Physical Sciences and Mathematics Commons^™

Planetary Boundaries: Exploring The Safe Operating Space For Humanity, Johan Rockström, W. L. Steffen, Kevin Noone, Åsa Persson, F. Stuart Chapin Iii, Eric Lambin, Timothy M. Lenton, Marten Scheffer, Carl Folke, Hans Joachim Schellnhuber, Björn Nykvist, Cynthia A. De Wit, Terry Hughes, Sander Van Der Leeuw, Henning Rodhe, Sverker Sörlin, Peter K. Snyder, Robert Costanza, Uno Svedin, Malin Falkenmark, Louise Karlberg, Robert W. Corell, Victoria J. Fabry, James Hansen, Brian Walker, Diana Liverman, Katherine Richardson, Paul Crutzen, Jonathan Foley

Institute for Sustainable Solutions Publications and Presentations

Anthropogenic pressures on the Earth System have reached a scale where abrupt global environmental change can no longer be excluded. We propose a new approach to global sustainability in which we define planetary boundaries within which we expect that humanity can operate safely. Transgressing one or more planetary boundaries may be deleterious or even catastrophic due to the risk of crossing thresholds that will trigger non-linear, abrupt environmental change within continental- to planetary-scale systems. We have identified nine planetary boundaries and, drawing upon current scientific understanding, we propose quantifications for seven of them. These seven are climate change (CO2 concentration …

Dark Current Behavior In Dslr Cameras, Justin Charles Dunlap, Oleg Sostin, Ralf Widenhorn, Erik Bodegom

Physics Faculty Publications and Presentations

Digital single-lens reflex (DSLR) cameras are examined and their dark current behavior is presented. We examine the influence of varying temperature, exposure time, and gain setting on dark current. Dark current behavior unique to sensors within such cameras is observed. In particular, heat is trapped within the camera body resulting in higher internal temperatures and an increase in dark current after successive images. We look at the possibility of correcting for the dark current, based on previous work done for scientific grade imagers, where hot pixels are used as indicators for the entire chip?s dark current behavior. Standard methods of …

Nano-Structure Formation Driven By Local Protonation Of Polymer Thin Films, Carsten Maedler, Harald Graaf, Mingdi Yan, Andres H. La Rosa

Physics Faculty Publications and Presentations

We report the creation of nano-structures via Dip Pen Nanolithography by locally exploiting the mechanical response of polymer thin films to an acidic environment. Protonation of cross linked poly(4-vinylpyridine) (P4VP) leads to a swelling of the polymer. We studied this process by using an AFM tip coated with a pH 4 buffer. Protons migrate through a water meniscus between tip and sample into the polymer matrix and interact with the nitrogen of the pyridyl group forming a pyridinium cation. The increase in film thickness, which is due to Coulomb repulsion between the charged centers, was investigated using Atomic Force Microscopy. …

Crystallography Open Database – An Open-Access Collection Of Crystal Structures, Saulius Grazulis, Daniel Chateigner, Robert T. Downs, A. F. T. Yokochi, Miguel Quirós, Luca Lutterotti, Elena Manakova, Justas Butkus, Peter Moeck, Armel Le Bail

Physics Faculty Publications and Presentations

The Crystallography Open Database (COD), which is a project that aims to gather all available inorganic, metal–organic and small organic molecule structural data in one database, is described. The database adopts an openaccess model. The COD currently contains 80,000 entries in crystallographic information file format, with nearly full coverage of the International Union of Crystallography publications, and is growing in size and quality.

Electron Microscopy And Optical Characterization Of Cadmium Sulphide Nanocrystals Deposited On The Patterned Surface Of Diatom Biosilica, Timothy Gutu, Debra K. Gale, Clayton Jeffryes, Wei Wang, Chih-Hung Chang, Gregory L. Rorrer, Jun Jiao

Physics Faculty Publications and Presentations

Intricately patterned biosilica obtained from the shell of unicellular algae called diatoms serve as novel templates for fabrication of optoelectronic nanostructures. In this study, the surface of diatom frustules that possessed hierarchical architecture ordered at the micro and nanoscale was coated with a nanostructured polycrystalline cadmium sulphide (CdS) thin film using a chemical bath deposition technique. The CdS thin film was composed of spherical nanoparticles with a diameter of about 75 nm. The CdS nanoparticle thin film imparted new photoluminescent properties to the intricately patterned diatom nanostructure. The imparted photoluminescent properties were dependent on the CdS coverage onto the frustules …

Report On Wintering Western Snowy Plovers At Coos Bay North Spit And Impacts To Plovers From The North Jetty Repair Project, Winter 2009, David J. Lauten, Kathleen J. Castelein, Eleanor P. Gaines

Institute for Natural Resources Publications

The Western Snowy Plover (Charadrius alexandrinus nivosus) breeds along the coast of the Pacific Ocean in California, Oregon, and Washington and at alkaline lakes in the interior of the western United States (Page et al. 1991). Loss of habitat, predation pressures, and disturbance have caused the decline of the coastal population of Snowy Plovers and led to the listing of the Pacific Coast Population of Western Snowy Plovers as Threatened on March 5, 1993 (U.S. Fish and Wildlife Service 1993). Oregon Western Snowy Plovers are known to winter along the coast of Oregon as well as migrate to …

Generation Of Novel Pikromycin Antibiotic Products Through Mutasynthesis, Shuchi Gupta, Venkatraman Lakshmanan, Beom Seok Kim, Robert Fecik, Kevin A. Reynolds

Chemistry Faculty Publications and Presentations

Mutasynthesis in pikromycin PKS: The amenability of pikromycin polyketide synthase to mutational biosynthesis has been demonstrated. A natural triketide and its analogues, activated as N-acetyl-cysteamine thioesters, were synthesized and fed to a pikAI-deleted strain; this led to the production of new antibiotics. A vinyl analogue was found to have better antibacterial activity than pikromycin.

Optimising The Synthesis And Red–Green–Blue Emission Of A Simple Organic Dye, Martha Sibrian-Vazquez, Robert M. Strongin

Chemistry Faculty Publications and Presentations

Synthetic dyes have been widely used in supramolecular chemistry not only to probe fundamental chemical interactions but also as components of functional materials. Most current efforts in this regard are directed at designing new host systems for the dyes. Herein we report on the study of a versatile new organic fluorophore. We describe a synthesis which affords improved yields in a convenient one pot procedure. Moreover, a simple method for predicting and controlling the dye’s responses to external stimuli affords a potentially practical method for achieving red–green–blue and concomitant white light generation.

Automated Traffic And The Finite Size Resonance, J. J. P. Veerman, Borko D. Stošić, F. M. Tangerman

Mathematics and Statistics Faculty Publications and Presentations

We investigate in detail what one might call the canonical (automated) traffic problem: A long string of N+1 cars (numbered from 0 to N) moves along a one-lane road “in formation” at a constant velocity and with a unit distance between successive cars. Each car monitors the relative velocity and position of only its neighboring cars. This information is then fed back to its own engine which decelerates (brakes) or accelerates according to the information it receives. The question is: What happens when due to an external influence—a traffic light turning green—the ‘zero’th’ car (the “leader”) accelerates?

As …

Structural Basis For Binding Specificity Between Subclasses Of Modular Polyketide Synthase Docking Domains, Tonia Buchholz, Todd W. Geders, Frank E. Bartley Iii, Kevin A. Reynolds, Janet L. Smith, David H. Sherman

Chemistry Faculty Publications and Presentations

Bacterial type I polyketide synthases (PKSs) assemble structurally diverse natural products of significant clinical value from simple metabolic building blocks. The synthesis of these compounds occurs in a processive fashion along a large multiprotein complex. Transfer of the acyl intermediate across interpolypeptide junctions is mediated, at least in large part, by N- and C-terminal docking domains. We report here a comprehensive analysis of the binding affinity and selectivity for the complete set of discrete docking domain pairs in the pikromycin and erythromycin PKS systems. Despite disconnection from their parent module, each cognate pair of docking domains retained exquisite binding selectivity. …

Unified Hybridization Of Discontinuous Galerkin, Mixed, And Continuous Galerkin Methods For Second Order Elliptic Problems, Bernardo Cockburn, Jay Gopalakrishnan, Raytcho Lazarov

Mathematics and Statistics Faculty Publications and Presentations

We introduce a unifying framework for hybridization of finite element methods for second order elliptic problems. The methods fitting in the framework are a general class of mixed-dual finite element methods including hybridized mixed, continu- ous Galerkin, non-conforming and a new, wide class of hybridizable discontinuous Galerkin methods. The distinctive feature of the methods in this framework is that the only globally coupled degrees of freedom are those of an approximation of the solution defined only on the boundaries of the elements. Since the associated matrix is sparse, symmetric and positive definite, these methods can be efficiently implemented. Moreover, the …

Precession Electron Diffraction And Its Advantages For Structural Fingerprinting In The Transmission Electron Microscope, Peter Moeck, Sergei Rouvimov

Physics Faculty Publications and Presentations

The foundations of precession electron diffraction in a transmission electron microscope are outlined. A brief illustration of the fact that laboratory-based powder X-ray diffraction fingerprinting is not feasible for nanocrystals is given. A procedure for structural fingerprinting of nanocrystals on the basis of structural data that can be extracted from precession electron diffraction spot patterns is proposed.

Calculating The Volume Of The May 18, 1980 Eruption Of Mount St. Helens, Dâvid Nuñez Wickham

Environmental Science and Management Professional Master's Project Reports

The May 18, 1980 eruption of Mount St. Helens created a massive amount of sediment and debris, thought to be as much as 5.5 billion cubic yards. This sediment causes infill of river stretches and collects along levees protecting southwest Washington State. The sediment must be removed to ensure these areas do not flood. The US Army Corps of Engineers (USACOE) is tasked with flood protection for southwest Washington State and the levees protecting the cities of Castle Rock, Lexington, Kelso, and Longview. The Sediment Retention Dam, opened in 1989 is able to filter out larger particulate but fine grain …

Downspout Disconnection Suitability And Incentives Analysis For The City Of Gresham, Oregon, Brian C. Fletcher

Environmental Science and Management Professional Master's Project Reports

The City of Gresham is developing a Downspout Disconnection Program, which encourages homeowners to disconnect their roof downspouts from the storm sewer system and divert the stormwater onto their lawn or rain garden. Downspout disconnection is being evaluated for its effectiveness to help the city meet stormwater discharge requirements in their NPDES-MS4 permit from Oregon DEQ. This study reviewed current Natural Resources Conservation Service (NRCS) soil data and developed a suitability map showing High, Medium and Low suitability zones for on-site stormwater management. To validate the map, 55 soil textural classes and 11 infiltration rates were determined at residences throughout …

A Photochemically Initiated Chemistry For Coupling Underivatized Carbohydrates To Gold Nanoparticles, Xin Wang, Olof Ramström, Mingdi Yan

Chemistry Faculty Publications and Presentations

The sensitive optoelectronic properties of metal nanoparticles make nanoparticle-based materials a powerful tool to study fundamental biorecognition processes. Here we present a new and versatile method for coupling underivatized carbohydrates to gold nanoparticles (Au NPs) via the photochemically induced reaction of perfluorophenylazide (PFPA). A one-pot procedure was developed where Au NPs were synthesized and functionalized with PFPA by a ligand-exchange reaction. Carbohydrates were subsequently immobilized on the NPs by a fast light activation. The coupling reaction was efficient, resulting in high coupling yield as well as high ligand surface coverage. A colorimetric system based on the carbohydrate-modified Au NPs was …

Exploring The Ph Dependence Of Viologen Reduction By Alpha-Carbon Radicals Derived From Hcy And Cys, Dong Wang, William E. Crowe, Robert M. Strongin, Martha Sibrian-Vazquez

Chemistry Faculty Publications and Presentations

The colorimetric reaction of homocysteine (HCy) with a series of viologen salts suggests a linear correlation between the mid-point reduction potential of Hcy-derived α-carbon radicals and pH.

Effect Of The Regiochemistry Of Butyl Amide Substituents On The Solution-State Structures Of Lanthanide(Iii) Dota-Tetraamide Complexes, Tomoyasu Mani, Gyula Tircsó, Piyu Zhao, A. Dean Sherry, Mark Woods

Chemistry Faculty Publications and Presentations

The coordination geometry adopted by the lanthanide complexes of DOTA-tetraamides is a critical factor in determining their water exchange kinetics. Controlling the water exchange kinetics of DOTA-tetraamide complexes, and by extension their coordination geometry, is of particular interest because of the potential application of this class of complex as PARACEST MRI contrast agents. To facilitate the maximum CEST effect at the lowest pre-saturation powers much slower exchange kinetics are required than are commonly observed with these types of chelates. Complexes that adopt the more slowly exchanging square antiprismatic coordination geometry are therefore preferred; however, the factors that govern which coordination …

A New Elasticity Element Made For Enforcing Weak Stress Symmetry, Bernardo Cockburn, Jay Gopalakrishnan, Johnny Guzmán

Mathematics and Statistics Faculty Publications and Presentations

We introduce a new mixed method for linear elasticity. The novelty is a simplicial element for the approximate stress. For every positive integer k, the row-wise divergence of the element space spans the set of polynomials of total degree k. The degrees of freedom are suited to achieve continuity of the normal stresses. What makes the element distinctive is that its dimension is the smallest required for enforcing a weak symmetry condition on the approximate stress. This is achieved using certain "bubble matrices", which are special divergence-free matrix-valued polynomials. We prove that the approximation error is of order k + …

Polynomial Extension Operators. Part Ii, Leszek Demkowicz, Jay Gopalakrishnan, Joachim Schöberl

Mathematics and Statistics Faculty Publications and Presentations

Consider the tangential trace of a vector polynomial on the surface of a tetrahedron. We construct an extension operator that extends such a trace function into a polynomial on the tetrahedron. This operator can be continuously extended to the trace space of H(curl ). Furthermore, it satisfies a commutativity property with an extension operator we constructed in Part I of this series. Such extensions are a fundamental ingredient of high order finite element analysis.

The Derivation Of Hybridizable Discontinuous Galerkin Methods For Stokes Flow, Bernardo Cockburn, Jay Gopalakrishnan

Mathematics and Statistics Faculty Publications and Presentations

In this paper, we introduce a new class of discontinuous Galerkin methods for the Stokes equations. The main feature of these methods is that they can be implemented in an efficient way through a hybridization procedure which reduces the globally coupled unknowns to certain approximations on the element boundaries. We present four ways of hybridizing the methods, which differ by the choice of the globally coupled unknowns. Classical methods for the Stokes equations can be thought of as limiting cases of these new methods.

Stability Of Linear Flocks On A Ring Road, J. J. P. Veerman, Carlos Martins Da Fonseca

Mathematics and Statistics Faculty Publications and Presentations

We discuss some stability problems when each agent of a linear flock on the line interacts with its two nearest neighbors (one on either side).

A Single Particle Impact Model For Motion In Avalanches, J. J. P. Veerman, Dacian Daescu, M. J. Romero-Vallés, P. J. Torres

Mathematics and Statistics Faculty Publications and Presentations

We describe the global behavior of the dynamics of a particle bouncing down an inclined staircase. For small inclinations all orbits eventually stop (independent of the initial condition). For large enough inclinations all orbits end up accelerating indefinitely (also independent of the initial conditions). There is an interval of inclinations of positive length between these two. In that interval the behavior of an orbit depends on its initial condition. In addition to stopping and accelerating orbits, there are also orbits with speeds bounded away from both zero and infinity. A second hallmark of the dynamics is that the orbits going …

Spatial Patterns Of Air Toxins In The Region, Linda Acha George, Vivek Shandas

Urban Studies and Planning Faculty Publications and Presentations

This Atlas draws on the Portland Air Toxics Assessment (PATA) study to explore the regional variation of air quality. The PATA study presents an extraordinary opportunity to think about how the creation of new information can help us better plan our cities, but it also challenges us to think about the impacts of the choices we make.

Evaluating Similarity-Based Trace Reduction Techniques For Scalable Performance Analysis, Kathryn Marie Mohror, Karen L. Karavanic

Computer Science Faculty Publications and Presentations

Event traces are required to correctly diagnose a number of performance problems that arise on today’s highly parallel systems. Unfortunately, the collection of event traces can produce a large volume of data that is difficult, or even impossible, to store and analyze. One approach for compressing a trace is to identify repeating trace patterns and retain only one representative of each pattern. However, determining the similarity of sections of traces, i.e., identifying patterns, is not straightforward. In this paper, we investigate pattern-based methods for reducing traces that will be used for performance analysis. We evaluate the different methods against several …

Finding Irc-Like Meshes Sans Layer 7 Payloads, Akshay Dua, Jim Binkley, Suresh Singh

Computer Science Faculty Publications and Presentations

We present an algorithm for detecting IRC-like chat networks that does not rely on Layer 7 payload information. The goal is to extract only those meshes from conventional flows where long-term periodic data is being exchanged between an external server and multiple internal clients. Flow data is passed through a series of filters that reduce the memory requirements needed for final candidate mesh sorting. Final outputs consist of two sorted lists including the fanout list, sorted by the number of client hosts in the mesh, and a secondary list called the evil sort. The latter consists of meshes with any …

Squeak By Example, Andrew P. Black, Stéphane Ducasse, Oscar Nierstrasz, Damien Pollet, Damien Cassou, Marcus Denker

Computer Science Faculty Publications and Presentations

Squeak is a modern open-source development environment for the classic Smalltalk-80 programming language. This book, intended for both students and developers, will guide you gently through the language and tools by means of a series of examples and exercises.

Additional material is available from the book's web page at SqueakByExample.org.

Computational Techniques For Reducing Spectra Of The Giant Planets In Our Solar System, Holly L. Grimes

Dissertations and Theses

The dynamic atmospheres of Jupiter, Saturn, Uranus, and Neptune provide a rich source of meteorological phenomena for scientists to study. To investigate these planets, scientists obtain spectral images of these bodies using various instruments including the Cooled Mid-Infrared Camera and Spectrometer (COMICS) at the Subaru Telescope Facility at Mauna Kea, Hawaii. These spectral images are two-dimensional arrays of double precision floating point values that have been read from a detector array. Such images must be reduced before the information they contain can be analyzed. The reduction process for spectral images from COMICS involves several steps:

1. Sky subtraction: the …

The ‘Benchmark Glacier’ Concept – Does It Work? Lessons From The North Cascade Range, Usa, Andrew G. Fountain, Matthew J. Hoffman, Frank Granshaw, Jon L. Riedel

Geology Faculty Publications and Presentations

Benchmark glaciers were established in many alpine areas during the 1960s as part of the International Hydrological Decade to represent ‘typical’ mass and energy processes on glaciers in different climatic regions around the world. These glaciers have received new interest in the past decade because they are used to infer the contribution of alpine glacier wastage to global sea-level rise. We compare South Cascade Glacier, the benchmark glacier for the northwest contiguous USA, and four other secondary glaciers, against the topographic, area and mass changes of 321 glaciers in the surrounding region. Results show that South Cascade Glacier is unusually …

Surface Energy Balance And Melt Thresholds Over 11 Years At Taylor Glacier, Antarctica, Matthew James Hoffman, Andrew G. Fountain, Glen E. Liston

Geography Faculty Publications and Presentations

In the McMurdo Dry Valleys, Victoria Land, Antarctica, melting of glacial ice is the primary source of water to streams, lakes, and associated ecosystems. To understand geochemical fluxes and ecological responses to past and future climates requires a physically based energy balance model. We applied a one-dimensional model to one site on Taylor Glacier using 11 years of daily meteorological data and seasonal ablation measurements. Inclusion of transmission of solar radiation into the ice was necessary to accurately model summer ablation and ice temperatures. Results showed good correspondence between calculated and measured ablation and ice temperatures over the 11 years. …

General Validity Of Reciprocity In Quantum Mechanics, P.T. Leung, H. Y. Xie, D. P. Tsai

Physics Faculty Publications and Presentations

The concept of reciprocity symmetry for matter-wave propagation is established for nonrelativistic quantum mechanics with previous results in the literature extended to include nonlocal interactions. Examples are given for cases with both local and nonlocal potentials, where we show in particular that reciprocity can be violated for the motion of a charged particle in an external electromagnetic field. In addition, this symmetry is applied to interpret a recent analysis [Phys. Rev. A 64, 042716 (2001)] on the symmetry of transmission through one-dimensional complex potentials, with the emphasis that the validity of reciprocity can go beyond that of time-reversal symmetry, such …