High-contrast adaptive optics systems, such as those needed to image extrasolar planets, are known to require excellent wavefront control and diffraction suppression. At the Laboratory for Adaptive Optics on the Extreme Adaptive Optics testbed, we have already demonstrated wavefront control of better than 1 nm rms within controllable spatial frequencies. Corresponding contrast measurements, however, are limited by amplitude variations, including those introduced by the micro-electrical-mechanical-systems (MEMS) deformable mirror. Results from experimental measurements and wave optic simulations of amplitude variations on the ExAO testbed are presented. We find systematic intensity variations of about 2% rms, and intensity variations with the MEMS to be 6%. Some errors are introduced by phase and amplitude mixing because the MEMS is not conjugate to the pupil, but independent measurements of MEMS reflectivity suggest that some error is introduced by small non-uniformities in the reflectivity.

Silica aerogel collector tiles have been employed for the collection of particles in low Earth orbit and, more recently, for the capture of cometary particles by NASA's Stardust mission. Reliable, reproducible methods for cutting these and future collector tiles from sample return missions are necessary to maximize the science output from the extremely valuable embedded particles. We present a means of macroscopic subdivision of collector tiles by generating large-scale cuts over several centimeters in silica aerogel with almost no material loss. The cut surfaces are smooth and optically clear allowing visual location of particles for analysis and extraction. This capability is complementary to the smaller-scale cutting capabilities previously described [Westphal (2004), Ishii (2005a, 2005b)] for removing individual impacts and particulate debris in tiny aerogel extractions. Macroscopic cuts enable division and storage or distribution of portions of aerogel tiles for immediate analysis of samples by certain techniques in situ or further extraction of samples suited for other methods of analysis.

We study the Collins mechanism contribution to the single transverse spin asymmetry in inclusive hadron production in pp scattering p{up_arrow}p {yields} {pi}X from the leading jet fragmentation. The azimuthal asymmetric distribution of hadron in the jet leads to a single spin asymmetry for the produced hadron in the Lab frame. The effect is evaluated in a transverse momentum dependent model that takes into account the transverse momentum dependence in the fragmentation process. We find the asymmetry is comparable in size to the experimental observation at RHIC at {radical}s = 200GeV.

Data collected by the Pierre Auger Observatory provide evidence for anisotropy in the arrival directions of cosmic rays (CRs) with energies >57 EeV that suggests a correlation with the positions of active galactic nuclei (AGN) located within {approx}75 Mpc. However, this analysis does not take into account AGN morphology. A detailed study of the sample of AGN whose positions correlate with the CR events shows that most of them are classified as Seyfert 2 and low-ionization nuclear emission-line region (LINER) galaxies which do not differ from other local AGN of the same types. Therefore, the claimed correlation between the CR events observed by the Pierre Auger Observatory and local active galaxies should be considered as resulting from a chance coincidence, if the production of the highest energy CRs is not episodic in nature, but operates in a single object on long ({ge} Myr) timescales. Additionally, most of the selected sources do not show significant jet activity, and hence--in the framework of the jet paradigm--there are no reasons for expecting them to accelerate CRs up to the highest energies, {approx}10{sup 20} eV, at all. If the extragalactic magnetic fields and the sources of these CRs are coupled with matter, it is …

We perform linear stability calculations for horizontal fluid bilayers that can undergo a phase transformation, taking into account both buoyancy effects and thermocapillary effects in the presence of a vertical temperature gradient. We compare the familiar case of the stability of two immiscible fluids in a bilayer geometry with the less-studied case that the two fluids represent different phases of a single-component material, e.g., the water-steam system. The two cases differ in their interfacial boundary conditions: the condition that the interface is a material surface is replaced by the continuity of mass flux across the interface, together with an assumption of thermodynamic equilibrium that in the linearized equations represents the Clausius-Clapeyron relation relating the interfacial temperature and pressures. For the two-phase case, we find that the entropy difference between the phases plays a crucial role in determining the stability of the system. For small values of the entropy difference between the phases, the two-phase system can be linearly unstable to either heating from above or below. The instability is due to the Marangoni effect in combination with the effects of buoyancy (for heating from below). For larger values of the entropy difference the two-phase system is unstable only for heating …

The slowing pace of commodity microprocessor performance improvements combined with ever-increasing chip power demands has become of utmost concern to computational scientists. As a result, the high performance computing community is examining alternative architectures that address the limitations of modern cache-based designs. In this work, we examine the potential of the using the forth coming STI Cell processor as a building block for future high-end computing systems. Our work contains several novel contributions. We are the first to present quantitative Cell performance data on scientific kernels and show direct comparisons against leading superscalar (AMD Opteron), VLIW (IntelItanium2), and vector (Cray X1) architectures. Since neither Cell hardware nor cycle-accurate simulators are currently publicly available, we develop both analytical models and simulators to predict kernel performance. Our work also explores the complexity of mapping several important scientific algorithms onto the Cells unique architecture. Additionally, we propose modest microarchitectural modifications that could significantly increase the efficiency of double-precision calculations. Overall results demonstrate the tremendous potential of the Cell architecture for scientific computations in terms of both raw performance and power efficiency.

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The Eap (extracellular adherence protein) of Staphylococcus aureus functions as a secreted virulence factor by mediating interactions between the bacterial cell surface and several extracellular host proteins. Eap proteins from different Staphylococcal strains consist of four to six tandem repeats of a structurally uncharacterized domain (EAP domain). We have determined the three-dimensional structures of three different EAP domains to 1.8, 2.2, and 1.35 {angstrom} resolution, respectively. These structures reveal a core fold that is comprised of an {alpha}-helix lying diagonally across a five-stranded, mixed {beta}-sheet. Comparison of EAP domains with known structures reveals an unexpected homology with the C-terminal domain of bacterial superantigens. Examination of the structure of the superantigen SEC2 bound to the {beta}-chain of a T-cell receptor suggests a possible ligand-binding site within the EAP domain (Fields, B. A., Malchiodi, E. L., Li, H., Ysern, X., Stauffacher, C. V., Schlievert, P. M., Karjalainen, K., and Mariuzza, R. (1996) Nature 384, 188-192). These results provide the first structural characterization of EAP domains, relate EAP domains to a large class of bacterial toxins, and will guide the design of future experiments to analyze EAP domain structure/function relationships.

Genome features of the Bacillus cereus group genomes (representative strains of Bacillus cereus, Bacillus anthracis and Bacillus thuringiensis sub spp israelensis) were analyzed and compared with the Bacillus subtilis genome. A core set of 1,381 protein families among the four Bacillus genomes, with an additional set of 933 families common to the B. cereus group, was identified. Differences in signal transduction pathways, membrane transporters, cell surface structures, cell wall, and S-layer proteins suggesting differences in their phenotype were identified. The B. cereus group has signal transduction systems including a tyrosine kinase related to two-component system histidine kinases from B. subtilis. A model for regulation of the stress responsive sigma factor sigmaB in the B. cereus group different from the well studied regulation in B. subtilis has been proposed. Despite a high degree of chromosomal synteny among these genomes, significant differences in cell wall and spore coat proteins that contribute to the survival and adaptation in specific hosts has been identified.

The reaction of ozone with the (100) plane of solid potassium iodide (KI) was investigated using atomic force microscopy (AFM). The reaction forming potassium iodate (KIO{sub 3}) initiates at step edges prior to reacting on the flat terraces. Small domains of KIO{sub 3}, initially 3.8 {angstrom} in height are formed on the top of step edges. Following reaction at the step edge, domains of KIO{sub 3} are formed across the terraces. With prolonged exposure to ozone, KIO{sub 3} domains nucleate further growth until the surface is evenly covered with KIO{sub 3} particles that are 4-6 nm in height, at which point the surface is passivated and the reaction terminates.

We review recent results for the chiral behavior of meson masses and decay constants and the determination of the light quark masses by the RBC and UKQCD collaborations. We find that one-loop SU(2) chiral perturbation theory represents the behavior of our lattice data better than one-loop SU(3) chiral perturbation theory in both the pion and kaon sectors. The simulations have been performed using the Iwasaki gauge action at two different lattice spacings with the physical spatial volume held approximately fixed at (2.7fm){sup 3}. The Domain Wall fermion formulation was used for the 2+1 dynamical quark flavors: two (mass degenerate) light flavors with masses as light as roughly 1/5 the mass of the physical strange quark mass and one heavier quark flavor at approximately the value of the physical strange quark mass, On the ensembles generated with the coarser lattice spacing, we obtain for the physical average up- and down-quark and strange quark masses m{sub ud}{sup {ovr MS}} (2 GeV) = 3.72(0.16){sub stat}(0.33){sub ren}(0.18){sub syst}MeV and m{sub s}{sup {ovr MS}} (2 GeV) = 107.3(4.4){sub stat}(9.7){sub ren}(4.9){sub syst} MeV, respectively, while they find for the pion and kaon decay constants f{sub {pi}} = 124.1(3.6){sub stat}(6.9){sub syst}MeV, f{sub K} = 149.6(3.6){sub stat}(6.3){sub syst} …

We describe the performance of various materials used as thethermal interface between silicon to silicon and silicon to copper jointswhen operated at ~;120K and loaded with ~;20 watts of thermal power. Wefind that only the indium based silicon-to-silicon joint isreliable.

The U.S. LHC Accelerator Research Program (LARP), a collaboration between BNL, FNAL, LBNL, and SLAC, has among its major objectives the development of advanced magnet technology for an LHC luminosity upgrade. The LBNL Superconducting Magnet Group supports this program with a broad effort involving design studies, Nb{sub 3}Sn conductor development, mechanical models, and basic prototypes. This paper describes the development of a large aperture Nb{sub 3}Sn racetrack quadrupole magnet using four racetrack coils from the LBNL Subscale Magnet (SM) Program. The magnet provides a gradient of 95 T/m in a 110 mm bore, with a peak field in the conductor of 11.2 T. The coils are prestressed by a mechanical structure based on a pre-tensioned aluminum shell, and axially supported with aluminum rods. The mechanical behavior has been monitored with strain gauges and the magnetic field has been measured. Results of the test are reported and analyzed.

The temperature equilibration rate in dense hydrogen (for both T{sub i} > T{sub e} and T{sub i} < T{sub e}) has been calculated with large-scale molecular dynamics simulations for temperatures between 10 and 300 eV and densities between 10{sup 20}/cc to 10{sup 24}/cc. Careful attention has been devoted to convergence of the simulations, including the role of semiclassical potentials. We find that for Coulomb logarithms L {approx}> 1, Brown-Preston-Singleton [Brown et al., Phys. Rep. 410, 237 (2005)] with the sub-leading corrections and the fit of Gericke-Murillo-Schlanges [Gericke et al., PRE 65, 036418 (2003)] to the T-matrix evaluation of the collision operator, agrees with the MD data to within the error bars of the simulation. For more strongly-coupled plasmas where L {approx}< 1, our numerical results are consistent with the fit of Gericke-Murillo-Schlanges.

The optical properties of epitaxially grown islands of InGaN are investigated with nanometer-scale spatial resolution using visible apertureless near-field scanning optical microscopy. Scattered light from the tip-sample system is modulated by cantilever oscillations and detected at the third harmonic of the oscillation frequency to distinguish the near-field signal from unwanted scattered background light. Scattered near-field measurements indicate that the as-grown InGaN islanded film may exhibit both inhomogeneous In composition and strain-induced changes that affect the optical signal at 633 nm and 532 nm. Changes are observed in the optical contrast for large 3D InGaN islands (100's of nm) of the same height. Near-field optical mapping of small grains on a finer scale reveals InGaN composition or strain-induced irregularities in features with heights of only 2 nm, which exhibit different near-field signals at 633 nm and 532 nm incident wavelengths. Optical signal contrast from topographic features as small as 30 nm is detected.

We use current theoretical estimates for the density of long cosmic strings to predict the number of strong gravitational lensing events in astronomical imaging surveys as a function of angular resolution and survey area. We show that angular resolution is the single most important factor, and that interesting limits on the dimensionless string tension G{mu}/c{sup 2} can be obtained by existing and planned surveys. At the resolution of the Hubble Space Telescope (0'.14), it is sufficient to survey of order a square degree -- well within reach of the current HST archive -- to probe the regime G{mu}/c{sup 2} {approx} 10{sup -8}. If lensing by cosmic strings is not detected, such a survey would improve the limit on the string tension by an order of magnitude on that available from the cosmic microwave background. At the resolution (0'.028) attainable with the next generation of large ground based instruments, both in the radio and the infra-red with adaptive optics, surveying a sky area of order ten square degrees will allow us to probe the G{mu}/c{sup 2} {approx} 10{sup -9} regime. These limits will not be improved significantly by increasing the solid angle of the survey.

Chromosomal mosaicism in human preimplantation embryos is a common cause ofspontaneous abortions, however, our knowledge of its etiology is limited. We used multicolor fluorescence in situ hybridization (FISH) painting to investigate whether paternally-transmitted chromosomal aberrations result in mosaicism in mouse 2-cell embryos. Paternal exposure to acrylamide, an important industrial chemical also found in tobacco smoke and generated during the cooking process of starchy foods, produced significant increases in chromosomally defective 2-cell embryos, however, the effects were transient primarily affecting the postmeiotic stages of spermatogenesis. Comparisons with our previous study of zygotes demonstrated similar frequencies of chromosomally abnormal zygotes and 2-cell embryos suggesting that there was no apparent selection against numerical or structural chromosomal aberrations. However, the majority of affected 2-cell embryos were mosaics showing different chromosomal abnormalities in the two blastomeric metaphases. Analyses of chromosomal aberrations in zygotes and 2-cell embryos showed a tendency for loss of acentric fragments during the first mitotic division ofembryogenesis, while both dicentrics and translocations apparently underwent propersegregation. These results suggest that embryonic development can proceed up to the end of the second cell cycle of development in the presence of abnormal paternal chromosomes and that even dicentrics can persist through cell division. The high …

I explore a different type of approximation to the exactanisotropic wave velocities as a function of incidence angle invertically transversely isotropic (VTI) media. This method extends theThomsen weak anisotropy approach to stronger anisotropy withoutsignificantly affecting the simplicity of the formulas. One importantimprovement is that the peak of the quasi-SV-wave speed vsv(theta) islocated at the correct incidence angle theta= theta max, rather thanalways being at the position theta = 45o, which universally holds forThomsen's approximation although max theta = 45o is actually nevercorrect for any VTI anisotropic medium. The magnitudes of all the wavespeeds are also more closely approximated for all values of the incidenceangle. Furthermore, the value of theta max (which is needed in the newformulas) can be deduced from the same data that are typically used inthe weak anisotropy data analysis. The two examples presented are basedon systems having vertical fractures. The first set of model fractureshas their axes of symmetry randomly oriented in the horizontal plane.Such a system is then isotropic in the horizontal plane and, therefore,exhibits vertical transverse isotropic (VTI) symmetry. The second set offractures also has axes of symmetry in the horizontal plane, but it isassumed these axes are aligned so that the system exhibits horizontaltransverse …

We report the scaling behavior of Barkhausen avalanches for every small field step along the hysteresis loop in CoCrPt alloy film having perpendicular magnetic anisotropy. Individual Barkhausen avalanche is directly observed utilizing a high-resolution soft X-ray microscopy that provides real space images with a spatial resolution of 15 nm. Barkhausen avalanches are found to exhibit power-law scaling behavior at all field steps along the hysteresis loop, despite their different patterns for each field step. Surprisingly, the scaling exponent of the power-law distribution of Barkhausen avalanches is abruptly altered from 1 {+-} 0.04 to 1.47 {+-} 0.03 as the field step is close to the coercive field. The contribution of coupling among adjacent domains to Barkhausen avalanche process affects the sudden change of the scaling behavior observed at the coercivity-field region on the hysteresis loop of CoCrPt alloy film.

We present an analysis of archival Chandra and VLA observations of the E0 galaxy NGC1399 and the E2 galaxy NGC4649 in which we investigate cavities in the surrounding X-ray emitting medium caused by the central AGN. We calculate the jet power required for the AGN to evacuate these cavities and find values of {approx} 8x10{sup 41} erg s-1 and {approx} 14x10{sup 41} erg s{sup -1} for the lobes of NGC1399 and {approx} 7x10{sup 41} erg s{sup -1} and {approx} 6x1041 erg s{sup -1} for those of NGC4649. We also calculate the k/f values for each cavity, where k is the ratio of the total particle energy to that of electrons radiating in the range of 10 MHz to 10 GHz, and f is the volume filling factor of the plasma in the cavity. We find that the values of k/f for the lobes of NGC1399 are {approx} 93 and {approx} 190, and those of the lobes of NGC4649 are {approx} 15000 and {approx} 12000. We conclude that the assumed spectrum describes the electron distribution in the lobes of NGC1399 reasonably well, and that there are few entrained particles. For NGC4649, either there are many entrained particles or the model spectrum …

We describe an efficient implementation and present aperformance study of an algebraic multilevel sub-structuring (AMLS)method for sparse eigenvalue problems. We assess the time and memoryrequirements associated with the key steps of the algorithm, and compareitwith the shift-and-invert Lanczos algorithm in computational cost. Oureigenvalue problems come from two very different application areas: theaccelerator cavity design and the normal mode vibrational analysis of thepolyethylene particles. We show that the AMLS method, when implementedcarefully, is very competitive with the traditional method in broadapplication areas, especially when large numbers of eigenvalues aresought.

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The development of radiological consequence lookup tables for postulated releases of radionuclides commonly used at Savannah River Site (SRS) and other Department of Energy (DOE) facilities requires the use of the MELCOR Accident Consequence Code System (MACCS)/MACCS2. MACCS2 users input site-specific data: such as stack or ground release, building wake effects, boundary distance from release source, and site-specific meteorological data. MACCS2 also allows the input of more general data such as plume rise and wet and/or dry deposition. The acceptance of such inputs gives the MACCS2 program a broad spectrum of uses at participating DOE facilities. The MACCS2 outputs are converted to an excel spreadsheet to facilitate fast and accurate results for various accident scenarios. Consequence lookup tables can be employed to determine the effects of radiological accident scenarios before they occur. The data is then used by DOE facilities to create regulations and controls to prepare for worst-case scenarios.

Internal magnetic field measurements and high-speed imaging at the Sustained Spheromak Physics Experiment (SSPX) [E. B. Hooper, L. D. Pearlstein, R. H. Bulmer, Nucl. Fusion 39, 863 (1999)] are used to study spheromak formation and field buildup. The measurements are analyzed in the context of a phenomenological model of magnetic helicity based on the topological constraint of minimum helicity in the open flux before reconnecting and linking closed flux. Two stages are analyzed: (1) the initial spheromak formation, i. e. when all flux surfaces are initially open and reconnect to form open and closed flux surfaces, and (2) the stepwise increase of closed flux when operating the gun on a new mode that can apply a train of high-current pulses to the plasma. In the first stage, large kinks in the open flux surfaces are observed in the high-speed images taken shortly after plasma breakdown, and coincide with large magnetic asymmetries recorded in a fixed insertable magnetic probe that spans the flux conserver radius. Closed flux (in the toroidal average sense) appears shortly after this. This stage is also investigated using resistive magnetohydrodynamic simulations. In the second stage, a time lag in response between open and closed flux surfaces after …