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The ExaStar project aims to deliver an efficient, versatile, and portable software ecosystem for multi-physics astrophysics simulations run on exascale machines. The code suite is a component-based multi-physics toolkit, built on the capabilities of current simulation codes (in particular Flash-X and Castro), and based on the massively parallel adaptive mesh refinement framework AMReX. It includes modules for hydrodynamics, advanced radiation transport, thermonuclear kinetics, and nuclear microphysics. The code will reach exascale efficiency by building upon current multi- and many-core packages integrated into an orchestration system that uses a combination of configuration tools, code translators, and a domain-specific asynchronous runtime to manage performance across a range of platform architectures. The target science includes multi-physics simulations of astrophysical explosions (such as supernovae and neutron star mergers) to understand the cosmic origin of the elements and the fundamental physics of matter and neutrinos under extreme conditions.

Among symptomatic outpatients, subgenomic RNA of severe acute respiratory syndrome coronavirus 2 in nasal midturbinate swab specimens was concordant with antigen detection but remained detectable in 13 (82.1%) of 16 nasopharyngeal swab specimens from antigen-negative persons. Subgenomic RNA in midturbinate swab specimens might be useful for routine diagnostics to identify active virus replication.

Flash-X is a highly composable multiphysics software system that can be used to simulate physical phenomena in several scientific domains. It derives some of its solvers from FLASH, which was first released in 2000. Flash-X has a new framework that relies on abstractions and asynchronous communications for performance portability across a range of increasingly heterogeneous hardware platforms. Flash-X is meant primarily for solving Eulerian formulations of applications with compressible and/or incompressible reactive flows. It also has a built-in, versatile Lagrangian framework that can be used in many different ways, including implementing tracers, particle-in-cell simulations, and immersed boundary methods., Comment: 16 pages, 5 Figures, published open access in SoftwareX

The impact of repeated sample collection on COVID-19 test performance is unknown. The FDA and CDC currently recommend the primary collection of diagnostic samples to minimize the perceived risk of false-negative findings. We therefore evaluated the association between repeated sample collection and test performance among 325 symptomatic patients undergoing COVID-19 testing in Atlanta, GA. High concordance was found between consecutively collected mid-turbinate samples with both molecular (n = 74, 100% concordance) and antigen-based (n = 147, 97% concordance, kappa = 0.95, CI = 0.88–1.00) diagnostic assays. Repeated sample collection does not decrease COVID-19 test performance, demonstrating that multiple samples can be collected for assay validation and clinical diagnosis.

While there has been significant progress in the development of rapid COVID-19 diagnostics, as the pandemic unfolds, new challenges have emerged, including whether these technologies can reliably detect the more infectious variants of concern and be viably deployed in non-clinical settings as “self-tests”. Multidisciplinary evaluation of the Abbott BinaxNOW COVID-19 Ag Card (BinaxNOW, a widely used rapid antigen test, included limit of detection, variant detection, test performance across different age-groups, and usability with self/caregiver-administration. While BinaxNOW detected the highly infectious variants, B.1.1.7 (Alpha) first identified in the UK, B.1.351 (Beta) first identified in South Africa, P.1 (Gamma) first identified in Brazil, B.1.617.2 (Delta) first identified in India and B.1.2, a non-VOC, test sensitivity decreased with decreasing viral loads. Moreover, BinaxNOW sensitivity trended lower when devices were performed by patients/caregivers themselves compared to trained clinical staff, despite universally high usability assessments following self/caregiver-administration among different age groups. Overall, these data indicate that while BinaxNOW accurately detects the new viral variants, as rapid COVID-19 tests enter the home, their already lower sensitivities compared to RT-PCR may decrease even more due to user error.

The National Institutes of Health (NIH) launched the Rapid Acceleration of Diagnostics (RADxSM) Tech initiative to support the development and commercialization of novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) point-of-care test devices. The primary objective of the Clinical Studies Core (CSC) was to perform SARS-CoV-2 device studies involving diverse populations and settings. Within a few months, the infrastructure for clinical studies was developed, including a master protocol, digital study platform, data management system, single IRB, and multi-site partnerships. Data from some studies are being used to support Emergency Use Authorization of novel SARS-CoV-2 test devices. The CSC reduced the typical time and cost of developing medical devices and highlighted the impactful role of academic and NIH partnership in addressing public health needs at a rapid pace during a global pandemic. The structure, deployment, and lessons learned from this experience are widely applicable to future in vitro diagnostic device clinical studies.

We address the calibration of a computationally expensive nuclear physics model for which derivative information with respect to the fit parameters is not readily available. Of particular interest is the performance of optimization-based training algorithms when dozens, rather than millions or more, of training data are available and when the expense of the model places limitations on the number of concurrent model evaluations that can be performed. As a case study, we consider the Fayans energy density functional model, which has characteristics similar to many model fitting and calibration problems in nuclear physics. We analyze hyperparameter tuning considerations and variability associated with stochastic optimization algorithms and illustrate considerations for tuning in different computational settings., 25-page article, 9-page supplement, 1-page notice

FLASH is a multiphysics software package that was created in 1998 by combining three preexisting packages and has undergone three major revisions. Software design and engineering practices were integrated early in the development and maintenance processes of FLASH, and these processes have evolved strongly at each of the revisions. As high-performance computing enters the age of exascale, challenges along the orthogonal axes of node-level hardware and solver heterogeneity force developers of complex multiphysics software to consider a software architecture overhaul. Because of the nature and scope of necessary changes, an effort to refactor and grow the architecture of the FLASH code has been launched as a separate software project. For this project to succeed, its development team must evaluate, improve, and modernize software processes and policies to meet the unique challenges posed by the exascale era. We describe here our experiences, lessons we have learned, and the methods that we have developed as part of this ongoing project. Within the context of the challenges posed by exascale, we review the FLASH design approach as well as some of the main software engineering processes and tools that have been implemented or updated throughout the lifetime of FLASH. Modernization applied to these processes and tools is also detailed. Reviewing and reevaluating the FLASH experience of establishing and updating software design and engineering practices have been helpful in understanding the needs of the project as it transitions to exascale and in planning the transition. We find that our historical design methodology is still important and relevant. We also believe that using a mixture of plan-based and agile methods is still the best for our project and is in accord with the guidance found in the literature. We present a section on inferences and lessons learned related to software design and engineering practices.

Nuclear density functional theory is the prevalent theoretical framework for accurately describing nuclear properties at the scale of the entire chart of nuclides. Given an energy functional and a many-body scheme (e.g., single- or multireference level), the predictive power of the theory depends strongly on how the parameters of the energy functionals have been calibrated with experimental data. Expanded algorithms and computing power have enabled recent optimization protocols to include data in deformed nuclei in order to optimize the coupling constants of the energy functional. The primary motivation of this work is to test the robustness of such protocols with respect to some of the technical and numerical details of the underlying calculations, especially when the calibration explores a large parameter space. To this end, we quantify the effect of these uncertainties on both the optimization and statistical emulation of composite objective functions. We also emphasize that Bayesian calibration can provide better estimates of the theoretical errors used to define objective functions., Comment: 23 pages, 3 figures, 4 tables, 67 references; Submitted to J. Phys. G: Nucl. Part. Phys

A correlated material in the vicinity of an insulator-metal transition (IMT) exhibits rich phenomenology and variety of interesting phases. A common avenue to induce IMTs in Mott insulators is doping, which inevitably leads to disorder. While disorder is well known to create electronic inhomogeneity, recent theoretical studies have indicated that it may play an unexpected and much more profound role in controlling the properties of Mott systems. Theory predicts that disorder might play a role in driving a Mott insulator across an IMT, with the emergent metallic state hosting a power law suppression of the density of states (with exponent close to 1; V-shaped gap) centered at the Fermi energy. Such V-shaped gaps have been observed in Mott systems but their origins are as yet unknown. To investigate this, we use scanning tunneling microscopy and spectroscopy to study isovalent Ru substitutions in Sr$_3$(Ir$_{1-x}$Ru$_x$)$_2$O$_7$ which drives the system into an antiferromagnetic, metallic state. Our experiments reveal that many core features of the IMT such as power law density of states, pinning of the Fermi energy with increasing disorder, and persistence of antiferromagnetism can be understood as universal features of a disordered Mott system near an IMT and suggest that V-shaped gaps may be an inevitable consequence of disorder in doped Mott insulators., Comment: 13 pages, 4 figures; A new version can be find in PNAS

p.p1 {margin: 0.0px 0.0px 0.0px 0.0px; font: 11.0px Menlo; color: #000000; background-color: #ffffff} span.s1 {font-variant-ligatures: no-common-ligatures} FLASH is a highly-configurable multiphysics software designed for solving a large class of problems that involve fluid flows and need adaptive mesh refinement (AMR). FLASH has been in existence for two decades and has undergone four major revisions. It is now undergoing its fifth major revision to deal with increasingly heterogeneous platforms. The architecture of previous versions of the code and the AMR package at its core, Paramesh, are inadequate to meet the challenges posed by heterogeneity. In this paper we describe our experience with refactoring the mesh interface of the code to work with a more modern AMR library, AMReX. The focus of the paper is the refactoring methodology and the attendant software process that we have found useful to ensure that code quality is maintained during the transition.

International audience; The direct imaging of exoplanet is a leading field of today’s astronomy. The photons coming from the planet carry precious information on the chemical composition of its atmosphere. The second-generation instrument, Spectro-Polarimetric High contrast Exoplanet Research (SPHERE), dedicated to detection, photometry and spectral characterization of Jovian-like planets, is now in operation on the European very large telescope. This instrument relies on an extreme adaptive optics (XAO) system to compensate for atmospheric turbulence as well as for internal errors with an unprecedented accuracy. We demonstrate the high level of performance reached by the SPHERE XAO system (SAXO) during the assembly integration and test (AIT) period. In order to fully characterize the instrument quality, two AIT periods have been mandatory. In the first phase at Observatoire de Paris, the performance of SAXO itself was assessed. In the second phase at IPAG Grenoble Observatory, the operation of SAXO in interaction with the overall instrument has been optimized. In addition to the first two phases, a final check has been performed after the reintegration of the instrument at Paranal Observatory, in the New Integration Hall before integration at the telescope focus. The final performance aimed by the SPHERE instrument with the help of SAXO is among the highest Strehl ratio pretended for an operational instrument (90% in H band, 43% in V band in a realistic turbulence r0, and wind speed condition), a limit R magnitude for loop closure at 15, and a robustness to high wind speeds. The full-width at half-maximum reached by the instrument is 40 mas for infrared in H band and unprecedented 18.5 mas in V band.; L'imagerie directe d'exoplanètes est un domaine phare de l'astronomie actuelle. Les photons issus de la planète sont porteurs d'une information précieuse sur la composition chimique de son atmosphère. L'instrument de seconde génération SPHERE, Spectro-Polarimetri High-contrast Exoplanet Research, dédié à la détection la photométrie et la caractérisation spectrale de planètes joviennes, est maintenant en opération sur le très grand télescope Européen (VLT). Cet instrument repose sur une optique adaptative à très hautes performances (XAO) pour compenser les turbulences atmosphériques, comme les défauts optiques internes de l'instrument lui-même. Nous démontrons les très hauts niveaux de performance atteint par l'instrument SPHERE et son système de XAO SAXO, pendant la phase d'intégration (AIT). Pour pleinement caractériser les performances de l'instrument, deux périodes d'AIT ont été obligatoires. Dans la première phase à l'Observatoire de Paris, les performances de l'optique adaptative seule ont été obtenues. Dans la seconde phase à l'observatoire de Grenoble, l'opération de SAXO en interaction avec le reste de l'instrument ont été optimisées. En sus, une vérification finale a été faite au foyer du télescope. Les performances atteintes par SPHERE avec l'aide de SAXO sont parmi les plus hauts rapports de Strehl jamais atteint pour un instrument opérationnel (90% en bande H, 43% en bande V, sous hypothèse de turbulence et de vent classiques), et surtout une magnitude limite de R=15. La FHWM (largeur à mi-hauteur, la résolution de l'instrument) atteinte en bande H est de 40mas, et atteint une valeur sans précédent de 18.5mas en bande V.

In November 2012, we installed an L-band annular groove phase mask (AGPM) vector vortex coronagraph (VVC) inside NACO, the adaptive optics camera of ESO’s Very Large Telescope. The mask, made out of diamond subwavelength gratings has been commissioned, science qualified, and is now offered to the community. Here we report ground-breaking on-sky performance levels in terms of contrast, inner working angle, and discovery space. This new practical demonstration of the VVC, coming a few years after Palomar’s and recent record-breaking lab experiments in the visible (E. Serabyn et al. 2013, these proceedings), shows once again that this new-generation coronagraph has reached a high level of maturity.

We describe a new technique to reduce tip and tilt vibrations via the design of adaptive optics controllers in a frequency framework. The method synthesizes controllers by minimizing an H2 norm of the tip and tilt residuals. In this approach, open loop slopes (pseudo-open-loop) are reconstructed from on-sky data and input into off-line simulations of the adaptive optics system. The proposed procedure executes a sequence of off-line closed-loop runs with increasing controller complexity and searches for the controller that minimizes the variance of residuals. Although the method avoids any identification of the vibration and turbulence models during the controller synthesis, the actual models are indirectly constructed as a by-product of the H2 norm minimization. The technique has been implemented on and tested with two operational instruments, namely Paranal's NACO and Gemini-South's GeMS, showing an effective rejection of the main vibrations in the loop and also improving the overall performance of the system over varying turbulence conditions. It is shown that a superior performance is obtained when compared to the standard integrator controller.

Context. High contrast imaging has thoroughly combed through the limited search space accessible with first-generation ground-based adaptive optics instruments and the Hubble Space Telescope. Only a few objects were discovered, and many non-detections reported and statistically interpreted. The field is now in need of a technological breakthrough. Aim. Our aim is to open a new search space with first-generation systems such as NACO at the Very Large Telescope, by providing ground-breaking inner working angle (IWA) capabilities in the L' band. The L' band is a sweet spot for high contrast coronagraphy since the planet-to-star brightness ratio is favorable, while the Strehl ratio is naturally higher. Methods. An annular groove phase mask (AGPM) vector vortex coronagraph optimized for the L' band, made from diamond subwavelength gratings was manufactured and qualified in the lab. The AGPM enables high contrast imaging at very small IWA, potentially being the key to unexplored discovery space. Results. Here we present the installation and successful on-sky tests of an L'-band AGPM coronagraph on NACO. Using angular differential imaging, which is well suited to the rotational symmetry of the AGPM, we demonstrated a \Delta L' > 7.5 mag contrast from an IWA ~ 0".09 onwards, during average seeing conditions, and for total integration times of a few hundred seconds., Comment: 4 pages, 4 figures

NACO is the famous and versatile diffraction limited NIR imager and spectrograph with which ESO celebrated 10 years of Adaptive Optics at the VLT. Since two years a substantial effort has been put in to understanding and fixing issues that directly affect the image quality and the high contrast performances of the instrument. Experiments to compensate the non-common-path aberrations and recover the highest possible Strehl ratios have been carried out successfully and a plan is hereafter described to perform such measurements regularly. The drift associated to pupil tracking since 2007 was fixed in October 2011. NACO is therefore even better suited for high contrast imaging and can be used with coronagraphic masks in the image plane. Some contrast measurements are shown and discussed. The work accomplished on NACO will serve as reference for the next generation instruments on the VLT, especially those working at the diffraction limit and making use of angular differential imaging (i.e. SPHERE, VISIR, possibly ERIS)., 14 pages, 5 figures, SPIE 2012 Astronomical Instrumentation Proceeding

The analysis of the laser behavior on sky and of the adaptive optics system of SINFONI is made systematically since a year. This campaign of measurements will continue during the first semester 2012. The analysis, the results and the proposed optimization will be presented in this proceeding.

This paper aims at giving an update on the most versatile adaptive optics fed instrument to date, the well known and successful NACO . Although NACO is only scheduled for about two more years at the Very Large Telescope (VLT), it keeps on evolving with additional operation modes bringing original astronomical results. The high contrast imaging community uses it creatively as a test-bench for SPHERE and other second generation planet imagers. A new visible wavefront sensor (WFS) optimized for Laser Guide Star (LGS) operations has been installed and tested, the cube mode is more and more requested for frame selection on bright sources, a seeing enhancer mode (no tip/tilt correction) is now offered to provide full sky coverage and welcome all kind of extragalactic applications, etc. The Instrument Operations Team (IOT) and Paranal engineers are currently working hard at maintaining the instrument overall performances but also at improving them and offering new capabilities, providing the community with a well tuned and original instrument for the remaining time it is being used. The present contribution delivers a non-exhaustive overview of the new modes and experiments that have been carried out in the past months., Comment: 10 pages, 7 figures, SPIE 2010 Astronomical Instrumentation Proceeding

This presentation provides interesting miscellaneous information regarding the instrumentation activities at Paranal Observatory. It introduces the suite of 23 instruments and auxiliary systems that are under the responsibility of the Paranal Instrumentation group, information on the type of instruments, their usage and downtime statistics. The data is based on comprehensive data recorded in the Paranal Night Log System and the Paranal Problem Reporting System whose principles are explained as well. The work organization of the 15 team members around the high number of instruments is laid out, which includes: - Maintaining older instruments with obsolete components - Receiving new instruments and supporting their integration and commissioning - Contributing to future instruments in their developing phase. The assignments of the Instrumentation staff to the actual instruments as well as auxiliary equipment (Laser Guide Star Facility, Mask Manufacturing Unit, Cloud Observation Tool) are explained with respect to responsibility and scheduling issues. The essential activities regarding hardware & software are presented, as well as the technical and organizational developments within the group towards its present and future challenges.

${\mathrm{BaFe}}_{2}{\mathrm{As}}_{2}$ exhibits properties that are characteristic of the parent compounds of the newly discovered iron (Fe)-based high-${T}_{C}$ superconductors. By combining real-space imaging of scanning tunneling microscopy and spectroscopy ($\mathrm{STM}+\mathrm{STS}$) with momentum-space quantitative low-energy electron diffraction (LEED), we have identified the surface plane of cleaved ${\mathrm{BaFe}}_{2}{\mathrm{As}}_{2}$ crystals as the As terminated Fe-As layer---the plane where superconductivity occurs. LEED and $\mathrm{STM}+\mathrm{STS}$ data on the ${\mathrm{BaFe}}_{2}{\mathrm{As}}_{2}(001)$ surface indicate an ordered arsenic (As) terminated metallic surface without reconstruction or lattice distortion. It is surprising that STM images the different Fe-As orbitals associated with the orthorhombic structure, but not the As atoms in the surface plane.

BaFe2As2 exhibits properties that are characteristic of the parent compounds of the newly discovered iron (Fe)-based high-T(C) superconductors. By combining real-space imaging of scanning tunneling microscopy and spectroscopy (STM+STS) with momentum-space quantitative low-energy electron diffraction (LEED), we have identified the surface plane of cleaved BaFe2As2 crystals as the As terminated Fe-As layer-the plane where superconductivity occurs. LEED and STM+STS data on the BaFe2As2(001) surface indicate an ordered arsenic (As) terminated metallic surface without reconstruction or lattice distortion. It is surprising that STM images the different Fe-As orbitals associated with the orthorhombic structure, but not the As atoms in the surface plane.

Here we present the installation and successful commissioning of an L'-band Annular Groove Phase Mask (AGPM) coronagraph on VLT/NACO. The AGPM is a vector vortex coronagraph made from diamond subwavelength gratings tuned to the L' band. The vector vortex coronagraph enables high contrast imaging at very small inner working angle (here 0″.09, the diffraction limit of the VLT at L'), potentially being the key to a new parameter space. During technical and science verification runs, we discovered a late-type companion at two beamwidths from an F0V star (Mawet et al. 2013), and imaged the inner regions of β Pictoris down to the previously unexplored projected radius of 1.75 AU. The circumstellar disk was also resolved from ≃ 1″ to 5″ (see J. Milli et al., these proceedings). These results showcase the potential of the NACO L-band AGPM over a wide range of spatial scales.