Protein-folding via divide-and-conquer optimization (open access)

Protein-folding via divide-and-conquer optimization

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Date: July 11, 2004
Creator: Oliva, Ricardo; Crivelli, Silvia & Meza, Juan
System: The UNT Digital Library
Asymmetric injection of cathodic arc plasma into a macroparticlefilter (open access)

Asymmetric injection of cathodic arc plasma into a macroparticlefilter

The cathodic arc plasmas produced by cathode spots usuallyinclude macroparticles, which is undesirable for many applications. Acommon way of removing macroparticles is to use curved solenoid filterswhich guide the plasma from the source to the substrate. In this work, anarc source with relatively small cathode is used, limiting the possiblelocations of plasma production. The relative position of cathodic arcsource and macroparticle filtered was systematically varied and thefiltered plasma current was recorded. It was found that axis-symmetricplasma injection leads to maximum throughput only if an anode aperturewas used, which limited the plasma to near-axis flow by scraping offplasma at larger angles to the axis. When the anode aperture was removed,more plasma could enter the filter. In this case, maximum filtered ioncurrent was achieved when the plasma was injected off-axis, namely offsetin the direction where the filter is curved. Such behavior wasanticipated because the plasma column in the filter is known to beshifted by ExB and centrifugal drift as well as by non-axis-symmetriccomponents of the magnetic field in the filter entrance and exit plane.The data have implications for plasma transport variations caused bydifferent spot locations on cathodes that are not small compared to thefilter cross section.
Date: February 11, 2004
Creator: Anders, Andre & MacGill, Robert A.
System: The UNT Digital Library
Multi-Tube Power Leads Tower for Bepcii Ir Magnets. (open access)

Multi-Tube Power Leads Tower for Bepcii Ir Magnets.

A power lead tower containing the multi-tube power leads is designed and under fabrication for the superconducting IR quadrupole magnets in the Beijing Electron Position Collider Upgrade (BEPCII). The lead tower consists of six pairs of gas-cooled leads for seven superconducting coils at various operating currents. The power lead is designed in a modular fashion, which can be easily applied to suit different operating current. The end copper block of the tube lead has a large cold mass that provide a large time constant in case of cooling flow interruption. A novel cryogenic electrical isolator is used for the leads.
Date: May 11, 2004
Creator: Jia, L. X.; Zhang, X. B.; Wang, L.; Wang, T. H. & Yao, Z. L.
System: The UNT Digital Library
Speckle Imaging of Titan at 2 microns: Surface Albedo, Haze Optical Depth, and Tropospheric Clouds 1996-1998 (open access)

Speckle Imaging of Titan at 2 microns: Surface Albedo, Haze Optical Depth, and Tropospheric Clouds 1996-1998

We present results from 14 nights of observations of Titan in 1996-1998 using near-infrared (centered at 2.1 microns) speckle imaging at the 10-meter W.M. Keck Telescope. The observations have a spatial resolution of 0.06 arcseconds. We detect bright clouds on three days in October 1998, with a brightness about 0.5% of the brightness of Titan. Using a 16-stream radiative transfer model (DISORT) to model the central equatorial longitude of each image, we construct a suite of surface albedo models parameterized by the optical depth of Titan's hydrocarbon haze layer. From this we conclude that Titan's equatorial surface albedo has plausible values in the range of 0-0.20. Titan's minimum haze optical depth cannot be constrained from this modeling, but an upper limit of 0.3 at this wavelength range is found. More accurate determination of Titan's surface albedo and haze optical depth, especially at higher latitudes, will require a model that fully considers the 3-dimensional nature of Titan's atmosphere.
Date: February 11, 2004
Creator: Gibbard, S. G.; Gavel, D.; Ghez, A. M.; de Pater, I.; Max, C. E.; Young, E. F. et al.
System: The UNT Digital Library
Letter to the Editors of Physics Today (open access)

Letter to the Editors of Physics Today

Two points in our recent article on Edward Teller's scientific life (Physics Today, August 2004, page 45) require correction. In our description of Teller's students, we incorrectly stated that Arthur Kantrowitz's thesis was on the generation of hypersonic molecular beams. Actually, his thesis was on heat capacity lags in gas dynamics. Kantrowitz's invention of high intensity sources for molecular beams came later in his career. Maurice Goldhaber has emphasized that the situation with respect to possible nuclear resonances in ({gamma},n) or ({gamma},fission) reactions was quite unclear at the time of George C. Baldwin and G. Stanley Klaiber's papers on these reactions. This was because the rapid rise of their yield to a prominent peak with increasing energy, followed by a slower fall off was then thought to have been due to the competition between the rapidly rising density of nuclear states and the eventual domination of other reaction channels at higher energies. Goldhaber realized, however, that there could be an analogy between a possible collective nuclear resonance and the restrahl resonance (essentially the transverse optical phonon mode) in polar crystals. Goldhaber sought out Teller because of his paper with Russell Lyddane and Robert Sachs, relating the restrahl frequency to the …
Date: November 11, 2004
Creator: Libby, S B & Weiss, M S
System: The UNT Digital Library
Thermal Fluid Modeling of Bepcii Ir Quadrupole Magnet Cryostat. (open access)

Thermal Fluid Modeling of Bepcii Ir Quadrupole Magnet Cryostat.

A pair of superconducting interaction region quadrupole magnets for BEPCII was designed and fabricated at Brookhaven National Laboratory, USA. The cryogenic system for the IR magnets was designed at Harbin Institute of Technology, China. This paper provides the results of thermal fluid modeling for the magnet cryostat. The numerical analyses were carried out for two types of cooling methods, the subcooled liquid helium and the supercritical helium flow. The pressure and temperature changes in the cooling circuits are given.
Date: May 11, 2004
Creator: Wang, L.; Tang, H. M.; Zhang, X. B.; Yang, G. D. & Jia, L. X.
System: The UNT Digital Library
NotCal04 - Comparison / Calibration 14C records 26-50 cal kBP (open access)

NotCal04 - Comparison / Calibration 14C records 26-50 cal kBP

The radiocarbon calibration curve, IntCal04, extends back to 26 cal kBP. While several high resolution records exist beyond this limit, these data sets exhibit discrepancies one to another of up to several millennia. As a result, no calibration curve for the time range 26-50 cal kBP can be recommended as yet, but in this paper the IntCal04 working group compares the available data sets and offers a discussion of the information that they hold.
Date: November 11, 2004
Creator: der Plicht, J. V.; Beck, J.; Bard, E. & Baille, M.
System: The UNT Digital Library
Optical Probes For Continuous Fabry-Perot Velocimetry Inside Materials (open access)

Optical Probes For Continuous Fabry-Perot Velocimetry Inside Materials

We have used velocimetry for many years at LLNL to measure velocity-time histories of surfaces in dynamic experiments. We have developed and now use special instrumentation to make continuous shock-velocity measurements inside of materials. The goal is to extend the field of velocimetry into a new area of application in shock physics. At the last Congress we reported the successful use of our new filter system for selectively eliminating most of the non- Doppler-shifted light. We showed one record of a fiber embedded inside an explosive making a continuous detonation velocity-time history. At that time it was difficult to obtain complete records. We have now carried out over 65 inexpensive experiments usually using small cylinders or rectangular blocks of explosives or metals. Most were started by detonating a 25 mm diam by 25 mm long cylinder of Comp B explosive to drive a shock into an adjacent material of similar dimensions, using our embedded fiber probes. In contrast to surface velocimetry, embedded measurements involve detailed hydrodynamic considerations in order to result in a successful record. Calculations have guided us in understanding of various failed and successful experiments. The homogeneity of the explosive, poor contact, the materials used in the cladding …
Date: August 11, 2004
Creator: Goosman, D.; Wade, J.; Garza, R.; Avara, G.; Crabtree, T.; Rivera, A. et al.
System: The UNT Digital Library
Single-State Electronic Structure Measurements Using Time-Resolved X-Ray Laser Induced Photoelectron Spectroscopy (open access)

Single-State Electronic Structure Measurements Using Time-Resolved X-Ray Laser Induced Photoelectron Spectroscopy

We demonstrate single-shot x-ray laser induced time-of-flight photoelectron spectroscopy on semiconductor and metal surfaces with picosecond time resolution. The LLNL COMET compact tabletop x-ray laser source provides the necessary high photon flux (>10{sup 12}/pulse), monochromaticity, picosecond pulse duration, and coherence for probing ultrafast changes in the city, chemical and electronic structure of these materials. Static valence band and shallow core-level photoemission spectra are presented for ambient temperature Ge(100) and polycrystalline Cu foils. Surface contamination was removed by UV ozone cleaning prior to analysis. In addition, the ultrafast nature of this technique lends itself to true single-state measurements of shocked and heated materials. Time-resolved electron time-of-flight photoemission results for ultra-thin Cu will be presented.
Date: November 11, 2004
Creator: Nelson, A J; Dunn, J; van Buuren, T & Hunter, J
System: The UNT Digital Library
High pT hadron spectra at RHIC: an overview (open access)

High pT hadron spectra at RHIC: an overview

Recent results on high transverse momentum (p{sub T}) hadron production in p+p, d+Au and Au+Au collisions at the Relativistic Heavy Ion Collider (RHIC) are reviewed. Comparison of the nuclear modification factors, R{sub dAu}(p{sub T}) and R{sub AA}(p{sub T}), demonstrates that the large suppression in central Au+Au collisions is due to strong final-state effects. Theoretical models which incorporate jet quenching via gluon Bremsstrahlung in the dense partonic medium that is expected in central Au+Au collisions at ultra-relativistic energies are shown to reproduce the shape and magnitude of the observed suppression over the range of collision energies so far studied at RHIC.
Date: October 11, 2004
Creator: Klay, J L
System: The UNT Digital Library
Comparison of Electron Cloud Simulation and Experiments in the High-Current Experiment (open access)

Comparison of Electron Cloud Simulation and Experiments in the High-Current Experiment

Contaminating clouds of electrons are a common concern for accelerators of positive-charged particles, but there are some unique aspects of heavy-ion accelerators for fusion and high-energy density physics which make modeling such clouds especially challenging. In particular, self-consistent electron and ion simulation is required, including a particle advance scheme which can follow electrons in regions where electrons are strongly, weakly, and un-magnetized. We describe our approach to such self-consistency, and in particular a scheme for interpolating between full-orbit (Boris) and drift-kinetic particle pushes that enables electron time steps long compared to the typical gyro period in the magnets. We present tests and applications: simulation of electron clouds produced by three different kinds of sources indicates the sensitivity of the cloud shape to the nature of the source; first-of-a-kind self-consistent simulation of electron-cloud experiments on the High-Current Experiment (HCX) at LBNL, in which the machine can be flooded with electrons released by impact of the ion beam on an end plate, demonstrate the ability to reproduce key features of the ion-beam phase space; and simulation of a two-stream instability of thin beams in a magnetic field demonstrate the ability of the large-timestep mover to accurately calculate the instability.
Date: November 11, 2004
Creator: Cohen, R H; Friedman, A; Covo, M K; Lund, S M; Molvik, A W; Bieniosek, F M et al.
System: The UNT Digital Library
Parallel Algebraic Multigrids for Structural mechanics (open access)

Parallel Algebraic Multigrids for Structural mechanics

This paper presents the results of a comparison of three parallel algebraic multigrid (AMG) preconditioners for structural mechanics applications. In particular, they are interested in investigating both the scalability and robustness of the preconditioners. Numerical results are given for a range of structural mechanics problems with various degrees of difficulty.
Date: May 11, 2004
Creator: Brezina, M; Tong, C & Becker, R
System: The UNT Digital Library
Top quark mass measurement at CDF Run-II (open access)

Top quark mass measurement at CDF Run-II

CDF has resumed the top quark mass measurement with upgraded detectors and Tevatron complex. High statistics should allow us to determine the top mass with an uncertainty of a few GeV/c{sup 2} by the end of Run II. The current measured value, using an integrated luminosity of {approx} 108 pb{sup -1}, is 177.5{sub -9.4}{sup +12.7} (stat.) {+-} 7.1(syst.) GeV/c{sup 2} (lepton + jets with one b-jet tagged mode: the current best mode), which is consistent with RunI measurements.
Date: May 11, 2004
Creator: Maruyama, T.
System: The UNT Digital Library
Leptogenesis from split fermions (open access)

Leptogenesis from split fermions

We present a new type of leptogenesis mechanism based on a two-scalar split-fermions framework. At high temperatures the bulk scalar vacuum expectation values (VEVs) vanish and lepton number is strongly violated. Below some temperature, T{sub c}, the scalars develop extra dimension dependent VEVs. This transition is assumed to proceed via a first order phase transition. In the broken phase the fermions are localized and lepton number violation is negligible. The lepton-bulk scalar Yukawa couplings contain sizable CP phases which induce lepton production near the interface between the two phases. We provide a qualitative estimation of the resultant baryon asymmetry which agrees with current observation. The neutrino flavor parameters are accounted for by the above model with an additional approximate U(1) symmetry.
Date: January 11, 2004
Creator: Nagatani, Yukinori & Perez, Gilad
System: The UNT Digital Library
Diagnostics for intense heavy ion beams in the HIF-VNL (open access)

Diagnostics for intense heavy ion beams in the HIF-VNL

Modern diagnostic techniques provide detailed information on beam conditions in injector, transport, and final focus experiments in the HIF-VNL. Parameters of interest include beam current, beam energy, transverse and longitudinal distributions, emittance, and space charge neutralization. Imaging techniques, based on kapton films and optical scintillators, complement and in some cases, may replace conventional techniques based on slit scans. Time-resolved optical diagnostics that provide 4-D transverse information on the experimental beams are in operation on the existing experiments. Current work includes a compact optical diagnostic suitable for insertion in transport lines, improved algorithms for optical data analysis and interpretation, a high-resolution electrostatic energy analyzer, and an electron beam probe. A longitudinal diagnostic kicker generates longitudinal space-charge waves that travel on the beam. Time of flight of the space charge waves and an electrostatic energy analyzer provide an absolute measure of the beam energy. Special diagnostics to detect secondary electrons and gases desorbed from the wall have been developed.
Date: June 11, 2004
Creator: Bieniosek, F. M.; Eylon, S.; Faltens, A.; Friedman, A.; Kwan, J. W.; Leitner, M. A. et al.
System: The UNT Digital Library
An Application of the Coda Methodology for Moment-Rate Spectra Using Broadband Stations in Turkey (open access)

An Application of the Coda Methodology for Moment-Rate Spectra Using Broadband Stations in Turkey

A recently developed coda magnitude methodology was applied to selected broadband stations in Turkey for the purpose of testing the coda method in a large, laterally complex region. As found in other, albeit smaller regions, coda envelope amplitude measurements are significantly less variable than distance-corrected direct wave measurements (i.e., L{sub g} and surface waves) by roughly a factor 3-to-4. Despite strong lateral crustal heterogeneity in Turkey, they found that the region could be adequately modeled assuming a simple 1-D, radially symmetric path correction. After calibrating the stations ISP, ISKB and MALT for local and regional distances, single-station moment-magnitude estimates (M{sub W}) derived from the coda spectra were in excellent agreement with those determined from multistation waveform modeling inversions, exhibiting a data standard deviation of 0.17. Though the calibration was validated using large events, the results of the calibration will extend M{sub W} estimates to significantly smaller events which could not otherwise be waveform modeled. The successful application of the method is remarkable considering the significant lateral complexity in Turkey and the simple assumptions used in the coda method.
Date: July 11, 2004
Creator: Eken Tuna, Kevin Mayeda, Abraham Hofstetter, Rengin Gok, Gonca Orgulu, Niyazi Turkelli
System: The UNT Digital Library
Vibroseis Monitoring of San Andreas Fault in California (open access)

Vibroseis Monitoring of San Andreas Fault in California

A unique data set of seismograms for 720 source-receiver paths has been collected as part of a controlled source Vibroseis experiment San Andreas Fault (SAF) at Parkfield. In the experiment, seismic waves repeatedly illuminated the epicentral region of the expected M6 event at Parkfield from June 1987 until November 1996. For this effort, a large shear-wave vibrator was interfaced with the 3-component (3-C) borehole High-Resolution Seismic Network (HRSN), providing precisely timed collection of data for detailed studies of changes in wave propagation associated with stress and strain accumulation in the fault zone (FZ). Data collected by the borehole network were examined for evidence of changes associated with the nucleation process of the anticipated M6 earthquake at Parkfield. These investigations reported significant traveltime changes in the S coda for paths crossing the fault zone southeast of the epicenter and above the rupture zone of the 1966 M6 earthquake. Analysis and modeling of these data and comparison with observed changes in creep, water level, microseismicity, slip-at-depth and propagation from characteristic repeating microearthquakes showed temporal variations in a variety of wave propagation attributes that were synchronous with changes in deformation and local seismicity patterns. Numerical modeling suggests 200 meters as an effective thickness …
Date: June 11, 2004
Creator: Korneev, Valeri & Nadeau, Robert
System: The UNT Digital Library
Resonance decay effects on anisotropy parameters (open access)

Resonance decay effects on anisotropy parameters

We present the elliptic flow v{sub 2} of pions produced from resonance decays. The transverse momentum p{sub T} spectra of the parent particles are taken from thermal model fits and their v{sub 2} are fit under the assumption that they follow a number-of-constituent-quark (NCQ) scaling law expected from quark-coalescence models. The v{sub 2} of pions from resonance particle decays is found to be similar to the measured pion v{sub 2}. We also propose the measurement of electron v{sub 2} as a means to extract open-charm v{sub 2} and investigate whether a thermalized system of quasi-free quarks and gluons (a quark-gluon plasma) is created in collisions of Au nuclei at RHIC.
Date: March 11, 2004
Creator: Dong, Xin; Esumi, S.; Sorensen, P.; Xu, Nu & Xu, Z.
System: The UNT Digital Library
Performance characteristics of the Cray X1 and their implicationsfor application performance tuning (open access)

Performance characteristics of the Cray X1 and their implicationsfor application performance tuning

During the last decade the scientific computing community has optimized many applications for execution on superscalar computing platforms. The recent arrival of the Japanese Earth Simulator has revived interest in vector architectures especially in the US. It is important to examine how to port our current scientific applications to the new vector platforms and how to achieve high performance. The success of porting these applications will also influence the acceptance of new vector architectures. In this paper, we first investigate the memory performance characteristics of the Cray X1, a recently released vector platform, and determine the most influential performance factors. Then, we examine how to optimize applications tuned on superscalar platforms for the Cray X1 using its performance characteristics as guidelines. Finally, we evaluate the different types of optimizations used, the effort for their implementations, and whether they provide any performance benefits when ported back to superscalar platforms.
Date: May 11, 2004
Creator: Shan, Hogzhang & Strohmaier, Erich
System: The UNT Digital Library
The effect of compression on natural graphite anode performance and matrix conductivity (open access)

The effect of compression on natural graphite anode performance and matrix conductivity

Anodes for lithium-ion cells were constructed from three types of natural graphite, two coated spherical and one flaky. Anode samples were compressed from 0 to 300 kg/cm2 and studied in half-cells to study the relations between anode density, SEI formation and anode cyclability. The C/25 formation of the SEI layer was found to depend on the nature of the graphite and the anode density. Compression of the uncoated graphite lead to an increased conductivity, but only slight improvements in the efficiency of the formation process. Compression of the anodes made from the amorphous-carbon-coated graphites greatly improved both the reversible capacity and first-cycle efficiency. In addition, the fraction of the irreversible charge associated with the surface of the graphite increased with compression, from both an increase in the electrolyte contact as well as compression of the amorphous layer. The cyclability of all of the anodes tended to improve with compression. This suggests that it is the improvement in the conductivity of the anode plays more of a role in the improvement in the cyclability than the formation process.
Date: March 11, 2004
Creator: Striebel, K.A.; Sierra, A.; Shim, J.; Wang, C.-W. & Sastry, A.M.
System: The UNT Digital Library
Type Ia supernova rate at a redshift of ~;0.1 (open access)

Type Ia supernova rate at a redshift of ~;0.1

We present the type Ia rate measurement based on two EROS supernova search campaigns (in 1999 and 2000). Sixteen supernovae identified as type Ia were discovered. The measurement of the detection efficiency, using a Monte Carlo simulation, provides the type Ia supernova explosion rate at a redshift {approx} 0.13. The result is 0.125{sub -0.034-0.028}{sup +0.044+0.028} h{sub 70}{sup 2} SNu where 1 SNu = 1 SN/10{sup 10} L{sub {circle_dot}}{sup B}/century. This value is compatible with the previous EROS measurement (Hardin et al. 2000), done with a much smaller sample, at a similar redshift. Comparison with other values at different redshifts suggests an evolution of the type Ia supernova rate.
Date: May 11, 2004
Creator: Blanc, G.; Afonso, C.; Alard, C.; Albert, J. N.; Aldering, G.; Amadon, A. et al.
System: The UNT Digital Library
Formation of hollow nanocrystals through the nanoscale kirkendall effect (open access)

Formation of hollow nanocrystals through the nanoscale kirkendall effect

We demonstrate that hollow nanocrystals can be synthesized through a mechanism analogous to the Kirkendall Effect, in which pores form due to the difference in diffusion rates between two components in a diffusion couple. Cobalt nanocrystals are chosen as a primary example to show that their reaction in solution with oxygen, sulfur or selenium leads to the formation of hollow nanocrystals of the resulting oxide and chalcogenides. This process provides a general route to the synthesis of hollow nanostructures of large numbers of compounds. A simple extension of this process yields platinum-cobalt oxide yolk-shell nanostructures which may serve as nanoscale reactors in catalytic applications.
Date: March 11, 2004
Creator: Yin, Yadong; Rioux, Robert M.; Erdonmez, Can K.; Hughes, Steven; Somorjai, Gabor A. & Alivisatos, A. Paul
System: The UNT Digital Library
Measurement and simulation of the UMERbeam in the sourceregion (open access)

Measurement and simulation of the UMERbeam in the sourceregion

As the beam propagates in the University of Maryland Electron Ring (UMER) complex transverse density structure including halos has been observed. A primary objective of the experiment is to understand the evolution of a space-charge-dominated beam as it propagates over a substantial distance. It is therefore important to understand which details of the beam structure result from propagation of the beam in the ring and which characteristics result from the specific details of the initial distribution. Detailed measurements of the initial beam characteristics have therefore been performed. These include direct measurement of the density using a phosphor screen, as well as pepper pot measurements of the initial transverse distribution function. Detailed measurements of the distribution function have also been obtained by scanning a pinhole aperture across a beam diameter, and recording phosphor screen pictures of the beam downstream of the pinhole. Simulations of the beam characteristics in the gun region have also been performed using the WARP P.I.C. code. From these simulations, the observed behavior has been attributed to a combination of perturbations to the transverse distribution by a cathode grid that is used to modulate the beam current, as well as the complex transverse dynamics that results from the …
Date: June 11, 2004
Creator: Haber, I.; Bernal, S.; Kishek, R. A.; O'Shea, P. G.; Quinn, B.; Reiser, M. et al.
System: The UNT Digital Library
CRYOGENIC SYSTEM FOR BEPCII SRF CAVITY, IR QUADRUPOLE AND DETECTOR SOLENOID MAGNETS. (open access)

CRYOGENIC SYSTEM FOR BEPCII SRF CAVITY, IR QUADRUPOLE AND DETECTOR SOLENOID MAGNETS.

Beijing Electron-Positron Collider Upgrade (BEPCII) requires three types of superconducting facilities, including one pair of SRF cavities, one pair of interaction region quadrupole magnets, and one detector solenoid magnet. The cryo-plant for BEPCII has a total cooling capacity of 1kW at 4.5K, which is composed of two separate helium refrigerators of 500W each. Two refrigerators share the same gas storage and recovery system. The engineering design for the cryogenic systems, including power leads, control dewars, subcooler, cryogenic valve boxes, cryogenic transfer-lines and cryogenic controls, is completed. The production of its subsystem is under way. This paper summarizes the progress in cryogenics of the BEPCII project.
Date: May 11, 2004
Creator: JIA,J. X. & L., WANG.
System: The UNT Digital Library