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Web-Ice: Integrated Data Collection and Analysis for Macromolecular Crystallography (open access)

Web-Ice: Integrated Data Collection and Analysis for Macromolecular Crystallography

New software tools are introduced to facilitate diffraction experiments involving largenumbers of crystals. While existing programs have long provided a framework for lattice indexing, Bragg spot integration, and symmetry determination, these initial data processing steps often require significant manual effort. This limits the timely availability of data analysis needed for high-throughput procedures, including the selection of the best crystals from a large sample pool, and the calculation of optimal data collection parameters to assure complete spot coverage with minimal radiation damage. To make these protocols more efficient, we developed a network of software applications and application servers, collectively known as Web-Ice. When the package is installed at a crystallography beamline, a programming interface allows the beamline control software (e.g., Blu-Ice / DCSS) to trigger data analysis automatically. Results are organized based on a list of samples that the user provides, and are examined within a Web page, accessible both locally at the beamline or remotely. Optional programming interfaces permit the user tocontrol data acquisition through the Web browser. The system as a whole is implemented to support multiple users and multiple processors, and can be expanded to provide additional scientific functionality. Web-Ice has a distributed architecture consisting of several stand-alone …
Date: October 10, 2007
Creator: Gonzalez, Ana; Gonzalez, Ana; Moorhead, Penjit; McPhillips, Scott E.; Song, Jinhu; Sharp, Ken et al.
System: The UNT Digital Library
InN Nanorods Grown on Different Planes of Al2O3 (open access)

InN Nanorods Grown on Different Planes of Al2O3

None
Date: March 10, 2007
Creator: Liliental-Weber, Z.; Park, H.J.; Mangum, J.; Anderson, T. & Kryliouk, O.
System: The UNT Digital Library
Shape Determination for Deformed Electromagnetic Cavities (open access)

Shape Determination for Deformed Electromagnetic Cavities

The measured physical parameters of a superconducting cavity differ from those of the designed ideal cavity. This is due to shape deviations caused by both loose machine tolerances during fabrication and by the tuning process for the accelerating mode. We present a shape determination algorithm to solve for the unknown deviations from the ideal cavity using experimentally measured cavity data. The objective is to match the results of the deformed cavity model to experimental data through least-squares minimization. The inversion variables are unknown shape deformation parameters that describe perturbations of the ideal cavity. The constraint is the Maxwell eigenvalue problem. We solve the nonlinear optimization problem using a line-search based reduced space Gauss-Newton method where we compute shape sensitivities with a discrete adjoint approach. We present two shape determination examples, one from synthetic and the other from experimental data. The results demonstrate that the proposed algorithm is very effective in determining the deformed cavity shape.
Date: December 10, 2007
Creator: Akcelik, Volkan; Ko, Kwok; Lee, Lie-Quan; Li, Zhenghai; Ng, Cho-Kuen & Xiao, Liling
System: The UNT Digital Library
The polarized SRF gun experiment. (open access)

The polarized SRF gun experiment.

RF electron guns are capable of producing electron bunches with high brightness, which outperform DC electron guns and may even be able to provide electron beams for the ILC without the need for a damping ring. However, all successful existing guns for polarized electrons are DC guns because the environment inside an RF gun is hostile to the GaAs cathode material necessary for polarization. While the typical vacuum pressure in a DC gun is better than 10{sup -11} torr the vacuum in an RF gun is in the order of 10{sup -9} torr. Experiments at BINP Novosibirsk show that this leads to strong ion back-bombardment and generation of dark currents, which destroy the GaAs cathode in a short time. The situation might be much more favorable in a (super-conducting) SRF gun. The cryogenic pumping of the gun cavity walls may make it possible to maintain a vacuum close to 10{sup -12} torr, solving the problem of ion bombardment and dark currents. Of concern would be contamination of the gun cavity by evaporating cathode material. This report describes an experiment that Brookhaven National Laboratory (BNL) in collaboration with Advanced Energy Systems (AES) is conducting to answer these questions.
Date: September 10, 2007
Creator: Kewisch, J.; Ben-Zvi, Ilan; Rao, T.; Burrill, A.; Pate, D.; Grover, R. et al.
System: The UNT Digital Library
The Formation of Contact and Very Close Binaries (open access)

The Formation of Contact and Very Close Binaries

We explore the possibility that all close binaries, i.e. those with periods {approx}< 3 d, including contact (W UMa) binaries, are produced from initially wider binaries (periods of say 10's of days) by the action of a triple companion through the medium of Kozai Cycles with Tidal Friction (KCTF).
Date: August 10, 2007
Creator: Kisseleva-Eggleton, L & Eggleton, P P
System: The UNT Digital Library
Plasma Suppression of Large Scale Structure Formation in the Universe (open access)

Plasma Suppression of Large Scale Structure Formation in the Universe

We point out that during the reionization epoch of the cosmic history, the plasma collective effect among the ordinary matter would suppress the large scale structure formation. The imperfect Debye shielding at finite temperature would induce a residual long-range electrostatic potential which, working together with the baryon thermal pressure, would counter the gravitational collapse. As a result the effective Jean's length, {tilde {lambda}}{sub J}, is increased by a factor, {tilde {lambda}}{sub J}/{lambda}{sub J} = {radical}8/5, relative to the conventional one. For scales smaller than the effective Jean's scale the plasma would oscillate at the ion-acoustic frequency. The modes that would be influenced by this effect depend on the starting time and the initial temperature of reionization, but roughly lie in the range 0.5hMpc{sup -1} < k, which corresponds to the region of the Lyman-{alpha} forest from the inter-galactic medium. We predict that in the linear regime of density-contrast growth, the plasma suppression of the matter power spectrum would approach 1 - ({Omega}{sub dm}/{Omega}{sub m}){sup 2} {approx} 1 -(5/6){sup 2} {approx} 30%.
Date: December 10, 2007
Creator: Chen, Pisin & Lai, Kwang-Chang
System: The UNT Digital Library
Lactonization and protonation of gluconic acid: a thermodynamicand kinetic study by potentiometry, nmr and esi-ms (open access)

Lactonization and protonation of gluconic acid: a thermodynamicand kinetic study by potentiometry, nmr and esi-ms

In acidic aqueous solutions, gluconate protonation is coupled with lactonization of gluconic acid. With the decrease of pC{sub H}, two lactones ({delta}/{gamma}) are sequentially formed. The {delta}-lactone forms more readily than the {gamma}-lactone. In 0.1 M gluconate solutions, if pC{sub H} is above 2.5, only the {delta}-lactone is generated. When pC{sub H} is decreased below 2.0, the formation of the {gamma}-lactone is observable although the {delta}-lactone predominates. At I = 0.1 M NaClO{sub 4} and room temperature, the deprotonation constant of the carboxylic group, using the NMR technique, was determined to be log K{sub a} = 3.30 {+-} 0.02; the {delta}-lactonization constant, by the batch potentiometric titrations, was obtained to be log K{sub L} = - (0.54 {+-} 0.04). Using ESI-MS, the rate constants of the {delta}-lactonization and the hydrolysis at pC{sub H} {approx} 5.0 were estimated to be k{sub 1} = 3.2 x 10{sup -5} s{sup -1} and k{sup -1} = 1.1 x 10{sup -4} s{sup -1}, respectively.
Date: January 10, 2007
Creator: Zhang, Z.; Gibson, P.; Clark, S.B.; Tian, G.; Zanonato, P. & Rao, L.
System: The UNT Digital Library
Nuclear Dynamics in Resonant Electron Collisions with SmallPolyatomic Molecules (open access)

Nuclear Dynamics in Resonant Electron Collisions with SmallPolyatomic Molecules

None
Date: September 10, 2007
Creator: Rescigno, Thomas N.; McCurdy, C. William; Haxton, Daniel J.; Trevisan, Cynthia S. & Orel, Ann E.
System: The UNT Digital Library
Soft X-Ray Laser Interferometry of Colliding Laser-Created Plasmas in Semi-Cylindrical Cavities (open access)

Soft X-Ray Laser Interferometry of Colliding Laser-Created Plasmas in Semi-Cylindrical Cavities

A table-top capillary discharge soft x-ray laser was used to acquire high contrast interferograms that map the evolution of dense aluminum plasmas created by laser irradiation of a 500 {micro}m diameter semi-cylindrical cavity with 120 ps optical laser pulses of {approx}1.1 x 10{sup 12} Wcm{sup -2} peak intensity. The measured electron density maps, that were compared with simulations, show that the plasma converges on axis, where it collides to form a localized region with density exceeding 1 x 10{sup 20} cm{sup -3}.
Date: December 10, 2007
Creator: Purvis, M. A.; Grava, J.; Filevich, J.; Marconi, M.; Dunn, J.; Moon, S. J. et al.
System: The UNT Digital Library
Anodic Behavior of SAM2X5 Material Applied as Amorphous Coatings (open access)

Anodic Behavior of SAM2X5 Material Applied as Amorphous Coatings

Iron-based amorphous alloys are desirable industrial materials since they are highly resistant to corrosion and possess enhanced hardness for wear resistance. The amorphous materials can be produced from the melt as powder and later spray deposited as coatings on large engineering structures. As a laboratory experiment, SAM2X5 powder was coated on electrochemical specimens of 304SS for testing. Results show that the coated specimens did not perform satisfactorily during the laboratory testing. This is because of partial devitrification during the deposition of the powder on the small specimen substrates.
Date: August 10, 2007
Creator: Hailey, P D; Farmer, J C; Day, S D & Rebak, R B
System: The UNT Digital Library
Superfluid Transition in a Chiron Gas (open access)

Superfluid Transition in a Chiron Gas

Low temperature measurements of the magnetic susceptibility of LSCO suggest that the superconducting transition is associated with the disappearance of a vortex liquid. In this note we wish to draw attention to the fact that spin-orbit-like interactions in a poorly conducting layered material can lead to a new type of quantum ground state with spin polarized soliton-like charge carriers as the important quantum degree of freedom. In 2-dimensions these solitons are vortex-like, while in 3-dimensional systems they are monopole-like. In either case there is a natural mechanism for the pairing of spin up and spin down solitons, and we find that at low temperatures there is a cross-over transition as a function of carrier density between a state where the solitons are free and a condensate state where the spin up and spin down solitons in neighboring layers are paired.
Date: December 10, 2007
Creator: Chapline, G. F.
System: The UNT Digital Library
Effect of High Temperature Aging on the Corrosion Resistance of Iron Based Amorphous Alloys (open access)

Effect of High Temperature Aging on the Corrosion Resistance of Iron Based Amorphous Alloys

Iron-based amorphous alloys can be more resistant to corrosion than polycrystalline materials of similar compositions. However, when the amorphous alloys are exposed to high temperatures they may recrystallize (or devitrify) thus losing their resistance to corrosion. Four different types of amorphous alloys melt spun ribbon specimens were exposed to several temperatures for short periods of time. The resulting corrosion resistance was evaluated in seawater at 90 C and compared with the as-prepared ribbons. Results show that the amorphous alloys can be exposed to 600 C for 1-hr. without losing the corrosion resistance; however, when the ribbons were exposed at 800 C for 1-hr. their localized corrosion resistance decreased significantly.
Date: August 10, 2007
Creator: Day, S D; Haslam, J J; Farmer, J C & Rebak, R B
System: The UNT Digital Library
Recent Progress in a Beam-Beam Simulation Code for Circular Hadron Machines (open access)

Recent Progress in a Beam-Beam Simulation Code for Circular Hadron Machines

While conventional tracking codes can readily provide higher-order optical quantities and give an estimate of dynamic apertures, they are unable to provide directly measurable quantities such as lifetimes and loss rates. The particle tracking framework Plibb aims at modeling a storage ring with sufficient accuracy and a sufficiently high number of turns and in the presence of beam-beam interactions to allow for an estimate of these quantities. We provide a description of new features of the codes; we also describe a novel method of treating chromaticity in ring sections in a symplectic fashion.
Date: September 10, 2007
Creator: Kabel, Andreas; Fischer, Wolfram & Sen, Tanaji
System: The UNT Digital Library
Structure of A = 10 - 13 Nuclei with Two- Plus Three-Nucleon Interactions from Chiral Effective Field Theory (open access)

Structure of A = 10 - 13 Nuclei with Two- Plus Three-Nucleon Interactions from Chiral Effective Field Theory

Properties of finite nuclei are evaluated with two-nucleon (NN) and three-nucleon (NNN) interactions derived within chiral effective field theory (EFT). The nuclear Hamiltonian is fixed by properties of the A = 2 system, except for two low-energy constants (LECs) that parameterize the short range NNN interaction. We constrain those two LECs by a fit to the A = 3 system binding energy and investigate sensitivity of {sup 4}He, {sup 6}Li, {sup 10,11}B and {sup 12,13}C properties to the variation of the constrained LECs. We identify a preferred choice that gives globally the best description. We demonstrate that the NNN interaction terms significantly improve the binding energies and spectra of mid-p-shell nuclei not just with the preferred choice of the LECs but even within a wide range of the constrained LECs. At the same time, we find that a very high quality description of these nuclei requires further improvements to the chiral Hamiltonian.
Date: January 10, 2007
Creator: Navratil, P; Gueorguiev, V; Vary, J P; Ormand, W E & Nogga, A
System: The UNT Digital Library
Ionization of polarized 3He+ ions in EBIS trap with slanted electrostatic mirror. (open access)

Ionization of polarized 3He+ ions in EBIS trap with slanted electrostatic mirror.

Methods of producing the nuclear polarized {sup 3}He{sup +} ions and their ionization to {sup 3}H{sup ++} in ion trap of the electron Beam Ion Source (EBIS) are discussed. Computer simulations show that injection and accumulation of {sup 3}He{sup +} ions in the EBIS trap with slanted electrostatic mirror can be very effective for injection times longer than the ion traversal time through the trap.
Date: September 10, 2007
Creator: Pikin, A.; Zelenski, A.; Kponou, A.; Alessi, J.; Beebe, E.; Prelee, K. et al.
System: The UNT Digital Library
p-Carbon polarimetry at RHIC. (open access)

p-Carbon polarimetry at RHIC.

The polarization measurement through elastic ({rvec p},C) reaction plays a crucial role in the polarized proton beam operation of Relativistic Heavy Ion collider at Brookhaven National Laboratory. As well as measuring the polarization, the unknown analyzing power A{sub N} of elastic ({rvec p},C) is determined as well in combination with the absolute polarization measurement by a H-jet polarimeter. The systematic uncertainty of the Run05 measurements are discussed as well as introducing the experimental apparatus of the polarimeter system.
Date: September 10, 2007
Creator: Nakagawa,I.; Makdisi,Y.; Alekseev, I.; Bazilesky, A.; Bravar, A.; Bunce, G. et al.
System: The UNT Digital Library
Field evidence for strong chemical separation of contaminants in the Hanford Vadose Zone (open access)

Field evidence for strong chemical separation of contaminants in the Hanford Vadose Zone

Water and chemical transport from a point source withinvadose zone sediments at Hanford were examined with a leak testconsisting of five 3800-liter aliquots of water released at 4.5 m depthevery week over a 4-week period. The third aliquot contained bromide, D2Oand 87Sr. Movement of the tracers was monitored for 9 months by measuringpore water compositions of samples from boreholes drilled 2-8 m from theinjection point. Graded sedimentary layers acting as natural capillarybarriers caused significant lateral spreading of the leak water. D2Oconcentrations>50 percent of the concentration in the tracer aliquotwere detected at 9-11 m depth. However, increased water contents, lowerd18O values, and geophysical monitoring of moisture changes at otherdepths signified high concentrations of leak fluids were added where D2Oconcentrations were<3 percent above background, suggesting limitedmixing between different aliquots of the leak fluids. Initially highbromide concentrations decreased more rapidly over time than D2O,suggesting enhanced transport of bromide due to anion exclusion. Nosignificant increase in 87Sr was detected in the sampled pore water,indicating strong retardation of Sr by the sediments. These resultshighlight some of the processes strongly affecting chemical transport inthe vadose zone and demonstrate the significant separation of contaminantplumes that can occur.
Date: April 10, 2007
Creator: Conrad, Mark E.; DePaolo, Donald J.; Maher, Katharine; Gee,Glendon W. & Ward, Anderson L.
System: The UNT Digital Library
HIGH ENERGY HADRON POLARIMETRY. (open access)

HIGH ENERGY HADRON POLARIMETRY.

Proton polarimetry at RHIC uses the interference of electromagnetic (EM) and hadronic scattering amplitudes. The EM spin-flip amplitude for protons is responsible for the proton's anomalous magnetic moment, and is large. This then generates a significant analyzing power for small angle elastic scattering. RHIC polarimetry has reached a 5% uncertainty on the beam polarization, and seem capable of reducing this uncertainty further. Polarized neutron beams ax also interesting for RHIC and for a polarized electron-polarized proton/ion collider in the fume. In this case, deuterons, for example, have a very small anomalous magnetic moment, making the approach used for protons impractical. Although it might be possible to use quasielastic scattering from the protons in the deuteron to monitor the polarization. 3-He beams can provide polarized neutrons, and do have a large anomalous magnetic moment, making a similar approach to proton polarimetry possible.
Date: September 10, 2007
Creator: BUNCE,G.
System: The UNT Digital Library
Absolute Polarimetry at RHIC (open access)

Absolute Polarimetry at RHIC

Precise and absolute beam polarization measurements are critical for the RHIC spin physics program. Because all experimental spin-dependent results are normalized by beam polarization, the normalization uncertainty contributes directly to final physics uncertainties. We aimed to perform the beam polarization measurement to an accuracy Of {Delta}P{sub beam}/P{sub beam} &lt; 5%. The absolute polarimeter consists of Polarized Atomic Hydrogen Gas Jet Target and left-right pairs of silicon strip detectors and was installed in the RHIC-ring in 2004. This system features proton-proton elastic scattering in the Coulomb nuclear interference (CNI) region. Precise measurements of the analyzing power A{sub N} of this process has allowed us to achieve {Delta}P{sub beam}/P{sub beam} = 4.2% in 2005 for the first long spin-physics run. In this report, we describe the entire set up and performance of the system. The procedure of beam polarization measurement and analysis results from 2004-2005 are described. Physics topics of AN in the CNI region (four-momentum transfer squared 0.001 &lt; -t &lt; 0.032 (GeV/c){sup 2}) are also discussed. We point out the current issues and expected optimum accuracy in 2006 and the future.
Date: September 10, 2007
Creator: Okada, H.; Bravar, A.; Bunce, G.; Gill, R.; Huang, H.; Makdisi, Y. et al.
System: The UNT Digital Library
Sona transition studies in the RHIC OPPIS. (open access)

Sona transition studies in the RHIC OPPIS.

In Optically Pumped Polarized Ion Sources (OPPIS), the atomic beam is first electron polarized, and then this polarization is transferred to the nucleus by a suitable perturbing magnetic field. In the BNL OPPIS, the electron polarized atomic beam experiences the perturbing field when it traverses a region where the axial magnetic field reverses direction in a controlled manner, strength and gradient. This is the so-called Sona Transition region, named after P. G. Sona, who fist suggested the technique. We have extensively studied how the magnetic field profile in the Sona region affects beam polarization. In these studies, we have observed oscillations in polarization for certain field profiles, and tried to explain them. We report on these studies.
Date: September 10, 2007
Creator: Kponou,A.; Zelenski, A.; Kokhanovski, S. & Zubets, V.
System: The UNT Digital Library
Influence of interface exchange coupling in perpendicular anisotropy [Pt/Co]50/TbFe bilayers (open access)

Influence of interface exchange coupling in perpendicular anisotropy [Pt/Co]50/TbFe bilayers

We present the magnetization evolution of perpendicular anisotropy TbFe and [Co/Pt]{sub 50} thin films either in direct contact resulting in antiferromagnetic interfacial coupling or separated by a thick Pt layer. Magnetometry and x-ray magnetic circular dichroism spectroscopy determine the spatially averaged magnetic properties. Resonant magnetic x-ray small-angle scattering and magnetic soft X-ray transmission microscopy probed the domain configurations and correlations in the reversal processes. While the Co/Pt multilayer reverses by domain propagation, the TbFe magnetization reversal is found to be dominated either by coherent magnetization reversal processes or by lateral domain formation depending on the interface exchange coupling. In the presence of lateral domains, dipolar field induced domain replication phenomena are observed.
Date: October 10, 2007
Creator: Mangin, S.; Hauet, T.; Fischer, P.; Kim, D.H.; Kortright, J.B.; Chesnel, K. et al.
System: The UNT Digital Library
Cyclic and Linear Polarization of Yttrium-Containing Iron-Based Amorphous Alloys (open access)

Cyclic and Linear Polarization of Yttrium-Containing Iron-Based Amorphous Alloys

Iron-based amorphous alloys are produced by rapid solidification from the melt. These alloys may possess unique mechanical and corrosion resistant properties. The chemical composition of the alloy may influence the cooling rate that is necessary for the alloys to be completely vitreous. At the same time, the corrosion resistance of the amorphous alloys may also depend on their chemical composition. This paper examines the anodic behavior of iron-based amorphous alloys containing three different concentrations (1, 3 and 5 atomic %) of yttrium (Y) in several electrolyte solutions. Results from polarization resistance potentiodynamic polarization show that when the alloy contains 5% atomic Y, the corrosion resistance decreases.
Date: August 10, 2007
Creator: Day, S D; Lian, T; Farmer, J C & Rebak, R B
System: The UNT Digital Library
The RHIC Optically-Pumped Polarized H Ion Source. (open access)

The RHIC Optically-Pumped Polarized H Ion Source.

The depolarization factors in the multi-step spin-transfer polarization technique and basic limitations on maximum polarization in the OPPIS (Optically-Pumped Polarized H{sup -} Ion Source) are discussed. Detailed studies of polarization losses in the RHIC OPPIS and the source parameters optimization resulted in the OPPIS polarization increase to 86-90%. This contributed to increasing polarization in the AGS and RHIC to 65-70%.
Date: September 10, 2007
Creator: Zelenski,A.; Zelenski, A.; Kokhanovski, S.; Kponou, A.; Ritter, J. & Zubets, V.
System: The UNT Digital Library
The Effect of Extending the Length of the Coupling Coils in a MuonIonization Cooling Channel (open access)

The Effect of Extending the Length of the Coupling Coils in a MuonIonization Cooling Channel

RF cavities are used to re-accelerate muons that have beencooled by absorbers that are in low beta regions of a muon ionizationcooling channel. A superconducting coupling magnet (or magnets) arearound or among the RF cavities of a muon ionization-cooling channel. Thefield from the magnet guides the muons so that they are kept within theiris of the RF cavities that are used to accelerate the muons. Thisreport compares the use of a single short coupling magnet with anextended coupling magnet that has one or more superconducting coils aspart of a muon-cooling channel of the same design as the muon ionizationcooling experiment (MICE). Whether the superconducting magnet is shortand thick or long and this affects the magnet stored energy and the peakfield in the winding. The magnetic field distribution also affects is themuon beam optics in the cooling cell of a muon coolingchannel.
Date: November 10, 2007
Creator: Green, Michael A.
System: The UNT Digital Library