Physical Sciences and Mathematics Commons^™

Delay Line As A Chemical Reaction Network, Josh Moles, Peter Banda, Christof Teuscher

Computer Science Faculty Publications and Presentations

Chemistry as an unconventional computing medium presently lacks a systematic approach to gather, store, and sort data over time. To build more complicated systems in chemistries, the ability to look at data in the past would be a valuable tool to perform complex calculations. In this paper we present the first implementation of a chemical delay line providing information storage in a chemistry that can reliably capture information over an extended period of time. The delay line is capable of parallel operations in a single instruction, multiple data (SIMD) fashion.

Using Michaelis-Menten kinetics, we describe the chemical delay line implementation …

Assessing Usual Care In Clinical Trials, Judith A. Erlen, Lisa K. Tamres, Nancy Reynolds, Carol E. Golin, Marc I. Rosen, Robert H. Remien, Julie W. Banderas, Neil Schneiderman, Glenn Wagner, David Bangsberg, Honghu Liu

OHSU-PSU School of Public Health Faculty Publications and Presentations

Researchers designing clinical trials often specify usual care received by participants as the control condition expecting that all participants receive usual care regardless of group assignment. The assumption is that the groups in the study are affected similarly. We describe the assessment of usual care within the 16 studies in MACH 14, a multi-site collaboration on adherence to antiretroviral therapy. Only five of the studies in MACH 14 assessed usual care. Assessment protocols varied as did the timing and frequency of assessments. All usual care assessments addressed patient education focused on HIV, HIV medications, and medication adherence. Our findings support …

Core Evolution Driven By Mantle Global Circulation, Peter Olson, Renaud Deguen, Maxwell L. Rudolph, Shijie Zhong

Geology Faculty Publications and Presentations

Reconstructions of the Phanerozoic history of mantle global circulation that include past plate motions are used to constrain the thermochemical evolution of the core. According to our mantle global circulation models, the present-day global average heat flux at the core-mantle boundary lies in the range 80-90 mW.m^-2, with peak-to-peak, long wavelength lateral variations up to 100 mW.m^-2 associated with compositional and thermal heterogeneity in the D”-layer. For core thermal conductivity in the range k=100-130 W.m^-1.K^-1 we infer that the present-day outer core is thermally unstable beneath the high seismic velocity regions in the …

Energy Efficiency And Conservation Attitudes: An Exploration Of A Landscape Of Choices, Mersiha Spahic Mcclaren

Dissertations and Theses

This study explored energy-related attitudes and energy-saving behaviors that are no- or low-cost and relatively simple to perform. This study relied on two data sources: a longitudinal but cross-sectional survey of 4,102 U.S. residents (five biennial waves of this survey were conducted from 2002 to 2010) and a 2010 cross-sectional survey of 2,000 California residents. These two surveys contained data on two no- and low-cost behaviors: changing thermostat setting to save energy (no-cost behavior) and CFL installation behavior (low-cost behavior). In terms of attitudes, two attitudinal measures emerged from these data following a Cronbach's alpha and Confirmatory Factor Analysis (CFA): …

Modeling Predator Habitat To Enhance Reintroduction Planning, Shiloh Michael Halsey, William J. Zielinski, Robert M. Scheller

Environmental Science and Management Faculty Publications and Presentations

Context

The success of species reintroduction often depends on predation risk and spatial estimates of predator habitat. The fisher (Pekania pennanti) is a species of conservation concern and populations in the western United States have declined substantially in the last century. Reintroduction plans are underway, but the ability of the species to establish a selfsustaining population is affected by predation from its primary predator, the bobcat (Lynx rufus).

Objectives

To develop a habitat model that incorporates both habitat of the focal species and the spatial patterning of predator habitat. To locate areas of densely aggregated habitat that would be suitable …

Beyond The Angle Of Repose: A Review And Synthesis Of Landslide Processes In Response To Rapid Uplift, Eel River, Northern Eel River, Northern California, Joshua J. Roering, Benjamin H. Mackey, Alexander L. Handwerger, Adam M. Booth, David A. Schmidt, Georgina L. Bennett, Corina Cerovski-Darriau

Geology Faculty Publications and Presentations

In mountainous settings, increases in rock uplift are often followed by a commensurate uptick in denudation as rivers incise and steepen hillslopes, making them increasingly prone to landsliding as slope angles approach a limiting value. For decades, the threshold slope model has been invoked to account for landslide-driven increases in sediment flux that limit topographic relief, but the manner by which slope failures organize themselves spatially and temporally in order for erosion to keep pace with rock uplift has not been well documented. Here, we review past work and present new findings from remote sensing, cosmogenic adionuclides, suspended sediment records, …

Bubble Mobility In Mud And Magmatic Volcanoes, Aaron Tran, Maxwell L. Rudolph, Michael Manga

Geology Faculty Publications and Presentations

The rheology of particle-laden fluids with a yield stress, such as mud or crystal-rich magmas, controls the mobility of bubbles, both the size needed to overcome the yield stress and their rise speed. We experimentally measured the velocities of bubbles and rigid spheres in mud sampled from the Davis-Schrimpf mud volcanoes adjacent to the Salton Sea, Southern California. Combined with previous measurements in the polymer gel Carbopol, we obtained an empirical model for the drag coefficient and bounded the conditions under which bubbles overcome the yield stress. Yield stresses typical of mud and basaltic magmas with sub-mm particles can immobilize …

Current State Of Strain In The Central Cascadia Margin Derived From Changes In Distance Between Gps Stations, Kenneth M. Cruikshank, Curt D. Peterson

Geology Faculty Publications and Presentations

Using continuously operating Global Positioning Stations in the Pacific Northwest of the United States, over 100 station-station baseline length changes were determined along seven West-East transects, two North-South transects and in three localized areas to determine both the average annual strains over the past several years, and the variation in strain over the central Cascadia convergent margin. The North-South transects (composed of multiple baselines) show shortening. Along West-East transects some baselines show shortening and others extension. The direction of the principle strains calculated for two areas 100 km from the deformation front are close to per-pendicular to the deformation front. …

Analysis Of The Surface Density And Reactivity Of Perfluorophenylazide And The Impact On Ligand Immobilization, Gilad Zorn, David G. Castner, Anuradha Tyagi, Xin Wang, Hui Wang, Mingdi Yan

Chemistry Faculty Publications and Presentations

Perfluorophenylazide (PFPA) chemistry is a novel method for tailoring the surface properties of solid surfaces and nanoparticles. It is general and versatile, and has proven to be an efficient way to immobilize graphene, proteins, carbohydrates, and synthetic polymers. The main thrust of this work is to provide a detailed investigation on the chemical composition and surface density of the PFPA tailored surface. Specifically, gold surfaces were treated with PFPA-derivatized (11-mercaptoundecyl) tetra(ethylene glycol) (PFPA-MUTEG) mixed with 2-[2-(2-mercaptoethoxy)ethoxy]ethanol (MDEG) at varying solution mole ratios. Complementary analytical techniques were employed to characterize the resulting films including Fourier transform infrared spectroscopy to detect fingerprints …

Fire Modulates Climate Change Response Of Simulated Aspen Distribution Across Topoclimatic Gradients In A Semi-Arid Montane Landscape, Jian Yang, Peter J. Weisberg, Douglas J. Shinneman, Thomas E. Dilts, Susan L. Earnst, Robert M. Scheller

Environmental Science and Management Faculty Publications and Presentations

Content Changing aspen distribution in response to climate change and fire is a major focus of biodiversity conservation, yet little is known about the potential response of aspen to these two driving forces along topoclimatic gradients.

Objective This study is set to evaluate how aspen distribution might shift in response to different climate-fire scenarios in a semi-arid montane landscape, and quantify the influence of fire regime along topoclimatic gradients.

Methods We used a novel integration of a forest landscape succession and disturbance model (LAN DIS-II) with a fine-scale climatic water deficit approach to simulate dynamics of aspen and associated conifer …

Surface Temperature Probability Distributions In The Narccap Hindcast Experiment: Evaluation Methodology, Metrics, And Results, Paul C. Loikith, Duane E. Waliser, Huikyo Lee, Jinwon Kim, J. David Neelin, Benjamin R. Lintner, Seth Mcginnis, Chris A. Mattmann, Linda O. Mears

Geography Faculty Publications and Presentations

Methodology is developed and applied to evaluate the characteristics of daily surface temperature distributions in a six-member regional climate model (RCM) hindcast experiment conducted as part of the North American Regional Climate Change Assessment Program (NARCCAP). A surface temperature dataset combining gridded station observations and reanalysis is employed as the primary reference. Temperature biases are documented across the distribution, focusing on the median and tails. Temperature variance is generally higher in the RCMs than reference, while skewness is reasonably simulated in winter over the entire domain and over the western United States and Canada in summer. Substantial differences in skewness …

Semi-Modular Delay Model Revisited In Context Of Relative Timing, Hoon Park, Anping He, Marly Roncken, Xiaoyu Song

Electrical and Computer Engineering Faculty Publications and Presentations

A new definition of semi-modularity to accommodate relative timing constraints in self-timed circuits is presented. While previous definitions ignore such constraints, the new definition takes them into account. The difference on a design solution for a well-known speed-independent circuit implementation of the Muller C element and a set of relative timing constraints that renders the implementation hazard free is illustrated. The old definition produces a false semi-modularity conflict that cannot exist due to the set of imposed constraints. The new definition correctly accepts the solution.

Isolation Of Diverse Members Of The Aquificales From Geothermal Springs In Tengchong, China, Brian P. Hedlund, Anna-Louise Reysenbach, Liuquin Huang, John C. Ong, Zizhang Liu, Jeremy A. Dodsworth, Reham Ahmed, Amanda J. Williams, Brandon R. Briggs, Yitai Liu, Weiguo Hou, Hailiang Dong

Biology Faculty Publications and Presentations

The order Aquificales (phylum Aquificae) consists of thermophilic and hyperthermophilic bacteria that are prominent in many geothermal systems, including those in Tengchong, Yunnan Province, China. However, Aquificales have not previously been isolated from Tengchong. We isolated five strains of Aquificales from diverse springs (temperature 45.2–83.3°C and pH 2.6–9.1) in the Rehai Geothermal Field from sites in which Aquificales were abundant. Phylogenetic analysis showed that four of the strains belong to the genera Hydrogenobacter, Hydrogenobaculum, andSulfurihydrogenibium, including strains distant enough to likely justify new species ofHydrogenobacter and Hydrogenobaculum. The additional strain may represent a …

Glacier Status And Contribution To Streamflow In The Olympic Mountains, Usa, Jon L. Riedel, Steve Wilson, William Baccus, Michael Larrabee, T.J. Fudge, Andrew G. Fountain

Geology Faculty Publications and Presentations

The Olympic Peninsula, Washington, USA, currently holds 184 alpine glaciers larger than 0.01 km² and their combined area is 30.2 ± 0.95km². Only four glaciers are >1km² and 120 of the others are -¹ (1900–80) to 0.54 km² a^-¹ (1980–2009). Thinning rates on four of the largest glaciers averaged nearly 1ma^-¹ from 1987 to 2010, resulting in estimated volume losses of 17–24%. Combined glacial snow, firn and ice melt in the Hoh watershed is in the range 63–79 ± 7 × 10⁶m³, or 9–15% of total May–September streamflow. In the critical August–September …

Hidden Formaldehyde In E-Cigarette Aerosols, R. Paul Jensen, Wentai Luo, James F. Pankow, Robert M. Strongin, David H. Peyton

Chemistry Faculty Publications and Presentations

This letter reports a chemical analysis of vapor from electronic cigarettes that shows high levels of formaldehyde, a known carcinogen. The authors project that the associated incremental lifetime risk of cancer could be higher than that from long-term smoking.

Class Of Unambiguous State Discrimination Problems Achievable By Separable Measurements But Impossible By Local Operations And Classical Communication, Scott M. Cohen

Physics Faculty Publications and Presentations

We consider an infinite class of unambiguous quantum state discrimination problems on multipartite systems, described by Hilbert space H, of any number of parties. Restricting consideration to measurements that act only on H, we find the optimal global measurement for each element of this class, achieving the maximum possible success probability of 1/2 in all cases. This measurement turns out to be both separable and unique, and by our recently discovered necessary condition for local quantum operations and classical communication (LOCC) it is easily shown to be impossible by any finite-round LOCC protocol. We also show that, quite generally, if …

Monomials And Basin Cylinders For Network Dynamics, Daniel Austin, Ian H. Dinwoodie

Mathematics and Statistics Faculty Publications and Presentations

We describe methods to identify cylinder sets inside a basin of attraction for Boolean dynamics of biological networks. Such sets are used for designing regulatory interventions that make the system evolve towards a chosen attractor, for example initiating apoptosis in a cancer cell. We describe two algebraic methods for identifying cylinders inside a basin of attraction, one based on the Groebner fan that finds monomials that define cylinders and the other on primary decomposition. Both methods are applied to current examples of gene networks.

Sensible Air To Air Heat Recovery Strategies In A Passive House, Santiago Martin Rodriguez-Anderson

Dissertations and Theses

Due to rising energy costs and concerns about global climate change, high performance buildings are more in demand than ever before. With roughly 20% of the total energy consumption in the United States being devoted to residential use, this sector represents a significant opportunity for future savings. There are many guidelines and standards for reducing building energy consumption. One of the most stringent is the Passive House Standard. The standard requires that that air infiltration is less than or equal to 0.6 air changes per hour at a 50 Pascal pressure difference (ACH 50), annual heating energy is less than …

Static Conflict Detection For A Policy Language, Alix Trou, Robert Dockins, Andrew Tolmach

Computer Science Faculty Publications and Presentations

We present a static control flow analysis used in the Simple Unified Policy Programming Language (SUPPL) compiler to detect internally inconsistent policies. For example, an access control policy can decide to both “allow” and “deny” access for a user; such an inconsistency is called a conflict. Policies in Suppl. follow the Event-Condition-Action paradigm; predicates are used to model conditions and event handlers are written in an imperative way. The analysis is twofold; it first computes a superset of all conflicts by looking for a combination of actions in the event handlers that might violate a user-supplied definition of conflicts. SMT …

Enzymatic Control Of The Related Pathways Of Fatty Acid And Undecylprodiginine Biosynthesis In Streptomyces Coelicolor, Renu Singh

Dissertations and Theses

Streptomyces coelicolor produces fatty acids for both primary metabolism and for production of the components of natural products such as undecylprodiginine. Primary metabolism makes the longer and predominantly branched-chain fatty acids, while undecylprodiginine utilizes shorter and almost exclusively straight chain fatty acids. The first step in fatty acid biosynthetic process is catalyzed by FabH (β-ketoacyl synthase III), which catalyzes a decarboxylative condensation of an acyl-CoA primer with malonyl-acyl carrier protein (ACP). The resulting 3-ketoacyl-ACP product is reduced by NADPH-dependent FabG into 3-hydroxyacyl-ACP, which is dehydrated by FabA to form enoyl-ACP. The NADH-dependent FabI (InhA) completes the cycle. Subsequent rounds of …

Putting Impact First: Community-University Partnerships To Advance Authentic Neighborhood Sustainability, Michelle L. Holliday, Tony Defalco, Jacob Sherman

Institute for Sustainable Solutions Publications and Presentations

This article profiles a partnership between the Living Cully ecodistrict and Portland State University’s Sustainable Neighborhoods Initiative. The case studies presented in this article explore how Living Cully leveraged PSU assets to advance their goals, highlighting successes and lessons learned. This article also addresses how the partnership was formed, what makes the partnership innovative, the role of interdisciplinary/intercommunity organizational strategies, and how the community partner commits to urban sustainability and social justice.

Strengthening The Resiliency Of Dryland Forest-Based Livelihoods In Ethiopia And South Sudan: A Review Of Literature On The Interaction Between Dryland Forests, Livelihoods And Forest Governance, Steven Lawry, Rebecca J. Mclain, Habtemariam Kassa

Institute for Sustainable Solutions Publications and Presentations

Dry forests account for nearly half of the world’s tropical and subtropical forests and provide a multitude of ecological services. They contribute to hydrological cycles and livestock and wildlife provisioning; and host pollinators and wild plants. They are also important ecological zones for dryland agriculture and pastoral livelihood strategies that support hundreds of millions of people around the world. Dry forests cover large areas and their biomass stores carbon and helps mitigate climate change. Dry forests are particularly important to people in Africa. They provide wood for construction and energy, contribute to local diets with wild fruits, vegetables, nuts, edible …

Whose Urban Forest? The Political Ecology Of Foraging Urban Nontimber Forest Products, Patrick T. Hurley, Marla R. Emery, Rebecca J. Mclain, Melissa R. Poe, Brain Grabbatin, Cari L. Goetcheus

Institute for Sustainable Solutions Publications and Presentations

Drawing on case studies of foraging in Philadelphia, Pennsylvania and Mt. Pleasant, South Carolina, we point to foraging landscapes and practices within diverse urban forest spaces. We examine these spaces in relation to U.S. conservation and development processes and the effects of management and governance on species valued by foragers. These case studies reveal the everyday landscapes of urban foraging and suggest that ideas about what constitutes the suite of appropriate human-environment interactions in the sustainable city are contested and accommodated in diverse ways.

Oregon Lake Watch, 2015 Annual Report, Samuel Cimino, Rich Miller, Angela L. Strecker

Center for Lakes and Reservoirs Publications and Presentations

The Oregon Lake Watch (OLW) volunteer monitoring program completed its third year of operation during 2015 with a focus on early detection of aquatic invasive species (AIS) and water quality status and trend assessments for the better management of Oregon’s lakes and reservoirs. AIS surveys emphasized the detection of Watch List aquatic plant and species that can have a negative impacts on the beneficial uses of our waterbodies. Water transparency and temperature measurements were used to track the condition of volunteers' lakes.

Thirty-one Oregon lakes have been surveyed during the OLW’s three years, 16 of which were surveyed during 2015. …

Analyzing Free-Base Nicotine Content In The Particulate Matter Of Mainstream Tobacco Smoke Using A Headpace Solid-Phase Microextraction Gc/Ms Method, Christopher S. Motti

Civil and Environmental Engineering Master's Project Reports

The acid/base chemistry of cigarette smoke allows nicotine, the primary drug in mainstream tobacco smoke, to exist in protonated and free-base forms. Evidence suggests that most of the nicotine present in mainstream tobacco smoke is in the particle phase. α_fb is the fraction of particle-phase nicotine in the free-base form. The magnitude and rate of nicotine deposition in the respiratory tract is dependent on α_fb because only the free-base form of nicotine can volatilize from the particle phase of an inhaled aerosol and, once gaseous, rapidly deposit. This study develops a headspace solid-phase microextraction technique coupled with gas …

Geotechnical Statistical Evaluation Of Lahore Site Data And Deep Excavation Design, Aiza Malik

Civil and Environmental Engineering Master's Project Reports

Geotechnical characterization for foundation design is critical during preliminary planning, designing and feasibility studies of various engineering projects. In this research, an effort has been made to develop a geotechnical database for the city of Lahore, Pakistan. This database would aid geologists and engineers involved in the geotechnical design and planning of engineering projects in Lahore. The project area has been divided into zones geographically. Soil profiles have been developed for all zones, which provide ranges of soil properties and SPT-N values at regular intervals. Furthermore, the research also focuses on deep excavations in urban areas of Lahore, Pakistan and …

Institute For Sustainable Solutions Annual Report (2013-2014), Portland State University. Institute For Sustainable Solutions

Institute for Sustainable Solutions Publications and Presentations

This brief annual report from Portland State University's Institute for Sustainable Solutions captures the highlights from the year and signals where sustainability at PSU is headed in the years to come.

Dispersion Modeling Of Nitrogen Dioxide (No2) And Fine Particulate Matter (Pm2.5) From Backup Generators At Data Centers In Prineville, Oregon, Brooke E. Harmon

Civil and Environmental Engineering Master's Project Reports

As our society becomes increasingly dependent on digital communication (e.g., social media and email) and computerized storage (e.g., digitized medical records and government documents), tech giants such as Google, Facebook, and Apple are constructing and managing an increasing number of massive Internet data centers. These data centers house a network’s most critical systems and are vital to the continuity of daily operations. Requiring as much electricity as a medium size city, data centers rely on complex auxiliary power systems to prevent disruption to service. These backup systems consist of tens of multi-megawatt diesel-powered generators that release combustion byproducts, including over …

An Ornithological Investigation Of The Relationships Among Species Assemblages In Diverse Landscapes In Portland, Oregon, Trevor Attenberg

Environmental Science and Management Professional Master's Project Reports

This study involves geographic variables of the urban landscape and how they affect bird species assemblage. I utilized bird point count data from observation sites in the Portland, OR metropolitan region provided by Portland Environmental Services. Species data and its relationship with environmental variables were evaluated using Bray-Curtis Dissimilarity measurements together with Non-metric Multidimensional scaling (NMDS) to provide a clear image of the spatial relationships between sites. Land classification, water and canopy in 500 m buffers were quantified in order to describe important geographic variability among collection areas of bird data. Patterns indicating spatial trends in the urban landscape emerged. …

Initial Evaluations Of A U.S. Navy Rapidly Relocatable Gulf Of Mexico/Caribbean Ocean Forecast System In The Context Of The Deepwater Horizon Oil Spill Disaster, Edward D. Zaron, Patrick J. Fitzpatrick, Scott L. Cross, John M. Harding, Frank L. Bub, Jerry D. Wiggert, Dong S. Ko, Yee Lau, Katharine Woodward, Christopher N.K. Mooers

Civil and Environmental Engineering Faculty Publications and Presentations

In response to the Deepwater Horizon (DwH) oil spill event in 2010, the Naval Oceanographic Office deployed a nowcast-forecast system covering the Gulf of Mexico and adjacent Caribbean Sea that was designated Americas Seas, or AMSEAS, which is documented in this manuscript. The DwH disaster provided a challenge to the application of available ocean-forecast capabilities, and also generated a historically large observational dataset. AMSEAS was evaluated by four complementary efforts, each with somewhat different aims and approaches: a university research consortium within an Integrated Ocean Observing System (IOOS) testbed; a petroleum industry consortium, the Gulf of Mexico 3-D Operational Ocean …