Knowledge of the thermophysical properties of materials at extreme pressure and temperature conditions is essential for improving our understanding of many planetary and detonation processes. Significant gaps in what is known about the behavior of materials at high density and high temperature exist, largely due to the limitations and dangers of performing experiments at the necessary extreme conditions. Modeling these systems through the use of equations of state and particle-based simulation methods significantly extends the range of pressures and temperatures that can be safely studied. The reliability of such calculations depends on the accuracy of the models used. Here we present an assessment of the united-atom version of the TraPPE (Transferable Potentials for Phase Equilibria) force field and single-site exp-6 representations for methane, methanol, oxygen, and ammonia at extreme conditions. As shown by Monte Carlo simulations in the isobaric-isothermal ensemble, the TraPPE models, despite being parameterized to the vapor-liquid coexistence curve (i.e. relatively mild conditions), perform remarkably well in the high pressure/high temperature regime. The single-site exp-6 models can fit experimental data in the high pressure/temperature regime very well, but the parameters are less transferable to ambient conditions.

Direct imaging of exoplanets is limited by bright quasi-static speckles in the point spread function (PSF) of the central star. This limitation can be reduced by subtraction of reference PSF images. We have developed an algorithm to construct an optimal reference PSF image from an arbitrary set of reference images. This image is built as a linear combination of all available images and is optimized independently inside multiple subsections of the image to ensure that the absolute minimum residual noise is achieved within each subsection. The algorithm developed is completely general and can be used with many high contrast imaging observing strategies, such as angular differential imaging (ADI), roll subtraction, spectral differential imaging, reference star observations, etc. The performance of the algorithm is demonstrated for ADI data. It is shown that for this type of data the new algorithm provides a gain in sensitivity by up 22 to a factor 3 at small separation over the algorithm previously used.

The importance of microenvironment and context in regulation of tissue-specific genes is finally well established. DNA exposure to, or sequestration from, nucleases can be used to detect differences in higher order chromatin structure in intact cells without disturbing cellular or tissue architecture. To investigate the relationship between chromatin organization and tumor phenotype, we utilized an established 3-D assay where normal and malignant human breast cells can be easily distinguished by the morphology of the structures they make (acinus-like vs tumor-like, respectively). We show that these phenotypes can be distinguished also by sensitivity to AluI digestion where the malignant cells are resistant to digestion relative to non-malignant cells. Reversion of the T4-2 breast cancer cells by either cAMP analogs, or a phospatidylinositol 3-kinase (P13K) inhibitor not only reverted the phenotype, but also the chromatin sensitivity to AluI. By using different cAMP-analogs, we show that the cAMP-induced phenotypic reversion, polarization, and shift in DNA organization act through a cAMP-dependent-protein-kinase A-coupled signaling pathway. Importantly, inhibitory antibody to fibronectin also reverted the malignant phenotype, polarized the acini, and changed chromatin sequestration. These experiments show not only that modifying the tumor microenvironment can alter the organization of tumor cells but also that architecture of the …

In this paper, we present a three-dimensional quasistatic model for high brightness beam dynamics simulation in rf/dc photoinjectors, rf linacs, and similar devices on parallel computers. In this model, electrostatic space-charge forces within a charged particle beam are calculated self-consistently at each time step by solving the three-dimensional Poisson equation in the beam frame and then transforming back to the laboratory frame. When the beam has a large energy spread, it is divided into a number of energy bins or slices so that the space-charge forces are calculated from the contribution of each bin and summed together. Image-charge effects from conducting photocathode are also included efficiently using a shifted-Green function method. For a beam with large aspect ratio, e.g., during emission, an integrated Green function method is used to solve the three-dimensional Poisson equation. Using this model, we studied beam transport in one Linac Coherent Light Sources photoinjector design through the first traveling wave linac with initial misalignment with respect to the accelerating axis.

Solid deuterium-tritium (D-T) fuel layers for inertial confinement fusion experiments were formed inside of a 2 mm diameter beryllium shell and were characterized using phase-contrast enhanced x-ray imaging. The solid D-T surface roughness is found to be 0.4 {micro}m for modes 7-128 at 1.5 K below the melting temperature. The layer roughness is found to increase with decreasing temperature, in agreement with previous visible light characterization studies. However, phase-contrast enhanced x-ray imaging provides a more robust surface roughness measurement than visible light methods. The new x-ray imaging results demonstrate clearly that the surface roughness decreases with time for solid D-T layers held at 1.5 K below the melting temperature.

We discuss new methods of measuring and interpreting the forbidden-to-intercombination line ratios of helium-like triplets in the X-ray spectra of O-type stars, including accounting for the spatial distribution of the X-ray emitting plasma and using the detailed photospheric UV spectrum. Measurements are made for four O stars using archival Chandra HETGS data. We assume an X-ray emitting plasma spatially distributed in the wind above some minimum radius R{sub 0}. We find minimum radii of formation typically in the range of 1.25 < R{sub 0}/R{sub *} < 1.67, which is consistent with results obtained independently from line profile fits. We find no evidence for anomalously low f/i ratios and we do not require the existence of X-ray emitting plasmas at radii that are too small to generate sufficiently strong shocks.

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We report here a comparative analysis of the genome sequence of Methanosarcina barkeri with those of Methanosarcina acetivorans and Methanosarcina mazei. All three genomes share a conserved double origin of replication and many gene clusters. M. barkeri is distinguished by having an organization that is well conserved with respect to the other Methanosarcinae in the region proximal to the origin of replication with interspecies gene similarities as high as 95%. However it is disordered and marked by increased transposase frequency and decreased gene synteny and gene density in the proximal semi-genome. Of the 3680 open reading frames in M. barkeri, 678 had paralogs with better than 80% similarity to both M. acetivorans and M. mazei while 128 nonhypothetical orfs were unique (non-paralogous) amongst these species including a complete formate dehydrogenase operon, two genes required for N-acetylmuramic acid synthesis, a 14 gene gas vesicle cluster and a bacterial P450-specific ferredoxin reductase cluster not previously observed or characterized in this genus. A cryptic 36 kbp plasmid sequence was detected in M. barkeri that contains an orc1 gene flanked by a presumptive origin of replication consisting of 38 tandem repeats of a 143 nt motif. Three-way comparison of these genomes reveals differing mechanisms …

The analysis of surface heat fluxes and sounding profiles from SHEBA indicated possible significant effects of subsidence on the structure of stably-stratified ABLs (Mirocha et al. 2005). In this study the influence of the large-scale subsidence rate on the stably stratified atmospheric boundary layer (ABL) over the Arctic Ocean during clear sky, winter conditions is investigated using a large-eddy simulation model. Simulations are conducted while varying the subsidence rate between 0, 0.001 and 0.002 ms{sup -1}, and the resulting quasi-equilibrium ABL structure and evolution are examined. Simulations conducted without subsidence yield ABLs that are deeper, more strongly mixed, and cool much more rapidly than were observed. The addition of a small subsidence rate significantly improves agreement between the simulations and observations regarding the ABL height, potential temperature profiles and bulk heating rates. Subsidence likewise alters the shapes of the surface-layer flux, stress and shear profiles, resulting in increased vertical transport of heat while decreasing vertical momentum transport. A brief discussion of the relevance of these results to parameterization of the stable ABL under subsiding conditions in large-scale numerical weather and climate prediction models is presented.

Time-of-flight secondary ion mass spectrometry (ToF-SIMS) is employed to examine specific features observed on a polycrystalline depleted uranium sample after exposure to high purity D{sub 2} gas. The ToF-SIMS investigation, being the first of its kind on uranium, investigates a site where the deuterated form of uranium hydride (UD{sub 3}) is clearly observed to have broken through the thin, air-formed oxide. Density functional theory calculations have been performed, which confirm the stability of, and also assign structural geometries to, the various uranium containing fragments observed with SIMS. An inclusion site was also investigated using ToF-SIMS, and these data suggest that the edges of such inclusions exhibit increased D ion, and hence H ion, diffusion when compared to the surrounding surface oxide. These results offer support to the previously published hypotheses that inclusion sites on uranium surfaces exhibit an increased probability to form hydride sites under H{sub 2} exposure.

The following article is an edited transcript based on the Turnbull Lecture given by Eugene E. Haller at the 2005 Materials Research Society Fall Meeting in Boston on November 29, 2005. The David Turnbull Lectureship is awarded to recognize the career of a scientist who has made outstanding contributions to understanding materials phenomena and properties through research, writing, and lecturing, as exemplified by the life work of David Turnbull. Haller was named the 2005 David Turnbull Lecturer for his 'pioneering achievements and leadership in establishing the field of isotopically engineered semiconductors; for outstanding contributions to materials growth, doping and diffusion; and for excellence in lecturing, writing, and fostering international collaborations'. The scientific interest, increased availability, and technological promise of highly enriched isotopes have led to a sharp rise in the number of experimental and theoretical studies with isotopically controlled semiconductor crystals. This article reviews results obtained with isotopically controlled semiconductor bulk and thin-film heterostructures. Isotopic composition affects several properties such as phonon energies, band structure, and lattice constant in subtle, but, for their physical understanding, significant ways. Large isotope-related effects are observed for thermal conductivity in local vibrational modes of impurities and after neutron transmutation doping. Spectacularly sharp photoluminescence lines …

An atmospheric chemistry-transport model is used to assess the impacts of sea-spray chemistry on the particle composition in and downwind of a coastal city--Vancouver, British Columbia. Reactions in/on sea-spray affect the entire particle ensemble and particularly the size distribution of particle nitrate. Urban air quality, and particularly airborne particles, is a major concern in terms of human health impacts. Sea-spray is known to be a major component of the particle ensemble at coastal sites yet relatively few air quality models include the interaction of gases with sea-spray and the fate of the particles produced. Sea-spray is not an inert addition to the particle ensemble because heterogeneous chemistry in/on sea-spray droplets changes the droplets composition and the particle size distribution, which impacts deposition and the ion balance in different particle size fractions. It is shown that the ISOPART model is capable of simulating gas and particle concentrations in the coastal metropolis of Vancouver and the surrounding valley. It is also demonstrated that to accurately simulate ambient concentrations of particles and reactive/soluble gases in a coastal valley it is absolutely critical to include heterogeneous chemistry in/on sea-spray. Partitioning of total particle-NO{sub 3}{sup -} between sea-spray and NH{sub 4}NO{sub 3} is highly sensitive …

In this chapter we review numerous diagnostics capable of measurements at or near the first wall, many of which contribute information useful for safe operation of a tokamak. There are sections discussing infrared cameras, visible and VUV cameras, pressure gauges and RGAs, Langmuir probes, thermocouples, and erosion and deposition measurements by insertable probes and quartz microbalance. Also discussed are dust measurements by electrostatic detectors, laser scattering, visible and IR cameras, and manual collection of samples after machine opening. In each case the diagnostic is discussed with a view toward application to a burning plasma machine such as ITER.

Control Banding (CB) strategies offer simplified solutions for controlling worker exposures to constituents often encountered in the workplace. The original CB model was developed within the pharmaceutical industry; however, the modern movement involves models developed for non-experts to input hazard and exposure potential information for bulk chemical processes, receiving control advice as a result. The CB approach utilizes these models for the dissemination of qualitative and semi-quantitative risk assessment tools being developed to complement the traditional industrial hygiene model of air sampling and analysis. It is being applied and tested in small and medium size enterprises (SMEs) within developed countries and industrially developing countries; however, large enterprises (LEs) have also incorporated these strategies within chemical safety programs. Existing research of the components of the most available CB model, the Control of Substances Hazardous to Health (COSHH) Essentials, has shown that exposure bands do not always provide adequate margins of safety, that there is a high rate of under-control errors, that it works better with dusts than with vapors, that there is an inherent inaccuracy in estimating variability, and that when taken together the outcomes of this model may lead to potentially inappropriate workplace confidence in chemical exposure reduction in some …

OpenMP [2] is an important API for shared memory programming, combining shared memory's potential for performance with a simple programming interface. Unfortunately, OpenMP lacks a critical tool for demonstrating whether programs are correct: a formal memory model. Instead, the current official definition of the OpenMP memory model (the OpenMP 2.5 specification [2]) is in terms of informal prose. As a result, it is impossible to verify OpenMP applications formally since the prose does not provide a formal consistency model that precisely describes how reads and writes on different threads interact. We expand on our previous work that focused on the formal verification of OpenMP programs through a formal memory model [?]. As in that work, our formalization, which is derived from the existing prose model [2], provides a two-step process to verify whether an observed OpenMP execution is conformant. This paper extends the model to cover the entire specification. In addition to this formalization, our contributions include a discussion of ambiguities in the current prose-based memory model description. Although our formal model may not capture the current informal memory model perfectly, in part due to these ambiguities, our model reflects our understanding of the informal model's intent. We conclude with …

The world is at a turning point, moving away from the Cold War nuclear legacy towards a future global nuclear enterprise; and this presents a transformational challenge for nuclear materials management. Achieving safety and security during this transition is complicated by the diversified spectrum of threat 'players' that has greatly impacted nonproliferation, counterterrorism, and homeland security requirements. Rogue states and non-state actors no longer need self-contained national nuclear expertise, materials, and equipment due to availability from various sources in the nuclear market, thereby reducing the time, effort and cost for acquiring a nuclear weapon (i.e., manifestations of latency). The terrorist threat has changed the nature of military and national security requirements to protect these materials. An Integrated Global Nuclear Materials Management (IGNMM) approach would address the existing legacy nuclear materials and the evolution towards a nuclear energy future, while strengthening a regime to prevent nuclear weapon proliferation. In this paper, some preliminary concepts and studies of IGNMM will be presented. A systematic analysis of nuclear materials, activities, and controls can lead to a tractable, integrated global nuclear materials management architecture that can help remediate the past and manage the future. A systems approach is best suited to achieve multi-dimensional and …

Solving Schroedinger equation in quantum mechanics presents a challenging task in numerical methods due to the high order behavior and high dimension characteristics in the wave functions, in addition to the highly coupled nature between wave functions. This work introduces orbital and polynomial enrichment functions to the partition of unity for solution of Schroedinger equation under the framework of HP-Clouds. An intrinsic enrichment of orbital function and extrinsic enrichment of monomial functions are proposed. Due to the employment of higher order basis functions, a higher order stabilized conforming nodal integration is developed. The proposed methods are implemented using the density functional theory for solution of Schroedinger equation. Analysis of several single and multi-electron/nucleus structures demonstrates the effectiveness of the proposed method.

The thesis of this extended abstract is simple. High productivity comes from high level infrastructures. To measure this, we introduce a methodology that goes beyond the tradition of timing software in serial and tuned parallel modes. We perform a classroom productivity study involving 29 students who have written a homework exercise in a low level language (MPI message passing) and a high level language (Star-P with MATLAB client). Our conclusions indicate what perhaps should be of little surprise: (1) the high level language is always far easier on the students than the low level language. (2) The early versions of the high level language perform inadequately compared to the tuned low level language, but later versions substantially catch up. Asymptotically, the analogy must hold that message passing is to high level language parallel programming as assembler is to high level environments such as MATLAB, Mathematica, Maple, or even Python. We follow the Kepner method that correctly realizes that traditional speedup numbers without some discussion of the human cost of reaching these numbers can fail to reflect the true human productivity cost of high performance computing. Traditional data compares low level message passing with serial computation. With the benefit of a …

This paper accompanies a poster that is being presented atthe SciDAC 2006 meeting in Denver, CO. This project focuses on leveragingscientific visualization and analytics software technology as an enablingtechnology for increasing scientific productivity and insight. Advancesincomputational technology have resultedin an "information big bang,"which in turn has createda significant data understanding challenge. Thischallenge is widely acknowledged to be one of the primary bottlenecks incontemporary science. The vision for our Center is to respond directly tothat challenge by adapting, extending, creating when necessary anddeploying visualization and data understanding technologies for ourscience stakeholders. Using an organizational model as a Visualizationand Analytics Center for Enabling Technologies (VACET), we are wellpositioned to be responsive to the needs of a diverse set of scientificstakeholders in a coordinated fashion using a range of visualization,mathematics, statistics, computer and computational science and datamanagement technologies.

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These proceedings contain papers prepared for the 28th Seismic Research Review: Ground-Based Nuclear Explosion Monitoring Technologies, held 19-21 September, 2006 in Orlando, Florida. These papers represent the combined research related to ground-based nuclear explosion monitoring funded by the National Nuclear Security Administration (NNSA), Air Force Technical Applications Center (AFTAC), Air Force Research Laboratory (AFRL), US Army Space and Missile Defense Command, Comprehensive Nuclear-Test-Ban Treaty Organization (CTBTO), and other invited sponsors. The scientific objectives of the research are to improve the United States capability to detect, locate, and identify nuclear explosions. The purpose of the meeting is to provide the sponsoring agencies, as well as potential users, an opportunity to review research accomplished during the preceding year and to discuss areas of investigation for the coming year. For the researchers, it provides a forum for the exchange of scientific information toward achieving program goals, and an opportunity to discuss results and future plans. Paper topics include: seismic regionalization and calibration; detection and location of sources; wave propagation from source to receiver; the nature of seismic sources, including mining practices; hydroacoustic, infrasound, and radionuclide methods; on-site inspection; and data processing.

In the quest for precision cosmology, one must ensure that the cosmology is accurate as well. We discuss figures of merit for determining from observations whether the dark energy is a cosmological constant or dynamical, with special attention to the best determined equation of state value, at the ``pivot'' or decorrelation redshift. We show this is not necessarily the best lever on testing consistency with the cosmological constant, and moreover is subject to bias. The standard parametrization of w(a)=w_0+w_a(1-a) by contrast is quite robust, as tested by extensions to higher order parametrizations and modified gravity. Combination of complementary probes gives strong immunization against inaccurate, but precise, cosmology.

Common-plane (CP) algorithm is widely used in Discrete Element Method (DEM) to model contact forces between interacting particles or blocks. A new simple contact detection algorithm is proposed to model contacts in FE/FD methods which is similar to the CP algorithm. The CP is defined as a plane separating interacting faces of FE/FD mesh instead of blocks or particles in the original CP method. The method does not require iterations. It is very robust and easy to implement both in 2D and 3D case.

We investigate jet formation in black-hole systems using 3-D General Relativistic Particle-In-Cell (GRPIC) and 3-D GRMHD simulations. GRPIC simulations, which allow charge separations in a collisionless plasma, do not need to invoke the frozen condition as in GRMHD simulations. 3-D GRPIC simulations show that jets are launched from Kerr black holes as in 3-D GRMHD simulations, but jet formation in the two cases may not be identical. Comparative study of black hole systems with GRPIC and GRMHD simulations with the inclusion of radiate transfer will further clarify the mechanisms that drive the evolution of disk-jet systems.