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StralSV: assessment of sequence variability within similar 3D structures and application to polio RNA-dependent RNA polymerase

Description: Most of the currently used methods for protein function prediction rely on sequence-based comparisons between a query protein and those for which a functional annotation is provided. A serious limitation of sequence similarity-based approaches for identifying residue conservation among proteins is the low confidence in assigning residue-residue correspondences among proteins when the level of sequence identity between the compared proteins is poor. Multiple sequence alignment methods are more s… more
Date: November 29, 2010
Creator: Zemla, A; Lang, D; Kostova, T; Andino, R & Zhou, C
Partner: UNT Libraries Government Documents Department
open access

Subduction Controls of Hf and Nd Isotopes in Lavas of the Aleutian Island Arc

Description: The Hf and Nd isotopic compositions of 71 Quaternary lavas collected from locations along the full length of the Aleutian island arc are used to constrain the sources of Aleutian magmas and to provide insight into the geochemical behavior of Nd and Hf and related elements in the Aleutian subduction-magmatic system. Isotopic compositions of Aleutian lavas fall approximately at the center of, and form a trend parallel to, the terrestrial Hf-Nd isotopic array with {var_epsilon}{sub Hf} of +12.0 to… more
Date: August 29, 2010
Creator: Yogodzinski, Gene; Vervoort, Jeffery; Brown, Shaun Tyler & Gerseny, Megan
Partner: UNT Libraries Government Documents Department
open access

In situ spectroscopic detection of SMSI effect in a Ni/CeO2 system: hydrogen-induced burial and dig out of metallic nickel

Description: In situ APPES technique demonstrates that the strong metal support interaction effect (SMSI) in the Ni-ceria system is associated with the decoration and burial of metallic particles by the partially reduced support, a phenomenon reversible by evacuation at high temperature of the previously absorbed hydrogen.
Date: June 29, 2010
Creator: Caballero, Alfonso; Holgado, Juan P.; Gonzalez-delaCruz, Victor M.; Habas, Susan e.; Herranz, Tirma & Salmeron, Miquel
Partner: UNT Libraries Government Documents Department
open access

Post-Shot Radiation Environment Following Low-Yield Shots Inside the National Ignition Facility

Description: A detailed model of the Target Bay (TB) at the National Ignition Facility (NIF) has been developed to estimate the post-shot radiation environment inside the facility. The model includes large number of structures and diagnostic instruments present inside the TB. These structures and instruments are activated by the few nanosecond pulse of neutrons generated during a shot and the resultant gamma dose rates are estimated at various decay times following the shot. The results presented in this pa… more
Date: October 29, 2010
Creator: Sitaraman, S.; Brereton, S.; Dauffy, L.; Hall, J.; Hansen, L.; Khater, H. et al.
Partner: UNT Libraries Government Documents Department
open access

Kalman filtering to suppress spurious signals in Adaptive Optics control

Description: In many scenarios, an Adaptive Optics (AO) control system operates in the presence of temporally non-white noise. We use a Kalman filter with a state space formulation that allows suppression of this colored noise, hence improving residual error over the case where the noise is assumed to be white. We demonstrate the effectiveness of this new filter in the case of the estimated Gemini Planet Imager tip-tilt environment, where there are both common-path and non-common path vibrations. We discuss… more
Date: March 29, 2010
Creator: Poyneer, L & Veran, J P
Partner: UNT Libraries Government Documents Department
open access

Oxidative cleavage of erucic acid for the synthesis of brassylic acid

Description: The main focus of this work is to synthesize Brassylic Acid (BA) using oxidative cleavage of Erucic Acid (EA). Crambe (Crambe abyssinica) is an industrial oilseed grown in North Dakota. Crambe has potential as an industrial fatty acid feedstock as a source of Erucic acid (EA). It has approximately 50-60 % of EA, a C{sub 22} monounsaturated fatty acid. Oxidative cleavage of unsaturated fatty acids derived from oilseeds produces long chain (9, 11, and 13 carbon atoms) dibasic and monobasic acids.… more
Date: October 29, 2010
Creator: Nasrullah, Mohammed J.; Thapliyal, Pooja; Pfarr, Erica N.; Dusek, Nicholas S.; Schiele, Kristofer L. & Bahr, James A.
Partner: UNT Libraries Government Documents Department
open access

Enzyme-Like Catalysis of the Nazarov Cyclization by Supramolecular Encapsulation

Description: A primary goal in the design and synthesis of molecular hosts has been the selective recognition and binding of a variety of guests using non-covalent interactions. Supramolecular catalysis, which is the application of such hosts towards catalysis, has much in common with many enzymatic reactions, chiefly the use of both spatially appropriate binding pockets and precisely oriented functional groups to recognize and activate specific substrate molecules. Although there are now many examples whic… more
Date: March 29, 2010
Creator: Hastings, Courtney; Pluth, Michael; Bergman, Robert & Raymond, Kenneth
Partner: UNT Libraries Government Documents Department
open access

Analysis Efforts Supporting NSTX Upgrades

Description: The National Spherical Torus Experiment (NSTX) is a low aspect ratio, spherical torus (ST) configuration device which is located at Princeton Plasma Physics Laboratory (PPPL) This device is presently being updated to enhance its physics by doubling the TF field to 1 Tesla and increasing the plasma current to 2 Mega-amperes. The upgrades include a replacement of the centerstack and addition of a second neutral beam. The upgrade analyses have two missions. The first is to support design of new co… more
Date: November 29, 2010
Creator: H.Zhang, P. Titus, P. Rogoff, A.Zolfaghari, D. Mangra, M. Smith
Partner: UNT Libraries Government Documents Department
open access

On the Performance of an Algebraic MultigridSolver on Multicore Clusters

Description: Algebraic multigrid (AMG) solvers have proven to be extremely efficient on distributed-memory architectures. However, when executed on modern multicore cluster architectures, we face new challenges that can significantly harm AMG's performance. We discuss our experiences on such an architecture and present a set of techniques that help users to overcome the associated problems, including thread and process pinning and correct memory associations. We have implemented most of the techniques in a … more
Date: April 29, 2010
Creator: Baker, A H; Schulz, M & Yang, U M
Partner: UNT Libraries Government Documents Department
open access

Finite temperature spin-dynamics and phase transitions in spin-orbital models

Description: We study finite temperature properties of a generic spin-orbital model relevant to transition metal compounds, having coupled quantum Heisenberg-spin and Ising-orbital degrees of freedom. The model system undergoes a phase transition, consistent with that of a 2D Ising model, to an orbitally ordered state at a temperature set by short-range magnetic order. At low temperatures the orbital degrees of freedom freeze-out and the model maps onto a quantum Heisenberg model. The onset of orbital excit… more
Date: April 29, 2010
Creator: Chen, C. C.
Partner: UNT Libraries Government Documents Department
open access

Tunneling density of states as a function of thickness in superconductor/ strong ferromagnet bilayers

Description: We have made an experimental study of the tunneling density of states (DOS) in strong ferromagnetic thin films (CoFe) in proximity with a thick superconducting film (Nb) as a function of d{sub F}, the ferromagnetic thickness. Remarkably, we find that as d{sub F} increases, the superconducting DOS exhibits a scaling behavior in which the deviations from the normal-state conductance have a universal shape that decreases exponentially in amplitude with characteristic length d* {approx} 0.4 nm. We … more
Date: April 29, 2010
Creator: Reymond, S.
Partner: UNT Libraries Government Documents Department
open access

A Southern Sky Survey with Fermi LAT and ASKAP

Description: We present the prospects for a future joint gamma-ray and radio survey of southern hemisphere sources using the Fermi Large Area Telescope (LAT) and the upcoming Australian Square Kilometre Array Pathfinder (ASKAP) radio telescope. ASKAP is a next generation radio telescope designed to perform surveys at GHz frequencies at a much higher survey speed than previous radio telescopes, and is scheduled to start engineering observations in 2011. The survey capabilities of both Fermi LAT and ASKAP are… more
Date: April 29, 2010
Creator: Cameron, Robert A. & /SLAC /KIPAC, Menlo Park
Partner: UNT Libraries Government Documents Department
open access

Origin of charge density at LaAlO3-on-SrTiO3 heterointerfacespossibility of intrinsic doping

Description: As discovered by Ohtomo et al., a large sheet charge density with high mobility exists at the interface between SrTiO{sub 3} and LaAlO{sub 3}. Based on transport, spectroscopic and oxygen-annealing experiments, we conclude that extrinsic defects in the form of oxygen vacancies introduced by the pulsed laser deposition process used by all researchers to date to make these samples is the source of the large carrier densities. Annealing experiments show a limiting carrier density. We also present … more
Date: April 29, 2010
Creator: Siemons, W.
Partner: UNT Libraries Government Documents Department
open access

Quasi-zero dimensional CuB2O4: a resonant inelastic X-ray scattering case study

Description: We explore the general phenomenology of resonant inelastic scattering (RIXS) using CuB{sub 2}O{sub 4}, a network of CuO{sub 4} plaquettes electronically isolated by B{sup +3} ions. Spectra show a small number of well-separated features, and we exploit the simple electronic structure to explore RIXS phenomenology by developing a calculation which allows for intermediate-state effects ignored in standard approaches. These effects are found to be non-negligible and good correspondence between our … more
Date: April 29, 2010
Creator: Hancock, J.N.
Partner: UNT Libraries Government Documents Department
open access

Introduction to Extra Dimensions

Description: Extra dimensions provide a very useful tool in addressing a number of the fundamental problems faced by the Standard Model. The following provides a very basic introduction to this very broad subject area as given at the VIII School of the Gravitational and Mathematical Physics Division of the Mexican Physical Society in December 2009. Some prospects for extra dimensional searches at the 7 TeV LHC with {approx}1 fb{sup -1} of integrated luminosity are provided.
Date: April 29, 2010
Creator: Rizzo, Thomas G.
Partner: UNT Libraries Government Documents Department
open access

Limits on tau lepton flavor violating decays in three charged leptons

Description: A search for the neutrinoless, lepton-flavor violating decay of the {tau} lepton into three charged leptons has been performed using an integrated luminosity of 468 fb{sup -1} collected with the BABAR detector at the PEP-II collider. In all six decay modes considered, the numbers of events found in data are compatible with the background expectations. Upper limits on the branching fractions are set in the range (1.8-3.3) x 10{sup -8} at 90% confidence level.
Date: April 29, 2010
Creator: Cervelli, Alberto
Partner: UNT Libraries Government Documents Department
open access

Kinetics of small particle activation in supersaturated vapors

Description: We examine the nucleated (with barrier) activation of perfectly wetting (zero contact angle) particles ranging from bulk size down to one nanometer. Thermodynamic properties of the particles, coated with liquid layers of varying thickness and surrounded by vapor, are analyzed. Nano-size particles are predicted to activate at relative humidity below the Kelvin curve on crossing a nucleation barrier, located at a critical liquid layer thickness such that the total particle size (core + liquid lay… more
Date: August 29, 2010
Creator: McGraw, R. & Wang, J.
Partner: UNT Libraries Government Documents Department
open access

AdS/QCD, LIight-Front Holography, and the Non-perturbative Running Coupling

Description: The combination of Anti-de Sitter space (AdS) methods with light-front (LF) holography provides a remarkably accurate first approximation for the spectra and wavefunctions of meson and baryon light-quark bound states. The resulting bound-state Hamiltonian equation of motion in QCD leads to relativistic light-front wave equations in terms of an invariant impact variable {zeta} which measures the separation of the quark and gluonic constituents within the hadron at equal light-front time. These e… more
Date: April 29, 2010
Creator: Brodsky, Stanley J.; de Teramond, Guy & Deur, Alexandre
Partner: UNT Libraries Government Documents Department
open access

Radiation Protection Studies for LCLS Tune Up Dump

Description: The Linac Coherent Light Source (LCLS) at the Stanford Linear Accelerator Center is a pioneer fourth generation hard x-ray free electron laser that shall start to deliver laser pulses in 2009. Among other components of LCLS that present radiation protection concerns, the tune up dump (tdund) is of special interest because it also constitutes an issue for machine protection, as it is placed close to radiation sensitive components, like electronic devices and permanent magnets in the undulators. … more
Date: April 29, 2010
Creator: Santana-Leitner, M.; Fass, A.; Mao, S.; Nuhn, H. D.; Roesler, S.; Rokni, S. et al.
Partner: UNT Libraries Government Documents Department
open access

A momentum-dependent perspective on quasiparticleinterference in Bi2Sr2CaCu2O_8+delta

Description: Angle Resolved Photoemission Spectroscopy (ARPES) probes the momentum-space electronic structure of materials, and provides invaluable information about the high-temperature superconducting cuprates. Likewise, cuprates real-space, inhomogeneous electronic structure is elucidated by Scanning Tunneling Spectroscopy (STS). Recently, STS has exploited quasiparticle interference (QPI) - wave-like electrons scattering off impurities to produce periodic interference patterns - to infer properties of t… more
Date: April 29, 2010
Creator: Vishik, I. M.
Partner: UNT Libraries Government Documents Department
open access

Evidence for weak electronic correlations in Fe-pnictides

Description: Using x-ray absorption and resonant inelastic x-ray scattering, charge dynamics at and near the Fe L edges is investigated in Fe pnictide materials, and contrasted to that measured in other Fe compounds. It is shown that the XAS and RIXS spectra for 122 and 1111 Fe pnictides are each qualitatively similar to Fe metal. Cluster diagonalization, multiplet, and density-functional calculations show that Coulomb correlations are much smaller than in the cuprates, highlighting the role of Fe metallici… more
Date: April 29, 2010
Creator: Yang, W.L.
Partner: UNT Libraries Government Documents Department
open access

DETERMINING THE EFFECTS OF RADIATION ON AGING CONCRETE STRUCTURES OF NUCLEAR REACTORS

Description: The U.S. Department of Energy Office of Environmental Management (DOE-EM) is responsible for the Decontamination and Decommissioning (D&D) of nuclear facilities throughout the DOE Complex. Some of these facilities will be completely dismantled, while others will be partially dismantled and the remaining structure will be stabilized with cementitious fill materials. The latter is a process known as In-Situ Decommissioning (ISD). The ISD decision process requires a detailed understanding of t… more
Date: January 29, 2010
Creator: Serrato, M.
Partner: UNT Libraries Government Documents Department
open access

Estimation of brassylic acid by gas chromatography-mass spectrometry

Description: The main focus of this work is to estimate Brassylic Acid (BA) using gas chromatography-mass spectrometry (GC-MS). BA is a product obtained from the oxidative cleavage of Erucic Acid (EA). BA has various applications for making nylons and high performance polymers. BA is a 13 carbon compound with two carboxylic acid functional groups at the terminal end. BA has a long hydrocarbon chain that makes the molecule less sensitive to some of the characterization techniques. Although BA can be characte… more
Date: October 29, 2010
Creator: Mohammed J. Nasrullah, Erica N. Pfarr, Pooja Thapliyal, Nicholas S. Dusek, Kristofer L. Schiele, Christy Gallagher-Lein, and James A. Bahr
Partner: UNT Libraries Government Documents Department
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