Physical Sciences and Mathematics Commons^™

Profile Combinatorics For Fragment Selection In Comparative Protein Structure Modeling, Deacon Sweeney, Travis E. Doom, Michael L. Raymer

Kno.e.sis Publications

Sequencing of the human genome was a great stride towards modeling cellular complexes, massive systems whose key players are proteins and DNA. A major bottleneck limiting the modeling process is structure and function annotation for the new genes. Contemporary protein structure prediction algorithms represent the sequence of every protein of known structure with a profile to which the profile of a protein sequence of unknown structure is compared for recognition. We propose a novel approach to increase the scope and resolution of protein structure profiles. Our technique locates equivalent regions among the members of a structurally similar fold family, and …

Electrical Characterization Of 1.8 Mev Proton-Bombarded Zno, F. D. Auret, S. A. Goodman, M. Hayes, M. J. Legodi, H. A. Van Laarhoven, David C. Look

Physics Faculty Publications

We report on the electrical characterization of single-crystal ZnO and Au Schottky contacts formed thereon before and after bombarding them with 1.8 MeV protons. From capacitance–voltage measurements, we found that ZnO is remarkably resistant to high-energy proton bombardment and that each incident proton removes about two orders of magnitude less carriers than in GaN. Deep level transient spectroscopy indicates a similar effect: the two electron traps detected are introduced in extremely low rates. One possible interpretation of these results is that the primary radiation-induced defects in ZnO may be unstable at room temperature and anneal out without leaving harmful defects …

Thermal Stability Of Isolated And Complexed Ga Vacancies In Gan Bulk Crystals, K. Saarinen, T. Suski, I. Grzegory, David C. Look

Physics Faculty Publications

We have applied positron annihilation spectroscopy to show that 2-MeV electron irradiation at 300 K creates primary Ga vacancies in GaN with an introduction rate of 1 cm^-1. The Ga vacancies recover in long-range migration processes at 500–600 K with an estimated migration energy of 1.5 (2) eV. Since the native Ga vacancies in as-grown GaN survive up to much higher temperatures (1300–1500 K), we conclude that they are stabilized by forming complexes with oxygen impurities. The estimated binding energy of 2.2 (4) eV of such complexes is in good agreement with the results of theoretical calculations.

Multiwavelength Monitoring Of The Narrow-Line Seyfert 1 Galaxy Arakelian 564. Iii. Optical Observations And The Optical--Uv--X-Ray Connection, O. Shemmer, P. Romano, R. Bertram, W. Brinkmann, S. Collier, K. A. Crowley, E. Detsis, A. V. Filippenko, C. Martin Gaskell, T. A. George, M. Gliozzi, M. E. Hiller, T. L. Jewell, Shai Kaspi, Elizabeth S. Klimek, M. H. Lannon, W D. Li, P. Martini, Smita Mathur, H. Negoro, Hagai Netzer, Iossif Papadakis, Ioannis Papamastorakis, Bradley M. Peterson, Bradley W. Peterson, Richard William Pogge, V. I. Pronik, Kenneth S. Rumstay, S. G. Sergeev, G. M. Stirpe, C. J. Taylor, R. R. Treffers, T. J. Turner, P. Uttley, Marianne Vestergaard, Kaspar Von Braun, R. M. Wagner, Z. Zheng

Department of Physics and Astronomy: Faculty Publications

We present the results of a 2 yr long optical monitoring program of the narrow-line Seyfert 1 galaxy Ark 564. The majority of this monitoring project was also covered by X-ray observations (RXT E), and for a period of ~50 days, we observed the galaxy in UV (HST) and X-rays (RXTE and ASCA) simultaneously with the ground-based observations. Rapid and large-amplitude variations seen in the X-ray band, on a daily and hourly timescale, were not detected at optical and UV wavelengths, which in turn exhibited much lower variability either on short (1 day) or long (several months) timescales. The only …

Fisheries Research Report No. 127 - A 12-Month Survey Of Recreational Fishing In The Peel-Harvey Estuary Of Western Australia During 1998-99, B E. Malseed, Neil R. Sumner

Fisheries research reports

A survey of recreational boat-based and shore-based fishing in the Peel-Harvey Estuary was conducted between August 1998 and July 1999. During the survey 1,996 interviews were conducted at boat ramps. Of these, 1,136 boats had been crabbing and 136 angling in the estuary (43 were both crabbing and angling). In addition to the interviews at boat ramps, 909 shore-based fishing parties were interviewed.

The survey estimated the total annual boat-based recreational fishing effort as 126,000 fisher days, with 88% of this effort targeting blue swimmer crabs. The total annual shore-based recreational fishing effort was estimated to be 191,000 fisher days, …

Fisheries Research Report No. 130 - Environmental Requirements And Tolerances Of Rainbow Trout (Oncorhynchus Mykiss) And Brown Trout (Salmo Trutta) With Special Reference To Western Australia: A Review, Brett W. Molony

Fisheries research reports

Both Oncorhynchus mykiss (rainbow trout) and Salmo trutta (brown trout) have a long history of translocation and culture and a wide knowledge base exists. O.mykiss is being considered as a candidate for inland aquaculture in the salinity affected areas of southern Western Australia and this review aims, in part, at providing relevant information to those considering a trout-framing venture in Western Australia. Both species of trout can survive a wide range of environmental conditions, including temperature, salinity, pH, dissolved oxygen and ammonia, with O.mykiss having a higher temperature tolerance than S.trutta. However, within the ranges of environmental conditions, each species …

Energetic Particles And Magnetohydrodynamic Activity In The Swarthmore Spheromak Experiment, G. Qin, Vyacheslav S. Lukin , '00, C. D. Cothran, Michael R. Brown, W. H. Matthaeus

Physics & Astronomy Faculty Works

Results from the Swarthmore Spheromak Experiment (SSX) [M. R. Brown, Phys. Plasmas 6, 1717 (1999)] indicate that formation and partial merging of two spheromak plasmas can be described well by a magnetohydrodynamic (MHD) picture in which there is substantial evolution towards force free states within each vessel, while reconnection activity, also described reasonably well by MHD, occurs in the region of interaction. MHD simulations [V. S. Lukin , Phys. Plasmas 8, 1600 (2001)] support and provide further detail to this interpretation. In the present study, test particle equations are integrated using MHD data from SSX simulations to further understand the …

A Dipolar Coupling Based Strategy For Simultaneous Resonance Assignment And Structure Determination Of Protein Backbones, Fang Tian, Homayoun Valafar, James H. Prestegard

Faculty Publications

A new approach for simultaneous protein backbone resonance assignment and structure determination by NMR is introduced. This approach relies on recent advances in high-resolution NMR spectroscopy that allow observation of anisotropic interactions, such as dipolar couplings, from proteins partially aligned in field ordered media. Residual dipolar couplings are used for both geometric information and a filter in the assembly of residues in a sequential manner. Experimental data were collected in less than one week on a small redox protein, rubredoxin, that was 15N enriched but not enriched above 1% natural abundance in 13C. Given the acceleration possible with partial 13C …

Inside Unlv, Betty Blodgett, Tom Flagg, Diane Russell

Inside UNLV

No abstract provided.

Groundwater Study Of The Lake Grace Townsite, Damien Addison

Resource management technical reports

A groundwater study was carried out at the Lake Grace townsite to accelerate the implementation of effective salinity management options. The study consisted of a drilling investigation, expansion of a piezometer network, a pumping test, groundwater flow modelling and flood risk analysis.

Influence Of Lithophysal Porosity On Stress-Strain Properties Of Topopah Spring Tuff - Numerical Analysis, Nick Hudyma, Moses Karakouzian, Amy J. Smiecinski

Publications (YM)

The purpose of the numerical analysis effort of Task 27 of cooperative agreement DE-FC08-98NV12081 was to investigate the effect of lithophysal porosity on the elastic stress-strain properties of the tuff rock mass. Rock mass properties without lithophysal cavities are designated matrix properties. Rock mass properties with lithophysal cavities are designated effective properties. The analysis will be performed for a 6" by 6" square cross-section with a uniform distribution of lithophysal cavities for a variety of porosities. The analyses will be performed using FLAG 2D version 3.5, a Department of Energy qualified software. The analyses will compare the matrix properties to …

Interpreting Fracture Patterns In Sandstones Interbedded With Ductile Strata At The Salt Valley Anticline, Arches National Park, Utah, John C. Lorenz, Scott P. Cooper

All U.S. Government Documents (Utah Regional Depository)

Sandstones that overlie or that are interbedded with evaporitic or other ductile strata commonly contain numerous localized domains of fractures, each covering an area of a few square miles. Fractures within the Entrada Sandstone at the Salt Valley Anticline are associated with salt mobility within the underlying Paradox Formation. The fracture relationships observed at Salt Valley (along with examples from Paleozoic strata at the southern edge of the Holbrook basin in northeastern Arizona, and sandstones of the Frontier Formation along the western edge of the Green River basin in southwestern Wyoming), show that although each fracture domain may contain consistently …

Using Ssm Proxies To Provide Efficient Multiple-Source Multicast Delivery, Daniel Zappala, Aaron Fabbri

Faculty Publications

We consider the possibility that single-source multicast (SSM) will become a universal multicast service, enabling large-scale distribution of content from a few well-known sources to a general audience. Operating under this assumption, we explore the problem of building the traditional IP model of any-source multicast on top of SSM. Toward this end, we design an SSM proxy service that allows any sender to efficiently deliver content to a multicast group. We demonstrate the performance improvements this service offers over standard SSM and describe extensions for access control, dynamic proxy discovery, and multicast proxy distribution.

Genetic And Environmental Risk Factors Associated With Colon Cancer, Shamma Rashed Khalfan Al-Naili Al-Shamsi

Theses

Colorectal cancer represents one of the most common causes of mortality in the world. A major number of populations develop an adenoma by the age of 40s. Over the past years, it has become clear that genetic factors are of crucial importance in colorectal tumorigenesis. Familial adenomatous polyposis (FAP) is responsible of developing numerous colorectal cancers cases by causing mutations in the germline in adenomatous polyposis coli (APC) genes.

Colon cancer is considered the second most frequent cause of death in most of the Western countries. Colonic cancer is common in women and rectal in men. It arise in adenomatous …

Polygonal Chains Cannot Lock In 4d, Roxana Cocan, Joseph O'Rourke

Computer Science: Faculty Publications

We prove that, in all dimensions d ≥ 4, every simple open polygonal chain and every tree may be straightened, and every simple closed polygonal chain may be convexified. These reconfigurations can be achieved by algorithms that use polynomial time in the number of vertices, and result in a polynomial number of “moves.” These results contrast to those known for d = 2, where trees can “lock,” and for d = 3, where open and closed chains can lock.

Lower Willamette River Model: Boundary Conditions And Model Setup, Herman G. Rodriguez, Robert Leslie Annear, Scott A. Wells, Chris Berger

Civil and Environmental Engineering Faculty Publications and Presentations

Water Environment Services of Clackamas County is in the process of planning upgrades on several of its sewage treatment plants which discharge into the Lower Willamette River. The goals of the modeling effort are to:

• Gather data to construct a computer simulation model of the Lower Willamette River system including part of the Lower Columbia River and the Willamette River above the Oregon City Falls; Because of the tidal influence in the Lower Willamette River, portions of the Columbia River that might affect the Lower Willamette River water quality were also modeled. Also, a section of the Willamette River …

Search For Narrow Diphoton Resonances And For Γγ+W/Z Signatures In Pp̅ Collisions At √S=1.8 Tev, T. Affolder, Kenneth A. Bloom, Collider Detector At Fermilab Collaboration

Kenneth Bloom Publications

We present results of searches for diphoton resonances produced both inclusively and also in association with a vector boson (W or Z) using 100 pb^-1 of pp̅ collisions using the CDF detector. We set upper limits on the product of cross section times branching ratio for both pp̅→ γγ+X and pp̅→ γγ+ W/Z. Comparing the inclusive production to the expectations from heavy sgoldstinos we derive limits on the supersymmetrybreaking scale √F in the TeV range, depending on the sgoldstino mass and the choice of other parameters. Also, using a NLO prediction for the associated …

Ca4Iro6, Ca3Mgiro6 And Ca3Zniro6, Matthew J. Davis, Mark D. Smith, Hans Conrad Zur Loye

Faculty Publications

Single crystals of tetracalcium iridium hexaoxide, Ca₄IrO₆, tricalcium magnesium iridium hexaoxide, Ca₃MgIrO₆, and tricalcium zinc iridium hexaoxide, Ca₃ZnIrO₆, were prepared via high-temperature flux growth and structurally characterized by single-crystal X-ray diffraction. The three compounds are isostructural and adopt the K₄CdCl₆ structure type, comprised of chains of alternating face-shared [CaO₆], [MgO₆] or [ZnO₆] trigonal prisms and [IrO₆] octahedra, surrounded by columns of Ca²⁺ ions.

Formula: Ca₄IrO₆, Ca_3.34Mg_0.66IrO₆ and …

Hypsometry And Volume Of The Arctic Ocean And Its Constituent's Seas, Martin Jakobsson

Center for Coastal and Ocean Mapping

No abstract provided.

Ecdis Development Laboratory And Navigation Technology Demonstration Center, Lee Alexander, Maxim F. Van Norden, Charles M. Fralick

Center for Coastal and Ocean Mapping

The U.S. Navy is undergoing a major transition from traditional, paper chart navigation to computer-based electronic charting. The Chief of Naval Operations (CNO) has mandated that all Navy ships will navigate strictly through electronic means by FY07. However, due to some recent groundings, the Navy is now striving to accelerate the full implementation of electronic navigation by FY04. The Naval Oceanographic Office (NAVOCEANO) is making a concerted effort to support this transition with upgrades to state-of-the-art survey ships, instrumentation, and data processing equipment. NAVOCEANO is increasing its capability to rapidly collect and process hydrographic survey data, and to quickly produce …

Fisheries Research Report No. 129 - Morphology And Incidence Of Yabby (Cherax Albidus) Burrows In Western Australia, Craig S. Lawrence

Fisheries research reports

Yabby (Cherax albidus) burrows were recorded from dams, channels and ponds in Western Australia. Twenty five sites were sampled during Spring, 1998 and the burrow morphology and density was described from six of these locations where burrows were present. To improve the sample size and address seasonal trends 49 commercially harvested yabby dams were sampled over the summer of 1999/2000 and the number and density of yabby burrows were recorded. Burrow incidence and morphology was also recorded from 25 research ponds at the Avondale Research Station between 1995-1997. Soil and water chemistry values are presented and their relationships with burrow …

Design And Construction Of A Space-Borne Optical Tweezer Apparatus, Andrew Resnick

Physics Faculty Publications

A compact optical tweezer package has been developed for use on a microscope to be flown on the International Space Station as part of a series of experiments in colloid crystallization. A brief introduction to the principles of single-beam optical tweezer operation will be presented, after which a detailed system layout will be shown. Special design requirements due to the spaceflight nature of the hardware will also be discussed. The tweezer apparatus is capable of trapping many particles through use of a two-axis acousto-optical deflector. The trap strength is sufficient to perform the required science (50 pN at Δn=0.2). The …

The Role Of Small And Medium Enterprises In The Economy Of Slovakia, Jaroslav Kling

Student Work

The aim of this paper is to analyze the role of small and medium enterprises in the economy of Slovakia. The changes of 1989 brought about the changes of society and economy as well. In the period of transformation of the Slovak economy, small and medium enterprises have been often considered to be a critical element of economic revival. The study answers to what extent this expectation has been met. Legal and institutional frameworks of the small and medium enterprises development are analyzed. Popular attitudes toward entrepreneurs, views and opinions of the key representatives of entrepreneurs and state representatives are …

Component-Based Software Development, Luiz Fernando Capretz, Miriam Capretz, Dahai Li

Electrical and Computer Engineering Publications

Component-based software development (CBSD) strives to achieve a set of pre-built, standardized software components available to fit a specific architectural style for some application domain; the application is then assembled using these components. Component-based software reusability will be at the forefront of software development technology in the next few years. This paper describes a software life cycle that supports component-based development under an object-oriented framework. Development time versus software life cycle phases, which is an important assessment of the component-based development model put forward, is also mentioned.

Hubble Space Telescope Wfpc2 Imaging Of Cassiopeia A, R. A. Fesen, J. A. Morse, R. A. Chevalier, K. J. Borkowski, C. L. Gerardy

Dartmouth Scholarship

The young galactic supernova remnant Cassiopeia A was imaged with Wide Field Planetary Camera 2 (WFPC2) aboard the Hubble Space Telescope through filters selected to capture the complete velocity range of the remnant's main shell in several emission lines. The primary lines detected, along with the specific WFPC2 filters used, were [O III] λλ4959, 5007 (F450W), [N II] λ6583 (F658N), [S II] λλ6716, 6731 + [O II] λλ7319, 7330 + [O I] λλ6300, 6364 (F675W), and [S III] λλ9069, 9532 (F850LP). About three-quarters of the remnant's 4' diameter main shell was imaged with all four filters in three WFPC2 pointings, …

Capillary Flow In Interior Corners: The Infinite Column, Mark M. Weislogel

Mechanical and Materials Engineering Faculty Publications and Presentations

Capillary flow of a sinusoidally perturbed liquid column in an interior corner of infinite extent is solved using lubrication theory. Due primarily to the length scales selected to nondimensionalize the momentum equation, an analytic time scale governing the settling of the perturbation is determined. The time scale, which is shown to be independent of a steady base state flow, proves useful in rapidly predicting transients for surface settling in certain liquid-bearing tanks of spacecraft employing interior corners for fluids management purposes. The asymptotic analysis is extended to address flows along interior corners whose faces are slightly nonplanar. The generalized formulation …

Privacy Protection For Transactions Of Digital Goods, Feng Bao, Robert H. Deng

Research Collection School Of Computing and Information Systems

In this paper we study the problem of how to protect users’ privacy in web transactions of digital goods. In particular, we introduce a system which allows a user to disclose his/her identity information (such as user account or credit card number) to a web site in exchange for a digital item, but prevents the web site from learning which specific item the user intends to obtain. The problem concerned here is orthogonal to the problem of anonymous transactions [RSG98], [RR98] but commensurate with the general problem of PIR (private information retrieval) [CGK95]

Pickup And Delivery Problem With Time Windows: Algorithms And Test Case Generation, Hoong Chuin Lau, Zhe Liang

Research Collection School Of Computing and Information Systems

In the pickup and delivery problem with time windows (PDPTW), vehicles have to transport loads from origins to destinations respecting capacity and time constraints. In this paper, we present a two-phase method to solve the PDPTW. In the first phase, we apply a novel construction heuristics to generate an initial solution. In the second phase, a tabu search method is proposed to improve the solution. Another contribution of this paper is a strategy to generate good problem instances and benchmarking solutions for PDPTW, based on Solomon's benchmark test cases for VRPTW. Experimental results show that our approach yields very good …

Application Of Morphometric Relationships To Active Flow Networks Within The Mammoth Cave Watershed, John Glennon

Masters Theses & Specialist Projects

Numerous quantitative relationships have been formulated to describe the nature of surface-drainage networks. These parameters have been used in various studies of geomorphology and surface-water hydrology, such as flood characteristics, sediment yield, and evolution of basin morphology. Little progress has been made in applying these quantitative descriptors to karst flow systems due to the lack of sufficiently complete data and inadequate technology for processing the large, complex data sets. However, as a result of four decades of investigation, an abundance of data now exists for the Mammoth Cave Watershed providing the opportunity for broader quantitative research in the organization of …

Concentration Gradient, Diffusion, And Flow Through Open Porous Medium Near Percolation Threshold Via Computer Simulations, Ras B. Pandey, J.F. Gettrust, D. Stauffer

Faculty Publications

The interacting lattice gas model is used to simulate fluid flow through an open percolating porous medium with the fluid entering at the source-end and leaving from the opposite end. The shape of the steady-state concentration profile and therefore the gradient field depends on the porosity (p). The root mean square (rms) displacements of fluid and its constituents (tracers) show a drift power-law behavior, R∝t in the asymptotic regime (t→∞). The flux current density (j) is found to scale with the porosity according to, j∝(Δp)^β with Δp …