National Center for Supercomputing Applications

BACKGROUND: The number of prokaryotic genome sequences becoming available is growing steadily and is growing faster than our ability to accurately annotate them. DESCRIPTION: We describe a fully automated service for annotating bacterial and archaeal genomes. The service identifies protein-encoding, rRNA and tRNA genes, assigns functions to the genes, predicts which subsystems are represented in the genome, uses this information to reconstruct the metabolic network and makes the output easily downloadable for the user. In addition, the annotated genome can be browsed in an environment that supports comparative analysis with the annotated genomes maintained in the SEED environment. The service normally makes the annotated genome available within 12-24 hours of submission, but ultimately the quality of such a service will be judged in terms of accuracy, consistency, and completeness of the produced annotations. We summarize our attempts to address these issues and discuss plans for incrementally enhancing the service. CONCLUSION: By providing accurate, rapid annotation freely to the community we have created an important community resource. The service has now been utilized by over 120 external users annotating over 350 distinct genomes.

NAMDis a molecular dynamics program designed for high-performance simulations of very large biological objects on CPU- and GPU-based architectures. NAMD offers scalable performance on petascale parallel supercomputers consisting of hundreds of thousands of cores, as well as on inexpensive commodity clusters commonly found in academic environments. It is written in C++ and leans on Charm++ parallel objects for optimal performance on low-latency architectures. NAMD is a versatile, multipurpose code that gathers state-of-the-art algorithms to carry out simulations in apt thermodynamic ensembles, using the widely popular CHARMM, AMBER, OPLS, and GROMOS biomolecular force fields. Here, we review the main features of NAMD that allow both equilibrium and enhanced-sampling molecular dynamics simulations with numerical efficiency. We describe the underlying concepts utilized by NAMD and their implementation, most notably for handling long-range electrostatics; controlling the temperature, pressure, and pH; applying external potentials on tailored grids; leveraging massively parallel resources in multiple-copy simulations; and hybrid quantum-mechanical/molecular-mechanical descriptions. We detail the variety of options offered by NAMD for enhanced-sampling simulations aimed at determining free-energy differences of either alchemical or geometrical transformations and outline their applicability to specific problems. Last, we discuss the roadmap for the development of NAMD and our current efforts toward achieving optimal performance on GPU-based architectures, for pushing back the limitations that have prevented biologically realistic billion-atom objects to be fruitfully simulated, and for making large-scale simulations less expensive and easier to set up, run, and analyze. NAMD is distributed free of charge with its source code at www.ks.uiuc.edu.

One of Feynman's early applications of path integrals was to superfluid $^{4}\mathrm{He}$. He showed that the thermodynamic properties of Bose systems are exactly equivalent to those of a peculiar type of interacting classical "ring polymer." Using this mapping, one can generalize Monte Carlo simulation techniques commonly used for classical systems to simulate boson systems. In this review, the author introduces this picture of a boson superfluid and shows how superfluidity and Bose condensation manifest themselves. He shows the excellent agreement between simulations and experimental measurements on liquid and solid helium for such quantities as pair correlations, the superfluid density, the energy, and the momentum distribution. Major aspects of computational techniques developed for a boson superfluid are discussed: the construction of more accurate approximate density matrices to reduce the number of points on the path integral, sampling techniques to move through the space of exchanges and paths quickly, and the construction of estimators for various properties such as the energy, the momentum distribution, the superfluid density, and the exchange frequency in a quantum crystal. Finally the path-integral Monte Carlo method is compared to other quantum Monte Carlo methods.

We compare the results of Eulerian hydrodynamic simulations of cluster formation against virial scaling relations between four bulk quantities: the cluster mass, the dark matter velocity dispersion, the gas temperature, and the cluster luminosity. The comparison is made for a large number of clusters at a range of redshifts in three different cosmological models (cold plus hot dark matter, cold dark matter, and open cold dark matter). We find that the analytic formulae provide a good description of the relations between three of the four numerical quantities. The fourth (luminosity) also agrees once we introduce a procedure to correct for the fixed numerical resolution. We also compute the normalizations for the virial relations and compare extensively to the existing literature, finding remarkably good agreement. The Press-Schechter prescription is calibrated with the simulations, again finding results consistent with other authors. We also examine related issues such as the size of the scatter in the virial relations, the effect of metallicity with a fixed passband, and the structure of the halos. All of this is done in order to establish a firm groundwork for the use of clusters as cosmological probes. Implications for the models are briefly discussed.

Abstract We present the first Event Horizon Telescope (EHT) observations of Sagittarius A* (Sgr A*), the Galactic center source associated with a supermassive black hole. These observations were conducted in 2017 using a global interferometric array of eight telescopes operating at a wavelength of λ = 1.3 mm. The EHT data resolve a compact emission region with intrahour variability. A variety of imaging and modeling analyses all support an image that is dominated by a bright, thick ring with a diameter of 51.8 ± 2.3 μ as (68% credible interval). The ring has modest azimuthal brightness asymmetry and a comparatively dim interior. Using a large suite of numerical simulations, we demonstrate that the EHT images of Sgr A* are consistent with the expected appearance of a Kerr black hole with mass ∼4 × 10 6 M ⊙ , which is inferred to exist at this location based on previous infrared observations of individual stellar orbits, as well as maser proper-motion studies. Our model comparisons disfavor scenarios where the black hole is viewed at high inclination ( i > 50°), as well as nonspinning black holes and those with retrograde accretion disks. Our results provide direct evidence for the presence of a supermassive black hole at the center of the Milky Way, and for the first time we connect the predictions from dynamical measurements of stellar orbits on scales of 10 3 –10 5 gravitational radii to event-horizon-scale images and variability. Furthermore, a comparison with the EHT results for the supermassive black hole M87* shows consistency with the predictions of general relativity spanning over three orders of magnitude in central mass.

article Free Access Share on The CAVE: audio visual experience automatic virtual environment Authors: Carolina Cruz-Neira Electronic Visualization Laboratory Electronic Visualization LaboratoryView Profile , Daniel J. Sandin Electronic Visualization Laboratory and the School of Art and Design at the University of Illinois at Chicago Electronic Visualization Laboratory and the School of Art and Design at the University of Illinois at ChicagoView Profile , Thomas A. DeFanti Department of Electrical Engineering and Computer Science, Electronic Visualization Laboratory and UIC Software Technologies Research Center Department of Electrical Engineering and Computer Science, Electronic Visualization Laboratory and UIC Software Technologies Research CenterView Profile , Robert V. Kenyon University of Illinois at Chicago University of Illinois at ChicagoView Profile , John C. Hart Electronic Visualization Laboratory, University of Illinois at Chicago and the National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign Electronic Visualization Laboratory, University of Illinois at Chicago and the National Center for Supercomputing Applications, University of Illinois at Urbana-ChampaignView Profile Authors Info & Claims Communications of the ACMVolume 35Issue 6June 1992 pp 64–72https://doi.org/10.1145/129888.129892Published:01 June 1992Publication History 993citation6,657DownloadsMetricsTotal Citations993Total Downloads6,657Last 12 Months550Last 6 weeks52 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF

This paper reports the results of a qualitative study of motivation and barriers to employee participation in virtual knowledge‐sharing communities of practice at Caterpillar Inc., a Fortune 100, multinational corporation. The study indicates that, when employees view knowledge as a public good belonging to the whole organization, knowledge flows easily. However, even when individuals give the highest priority to the interests of the organization and of their community, they tend to shy away from contributing knowledge for a variety of reasons. Specifically, employees hesitate to contribute out of fear of criticism, or of misleading the community members (not being sure that their contributions are important, or completely accurate, or relevant to a specific discussion). To remove the identified barriers, there is a need for developing various types of trust, ranging from the knowledge‐based to the institution‐based trust. Future research directions and implications for KM practitioners are formulated.

This paper describes the Sixth Data Release of the Sloan Digital Sky Survey. With this data release, the imaging of the northern Galactic cap is now complete. The survey contains images and parameters of roughly 287 million objects over 9583 deg 2 , including scans over a large range of Galactic latitudes and longitudes. The survey also includes 1.27 million spectra of stars, galaxies, quasars, and blank sky (for sky subtraction) selected over 7425 deg 2 . This release includes much more stellar spectroscopy than was available in previous data releases and also includes detailed estimates of stellar temperatures, gravities, and metallicities. The results of improved photometric calibration are now available, with uncertainties of roughly 1% in g , r , i , and z , and 2% in u , substantially better than the uncertainties in previous data releases. The spectra in this data release have improved wavelength and flux calibration, especially in the extreme blue and extreme red, leading to the qualitatively better determination of stellar types and radial velocities. The spectrophotometric fluxes are now tied to point-spread function magnitudes of stars rather than fiber magnitudes. This gives more robust results in the presence of seeing variations, but also implies a change in the spectrophotometric scale, which is now brighter by roughly 0.35 mag. Systematic errors in the velocity dispersions of galaxies have been fixed, and the results of two independent codes for determining spectral classifications and redshifts are made available. Additional spectral outputs are made available, including calibrated spectra from individual 15 minute exposures and the sky spectrum subtracted from each exposure. We also quantify a recently recognized underestimation of the brightnesses of galaxies of large angular extent due to poor sky subtraction; the bias can exceed 0.2 mag for galaxies brighter than r = 14 mag.

We compare the results of Eulerian hydrodynamic simulations of cluster formation against virial scaling relations between four bulk quantities: the cluster mass, the dark matter velocity dispersion, the gas temperature and the cluster luminosity. The comparison is made for a large number of clusters at a range of redshifts in three different cosmological models (CHDM, CDM and OCDM). We find that the analytic formulae provide a good description of the relations between three of the four numerical quantities. The fourth (luminosity) also agrees once we introduce a procedure to correct for the fixed numerical resolution. We also compute the normalizations for the virial relations and compare extensively to the existing literature, finding remarkably good agreement. The Press-Schechter prescription is calibrated with the simulations, again finding results consistent with other authors. We also examine related issues such as the size of the scatter in the virial relations, the effect of metallicity with a fixed pass-band, and the structure of the halos. All of this is done in order to establish a firm groundwork for the use of clusters as cosmological probes. Implications for the models are briefly discussed.

We present cosmological results from a combined analysis of galaxy clustering and weak gravitational lensing, using 1321 deg 2 of griz imaging data from the first year of the Dark Energy Survey (DES Y1). We combine three two-point functions: (i) the cosmic shear correlation function of 26 million source galaxies in four redshift bins, (ii) the galaxy angular autocorrelation function of 650,000 luminous red galaxies in five redshift bins, and (iii) the galaxy-shear cross-correlation of luminous red galaxy positions and source galaxy shears. To demonstrate the robustness of these results, we use independent pairs of galaxy shape, photometric-redshift estimation and validation, and likelihood analysis pipelines. To prevent confirmation bias, the bulk of the analysis was carried out while "blind" to the true results; we describe an extensive suite of systematics checks performed and passed during this blinded phase. The data are modeled in flat CDM and wCDM cosmologies, marginalizing over 20 nuisance parameters, varying 6 (for CDM) or 7 (for wCDM) cosmological parameters including the neutrino mass density and including the 457 457 element analytic covariance matrix. We find consistent cosmological results from these three two-point functions and from their combination obtain S 8 8 m =0.3 0.5 0.773 0.026 -0.020 and m 0.267 0.030 -0.017 for CDM; for wCDM, we find S 8 0.782 0.036 -0.024 , m 0.284 0.033 -0.030 , and w -0.82 0.21 -0.20 at 68% C.L. The precision of these DES Y1 constraints rivals that from the Planck cosmic microwave background measurements, allowing a comparison of structure in the very

We present the first cosmology results from large-scale structure using the full 5000 deg 2 of imaging data from the Dark Energy Survey (DES) Data Release 1. We perform an analysis of large-scale structure combining three two-point correlation functions (3 2pt): (i) cosmic shear using 100 million source galaxies, (ii) galaxy clustering, and (iii) the cross-correlation of source galaxy shear with lens galaxy positions, galaxy-galaxy lensing. To achieve the cosmological precision enabled by these measurements has required updates to nearly every part of the analysis from DES Year 1, including the use of two independent galaxy clustering samples, modeling advances, and several novel improvements in the calibration of gravitational shear and photometric redshift inference. The analysis was performed under strict conditions to mitigate confirmation or observer bias; we describe specific changes made to the lens galaxy sample following unblinding of the results and tests of the robustness of our results to this decision. We model the data within the flat CDM and wCDM cosmological models, marginalizing over 25 nuisance parameters. We find consistent cosmological results between the three two-point correlation functions; their combination yields clustering amplitude S 8 0.776 0.017 -0.017 and matter density m 0.339 0.032 -0.031 in CDM, mean with

Abstract The fourth generation of the Sloan Digital Sky Survey (SDSS-IV) has been in operation since 2014 July. This paper describes the second data release from this phase, and the 14th from SDSS overall (making this Data Release Fourteen or DR14). This release makes the data taken by SDSS-IV in its first two years of operation (2014–2016 July) public. Like all previous SDSS releases, DR14 is cumulative, including the most recent reductions and calibrations of all data taken by SDSS since the first phase began operations in 2000. New in DR14 is the first public release of data from the extended Baryon Oscillation Spectroscopic Survey; the first data from the second phase of the Apache Point Observatory (APO) Galactic Evolution Experiment (APOGEE-2), including stellar parameter estimates from an innovative data-driven machine-learning algorithm known as “The Cannon”; and almost twice as many data cubes from the Mapping Nearby Galaxies at APO (MaNGA) survey as were in the previous release (N = 2812 in total). This paper describes the location and format of the publicly available data from the SDSS-IV surveys. We provide references to the important technical papers describing how these data have been taken (both targeting and observation details) and processed for scientific use. The SDSS web site ( www.sdss.org ) has been updated for this release and provides links to data downloads, as well as tutorials and examples of data use. SDSS-IV is planning to continue to collect astronomical data until 2020 and will be followed by SDSS-V.

Domestic yaks (Bos grunniens) provide meat and other necessities for Tibetans living at high altitude on the Qinghai-Tibetan Plateau and in adjacent regions. Comparison between yak and the closely related low-altitude cattle (Bos taurus) is informative in studying animal adaptation to high altitude. Here, we present the draft genome sequence of a female domestic yak generated using Illumina-based technology at 65-fold coverage. Genomic comparisons between yak and cattle identify an expansion in yak of gene families related to sensory perception and energy metabolism, as well as an enrichment of protein domains involved in sensing the extracellular environment and hypoxic stress. Positively selected and rapidly evolving genes in the yak lineage are also found to be significantly enriched in functional categories and pathways related to hypoxia and nutrition metabolism. These findings may have important implications for understanding adaptation to high altitude in other animal species and for hypoxia-related diseases in humans.

Variational and fixed-node Green's-function Monte Carlo calculations have been performed to find the ground-state properties of the two-dimensional electron gas in the density range 1\ensuremath{\le}${r}_{s}$\ensuremath{\le}100. Our calculations predict a Wigner crystallization at the density ${r}_{s}$\ensuremath{\simeq}37\ifmmode\pm\else\textpm\fi{}5. The electron system is found to be in the normal- (paramagnetic) fluid state below the transition density, but the fully polarized state is very close in energy. We have tabulated the values of pair distribution function g(r), the static structure factor S(k), and the momentum distribution n(k) at several densities of interest both in the normal and the polarized phases. An estimate of the spin susceptibility \ensuremath{\chi} is also given.

We present UV, optical, and near-infrared (NIR) photometry of the first electromagnetic counterpart to a gravitational wave source from Advanced Laser Interferometer Gravitational-wave Observatory (LIGO)/Virgo, the binary neutron star merger GW170817. Our data set extends from the discovery of the optical counterpart at 0.47–18.5 days post-merger, and includes observations with the Dark Energy Camera (DECam), Gemini-South/FLAMINGOS-2 (GS/F2), and the Hubble Space Telescope ( HST ). The spectral energy distribution (SED) inferred from this photometry at 0.6 days is well described by a blackbody model with K, a radius of cm (corresponding to an expansion velocity of ), and a bolometric luminosity of erg s −1 . At 1.5 days we find a multi-component SED across the optical and NIR, and subsequently we observe rapid fading in the UV and blue optical bands and significant reddening of the optical/NIR colors. Modeling the entire data set, we find that models with heating from radioactive decay of 56 Ni, or those with only a single component of opacity from r -process elements, fail to capture the rapid optical decline and red optical/NIR colors. Instead, models with two components consistent with lanthanide-poor and lanthanide-rich ejecta provide a good fit to the data; the resulting "blue" component has and , and the "red" component has and . These ejecta masses are broadly consistent with the estimated r -process production rate required to explain the Milky Way r -process abundances, providing the first evidence that binary neutron star (BNS) mergers can be a dominant site of r -process enrichment.

In this work, we present our discovery and characterization of a new kagome prototype structure, ${\mathrm{KV}}_{3}{\mathrm{Sb}}_{5}$. We also present the discovery of the isostructural compounds ${\mathrm{RbV}}_{3}{\mathrm{Sb}}_{5}$ and ${\mathrm{CsV}}_{3}{\mathrm{Sb}}_{5}$. All materials exhibit a structurally perfect two-dimensional kagome net of vanadium. Density-functional theory calculations indicate that the materials are metallic, with the Fermi level in close proximity to several Dirac points. Powder and single-crystal syntheses are presented, with postsynthetic treatments shown to deintercalate potassium from single crystals of ${\mathrm{KV}}_{3}{\mathrm{Sb}}_{5}$. Considering the proximity to Dirac points, deintercalation provides a convenient means to tune the Fermi level. Magnetization measurements indicate that ${\mathrm{KV}}_{3}{\mathrm{Sb}}_{5}$ exhibits behavior consistent with a the Curie-Weiss model at high temperatures, although the effective moment is low $(0.22{\ensuremath{\mu}}_{\text{B}}$ per vanadium ion). An anomaly is observed in both magnetization and heat capacity measurements at 80 K, below which the moment is largely quenched. Elastic neutron scattering measurements find no obvious evidence of long-range or short-range magnetic ordering below 80 K. The possibility of an orbital-ordering event is considered. Single-crystal resistivity measurements show the effect of deintercalation on the electron transport and allow estimation of the Kadowaki-Woods ratio in ${\mathrm{KV}}_{3}{\mathrm{Sb}}_{5}$. We find that $A/{\ensuremath{\gamma}}^{2}\ensuremath{\sim}61\phantom{\rule{4pt}{0ex}}\ensuremath{\mu}\mathrm{Ohm}$ cm ${\mathrm{mol}}_{\text{FU}}^{2}\phantom{\rule{4pt}{0ex}}{\mathrm{K}}^{2}\phantom{\rule{4pt}{0ex}}{\mathrm{J}}^{\ensuremath{-}2}$, suggesting that correlated electron transport may be possible. ${\mathrm{KV}}_{3}{\mathrm{Sb}}_{5}$ and its cogeners ${\mathrm{RbV}}_{3}{\mathrm{Sb}}_{5}$ and ${\mathrm{CsV}}_{3}{\mathrm{Sb}}_{5}$ represent a new family of kagome metals, and our results demonstrate that they deserve further study as potential model systems.

This report documents the results of a study to address the long range, strategic planning required by NASA's Revolutionary Computational Aerosciences (RCA) program in the area of computational fluid dynamics (CFD), including future software and hardware requirements for High Performance Computing (HPC). Specifically, the Vision 2030 CFD study is to provide a knowledge-based forecast of the future computational capabilities required for turbulent, transitional, and reacting flow simulations across a broad Mach number regime, and to lay the foundation for the development of a future framework and/or environment where physics-based, accurate predictions of complex turbulent flows, including flow separation, can be accomplished routinely and efficiently in cooperation with other physics-based simulations to enable multi-physics analysis and design. Specific technical requirements from the aerospace industrial and scientific communities were obtained to determine critical capability gaps, anticipated technical challenges, and impediments to achieving the target CFD capability in 2030. A preliminary development plan and roadmap were created to help focus investments in technology development to help achieve the CFD vision in 2030.

Abstract Astrophysical black holes are expected to be described by the Kerr metric. This is the only stationary, vacuum, axisymmetric metric, without electromagnetic charge, that satisfies Einstein’s equations and does not have pathologies outside of the event horizon. We present new constraints on potential deviations from the Kerr prediction based on 2017 EHT observations of Sagittarius A* (Sgr A*). We calibrate the relationship between the geometrically defined black hole shadow and the observed size of the ring-like images using a library that includes both Kerr and non-Kerr simulations. We use the exquisite prior constraints on the mass-to-distance ratio for Sgr A* to show that the observed image size is within ∼10% of the Kerr predictions. We use these bounds to constrain metrics that are parametrically different from Kerr, as well as the charges of several known spacetimes. To consider alternatives to the presence of an event horizon, we explore the possibility that Sgr A* is a compact object with a surface that either absorbs and thermally reemits incident radiation or partially reflects it. Using the observed image size and the broadband spectrum of Sgr A*, we conclude that a thermal surface can be ruled out and a fully reflective one is unlikely. We compare our results to the broader landscape of gravitational tests. Together with the bounds found for stellar-mass black holes and the M87 black hole, our observations provide further support that the external spacetimes of all black holes are described by the Kerr metric, independent of their mass.

We use 26 10 6 galaxies from the Dark Energy Survey (DES) Year 1 shape catalogs over 1321 deg 2 of the sky to produce the most significant measurement of cosmic shear in a galaxy survey to date. We constrain cosmological parameters in both the flat CDM and the wCDM models, while also varying the neutrino mass density. These results are shown to be robust using two independent shape catalogs, two independent photo-z calibration methods, and two independent analysis pipelines in a blind analysis. We find a 3.5% fractional uncertainty on 8 m =0.3 0.5 0.782 0.027 -0.027 at 68% C.L., which is a factor of 2.

The Very Large Array Sky Survey (VLASS) is a synoptic, all-sky radio sky survey with a unique combination of high angular resolution (≈2."5), sensitivity (a 1σ goal of 70 μJy/beam in the coadded data), full linear Stokes polarimetry, time domain coverage, and wide bandwidth (2–4 GHz). The first observations began in 2017 September, and observing for the survey will finish in 2024. VLASS will use approximately 5500 hr of time on the Karl G. Jansky Very Large Array (VLA) to cover the whole sky visible to the VLA (decl. > −40°), a total of 33 885 deg². The data will be taken in three epochs to allow the discovery of variable and transient radio sources. The survey is designed to engage radio astronomy experts, multi-wavelength astronomers, and citizen scientists alike. By utilizing an "on the fly" interferometry mode, the observing overheads are much reduced compared to a conventional pointed survey. In this paper, we present the science case and observational strategy for the survey, and also results from early survey observations.