Physical Sciences and Mathematics Commons^™

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.

A Framework For Relationship Pattern Languages, Sudarshan Murthy, David Maier

Computer Science Faculty Publications and Presentations

A relationship pattern is an abstraction of a recurring need when establishing relationships among information elements in specific contexts. By developing or leveraging a relationship pattern, modelers can solve a class of problems once and describe many relationship types at once. We have developed a framework for specifying relationship patterns and pattern languages (sets of patterns) in both modeling-language-independent and modeling-language-specific ways. We describe this framework both informally and formally. We provide examples of some commonly observed relationship patterns and show how to use them in ER with the help of a relationship pattern language called Exemplar. We also provide …

Multisymplectic Theory Of Balance Systems, I, Serge Preston

Mathematics and Statistics Faculty Publications and Presentations

In this paper we are presenting the theory of balance equations of the Continuum Thermodynamics (balance systems) in a geometrical form using Poincare-Cartan formalism of the Multisymplectic Field Theory. A constitutive relation C of a balance system B_C is realized as a mapping between a (partial) 1-jet bundle of the configurational bundle π : Y ͢ X and the extended dual bundle similar to the Legendre mapping of the Lagrangian Field Theory. Invariant (variational) form of the balance system BC is presented in three different forms and the space of admissible variations is defined and studied. Action of automorphisms …

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.

Temporal Variations In Physical And Chemical Features Of Cryoconite Holes On Canada Glacier, Mcmurdo Dry Valleys, Antarctica, Andrew G. Fountain, Thomas H. Nylen, Martyn Tranter, Elizabeth A. Bagshaw

Geography Faculty Publications and Presentations

Cryoconite holes in the McMurdo Dry Valleys are ice-lidded, thus isolating the pools of water from the atmosphere and from potential surface melt. Hourly measurements of ice and water temperature and water electrical conductivity (EC) were recorded to broadly characterize the physical and chemical changes on daily to seasonal timescales. Overall, subsurface ice/water temperatures were typically several degrees warmer than air temperatures, underscoring the importance of subsurface solar heating. At no time was surface melt observed and the holes melted from within. Detailed differences in the timing and magnitude of both temperature and EC variations during melt-out and freezeup existed …

Modulation Of Water Exchange In Europium(Iii) Dota–Tetraamide Complexes Via Electronic Substituent Effects, S. James Ratnakar, Mark Woods, Angelo J.M. Lubag, Zoltan Kovacs, A. Dean Sherry

Chemistry Faculty Publications and Presentations

The chemical exchange saturation transfer (CEST) efficiency for a series Eu³⁺-based tetraamide complexes bearing p-substituents on a single coordinating pendant arm is highly sensitive to water exchange rates. The CEST effect increases in the order Me < MeO < F ∼ CO₂^tBu < CN ≪ H. These results show that CEST contrast can be modulated by changes in electron density at a single ligating atom, and this forms the basis of creating imaging agents that respond to chemical oxidation and reduction.

Inventory And Mapping Of Aquatic Plants At Lake Roosevelt National Recreation Area, Mark D. Sytsma, Rich Miller

Center for Lakes and Reservoirs Publications and Presentations

Lake Roosevelt is a large reservoir in northeast Washington State formed by the Grand Coulee Dam. The reservoir, which inundates portions of the Columbia River, the Spokane River, and other rivers and streams, is the focus of the Lake Roosevelt National Recreation Area (LARO) that is managed by the National Park Service. LARO encompasses 100,390 acres (40,625 ha) and includes significant cultural and recreational resources. The surface area, volume, and shoreline length of Lake Roosevelt at full pool is 82,691 acres (33,490 ha), 9.41 × 10¹⁰ acre-ft (1.16 × 10¹⁰ m³) (Nigro et. al. 1981), and …

Constructive Perception Of Self-Motion, Jan E. Holly, Gin Mccollum

Gin McCollum

This review focusses attention on a ragged edge of our knowledge of self-motion perception, where understanding ends but there are experimental results to indicate that present approaches to analysis are inadequate. Although self-motion perception displays processes of “top-down” construction, it is typically analyzed as if it is nothing more than a deformation of the stimulus, using a “bottom-up” and input/output approach beginning with the transduction of the stimulus. Analysis often focusses on the extent to which passive transduction of the movement stimulus is accurate. Some perceptual processes that deform or transform the stimulus arise from the way known properties of …

The Ownership Of The Internet And The World Wide Web In Vermont, Ida Kubiszewski

Institute for Sustainable Solutions Publications and Presentations

The internet is an interesting case, since it was created entirely with taxpayer's money by DARPA, while the world wide web was created at CERN in Switzerland and placed into the public domain voluntarily in 1993. The internet and web have many features of a commons, and many people refer to the "internet commons". Kubiszewski (pronounced cube- ih-shefski) explores the intricacies of the internet and world wide web to determine if internet companies are extracting economic rent from the public and how it could be recovered. She finds that companies are making a substantial profit by utilizing a resource that …

Floodplains: Balancing Nature And Human Needs, Vivek Shandas, Meg Merrick

Institute for Sustainable Solutions Publications and Presentations

For countless years, the interaction between climatic conditions and water flow has forged the rolling hills and rivers in the metroscape. The floods that forced a deluge of water down the Columbia River between 13 and 17 thousand years ago established the fertile and absorptive landscape of the Willamette Valley. The lush vegetation controlled the regional climate and stabilized the soils, while the thirsty wetlands reduced flood potential, provided habitat, and purified the water. Over geological time, these natural processes have created ideal conditions for humans. The Pacific Northwest was home to some of the most densely populated communities of …

Introduction To Special Section On Microcosms In Ice: The Biogeochemistry Of Cryoconite Holes, Andrew G. Fountain, Martyn Tranter

Geology Faculty Publications and Presentations

Cryoconite holes are small, water filled, cylindrical melt-holes on glacial ice surface. Cryoconite, 'cold dust,' refers to the thin layer of sediment at the hole bottom. The holes form from surficial sediment patches that absorbs more solar radiation than the surrounding ice and which preferentially melt into the glacier forming a cylindrical water-filled hole. These holes form on the ice-covered, as opposed to snow covered, parts of glaciers world-wide, wherever there is sufficient energy for melting. Biogeochemically, cryoconite holes are interesting because the sediment is inncoculated with biologic material, a fraction of which thrives in the cryoconite environment of near-freezing …

Hydrologic Response To Extreme Warm And Cold Summers In The Mcmurdo Dry Valleys, East Antarctica, Peter T. Doran, Christopher P. Mckay, Andrew G. Fountain, Thomas H. Nylen, Diane M. Mcknight, Chris Jaros, John E. Barrett

Geography Faculty Publications and Presentations

The meteorological characteristics and hydrological response of an extreme warm, and cold summer in the McMurdo Dry Valleys are compared. The driver behind the warmer summer conditions was the occurrence of down-valley winds, which were not present during the colder summer. Occurrence of the summer down-valley winds coincided with lower than typical mean sea level pressure in the Ross Sea region. There was no significant difference in the amount of solar radiation received during the two summers. Compared to the cold summer, glaciological and hydrological response to the warm summer in Taylor Valley included significant glacier mass loss, and 3- …

Glacial Ecosystems, Amy Hodson, Alexandre M. Anesio, Martyn Tranter, Andrew G. Fountain, Mark Osborn, John Charles Priscu, Johanna Laybourn-Perry, Birgit Sattler

Geography Faculty Publications and Presentations

There is now compelling evidence that microbially mediated reactions impart a significant effect upon the dynamics, composition, and abundance of nutrients in glacial melt water. Consequently, we must now consider ice masses as ecosystem habitats in their own right and address their diversity, functional potential, and activity as part of alpine and polar environments. Although such research is already underway, its fragmentary nature provides little basis for developing modern concepts of glacier ecology. This paper therefore provides a much-needed framework for development by reviewing the physical, biogeochemical, and microbiological characteristics of microbial habitats that have been identified within glaciers and …

Plagioclase Populations And Zoning In Dacite Of The 2004–2005 Mount St. Helens Eruption: Constraints For Magma Origin And Dynamics, Martin J. Streck, Cindy A. Broderick, Carl R. Thornber, Michael A. Clynne, John S. Pallister

Geology Faculty Publications and Presentations

We investigated plagioclase phenocrysts in dacite of the 2004–5 eruption of Mount St. Helens to gain insights into the magmatic processes of the current eruption, which is char­acterized by prolonged, nearly solid-state extrusion, low gas emission, and shallow seismicity. In addition, we investigated plagioclase of 1980–86 dacite.

Light and Nomarski microscopy were used to texturally characterize plagioclase crystals. Electron microprobe analy­ses measured their compositions. We systematically mapped and categorized all plagioclase phenocrysts in a preselected area according to the following criteria: (1) occurrence of zones of acicular orthopyroxene inclusions, (2) presence of dissolution surface(s), and (3) spatial association of 1 …

Rapid Assessment Of 2008-2012 Highway Development Projects In Region 6: Threats And Opportunities To Terrestrial Wildlife Resources, Sandra L. Jacobson, Catherine E. De Rivera, Kathleen Armstrong, Rebecca Aaby, Nadia Jones

Environmental Science and Management Faculty Publications and Presentations

Summaries of Highway Development Projects in Region 6 National Forests.

This document contains a summary of higher complexity projects selected for their interest to line officers and resource managers. These projects represent not only the current Statewide Transportation Improvement Plan (STIP) projects but also a sample of the types of projects that will be on future STIPs. Thus, readers are urged to glance at the tracking tools and narratives for all forests to gain a quick glimpse of the types of projects potentially facing each forest. The summary has extracted brief information on project locations and types, the program year …

Nutrient Uptake By Intact And Disturbed Roots Of Loblolly Pine Seedlings, Melissa S. Lucash, Ruth D. Yanai, J. Devereux Joslin

Environmental Science and Management Faculty Publications and Presentations

Most measurements of nutrient uptake use either hydroponic systems or soil-grown roots that have been disturbed by excavation. The first objective of this study was to test how root excavation affects nitrate uptake. Rates of NO3− uptake by mycorrhizal loblolly pine (Pinus taeda L.) seedlings were measured in intact sand-filled columns, hydroponics, and disturbed sand-filled columns. Total nitrate uptake in intact sand-filled columns was higher than in disturbed columns, indicating that disturbance lowers uptake. Transferring plants from the sand-filled columns to hydroponics had little effect on NO3− uptake beyond delaying uptake for an hour. The second objective of this study …

Superior Adaptation To Drought In Rubus Armeniacus (Himalayan Blackberry) In Northwest Oregon, J. Alan Yeakley, Joshua S. Caplan

Environmental Science and Management Faculty Publications and Presentations

Despite the status Rubus armeniacus (Himalayan blackberry) has as one of the most prolific and damaging plant invaders in the Pacific Northwest, we know little about the role of water relations in its success. The information available on invasive blackberry water relations (Fotelli et al. 2001; McDowell and Turner 2002) suggests that an ability to avoid water stress has been critically important to their proliferation in regions with Mediterranean climates (Amor et al. 1998). We had two objectives regarding the role of water relations in the invasive success of R. armeniacus:

Objective 1. Determine if R. armeniacus is better adapted …

Engaging Recreational Fishers In Management And Conservation: Global Case Studies, Elise F. Granek, Elizabeth M.P. Madin, M. A. Brown, Will F. Figueira, Darren S. Cameron, Zeb Hogan, Gerry Kristianson, Pierre De Villiers, Jack E. Williams, John R. Post, S. Zahn, R. Arlinghaus

Environmental Science and Management Faculty Publications and Presentations

Globally, the number of recreational fishers is sizeable and increasing in many countries. Associated with this trend is the potential for negative impacts on fish stocks through exploitation or management measures such as stocking and introduction of non-native fishes. Nevertheless, recreational fishers can be instrumental in successful fisheries conservation through active involvement in, or initiation of, conservation projects to reduce both direct and external stressors contributing to fishery declines. Understanding fishers’ concerns for sustained access to the resource and developing methods for their meaningful participation can have positive impacts on conservation efforts. We examined a suite of case studies that …

Controlled Fabrication Of High-Yield Cds Nanostructures By Compartment Arrangement, Joshua M. Green, Juno Lawrance, Jun Jiao

Physics Faculty Publications and Presentations

High-yield, high-purity CdS nanostructures were synthesized in a turf-like configuration using an improved vapor-liquid-solid method. To increase the yield, a compartment arrangement was employed. The specific kind of nanostructure fabricated was found to be directly dependent on the temperature in the compartment. Along with the high-yield growth of CdS nanorods, nanowires, and nanobelts, intertwined structures were also observed, and the electron field emission property of the intertwined structures was investigated and compared with that of other type of nanostructures. Photoluminescence measurements at 10 K showed a peak emission from the CdS nanostructures at 485 nm.

Differential Effects Of Understory And Overstory Gaps On Tree Regeneration, Brian Beckage, Brian D. Kloeppel, J. Alan Yeakley, Sharon F. Taylor, David C. Coleman

Environmental Science and Management Faculty Publications and Presentations

Gaps in the forest canopy can increase the diversity of tree regeneration. Understory shrubs also compete with tree seedlings for limited resources and may depress tree recruitment. We compared effects of shrub removal and canopy windthrow gaps on seedling recruitment and understory resource levels. Shrub removal, with the canopy left intact, was associated with increased levels of understory light and soil moisture and coincided with increased species richness and diversity of tree regeneration compared to both control plots and canopy gaps. Canopy windthrow gaps, however, resulted in a more than 500 fold increase in soil nitrate concentrations, and seedling growth …

Invasive Predator, Bythotrephes, Has Varied Effects On Ecosystem Function In Freshwater Lakes, Angela L. Strecker, Shelley E. Arnott

Environmental Science and Management Faculty Publications and Presentations

Bythotrephes longimanus is an invertebrate predator that has invaded the North American Great Lakes and a number of inland lakes, where it preys on crustacean zooplankton. We examined the effect of Bythotrephes on two measures of ecosystem function during a four month observational study of freshwater lakes on the boreal shield. Bythotrephes-invaded lakes had significantly lower epilimnetic zooplankton abundance and production compared to reference lakes. On average, Bythotrephes consumed 34% ofzooplankton production when it was present in lakes. There was some evidence of changes in the timing of zooplankton production, as well as shifts to cooler, less productive habitats, which …

Multigrid Convergence For Second Order Elliptic Problems With Smooth Complex Coefficients, Jay Gopalakrishnan, Joseph E. Pasciak

Mathematics and Statistics Faculty Publications and Presentations

The finite element method when applied to a second order partial differential equation in divergence form can generate operators that are neither Hermitian nor definite when the coefficient function is complex valued. For such problems, under a uniqueness assumption, we prove the continuous dependence of the exact solution and its finite element approximations on data provided that the coefficients are smooth and uniformly bounded away from zero. Then we show that a multigrid algorithm converges once the coarse mesh size is smaller than some fixed number, providing an efficient solver for computing discrete approximations. Numerical experiments, while confirming the theory, …

The Indefinite Metric Of R. Mrugala And The Geometry Of The Thermodynamical Phase Space, Serge Preston, James Vargo

Mathematics and Statistics Faculty Publications and Presentations

We study an indefinite metric G which was introduced by R. Mrugala and is defined on the contact phase space (P, θ) of a homogeneous thermodynamical system. We describe the curvature properties and the isometry group of the metric G. We established an isomorphism of the space (P, θ, G) with the Heisenberg Lie group H_n, endowed with the right invariant contact structure and the right invariant indefinite metric. The lift of the metric G to the symplectization of contact space (P, θ) and its properties are studied. Finally we introduce the "hyperbolic projectivization" of the space …

A Mixed Method For Axisymmetric Div-Curl Systems, Dylan M. Copeland, Jay Gopalakrishnan, Joseph E. Pasciak

Mathematics and Statistics Faculty Publications and Presentations

We present a mixed method for a three-dimensional axisymmetric div-curl system reduced to a two-dimensional computational domain via cylindrical coordinates. We show that when the meridian axisymmetric Maxwell problem is approximated by a mixed method using the lowest order Nédélec elements (for the vector variable) and linear elements (for the Lagrange multiplier), one obtains optimal error estimates in certain weighted Sobolev norms. The main ingredient of the analysis is a sequence of projectors in the weighted norms satisfying some commutativity properties.

Asymptotic And Numerical Techniques For Resonances Of Thin Photonic Structures, Jay Gopalakrishnan, Shari Moskow, Fadil Santosa

Mathematics and Statistics Faculty Publications and Presentations

We consider the problem of calculating resonance frequencies and radiative losses of an optical resonator. The optical resonator is in the form of a thin membrane with variable dielectric properties. This work provides two very different approaches for doing such calculations. The first is an asymptotic method which exploits the small thickness and high index of the membrane. We derive a limiting resonance problem as the thickness goes to zero, and for the case of a simple resonance, find a first order correction. The limiting problem and the correction are in one less space dimension, which can make the approach …

Quantifying Twentieth Century Glacier Change In The Sierra Nevada, California, Hassan J. Basagic

Dissertations and Theses

Numerous small alpine glaciers occupy the high elevation regions of the central and southern Siena Nevada, California. These glaciers change size in response to variations in climate and are therefore important indicators of climate change. An inventory based on USGS topographic maps (l :24,000) revealed 1719 glaciers and perennial snow and ice features for a total area of 39.l5 ±7.52 km². The number of 'true' glaciers, versus non-moving ice, is estimated to be 118, covering 15.87 ± 1.69 Km². All glaciers were located on north to northeast aspects, at elevations >3000 m. Historical photographs, geologic evidence, …

New Particle Formation In The Front Range Of The Colorado Rocky Mountains, Micahel Boy, Thomas Karl, Andrew Turnipseed, Roy Lee Mauldin, Edward Kosciuch, James Greenberg, Jeff Rathbone, James Smith, Andreas Held, Kelley Barsanti, Alex Guenther

Civil and Environmental Engineering Faculty Publications and Presentations

New particle formation is of interest because of its influence on the properties of aerosol population, and due to the possible contribution of newly formed particles to cloud condensation nuclei. Currently no conclusive evidence exists as to the mechanism or mechanisms of nucleation and subsequent particle growth. However, nucleation rates exhibit a clear dependence on ambient sulphuric acid concentrations and particle growth is often attributed to the condensation of organic vapours. A detailed study of new particle formation in the Front Range of the Colorado Rocky Mountains is presented here. Gas and particle measurement data for 32 days was analyzed …

Electrical Detection Of The Temperature Induced Melting Transition Of A Dna Hairpin Covalently Attached To Gold Interdigitated Microelectrodes, Greg P. Brewood, Yaswanth Rangineni, Daniel J. Fish, Ashwini Bhandiwad, David R. Evans, Raj Solanki, Albert S. Benight

Chemistry Faculty Publications and Presentations

The temperature induced melting transition of a self-complementary DNA strand covalently attached at the 5' end to the surface of a gold interdigitated microelectrode (GIME) was monitored in a novel, label-free, manner. The structural state of the hairpin was assessed by measuring four different electronic properties of the GIME (capacitance, impedance, dissipation factor and phase angle) as a function of temperature from 25 degrees C to 80 degrees C. Consistent changes in all four electronic properties of the GIME were observed over this temperature range, and attributed to the transition of the attached single-stranded DNA (ssDNA) from an intramolecular, folded …

Unsymmetric Aryl–Alkyl Disulfide Growth Inhibitors Of Methicillin-Resistant Staphylococcus Aureus And Bacillus Anthracis, Edward Turos, Kevin D. Revell, Praveen Ramaraju, Danielle A. Gergeres, Kerriann Greenhalgh, Ashley Young, Nalini Sathyanarayan, Sonja Dickey, Daniel Lim, Mamoun M. Alhamadsheh, Kevin A. Reynolds

Chemistry Faculty Publications and Presentations

This study describes the antibacterial properties of synthetically-produced mixed aryl alkyl disulfide compounds as a means to control the growth of Staphylococcus aureus and Bacillus anthracis. Some of these compounds exerted strong in vitro bioactivity. Our results indicate that among the twelve different aryl substituents examined, nitrophenyl derivatives provide the strongest antibiotic activities. This may be the result of electronic activation of the arylthio moiety as a leaving group for nucleophilic attack on the disulfide bond. Small alkyl residues on the other sulfur provide the best activity as well, which for different bacteria appears to be somewhat dependent on …

The Cis-Δ2,3-Double Bond Of Phoslactomycins Is Generated By A Post-Pks Tailoring Enzyme, Nadaraj Palaniappan, Mamoun M. Alhamadsheh, Kevin A. Reynolds

Chemistry Faculty Publications and Presentations

The antifungal phoslactomycins (PLM A-F), produced by Streptomyes sp HK803, are structurally unusual in that three of their four double bonds are in the cis form (Δ^12,13, Δ^14,15, Δ^2,3). The PLM polyketide synthase (PKS) has the predicted dehydratase catalytic domain in modules 1,2 and 5 required for establishing two of these cis double bonds (Δ^12,13Δ^14,15), as well as the only trans Δ^6,7double bond. By contrast, the formation of the cis Δ^2,3 in the unsaturated lactone moiety of PLMs has presented an enigma because the predicted dehydratase domain …