Physical Sciences and Mathematics Commons^™

Haskell For The Cloud, Andrew P. Black

Computer Science Faculty Publications and Presentations

We present Cloud Haskell, a domain specific language for developing programs for a distributed-memory computing environment. Implemented as a shallow embedding in Haskell, it provides a message-passing communication model, inspired by Erlang, without introducing incompatibility with Haskell's established sharedmemory concurrency. A key contribution is a method for serializing function closures for transmission across the network. Cloud Haskell has been implemented; we present example code and some preliminary performance measurements.

Finding Haystacks With Needles: Ranked Search For Data Using Geospatial And Temporal Characteristics, Veronika Margaret Megler, David Maier

Computer Science Faculty Publications and Presentations

The past decade has seen an explosion in the number and types of environmental sensors deployed, many of which provide a continuous stream of observations. Each individual observation consists of one or more sensor measurements, a geographic location, and a time. With billions of historical observations stored in diverse databases and in thousands of datasets, scientists have difficulty finding relevant observations. We present an approach that creates consistent geospatial-temporal metadata from large repositories of diverse data by blending curated and automated extracts. We describe a novel query method over this metadata that returns ranked search results to a query with …

Can Transportation Researchers Reuse Project Datasets And Programs?, Tyler Hayes, Lois Delcambre, Leonard Shapiro

Computer Science Faculty Publications and Presentations

Data users involved in research and analysis typically invest a lot of eort cleaning and manipu- lating their data as they work. Based on this observation, we have investigated two hypotheses: 1) reuse of datasets and procedures is difficult, and 2) the inability to reuse datasets and procedures is primarily due to a lack of documentation. To test these hypotheses we conducted structured interviews with data users asking questions regarding the struggles in their work pertaining to data, their documentation habits, and the importance of documentation. The interviews revealed that the data users rarely reused data or procedures, frequently encountered …

Relativistic Red-Black Trees, Philip William Howard, Jonathan Walpole

Computer Science Faculty Publications and Presentations

Operating system performance and scalability on sharedmemory many-core systems depends critically on efficient access to shared data structures. Scalability has proven difficult to achieve for many data structures. In this paper we present a novel and highly scalable concurrent red-black tree. Red-black trees are widely used in operating systems, but typically exhibit poor scalability. Our red-black tree has linear read scalability, uncontended read performance that is at least 25% faster than other known approaches, and deterministic lookup times for a given tree size, making it suitable for realtime applications.

The Ordering Requirements Of Relativistic And Reader-Writer Locking Approaches To Shared Data Access, Philip William Howard, Josh Triplett, Jonathan Walpole, Paul E. Mckenney

Computer Science Faculty Publications and Presentations

The semantics of reader-writer locks allow read-side concurrency. Unfortunately, the locking primitives serialize access to the lock variable to an extent that little or no concurrency is realized in practice for small critical sections. Relativistic programming is a methodology that also allows read- side concurrency. Relativistic programming uses dfferent ordering constraints than reader-writer locking. The different ordering constraints allow relativistic readers to proceed without synchronization so relativistic readers scale even for very short critical sections. In this paper we explore the diferences between the ordering constraints for reader-writer locking and relativistic programs. We show how and why the dfferent ordering …

Potential For Speciation In Mammals Following Vast, Late Miocene Volcanic Interruptions In The Pacific Northwest, Ryan Thomas Mckenna

Dissertations and Theses

The impact of large-scale volcanic eruptions on landscapes can affect many processes ranging from interrupting or redirecting regional soil forming processes and hydrological systems to generating temporary changes in global climate. Though more studies exist every year, less is known of the direct impact of large-scale volcanic eruptions on ecosystems and extinction, while even less is known of their impact on speciation. In deposits throughout the Pacific Northwest a special combination and association of volcanic magnitude with palaeoecological yield frequently presents unique prospects for inquiry. In this study, particular attention is given to large, late Miocene ash-flow tuffs of central …

Physical And Electrical Characterization Of Triethanolamine Based Sensors For No₂ Detection And The Influence Of Humidity On Sensing Response, Zachariah Marcus Peterson

Dissertations and Theses

Triethanolamine (TEA) is a semiconducting polymer which exhibits a resistance change when exposed to various gases. The polymer also exhibits a number of reactions with nitrogen dioxide, with the reaction products being heavily dependent on the presence or absence of water vapor. Previous studies have attempted the incorporation of a TEA-carbon nanoparticle composite as the active sensing layer in a chemresistive sensor for detection of NO₂. The incorporation of carbon nanoparticles in the polymer nanocomposite was thought to amplify the sensor's response. There are a number of chemical reactions that can occur between TEA and NO₂, with the reaction products …

Interception In Open-Grown Douglas-Fir (Pseudotsuga Menziesii) Urban Canopy, Mitchell Bixby

Dissertations and Theses

I hypothesized that Douglas-fir trees (Pseudotsuga menziesii) standing apart from other trees ('open-grown') will intercept more rainfall than Douglas-fir trees standing near other trees ('closed-canopy'). Open-grown trees differ structurally and are more common in urban settings, yet have been infrequently studied. Existing literature, based primarily on closed-canopy trees, suggests Douglas-fir trees in Pacific Northwest forests intercept approximately 25% of rainfall annually. Because open-grown trees have more vertical leaf area than individual trees in closed-canopy forests, I expected to find higher interception by open-grown trees.

I collected throughfall under four open-grown Douglas-firs using six static collectors ('buckets') per tree, …

Floorplan Design And Yield Enhancement Of 3-D Integrated Circuits, Rajeev Kumar Nain

Dissertations and Theses

We have developed a placement-aware 3-D floorplanning algorithm that enables additional wirelength reduction by planning for 3-D placement of logic gates in selected circuit modules during the floorplanning stage. Thus it also bridges the existing gap between 3-D floorplanning and 3-D placement. To reduce the solution space of 3-D floorplanning which is known to be an NP-hard problem, we derive a set of feasibility conditions on the topological representation of a floorplan. In addition, we have designed a fast module packing algorithm that satisfies a set of constraints for placement-aware 3-D floorplanning. Furthermore, we have designed an efficient evolutionary algorithm …

Direct And Indirect Effects Of An Invasive Planktonic Predator On Pelagic Food Webs, Angela L. Strecker, Beatrix E. Beisner, Shelley E. Arnott, Andrew M. Paterson, Jennifer G. Winter, Ora E. Johannsson, Norman D. Yan

Environmental Science and Management Faculty Publications and Presentations

The relative importance of top-down invader effects relative to environmental drivers was determined by sampling crustacean zooplankton, rotifer, and phytoplankton communities in a set of invaded and noninvaded reference lakes. The non-native invertebrate predator Bythotrephes had significant effects on zooplankton community size structure, rotifers, and phytoplankton taxonomic composition, but no significant effects on crustacean zooplankton taxonomic and functional group composition. Part of the variation in phytoplankton communities was explained by the presence of the invader. Because Bythotrephes is generally known to be a carnivore and to not consume phytoplankton, this effect is likely mediated by the zooplankton community’s response to …

A 1-D Mechanistic Model For The Evolution Of Earthflow-Prone Hillslopes, Adam M. Booth, Joshua J. Roering

Geology Faculty Publications and Presentations

In mountainous terrain, deep‐seated landslides transport large volumes of material on hillslopes, exerting a dominant control on erosion rates and landscape form. Here, we develop a mathematical landscape evolution model to explore interactions between deep‐seated earthflows, soil creep, and gully processes at the drainage basin scale over geomorphically relevant (>10³ year) timescales. In the model, sediment flux or incision laws for these three geomorphic processes combine to determine the morphology of actively uplifting and eroding steady state topographic profiles. We apply the model to three sites, one in the Gabilan Mesa, California, with no earthflow activity, and two …

Volcanism And Astrobiology: Life On Earth And Beyond, Charles S. Cockell, Sherry L. Cady, Nicola Mcloughlin

Geology Faculty Publications and Presentations

Editorial Introduction to the 2011 Special Issue of Astrobiology.

Potential Fossil Endoliths In Vesicular Pillow Basalt, Coral Patch Seamount, Eastern North Atlantic Ocean, Barbara Cavalazzi, Frances Westall, Sherry L. Cady, Roberto Barbieri, Frédéric Foucher

Geology Faculty Publications and Presentations

The chilled rinds of pillow basalt from the Ampere-Coral Patch Seamounts in the eastern North Atlantic were studied as a potential habitat of microbial life. A variety of putative biogenic structures, which include filamentous and spherical microfossil-like structures, were detected in K-phillipsite-filled amygdules within the chilled rinds. The filamentous structures (similar to 2.5 mu m in diameter) occur as K-phillipsite tubules surrounded by an Fe-oxyhydroxide (lepidocrocite) rich membranous structure, whereas the spherical structures (from 4 to 2 mu m in diameter) are associated with Ti oxide (anatase) and carbonaceous matter. Several lines of evidence indicate that the microfossil-like structures in …

'Sticky Spots' And Subglacial Lakes Under Ice Streams Of The Siple Coast, Antarctica, Olga V. Sergienko, Christina L. Hulbe

Geology Faculty Publications and Presentations

Locations of subglacial lakes discovered under fast-moving West Antarctic ice streams tend to be associated with topographic features of the subglacial bed or with areas that have strong variations in basal conditions. Inversion of ice-stream surface velocity indicates that basal conditions under ice streams can be highly variable and that there can be widespread regions where basal traction is high. To seek an explanation for why lakes appear to be sited near areas with high basal traction, we use numerical models to simulate ice-stream dynamics, thermodynamics and subglacial water flow. We demonstrate that the ice flow over high basal traction …

Urban And Rural-Residential Land Uses: Their Role In Watershed Health And The Rehabilitation Of Oregon’S Wild Salmonids, Michael Harte, Victor W. Kaczynski, Clinton C. Shock, J. Alan Yeakley, Robert M. Hughes, Nancy Molina, Carl B. Schreck

Environmental Science and Management Faculty Publications and Presentations

This technical report by the Independent Multidisciplinary Science Team (IMST) is a comprehensive review of how human activities in urban and rural-residential areas can alter aquatic ecosystems and resulting implications for salmonid recovery, with a geographic focus on the state of Oregon. The following topics are considered in the form of science questions, and comprise the major components of this report:

1. The effects of urban and rural-residential development on Oregon’s watersheds and native wild salmonids.
2. Actions that can be used to avoid or mitigate undesirable changes to aquatic ecosystems near developing urban and rural-residential areas.
3. The benefits and pitfalls of …

Interview With Brendan Phillips, Sisters Of The Road, 2010 (Audio), Brendan Phillips

All Sustainability History Project Oral Histories

Interview of Brendan Phillips by Brandon Green in Portland, Oregon on December 8th, 2010.

The interview index is available for download.

Reconstructability Analysis Of Epistasis, Martin Zwick

Systems Science Faculty Publications and Presentations

The literature on epistasis describes various methods to detect epistatic interactions and to classify different types of epistasis. Reconstructability analysis (RA) has recently been used to detect epistasis in genomic data. This paper shows that RA offers a classification of types of epistasis at three levels of resolution (variable-based models without loops, variable-based models with loops, state-based models). These types can be defined by the simplest RA structures that model the data without information loss; a more detailed classification can be defined by the information content of multiple candidate structures. The RA classification can be augmented with structures from related …

Random Automata Networks: Why Playing Dice Is Not A Vice, Christof Teuscher

Systems Science Friday Noon Seminar Series

Random automata networks consist of a set of simple compute nodes interacting with each other. In this generic model, one or multiple model parameters, such as the the node interactions and/or the compute functions, are chosen at random. Random Boolean Networks (RBNs) are a particular case of discrete dynamical automata networks where both time and states are discrete. While traditional RBNs are generally credited to Stuart Kauffman (1969), who introduced them as simplified models of gene regulation, Alan Turing proposed unorganized machines as early as 1948. In this talk I will start with Alan Turing's early work on unorganized machines, …

Recreational Boats As Potential Vectors Of Marine Organisms At An Invasion Hotspot, Ian C. Davidson, Chela J. Zabin, Andrew L. Chang, Christopher W. Brown, Mark Sytsma, Gregory M. Ruiz

Center for Lakes and Reservoirs Publications and Presentations

With more than 200 aquatic nonindigenous species (NIS), San Francisco Bay (California, USA) is among the world’s most invaded harbors. Hard-substratum benthic (biofouling) organisms, which dominate NIS richness, have arrived primarily as a result of shipping and aquaculture activity over past centuries. To date there has been no assessment of the leisure craft vector in the Bay. We aimed to characterize (1) biofouling on boats’ submerged surfaces and (2) boater behavior likely to affect the risk of NIS transfers. We used an underwater pole-cam, specimen collections, and a boater questionnaire to quantify the extent and composition of biofouling on recreational …

Interview With Dan Mcfarling, Aorta, 2010 (Audio), Dan Mcfarling

All Sustainability History Project Oral Histories

Interview of Dan McFarling by Andrew Scanlan at Union Station, Portland, Oregon on December 1st, 2010.

The interview index is available for download.

Amaila Falls Hydroelectric Project Model Development And Scenarios, Chris Berger, Scott A. Wells, Vanessa Wells

Civil and Environmental Engineering Faculty Publications and Presentations

The focus of this present study is to perform the following tasks:

* Develop a hydrodynamic and water quality model of the reservoir formed by the Amaila Falls Hydroelectric Project

* Develop and run modeling scenarios

Water quality model simulations of the 23.3 km² reservoir for Amaila Falls Hydroelectric Project were conducted for low, average, and high flow years. A scenario with no vegetation removed from the reservoir for an average flow was also simulated. Conditions downstream of the reservoir were also modeled using a river model.

The model used for the reservoir formed by Amaila Falls Hydroelectric Project …

Apertureless Near-Field/Far-Field Cw Two-Photon Microscope For Biological And Material Imaging And Spectroscopic Applications, Derek Brant Nowak, Andrew James Lawrence, Erik J. Sánchez

Physics Faculty Publications and Presentations

We present the development of a versatile spectroscopic imaging tool to allow for imaging with single-molecule sensitivity and high spatial resolution. The microscope allows for near-field and subdiffraction-limited far-field imaging by integrating a shear-force microscope on top of a custom inverted microscope design. The instrument has the ability to image in ambient conditions with optical resolutions on the order of tens of nanometers in the near field. A single low-cost computer controls the microscope with a field programmable gate array data acquisition card. High spatial resolution imaging is achieved with an inexpensive CW multiphoton excitation source, using an apertureless probe …

The Distribution And Reproductive Success Of The Western Snowy Plover Along The Oregon Coast - 2010, David J. Lauten, Kathleen J. Castelein, J. Daniel Farrar, Adam A. Kotaich, Eleanor P. Gaines

Institute for Natural Resources Publications

From 8 April – 27 September 2010 we monitored the distribution, abundance and productivity of the federally Threatened Western Snowy Plover (Charadrius alexandrinus nivosus) along the Oregon coast. From north to south, we surveyed and monitored plover activity at Sutton Beach, Siltcoos River estuary, the Dunes Overlook, North Tahkenitch Creek, Tenmile Creek, Coos Bay North Spit, Bandon Beach, New River, and Floras Lake. Our objectives for the Oregon coastal population in 2010 were to: 1) estimate the size of the adult Snowy Plover population, 2) locate plover nests, 3) continue selective use of mini-exclosures (MEs) to protect nests …

Phosphorus Export From A Restored Wetland Ecosystem In Response To Natural And Experimental Hydrologic Fluctuations, Marcelo Ardón, Shaena Montanari, Jennifer L. Morse, Martin W. Doyle, Emily S. Bernhardt

Environmental Science and Management Faculty Publications and Presentations

Wetland restoration is a commonly used approach to reduce nutrient loading to freshwater and coastal ecosystems, with many wetland restoration efforts occurring in former agricultural fields. Restored wetlands are expected to be effective at retaining or removing both nitrogen and phosphorus (P), yet restoring wetland hydrology to former agricultural fields can lead to the release of legacy fertilizer P. Here, we examined P cycling and export following rewetting of the Timberlake Restoration Project, a 440 ha restored riverine wetland complex in the coastal plain of North Carolina. We also compared P cycling within the restored wetland to two minimally disturbed …

Effect Of Network Structure On The Stability Margin Of Large Vehicle With Distributed Control, He Hao, Prabir Barooah, J. J. P. Veerman

Mathematics and Statistics Faculty Publications and Presentations

We study the problem of distributed control of a large network of double-integrator agents to maintain a rigid formation. A few lead vehicles are given information on the desired trajectory of the formation; while every other vehicle uses linear controller which only depends on relative position and velocity from a few other vehicles, which are called its neighbors. A predetermined information graph defines the neighbor relationships. We limit our attention to information graphs that are D-dimensional lattices, and examine the stability margin of the closed loop, which is measured by the real part of the least stable eigenvalue of …

Interview With Michael O'Brien, Osd, 2010 (Audio), Michael O'Brien

All Sustainability History Project Oral Histories

Interview of Michael O'Brien by Ian Caputo in North Portland, Oregon on November 22nd, 2010.

The interview index is available for download.

Interview With Brighton West, Friends Of Trees, 2010 (Audio), Brighton West

All Sustainability History Project Oral Histories

Interview of Brighton West by Brigitta Bazso at Portland State University on November 18th, 2010.

The interview index is available for download.

Interview With Renee Loveland, Gerding Edlen, 2010 (Audio), Renee Loveland

All Sustainability History Project Oral Histories

Interview of Renee Loveland by Jena Orr at Gerding Edlen, Portland, Oregon on November 17th, 2010.

The interview index is available for download.

Bandwidth Tuning Triggers Interplay Of Charge Order And Superconductivity In Two-Dimensional Organic Materials, S. Kaiser, M. Dressel, Y. Sun, A. Greco, J. A. Schlueter, Gary L. Gard, N. Drichko

Chemistry Faculty Publications and Presentations

We observe charge-order fluctuations in the quasi-two-dimensional organic superconductor β″-(BEDT-TTF)₂SF₅CH₂CF₂SO₃, both by means of vibrational spectroscopy, locally probing the fluctuating charge order, and by investigating the in-plane dynamical response by infrared reflectance spectroscopy. The decrease of the effective electronic interaction in an isostructural metal suppresses both charge-order fluctuations and superconductivity, pointing to their interplay. We compare the results of our experiments with calculations on the extended Hubbard model.

Accelerated Erosion Of Saltmarshes Infested By The Non-Native Burrowing Crustacean Sphaeroma Quoianum, Timothy Mathias Davidson, Catherine E. De Rivera

Environmental Science and Management Faculty Publications and Presentations

Lateral erosion of saltmarshes is affected by many abiotic and biotic factors. While abiotic factors are typically regarded as primary drivers of erosion, biotic influences such as burrowing or bioturbating taxa can also extensively modify the physical structure of this marine habitat. Many estuaries on the Pacific coast of North America have been invaded by populations of the burrowing non-native isopod Sphaeroma quoianum, which are thought to exacerbate the erosion of saltmarshes. We conducted a mensurative experiment to examine the relationship between populations of S. quoianum and lateral erosion rate of saltmarshes in Coos Bay, Oregon, USA. After 1 …