteine that is prone to oxidation in vivo. Here, we report the crystal structure of a mutant of Bacillus subtilis QueF, which reveals an unanticipated intramolecular disulfide formed between the catalytic Cys55 and a conserved Cys99 located near the active site. This structure is more symmetric than the substrate-bound structure and exhibits major rearrangement of …

Nesterov's Smoothing Technique And Minimizing Differences Of Convex Functions For Hierarchical Clustering, Mau Nam Nguyen, Wondi Geremew, Sam Raynolds, Tuyen Tran

Mathematics and Statistics Faculty Publications and Presentations

A bilevel hierarchical clustering model is commonly used in designing optimal multicast networks. In this paper we will consider two different formulations of the bilevel hierarchical clustering problem -- a discrete optimization problem which can be shown to be NP-hard. Our approach is to reformulate the problem as a continuous optimization problem by making some relaxations on the discreteness conditions. This approach was considered by other researchers earlier, but their proposed methods depend on the square of the Euclidian norm because of its differentiability. By applying the Nesterov smoothing technique and the DCA -- a numerical algorithm for minimizing differences …

Using Satellite Observations To Characterize The Response Of Estuarine Turbidity Maxima To External Forcing, Austin S. Hudson, Stefan A. Talke, David A. Jay

Civil and Environmental Engineering Faculty Publications and Presentations

This study explores the spatial and temporal character of turbidity maxima in the Columbia River Estuary (CRE) using satellite observations. Surface reflectance data measured by the Moderate Imaging Spectroradiometer (MODIS) were calibrated against in situ measurements of surface turbidity (R2 = 0.85 for 205 measurements). More than 1500 satellite images from 2000 to 2015 were then conditionally sampled to explore the physical processes that drive the spatial distribution of the turbidity field. We find satellite measurements are able to describe seasonal, spring–neap, and spatial features of the estuarine turbidity maxima (ETM) that are not easily observable by other means. System-wide …

Some Remarks On Interpolation And Best Approximation, Randolph E. Bank, Jeffrey S. Ovall

Mathematics and Statistics Faculty Publications and Presentations

Sufficient conditions are provided for establishing equivalence between best approximation error and projection/interpolation error in finite-dimensional vector spaces for general (semi)norms. The results are applied to several standard finite element spaces, modes of interpolation and (semi)norms, and a numerical study of the dependence on polynomial degree of constants appearing in our estimates is provided.

Space-Time Cfosls Methods With Amge Upscaling, Martin Neumüller, Panayot Vassilevski, Umberto E. Villa

Mathematics and Statistics Faculty Publications and Presentations

This work considers the combined space-time discretization of time-dependent partial differential equations by using first order least square methods. We also impose an explicit constraint representing space-time mass conservation. To alleviate the restrictive memory demand of the method, we use dimension reduction via accurate element agglomeration AMG coarsening, referred to as AMGe upscaling. Numerical experiments demonstrating the accuracy of the studied AMGe upscaling method are provided.

Network Analysis Of Wildfire Transmission And Implications For Risk Governance, Alan A. Ager, Cody Evers, Michelle A. Day, Haiganoush K. Preisler, Ana M.G. Barros, Max Nielsen-Pincus

Environmental Science and Management Faculty Publications and Presentations

We characterized wildfire transmission and exposure within a matrix of large land tenures (federal, state, and private) surrounding 56 communities within a 3.3 million ha fire prone region of central Oregon US. Wildfire simulation and network analysis were used to quantify the exchange of fire among land tenures and communities and analyze the relative contributions of human versus natural ignitions to wildfire exposure. Among the land tenures examined, the area burned by incoming fires averaged 57% of the total burned area. Community exposure from incoming fires ignited on surrounding land tenures accounted for 67% of the total area burned. The …

The Influence Of Föhn Winds On Glacial Lake Washburn And Palaeotemperatures In The Mcmurdo Dry Valleys, Antarctica, During The Last Glacial Maximum, Maciej Obryk, Peter Doran, Ed Waddington, Chris Mckay

Geology Faculty Publications and Presentations

Large glacial lakes, including Glacial Lake Washburn, were present in the McMurdo Dry Valleys, Antarctica, during the Last Glacial Maximum (LGM) despite a colder and drier climate. To address the mechanism capable of generating enough meltwater to sustain these large lakes, a conceptual model was developed based on the warming potential of infrequent contemporary föhn winds. The model suggests that föhn winds were capable of generating enough meltwater to sustain large glacial lakes during the LGM by increasing degree days above freezing (DDAF) and prolonging the melt season. A present-day relationship between infrequent summer föhn winds and DDAF was established. …

Ground-Rupturing Earthquakes On The Northern Big Bend Of The San Andreas Fault, California, 800 A.D. To Present, Katherine Scharer, Ray J. Weldon Ii, Glenn Biasi, Ashley Streig, Thomas Fumal

Geology Faculty Publications and Presentations

Paleoseismic data on the timing of ground-rupturing earthquakes constrain the recurrence behavior of active faults and can provide insight on the rupture history of a fault if earthquakes dated at neighboring sites overlap in age and are considered correlative. This study presents the evidence and ages for 11 earthquakes that occurred along the Big Bend section of the southern San Andreas Fault at the Frazier Mountain paleoseismic site. The most recent earthquake to rupture the site was the Mw7.7–7.9 Fort Tejon earthquake of 1857. We use over 30 trench excavations to document the structural and sedimentological evolution of a small …

Electrical Properties Of Covalently Functionalized Graphene, Paul Plachinda, David Evans, Raj Solanki

Physics Faculty Publications and Presentations

We have employed first-principle calculations to study transformation of graphene’s electronic structure under functionalization by covalent bonds with different atomic and molecular groups - epoxies, amines, PFPA. It is shown that this functionalization leads to an opening in the graphene’s band gap on order of tens meV, but also leads to reduction of electrical conductivity. We also discuss the influence of charge exchange between the functionalizing molecule and graphene’s conjugated electrons on electron transport properties.

Watershed Response To Climate Change And Fire-Burns In The Upper Umatilla River Basin, Usa, Kimberly Crystal Yazzie, Heejun Chang

Geography Faculty Publications and Presentations

This study analyzed watershed response to climate change and forest fire impacts in the upper Umatilla River Basin (URB), Oregon, using the precipitation runoff modeling system. Ten global climate models using Coupled Intercomparison Project Phase 5 experiments with Representative Concentration Pathways (RCP) 4.5 and 8.5 were used to simulate the effects of climate and fire-burns on runoff behavior throughout the 21st century. We observed the center timing (CT) of flow, seasonal flows, snow water equivalent (SWE) and basin recharge. In the upper URB, hydrologic regime shifts from a snow-rain-dominated to rain-dominated basin. Ensemble mean CT occurs 27 days earlier in …

Hydrodynamic And Water Quality Modeling Of The Chehalis River Using Ce-Qual-W2, Sarah Van Glubt

Dissertations and Theses

The Chehalis River Basin is located in the southwest region of Washington State, originating in the Olympic Mountains and flowing to Grays Harbor and the Pacific Ocean. The Chehalis River is over 125 miles, exists within five counties, and flows through agricultural, residential, industrial, and forest land areas. Four major rivers discharge to the Chehalis River, as well as many smaller creeks, five wastewater treatment plants, and groundwater flows.

Flooding is a major problem in the relatively flat areas surrounding the cities of Chehalis and Centralia, with severe consequences for property, safety and transportation. As a result, construction of a …

Solvent Chemistry In The Electronic Cigarette Reaction Vessel, Robert Paul Jensen, Robert M. Strongin, David H. Peyton

Chemistry Faculty Publications and Presentations

Knowledge of the mechanism of formation, levels and toxicological profiles of the chemical products in the aerosols (i.e., vapor plus particulate phases) of e-cigarettes is needed in order to better inform basic research as well as the general public, regulators, and industry. To date, studies of e-cigarette emissions have mainly focused on chromatographic techniques for quantifying and comparing the levels of selected e-cigarette aerosol components to those found in traditional cigarettes. E-cigarettes heat and aerosolize the solvents propylene glycol (PG) and glycerol (GLY), thereby affording unique product profiles as compared to traditional cigarettes. The chemical literature strongly suggests that there …

Holocene History Of Deep-Seated Landsliding In The North Fork Stillaguamish River Valley From Surface Roughness Analysis, Radiocarbon Dating, And Numerical Landscape Evolution Modeling, Adam M. Booth, Sean R. Lahusen, Alison R. Duvall, David R. Montgomery

Geology Faculty Publications and Presentations

Documenting spatial and temporal patterns of past landsliding is a challenging step in quantifying the effect of landslides on landscape evolution. While landslide inventories can map spatial distributions, lack of dateable material, landslide reactivations, or time, access, and cost constraints generally limit dating large numbers of landslides to analyze temporal patterns. Here we quantify the record of the Holocene history of deep-seated landsliding along a 25 km stretch of the North Fork Stillaguamish River valley, Washington State, USA, including the 2014 Oso landslide, which killed 43 people. We estimate the ages of more than 200 deep-seated landslides in glacial sediment …

Divergent Trends In Ecosystem Services Under Different Climate-Management Futures In A Fire-Prone Forest Landscape, Joshua S. Halofsky, Jessica E. Halofsky, Miles A. Hemstrom, Anita T. Morzillo, Xiaoping Zhou, Daniel C. Donato

Institute for Natural Resources Publications

While ecosystem services and climate change are often examined independently, quantitative assessments integrating these fields are needed to inform future land management decisions. Using climate-informed state-and-transition simulations, we examined projected trends and trade-offs for a suite of ecosystem services under four climate change scenarios and two management scenarios (active management emphasizing fuel treatments and no management other than fire suppression) in a fire-prone landscape of dry and moist mixed-conifer forests in central Oregon, USA. Focal ecosystem services included fire potential (regulating service), timber volume (provisioning service), and potential wildlife habitat (supporting service). Projections without climate change suggested active management in …

Incorporating Sociocultural Phenomena Into Ecosystem-Service Valuation: The Importance Of Critical Pluralism, Carena J. Van Riper, Adam C. Landon, Sarah Kidd, Patrick Bitterman, Lee A. Fitzgerald, Elise F. Granek, Sonia Ibarra, David Iwaniec, Christopher Raymond, David Toledo

Environmental Science and Management Faculty Publications and Presentations

Ecosystem-services scholarship has largely focused on monetary valuation and the material contributions of ecosystems to human well-being. Increasingly, research is calling for a deeper understanding of how less tangible, nonmaterial values shape management and stakeholder decisions. We propose a framework that characterizes a suite of sociocultural phenomena rooted in key social science disciplines that are currently underrepresented in the ecosystem-services literature. The results from three example studies are presented to demonstrate how the tenets of this conceptual model can be applied in practice. We consider the findings from these studies in light of three priorities for future research: (1) complexities …

Forest Management Scenarios In A Changing Climate: Trade-Offs Between Carbon, Timber, And Old Forest, Robert M. Scheller, Megan K. Creutzburg, Melissa S. Lucash, Stephen D. Leduc, Mark G. Johnson

Environmental Science and Management Faculty Publications and Presentations

Balancing economic, ecological, and social values has long been a challenge in the forests of the Pacific Northwest, where conflict over timber harvest and old-growth habitat on public lands has been contentious for the past several decades. The Northwest Forest Plan, adopted two decades ago to guide management on federal lands, is currently being revised as the region searches for a balance between sustainable timber yields and habitat for sensitive species. In addition, climate change imposes a high degree of uncertainty on future forest productivity, sustainability of timber harvest, wildfire risk, and species habitat. We evaluated the long-term, landscape-scale trade-offs …

Increased Habitat Connectivity Homogenizes Freshwater Communities: Historical And Landscape Perspectives, Angela L. Strecker, Jeffrey Thomas Brittain

Environmental Science and Management Faculty Publications and Presentations

1. Increases in habitat connectivity can have consequences for taxonomic, functional, and genetic diversity of communities. Previously isolated aquatic habitats were connected with canals and pipelines in the largest water development project in the US history, the Columbia Basin Project (CBP; eastern Washington, USA), which also altered environmental conditions; however, the ecological consequences are largely unknown.

2. Using a historical dataset, we examined long-term patterns in zooplankton communities, water chemistry and clarity, testing the hypothesis that increased connectivity will result in taxonomic homogenization. Further, we tested contemporary drivers of communities using a comprehensive set of environmental and landscape variables.

3. Waterbodies were sampled …

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Legacies Of Stream Channel Modification Revealed Using General Land Office Surveys, With Implications For Water Temperature And Aquatic Life, Seth M. White, Casey Justice, Denise A. Kelsey, Dale A. Mccullough, Tyanna Smith

Environmental Science and Management Faculty Publications and Presentations

Land use legacies can have a discernible influence in present-day watersheds and should be accounted for when designing conservation strategies for riverine aquatic life. We describe the environmental history of three watersheds within the Grande Ronde subbasin of the Columbia River using General Land Office survey field notes from the 19th century. In the two watersheds severely impacted by Euro-American land use, stream channel widths—a metric representing habitat simplification—increased from an average historical width of 16.8 m to an average present width of 20.8 m in large streams; 4.3 m to 5.5 m in small, confined or partly confined streams; …

Plans And Living Practices For The Green Campus Of Portland State University, Yoon Jung Choi, Minjung Oh, Jihye Kang, Loren Lutzenhiser

Urban Studies and Planning Faculty Publications and Presentations

This study aims to comprehend Portland State University (PSU)’s green campus strategies, and students’ level of knowledge and living practices relating to green campus. PSU’s sustainable campus plan has been nationally and internationally recognized. A literature review, field investigation, and interviews were conducted to ascertain the PSU green campus strategies. This study also used a survey to understand students’ level of knowledge and practices. The survey results were analyzed by SPSS. Green campus projects at PSU were operated by official organizations and funded according to PSU’s long term plans in 12 multilateral categories: administration, energy, water, climate action, green buildings, …

Developing A Representative Snow-Monitoring Network In A Forested Mountain Watershed, Kelly E. Gleason, Anne Nolin, Travis R. Roth

Environmental Science and Management Faculty Publications and Presentations

A challenge in establishing new ground-based stations for monitoring snowpack accumulation and ablation is to locate the sites in areas that represent the key processes affecting snow accumulation and ablation. This is especially challenging in forested montane watersheds where the combined effects of terrain, climate, and land cover affect seasonal snowpack. We present a coupled modeling approach used to objectively identify representative snow-monitoring locations in a forested watershed in the western Oregon Cascades mountain range. We used a binary regression tree (BRT) non-parametric statistical model to classify peak snow water equivalent (SWE) based on physiographic landscape characteristics in an average …

Novel Compound, 84f2, Inhibits Calmodulin Deficient Ryr2, Robert Carl Klipp

Dissertations and Theses

The cardiac ryanodine receptor (RyR2) plays a key role in excitation-contraction coupling (ECC). Mutations in RyR2 are known to be linked to the arrhythmogenic disorder, catecholaminergic polymorphic ventricular tachycardia (CPVT), a deadly disease which is characterized by a leak of calcium from sarcoplasmic reticulum and a decrease in calmodulin (CaM) binding. A novel drug, 84F2, shown to inhibit arrhythmias in RyR2-R176Q heterozygous CPVT mouse hearts (2.5 µg/kg), decrease spark frequency in cells derived from CPVT mice (IC₅₀ = 35 nM), and inhibit RyR2 single channel activity at low nanomolar concentrations (IC₅₀ = 8 nM). When CaM is added …

Building A Multivariable Linear Regression Model Of On-Road Traffic For Creation Of High Resolution Emission Inventories, James Eckhardt Powell

Dissertations and Theses

Emissions inventories are an important tool, often built by governments, and used to manage emissions. To build an inventory of urban CO₂ emissions and other fossil fuel combustion products in the urban atmosphere, an inventory of on-road traffic is required. In particular, a high resolution inventory is necessary to capture the local characteristics of transport emissions. These emissions vary widely due to the local nature of the fleet, fuel, and roads.

Here we show a new model of ADT for the Portland, OR metropolitan region. The backbone is traffic counter recordings made by the Portland Bureau of Transportation at …

Far-Red And Near-Infrared Seminaphthofluorophores For Targeted Pancreatic Cancer Imaging, Lei Wang, Connor W. Barth, Martha Sibrian-Vazquez, Jorge O. Escodedo, Mark Lowry, John Muschler, Haiyan Li, Summer L. Gibbs, Robert Strongin

Chemistry Faculty Publications and Presentations

Molecular probes that selectively highlight pancreatic cancer (PC) tissue have the potential to improve pancreatic ductal adenocarcinoma (PDAC) margin assessment through the selective highlighting of individual PC cells. Herein, we report a simple and unique family of systematically modified red and near-infrared fluorescent probes that exhibit a field-effect-derived redshift. Two of thirteen probes distributed to the normal mouse pancreas following systemic administration. One selectively accumulated in genetically modified mouse models of PDAC. The probe exhibited intracellular accumulation and enabled visualization of four levels of the structure, including the whole organ, resected tissue, individual cells, and subcellular organelles. In contrast to …