Different microbial species are thought to occupy distinct ecological niches, subjecting each species to unique selective constraints, which may leave a recognizable signal in their genomes. Thus, it may be possible to extract insight into the genetic basis of ecological differences among lineages by identifying unusual patterns of substitutions in orthologous gene or protein sequences. We use the ratio of substitutions in slow versus fast-evolving sites (nucleotides in DNA, or amino acids in protein sequence) to quantify deviations from the typical pattern of selective constraint observed across bacterial lineages. We propose that elevated S:F in one branch (an excess of slow-site substitutions) can indicate a functionally-relevant change, due to either positive selection or relaxed evolutionary constraint. In a genome-wide comparative study of gamma-proteobacterial proteins, we find that cell-surface proteins involved with motility and secretion functions often have high S:F ratios, while information-processing genes do not. Change in evolutionary constraints in some species is evidenced by increased S:F ratios within functionally-related sets of genes (e.g., energy production in Pseudomonas fluorescens), while other species apparently evolve mostly by drift (e.g., uniformly elevated S:F across most genes in Buchnera spp.). Overall, S:F reveals several species-specific, protein-level changes with potential functional/ecological importance. As microbial …

Transient processes in radiative transfer have recently become of interest in the modeling of astrophysical phenomena, particularly with regard to the brightness of novae, supernovae, and perhaps even galactic clouds adjacent to quasars. Analytic solutions to a particular class of Marshak wave problems are presented with and without the Marshak (Milne) boundary condition. The choice of boundary condition can have a decisive effect on the coupling of radiative energy to the material energy in the vicinity of a material boundary. The analytic solution obtained can be useful as a tool for calibrating numerical calculation techniques.

The prospect of using computer simulations to calculate radiation-induced defect production and its influence on microstructure evolution and mechanical property changes during prolonged irradiation of nuclear materials has been a beckoning, yet elusive goal for many years. However, the enormous progress achieved in computational physics for calculating reliable, yet tractable interatomic potentials, coupled with vast improvements in computational power have brought this hope to near reality. In order to develop modeling and simulation tools for predicting the irradiation response of nuclear structural materials, models must be implemented and tested across all relevant length and time scales. We discuss the development and implementation of a modeling methodology that consists of the linkage and hierarchical use of ab initio electronic structure calculations, molecular dynamics (MD) simulations, and kinetic Monte Carlo (KMC) simulations. This methodology can describe length and time scales from nanometers to hundreds of microns and from picoseconds to years, respectively. The ideas are demonstrated in two applications. First, we describe simulations that describe the irradiation and subsequent isochronal annealing of Pb, a low melting point fcc metal, and compare the results to experiments. Second, we show how these methods can be used to investigate damage production and freely migrating defect …

Inelastic nuclear scattering of X-rays from the 14.413 keV nuclear resonance of {sup 57}Fe was employed to measure directly the Fe-projected phonon density of states (DOS) in MBE-grown Fe/Cr(00l) superlattices on MgO(001). The Moessbauer-inactive {sup 56}Fe isotope was used in the Fe layers. A 1{angstrom} thick Moessbauer-active {sup 57}Fe-probe layer (95% enriched) was placed at different locations within the Fe layers. This procedure permits one to distinguish phonon density of states at the Fe-Cr-interface from that at the center of the Fe-film. Distinct differences have been observed in the DOS of our samples. The phonon DOS of an amorphous Tb{sub 33}Fe{sub 67} alloy film was found to be a broad and structureless hump, contrary to that of an epitaxial TbFe{sub 2} film, which exhibits characteristic features.

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The electrical resistivities of polycrystalline samples of La, Pr, Nd, and Sm are reported in the temperature range 1.3 to 300 deg K. La exhibits a superconducting transition at 5.8 deg K. The curve for Pr has slope changes at 61 and 95 deg K. The Nd curve shows small jumps at 5 and 20 deg K. Sm shows slope changes at 14 and 106 deg K. (auth)

This work explores the potential reach of the 7 TeV LHC to new colored states in the context of simplified models and addresses the issue of which search regions are necessary to cover an extensive set of event topologies and kinematic regimes. This article demonstrates that if searches are designed to focus on specific regions of phase space, then new physics may be missed if it lies in unexpected corners. Simple multiregion search strategies can be designed to cover all of kinematic possibilities. A set of benchmark models are created that cover the qualitatively different signatures and a benchmark multiregion search strategy is presented that covers these models.

Experiment E769 at Fermilab obtained charm hadroproduction data during the 1987-88 Fixed Target running period with a 250 GeV hadron beam incident on thin target foils of Be, Al, Cu, and W. From an analysis of 25% of the recorded 400M trigger sample we have explored the Feynman x, p{sub t}{sup 2} and the atomic number dependence of charm quark production using samples of D{sup +} and D{sup 0} mesons. 7 refs., 4 figs.

The central goal of the National Ignition Facility (NIF) is demonstration of controlled thermonuclear ignition. The mainline ignition target is a low-Z, single-shell cryogenic capsule designed to have weakly nonlinear Rayleigh-Taylor growth of surface perturbations. Double-shell targets are an alternative design concept that avoids the complexity of cryogenic preparation but has greater physics uncertainties associated with performance-degrading mix. A typical double-shell design involves a high-Z inner capsule filled with DT gas and supported within a low-Z ablator shell. The largest source of uncertainty for this target is the degree of highly evolved nonlinear mix on the inner surface of the high-Z shell. High Atwood numbers and feed-through of strong outer surface perturbation growth to the inner surface promote high levels of instability. The main challenge of the double-shell target designs is controlling the resulting nonlinear mix to levels that allow ignition to occur. Design and analysis of a suite of indirect-drive NIF double-shell targets with hohlraum temperatures of 200 eV and 250 eV are presented. Analysis of these targets includes assessment of two-dimensional radiation asymmetry as well as nonlinear mix. Two-dimensional integrated hohlraum simulations indicate that the x-ray illumination can be adjusted to provide adequate symmetry control in hohlraums specially …

We have studied the intrinsic normal and superconducting properties of the oxypnictide LaFePO. These samples exhibit bulk superconductivity and the evidence suggests that stoichiometric LaFePO is indeed superconducting, in contrast to other reports. We find that superconductivity is independent of the interplane residual resistivity {rho}{sub 0} and discuss the implications of this on the nature of the superconducting order parameter. Finally we find that, unlike T{sub c}, other properties in single-crystal LaFePO including the resistivity and magnetoresistance, can be very sensitive to disorder.

We demonstrate the application code ''rap'' which is part of the ''Overture'' library. A CAD geometry imported from an IGES file is first cleaned up and simplified to suit the needs of mesh generation. Thereafter, the topology of the model is computed and a water-tight surface triangulation is created on the CAD surface. This triangulation is used to speed up the projection of points onto the CAD surface during the generation of overlapping surface grids. From each surface grid, volume grids are grown into the domain using a hyperbolic marching procedure. The final step is to fill any remaining parts of the interior with background meshes.

Arc and glow discharges are defined based on their cathode processes. Arcs are characterized by collective electron emission, which can be stationary with hot cathodes (thermionic arcs), or non-stationary with cold cathodes (cathodic arcs). A brief review on cathodic arc properties serves as the starting point to better understand arcing phenomena in sputtering. Although arcing occurs in both metal and reactive sputtering, it is more of an issue in the reactive case. Arcing occurs if sufficiently high field strength leads to thermal runaway of an electron emission site. The role of insulating layers and surface potential adjustment through current leakage is highlighted. In the situation of magnetron sputtering with ''racetrack'', the need for a model with two spatial dimensions is shown. In many cases, arcing is initiated by breakdown of dielectric layers and inclusions. It is most efficiently prevented if formation and excessive charge-up of dielectric layers and inclusions can be avoided.

Arcing is a well-known, unwanted discharge regime observed on the surface of sputtering targets. The discharge voltage breaks down to less than 50 V while the current jumps to elevated levels. Arcing is unwanted because it prevents uniform deposition and creates particulates. The issue of arcing has been dealt with by target surface conditioning and by using modern power supplies that have arc suppression incorporated. With increasing quality requirements in terms of uniformity of coatings, and absence of particulates, especially for electrochromic and other advanced coatings applications, the issue of arcing warrants a closer examination with the goal to find other, physics-based, and hopefully better approaches of arcing prevention. From a physics point of view, the onset of arcing is nothing else than the transition of the discharge to a cathodic arc mode, which is characterized by the ignition of non-stationary arc spots. Arc spots operate by a sequence of microexplosions, enabling explosive electron emission, as opposed to secondary electron emission. Arc spots and their fragments have a size distribution in the micrometer and sub-micrometer range, and a characteristic time distribution that has components shorter than microseconds. Understanding the ignition conditions of arc spots are of central physical interest. Spot …

It is argued that detection of heavy leptons at the Superconducting Super Collider seems to be very difficult but perhaps not impossible. The feasibility is shown to depend critically upon the ability to identify events with W's decaying hadronically and missing transverse momentum. (LEW)

Multiple current limiting mechanisms exist from the nanometer to millimeter scale in Ag-sheathed (Bi,Pb)-2223 tapes. Recent studies of the zero-field critical current density (J{sub c} (0T, 77K)), the irreversibility field (H*) and the crack microstructure elucidate these properties. We show that H*(77K) can vary significantly over the range {approximately}120-260 mT, independently of J{sub c} (0T, 77K). Cracks, actual or incipient, exist on the sub to several hundred micron scale. Surface magneto optical imaging of whole tapes, correlated to subsequent ultrasonic fracture analysis of. the bare 2223 filaments extracted by dissolving away the Ag shows that even composites having J{sub c} (0T, 77K) values of 60 kA/cm{sup 2} exhibit strong signs of unhealed rolling damage. These combined studies show that today's very best 2223 tapes are still far from full optimization.

The new generation of powerful DSM and SMP cluster computers enables simulations of fluid dynamics at sufficient resolution to compute the complex nonlinear interactions of small-scale turbulent motions with a large-scale driving flow. With a new programming model of hierarchical shared memory multitasking, it is possible to exploit these new systems without disrupting the flow of small and medium-sized jobs that makes their existence possible.

Velocity bunching has been recently proposed as a tool for compressing electron beam pulses in modern high brightness photoinjector sources. This tool is familiar from earlier schemes implemented for bunching dc electron sources, but presents peculiar challenges when applied to high current, low emittance beams from photoinjectors. The main difficulty foreseen is control of emittance oscillations in the beam in this scheme, which can be naturally considered as an extension of the emittance compensation process at moderate energies. This paper presents two scenarios in which velocity bunching, combined with emittance control, is to play a role in nascent projects. The first is termed ballistic bunching, where the changing of relative particle velocities and positions occur in distinct regions, a short high gradient linac, and a drift length. This scenario is discussed in the context of the proposed ORION photoinjector. Simulations are used to explore the relationship between the degree of bunching, and the emittance compensation process. Experimental measurements performed at the UCLA Neptune Laboratory of the surprisingly robust bunching process, as well as accompanying deleterious transverse effects, are presented. An unanticipated mechanism for emittance growth in bends for highly momentum chirped beam was identified and studied in these experiments. The …

Coupled modelling of fluid flow and reactive transport ingeothermal systems is challenging because of reservoir conditions such ashigh temperatures, elevated pressures and sometimes high salinities ofthe formation fluids. Thermal hydrological-chemical (THC) codes, such asFRACHEM and TOUGHREACT, have been developed to evaluate the long-termhydrothermal and chemical evolution of exploited reservoirs. In thisstudy, the two codes were applied to model the same geothermal reservoir,to forecast reservoir evolution using respective thermodynamic andkinetic input data. A recent (unreleased) TOUGHREACT version allows theuse of either an extended Debye-Hu?ckel or Pitzer activity model forcalculating activity coefficients, while FRACHEM was designed to use thePitzer formalism. Comparison of models results indicate that differencesin thermodynamic equilibrium constants, activity coefficients andkinetics models can result in significant differences in predictedmineral precipitation behaviour and reservoir-porosity evolution.Differences in the calculation schemes typically produce less differencein model outputs than differences in input thermodynamic and kineticdata, with model results being particularly sensitive to differences inion-interaction parameters for highsalinity systems.

To better understand the contribution of cosmic ray muons to the CUORICINO background, ten plastic scintillator detectors were installed at the CUORICINO siteand operated during the final 3 months of the experiment. From these measurements, an upper limit of 0.0021 counts/(keV.kg.yr) (95percent c.l.) was obtained on the cosmicray induced background in the neutrinoless double beta decay region of interest. The measurements were also compared to Geant4 simulations.

The new barrel Instrumented Flux Return (IFR) of BABAR detector will be reported here. Limited Streamer Tubes (LSTs) have been chosen to replace the existing RPCs as active elements of the barrel IFR. The layout of the new detector will be discussed: in particular, a cell bigger than the standard one has been used to improve efficiency and reliability. The extruded profile is coated with a resistive layer of graphite having a typical surface resistivity between 0.2 and 0.4 MOhm/square. The tubes are assembled in modules and installed in 12 active layers of each sextant of the IFR detector. R&D studies to choose the final design and Quality Control procedure adopted during the tube production will be briefly discussed. Finally the performances of installed LSTs into 2/3 of IFR after 8 months of operations will be reported.

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Discretization of optimal shape design problems leads to very large nonlinear optimization problems. For attaining maximum computational efficiency, a sequential quadratic programming (SQP) algorithm should achieve superlinear convergence while preserving sparsity and convexity of the resulting quadratic programs. Most classical SQP approaches violate at least one of the requirements. We show that, for a very large class of optimization problems, one can design SQP algorithms that satisfy all these three requirements. The improvements in computational efficiency are demonstrated for a cam design problem.

The boreal summer intraseasonal variability (BSISV) associated with the 30-50 day mode is represented by the co-existence of three components, poleward propagation of convection over the Indian and tropical west Pacific longitudes and eastward propagation along the equator. The hypothesis that the three components influence each other has been investigated using observed OLR, NCEP-NCAR reanalysis, and solutions from an idealized linear model. The null hypothesis is that the three components are mutually independent. Cyclostationary EOF (CsEOF) analysis is applied on filtered OLR to extract the life-cycle of the BSISV. The dominant mode of CsEOF is significantly tied to observed rainfall over the Indian subcontinent. The components of the heating patterns from CsEOF analysis serve as prescribed forcings for the linear model. This allows us to ascertain which heat sources and sinks are instrumental in driving the large-scale monsoon circulation during the BSISV life-cycle. We identify three new findings: (1) the circulation anomalies that develop as a Rossby wave response to suppressed convection over the equatorial Indian Ocean associated with the previous break phase of the BSISV precondition the ocean-atmosphere system in the western Indian Ocean and trigger the next active phase of the BSISV, (2) the development of convection over …

The electronic contribution to friction at semiconductor surfaces was investigated by using a Pt-coated tip with 50nm radius in an atomic force microscope sliding against an n-type GaAs(100) substrate. The GaAs surface was covered by an approximately 1 nm thick oxide layer. Charge accumulation or depletion was induced by the application of forward or reverse bias voltages. We observed a substantial increase in friction force in accumulation (forward bias) with respect to depletion (reverse bias). We propose a model based on the force exerted by the trapped charges that quantitatively explains the experimental observations of excess friction.