Physical Sciences and Mathematics Commons^™

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 …

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 …

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 …

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 …

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 …

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.

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.

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 …

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 …

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).

Interview With Crystal Benson, Green Building Services, 2010 (Audio), Crystal Benson

All Sustainability History Project Oral Histories

Interview of Crystal M. Benson by Alex Woolery at Green Building Services Portland, Oregon on August 12th, 2010.

The interview index is available for download.

Interview With Brandon Hill, Bamboo Sushi, 2010 (Audio), Brandon Hill

All Sustainability History Project Oral Histories

Interview of Brandon Hill by Jeff Francoeur at Bamboo Sushi, SE Portland, Oregon on August 10, 2010.

The interview index is available for download.

Interview With Farhad Ghafarzade, Green Drop Garage, 2010 (Audio), Farhad Ghafarzade

All Sustainability History Project Oral Histories

Interview of Farhad Ghafarzade by Jeff Howard in SE Portland, Oregon on August 6th, 2010.

The interview index is available for download.

Interview With Nicole Stein, Umpqua Bank, 2010 (Audio), Nicole Stein

All Sustainability History Project Oral Histories

Interview of Nicole Stein by Shivon Van Allen at SW Portland, Oregon on August 5th, 2010.

The interview index is available for download.

Interview With Garrett Moon, The Commons Project, 2010 (Audio), Garrett Moon

All Sustainability History Project Oral Histories

Interview of Garrett Moon by Rayne Walter-Young at Portland State University on August 3rd, 2010.

The interview index is available for download.

Contribution Of Membrane Elastic Energy To Rhodopsin Function, Olivier Soubias, Walter E. Teague, Kirk G. Hines, Drake C. Mitchell, Klaus Gawrisch

Physics Faculty Publications and Presentations

We considered the issue of whether shifts in the metarhodopsin I (MI)-metarhodopsin II (MII) equilibrium from lipid composition are fully explicable by differences in bilayer curvature elastic stress. A series of six lipids with known spontaneous radii of monolayer curvature and bending elastic moduli were added at increasing concentrations to the matrix lipid 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and the MI-MII equilibrium measured by flash photolysis followed by recording UV-vis spectra. The average area-per-lipid molecule and the membrane hydrophobic thickness were derived from measurements of the 2H NMR order parameter profile of the palmitic acid chain in POPC. For the series of ethanolamines …

Climate Change And Globalization In The Americas: Case Studies Of Mitigation And Adaptation, Mary Finley-Brook, Melissa Haeffner, Charmaine Heslop-Thomas, Elma Montaña, Leah Sprain

Environmental Science and Management Faculty Publications and Presentations

Robin Leichenko and Karen O‘Brien have proposed ―double exposure‖ as a conceptual framework to demonstrate how processes of globalization and global environmental change (GEC) redefine risk and encourage new, interrelated responses to social and ecological transitions (O‘Brien and Leichenko, 2000; Leichenko and O'Brien, 2008). In particular, the concept encourages researchers and policy makers to consider interplay between global climate change and globalization and how this is expressed unevenly across space. After reviewing the ways double exposure has been used in the literature, we consider four case studies to investigate the utility of the framework for analyzing and understanding climate change …

Biosynthesis Of Salinosporamides From Α,Β-Unsaturated Fatty Acids: Implications For Extending Polyketide Synthase Diversity, Yuan Liu, Christopher Hazzard, Alessandra S. Eustáquio, Kevin A. Reynolds, Bradley S. Moore

Chemistry Faculty Publications and Presentations

A new series of coenzyme A-tethered polyketide synthase extender units were discovered in relation to the biosynthesis of the salinosporamide family of anticancer agents from the marine bacterium Salinispora tropica. In vivo and in vitro experiments revealed that the crotonyl-CoA reductase/carboxylase SalG has broad substrate tolerance toward 2-alkenyl-CoAs that give rise to the salinosporamide C-2 substitution pattern.

Supplementary Balance Laws And The Entropy Principle, Serge Preston

Mathematics and Statistics Faculty Publications and Presentations

In this work we study the mathematical aspects of the development in the continuum thermodynamics known as the “Entropy Principle”. It started with the pioneering works of B.Coleman, W.Noll and I. Muller in 60th of XX cent. and got its further development mostly in the works of G. Boillat, I-Shis Liu and T.Ruggeri. “Entropy Principle” combines in itself the structural requirement on the form of balance laws of the thermodynamical system (denote such system (C)) and on the entropy balance law with the convexity condition of the entropy density. First of these requirements has pure mathematical form defining so called …

Non-­Native Invasive Aquatic Plant And Mussel Survey Of Six Umpqua National Forest Area Lakes, Mark Sytsma, Rich Miller, Rupa Shrestha

Center for Lakes and Reservoirs Publications and Presentations

Six lakes and ponds located within or near the Umpqua National Forest were surveyed for non-­native aquatic plants and mussels during August, 2009. A diverse assemblage of native plants was identified along with one possible non-­native aquatic plant hybrid in Herberts Pond. The possible hybrid between the non-­native species Myriophyllum spicatum and the native species M. sibiricum requires genetic analysis for identification. Water chemistry is suitable for the establishment of invasive mussels in Buckeye Lake; however, no zebra or quagga mussel veligers were detected in any of the lakes.

Climate Change, Its Effect On Migration Patterns Of The Cackling Goose And White-Fronted Goose In The Willamette Valley, And Implications For Goose Management, Kelly Warren

Environmental Science and Management Professional Master's Project Reports

This thesis considers the question of whether climate change is affecting the migration patterns of geese in the Pacific Flyway, specifically cackling geese (Branta hutchinsii minima) and Pacific white-fronted geese (Anser albifrons frontalis). Ancillary questions that are considered are as follows:

• If global warming is affecting these species, what is the nature of the effects?

• How are the changes affecting the human environment and what can be done about these effects?

In 1994, the majority of the cackler population in the Pacific Flyway began to winter in Oregon's Willamette Valley rather than in their …

Symmetries Of The Central Vestibular System: Forming Movements For Gravity And A Three-Dimensional World, Gin Mccollum, Douglas Hanes

Mathematics and Statistics Faculty Publications and Presentations

Intrinsic dynamics of the central vestibular system (CVS) appear to be at least partly determined by the symmetries of its connections. The CVS contributes to whole-body functions such as upright balance and maintenance of gaze direction. These functions coordinate disparate senses (visual, inertial, somatosensory, auditory) and body movements (leg, trunk, head/neck, eye). They are also unified by geometric conditions. Symmetry groups have been found to structure experimentally-recorded pathways of the central vestibular system. When related to geometric conditions in three-dimensional physical space, these symmetry groups make sense as a logical foundation for sensorimotor coordination.

Interview With Brad Bateman, Costco, 2010 (Audio), Brad Bateman

All Sustainability History Project Oral Histories

Interview of Brad Bateman by Nemah Dalai at Costco Clackamas, Oregon on June 10th, 2010.

The interview index is available for download.

Outcomes Of A One-Week Teaching Training In Community-Based Ecological Research, Kara Gonsler

Environmental Science and Management Professional Master's Project Reports

The goal of this project was to expand on potential audiences and partnerships within the Teaching Ecological Complexity Project, by creating a one-week teacher training workshop in collaboration with a local natural resource management partner. The training sought to increase teachers’ understanding of ecology and qualitative conceptual models through immersion in field research and partnerships with local scientists and natural resource managers. Ecological knowledge was measured by comparing pre and post qualitative conceptual models, which were scored with a rubric and analyzed using the Wilcoxon Signed Ranks Test. Classroom implementation of an inquiry-based ecological research project was expected of participants. …

Food Delivery Footprint: Addressing Transportation, Packaging, And Waste In The Food Supply Chain, Madeleine E. Pullman, Robin Fenske, Wayne Wakeland

Business Faculty Publications and Presentations

Transportation of food accounts for a significant fraction of the carbon dioxide emissions believed to be adversely impacting climate and the environment. And this impact is increasing as food supply chains become longer and more complex, and food packaging requirements lead to increased waste. Many organizations such as hospitals and upper level education are becoming increasingly concerned about sustainability. In this study, college, university, and hospital food purchasing behavior were assessed using interviews, surveys, and modeling to evaluate the environmental implications of decisions regarding food transportation and packaging. Current purchasing practices, corresponding transportation modes, packaging, recycling, and waste removal were …

Interview With Marisa Ferro, Portland State University, 2010 (Audio), Marisa Ferro

All Sustainability History Project Oral Histories

Interview of Marisa Ferro by Hamza Sherwani at Portland State University on June 1st, 2010.

The interview index is available for download.