Physical Sciences and Mathematics Commons^™

Electron Crystallography Of Aquaporins, Simeon Andrews, Steve Reichow, Tamir Gonen

Chemistry Faculty Publications and Presentations

Aquaporins are a family of ubiquitous membrane proteins that form a pore for the permeation of water. Both electron and X-ray crystallography played major roles in determining the atomic structures of a number of aquaporins. This review focuses on electron crystallography, and its contribution to the field of aquaporin biology. We briefly discuss electron crystallography and the two-dimensional crystallization process. We describe features of aquaporins common to both electron and X-ray crystallographic structures; as well as some structural insights unique to electron crystallography, including aquaporin junction formation and lipid-protein interactions.

Peroxynitrite Chemistry: Formation, Decomposition And Possible Deactivation Mechanisms By Thiols, Olufunke Modupe Olagunju

Dissertations and Theses

Kinetics of formation and decomposition of peroxynitrite was studied in acidic and buffer solutions. Peroxynitrous acid was formed in acidic media by the reaction of H₂O₂ with HNO^₂ and NO +. Bimolecular rate constant for reaction of H²O² with HNO^₂ at 25°C was determined to be 3.7 × 10 3 M-¹ s-¹. Peroxynitrous acid formed is highly unstable with half life of approximately 1 second. Decomposition of peroxynitrite is highly pH-dependent. In acidic media, peroxynitrous acid decomposes to nitrate while at neutral to slightly basic media, products of decomposition …

Theoretical Investigations And Microarray Applications Of Dna Multiplex Hybridization Reactions, Michael Todd Horne

Dissertations and Theses

General equilibrium and kinetic models with numerical solutions describing DNA multiplex hybridization reactions are developed and presented. Theoretical investigations on example multiplex systems were carried out in order to test the sensitivity of the model system to a variety of experimental and model parameters. A spotted microarray platform was calibrated to yield quantitative results, and the theoretical model motivated the design of an effective kinetic assay to discriminate SNPs in a multiplex fashion. Effects of duplex length, %G+C and relative position of the SNP on duplex hybridization and SNP resolution were determined. The theoretical model of multiplex hybridization accurately predicted …

Interview With Michael Menzies, Braeside Farms, 2008 (Audio), Michael Menzies

All Sustainability History Project Oral Histories

Interview of Michael Menzies by Joel DaMetz at Braeside Farms in Estacada, Oregon on June 6th, 2008.

The interview index is available for download.

Development And Investigation Of Unique Organic Materials To Detect Disease Biomarkers, George Kiplimo Samoei

Dissertations and Theses

Chemomechanical polymer gels with the capability of recognizing specific biological molecules are promising materials for many biomedical applications. Glucose-selective hydrogels have potential utility in the continuous monitoring of glucose and glucose-triggered insulin delivery for the management of diabetes. Herein, the development and study of the first material which detects glucose via significant volume changes in the challenging matrix human blood plasma is described. The material was created via the modification of PMMA with supramolecular binding sites. The polymer exhibits excellent selectivity and reversibility including continuous expansion-contraction cycles.

Interview With David Shonk, Bumblebee Farm, 2008 (Audio), David Shonk

All Sustainability History Project Oral Histories

Interview of David Shonk by Brian Francetich at Troutdale, Oregon on June 4th, 2008.

The interview index is available for download.

How Students Use Mathematical Resources In An Electrostatics Context, Dawn C. Meredith, Karen A. Marrongelle

Mathematics and Statistics Faculty Publications and Presentations

We present evidence that although students’ mathematical skills in introductory calculus-based physics classes may not be readily applied in physics contexts, these students have strong mathematical resources on which to build effective instruction. Our evidence is based on clinical interviews of problem solving in electrostatics, which are analyzed using the framework of Sherin’s symbolic forms. We find that students use notions of “dependence” and “parts-of-a-whole” to successfully guide their work, even in novel situations. We also present evidence that students’ naive conceptions of the limit may prevent them from viewing integrals as sums.

Dynamical Evolution Of Volume Fractions In Multipressure Multiphase Flow Models, C. H. Chang, John D. Ramshaw

Physics Faculty Publications and Presentations

Compared to single-pressure models, multipressure multiphase flow models require additional closure relations to determine the individual pressures of the different phases. These relations are often taken to be evolution equations for the volume fractions. We present a rigorous theoretical framework for constructing such equations for compressible multiphase mixtures in terms of submodels for the relative volumetric expansion rates ∆Ei of the phases. These quantities are essentially the rates at which the phases dynamically expand or contract in response to pressure differences, and represent the general tendency of the volume fractions to relax toward values that produce local pressure equilibrium. We …

Interview With Shari Sirkin, Dancing Roots Farm, 2008 (Audio), Shari Sirkin

All Sustainability History Project Oral Histories

Interview of Shari Sirkin by Brian Francetich at Troutdale, Oregon on May 28th, 2008.

The interview index is available for download.

Interview With Jill And Michael J. Paine, Gaining Ground Farm, 2008 (Audio), Jill Paine, Michael J. Paine

All Sustainability History Project Oral Histories

Interview of Jill and Michael J. Pain by James Pritchett in Yamhill, Oregon on May 28th, 2008.

The interview index is available for download.

Interview With Melanie Plies, Backyard Bounty, 2008 (Audio), Melanie Plies

All Sustainability History Project Oral Histories

Interview of Melanie Plies by Stephenie Bitz on May 21st, 2008.

The interview index is available for download.

Interview With Louisa Depaiva, Purple Rain Vineyard, 2008 (Audio), Louisa Depaiva

All Sustainability History Project Oral Histories

Interview of Louisa DePaiva by Stephenie Bitz at Brush Prairie, Washington on May 10th, 2008.

The interview index is available for download.

Interview With John Martinson Jr., Birds & Bees Community Farm, 2008 (Audio), John Martinson Jr.

All Sustainability History Project Oral Histories

Interview of John Martinson Jr. by Clint Anderson in Oregon City, Oregon on May 8th, 2008.

The interview index is available for download.

Simpol.1: A Simple Group Contribution Method For Predicting Vapor Pressures And Enthalpies Of Vaporization Of Multifunctional Organic Compounds, James F. Pankow, William E. Asher

Physics Faculty Publications and Presentations

The SIMPOL.1 group contribution method is developed for predicting the liquid vapor pressure p^o_L (atm) and enthalpy of vaporization Δ H_vap (kJ mol^-1) of organic compounds as functions of temperature (T). For each compound i, the method assumes log₁₀p^o_L,i (T)=∑_kν_k,ib_k(T) where ν_k,i is the number of groups of type k, and b_k (T) is the contribution to log₁₀p^o_L,i (T) by each group of type k. A …

Unipolar Transport And Interface Charge Transfer In Nanostructured Cdte/Polymer Hybrid Films, Rolf Kӧnenkamp, Robert Meier, Robert Campbell Word, Athavan Nadarajah

Physics Faculty Publications and Presentations

We report detailed photoconductance measurements on hybrid semiconductor films consisting of CdTe nanoparticles in a poly[2-methoxy-5-(2′-ethyl-hexyloxy)-1,4-phenylene vinylene (MEH-PPV) matrix. Our results show that a staggered band alignment between organic and inorganic semiconductors produces an efficient separation of photoexcited electron-hole pairs and promotes a unipolar transport in each of the semiconductors. Hole drift mobilities in the MEH-PPV film and electron drift mobilities in the CdTe nanoparticle network are determined. We find clear evidence for the transport in the two phases of the hybrid film to be electrically uncoupled, and we conclude that these properties can lead to improved electron transport properties.

Iron(Iii)-Salophene: An Organometallic Compound With Selective Cytotoxic And Anti-Proliferative Properties In Platinum-Resistant Ovarian Cancer Cells, Thilo S. Lange, Kyu Kwang Kim, Rakesh K. Singh, Robert M. Strongin, Carolyn Mccourt, Laurent Brard

Chemistry Faculty Publications and Presentations

Background: In this pioneer study to the biological activity of organometallic compound Iron(III)-salophene (Fe-SP) the specific effects of Fe-SP on viability, morphology, proliferation, and cell-cycle progression on platinum-resistant ovariancancer cell lines were investigated.

Methodology/Principal Findings: Fe-SP displayed selective cytotoxicity against SKOV-3 and OVCAR-3 (ovarian epithelial adenocarcinoma) cell lines at concentrations between 100 nM and 1 μM, while the viability of HeLa cells (epithelial cervix adenocarcinoma) or primary lung or skin fibroblasts was not affected. SKOV-3 cells in contrast to fibroblasts after treatment with Fe-SP revealed apparent hallmarks of apoptosis including densely stained nuclear granular bodies within fragmented nuclei, highly condensed …

Bioinspired Broadband Antireflection Coatings On Gasb, Wei-Lun Min, Amaury P. Betancourt, Peng Jiang, Bin Jiang

Mathematics and Statistics Faculty Publications and Presentations

We report an inexpensive yet scalable templating technique for fabricating moth-eye antireflection gratings on gallium antimonide substrates. Non-close-packed colloidal monolayers are utilized as etching masks to pattern subwavelength-structured nipple arrays on GaSb. The resulting gratings exhibit superior broadband antireflection properties and thermal stability than conventional multilayer dielectric coatings. The specular reflection of the templated nipple arrays match with the theoretical predictions using a rigorous coupled-wave analysis model. The effect of the nipple shape and size on the antireflection properties has also been investigated by the same model. These biomimetic coatings are of great technological importance in developing efficient thermophotovoltaic cells.

Towards The Rational Design Of Mri Contrast Agents: Electron Spin Relaxation Is Largely Unaffected By The Coordination Geometry Of Gadolinium(Iii)–Dota-Type Complexes, Alain Borel, Jonathan F. Bean, Robert B. Clarkson, Lothar Helm, Loïck Moriggi, A. Dean Sherry, Mark Woods

Chemistry Faculty Publications and Presentations

Electron‐spin relaxation is one of the determining factors in the efficacy of MRI contrast agents. Of all the parameters involved in determining relaxivity it remains the least well understood, particularly as it relates to the structure of the complex. One of the reasons for the poor understanding of electron‐spin relaxation is that it is closely related to the ligand‐field parameters of the Gd³⁺ ion that forms the basis of MRI contrast agents and these complexes generally exhibit a structural isomerism that inherently complicates the study of electron spin relaxation. We have recently shown that two DOTA‐type ligands could be …

Economics Of Soil Conservation Adoption In High-Rainfall Areas Of The Ethiopian Highlands, Menale Kassie, Stein Holden, Gunnar Köhlin, Randall Bluffstone

Economics Faculty Publications and Presentations

This study measures the impact of fanya juu bunds (an important soil and water conservation technology and the most popular type of contour bund in east Africa) on the value of crop production in a high-rainfall area in the Ethiopian highlands using cross-sectional multiple plot observations. We applied switching regression, stochastic dominance analysis (SDA), and decomposition and propensity score matching methods to ensure robustness. The switching regression, SDA, and decomposition analyses relied on matched observations, which was important because regression and SDA often do not ensure that comparable plots with conservation technology (conserved) and plots without (unconserved) actually exist in …

Structural Identification Of Cubic Iron-Oxide Nanocrystal Mixtures: X-Ray Powder Diffraction Versus Quasi-Kinematic Transmission Electron Microscopy, Peter Moeck

Physics Faculty Publications and Presentations

Two novel (and proprietary) strategies for the structural identification of a nanocrystal from either a single high-resolution (HR) transmission electron microscopy (TEM) image or a single precession electron diffraction pattern are proposed and their advantages discussed in comparison to structural fingerprinting from powder X-ray diffraction patterns. Simulations for cubic magnetite and maghemite nanocrystals are used as examples.

Determination Of Enantiomeric Compositions Of Analytes Using Novel Fluorescent Chiral Molecular Micelles And Steady State Fluorescence Measurements, Alicia A. Williams, Sayo O. Fakayode, Onur Alptürk, Christina M. Jones, Mark Lowry, Robert M. Strongin, Isiah M. Warner

Chemistry Faculty Publications and Presentations

Novel fluorescent chiral molecular micelles (FCMMs) were synthesized, characterized, and employed as chiral selectors for enantiomeric recognition of non-fluorescent chiral molecules using steady state fluorescence spectroscopy. The sensitivity of the fluorescence technique allowed for investigation of low concentrations of chiral selector (3.0 x 10(-5) M) and analyte (5.0 x 10(-6) M) to be used in these studies. The chiral interactions of glucose, tartaric acid, and serine in the presence of FCMMs poly(sodium N-undecanoyl-L-tryptophanate) [poly-L-SUW], poly(sodium N-undecanoyl-L-tyrosinate) [poly-L-SUY], and poly(sodium N-undecanoyl-L-phenylalininate) [poly-SUF] were based on diastereomeric complex formation. Poly-L-SUW had a significant fluorescence emission spectral difference as compared to poly-L-SUY and …

Prostate Segmentation On Pelvic Ct Images Using A Genetic Algorithm, Payel Ghosh, Melanie Mitchell

Computer Science Faculty Publications and Presentations

A genetic algorithm (GA) for automating the segmentation of the prostate on pelvic computed tomography (CT) images is presented here. The images consist of slices from three-dimensional CT scans. Segmentation is typically performed manually on these images for treatment planning by an expert physician, who uses the “learned” knowledge of organ shapes, textures and locations to draw a contour around the prostate. Using a GA brings the flexibility to incorporate new “learned” information into the segmentation process without modifying the fitness function that is used to train the GA. Currently the GA uses prior knowledge in the form of texture …

Semantic Components: A Model For Enhancing Retrieval Of Domain- Specific Information, Susan Loucette Price

Dissertations and Theses

Despite the success of general Internet search engines, information retrieval remains an incompletely solved problem. Our research focuses on supporting domain experts when they search domain-specific libraries to satisfy targeted information needs. The semantic components model introduces a schema specific to a particular document collection. A semantic component schema consists of a two-level hierarchy, document classes and semantic components. A document class represents a document grouping, such as topic type or document purpose. A semantic component is a characteristic type of information that occurs in a particular document class and represents an important aspect of the document’s main topic. …

Green Crab Control: A Removal Effort In A Shallow Central California Estuary, Amy A. Larson, C. E. De Rivera, G. M. Ruiz, E. D. Grosholz, Mark D. Sytsma

Environmental Science and Management Faculty Publications and Presentations

Goal: To test the feasibility and effects of locally removing a well-established population of a marine organism with pelagic larvae. Removal of adult European green crabs (Carcinus maenas) from Bodega Harbor as a model system to develop and inform management options for eradication, rapid response, and control of marine invaders.

An Integrative Approach To Quality Of Life Measurement, Research, And Policy, Robert Costanza, Brendan Fisher, Saleem H. Ali, Caroline C. Beer, Lynne A. Bond, Roelof Boumans, Nicholas Louis Danigelis, Jennifer Alvarez Dickinson, Carolyn M. Elliott, Joshua C. Farley, Diane Elliott Gayer, Linda Macdonald Glenn, Thomas Richard Hudspeth, Dennis F. Mahoney, Laurence E. Mccahill, Barbara Mcintosh, Brian V. Reed, S. Abu Rizvi, Donna Marie Rizzo, Thomas A. Simpatico, Robert Raymond Snapp

Institute for Sustainable Solutions Publications and Presentations

While Quality of Life (QOL) has long been an explicit or implicit policy goal, adequate definition and measurement have been elusive. Diverse "objective" and "subjective" indicators across a range of disciplines and scales, and recent work on subjective well-being (SWB) surveys and the psychology of happiness have spurred renewed interest. Drawing from multiple disciplines, we present an integrative definition of QOL that combines measures of human needs with subjective well-being or happiness. QOL is proposed as a multiscale, multi-dimensional concept that contains interacting objective and subjective elements. We relate QOL to the opportunities that are provided to meet human needs …

Templated Biomimetic Multifunctional Coatings, Chih-Hung Sun, Adriel Gonzalez, Nicholas C. Linn, Peng Jiang, Bin Jiang

Mathematics and Statistics Faculty Publications and Presentations

We report a bioinspired templating technique for fabricating multifunctional optical coatings that mimic both unique functionalities of antireflective moth eyes and superhydrophobic cicada wings. Subwavelength-structured fluoropolymer nipple arrays are created by a soft-lithography-like process. The utilization of fluoropolymers simultaneously enhances the antireflective performance and the hydrophobicity of the replicated films. The specular reflectivity matches the optical simulation using a thin-film multilayer model. The dependence of the size and the crystalline ordering of the replicated nipples on the resulting antireflective properties have also been investigated by experiment and modeling. These biomimetic materials may find important technological application in self-cleaning antireflection coatings.

Dark Current Measurements In A Cmos Imager, William C. Porter, Bradley Kopp, Justin Charles Dunlap, Ralf Widenhorn, Erik Bodegom

Physics Faculty Publications and Presentations

We present data for the dark current of a commercially available CMOS image sensor for different gain settings and bias offsets over the temperature range of 295 to 340 K and exposure times of 0 to 500 ms. The analysis of hot pixels shows two different sources of dark current. One source results in hot pixels with high but constant count for exposure times smaller than the frame time. Other hot pixels exhibit a linear increase with exposure time. We discuss how these hot pixels can be used to calculate the dark current for all pixels. Finally, we show that …

Measurements Of Dark Current In A Ccd Imager During Light Exposures, Ralf Widenhorn, Ines Hartwig, Justin Charles Dunlap, Erik Bodegom

Physics Faculty Publications and Presentations

Thermal excitation of electrons is a major source of noise in Charge-Coupled Device (CCD) imagers. Those electrons are generated even in the absence of light, hence the name dark current. Dark current is particularly important for long exposure times and elevated temperatures. The standard procedure to correct for dark current is to take several pictures under the same condition as the real image, except with the shutter closed. The resulting dark frame is later subtracted from the exposed image. We address the question of whether the dark current produced in an image taken with a closed shutter is identical to …

Better Refactoring Tools For A Better Refactoring Strategy, Andrew P. Black

Computer Science Faculty Publications and Presentations

Refactoring tools can improve the speed and accuracy with which we create and maintain software – but only if they are used. In practice, tools are not used as much as they could be; this seems to be because they do not align with the refactoring strategy preferred by the majority of programmers: floss refactoring. We propose five principles that characterize successful floss refactoring tools – principles that can help programmers to choose the most appropriate refactoring tools and also help toolsmiths to design more usable tools.

Discrete Sums For The Rapid Determination Of Exponential Decay Constants, Michael A. Everest, Dean B. Atkinson

Chemistry Faculty Publications and Presentations

Several computational methods are presented for the rapid extraction of decay time constants from discrete exponential data. Two methods are found to be comparably fast and highly accurate. They are corrected successive integration and a method involving the Fourier transform (FT) of the data and the application of an expression that does not assume continuous data. FT methods in the literature are found to introduce significant systematic error owing to the assumption that data are continuous. Corrected successive integration methods in the literature are correct, but we offer a more direct way of applying them which we call linear regression …