Physical Sciences and Mathematics Commons^™

Composition And Dispersal Dynamics Of Vegetation Communities In Urban Riparian Forests, Christa Von Behren

Dissertations and Theses

In urban riparian areas, vegetation composition may be affected by urban land use changes at both the stream reach and the watershed scale. Moreover, the mechanisms by which seeds disperse may be affected both by reduction in seed sources due to vegetation removal and by the urban stream syndrome that produces flashier hydrographs and incised channels. I hypothesized that vegetation communities with high cover of native and hydrophilic species would be found in watersheds with high forest cover, while more limited cover of these species would be found in highly developed watersheds. Additionally, to examine the dispersal mechanisms contributing to …

A Study Of Fragmentation And Spontaneous Covalent Self-Assembly Of The Azaorcus Ribozyme From Multiple Small Inactive Rna Fragments, Tharuka Sewwandi Jayathilaka

Dissertations and Theses

The question about the origins of life often appears as a difficult question to answer. A more reliable candidate molecule for the chemical origins of life would be a molecule that is capable of making copies of itself from simple precursors. With the finding of the catalytic activities of RNA molecules by Thomas Cech and Sid Altman in late 1980s, the term ribozyme was introduced to define an RNA molecule with catalytic activity. The RNA World is a conceptual period in the early stages in the development of life because RNA simultaneously possesses evolvability and catalytic function. An RNA molecule …

The Dispute Over The Commons: Seed And Food Sovereignty As Decommodification In Chiapas, Mexico, Carol Frances HernáNdez RodríGuez

Dissertations and Theses

Seeds have become one of the most contested resources in our society. Control over seeds has intensified under neoliberalism, and today four large multinational corporations control approximately 70 percent of the global seed market. In response to this concentration of corporate power, an international social movement has emerged around the concept of seed sovereignty, which reclaims seeds and biodiversity as commons and public goods. This study examines the relationship between the global dynamics of commodification and enclosure of seeds, and the seed sovereignty countermovement for decommodification. I approach this analysis through an ethnographic case study of one local seed sovereignty …

Wind Energy And Wind-Energy-Inspired Turbulent Wakes: Modulation Of Structures, Mechanisms And Flow Regimes, Elizabeth H. Camp

Dissertations and Theses

The interaction of turbulent wakes with one another and with the adjacent fluid directly impacts the generation of electricity in wind turbine arrays. Computational modeling is well suited to the repeated iterations of data generation that may be required to inform understanding of the function of wind farms as well as to develop control schemes for plant function. In order to perform such computational studies, a simplified model of the turbine must be implemented. One of the most computationally efficient parametrizations of the blade utilizes a stationary disk which has a prescribed drag and produces a wake. However, since accurate …

Cox Processes For Counting By Detection, Purnima Rajan, Yongming Ma, Bruno Jedynak

Portland Institute for Computational Science Publications

In this work, doubly stochastic Poisson (Cox) processes and convolutional neural net (CNN) classifiers are used to estimate the number of instances of an object in an image. Poisson processes are well suited to model events that occur randomly in space, such as the location of objects in an image or the enumeration of objects in a scene. The proposed algorithm selects a subset of bounding boxes in the image domain, then queries them for the presence of the object of interest by running a pre-trained CNN classifier. The resulting observations are then aggregated, and a posterior distribution over the …

Baroclinic Tidal Sea Level From Exact-Repeat Mission Altimetry, Edward Zaron

Portland Institute for Computational Science Publications

A near-global model for the sea-surface expression of the baroclinic tide has been developed using exact-repeat mission altimetry. The methodology used differs in detail from other altimetry-based estimates of the open ocean baroclinic tide, but it leads to estimates which are broadly similar to previous results. It may be used for prediction of the baroclinic sea level anomaly at the frequencies of the main diurnal and semidiurnal tides, K₁, O₁, M₂, S₂, as well as the annual modulates of M₂, denoted MA₂ and MB₂. Based on a …

Space-Time Discretizations Using Constrained First-Order System Least Squares (Cfosls), Kirill Voronin, Chak Shing Lee, Martin Neumüller, Paulina Sepulveda, Panayot S. Vassilevski

Portland Institute for Computational Science Publications

This paper studies finite element discretizations for three types of time-dependent PDEs, namely heat equation, scalar conservation law and wave equation, which we reformulate as first order systems in a least-squares setting subject to a space-time conservation constraint (coming from the original PDE). Available piece- wise polynomial finite element spaces in (n + 1)-dimensions for functional spaces from the (n + 1)-dimensional de Rham sequence for n = 3, 4 are used for the implementation of the method. Computational results illustrating the error behavior, iteration counts and performance of block-diagonal and monolithic geometric multi- grid preconditioners are …

Gaussian Processes With Context-Supported Priors For Active Object Localization, Bruno Jedynak

Portland Institute for Computational Science Publications

We devise an algorithm using a Bayesian optimization framework in conjunction with contextual visual data for the efficient localization of objects in still images. Recent research has demonstrated substantial progress in object localization and related tasks for computer vision. However, many current state-of-the-art object localization procedures still suffer from inaccuracy and inefficiency, in addition to failing to provide a principled and interpretable system amenable to high-level vision tasks. We address these issues with the current research.

Our method encompasses an active search procedure that uses contextual data to generate initial bounding-box proposals for a target object. We train a convolutional …

Sediment Chemistry Of Urban Stormwater Ponds And Controls On Denitrification, Joanna R. Blaszczak, Meredith Steele, Brian D. Badgley, James B. Heffernan, Sarah E. Hobbie, Jennifer L. Morse, Erin N. Rivers, Sharon J. Hall, Christopher Neill, Diane E. Pataki, Peter M. Groffman, Emily S. Bernhardt

Environmental Science and Management Faculty Publications and Presentations

Stormwater ponds and retention basins are ubiquitous features throughout urban landscapes. These ponds are potentially important control points for nitrogen (N) removal from surface water bodies via denitrification. However, there are possible trade-offs to this water quality benefit if high N and contaminant concentrations in stormwater pond sediments decrease the complete reduction of nitrous oxide (N₂O), a potent greenhouse gas, to dinitrogen (N₂) during denitrification. This may occur through decreasing the abundance or efficiency of denitrifiers capable of producing the N₂O reductase enzyme. We predicted that ponds draining increasingly urbanized landscapes would have higher …

Investigating Environmental Migration And Other Rural Drought Adaptation Strategies In Baja California Sur, Mexico, Melissa Haeffner, Jacopo A. Baggio, Kathleen Galvin

Environmental Science and Management Faculty Publications and Presentations

This paper explores the relationship between specific household traits (region of residence, head of household occupation, financial diversity, female level of education, land and animal ownership, social capital, and climate perception) and choice of specific adaptation strategies used by households in two sites in Baja California Sur, Mexico, during a severe drought from 2006 to 2012 using survey data and key informant interviews. We analyzed the co-occurrence of household traits adopting different drought adaptation strategies, then applied Qualitative Comparative Analysis (QCA) to examine the relationship between traits and strategies and integrated interview data to understand how rancheros perceive associations. We …

Garden Pollinators And The Potential For Ecosystem Service Flow To Urban And Peri-Urban Agriculture, Gail A. Langellotto, Andony Melathopoulos, Isabella Messer, Aaron Anderson, Nathan Mcclintock, Lucas Costner

Urban Studies and Planning Faculty Publications and Presentations

Hedgerows, flowering strips, and natural areas that are adjacent to agricultural land have been shown to benefit crop production, via the provision of insect pollinators that pollinate crops. However, we do not yet know the extent to which bee habitat in the form of urban gardens might contribute to pollination services in surrounding crops. We explored whether gardens might provision pollinators to adjacent agricultural areas by sampling bees from gardens in the Portland, Oregon metropolitan area, and estimating typical foraging distances in the context of commercialand residential-scale pollination-dependent crops up to 1000 m from garden study sites. We estimate that …

Sensing Building Structure Using Uwb Radios For Disaster Recovery, Jeong Eun Lee

Dissertations and Theses

This thesis studies the problem of estimating the interior structure of a collapsed building using embedded Ultra-Wideband (UWB) radios as sensors. The two major sensing problems needed to build the mapping system are determining wall type and wall orientation. We develop sensing algorithms that determine (1) load-bearing wall composition, thickness, and location and (2) wall position within the indoor cavity. We use extensive experimentation and measurement to develop those algorithms.

In order to identify wall types and locations, our research approach uses Received Signal Strength (RSS) measurement between pairs of UWB radios. We create an extensive database of UWB signal …

Analytical And Toxicological Evaluation Of Flavor Chemicals In Electronic Cigarette Refill Fluids, Rachel Z. Behar, Wentai Luo, Kevin J. Mcwhirter, James F. Pankow, Prue Talbot

Chemistry Faculty Publications and Presentations

Thousands of electronic cigarette refill fluids are commercially available. The concentrations of nicotine and the solvents, but not the flavor chemicals, are often disclosed on product labels. The purpose of this study was to identify and quantify flavor chemicals in 39 commercial refill fluids that were previously evaluated for toxicity. Twelve flavor chemicals were identified with concentrations ≥1 mg/ml: cinnamaldehyde, menthol, benzyl alcohol, vanillin, eugenol, p-anisaldehyde, ethyl cinnamate, maltol, ethyl maltol, triacetin, benzaldehyde, and menthone. Transfer of these flavor chemicals into aerosols made at 3V and 5V was efficient (mean transfer = 98%). We produced lab-made refill fluids containing …

An Analysis Of Green Infrastructure Implementation Strategies In Portland And Other Global Leaders In Climate Action, Rachel L.R. Lemont

University Honors Theses

Green infrastructure has become increasingly popular as a way to mitigate and adapt to the effects of climate change in urban environments. Cities all over the world, including Portland, have developed their own strategies which inform local organizations on the actions they should take to be climate resilient - and many of these strategies include the implementation of green infrastructure. This thesis compares Portland's green infrastructure implementation strategies to those known around the world, and utilizes themes found in those strategies to create a survey on local green infrastructure initiatives in the Portland area. This information will be important for …

Designing Model Experiments Around Harriet Tubman Middle School, Ryan Crist, Sarah Smith, Greg Sakradse, Ryan Scott

Undergraduate Research & Mentoring Program

Air quality is of concern in densely populated areas and especially near sources of inefficiently exhausted fossil fuel such as near the highway. Harriet Tubman middle school in North Portland, Oregon is situated alongside highway 5. Here, model experiments are designed and proposed to observe the instantaneous flow fields reflect modifications. LIDAR data was used to model the school and surrounding topography three-dimensionally in order to construct a model school and surrounding area from laser cut cardboard with a surface smoothed with paper mache. This model will be placed in the Portland State University wind tunnel; transport of mean and …

Clock Jitter In Communication Systems, Andrew Wayne Martwick

Dissertations and Theses

For reliable digital communication between devices, the sources that contribute to data sampling errors must be properly modeled and understood. Clock jitter is one such error source occurring during data transfer between integrated circuits. Clock jitter is a noise source in a communication link similar to electrical noise, but is a time domain noise variable affecting many different parts of the sampling process. Presented in this dissertation, the clock jitter effect on sampling is modeled for communication systems with the degree of accuracy needed for modern high speed data communication. The models developed and presented here have been used to …

Using Quenching To Detect Corrosion On Sculptural Metalwork: A Real-World Application Of Fluorescence Spectroscopy, Cory Hensen, Tami Lasseter Clare, Jack Barbera

Chemistry Faculty Publications and Presentations

Fluorescence spectroscopy experiments are a frequently taught as part of upper-division teaching laboratories. To expose undergraduate students to an applied fluorescence technique, a corrosion detection method, using quenching, was adapted from authentic research for an instrumental analysis laboratory. In the experiment, students acquire fluorescence spectra of sensing molecules in the presence of mock sculpture samples and discuss the condition of the sculptures based on the levels of soluble iron detected. This real-world-based experiment allows students the chance to engage with ongoing research and further understand the challenges with early detection of corrosion. Most students successfully completed the experiment, wrote a …

A New Finite Difference Time Domain Method To Solve Maxwell's Equations, Timothy P. Meagher

Dissertations and Theses

We have constructed a new finite-difference time-domain (FDTD) method in this project. Our new algorithm focuses on the most important and more challenging transverse electric (TE) case. In this case, the electric field is discontinuous across the interface between different dielectric media. We use an electric permittivity that stays as a constant in each medium, and magnetic permittivity that is constant in the whole domain. To handle the interface between different media, we introduce new effective permittivities that incorporates electromagnetic fields boundary conditions. That is, across the interface between two different media, the tangential component, E_r(x,y), …

E-Cigarettes Can Emit Formaldehyde At High Levels Under Conditions That Have Been Reported To Be Non-Averse To Users, James C. Salamanca, Jiries Meehan-Attrash, Shawna Vreeke, Jorge O. Escobedo, David H. Peyton, Robert M. Strongin

Chemistry Faculty Publications and Presentations

E-cigarette aerosol emission studies typically focus on benchmarking toxicant levels versus those of cigarettes. However, such studies do not fully account for the distinct chemical makeup of e-liquids and their unique properties. These approaches often conclude that there are fewer and lower levels of toxins produced by e-cigarettes than by cigarettes. In 2015, we reported the discovery of new hemiacetals derived from the reaction of formaldehyde and the e-liquid solvents. The main finding was that they constituted a significant proportion of potentially undetected formaldehyde. Moreover, unlike gaseous formaldehyde, the hemiacetals reside in the aerosol particulate phase, and thus are capable …

Transient Reactivation Of A Deep-Seated Landslide By Undrained Loading Captured With Repeat Airborne And Terrestrial Lidar, Adam M. Booth, Justin Mccarley, Jason Hinkle, Jean-Paul Ampuero, Michael P. Lamb

Geology Faculty Publications and Presentations

Landslides reactivate due to external environmental forcing or internal mass redistribution, but the process is rarely documented quantitatively. We capture the three-dimensional, 1-m resolution surface deformation field of a transiently reactivated landslide with image correlation of repeat airborne lidar. Undrained loading by two debris flows in the landslide’s head, rather than external forcing, triggered reactivation. After that loading, the lower 2 km of the landslide advanced by up to 14 m in 2 years before completely stopping. The displacement field over those 2 years implies that the slip surface gained 1 kPa of shear strength, which was likely accomplished by …

Diagnostic Platform For Current Health Status Monitoring, Albert S. Benight, Megan M. Koslen, Matthew W. Eskew

Student Research Symposium

Our approach is based on physical measurements of blood plasma and exploits the plethora of information contained in the human plasma proteome, as a reporter of human health status. The assay involves collection and analysis ofthermograms of plasma from human blood measured by differential scanning calorimetry (DSC).

Plasma thermograms arise from the temperature-induced denaturation profile of proteins within blood plasma measured by DSC. This insightful measurement thereby provides a snapshot of the current state of the human plasma proteome which directly informs on overall systemic health. Such measurements have been shown to be highly accurate and sensitive indicators of health …

Metallodithiolate Ligands For Reversing Metal Ion Induced Aggregation Of Beta Amyloid, Eleanor K. Adams, Marilyn Rampersad Mackiewicz

Student Research Symposium

Alzheimer’s Disease (AD) is the sixth leading cause of death in the United States with no known methods to cure, reverse or halt disease progression. The “metal hypothesis” states that Fe^II, Cu^II, Zn^II, and Al^II bind to truncated Aβ peptides and form soluble oligomers which deposit as senile plaques. These plaques play a crucial role in AD pathogenesis. For example, metallated-Aβ aggregates are hypothesized to disrupt membranes or generate a reactive oxygen species (ROS) through redox cycling in the presence of Cu^I/II or Fe^III/II and a reducing agent. ROS can lead …

Assessment Of Observed Increases In Extreme Warm Exceedances In Locations With Short Warm Side Tails, Jacob S. Hunter, Paul C. Loikith, J. David Neelin

Student Research Symposium

Regions of shorter-than-Gaussian temperature distribution tails have been shown to occur in spatially coherent patterns in the current climate using reanalysis. Under such conditions, future changes in extremes due to global warming may manifest in more complex ways than if the underlying distribution were closer to Gaussian. For instance, under a uniform warm shift, the simplest prototype for future warming, a location with a short warm side tail would experience a greater increase in exceedances than if the distribution were Gaussian. This carries meaningful societal and environmental implications including but not limited to negative impacts on human and ecosystem health, …

Estimating Sand Loss: Using Eolian Sand Ramps As A Proxy For Estimating Past Erosion Within The Lincoln City Dune Sheet; Lincoln City, Oregon, Kara E. P. Kingen, John Bershaw, Curt D. Peterson

Student Research Symposium

Eolian sand ramps are features that are sculpted from beach sand blowing up against sea cliffs or bluffs. In some coastal areas, sand ramp deposits only appear as the erosional remnants of pre-existing ramps that have been truncated at eroded shorelines, separating them from their previous sediment supply. Although sand ramp features have been observed in other areas on the western coast of the United States , they had not been studied or documented within the Lincoln City Dune Sheet (LINC) prior to this study – which documents the existence of truncated eolian sand ramps in LINC and uses them …

Opportunities In Physics Education: Low-Cost Position Tracking For Use In Kinematics Labs, Paul R. Destefano, Cora Siebert, Roberto Perez-Franco, Thomas Allen, Gabriel Mukobi, Ralf Widenhorn

Student Research Symposium

Traditional introductory physics kinematics laboratories utilized a few different instruments for locating objects in motion, all of which have shortcomings. Some provide only timing data, which heavily restricts trajectories and data collection. Some instruments provide more measurements but restrict object shapes, orientations, and textures. Still others require extensive pre-processing. None of these traditional instruments provide two- or three-dimensional position data. New, low-cost, local positioning technology, based on radio frequency wireless communications, is available that enables novel redesigns of physics laboratories. This technology provides two- and three-dimensional position measurements, continuously, at data rates of 10 Hz or faster, from any object …

Clustering And Multifacility Location With Constraints Via Distance Function Penalty Methods And Dc Programming, Tuyen Tran, Samuel Reynolds, Thai An Nguyen, Mau Nam Nguyen

Student Research Symposium

This is a continuation of our effort in using mathematical optimization involving DC programming in clustering and multifacility location. We study a penalty method based on distance functions and apply it particularly to a number of problems in clustering and multi- facility location in which the centers to be found must lie in some given set constraints. We also provide numerical examples to test our method.

Using Reservoir Computing To Build A Robust Interface With Dna Circuits In Determining Genetic Similarities Between Pathogens, Christopher Neighbor, Christof Teuscher

Student Research Symposium

As computational power increases, the field of neural networks has advanced exponentially. In particular recurrent neural networks (RNNs) are being utilized to simulate dynamic systems and to learn to predict time series data. Reservoir computing is an architecture which has the potential to increase training speed while reducing computational costs. Reservoir computing consists of a RNN with a fixed connections “reservoir” while only the output layer is trained. The purpose of this research is to explore the effective use of reservoir computing networks with the eventual application towards use in a DNA based molecular computing reservoir for use in pathogen …

The Auxiliary Space Preconditioner For The De Rham Complex, Jay Gopalakrishnan, Martin Neumüller, Panayot S. Vassilevski

Portland Institute for Computational Science Publications

We generalize the construction and analysis of auxiliary space preconditioners to the n-dimensional finite element subcomplex of the de Rham complex. These preconditioners are based on a generalization of a decomposition of Sobolev space functions into a regular part and a potential. A discrete version is easily established using the tools of finite element exterior calculus. We then discuss the four-dimensional de Rham complex in detail. By identifying forms in four dimensions (4D) with simple proxies, form operations are written out in terms of familiar algebraic operations on matrices, vectors, and scalars. This provides the basis for our implementation of …

Multivalency Regulates Activity In An Intrinsically Disordered Transcription Factor, Sarah Clark, Janette B. Myers, Ashleigh King, Radovan Fiala, Jiri Novacek, Grant Pearce, Steve L. Reichow, Elisar J. Barbar

Chemistry Faculty Publications and Presentations

The transcription factor ASCIZ (ATMIN, ZNF822) has an unusually high number of recognition motifs for the product of its main target gene, the hub protein LC8 (DYNLL1). Using a combination of biophysical methods, structural analysis by NMR and electron microscopy, and cellular transcription assays, we developed a model that proposes a concerted role of intrinsic disorder and multiple LC8 binding events in regulating LC8 transcription. We demonstrate that the long intrinsically disordered C-terminal domain of ASCIZ binds LC8 to form a dynamic ensemble of complexes with a gradient of transcriptional activity that is inversely proportional to LC8 occupancy. The preference …

The Economic Contribution Of Stewardship Contracting: Two Case Studies From The Mount Hood National Forest, Jean M. Daniels, Max Nielsen-Pincus, Mike Paruszkiewicz, Nathan Poage

Environmental Science and Management Faculty Publications and Presentations

We conducted an economic analysis of two case study stewardship contracts on the Mount Hood National Forest in western Oregon. Stewardship contracting has been embraced by some federal managers to achieve restoration goals while providing economic benefits to local communities. Little is known about economic contributions from stewardship contracts, including how they compare against Secure Rural Schools funding or the century-old payments to counties revenue sharing system. Using expenditure data from sale purchasers, contractors, and fiscal agents, we developed methodology to track spending and used IMPLAN software to estimate economic contributions and multipliers. Results showed that (1) commercial thinning, service …