This report talks about Integrated Safety Management Summit i Knoxville, TN

Gene families are growing rapidly, but standard methods for inferring phylogenies do not scale to alignments with over 10,000 sequences. We present FastTree, a method for constructing large phylogenies and for estimating their reliability. Instead of storing a distance matrix, FastTree stores sequence profiles of internal nodes in the tree. FastTree uses these profiles to implement neighbor-joining and uses heuristics to quickly identify candidate joins. FastTree then uses nearest-neighbor interchanges to reduce the length of the tree. For an alignment with N sequences, L sites, and a different characters, a distance matrix requires O(N^2) space and O(N^2 L) time, but FastTree requires just O( NLa + N sqrt(N) ) memory and O( N sqrt(N) log(N) L a ) time. To estimate the tree's reliability, FastTree uses local bootstrapping, which gives another 100-fold speedup over a distance matrix. For example, FastTree computed a tree and support values for 158,022 distinct 16S ribosomal RNAs in 17 hours and 2.4 gigabytes of memory. Just computing pairwise Jukes-Cantor distances and storing them, without inferring a tree or bootstrapping, would require 17 hours and 50 gigabytes of memory. In simulations, FastTree was slightly more accurate than neighbor joining, BIONJ, or FastME; on genuine alignments, FastTree's …

None

We have studied the oxidation of carbon monoxide over a lanthanum substituted perovskite (La0.5Sr0.5CoO3-d) catalyst prepared by spray pyrolysis. Under the assumption of a first-order kinetics mechanism for CO, it has been found that the activation energy barrier of the reaction changes from 80 to 40 kJ mol-1 at a threshold temperature of ca. 320 oC. In situ XPS near-ambient pressure ( 0.2 torr) shows that the gas phase oxygen concentration over the sample decreases sharply at ca. 300 oC. These two observations suggest that the oxidation of CO undergoes a change of mechanism at temperatures higher than 300 oC.

This poster shows the benefits of integrating a workflow management system with logging and log mining capabilities. By combing two existing, mature technologies: Pegasus-WMS and Netlogger, we are able to efficiently process execution logs of earthquake science workflows consisting of hundreds of thousands to one million tasks. In particular we show results of processing logs of CyberShake, a workflow application running on the TeraGrid. Client-side tools allow scientists to quickly gather statistics about a workflow run and find out which tasks executed, where they were executed, what was their runtime, etc. These statistics can be used to understand the performance characteristics of a workflow and help tune the execution parameters of the workflow management system. This poster shows the scalability of the system presenting results of uploading task execution records into the system and by showing results of querying the system for overall workflow performance information.

The next generation of synchrotrons and free electron lasersrequires x-ray optical systems with extremely high-performance,generally, of diffraction limited quality. Fabrication and use of suchoptics requires highly accurate metrology. In the present paper, wediscuss a way to improve the performance of the Long Trace Profiler(LTP), a slope measuring instrument widely used at synchrotron facilitiesto characterize x-ray optics at high-spatial-wavelengths fromapproximately 2 mm to 1 m. One of the major sources of LTP systematicerror is the detector. For optimal functionality, the detector has topossess the smallest possible pixel size/spacing, a fast method ofshuttering, and minimal non-uniformity of pixel-to-pixel photoresponse.While the first two requirements are determined by choice of detector,the non-uniformity of photoresponse of typical detectors such as CCDcameras is around 2-3 percent. We describe a flat-field calibration setupspecially developed for calibration of CCD camera photo-response and darkcurrent with an accuracy of better than 0.5 percent. Such accuracy isadequate for use of a camera as a detector for an LTP with performance of~;0.1 microradian (rms). We also present the design details of thecalibration system and results of calibration of a DALSA CCD camera usedfor upgrading our LTP-II instrument at the ALS Optical MetrologyLaboratory.

Small carbon clusters (Cn, n = 2-15) are produced in amolecular beam by pulsed laser vaporization and studied with vacuumultraviolet (VUV) photoionization mass spectrometry. The required VUVradiation in the 8-12 eV range is provided by the Advanced Light Source(ALS) at the Lawrence Berkeley National Laboratory. Mass spectra atvarious ionization energies reveal the qualitative relative abundances ofthe neutral carbon clusters produced. By far the most abundant species isC3. Using the tunability of the ALS, ionization threshold spectra arerecorded for the clusters up to 15 atoms in size. The ionizationthresholds are compared to those measured previously with charge-transferbracketing methods. To interpret the ionization thresholds for differentcluster sizes, new ab initio calculations are carried out on the clustersfor n = 4-10. Geometric structures are optimized at the CCSD(T) levelwith cc-pVTZ (or cc-pVDZ) basis sets, and focal point extrapolations areapplied to both neutral and cation species to determine adiabatic andvertical ionization potentials. The comparison of computed and measuredionization potentials makes it possible to investigate the isomericstructures of the neutral clusters produced in this experiment. Themeasurements are inconclusive for the n = 4-6 species because ofunquenched excited electronic states. However, the data provide evidencefor the prominence of linear structures for the n = 7, 9, …

Ga-acceptor nanowires were embedded in crystalline Si using focused-ion beams. The dc current-voltage characteristics of these wires after annealing are highly nonlinear at low temperatures, and a threshold voltage of less than 50 mV is observed independent of Ga+ dosage and implant beam overlap. These features suggest a Coulomb blockade transport mechanism presumably caused by a network of Ga precipitates in the substrate. This granular scenario is further supported by measurements of gated nanowires. Nanowires with metallic conductance at low temperatures could be achieved by reducing the current density of the focused-ion beams.

Accelerator-based neutron sources offer many advantages, in particular tunability of the neutron beam in energy and width to match the needs of the application. Using a recently constructed neutron beam line at the 88-Inch Cyclotron at LBNL, tunable high-intensity sources of quasi-monoenergetic and broad spectrum neutrons from deuteron breakup are under development for a variety of applications.

We present results of direct numerical simulations of impact of hypervelocity particle stream with a target. The stream of interest consists of submillimeter (30-300 micron) brittle ceramic particles. Current supercomputer capabilities make it possible to simulate a realistic size of streams (up to 20 mm in diameter and 500 mm in length) while resolving each particle individually. Such simulations make possible to study the damage of the target from synergistic effects of individual impacts. In our research we fixed the velocity distribution along the axis of the stream (1-4 km/s) and volume fraction of the solid material (1-10%) and study effects of particle size variation, particle and target material properties and surrounding air properties. We ran 3D calibration simulations with up to 10 million individual particles and conducted sensitivity studies with 2D cylindrically symmetric simulations. We used an Eulerian Godunov hydrocode with adaptive mesh refinement. The particles, target material and air are represented with volume-of-fluid approach. Brittle particle and target material has been simulated with pressure-dependent yield strength and Steinberg model has been used for metal targets. Simulations demonstrated penetration depth and a hole diameter similar to experimental observations and can explain the influence of parameters of the stream on …

The National Ignition Facility (NIF) requires optical diagnostics for measuring shock velocities in shock physics experiments. The nature of the NIF facility requires the alignment of complex three-dimensional optical systems of very long distances. Access to the alignment mechanisms can be limited, and any alignment system must be operator friendly. The Velocity Interferometer System for Any Reflector measures shock velocities, shock breakout times, and emission of 1- to 5-mm targets at a location remote to the NIF target chamber. Three optical systems using the same vacuum chamber port each have a total track of 21 meters. All optical lenses are on kinematic mounts or sliding rails, enabling pointing accuracy of the optical axis to be checked. Counter-propagating laser beams (orange and red) align these diagnostics to a listing of tolerances. Movable aperture cards, placed before and after lens groups, show the spread of alignment spots created by the orange and red alignment lasers. Optical elements include 1-in. to 15-in. diameter mirrors, lenses with up to 10.5-in. diameters, beamsplitters, etalons, dove prisms, filters, and pellicles. Alignment of more than 75 optical elements must be verified before each target shot. Archived images from eight alignment cameras prove proper alignment before each shot.

The development of third generation light sources like theAdvanced Light Source (ALS) or BESSY II brought to a focus the need forhigh performance synchrotron optics with unprecedented tolerances forslope error and micro roughness. Proposed beam lines at Free ElectronLasers (FEL) require optical elements up to a length of one meter,characterized by a residual slope error in the range of 0.1murad (rms),and rms values of 0.1 nm for micro roughness. These optical elements mustbe inspected by highly accurate measuring instruments, providing ameasurement uncertainty lower than the specified accuracy of the surfaceunder test. It is essential that metrology devices in use at synchrotronlaboratories be precisely characterized and calibrated to achieve thistarget. In this paper we discuss a proposal for a Universal Test Mirror(UTM) as a realization of a high performance calibration instrument. Theinstrument would provide an ideal calibration surface to replicate aredundant surface under test of redundant figure. The application of asophisticated calibration instrument will allow the elimination of themajority of the systematic error from the error budget of an individualmeasurement of a particular optical element. We present the limitationsof existing methods, initial UTM design considerations, possiblecalibration algorithms, and an estimation of the expectedaccuracy.

The Gordon Research Conference (GRC) on MOLECULAR & IONIC CLUSTERS was held at Crowne Plaza from 2/19/2006 thru 2/24/2006. The Conference was well-attended with 89 participants (attendees list attached). The attendees represented the spectrum of endeavor in this field coming from academia, industry, and government laboratories, both U.S. and foreign scientists, senior researchers, young investigators, and students. In designing the formal speakers program, emphasis was placed on current unpublished research and discussion of the future target areas in this field. There was a conscious effort to stimulate lively discussion about the key issues in the field today. Time for formal presentations was limited in the interest of group discussions. In order that more scientists could communicate their most recent results, poster presentation time was scheduled. Attached is a copy of the formal schedule and speaker program and the poster program. In addition to these formal interactions, ''free time'' was scheduled to allow informal discussions. Such discussions are fostering new collaborations and joint efforts in the field.

Following our earlier study on the dynamics of low energy electron attachment to formic acid, we report the results of elastic low-energy electron collisions with formic acid. Momentum transfer and angular differential cross sections were obtained by performing fixed-nuclei calculations employing the complex Kohn variational method. We make a brief description of the technique used to account for the polar nature of this polyatomic target and compare our results with available experimental data.

None

In a study of B{sup +} {yields} J/{psi}{gamma}K{sup +} decays, they find evidence for the radiative decay X(3872) {yields} J/{psi}{gamma} with a statistical significance of 3.4{sigma}. They measure the product of branching fractions {Beta}(B{sup +} {yields} X(3872)K{sup +}) {center_dot} {Beta}(X(3872) {yields} J/{psi}{gamma}) = (3.3 {+-} 1.0 {+-} 0.3) x 10{sup -6}, where the uncertainties are statistical and systematic, respectively. They also measure the branching fraction {Beta}(B{sup +} {yields} {chi}{sub c1}K{sup +}) = (4.9 {+-} 0.20 {+-} 0.4) x 10{sup -4}. These results are obtained from (287 {+-} 3) million B{bar B} decays collected at the {Upsilon}(4S) resonance with the BABAR detector at the PEP-II B Factory at SLAC.

A search for the decay B{+-} {yields} a{sub 0}{sup {+-}}{pi}{sup 0} with the a{sub 0}{sup +} decaying to an {eta} and a {pi}{sup +} was carried out at the Stanford Linear Accelerator Center using the BABAR detector coupled with the PEP-II collider. The analysis used a data sample comprised of approximately 252 million B{bar B} pairs collected at the {Upsilon}(4S) resonance. No signal was observed and a 90% confidence level upper limit on the branching fraction was set at 1.32 x 10{sup -6}.

The authors search for B{sup 0} meson decays into two-body combinations of K{sup 0}, {eta}, {eta}', and {phi} mesons in 324 million B{bar B} pairs collected with the BABAR detector at the PEP-II asymmetric-energy e{sup +}e{sup -} collider at SLAC. They measure the following branching fractions (upper limits at 90% confidence level) in units of 10{sup -6}: {Beta}(B{sup 0} {yields} {eta}K{sup 0}) = 1.8{sub -0.6}{sup +0.7} {+-} 0.1 (< 2.9), {Beta}(B{sup 0} {yields} {eta}{eta}) = 1.1{sub -0.4}{sup +0.5} {+-} 0.1(< 1.8), {Beta}(B{sup 0} {yields} {eta}{phi}) = 0.1 {+-} 0.2 {+-} 0.1(< 0.6), {Beta}(B{sup 0} {yields} {eta}'{phi}) = 0.2{sub -0.3}{sup +0.4} {+-} 0.1(< 1.0), and {Beta}(B{sup 0} {yields} {eta}'{eta}') = 1.0{sub -0.6}{sup +0.8} {+-} 0.1 (< 2.4), where the first error is statistical and the second systematic.

We demonstrate the use of micro-scale nuclear magneticresonance (NMR) for studying the transfer of spin coherence innon-equilibrium chemical processes, using spatially separated NMRencoding and detection coils. As an example, we provide the map ofchemical shift correlations for the amino acid alanine as it transitionsfrom the zwitterionic to the anionic form. Our method is unique in thesense that it allows us to track the chemical migration of encodednuclear spins during the course of chemical transformations.

We present strange particle spectra and yields measured atmid-rapidity in sqrt text s=200 GeV proton-proton (p+p) collisions atRHIC. We find that the previously observed universal transverse mass(mathrm mT \equiv\sqrt mathrm p_T 2+\mathrm m2) scaling of hadronproduction in p+p collisions seems to break down at higher \mt and thatthere is a difference in the shape of the \mt spectrum between baryonsand mesons. We observe mid-rapidity anti-baryon to baryon ratios nearunity for Lambda and Xi baryons and no dependence of the ratio ontransverse momentum, indicating that our data do not yet reach thequark-jet dominated region. We show the dependence of the mean transversemomentum (\mpt) on measured charged particle multiplicity and on particlemass and infer that these trends are consistent with gluon-jet dominatedparticle production. The data are compared to previous measurements fromCERN-SPS, ISR and FNAL experiments and to Leading Order (LO) and Next toLeading order (NLO) string fragmentation model predictions. We infer fromthese comparisons that the spectral shapes and particle yields from $p+p$collisions at RHIC energies have large contributions from gluon jetsrather than quark jets.

We are studying the flashover of vacuum insulators for applications where high voltage conditioning of the insulator and electrodes is not practical and for pulse lengths on the order of several microseconds. The study is centered about experiments performed with a 100-kV, 10-ms pulsed power system and supported by a combination of theoretical and computational modeling. The base line geometry is a cylindrically symmetric, +45{sup o} insulator between flat electrodes. In the experiments, flashovers or breakdowns are localized by operating at field stresses slightly below the level needed for explosive emissions with the base line geometry. The electrodes and/or insulator are then seeded with an emission source, e.g. a tuft of velvet, or a known mechanical defect. Various standard techniques are employed to suppress cathode-originating flashovers/breakdowns. We present the results of our experiments and discuss the capabilities of modeling insulator flashover.

We have constructed a fast-neutron double-scatter spectrometer that efficiently measures the neutron spectrum and direction of a spontaneous fission source. The device consists of two planes of organic scintillators, each having an area of 125 cm{sup 2}, efficiently coupled to photomultipliers. The four scintillators in the front plane are 2 cm thick, giving almost 25% probability of detecting an incident fission-spectrum neutron at 2 MeV by proton recoil and subsequent ionization. The back plane contains four 5-cm-thick scintillators which give a 40% probability of detecting a scattered fast neutron. A recordable double-scatter event occurs when a neutron is detected in both a front plane detector and a back plane detector within an interval of 500 nanoseconds. Each double-scatter event is analyzed to determine the energy deposited in the front plane, the time of flight between detectors, and the energy deposited in the back plane. The scattering angle of each incident neutron is calculated from the ratio of the energy deposited in the first detector to the kinetic energy of the scattered neutron.

The Long Trace Profiler (LTP) is a useful optical metrology instrument for measuring the figure and slope error of cylindrical aspheres commonly used as synchrotron radiation (SR) optics. It is used extensively at a number of synchrotron radiation laboratories around the world. In order to improve SR beam line quality and resolution, the National Synchrotron Radiation Laboratory (NSRL) of China is developing a versatile LTP that can be used to measure both SR optics and more conventional ''normal'' optical surfaces. The optical metrology laboratories at Brookhaven National Laboratory (BNL) and NSRL are collaborating in developing a multiple functions LTP (LTP-MF). Characteristics of the LTP-MF are: a very compact and lightweight optical head, a large angular test range ({+-} 16 mad) and high accuracy. The LTP-MF can be used in various configurations: as a laboratory-based LTP, an in-situ LTP or penta-prism LTP, as an angle monitor, a portable LTP, and a small radius of curvature test instrument. The schematic design of the compact optical head and a new compact slide are introduced. Analysis of different measurements modes and systematic error correction methods are introduced.

New results from studies of coplanar-grid CdZnTe (CZT) detectors are presented. The coplanar-grid detectors, were investigated by using a highly collimated X-ray beam available at Brookhaven's National Synchrotron Light Source and by applying a pulse-shape analysis. The coplanar-grid detector operates as a single-carrier device. Despite the fact that its operational principle is well known and has been investigated by many groups in the past, we found some new details that may explain the performance limits of these types of devices. The experimental results have been confirmed by extensive computer modeling.