Physical Sciences and Mathematics Commons^™

Statistical Thermodynamics And Kinetics Of Dna Multiplex Hybridization Reactions, Albert S. Benight, M. T. Horne, D. J. Fish

Chemistry Faculty Publications and Presentations

A general analytical description of the equilibrium and reaction kinetics of DNA multiplex hybridization has been developed. In this approach, multiplex hybridization is considered to be a competitive multichannel reaction process: a system wherein many species can react both specifically and nonspecifically with one another. General equations are presented that can consider equilibrium and kinetic models of multiplex hybridization systems comprised, in principle, of any number of targets and probes. Numerical solutions to these systems for both equilibrium and kinetic behaviors are provided. Practical examples demonstrate clear differences between results obtained from more common simplex methods, in which individual hybridization …

The Distribution And Reproductive Success Of The Western Snowy Plover Along The Oregon Coast - 2006, David J. Lauten, Kathleen J. Castelein, Susan Weston, Krista Eucken, Eleanor P. Gaines

Institute for Natural Resources Publications

Part of the Oregon Bidiversity Information Center Report

Gridfields: Model-Driven Data Transformation In The Physical Sciences, Bill Howe

Dissertations and Theses

Scientists' ability to generate and store simulation results is outpacing their ability to analyze them via ad hoc programs. We observe that these programs exhibit an algebraic structure that can be used to facilitate reasoning and improve performance. In this dissertation, we present a formal data model that exposes this algebraic structure, then implement the model, evaluate it, and use it to express, optimize, and reason about data transformations in a variety of scientific domains.

Simulation results are defined over a logical grid structure that allows a continuous domain to be represented discretely in the computer. Existing approaches for manipulating …

Interview With Alisa Kane, Office Of Sustainable Development, 2006 (Audio), Alisa Kane

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Interview of Alisa Kane by Daniel Woodward at City of Portland Office of Sustainable Development, Oregon on November 30th, 2006.

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Interview With Michael Zilis, Walker Macy, 2006 (Audio), Michael Zilis

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Interview of Michael Zilis by Gerald Bones at Portland, Oregon on November 29th, 2006.

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Interview With Jessica Green, Macdonald Environmental Planning, 2006 (Audio), Jessica Green

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Interview of Jessica Green by Cory Angell in SW Portland, Oregon on November 29th, 2006.

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Interview With Christopher Weaver, Plm, 2006 (Audio), Christopher Weaver

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Interview of Christopher Weaver by Gerald Bones at Hillsboro, Oregon on November 29th, 2006.

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Interview With Laurel Macdonald-Bonnell, Macdonald Environmental, 2006 (Audio), Laurel Macdonald-Bonnell

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Interview of Laurel McDonald by Chloe Collins at MacDonald Environmental Planning on November 29th, 2006.

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Interview With Dell M. Turner, Green Roofing Contractor, 2006 (Audio), Dell M. Turner

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Interview of Dell M. Turner by Padraic Keene at Portland State University on November 28th, 2006.

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Interview With Brian Croak, Croak Creations, 2006 (Audio), Brian Croak

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Interview of Brian Croak by Chloe Collins on November 28th, 2006.

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Interview With Chelsea Cochran, Walker Macy, 2006 (Audio), Chelsea Cochran

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Interview of Chelsea Cochran by Cory Angell at Walker Macy, Portland Oregon on November 27th, 2006.

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Interview With Jason Desanto, Our United Villages, 2006 (Audio), Jason Desanto

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Interview of Jason DeSanto by Joe Arbow in Portland, Oregon on November 16th, 2006.

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A New Vision For New Orleans And The Mississippi Delta: Applying Ecological Economics And Ecological Engineering, Robert Costanza, John W. Day, William J. Mitsch

Institute for Sustainable Solutions Publications and Presentations

The restoration of New Orleans and the rest of the Mississippi delta after Hurricane Katrina can become another disaster waiting to happen, or it can become a model of sustainable development. Sea level is rising, precipitation patterns are changing, hurricane intensity is increasing, energy costs are predicted to soar, and the city is continuing to sink. Most of New Orleans is currently from 0.6 to 5 m (2?15 feet) below sea level. The conventional approach of simply rebuilding the levees and the city behind them will only delay the inevitable. If New Orleans, and the delta in which it is …

Pend Oreille River, Box Canyon Model: Model Development And Calibration, Robert Leslie Annear, Chris Berger, Scott A. Wells

Civil and Environmental Engineering Faculty Publications and Presentations

The purpose of this study was to improve the existing Version 3.0 application of CE-QUAL-W2 of the Pend Oreille River between Box Canyon Dam and Albeni Falls Dam by performing the tasks outlined above. In addition, the use of field data from 2004 as an additional calibration year would improve the confidence in the model’s predictive ability for temperature. The model simulations were run from January 1st to December 31st in each of the 3 years of model simulation: 1997, 1998 and 2004.

The model chosen for development is CE-QUAL-W2 Version 3.5 (Cole and Wells, 2006). This is a twodimensional …

Capillary-Driven Flows Along Rounded Interior Corners, Yongkang Chen, Mark M. Weislogel, Cory L. Nardin

Mechanical and Materials Engineering Faculty Publications and Presentations

The problem of low-gravity isothermal capillary flow along interior corners that are rounded is revisited analytically in this work. By careful selection of geometric length scales and through the introduction of a new geometric scaling parameter Tc, the Navier–Stokes equation is reduced to a convenient∼O(1) form for both analytic and numeric solutions for all values of corner half-angle α and corner roundedness ratio λ for perfectly wetting fluids. The scaling and analysis of the problem captures much of the intricate geometric dependence of the viscous resistance and significantly reduces the reliance on numerical data compared with several previous solution methods …

A Transmission Electron Microscope For Lecture Demonstrations, J. A. Panitz, Gertrude Rempfer

Physics Faculty Publications and Presentations

A simple transmission electron microscope (TEM) suitable for lecture demonstrations is described. In this TEM electrons are created in a glow discharge between two parallel electrodes in air at a reduced pressure. The electrons are collimated by a small hole in theanode, focused by a solenoid that acts as an electromagnetic lens, and imaged on a thin layer of phosphor deposited inside an Erlenmeyer flask. An image of a biological sample placed between the source and the lens can be magnified about 20 times. The microscope uses inexpensive components that can be quickly assembled during a demonstration. The TEMprovides a …

Transmission Electron Goniometry And Its Relation To Electron Tomography For Materials Science Apoplications, Peter Moeck, P. Fraundorf

Physics Faculty Publications and Presentations

Aspects of transmission electron goniometry are discussed. Combined with high resolution phase contrast transmission electron microscopy (HRTEM) and atomic resolution scanning TEM (STEM) in the atomic number contrast (Z-STEM) or the phase contrast bright field mode, transmission electron goniometry offers the opportunity to develop dedicated methods for the crystallographic characterization of nanocrystals in three dimensions. The relationship between transmission electron goniometry and electron tomography for materials science applications is briefly discussed. Internet based java applets that facilitate the application of transmission electron goniometry for cubic crystals with calibrated tilt-rotation and double-tilt specimen holders/goniometers are mentioned. The so called cubic-minimalistic tilt …

Idaho Pend Oreille River Model: Model Development And Calibration, Robert Leslie Annear, Chris Berger, Scott A. Wells

Civil and Environmental Engineering Faculty Publications and Presentations

The objectives of this project were to:

• Develop a hydrodynamic and temperature model of Pend Oreille River using CE-QUAL-W2 Version 3.2

• Calibrate the CE-QUAL-W2 model to field data collected during 2004 and 2005 using the following water quality variables:

• flow, water surface elevation, and velocity
• temperature o dissolved oxygen
• nutrients (NO3-N+NO2-N, NH4-N, PO4-P)
• algae – chlorophyll a
• BOD5 and dissolved organic matter and particulate organic matter compartments (both labile and refractory) for the organic matter cycling with algae
• periphyton

The model chosen for development was CE-QUAL-W2 Version 3.2 (Cole and Wells, 2004). This is a two-dimensional unsteady hydrodynamic …

Fermiology And Superconductivity At High Magnetic Fields In A Completely Organic Cation Radical Salt, J. S. Brooks, V. Williams, E. Choi, D. Graf, M. Tokumoto, S. Uji, F. Zuo, J. Wosnitza, J. A. Schlueter, H. David, Rolf Walter Winter, Gary L. Gard, K. Storr

Chemistry Faculty Publications and Presentations

We report specialized interplane magnetoresistance (MR) measurements on the organic superconducting compound β″–(BEDT-TTF)₂SF₅CH₂CF₂SO₃ (where BEDT-TTF is bis(ethylenedithio)tetrathiafulvalene) in both the superconducting (Tc ∼ 5K) and normal states versus magnetic field direction. In the normal state, detailed angular-dependent magnetoresistance oscillation (AMRO) studies reveal peculiar features of the Fermi surface topology of this compound, and very high magnetic field studies further support the unusual nature of the electronic structure. In the superconducting state we investigate, through detailedAMRO measurements, the anomalous MR peak that appears within the superconducting field-temperature phase diagram. Our results reveal a direct connection between the superconducting state determined from …

Efficient Support For Application-Specific Video Adaptation, Jie Huang

Dissertations and Theses

As video applications become more diverse, video must be adapted in different ways to meet the requirements of different applications when there are insufficient resources. In this dissertation, we address two sorts of requirements that cannot be addressed by existing video adaptation technologies: (i) accommodating large variations in resolution and (ii) collecting video effectively in a multi-hop sensor network. In addition, we also address requirements for implementing video adaptation in a sensor network.

Accommodating large variation in resolution is required by the existence of display devices with widely disparate screen sizes. Existing resolution adaptation technologies usually aim at adapting video …

Oregon Ballast Water Task Force Report On Ballast Water Management In Oregon, Christina Simkanin, Mark Sytsma

Center for Lakes and Reservoirs Publications and Presentations

This report provides information and analysis on the current ballast water regulations at international, federal, regional and state levels; ballast water discharge trends in Oregon; the shipping industry’s compliance with Oregon law; and current and emerging issues affecting Oregon’s ballast water legislation. The report also provides recommendations for strengthening Oregon’s management of shipping-related pathways of invasive species introduction.

Koll Center Wetlands Natural Resources Maintenance Management Plan, Meredith Clayton

Environmental Science and Management Professional Master's Project Reports

The intention of this plan is to provide a vision and guidelines for maintaining and improving the ecological health of Koll Center Wetlands in the short and long term. Although the plan will change over time, the goal is to quantify natural resource needs spatially, temporally, and economically.

Koll Center Wetlands is part of the Greenway/Fanno Creek/Koll Center Wetlands Park complex. The nearly 13 acre park is dominated by aquatic habitats that attract a wide variety of wildlife, particularly birds. The park grounds are not easily traversed and experience limited human use, but there are many viewpoints from which the …

India’S Rise As A Software Power: Governmental Policy Factors, Tad Drozdowski, Hai Huynh, Brian Lininger, Yicheng Peng, Naruedom Sakulyong

Engineering and Technology Management Student Projects

The Indian government’s policies toward an open, global market, support of educational institutions, and enhancement of appropriate infrastructure helped enable their software industry to become critical components of India’s economic growth in the 1990s. The Technical, Organizational, and Personal perspective (T, O, and P) model is utilized to examine different affects that each perspective, inclusive of government policies, has on a socio-technical system (Software development in India). The Indian government has provided substantial economic liberalization to support their software industries, though continued reform is necessary to ensure that they remain a software superpower.

A Pattern Language For Extensible Program Representation, Andrew P. Black, Daniel Vainsencher

Computer Science Faculty Publications and Presentations

For the last 15 years, implementors of multiple view programming environments have sought a single code model that would form a suitable basis for all of the program analyses and tools that might be applied to the code. They have been unsuccessful. The consequences are a tendency to build monolithic, single-purpose tools, each of which implements its own specialized analyses and optimized representation. This restricts the availability of the analyses, and also limits the reusability of the representation by other tools. Unintegrated tools also produce inconsistent views, which reduce the value of multiple views. This article describes a set of …

A Rough Guide To Interdisciplinarity: Graduate Student Perspectives, Jessica K. Graybill, Sarah Dooling, Vivek Shandas, John Withey, Adrienne I. Greve, Gregory L. Simon

Institute for Sustainable Solutions Publications and Presentations

A widely held belief is that only through interdisciplinarity can academics effectively address today's complex ecological problems, because these problems demand cross-disciplinary efforts and specialized knowledge from natural and social scientists. Innovative interdisciplinary research and curricula have been created to train a new generation of scientists to engage with complex issues. It seems critical that those most affected by interdisciplinary education—doctoral students—provide feedback about such innovations. Without understanding students' experiences in interdisciplinary programs, faculty will not know whether they are "getting it right" for future generations of interdisciplinarians. From our experiences as doctoral students, we provide reflections and perspectives on …

Relativistic Corrections To A Generalized Sum Rule, P.T. Leung, H. Sinky

Physics Faculty Publications and Presentations

Relativistic corrections to a previously established generalized sum rule are obtained using the Foldy-Wouthysen transformation. This sum rule derived previously by Wang [Phys. Rev. A 60, 262 (1999)] for a nonrelativistic system contains both the well-known Thomas-Reiche-Kuhn and Bethe sum rules, for which relativistic corrections have been obtained in the literature. Our results for the generalized formula will be applied to recover several results obtained previously in the literature, as well as to another sum rule whose relativistic corrections will be obtained.

Mapped Overland Distance Of Paleotsunami High-Velocity Inundation N Back-Barrier Wetlands Of The Central Cascadia Margin, U.S.A, Robert B. Schlichting, Curt D. Peterson

Geology Faculty Publications and Presentations

Investigations of back-barrier, open-coastal plain settings have been used to establish minimum inundation distances of prehistoric tsunamis produced by great subduction zone earthquakes in the central Cascadia margin. Distinctive sand sheets were characterized at four localities within the central Cascadia margin, a shoreline distance of about 250 km. The sand sheets vary in thickness from 0.2 to 25 cm. They thin in the landward direction and consist of well-sorted beach sand that fines upsection. Many of the sand sheets include capping layers of organic-rich detritus, as well as assimilated mud rip-up clasts and soil litter. Marine diatoms and bromine (i.e., …

Interview With Ted Morris, Dayton Meat Company, 2006 (Audio), Ted Morris

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Interview of Ted Morris by Matt Witke on August 17th, 2006.

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Interview With Oscar Lozano, Dayton Meat Company, 2006 (Audio), Oscar Lozano

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Interview of Oscar Lozano by Brad Schuler on August 14th, 2006.

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Interview With Ed Mays, Endura Wood Products, 2006 (Audio), Ed Mays

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Interview of Ed Mays by Damon Quint in Portland, Oregon on August 11th, 2006.

The interview index is available for download.