Physical Sciences and Mathematics Commons^™

Urban And Rural-Residential Land Uses: Their Role In Watershed Health And The Rehabilitation Of Oregon’S Wild Salmonids, Michael Harte, Victor W. Kaczynski, Clinton C. Shock, J. Alan Yeakley, Robert M. Hughes, Nancy Molina, Carl B. Schreck

Environmental Science and Management Faculty Publications and Presentations

This technical report by the Independent Multidisciplinary Science Team (IMST) is a comprehensive review of how human activities in urban and rural-residential areas can alter aquatic ecosystems and resulting implications for salmonid recovery, with a geographic focus on the state of Oregon. The following topics are considered in the form of science questions, and comprise the major components of this report:

1. The effects of urban and rural-residential development on Oregon’s watersheds and native wild salmonids.
2. Actions that can be used to avoid or mitigate undesirable changes to aquatic ecosystems near developing urban and rural-residential areas.
3. The benefits and pitfalls of …

Interview With Brendan Phillips, Sisters Of The Road, 2010 (Audio), Brendan Phillips

All Sustainability History Project Oral Histories

Interview of Brendan Phillips by Brandon Green in Portland, Oregon on December 8th, 2010.

The interview index is available for download.

Reconstructability Analysis Of Epistasis, Martin Zwick

Systems Science Faculty Publications and Presentations

The literature on epistasis describes various methods to detect epistatic interactions and to classify different types of epistasis. Reconstructability analysis (RA) has recently been used to detect epistasis in genomic data. This paper shows that RA offers a classification of types of epistasis at three levels of resolution (variable-based models without loops, variable-based models with loops, state-based models). These types can be defined by the simplest RA structures that model the data without information loss; a more detailed classification can be defined by the information content of multiple candidate structures. The RA classification can be augmented with structures from related …

Random Automata Networks: Why Playing Dice Is Not A Vice, Christof Teuscher

Systems Science Friday Noon Seminar Series

Random automata networks consist of a set of simple compute nodes interacting with each other. In this generic model, one or multiple model parameters, such as the the node interactions and/or the compute functions, are chosen at random. Random Boolean Networks (RBNs) are a particular case of discrete dynamical automata networks where both time and states are discrete. While traditional RBNs are generally credited to Stuart Kauffman (1969), who introduced them as simplified models of gene regulation, Alan Turing proposed unorganized machines as early as 1948. In this talk I will start with Alan Turing's early work on unorganized machines, …

Recreational Boats As Potential Vectors Of Marine Organisms At An Invasion Hotspot, Ian C. Davidson, Chela J. Zabin, Andrew L. Chang, Christopher W. Brown, Mark Sytsma, Gregory M. Ruiz

Center for Lakes and Reservoirs Publications and Presentations

With more than 200 aquatic nonindigenous species (NIS), San Francisco Bay (California, USA) is among the world’s most invaded harbors. Hard-substratum benthic (biofouling) organisms, which dominate NIS richness, have arrived primarily as a result of shipping and aquaculture activity over past centuries. To date there has been no assessment of the leisure craft vector in the Bay. We aimed to characterize (1) biofouling on boats’ submerged surfaces and (2) boater behavior likely to affect the risk of NIS transfers. We used an underwater pole-cam, specimen collections, and a boater questionnaire to quantify the extent and composition of biofouling on recreational …

Interview With Dan Mcfarling, Aorta, 2010 (Audio), Dan Mcfarling

All Sustainability History Project Oral Histories

Interview of Dan McFarling by Andrew Scanlan at Union Station, Portland, Oregon on December 1st, 2010.

The interview index is available for download.

Effect Of Network Structure On The Stability Margin Of Large Vehicle With Distributed Control, He Hao, Prabir Barooah, J. J. P. Veerman

Mathematics and Statistics Faculty Publications and Presentations

We study the problem of distributed control of a large network of double-integrator agents to maintain a rigid formation. A few lead vehicles are given information on the desired trajectory of the formation; while every other vehicle uses linear controller which only depends on relative position and velocity from a few other vehicles, which are called its neighbors. A predetermined information graph defines the neighbor relationships. We limit our attention to information graphs that are D-dimensional lattices, and examine the stability margin of the closed loop, which is measured by the real part of the least stable eigenvalue of …

Apertureless Near-Field/Far-Field Cw Two-Photon Microscope For Biological And Material Imaging And Spectroscopic Applications, Derek Brant Nowak, Andrew James Lawrence, Erik J. Sánchez

Physics Faculty Publications and Presentations

We present the development of a versatile spectroscopic imaging tool to allow for imaging with single-molecule sensitivity and high spatial resolution. The microscope allows for near-field and subdiffraction-limited far-field imaging by integrating a shear-force microscope on top of a custom inverted microscope design. The instrument has the ability to image in ambient conditions with optical resolutions on the order of tens of nanometers in the near field. A single low-cost computer controls the microscope with a field programmable gate array data acquisition card. High spatial resolution imaging is achieved with an inexpensive CW multiphoton excitation source, using an apertureless probe …

Phosphorus Export From A Restored Wetland Ecosystem In Response To Natural And Experimental Hydrologic Fluctuations, Marcelo Ardón, Shaena Montanari, Jennifer L. Morse, Martin W. Doyle, Emily S. Bernhardt

Environmental Science and Management Faculty Publications and Presentations

Wetland restoration is a commonly used approach to reduce nutrient loading to freshwater and coastal ecosystems, with many wetland restoration efforts occurring in former agricultural fields. Restored wetlands are expected to be effective at retaining or removing both nitrogen and phosphorus (P), yet restoring wetland hydrology to former agricultural fields can lead to the release of legacy fertilizer P. Here, we examined P cycling and export following rewetting of the Timberlake Restoration Project, a 440 ha restored riverine wetland complex in the coastal plain of North Carolina. We also compared P cycling within the restored wetland to two minimally disturbed …

Amaila Falls Hydroelectric Project Model Development And Scenarios, Chris Berger, Scott A. Wells, Vanessa Wells

Civil and Environmental Engineering Faculty Publications and Presentations

The focus of this present study is to perform the following tasks:

* Develop a hydrodynamic and water quality model of the reservoir formed by the Amaila Falls Hydroelectric Project

* Develop and run modeling scenarios

Water quality model simulations of the 23.3 km² reservoir for Amaila Falls Hydroelectric Project were conducted for low, average, and high flow years. A scenario with no vegetation removed from the reservoir for an average flow was also simulated. Conditions downstream of the reservoir were also modeled using a river model.

The model used for the reservoir formed by Amaila Falls Hydroelectric Project …

The Distribution And Reproductive Success Of The Western Snowy Plover Along The Oregon Coast - 2010, David J. Lauten, Kathleen J. Castelein, J. Daniel Farrar, Adam A. Kotaich, Eleanor P. Gaines

Institute for Natural Resources Publications

From 8 April – 27 September 2010 we monitored the distribution, abundance and productivity of the federally Threatened Western Snowy Plover (Charadrius alexandrinus nivosus) along the Oregon coast. From north to south, we surveyed and monitored plover activity at Sutton Beach, Siltcoos River estuary, the Dunes Overlook, North Tahkenitch Creek, Tenmile Creek, Coos Bay North Spit, Bandon Beach, New River, and Floras Lake. Our objectives for the Oregon coastal population in 2010 were to: 1) estimate the size of the adult Snowy Plover population, 2) locate plover nests, 3) continue selective use of mini-exclosures (MEs) to protect nests …

Interview With Michael O'Brien, Osd, 2010 (Audio), Michael O'Brien

All Sustainability History Project Oral Histories

Interview of Michael O'Brien by Ian Caputo in North Portland, Oregon on November 22nd, 2010.

The interview index is available for download.

Interview With Brighton West, Friends Of Trees, 2010 (Audio), Brighton West

All Sustainability History Project Oral Histories

Interview of Brighton West by Brigitta Bazso at Portland State University on November 18th, 2010.

The interview index is available for download.

Interview With Renee Loveland, Gerding Edlen, 2010 (Audio), Renee Loveland

All Sustainability History Project Oral Histories

Interview of Renee Loveland by Jena Orr at Gerding Edlen, Portland, Oregon on November 17th, 2010.

The interview index is available for download.

Bandwidth Tuning Triggers Interplay Of Charge Order And Superconductivity In Two-Dimensional Organic Materials, S. Kaiser, M. Dressel, Y. Sun, A. Greco, J. A. Schlueter, Gary L. Gard, N. Drichko

Chemistry Faculty Publications and Presentations

We observe charge-order fluctuations in the quasi-two-dimensional organic superconductor β″-(BEDT-TTF)₂SF₅CH₂CF₂SO₃, both by means of vibrational spectroscopy, locally probing the fluctuating charge order, and by investigating the in-plane dynamical response by infrared reflectance spectroscopy. The decrease of the effective electronic interaction in an isostructural metal suppresses both charge-order fluctuations and superconductivity, pointing to their interplay. We compare the results of our experiments with calculations on the extended Hubbard model.

Accelerated Erosion Of Saltmarshes Infested By The Non-Native Burrowing Crustacean Sphaeroma Quoianum, Timothy Mathias Davidson, Catherine E. De Rivera

Environmental Science and Management Faculty Publications and Presentations

Lateral erosion of saltmarshes is affected by many abiotic and biotic factors. While abiotic factors are typically regarded as primary drivers of erosion, biotic influences such as burrowing or bioturbating taxa can also extensively modify the physical structure of this marine habitat. Many estuaries on the Pacific coast of North America have been invaded by populations of the burrowing non-native isopod Sphaeroma quoianum, which are thought to exacerbate the erosion of saltmarshes. We conducted a mensurative experiment to examine the relationship between populations of S. quoianum and lateral erosion rate of saltmarshes in Coos Bay, Oregon, USA. After 1 …

Understanding, Modeling And Valuing Ecosystem Services, Robert Costanza

Systems Science Friday Noon Seminar Series

Ecosystem services (ES) are the direct and indirect contributions of ecosystems (in combination with other inputs) to human well-being. An ES-based approach can assess the trade-offs inherent in managing humans embedded in ecological systems. Evaluating trade-offs requires both an understanding of the biophysical magnitudes of ES changes that result from human actions, as well as an understanding of their impact on human well-being, broadly conceived. This talk discusses the state of the art of ES assessment, valuation, and modeling, including the potential of integrated ecological economic modeling. Valuation is about assessing trade-offs – not necessarily about trades (exchanges) in markets …

Accurate Description Of The Optical Response Of A Multilayered Spherical System In The Long Wavelength Approximation, H. Y. Chung, G. Y. Guo, Hai-Pang Chiang, D. P. Tsai, P.T. Leung

Physics Faculty Publications and Presentations

The optical response of a multilayered spherical system of unlimited number of layers (a “matryoshka”) in the long wavelength limit can be accounted for from the knowledge of the static multipole polarizability of the system to first-order accuracy. However, for systems of ultrasmall dimensions or systems with sizes not-too-small compared to the wavelength, this ordinary quasistatic long wavelength approximation (LWA) becomes inaccurate. Here we introduce two significant modifications of the LWA for such a nanomatryoshka in each of the two limits: the nonlocal optical response for ultrasmall systems (<10 >nm), and the “finite-wavelength corrections” for systems ∼100 nm. This is …

Scoring Function To Predict Solubility Mutagenesis, Ye Tian, Christopher Deutsch, Bala Krishnamoorthy

Chemistry Faculty Publications and Presentations

Background: Mutagenesis is commonly used to engineer proteins with desirable properties not present in the wild type (WT) protein, such as increased or decreased stability, reactivity, or solubility. Experimentalists often have to choose a small subset of mutations from a large number of candidates to obtain the desired change, and computational techniques are invaluable to make the choices. While several such methods have been proposed to predict stability and reactivity mutagenesis, solubility has not received much attention. Results: We use concepts from computational geometry to define a three body scoring function that predicts the change in protein solubility due to …

Tabor To The River: An Evaluation Of Outreach Efforts And Opportunities For Engaging Residents In Stormwater Management, Vivek Shandas, Anne Nelson, Carine Arendes, Cathy Cibor

Institute for Sustainable Solutions Publications and Presentations

This report summarizes the key findings from a neighborhood survey that focused on household perceptions of sustainable stormwater systems. The survey was conducted in collaboration with the City of Portland?s Bureau of Environmental Services (BES) and Portland State University?s Center for Urban Studies.

A Class Of Discontinuous Petrov–Galerkin Methods. Part Iv: The Optimal Test Norm And Time-Harmonic Wave Propagation In 1d., Jeffrey Zitelli, Leszek Demkowicz, Jay Gopalakrishnan, D. Pardo, V. M. Calo

Mathematics and Statistics Faculty Publications and Presentations

The phase error, or the pollution effect in the finite element solution of wave propagation problems, is a well known phenomenon that must be confronted when solving problems in the high-frequency range. This paper presents a new method with no phase errors for one-dimensional (1D) time-harmonic wave propagation problems using new ideas that hold promise for the multidimensional case. The method is constructed within the framework of the discontinuous Petrov–Galerkin (DPG) method with optimal test functions. We have previously shown that such methods select solutions that are the best possible approximations in an energy norm dual to any selected test …

Extensive Aerosol Optical Properties And Aerosol Mass Related Measurements During Tramp/Texaqs 2006 – Implications For Pm Compliance And Planning, Monica Elizabeth Wright, Dean B. Atkinson, Luke Ziemba, Robert Griffin, Naruki Hiranuma, Sarah D. Brooks, James Flynn, Ryan Perna, Bernhard Rappenglück, Winston Luke, Paul Kelley

Chemistry Faculty Publications and Presentations

Extensive aerosol optical properties, particle size distributions, and Aerodyne quadrupole aerosol mass spectrometer measurements collected during TRAMP/TexAQS 2006 were examined in light of collocated meteorological and chemical measurements. Much of the evident variability in the observed aerosol-related air quality is due to changing synoptic meteorological situations that direct emissions from various sources to the TRAMP site near the center of the Houston-Galveston-Brazoria (HGB) metropolitan area. In this study, five distinct long-term periods have been identified. During each of these periods, observed aerosol properties have implications that are of interest to environmental quality management agencies. During three of the periods, long …

Facile Pyrolytic Synthesis Of Silicon Nanowires, Joo C. Chan, Hoang Tran, James W. Pattison, Shankar B. Rananavare

Chemistry Faculty Publications and Presentations

One-dimensional nanostructures such as silicon nanowires (SiNW) are attractive candidates for low power density electronic and optoelectronic devices including sensors. A new simple method for SiNW bulk synthesis[1, 2] is demonstrated in this work, which is inexpensive and uses low toxicity materials, thereby offering a safe, energy efficient and green approach. The method uses low flammability liquid phenylsilanes, offering a safer avenue for SiNW growth compared with using silane gas. A novel, duo-chamber glass vessel is used to create a low-pressure environment where SiNWs are grown through vapor-liquid-solid mechanism using gold nanoparticles as a catalyst. The catalyst decomposes silicon precursor …

Structure Of The Cholera Toxin Secretion Channel In Its Closed State, Steve Reichow, Konstantin V. Korotkov, Wim Gj Hol, Tamir Gonen

Chemistry Faculty Publications and Presentations

The type II secretion system (T2SS) is a macromolecular complex spanning the inner and outer membranes of Gram-negative bacteria. Remarkably, the T2SS secretes folded proteins including multimeric assemblies like cholera toxin and heat-labile enterotoxin from Vibrio cholerae and enterotoxigenic Escherichia coli, respectively. The major outer membrane T2SS protein is the “secretin” GspD. Electron cryomicroscopy reconstruction of the V. cholerae secretin at 19 Å resolution reveals a dodecameric structure reminiscent of a barrel with a large channel at its center that appears to contain a closed periplasmic gate. The GspD periplasmic domain forms a vestibule with a conserved constriction, and binds …

Cooperative Interaction Of Transcription Termination Factors With The Rna Polymerase Ii C-Terminal Domain, Bradley M. Lunde, Steve Reichow, Minkyu Kim, Hyunsuk Suh, Thomas C. Leeper, Fan Yang, Hannes Mutschler, Stephen Buratowski, Anton Meinhart, Gabriele Varani

Chemistry Faculty Publications and Presentations

Phosphorylation of the C-terminal domain of RNA polymerase II controls the co-transcriptional assembly of RNA processing and transcription factors. Recruitment relies on conserved CTDinteracting domains that recognize different CTD phosphoisoforms during the transcription cycle, but the molecular basis for their specificity remains unclear. We show that the CTD-interacting domains of two transcription termination factors, Rtt103 and Pcf11, achieve high affinity and specificity both by specifically recognizing the phosphorylated CTD and by cooperatively binding to neighboring CTD repeats. Single amino acid mutations at the protein-protein interface abolish cooperativity and affect recruitment at the 3′-end processing site in vivo. We suggest that …

Systems For Assessing And Enhancing The Performance Of Scanning Electron Microscopes By Quantifying And Enforcing Symmetries And Periodicities In Two Dimensions, Peter Moeck

Physics Faculty Publications and Presentations

Scanning probe microscope (SPM) images are enhanced by enforcing one or more symmetries that can be selected based on suitable Fourier coefficient amplitude or phase angle residuals, and/ or geometric Akaike information criteria, and/ or cross correlation techniques. Alternatively, this selection can be based on prior knowledge of specimen characteristics. In addition, a scanning microscope point spread function is obtained based on the evaluation of a calibration image by enforcing at least one symmetry and can be applied to other image acquisitions.

The Perfect Spill: Solutions For Averting The Next Deepwater Horizon, Robert Costanza, David Batker, John W. Day, Rusty A. Feagin, M. Luisa Martinez, Joe Roman

Institute for Sustainable Solutions Publications and Presentations

In this article the authors comment on the oil spill incident from the Deepwater Horizon, particularly on its economic and ecological damages. The authors highlighted the disaster as an event wherein much is needed to be learned so that future oil spills can be avoided. One lesson refers to the valuability of natural capital assets and other public entities that are at risks due to private interests and that better regulations and incentives are needed to protect these assets against risks.

The Effectiveness Of Vertebrate Passage And Prevention Structures: A Study Of Boeckman Road In Wilsonville, Catherine E. De Rivera, Leslie L. Bliss-Ketchum

Environmental Science and Management Faculty Publications and Presentations

One of the most obvious impacts roads have on the natural world is direct mortality to individual animals that attempt to cross roads. A less obvious but likely more important impact of roads on many species is habitat fragmentation. The ability for individuals to travel between subpopulations is the key to genetic diversity as well as ultimately the survival of the species. Considering these impacts and management goals to increase habitat connectivity, increased attention has been given to creating road design that reduces wildlife collisions. Most studies, however, have been in other countries or regions and most focus on connectivity …

Modeling Acoustic Scattering From The Seabed Using Transport Theory, Jorge Quijano, Lisa M. Zurk

Electrical and Computer Engineering Faculty Publications and Presentations

Radiative Transfer (RT) theory has established itself as an important tool for electromagnetic remote sensing in parallel plane geometries with random distributions of scatterers, and most recently it has also been proposed as a model for the propagation of elastic waves in layered ocean sediments. In this work the capabilities of this model are illustrated, as the RT method is used to predict backscattering strength from laboratory models of random media. The RT model is characterized by its flexibility on accommodating scatterers in a broad variety of sizes, shapes, and acoustic contrast relative to the background media. Additionally, this formulation …

Virus Silicification Under Simulated Hot Spring Conditions, James R. Laidler, Kenneth M. Stedman

Biology Faculty Publications and Presentations

Silicification of organisms in silica-depositing environments can impact both their ecology and their presence in the fossil record. Although microbes have been silicified under laboratory and environmental conditions, viruses have not. Bacteriophage T4 was successfully silicified under laboratory conditions that closely simulated those found in silica-depositing hot springs. Virus morphology was maintained, and a clear elemental signature of phosphorus was detected by energy-dispersive X-ray spectrophotometry (EDS).