Physical Sciences and Mathematics Commons^™

On The Effect Of Criticality And Topology On Learning In Random Boolean Networks, Alireza Goudarzi

Systems Science Friday Noon Seminar Series

Random Boolean networks (RBN) are discrete dynamical systems composed of N automata with a binary state, each of which interacts with other automata in the network. RBNs were originally introduced as simplified models of gene regulation. In this presentation, I will present recent work done conjointly with Natali Gulbahce (UCSF), Thimo Rohlf (MPI, CNRS), and Christof Teuscher (PSU). We extend the study of learning in feedforward Boolean networks to random Boolean networks (RBNs) and systematically explore the relationship between the learning capability, the network topology, the system size N, the training sample T, and the complexity of the computational task. …

Information Disclosure And Environmental Performance, Mark Stephan

Systems Science Friday Noon Seminar Series

Scholars and policymakers increasingly argue that information disclosure programs such as the Toxics Release Inventory (TRI) should be used to supplement conventional environmental regulation. Yet we lack a clear understanding of how such programs work as well as the empirical data to confirm their success in achieving environmental quality objectives. To better understand the impacts of environmental information disclosure on corporate decision making, this paper develops an analytic framework drawn from theories of risk perception and communication, individual and corporate decision making, and social capital. I examine the importance of the TRI for facility level behavior through an analysis of …

Making Ecodistricts: City-Scale Climate Action One Neighborhood At A Time, Ethan Seltzer, Ellen M. Bassett, Joseph Cortright, Vivek Shandas, Timothy W. Smith

Institute for Sustainable Solutions Publications and Presentations

As part of its approach to meeting Climate Action Plan goals, the City of Portland has joined with the Portland Sustainability Institute to create "EcoDistricts" in Portland neighborhoods to seek neighborhood engagement on behalf of city climate action goals. EcoDistricts, like neighborhoods, offer a scale at which individuals can be affective and empowered to make climate-positive choices, but in a manner that can scale up to make citywide climate action real.

Urban Water Demand Modeling: Review Of Concepts, Methods, And Organizing Principles, Heejun Chang, Lily House-Peters

Institute for Sustainable Solutions Publications and Presentations

In this paper, we use a theoretical framework of coupled human and natural systems to review the methodological advances in urban water demand modeling over the past 3 decades. The goal of this review is to quantify the capacity of increasingly complex modeling techniques to account for complex human and natural processes, uncertainty, and resilience across spatial and temporal scales. This review begins with coupled human and natural systems theory and situates urban water demand within this framework. The second section reviews urban water demand literature and summarizes methodological advances in relation to four central themes: (1) interactions within and …

Approximating Confidence Intervals About Discrete Time Survival/Cumulative Incidence Estimates Using The Delta Method, Alexis Dinno, Jong-Sung Kim

Community Health Faculty Publications and Presentations

Poster focuses on answering the questions whether and when and event will happen in a population at risk.

Prioritizing Zebra And Quagga Mussel Monitoring In The Columbia River Basin, Steve W. Wells, Timothy D. Counihan, Amy Puls, Mark Sytsma, Brian Adair

Center for Lakes and Reservoirs Publications and Presentations

The purpose of this report is to provide a framework for the prioritization of water bodies in the Columbia River Basin and the Greater Northwest region (surrounding areas in Oregon, Washington, California, Nevada, Idaho, Utah, and Wyoming) for early detection monitoring for dreissenid mussels. Our ability to assess the relative risk of establishment and introduction of dreissenid mussels was confounded by significant gaps in the data necessary to rigorously predict where dreissenid mussels will become introduced and subsequently established. Consequently, local jurisdictions should evaluate the prioritized lists provided critically and make adjustments where local knowledge and additional information dictates. Further, …

Toward An Integrated History To Guide The Future, Sander Van Der Leeuw, Robert Costanza, Steve Aulenbach, Simon Brewer, Michael Burek, Sarah Cornell, Carole L. Crumley, J. A. Dearing, Catherine Downy, Lisa J. Graumlich, Scott Heckbert, Michelle Hegmon, Kathy A. Hibbard, Stephen T. Jackson, Ida Kubiszewski, Paul Sinclair, Sverker Sörlin, W. L. Steffen

Institute for Sustainable Solutions Publications and Presentations

Many contemporary societal challenges manifest themselves in the domain of human?environment interactions. There is a growing recognition that responses to these challenges formulated within current disciplinary boundaries, in isolation from their wider contexts, cannot adequately address them. Here, we outline the need for an integrated, transdisciplinary synthesis that allows for a holistic approach, and, above all, a much longer time perspective. We outline both the need for and the fundamental characteristics of what we call ?integrated history.? This approach promises to yield new understandings of the relationship between the past, present, and possible futures of our integrated human?environment system. We …

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

Mathematics and Statistics Faculty Publications and Presentations

In this concluding part of a series of papers on tetrahedral polynomial extension operators, the existence of a polynomial extension operator in the Sobolev space H(div) is proven constructively. Specifically, on any tetrahedron K, given a function w on the boundary ∂K that is a polynomial on each face, the extension operator applied to w gives a vector function whose components are polynomials of at most the same degree in the tetrahedron. The vector function is an extension in the sense that the trace of its normal component on the boundary ∂K coincides with w. Furthermore, the extension operator is …

Strategies For Labeling Proteins With Paracest Agents, Olga Vasalatiy, Piyu Zhao, Mark Woods, Andrei Marconescu, Aminta Castillo-Muzquiz, Philip Thorpe, Garry Kiefer, A. Dean Sherry

Chemistry Faculty Publications and Presentations

Reactive surface lysine groups on the chimeric monoclonal antibody (3G4) and on human serum albumin (HSA) were labeled with two different PARACEST chelates. Between 7.4 – 10.1 chelates were added per 3G4 molecule and between 5.6 – 5.9 chelates per molecule of HSA, depending upon which conjugation chemistry was used. The immunoreactivity of 3G4 as measured by ELISA assays was highly dependent upon the number of attached chelates: 88% immunoreactivity with 7.4 chelates per antibody versus only 17% immunoreactivity with 10.1 chelates per antibody. Upon conjugation to 3G4, the bound water lifetime of Eu-1 increased only marginally, up from …

Analysis Of The Dpg Method For The Poisson Equation, Leszek Demkowicz, Jay Gopalakrishnan

Mathematics and Statistics Faculty Publications and Presentations

We give an error analysis of the recently developed DPG method applied to solve the Poisson equation and a convection-dffusion problem. We prove that the method is quasioptimal. Error estimates in terms of both the mesh size h and the polynomial degree p (for various element shapes) can be derived from our results. Results of extensive numerical experiments are also presented.

A Second Elasticity Element Using The Matrix Bubble, Jay Gopalakrishnan, Johnny Guzmán

Mathematics and Statistics Faculty Publications and Presentations

We presented a family of finite elements that use a polynomial space augmented by certain matrix bubbles in Cockburn et al. (2010) A new elasticity element made for enforcing weak stress symmetry. Math. Comput., 79, 1331–1349 . In this sequel we exhibit a second family of elements that use the same matrix bubble. This second element uses a stress space smaller than the first while maintaining the same space for rotations (which are the Lagrange multipliers corresponding to a weak symmetry constraint). The space of displacements is of one degree less than the first method. The analysis, while similar to …

Computational Approach To Dark Current Spectroscopy In Ccds As Complex Systems. Ii. Numerical Analysis Of The Uniqueness Parameters Evaluation, Ionel Tunaru, Ralf Widenhorn, Dan A. Iordache, Erik Bodegom

Physics Faculty Publications and Presentations

The evaluation of the uniqueness parameters of the temperature dependence in CCDs is difficult to the considerable number of input parameters and to the strongly nonlinear (exponential) theoretical relations. For this reason, the elaborated computer programs are very sensitive to the choice of the zero-order approximations of the effective (Si) energy gap, and of the weights associated to the experimentally determined dark current. The main goal of this work was to study the rather narrow stability domains of the zero-order approximations, which lead to attractors with physical meaning. It was found that the stability domains are surrounded by (usually in …

Nonlinear Time Dependence Of Dark Current In Charge-Coupled Devices, Justin Charles Dunlap, Erik Bodegom, Ralf Widenhorn

Physics Faculty Publications and Presentations

It is generally assumed that charge-coupled device (CCD) imagers produce a linear response of dark current versus exposure time except near saturation. We found a large number of pixels with nonlinear dark current response to exposure time to be present in two scientific CCD imagers. These pixels are found to exhibit distinguishable behavior with other analogous pixels and therefore can be characterized in groupings. Data from two Kodak CCD sensors are presented for exposure times from a few seconds up to two hours. Linear behavior is traditionally taken for granted when carrying out dark current correction and as a result, …

Dark Current In An Active Pixel Complementary Metal-Oxide-Semiconductor Sensor, Justin Charles Dunlap, William Christian Porter, Erik Bodegom, Ralf Widenhorn

Physics Faculty Publications and Presentations

We present an analysis of dark current from a complementary metal?oxide?semiconductor (CMOS) active pixels sensor with global shutter. The presence of two sources of dark current, one within the collection area of the pixel and another within the sense node, present complications to correction of the dark current. The two sources are shown to generate unique and characteristic dark current behavior with respect to varying exposure time, temperature, and/or frame rate. In particular, a pixel with storage time in the sense node will show a dark current dependence on frame rate and the appearance of being a ?stuck pixel? with …

Photoelectron Emission Control With Polarized Light In Plasmonic Metal Random Structures, Robert Campbell Word, Joseph Fitzgerald, Rolf Kӧnenkamp

Physics Faculty Publications and Presentations

The authors report on the possibility of switching the emission rate of photoelectrons by polarization changes in the plasmon excitation light. Photoelectron emission is strongly enhanced in the near-field of localized surface plasmons and occurs from areas with typical diameters of 20-70 nm. The underlying physical process involves excitation of a localized surface plasmon polariton with a femtosecond laser pulse, and a subsequent multi-photon photoemission process. The non-linearity of this process leads to a sharp polarization dependence that allows efficient switching of the emission. We demonstrate that a 90° polarization change can result in on/off ratios of ∼100 for electron …

Acousto Characterization Of Fluid-Like Mesoscopic Films Under Shear, Rodolfo Fernandez, Xiaohua Wang, Andres H. La Rosa

Physics Faculty Publications and Presentations

Full understanding of the physics underlying the striking changes-in viscoelasticity, relaxation time, and phase transitions-that mesoscopic fluid-like systems undergo when placed under confinement or when adsorbed at solid surfaces constitutes a long standing scientific challenge. One of the methods used to characterize these films consists of bringing a solid boundary closer to another solid boundary (while in relative lateral periodic motion) with a liquid trapped in between. In addition, using a tapered probe (~ 50 nm apex diameter) as one of the boundaries improves the lateral resolution of the measurement. In this scenario, the dynamics of the fluid is inferred …

Crystallite Phase And Orientation Determinations Of (Mn, Ga) As/Gaas-Crystallites Using Analyzed (Precession) Electron Diffraction Patterns, Ines Häusler, Stavros Nicolopoulos, Edgar F. Rauch, K. Volz, Peter Moeck

Physics Faculty Publications and Presentations

Outline of the presentation:

1. Material system: (Mn,Ga)As/GaAs-crystallites

2. Structure analysis using Nano-beam Diffraction (NBD) Precession Electron Diffraction Technique (PED) --> Structure type I + II

3. Phase and orientation mapping using ASTAR

4. Conclusion

The Sociology Of Landowner Interest In Restoring Fire-Adapted, Biodiverse Habitats In The Wildland-Urban Interface Of Oregon's Willamette Valley Ecoregion, Max Nielsen-Pincus

Environmental Science and Management Faculty Publications and Presentations

In many parts of the world, the combined effects of wildfire, climate change, and population growth in the wildland-urban interface pose increasing risks to both people and biodiversity. These risks are exemplified in western Oregon’s Willamette Valley Ecoregion, where population is projected to double by 2050 and climate change is expected to increase wildfire risk. Restoring elements of the region’s historic fire-adapted prairie, savanna, and woodland habitats may help to reduce future wildfire risk and help conserve the region’s threatened biodiversity. We report on a mail survey (n = 939) examining the socio-demographic factors influencing private landowners’ likelihood of restoring …

Detecting Specific Saccharides Via A Single Indicator, Soojin Lim, Jorge O. Escobedo, Mark Lowry, Robert M. Strongin

Chemistry Faculty Publications and Presentations

An improved synthesis of a rhodamine boronic acid indicator is reported. This compound is used in an optimized data collection protocol for wavelength- and time-dependent selectivity of sugars such as fructose and ribose derivatives. One indicator is thus used to selectively distinguish structurally related sugar analytes.

Foliar Nutrient Concentrations Related To Soil Sources Across A Range Of Sites In The Northeastern United States, Melissa S. Lucash, Ruth D. Yanai, Joel D. Blum, B. B. Park

Environmental Science and Management Faculty Publications and Presentations

Understanding the supply of nutrients from various soil sources and the sensitivity of tree species to soil nutrient availability is critical for predicting the effects of declines in base cations due to acid rain and forest harvesting on forest health and productivity. We collected soil samples from 19 sites in the northeastern United States, chemically analyzed them using a sequential extraction procedure, and compared them to the chemical composition of foliage of the dominant tree species. Concentrations of Ca and Mg in foliage were correlated with exchangeable Ca and Mg concentrations in the upper mineral soil; for most tree species …

Can Salmonids (Oncorhynchus Spp.) Be Identified To Species Using Vertebral Morphometrics?, Harriet R. Huber, Jeffery C. Jorgensen, Virginia L. Butler, Greg Baker, Rebecca Stevens

Anthropology Faculty Publications and Presentations

Remains of anadromous Pacific salmon and trout (genus Oncorhynchus) are common in archaeological sites from California to Alaska; however, morphological similarity generally precludes species identification, limiting the range of questions that salmonid remains can address in relation to past human use and ongoing efforts in conservation biology. We developed a relatively simple, rapid, and non-destructive way to classify salmon and trout vertebrae from archaeological contexts to species using length, height and the ratio of length to height. Modern reference material was obtained from all seven anadromous Oncorhynchus species native to the west coast of North America. A minimum of ten …

Symmetric Nonconforming Mixed Finite Elements For Linear Elasticity, Jay Gopalakrishnan, Johnny Guzmán

Mathematics and Statistics Faculty Publications and Presentations

We present a family of mixed methods for linear elasticity that yield exactly symmetric, but only weakly conforming, stress approximations. The method is presented in both two and three dimensions (on triangular and tetrahedral meshes). The method is efficiently implementable by hybridization. The degrees of freedom of the Lagrange multipliers, which approximate the displacements at the faces, solve a symmetric positive-definite system. The design and analysis of this method is motivated by a new set of unisolvent degrees of freedom for symmetric polynomial matrices. These new degrees of freedom are also used to give a new simple calculation of the …

Balance Systems And The Variational Bicomplex, Serge Preston

Mathematics and Statistics Faculty Publications and Presentations

In this work we show that the systems of balance equations (balance systems) of continuum thermodynamics occupy a natural place in the variational bicomplex formalism. We apply the vertical homotopy decomposition to get a local splitting (in a convenient domain) of a general balance system as the sum of a Lagrangian part and a complemental "pure non-Lagrangian" balance system. In the case when derivatives of the dynamical fields do not enter the constitutive relations of the balance system, the "pure non-Lagrangian" systems coincide with the systems introduced by S. Godunov [Soviet Math. Dokl. 2 (1961), 947–948] and, later, asserted as …

The Integrated Wrf/Urban Modeling System: Development, Evaluation, And Applications To Urban Environmental Problems, Fei Chen, Hiroyuki Kusaka, Robert Bornstein, Jason Ching, C.S.B. Grimmond, Susanne Grossman-Clarke, Thomas Loridan, Kevin W. Manning, Alberto Martilli, Shiguang Miao, David J. Sailor, Francisco P. Salamanca, Haider Taha, Mukul Tewari, Xuemei Wang, Andrzej A. Wyszogrodzki, Chaolin Zhang

Mechanical and Materials Engineering Faculty Publications and Presentations

To bridge the gaps between traditional mesoscale modeling and microscale modeling, the National Center for Atmospheric Research (NCAR), in collaboration with other agencies and research groups, has developed an integrated urban modeling system coupled to the Weather Research and Forecasting (WRF) model as a community tool to address urban environmental issues. The core of this WRF/urban modeling system consists of: 1) three methods with different degrees of freedom to parameterize urban surface processes, ranging from a simple bulk parameterization to a sophisticated multi-layer urban canopy model with an indoor outdoor exchange sub-model that directly interacts with the atmospheric boundary layer, …

Sources And Pathways To The Environment And Environmental Presence, Tess Chadil

Environmental Science and Management Professional Master's Project Reports

In an attempt to successfully address and reduce contamination from toxic chemicals and other pollutants in the Oregon environment, the Oregon Department of Environmental Quality is in the early stages of developing a comprehensive agency-wide toxics reduction plan. The plan seeks to find a more efficient, sustainable approach to addressing contaminants of concern to human and ecological health. Team Toxics, a work group compromised of members from various DEQ departments, has been created to collaborate and create the framework for developing these strategies. In summer 2009, Team Toxics was in the very early stages of development, and found the need …

Imaging The Extracellular Ph Of Tumors By Mri After Injection Of A Single Cocktail Of T1 And T2 Contrast Agents, Gary V. Martinez, Xiaomeng Zhang, María L. García-Martín, David L. Morse, Mark Woods, A. Dean Sherry, Robert J. Gillies

Chemistry Faculty Publications and Presentations

The extracellular pH (pH(e) ) of solid tumors is acidic, and there is evidence that an acidic pH(e) is related to invasiveness. Herein, we describe an MRI single-infusion method to measure pH(e) in gliomas using a cocktail of contrast agents (CAs). The cocktail contained gadolinium-1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraaminophosphonate (GdDOTA-4AmP) and dysprosium-1,4,7,10-tetraazacyclododecane-N,N',N'',N'''-tetrakis(methylenephosphonic acid) (DyDOTP), whose effects on relaxation are sensitive and insensitive to pH, respectively. The Gd-CA dominated the spin-lattice relaxivity ΔR(1) , whereas the Dy-CA dominated the spin-spin relaxivity ΔR(2)*. The ΔR(2)* effects were used to determine the pixel-wise concentration of [Dy] which, in turn, was used to calculate a value for [Gd] …

Commuting Smoothed Projectors In Weighted Norms With An Application To Axisymmetric Maxwell Equations, Jay Gopalakrishnan, Minah Oh

Mathematics and Statistics Faculty Publications and Presentations

We construct finite element projectors that can be applied to functions with low regularity. These projectors are continuous in a weighted norm arising naturally when modeling devices with axial symmetry. They have important commuting diagram properties needed for finite element analysis. As an application, we use the projectors to prove quasioptimal convergence for the edge finite element approximation of the axisymmetric time-harmonic Maxwell equations on nonsmooth domains. Supplementary numerical investigations on convergence deterioration at high wavenumbers and near Maxwell eigenvalues and are also reported.

Analysis Of Hdg Methods For Stokes Flow, Bernardo Cockburn, Jay Gopalakrishnan, Ngoc Cuong Nguyen, Jaume Peraire, Francisco-Javier Sayas

Mathematics and Statistics Faculty Publications and Presentations

In this paper, we analyze a hybridizable discontinuous Galerkin method for numerically solving the Stokes equations. The method uses polynomials of degree $ k$ for all the components of the approximate solution of the gradient-velocity-pressure formulation. The novelty of the analysis is the use of a new projection tailored to the very structure of the numerical traces of the method. It renders the analysis of the projection of the errors very concise and allows us to see that the projection of the error in the velocity superconverges. As a consequence, we prove that the approximations of the velocity gradient, the …

(Editorial) A Long Term View Of Rare Plant Reintroduction. A Response To Godefroid Et Al. 2011: How Successful Are Plant Reintroductions?, Matthew A. Albrecht, Edward O. Guerrant Jr., Joyce Maschinski, Kathryn Kennedy

Environmental Science and Management Faculty Publications and Presentations

This is an editorial response to Godefroidet al. (2011). How successful are plant species reintroductions? Biological Conservation 144, 672-682.

Quantifying Uncertainty In Urban Flooding Analysis Considering Hydro-Climatic Projection And Urban Development Effects, Il-Won Jung, Heejun Chang, Hamid Moradkhani

Geography Faculty Publications and Presentations

How will the combined impacts of land use change, climate change, and hydrologic modeling influence changes in urban flood frequency and what is the main uncertainty source of the results? Will such changes differ by catchment with different degrees of current and future urban development? We attempt to answer these questions in two catchments with different degrees of urbanization, the Fanno catchment with 84% urban land use and the Johnson catchment with 36% urban land use, both located in the Pacific Northwest of the US. Five uncertainty sources – general circulation model (GCM) structures, future greenhouse gas (GHG) emission scenarios, …