Physical Sciences and Mathematics Commons^™

Analysis Of The Execution Time Variation Of Openmp-Based Applications On The Intel Xeon Phi, Roberto Camacho Barranco, Patricia J. Teller

Departmental Technical Reports (CS)

The Intel Xeon Phi accelerator is currently being used in several large-scale computer clusters and supercomputers to enhance the execution-time performance of computation-intensive applications. While performing a comprehensive profiling of the Intel Xeon Phi execution-time behavior of different applications included in the Rodinia Benchmark suite, we observed large variations in application execution times. In this report we present the average execution times for different runs of each application. In addition, we describe the different steps taken to try to solve this problem.

For example, a brief study was performed using one of these applications, i.e., a matrix-multiply kernel. By improving …

What Will Make Computers Faster: An Approach Based On Computational Complexity, Vladik Kreinovich

Departmental Technical Reports (CS)

No abstract provided.

How To Transform Partial Order Between Degrees Into Numerical Values, Olga Kosheleva, Vladik Kreinovich, Joe Lorkowski, Martha Osegueda Escobar

Departmental Technical Reports (CS)

Fuzzy techniques are a successful way to handle expert knowledge, enabling us to capture different degrees of expert's certainty in their statements. To use fuzzy techniques, we need to describe expert's degree of certainty in numerical terms. Some experts can provide such numbers, but others can only describe their degrees by using natural-language words like "very", "somewhat", "to some extent", etc. In general, all we know about these word-valued degrees is that there is a natural partial order between these degrees: e.g., "very small" is clearly smaller than "somewhat small". In this paper, we propose a natural way to transform …

Defect Driven Magnetism In Doped Sno2 Nanoparticles: Surface Effects, Pushpa Raghani, Pankaj Kumar, Balaji Ramanujam, Alex Punnoose

Physics Faculty Publications and Presentations

Magnetism and energetics of intrinsic and extrinsic defects and defect clusters in bulk and surfaces of SnO₂ is investigated using first-principles to understand the role of surfaces in inducing magnetism in Zn doped nanoparticles. We find that Sn vacancies induce the largest magnetic moment in bulk and on surfaces. However, they have very large formation energies in bulk as well as on surfaces. Oxygen vacancies on the other hand are much easier to create than V_Sn, but neutral and V_O⁺² vacancies do not induce any magnetism in bulk as well as on surfaces. V_{O …}

Putting Prep Into Practice: Lessons Learned From Early-Adopting U.S. Providers' Firsthand Experiences Providing Hiv Pre-Exposure Prophylaxis And Associated Care, S. K. Calabrese, Manya Magnus, K. H. Mayer, D. S. Krakower, A. I. Eldahan, L. A. Gaston Hawkins, +5 Additional Authors

Epidemiology Faculty Publications

Optimizing access to HIV pre-exposure prophylaxis (PrEP), an evidence-based HIV prevention resource, requires expanding healthcare providers' adoption of PrEP into clinical practice. This qualitative study explored PrEP providers' firsthand experiences relative to six commonly-cited barriers to prescription-financial coverage, implementation logistics, eligibility determination, adherence concerns, side effects, and anticipated behavior change (risk compensation)-as well as their recommendations for training PrEP-inexperienced providers. U.S.-based PrEP providers were recruited via direct outreach and referral from colleagues and other participants (2014-2015). One-on-one interviews were conducted in person or by phone, transcribed, and analyzed. The sample (n = 18) primarily practiced in the Northeastern (67%) or …

Approximate Analytical Solution Of Boussinesq Equation In Homogeneous Medium With Leaky Base, Rajeev K. Bansal

Applications and Applied Mathematics: An International Journal (AAM)

Approximate analytical solutions of Boussinesq equation are widely used for approximation of subsurface seepage flow in confined and unconfined aquifers under varying hydrological conditions. In this paper, we use a 2-dimensional linearized Boussinesq equation to simulate the water table fluctuations in an isotropic aquifer overlying a semi pervious bed under multiple localized recharge and withdrawal. The unconfined aquifer is considered to be in contact with two water bodies of constant water head along opposite cost lines, while the remaining two faces have no flow condition. The mathematical model is solved analytically using finite Fourier sine transform and the application of …

Statistical Methodology For Data With Multiple Limits Of Detection, Robert M. Flikkema

Dissertations

Limitations of instruments used to collect continuous data sometimes lead to obtaining observations lower than a limit of detection. These observations are known as nondetects. They could be zeroes, or positive numbers, but they are too small to be recorded by a measuring device. Nondetects frequently occur in environmental data. Trace amounts of chemicals can exist in soil or groundwater and are undetectable by a machine reading. These observations pose a problem to researchers since the true values are unknown.

Simulations in the literature have led to inconsistent conclusions regarding what estimation technique to use with nondetect data when estimating …

Accelerating Hash Grid And Screen-Space Photon Mapping In 3d Interactive Applications With Opencl, Nikolai Shkurkin

Computer Science and Software Engineering

Achieving interactive and realistic rendering is only possible with a combination of rendering algorithms, rendering pipelines, multi-core hardware, and parallelization APIs. This project explores and implements two photon mapping pipelines based on the work of Mara et. al [5] and Singh et. al [7] to achieve interactive rendering performance for a set of simple scenes using OpenCL and C++ to work with a GPU. In particular, both a 3D hash grid and a screen-space tiling algorithm are parallelized to accelerate photon lookup in order to compute direct and indirect lighting on visible surfaces in a scene. By using OpenCL with …

Improvements To Digital Democracy's Transcription Tool, Andrew Reinman

Computer Science and Software Engineering

Digital Democracy is a website that hosts legislative court hearings along with their transcripts and other information. The current process for getting these videos onto the website is quite tedious. By improving the tool currently used, I will automate a lot of the current work in order to greatly reduce the time spent getting videos on our website.

Raspberry Pi Radio Scanner Control Web Application, Jackson Marshall Strand

Computer Science and Software Engineering

In this senior project I design and develop software for the Raspberry Pi which allows the user to listen to and control a scanner radio anywhere in their home. The solution involves utilizing a Raspberry Pi 2 interfaced with the radio, a software package to communicate directly with the radio, and a web app hosting a web client providing the interface for user control. Audio streaming is achieved through the use of FFmpeg. Listening on the client is achieved by using an external software such as Video Lan (VLC) to open the audio stream. We provide an operable proof-of-concept with …

Black Holes Modeled As Fluid Droplets On Membranes, Anthony Bardessono

Physics

No abstract provided.

Real-Time, Non-Contact Heart Rate Monitor, Daniel Blike

Computer Engineering

No abstract provided.

Positive And Negative Gps-Tec Ionospheric Storm Effects During The Extreme Space Weather Event Of March 2015 Over The Brazilian Sector, P. R. Fagundes, F. A. Cardoso, B. G. Fejer, K. Venkatsch, B.A. G. Ribeiro, V. G. Pillat

All Physics Faculty Publications

We studied the response of the ionosphere (F region) in the Brazilian sector during extreme space weather event of 17 March 2015 using a large network of 102 GPS- total electron content (TEC) stations. It is observed that the vertical total electron content (VTEC) was severely disturbed during the storm main and recovery phases. A wavelike oscillation with three peaks was observed in the TEC diurnal variation from equator to low latitudes during the storm main phase on 17_18 March 2015. The latitudinal extent of the wavelike oscillation peaks decreased from the beginning of the main phase toward the recovery …

Mechanism Of Lysine 48 Selectivity During Polyubiquitin Chain Formation By The Ube2r1/2 Ubiquitin-Conjugating Enzyme, Spencer Hill, Joseph S. Harrison, Steven M. Lewis, Brian Kuhlman, Gary Kleiger

College of the Pacific Faculty Articles

Lysine selectivity is of critical importance during polyubiquitin chain formation because the identity of the lysine controls the biological outcome. Ubiquitins are covalently linked in polyubiquitin chains through one of seven lysine residues on its surface and the C terminus of adjacent protomers. Lys 48-linked polyubiquitin chains signal for protein degradation; however, the structural basis for Lys 48 selectivity remains largely unknown. The ubiquitin-conjugating enzyme Ube2R1/2 has exquisite specificity for Lys 48, and computational docking of Ube2R1/2 and ubiquitin predicts that Lys 48 is guided to the active site through a key electrostatic interaction between Arg 54 on ubiquitin and …

An Investigation Into The Use Of Polymer Bound Boronic Acid For Glucose Detection In Paper Based Microfluidic Devices, Spencer A. Schultz

Master's Theses

Paper Based Microfluidic Devices (microPADs) are a new platform for point-of-care diagnostic assays for use in resource-limited settings. These devices rely typically on enzymatic assays to produce their results, which makes them susceptible to degradation when exposed to extreme environmental conditions such as high temperature. In order to overcome this limitation, this research project focused on investigating the use of polymers instead of enzymes to detect analytes on microPADs.

Polymer-bound boronic acid, a glucose and pH sensitive polymer, was incorporated into microPADs in order to develop a chronometric, paper-based glucose assay. The polymer was tested with both lateral and vertical …

Enhancing Digestibility And Ethanol Yield Of Populus Wood Via Expression Of An Engineered Monolignol 4-O-Methyltransferase, Yuanheng Cai, Kewei Zhang, Hoon Kim, Guichuan Hou, Xuebin Zhang, Huijun Yang, Huan Feng, Lisa Miller, John Ralph, Chang-Jun Liu

Department of Earth and Environmental Studies Faculty Scholarship and Creative Works

Producing cellulosic biofuels and bio-based chemicals from woody biomass is impeded by the presence of lignin polymer in the plant cell wall. Manipulating the monolignol biosynthetic pathway offers a promising approach to improved processability, but often impairs plant growth and development. Here, we show that expressing an engineered 4-O-methyltransferase that chemically modifies the phenolic moiety of lignin monomeric precursors, thus preventing their incorporation into the lignin polymer, substantially alters hybrid aspens’ lignin content and structure. Woody biomass derived from the transgenic aspens shows a 62% increase in the release of simple sugars and up to a 49% increase in the …

Book Reviews: A Chorus Of Cranes: The Cranes Of North America And The World. Paul A. Johnsgard (With Photographs By Thomas D. Mangelsen, And Drawings And Maps By Paul A. Johnsgard)., John G. Sidle

The Prairie Naturalist

Once again, naturalist and author Paul A. Johnsgard invites us to dance and chorus with cranes, and to appreciate their beauty and links to another species, Homo sapiens. A Chorus of Cranes is about natural history but also is a plea for conservation, which is a common foreword, prologue, preface, and/or epilogue of many wildlife books. It is vintage Paul Johnsgard text from preface to epilogue, words that emerge after a long wade through countless papers and reports, and a prolonged career of observation and reflection in the field. He has beckoned us before to cherish cranes and the natural …

Resource Selection By Black-Backed Woodpeckers (Picoides Arcticus) And American Three-Toed Woodpeckers (P. Dorsalis) In South Dakota And Wyoming, Sean R. Mohren, Mark A. Rumble, Chadwick P. Lehman, Stanley H. Anderson

The Prairie Naturalist

Black-backed woodpeckers (Picoides arcticus, [BBWO]) and American three-toed woodpeckers (P. dorsalis, [ATTW]) are uncommon inhabitants of conifer forests and are sympatric in some areas, including the Black Hills. Both species exhibit genetic characteristics associated with isolated populations, are species of special management concern, and for which data are lacking concerning populations and habitats. We developed resource selection models of forest vegetation within 500 m radius plots (78.5 ha) for BBWOs and ATTWs to provide forest managers with stand-level information to estimate how forest management might affect habitat for these species in the Black Hills. Relative probability of selection by BBWOs …

Missing The Point, Christopher N. Jacques

The Prairie Naturalist

Greetings GPNSS members! I hope summer finds you well and enjoying the Great Plains in some way, whether that be getting your hands dirty with field work, a reprieve from the office, anxiously awaiting the crappie bite at your favorite lake, or taking a much needed vacation. For those who enjoy cooler temperatures, summer heat and humidity are challenging and even the most seasoned field biologists among us are tested when fighting the conditions doing what we are passionate about. I personally prefer the fall and winter seasons, though also look forward to summer because it offers me a break …

The Science Of Open Spaces: Theory And Practice For Conserving Large, Complex Systems. Charles G. Curtin., Michelle L. Hellman, Caleb P. Roberts, Hannah Birge, Zachary Warren, Craig R. Allen

The Prairie Naturalist

The phrase “open spaces,” may bring to mind expansive tracts of prairie, rangeland, or even desert, stretching lonely and unchanged to the horizon. Open spaces also could conjure open oceans or interstitial rural lands between urbanized hubs, dotted with farms, fields, and woodlands. In an abstract sense, open spaces could represent gaps in human understanding or blank spaces on a map. In his book The Science of Open Spaces, landscape ecologist Charles Curtin combines all these perspectives, expanding the definition of “open spaces” to multi-layered and multi-scaled complex systems that are “greater than the sum of their parts.” He populates …

Book Review: Better Birding: Tips, Tools, And Concepts For The Field. George L. Armistead And Brian L. Sullivan., Stephen J. Dinsmore

The Prairie Naturalist

George Armistead and Brian Sullivan have written a book whose aim is to provide birders with a solid foundation upon which to develop better birding skills. They advocate a more holistic approach to bird identification than simply looking at a set of predetermined field marks. To that end, their approach combines traditional field identification approaches with behavioral and habitat cues, as well as natural history, to broaden bird identification skills. This is not the first book to make a case for looking at bird identification more broadly, although their specific approach seems unique. The authors offer constructive criticism of “traditional” …

Mink Predation Of Brown Trout In A Black Hills Stream, Jake Davis, Jerry W. Wilhite, Steven R. Chipps

The Prairie Naturalist

In the early 2000’s, declines in the brown trout (Salmo trutta) fishery in Rapid Creek, South Dakota, caused concern for anglers and fisheries managers. We conducted a radio telemetry study in 2010 and 2011 to identify predation mortality associated with mink, using hatchery-reared (2010) or wild (2011) brown trout. Estimated predation rates by mink (Mustela vison) on radio-tagged brown trout were 30% for hatchery fish and 32% for wild fish. Size frequency analysis revealed that the size distribution of brown trout lost to predation was similar to that of other, radio-tagged brown trout. In both years, a higher proportion of …

Estimability Tools For Package Developers, Russell V. Lenth

The R Journal

When a linear model is rank-deficient, then predictions based on that model become questionable because not all predictions are uniquely estimable. However, some of them are, and the estimability package provides tools that package developers can use to tell which is which. With the use of these tools, a model object’s predict method could return estimable predictions as-is while f lagging non-estimable ones in some way, so that the user can know which predictions to believe. The estimability package also provides, as a demonstration, an estimability-enhanced epredict method to use in place of predict for models fitted using the stats …

Raspberry Pi Vpn Travel Router, Daniel S. Pierson

Computer Science and Software Engineering

Consumers are increasingly relying on public wireless hotspots to access the internet from a growing number of devices. Usage of these hotspots has expanded from just laptops to everything from iPhones to tablets, which are expected to be internet-connected for full functionality. It has become common for one to check if there’s an open wireless hotspot connection available at places like coffee shops, hotels, restaurants, or even a doctor’s waiting room. The issue that arises is that these public connections present an inherent security risk, as anyone can connect and gain access to the network. For increased security, the use …

Dallimi Mes Agile Dhe Plan Driven, Dea Macula

Theses and Dissertations

Softueri ka qenë pjesë e tregut modern për shumë vite. Kemi disa metodologji të zhvillimit që përdoren në ditët e sotme. Burimet e pakta, konkurenca e ashpër si dhe kërkesat gjithnjë e në ndryshim të biznesit kërkojnë modele të zhvillimit të softuerit që janë sa më efikase dhe fleksibile. Edhe pse disa prej kompanive kanë metodologjinë e tyre përshtatëse të zhvillimit, pjesa më e madhe përodrin dy prej llojeve më të njohur siq janë: Plan Drvien dhe Agile metodologjitë. Plan Driven metodologjitë konsiderohen si formë tradicionale e zhvillimit të softuerit që përkrahin planifikimin e plotë, dokumentacion të detajuar dhe dizjan …

Prosense, Johnny Favazza Ii, Casey Glasgow, Matt Epperson

Computer Engineering

This project aims to gather advanced data sets from MEMS sensors and GPS and deliver it to the user, who can capitalize on the data. The once negligible half-degree difference of your board barreling down a wave can be recorded from a gyro and exploited for the perfect turn. The exact speed dreaded by longboarders where speed wobbles turn into a road rash can be analysed and consequently avoided. Ascertaining the summit of your flight using combined GPS sensors from the ski ramp allows for the correct timing of tricks. When it comes to pursuing excellence in professional sports, amateur …

Musictrakr, Benjamin Lin

Computer Engineering

MusicTrackr is an IoT device that musicians attach to their instruments. The device has a start and stop button that allows users to record their playing sessions. Each recorded session is sent wirelessly to a cloud database. An accompanying website displays all of the recorded sessions, organized by date. After picking a specific date, the user can view graphs showing total practice time and average session length as well play back any recordings during that date. In addition, the user may add comments to any specific date or recording. Lastly, the user may tag a specific date with a color …

Development Of Utility Theory And Utility Paradoxes, Timothy E. Dahlstrom

Lawrence University Honors Projects

Since the pioneering work of von Neumann and Morgenstern in 1944 there have been many developments in Expected Utility theory. In order to explain decision making behavior economists have created increasingly broad and complex models of utility theory. This paper seeks to describe various utility models, how they model choices among ambiguous and lottery type situations, and how they respond to the Ellsberg and Allais paradoxes. This paper also attempts to communicate the historical development of utility models and provide a fresh perspective on the development of utility models.

Electron Beam Effects In Ge–Se Thin Films And Resistance Change Memory Devices, Kasandra Wolf, Hugh Barnaby, Mahesh S. Ailavajhala, Micahel N. Kozicki, Dmitri A. Tenne, Maria Mitkova

Physics Faculty Publications and Presentations

Chalcogenide glasses are the advanced materials of choice for the emerging nanoionic memory devices – conductive bridge random access memory (CBRAM). To understand the nature of the effects occurring in these devices under influence of electron-beam radiation, the interaction of blanked chalcogenide films and nanostructured films containing chalcogenide glass and silver (Ag) source are studied. Raman spectroscopy, energy-dispersive X-ray spectroscopy and X-ray diffraction are used for establishing the structural and compositional effects occurring under radiation. They have strong compositional dependence with the stoichiometric compositions being most stable showing less structural changes after radiation. These effects are associated with the availability …

Farmstead Planning: Old Farm Buildings Repurposed For Better Farming: How To Develop A Complex, Stephen F. Higgins, Lee Moser

Agriculture and Natural Resources Publications

Farming is probably one of the most complex means of earning a living that has been devised. The many components of a farming operation that have to be managed would create an extensive list. Many beef cattle producers might focus on reproduction, nutrition, forages, health, and handling. However, there are many others operational considerations that are just as important.