Physical Sciences and Mathematics Commons^™

Mechanisms Of Methane Transport Through Populus Trichocarpa, Ellynne Marie Kutschera, M. A. K. Khalil, Andrew Rice, Todd Rosenstiel

Physics Faculty Publications and Presentations

Although the dynamics of methane (CH4) emission from croplands and wetlands have been fairly well investigated, the contribution of trees to global CH4 emission and the mechanisms of tree transport are relatively unknown. CH4 emissions from the common wetland tree species Populus trichocarpa (black cottonwood) native to the Pacific Northwest were measured under hydroponic conditions in order to separate plant transport mechanisms from the influence of soil processes. Roots were exposed to CH4 enriched water and canopy emissions of CH4 were measured. The average flux for 34 trials (at temperatures ranging from 17 to 25 °C) was 2.8 ± 2.2 …

Assessing The Impacts Of Federal Forest Planning On Wildfire Risk Mitigation In The Pacific Northwest, Usa, Alan A. Ager, Michelle A. Day, Karen C. Short, Cody R. Evers

Environmental Science and Management Faculty Publications and Presentations

We analyzed the impact of amenity and biodiversity protection as mandated in national forest plans on the implementation of hazardous fuel reduction treatments aimed at protecting the wildland urban interface (WUI) and restoring fire resilient forests. We used simulation modeling to delineate areas on national forests that can potentially transmit fires to adjacent WUI. We then intersected these areas with national forest planning maps to determine where mechanical treatments are allowed for restoration and fire protection, versus areas where they are prohibited. We found that a large proportion of the national forest lands (79%) can spawn fires that burn adjacent …

Ecosystem Services In Managing Residential Landscapes: Priorities, Value Dimensions, And Cross-Regional Patterns, Kelli L. Larson, Jennifer L. Morse, Peter M. Groffman, Neil D. Bettez, Tara Trammell

Environmental Science and Management Faculty Publications and Presentations

Although ecosystem services have been intensively examined in certain domains (e.g., forests and wetlands), little research has assessed ecosystem services for the most dominant landscape type in urban ecosystems—namely, residential yards. In this paper, we report findings of a cross-site survey of homeowners in six U.S. cities to 1) examine how residents subjectively value various ecosystem services, 2) explore distinctive dimensions of those values, and 3) test the urban homogenization hypothesis. This hypothesis posits that urbanization leads to similarities in the social-ecological dynamics across cities in diverse biomes. By extension, the thesis suggests that residents’ ecosystem service priorities for residential …

Carbon Sequestration In Managed Temperate Coniferous Forests Under Climate Change, Caren C. Dymond, Sarah Beukema, Craig R. Nitschke, K. David Coates, Robert M. Scheller

Environmental Science and Management Faculty Publications and Presentations

Management of temperate forests has the potential to increase carbon sinks and mitigate climate change. However, those opportunities may be confounded by negative climate change impacts. We therefore need a better understanding of climate change alterations to temperate forest carbon dynamics before developing mitigation strategies. The purpose of this project was to investigate the interactions of species composition, fire, management, and climate change in the Copper–Pine Creek valley, a temperate coniferous forest with a wide range of growing conditions. To do so, we used the LANDIS-II modelling framework including the new Forest Carbon Succession extension to simulate forest ecosystems under …

Mapping Of Defects In Individual Silicon Nanocrystals Using Real- Space Spectroscopy, Dmitry A. Kislitsyn, Vancho Kocevski, Jon M. Mills, Sheng-Kuei Chiu, Christian F. Gervasi, Benjamen N. Taber, Ariel E. Rosenfield, Olle Eriksson, Ján Rusz, Andrea Mitchell Goforth, George V. Nazin

Chemistry Faculty Publications and Presentations

The photophysical properties of silicon semiconductor nanocrystals (SiNCs) are extremely sensitive to the presence of surface chemical defects, many of which are easily produced by oxidation under ambient conditions. The diversity of chemical structures of such defects and the lack of tools capable of probing individual defects continue to impede understanding of the roles of these defects in SiNC photophysics. We use scanning tunneling spectroscopy to study the impact of surface defects on the electronic structures of hydrogen-passivated SiNCs supported on the Au(111) surface. Spatial maps of the local electronic density of states (LDOS) produced by our measurements allowed us …

Climate Change Decreases Nitrogen Pools And Mineralization Rates In Northern Hardwood Forests, Jorge Durán, Jennifer L. Morse, Peter M. Groffman, John L. Campbell, Lynn M. Christenson, Charles T. Driscoll, Timothy J. Fahey, Melany C. Fisk, Gene E. Likens, Jerry M. Melillo, Myron J. Mitchell, Pamela H. Templer, Matthew A. Vadeboncoeur

Environmental Science and Management Faculty Publications and Presentations

Nitrogen (N) supply often limits the productivity of temperate forests and is regulated by a complex mix of biological and climatic drivers. In excess, N is linked to a variety of soil, water, and air pollution issues. Here, we use results from an elevation gradient study and historical data from the long-term Hubbard Brook Ecosystem Study (New Hampshire, USA) to examine relationships between changes in climate, especially during winter, and N supply to northern hardwood forest ecosystems. Low elevation plots with less snow, more soil freezing, and more freeze/thaw cycles supported lower rates of N mineralization than high elevation plots, …

Pharmaceutical Contaminants As Stressors On Rocky Intertidal And Estuarine Organisms: A Case Study Of Fluoxetine, Joseph Richard Peters

Dissertations and Theses

Contaminants such as pharmaceuticals are of increasing concern due to their ubiquitous use and persistence in surface waters worldwide. Limited attention has been paid to the effects of pharmaceuticals on marine life, despite widespread detection of these contaminants in the marine environment. Of the existing studies, the majority assess the negative effects of pharmaceuticals over an exposure period of 30 days or less and focus on cellular and subcellular biomarkers. Longer studies are required to determine if chronic contaminant exposure poses risks to marine life at environmentally relevant concentrations. Also scarce in the literature is examination of whole organism effects …

Satisfaction, Water And Fertilizer Use In The American Residential Macrosystem, Peter M. Groffman, J. Morgan Grove, Colin Polsky, Neil D. Bettez, Jennifer L. Morse, Jeannine Cavender-Bares, Sharon J. Hall, James B. Heffernan, Sarah E. Hobbie, Kelli L. Larson, Christopher Neill, Kristen C. Nelson, Laura A. Ogden, Jarlath O'Neil-Dunne, Diane E. Pataki, Rinku Roy Chowdhury, Dexter H. Locke

Environmental Science and Management Faculty Publications and Presentations

Residential yards across theUSlook remarkably similar despite marked variation in climate and soil, yet the drivers of this homogenization are unknown. Telephone surveys of fertilizer and irrigation use and satisfaction with the natural environment, and measurements of inherent water and nitrogen availability in sixUScities (Boston, Baltimore, Miami, Minneapolis-St. Paul, Phoenix, Los Angeles) showed that the percentage of people using irrigation at least once in a year was relatively invariant with little difference between the wettest (Miami,85%) and driest (Phoenix,89%) cities. The percentage of people using fertilizer at least once in a year also ranged narrowly (52%–71%), while soil nitrogen supply …

Field Geology And Petrologic Investigation Of The Strawberry Volcanics, Northeast Oregon, Arron Richard Steiner

Dissertations and Theses

The Strawberry Volcanics of Northeast Oregon are a group of geochemically related lavas with a diverse chemical range (basalt to rhyolite) that erupted between 16.2 and 12.5 Ma and co-erupted with the large, (~200,000 km3) Middle Miocene tholeiitic lavas of the Columbia River Basalt Group (CRBG), which erupted near and geographically surround the Strawberry Volcanics. The rhyolitic lavas of the Strawberry Volcanics produced the oldest 40Ar/39Ar ages measured in this study with ages ranging from 16.2 Ma to 14.6 Ma, and have an estimated total erupted volume of 100 km3. The mafic and intermediate lavas of the Strawberry Volcanics include …

Determination Of The Goos-Hänchen Shift In Dielectric Waveguides Via Photo Emission Electron Microscopy In The Visible Spectrum, Theodore Stedmark, Robert Campbell Word, Rolf Kӧnenkamp

Physics Faculty Publications and Presentations

Photoemission Electron Microscopy (PEEM) is a versatile tool that relies on the photoelectric effect to produce high-resolution images. Pulse lasers allow for multi-photon PEEM where multiple photons are required excite a single electron. This non-linear process can directly image the near field region of electromagnetic fields in materials. We use this ability here to analyze wave propagation in a linear dielectric waveguide with wavelengths of 410nm and 780nm. The propagation constant of the waveguide can be extracted from the interference pattern created by the coupled and incident light and shows distinct polarization dependence. The electromagnetic field interaction at the boundaries …

One-Dimensional Nanostructure And Sensing Applications: Tin Dioxide Nanowires And Carbon Nanotubes, Hoang Anh Tran

Dissertations and Theses

The key challenge for a nanomaterial based sensor is how to synthesize in bulk quantity and fabricate an actual device with insightful understanding of operational mechanisms during performance. I report here effective, controllable methods that exploit the concepts of the "green approach" to synthesize two different one-dimensional nanostructures, including tin oxide nanowires and carbon nanotubes. The syntheses are followed by product characterization and sensing device fabrications as well as sensor performance understanding at the molecular level. Sensor-analyte response and recovery kinetics are also presented.

The first part of the thesis describes bulk-scale synthesis and characterization of tin oxide nanowires by …

Incorporating Priors For Medical Image Segmentation Using A Genetic Algorithm, Payel Ghosh, Melanie Mitchell, James A. Tanyi, Arthur Y. Hung

Computer Science Faculty Publications and Presentations

Medical image segmentation is typically performed manually by a physician to delineate gross tumor volumes for treatment planning and diagnosis. Manual segmentation is performed by medical experts using prior knowledge of organ shapes and locations but is prone to reader subjectivity and inconsistency. Automating the process is challenging due to poor tissue contrast and ill-defined organ/tissue boundaries in medical images. This paper presents a genetic algorithm for combining representations of learned information such as known shapes, regional properties and relative position of objects into a single framework to perform automated three-dimensional segmentation. The algorithm has been tested for prostate segmentation …

Slow Slip Events And Time-Dependent Variations In Locking Beneath Lower Cook Inlet Of The Alaska-Aleutian Subduction Zone, Shanshan Li, Jeffrey Freymueller, Robert Mccaffrey

Geology Faculty Publications and Presentations

We identify a series of abrupt changes in GPS site velocities in Lower Cook Inlet, Alaska, in late 2004, early 2010, and late 2011. The site motions during each time period are nearly linear. The surface deformations inferred from GPS for pre-2004 and 2010–2011 are similar to each other, as are 2004–2010 and post-2011. We estimate the slip distribution on the Alaska-Aleutian subduction plate interface accounting for upper plate block rotations and interpret this toggling between two deformation patterns as caused by transient slip. We find that by allowing negative slip deficit rates (i.e., creep rates in excess of relative …

Characterization And Comparative Analysis Of 2,4-Toluene Diisocyanate And 1,6-Hexamethylene Diisocyanate Haptenated Human Serum Albumin And Hemoglobin, Morgen Mhike, Ita Chipinda, Brandon F. Law, Toni A. Bledsoe, Angela R. Lemons, Ajay P. Nayak, Brett J. Green, Donald H. Beezhold, Reuben H. Simoyi, Paul D. Siegel

Chemistry Faculty Publications and Presentations

Diisocyanates (dNCOs) are lowmolecularweight chemical sensitizers that reactwith autologous proteins to produce neoantigens. dNCO-haptenated proteins have been used as immunogens for generation of dNCO-specific antibodies and as antigens to screen for dNCO-specific antibodies in exposed individuals. Detection of dNCOspecific antibodies in exposed individuals for diagnosis of dNCO asthma has been hampered by poor sensitivities of the assay methods in that specific IgE can only be detected in approximately 25% of the dNCO asthmatics. Apart from characterization of the conjugates used for these immunoassays, the choice of the carrier protein and the dNCO used are important parameters that can influence the …

Micrometeorological Simulations To Predict The Impacts Of Heat Mitigation Strategies On Pedestrian Thermal Comfort In A Los Angeles Neighborhood, Mohammad Taleghani, David J. Sailor, George A. Ban-Weiss

Mechanical and Materials Engineering Faculty Publications and Presentations

The urban heat island impacts the thermal comfort of pedestrians in cities. In this paper, the effects of four heat mitigation strategies on micrometeorology and the thermal comfort of pedestrians were simulated for a neighborhood in eastern Los Angeles County. The strategies investigated include solar reflective ‘cool roofs’, vegetative ‘green roofs’, solar reflective ‘cool pavements’, and increased streetlevel trees. Aseries of micrometeorological simulations for an extreme heat day were carried out assuming widespread adoption of each mitigation strategy. Comparing each simulation to the control simulation assuming current land cover for the neighborhood showed that additional street-trees and cool pavements reduced …

The Elusive Quest For Rna Knots, Aaron S. Burton, Marco Di Stefano, Niles Lehman, Henri Orland, Cristian Micheletti

Chemistry Faculty Publications and Presentations

Physical entanglement, and particularly knots arise spontaneously in equilibrated polymers that are sufficiently long and densely packed. Biopolymers are no exceptions: knots have long been known to occur in proteins as well as in encapsidated viral DNA. The rapidly growing number of RNA structures has recently made it possible to investigate the incidence of physical knots in this type of biomolecule, too. Strikingly, no knots have been found to date in the known RNA structures. In this Point of View Article we discuss the absence of knots in currently available RNAs and consider the reasons why knots in RNA have …

The Log-Exponential Smoothing Technique And Nesterov’S Accelerated Gradient Method For Generalized Sylvester Problems, N. T. An, Daniel J. Giles, Nguyen Mau Nam, R. Blake Rector

Mathematics and Statistics Faculty Publications and Presentations

The Sylvester or smallest enclosing circle problem involves finding the smallest circle enclosing a finite number of points in the plane. We consider generalized versions of the Sylvester problem in which the points are replaced by sets. Based on the log-exponential smoothing technique and Nesterov’s accelerated gradient method, we present an effective numerical algorithm for solving these problems.

Minimizing Differences Of Convex Functions With Applications To Facility Location And Clustering, Mau Nam Nguyen, R. Blake Rector, Daniel J. Giles

Mathematics and Statistics Faculty Publications and Presentations

In this paper we develop algorithms to solve generalized Fermat-Torricelli problems with both positive and negative weights and multifacility location problems involving distances generated by Minkowski gauges. We also introduce a new model of clustering based on squared distances to convex sets. Using the Nesterov smoothing technique and an algorithm for minimizing differences of convex functions called the DCA introduced by Tao and An, we develop effective algorithms for solving these problems. We demonstrate the algorithms with a variety of numerical examples.

Distributed Modeling Of Ablation (1996–2011) And Climate Sensitivity On The Glaciers Of Taylor Valley, Antarctica, Matthew J. Hoffman, Andrew G. Fountain, Glen E. Liston

Geology Faculty Publications and Presentations

The McMurdo Dry Valleys of Antarctica host the coldest and driest ecosystem on Earth, which is acutely sensitive to the availability of water coming from glacial runoff. We modeled the spatial variability in ablation and assessed climate sensitivity of the glacier ablation zones using 16 years of meteorological and surface mass-balance observations collected in Taylor Valley. Sublimation was the primary form of mass loss over much of the ablation zones, except for near the termini where melt, primarily below the surface, dominated. Microclimates in ~10 m scale topographic basins generated melt rates up to ten times higher than over smooth …

Processes Controlling Carbon Cycling In Antarctic Glacier Surface Ecosystems, Elizabeth A. Bagshaw, Martyn Tranter, Jemma L. Wadham, Andrew G. Fountain, A. Dubnick, S. Fitzsimons

Geology Faculty Publications and Presentations

Glacier surface ecosystems, including cryoconite holes and cryolakes, are significant contributors to regional carbon cycles. Incubation experiments to determine the net production (NEP) of organic matter in cryoconite typically have durations of 6-24 hours, and produce a wide range of results, many of which indicate that the system is net heterotrophic. We employ longer term incubations to examine the temporal variation of NEP in cryoconite from the McMurdo Dry Valleys, Antarctica to examine the effect of sediment disturbance on system production, and to understand processes controlling production over the lifetimes of glacier surface ecosystems. The shorter-term incubations have durations of …

Efficient Bimolecular Mechanism Of Photochemical Hydrogen Production Using Halogenated Boron-Dipyrromethene (Bodipy) Dyes And A Bis(Dimethylglyoxime) Cobalt(Iii) Complex, Randy Pat Sabatini, Brian M. Lindley, Theresa M. Mccormick, Theodore Lazarides, William Brennessel, David W. Mccamant, Richard Eisenberg

Chemistry Faculty Publications and Presentations

A series of Boron-­dipyrromethene (Bodipy) dyes were used as photosensitizers for photochemical hydrogen production in conjunction with [Co^III(dmgH)2pyCl] (where dmgH = dimethylglyoximate, py = pyridine) as the catalyst and triethanolamine (TEOA) as the sacrificial electron donor. The Bodipy dyes are fully characterized by electrochemistry, x-­‐ray crystallography, quantum chemistry calculations, femtosecond transient absorption and time-­‐resolved fluorescence, as well as in long-­‐term hydrogen production assays. Consistent with other recent reports, only systems containing halogenated chromophores were active for hydrogen production, as the long-­‐lived triplet state is necessary for efficient bimolecular electron transfer. Here, it is shown that the photostability of …

Slope Failure Detection Through Multi-Temporal Lidar Data And Geotechnical Soils Analysis Of The Deep-Seated Madrone Landslide, Coast Range, Oregon, Michael Scott Marshall

Dissertations and Theses

Landslide hazard assessment of densely forested, remote, and difficult to access areas can be rapidly accomplished with airborne light detection and ranging (lidar) data. An evaluation of geomorphic change by lidar-derived digital elevation models (DEMs) coupled with geotechnical soils analysis, aerial photographs, ground measurements, precipitation data, and numerical modeling can provide valuable insight to the reactivation process of unstable landslides. A landslide was selected based on previous work by Mickleson (2011) and Burns et al. (2010) that identified the Madrone Landslide with significant volumetric changes. This study expands on previous work though an evaluation of the timing and causation of …

Reactivity Measurement In Estimation Of Benzoquinone And Benzoquinone Derivatives’ Allergenicity, Wilbes Mbiya, Ita Chipinda, Reuben H. Simoyi, Paul D. Siegel

Chemistry Faculty Publications and Presentations

Benzoquinone (BQ) and benzoquinone derivatives (BQD) are used in the production of dyes and cosmetics. While BQ, an extreme skin sensitizer, is an electrophile known to covalently modify proteins via Michael Addition (MA) reaction whilst halogen substituted BQD undergo nucleophilic vinylic substitution (SNV) mechanism onto amine and thiol moieties on proteins, the allergenic effects of adding substituents on BQ have not been reported. The effects of inserting substituents on the BQ ring has not been studied in animal assays. However, mandated reduction/elimination of animals used in cosmetics testing in Europe has led to an increased need for alternatives for the …

3d Fpga Cell Matrix By Self-Assembly, Jeffrey Udall

Undergraduate Research & Mentoring Program

Physical size limitations in miniaturizing two-dimensional (2D) transistors are becoming more difficult to overcome. In order to continue increasing the processing power of electronic circuits, new design paradigms are needed. Three-dimensional (3D) architectures provide a solution to this issue and are currently being implemented via wafer stacking. However, more significant gains in terms of packing and speed can be achieved by CMOS components with truly integrated 3D cellular architectures. One of these is the Cell Matrix, a self-configurable defect- and fault-tolerant architecture, which is ideally suited for ultra large-scale integration. For this project, we worked to expand the Cell Matrix …

Emerging Adaptive Architectures For Biomolecular Computation, Matthew Fleetwood

Undergraduate Research & Mentoring Program

The goal of this work is to explore applications of reservoir computing in biomolecular computation. Reservoir computing is a unique model for representing a mapping from one instance in time to a specific output. A neural network of randomly connected neurons is linked with a single output neuron or multiple output neurons. The output neurons are capable of mapping inputs to desired outputs using adaptable algorithms. This framework is investigated by using the Python programming language and object oriented design and programming. Neurons are created in programs by bundling information like input data and attributes of the network, which utilize …

Assessment Of Tmdl Implementation And Water Quality Status And Trends In Amazon Creek And Coyote Creek Watersheds, Stosh Zydek

Environmental Science and Management Professional Master's Project Reports

In this project, I analyzed the status and trends of water quality data describing fecal bacteria (E. coli) and DO in the Amazon and Coyote Creek watersheds of the Southern Willamette Valley, Oregon. I also examined TMDL implementation plans produced by DMAs, determined if and how implementation activities corresponded to changes in water quality, compared management and planning of DMAs in the watersheds, discussed aspects of the current TMDL, and compared state regulations and standards in other states. I concluded by making management recommendations to better facilitate future status and trend analysis.

Amazon Creek, Amazon Diversion Channel, A-3 …

Complex Capillary Fluidic Phenomena For Passive Control Of Liquids In Low-Gravity Environments, Logan Torres

Undergraduate Research & Mentoring Program

In an effort to further apply the recent results of puddle jumping research, we seek to expand the oblique droplet impact studies of others by exploiting large liquid droplets in the near weightless environment of a drop tower. By using the spontaneous puddle jump mechanism, droplets of volumes 1 mL ≤ V ≤ 3 mL with corresponding Weber numbers of We ≈ 1 are impinged on surfaces inclined in the range 40° ≤ α ≤ 80° (measured from the horizontal plane). Impact surface wetting characteristics exhibit static contact angles θstatic = 165 ± 5°. All impacts result in complete rebound. …

3d Hydrodynamic Model Development And Verification, Hussein A. M. Al-Zubaidi

Civil and Environmental Engineering Master's Project Reports

A three-dimensional numerical model was developed to simulate hydrodynamic, temperature, and water quality distributions in rivers and lakes. In an attempt to get rid of the extra approximation and complexity, no coordinate transformation has been done and z-coordinate system has been employed. The governing equations are the continuity equation, free surface equation, momentum equations, and conservation equations of temperature and water quality. The model employs the time splitting technique which allows splitting the directions in which we end with two-dimensional governing equations and eventually the solution ends with a tri-diagonal matrix, which is easily solved by Thomas algorithm. The first …

A Study On The Current State Of Contaminants Of Concern Research, With A Focus On Biosolids And Regulations, Maren Mariah Fulton

Civil and Environmental Engineering Master's Project Reports

Wastewater treatment plants are a major source of contaminants of emerging concern, as these facilities are the main receptors of these products via household, commercial, and industrial drains, and transport via stormwater runoff. Biosolids are composed of numerous constituents, with a number of environmentally persistent and potentially toxic contaminants of emerging concern identified as present in large concentrations. Research is needed to understand the transport and fate mechanisms of these compounds in biosolids. Additionally, this research is needed to determine a new priority framework to regulate CECs, both on the national level and regional levels. Wastewater treatment plant influent and …

Greenroof Study: Final Report, An Assessment Of Greenroof Design And Maintenance In Portland, Oregon: 2011 – 2013, Windy Carney Beck

Environmental Science and Management Professional Master's Project Reports

In 1999 the City of Portland (City) began to require that stormwater management facilities (SMF) be built when private property is newly developed or redeveloped (City Code Chapter 17.38). Proper maintenance and upkeep of SMFs is essential to ensuring they function appropriately. The City's Maintenance Inspection Program (MIP) is tasked with inspecting stormwater management facilities on private properties in order to ensure that they are being properly operated and maintained and to meet provisions of the City's NPDES Municipal Separated Storm Sewer System (MS4) permit.

Greenroofs are one type of SMF that are installed to satisfy this requirement. Understanding the …