Computational science research components were vital parts of the SciDAC-1 accelerator project and are continuing to play a critical role in newly-funded SciDAC-2 accelerator project, the Community Petascale Project for Accelerator Science and Simulation (ComPASS). Recent advances and achievements in the area of computational science research in support of petascale electromagnetic modeling for accelerator design analysis are presented, which include shape determination of superconducting RF cavities, mesh-based multilevel preconditioner in solving highly-indefinite linear systems, moving window using h- or p- refinement for time-domain short-range wakefield calculations, and improved scalable application I/O.

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The Linac Coherent Light Source (LCLS) is a SASE x-ray Free-Electron Laser (FEL) project under construction at SLAC [1]. The injector section, from drive-laser and RF photocathode gun through the first bunch compressor, was commissioned in the spring and summer of 2007. The second phase of commissioning, including the second bunch compressor and various main linac modifications, was completed in January through August of 2008. We report here on experience gained during this second phase of machine commissioning, including the injector, the first and second bunch compressor stages, the linac up to 14 GeV, and beam stability measurements. The final commissioning phase, including the undulator and the long transport line from the linac, is set to begin in December 2008, with first light expected in July 2009.

A recent article in which John Searle claims to refute dualism is examined from a scientific perspective. John Searle begins his recent article 'Dualism Revisited' by stating his belief that the philosophical problem of consciousness has a scientific solution. He then claims to refute dualism. It is therefore appropriate to examine his arguments against dualism from a scientific perspective. Scientific physical theories contain two kinds of descriptions: (1) Descriptions of our empirical findings, expressed in an every-day language that allows us communicate to each other our sensory experiences pertaining to what we have done and what we have learned; and (2) Descriptions of a theoretical model, expressed in a mathematical language that allows us to communicate to each other certain ideas that exist in our mathematical imaginations, and that are believed to represent, within our streams of consciousness, certain aspects of reality that we deem to exist independently of their being perceived by any human observer. These two parts of our scientific description correspond to the two aspects of our general contemporary dualistic understanding of the total reality in which we are imbedded, namely the empirical-mental aspect and the theoretical-physical aspect. The duality question is whether this general dualistic understanding …

We present a preliminary analysis of the decays B{sup 0} {yields} K*{sup 0}{gamma} and B{sup +} {yields} K*{sup +}{gamma} using a sample of 383 million B{bar B} events collected with the BABAR detector at the PEP-II asymmetric energy B factory. We measure the branching fractions {Beta}(B{sup 0} {yields} K*{sup 0}{gamma}) = (4.58 {+-} 0.10 {+-} 0.16) x 10{sup -5} and {Beta}(B{sup +} {yields} K*{sup +}{gamma}) = (4.73 {+-} 0.15 {+-} 0.17) x 10{sup -5}. We measure the direct CP asymmetry to be -0.043 < {Alpha}(B {yields} K*{gamma}) < 0.025 and the isospin asymmetry to be -0.021 < {Delta}{sub 0-} < 0.079, where the limits are determined at the 90% confidence interval and include both the statistical and systematic uncertainties.

Tritium movement and accumulation in the Next Generation Nuclear Plant (NGNP) employing either a high-temperature electrolysis (HTE) process or a thermochemical water-splitting Sulfur-Iodine (SI) process to produce hydrogen is estimated by a numerical code, THYTAN, as a function of design, operational and material parameters. Estimated tritium concentrations in the hydrogen product and in the process chemicals of the hydrogen plant using the HTE process are slightly higher than the limit in drinking water defined by the U.S. Environmental Protection Agency (EPA) and in effluent at the boundary of an unrestricted area defined by the U.S. Nuclear Regulatory Commission (NRC), respectively. Estimated tritium concentrations in the NGNP using the SI hydrogen production process are significantly higher, and are largely affected by undetermined parameters (i.e., tritium permeability of heat exchanger materials, hydrogen concentration in the helium energy transport fluids, equilibrium constant of the tritium isotope exchange reaction between HT and H{sub 2}SO{sub 4}). These parameters should be measured or estimated in the near future, as should the tritium generation and release rate from the NGNP nuclear reactor core. Decreasing the tritium permeation rate between the primary and secondary heat transport circuits is an effective measure to decrease the tritium concentrations in the …

This Report describes Molecular & Cellular Bioenergetics.

An optical spectroscopy approach is demonstrated allowing for critical parameters during RF ablation of cardiac tissue to be evaluated in real time. The method is based on incorporating in a typical ablation catheter transmitting and receiving fibers that terminate at the tip of the catheter. By analyzing the spectral characteristics of the NIR diffusely reflected light, information is obtained on such parameters as, catheter-tissue proximity, lesion formation, depth of penetration of the lesion, formation of char during the ablation, formation of coagulum around the ablation site, differentiation of ablated from healthy tissue, and recognition of micro-bubble formation in the tissue.

Bulk chemical and oxygen, magnesium and silicon isotopic compositions were measured for each of 17 Types A and B refractory inclusions from CV3 chondrites. After bulk chemical compositions were corrected for non-representative sampling in the laboratory, the Mg and Si isotopic compositions of each inclusion were used to calculate its original chemical composition assuming that the heavy-isotope enrichments of these elements are due to Rayleigh fractionation that accompanied their evaporation from CMAS liquids. The resulting pre-evaporation chemical compositions are consistent with those predicted by equilibrium thermodynamic calculations for high-temperature nebular condensates but only if different inclusions condensed from nebular regions that ranged in total pressure from 10{sup -6} to 10{sup -1} bar, regardless of whether they formed in a system of solar composition or in one enriched in OC dust relative to gas by a factor of ten relative to solar composition. This is similar to the range of total pressures predicted by dynamic models of the solar nebula for regions whose temperatures are in the range of silicate condensation temperatures. Alternatively, if departure from equilibrium condensation and/or non-representative sampling of condensates in the nebula occurred, the inferred range of total pressure could be smaller. Simple kinetic modeling of evaporation …

The computational challenge of predicting shock-turbulence interactions stems from the fundamentally different physics at play. Shock waves are microscopically thin regions wherein flow properties change rapidly over a distance roughly equal to the molecular mean free path; hence, they are essentially strong discontinuities in the flow field. Turbulence, on the other hand, is a chaotic phenomenon with broadband spatial and temporal scales of motion. Most shock-capturing methods rely on strong numerical dissipation to artificially smooth the discontinuity, such that it can be resolved on the computational grid. Unfortunately, the artificial dissipation necessary for capturing shocks has a deleterious effect on turbulence. An additional problem is the fact that shock-capturing schemes are typically based on one-dimensional Riemann solutions that are not strictly valid in multiple dimensions. This can lead to anisotropy errors and grid-seeded perturbations. Other complications arising from upwinding, flux limiting, operator splitting etc., can seriously degrade performance and generate significant errors, especially in multiple dimensions. The purpose of this work is to design improved algorithms, capable of capturing both shocks and turbulence, which also scale to tens of thousands of processors. We have evaluated two new hydrodynamic algorithms, in relation to the widely used WENO method, on a suite …

This paper compares various approaches to stability analysis of linear (and of linearized) circuits. In particular it clarifies the limits of application of a widely used but generally erroneous method. It also compares the criteria formulated in terms of impedances versus those expressed in S-parameters.

We report measurements of hadronic final states produced in e{sup +}e{sup -} annihilations from the BABAR and Belle experiments. In particular, we present cross sections measured in several different processes, including two-photon physics, Initial-State Radiation, and exclusive hadron productions at center-of-mass energies near 10.58 GeV. Results are compared with theoretical predictions.

The equilibrium structure of embedded nanocrystals formed from strongly segregating binary-alloys is considered within a simple thermodynamic model. The model identifies two dimensionlessinterface energies that dictate the structure, and allows prediction of the stable structure for anychoice of these parameters. The resulting structure map includes three distinct nanocrystal mor-phologies: core/shell, lobe/lobe, and completely separated spheres.

In the mammary gland, epithelial cells are embedded in a 'soft' environment and become functionally differentiated in culture when exposed to a laminin-rich extracellular matrix gel. Here, we define the processes by which mammary epithelial cells integrate biochemical and mechanical extracellular cues to maintain their differentiated phenotype. We used single cells cultured on top of gels in conditions permissive for {beta}-casein expression using atomic force microscopy to measure the elasticity of the cells and their underlying substrata. We found that maintenance of {beta}-casein expression required both laminin signalling and a 'soft' extracellular matrix, as is the case in normal tissues in vivo, and biomimetic intracellular elasticity, as is the case in primary mammary epithelial organoids. Conversely, two hallmarks of breast cancer development, stiffening of the extracellular matrix and loss of laminin signalling, led to the loss of {beta}-casein expression and non-biomimetic intracellular elasticity. Our data indicate that tissue-specific gene expression is controlled by both the tissues unique biochemical milieu and mechanical properties, processes involved in maintenance of tissue integrity and protection against tumorigenesis.

We present updated measurements of time-dependent CP asymmetries in fully reconstructed neutral B decays containing a charmonium meson. The measurements reported here use a data sample of (465 {+-} 5) x 10{sup 6} {Upsilon}(4S) {yields} B{bar B} decays collected with the BABAR detector at the PEP-II B factory. The time-dependent CP asymmetry parameters measured from J/{psi}K{sub S}{sup 0}, J/{psi}K{sub L}{sup 0}, {psi}(2S)K{sub S}{sup 0}, {chi}{sub c1}K{sub S}{sup 0}, {eta}{sub c}K{sub S}{sup 0}, and J/{psi}K*{sup 0} decays are: (1) C{sub f} = 0.026 {+-} 0.020(stat) {+-} 0.016(syst); and (2) S{sub f} = 0.691 {+-} 0.029(stat) {+-} 0.014(syst).

Scanning tunneling microscopy (STM) and x-ray absorption spectroscopy (XAS) have been used to study the structures produced by water on Ru(0001) at temperatures above 140 K. It was found that while undissociated water layers are metastable below 140 K, heating above this temperature produces drastic transformations whereby a fraction of the water molecules partially dissociate and form mixed H{sub 2}O-OH structures. XPS and XAS revealed the presence of hydroxyl groups with their O-H bond essentially parallel to the surface. STM images show that the mixed H{sub 2}O-OH structures consist of long narrow stripes aligned with the three crystallographic directions perpendicular to the close-packed atomic rows of the Ru(0001) substrate. The internal structure of the stripes is a honeycomb network of H-bonded water and hydroxyl species. We found that the metastable low temperature molecular phase can also be converted to a mixed H{sub 2}O-OH phase through excitation by the tunneling electrons when their energy is 0.5 eV or higher above the Fermi level. Structural models based on the STM images were used for Density Functional Theory optimizations of the stripe geometry. The optimized geometry was then utilized to calculate STM images for comparison with the experiment.

Temporary trapping of atomic xenon in functionalized cryptophane cages makes the high sensitivity of hyperpolarized (hp) 129Xe available for highly specific NMR detection of biomolecules like proteins in solution. Here, we study the signal transfer onto a reservoir of unbound hp xenon by gating the residence time of the nuclei in the cage through the temperature-dependent exchange rate. Temperature changes were detectable immediately as an altered reservoir signal and yielded a sensitivity of 0.6 K. The temperature response is adjustable with lower concentrations of caged xenon providing more sensitivity at higher temperatures and allows ultra-sensitive detection of such molecular cages at 310 K. Functionalized cryptophane could be detected at concentrations as low as 10nM which corresponds to a 4000-fold sensitivity enhancement compared to conventional detection. This sensitivity makes hp-NMR capable of detecting such constructs in concentrations far belowthe detection limit by UV-visible light absorbance.

Jet quenching measurements using leading particles and their correlations suffer from known biases, which can be removed via direct reconstruction of jets in central heavy ion collisions. In this talk, we discuss several modern jet reconstruction algorithms and background subtraction techniques that are appropriate to heavy ion collisions.

X-ray absorption spectroscopy (XAS) and magnetic circular dichroism (MCD) at the V L2,3 and C and N K edges reveal bonding/backbonding interactions in films of the 400 K magnetic semiconductor V[TCNE]x~;;2. In V spectra, dxy-like orbitals are modeled assuming V2+ in an octahedral ligand field, while dz2 and dx2-y2 orbitals involved in strong covalent bonding cannot be modeled by atomic calculations. C and N MCD, and differences in XAS from neutral TCNE molecules, reveal spin-polarized molecular orbitals in V[TCNE]x~;;2 associated with backbonding interactions that yield its novel properties.

Experiments involving the interaction of a high-power laser beam with metal targets demonstrate that combustion plays an important role. This process depends on reactions within an oxide layer, together with oxygenation and removal of this layer by the wind. We present an analytical model of laser-induced combustion. The model predicts the threshold for initiation of combustion, the growth of the combustion layer with time, and the threshold for self-supported combustion. Solutions are compared with detailed numerical modeling as benchmarked by laboratory experiments.

The authors measure the time-dependent CP asymmetry in B{sup 0} {yields} K{sub S}{sup 0}{pi}{sup 0}{gamma} decays for two regions of K{sub S}{sup 0}-{pi}{sup 0} invariant mass, m(K{sub S}{sup 0}{pi}{sup 0}), using the final BABAR data set of 467 x 10{sup 6} B{bar B} pairs collected at the PEP-II e{sup +}e{sup -} collider at SLAC. They find 339 {+-} 24 B{sup 0} {yields} K*{sup 0}{gamma} candidates and measure S{sub K*{gamma}} = -0.03 {+-} 0.29 {+-} 0.03 and C{sub K*{gamma}} = -0.14 {+-} 0.16 {+-} 0.03. In the range 1.1 < m(K{sub S}{sup 0}{pi}{sup 0}) < 1.8 GeV/c{sup 2} they find 133 {+-} 20 B{sup 0} {yields} K{sub S}{sup 0}{pi}{sup 0}{gamma} candidates and measure S{sub K{sub S}{sup 0}{pi}{sup 0}{gamma}} = -0.78 {+-} 0.59 {+-} 0.09 and C{sub K{sub S}{sup 0}{pi}{sup 0}{gamma}} = -0.36 {+-} 0.33 {+-} 0.04. The uncertainties are statistical and systematic, respectively.

We report on the L-band RF power distribution system (PDS) developed at SLAC for Fermilab's NML superconducting test accelerator facility. The makeup of the system, which allows tailoring of the power distribution to cavities by pairs, is briefly described. Cold test measurements of the system and the results of high power processing are presented. We also investigate the feasibility of eliminating the expensive, lossy circulators from the PDS by pair-feeding cavities through custom 3-dB hybrids. A computational model is used to simulate the impact on cavity field stability due to the reduced cavity-to-cavity isolation.

Demand response (DR) is an emerging research field and an effective tool that improves grid reliability and prevents the price of electricity from rising, especially in deregulated markets. This paper introduces the definition of DR and Automated Demand Response (Auto-DR). It describes the Auto-DR technology utilized at a commercial building in the summer of 2006 and the methodologies to evaluate associated demand savings. On the basis of field tests in a large office building, Auto-DR is proven to be a reliable and credible resource that ensures a stable and economical operation of the power grid.

Molybdenum-containing amorphous carbon (a-C:Mo) thin films were prepared using a dual-cathode filtered cathodic arc plasma source with a molybdenum and a carbon (graphite) cathode. The Mo content in the films was controlled by varying the deposition pulse ratio of Mo and C. Film sheet resistance was measured in situ at process temperature, which was close to room temperature, as well as ex situ as a function of temperature (300-515 K) in ambient air. Film resistivity and electrical activation energy were derived for different Mo and C ratios and substrate bias. Film thickness was in the range 8-28 nm. Film resistivity varied from 3.55x10-4 Omega m to 2.27x10-6 Omega m when the Mo/C pulse ratio was increased from 0.05 to 0.4, with no substrate bias applied. With carbon-selective bias, the film resistivity was in the range of 4.59x10-2 and 4.05 Omega m at a Mo/C pulse ratio of 0.05. The electrical activation energy decreased from 3.80x10-2 to 3.36x10-4 eV when the Mo/C pulse ratio was increased in the absence of bias, and from 0.19 to 0.14 eV for carbon-selective bias conditions. The resistivity of the film shifts systematically with the amounts of Mo and upon application of substrate bias voltage. The …