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At least 1,675 records · Page 93

Local-to-global signal transduction at the core of a Mn 2+ sensing riboswitch

The widespread Mn 2+ -sensing yybP-ykoY riboswitch controls the expression of bacterial Mn 2+ homeostasis genes. Here, we first determine the crystal structure of the ligand-bound yybP-ykoY riboswitch aptamer from Xanthomonas oryzae at 2.96 Å resolution, revealing two conformations with docked four-way junction (4WJ) and incompletely coordinated metal ions. In >100 µs of MD simulations, we observe that loss of divalents from the core triggers local structural perturbations in the adjacent docking interface, laying the foundation for signal transduction to the regulatory switch helix. Using single-molecule FRET, we unveil a previously unobserved extended 4WJ conformation that samples transient docked states in the presence of Mg 2+ . Only upon adding sub-millimolar Mn 2+ , however, can the 4WJ dock stably, a feature lost upon mutation of an adenosine contacting Mn 2+ in the core. These observations illuminate how subtly differing ligand preferences of competing metal ions become amplified by the coupling of local with global RNA dynamics.

59 BASIC BIOLOGICAL SCIENCES↗

THE DIFFERENCE IMAGING PIPELINE FOR THE TRANSIENT SEARCH IN THE DARK ENERGY SURVEY

We describe the operation and performance of the difference imaging pipeline (DiffImg) used to detect transients in deep images from the Dark Energy Survey Supernova program (DES-SN) in its first observing season from 2013 August through 2014 February. DES-SN is a search for transients in which ten 3 deg{sup 2} fields are repeatedly observed in the g, r, i, z passbands with a cadence of about 1 week. The observing strategy has been optimized to measure high-quality light curves and redshifts for thousands of Type Ia supernovae (SNe Ia) with the goal of measuring dark energy parameters. The essential DiffImg functions are to align each search image to a deep reference image, do a pixel-by-pixel subtraction, and then examine the subtracted image for significant positive detections of point-source objects. The vast majority of detections are subtraction artifacts, but after selection requirements and image filtering with an automated scanning program, there are ∼130 detections per deg{sup 2} per observation in each band, of which only ∼25% are artifacts. Of the ∼7500 transients discovered by DES-SN in its first observing season, each requiring a detection on at least two separate nights, Monte Carlo (MC) simulations predict that 27% are expected to be SNe Ia or core-collapse SNe. Another ∼30% of the transients are artifacts in which a small number of observations satisfy the selection criteria for a single-epoch detection. Spectroscopic analysis shows that most of the remaining transients are AGNs and variable stars. Fake SNe Ia are overlaid onto the images to rigorously evaluate detection efficiencies and to understand the DiffImg performance. The DiffImg efficiency measured with fake SNe agrees well with expectations from a MC simulation that uses analytical calculations of the fluxes and their uncertainties. In our 8 “shallow” fields with single-epoch 50% completeness depth ∼23.5, the SN Ia efficiency falls to 1/2 at redshift z ≈ 0.7; in our 2 “deep” fields with mag-depth ∼24.5, the efficiency falls to 1/2 at z ≈ 1.1. A remaining performance issue is that the measured fluxes have additional scatter (beyond Poisson fluctuations) that increases with the host galaxy surface brightness at the transient location. This bright-galaxy issue has minimal impact on the SNe Ia program, but it may lower the efficiency for finding fainter transients on bright galaxies.

79 ASTRONOMY AND ASTROPHYSICS↗

Mapping the particle acceleration in the cool core of the galaxy cluster RX J1720.1+2638

We present new deep, high-resolution radio images of the diffuse minihalo in the cool core of the galaxy cluster RX J1720.1+2638. The images have been obtained with the Giant Metrewave Radio Telescope at 317, 617, and 1280 MHz and with the Very Large Array at 1.5, 4.9, and 8.4 GHz, with angular resolutions ranging from 1'' to 10''. This represents the best radio spectral and imaging data set for any minihalo. Most of the radio flux of the minihalo arises from a bright central component with a maximum radius of ∼80 kpc. A fainter tail of emission extends out from the central component to form a spiral-shaped structure with a length of ∼230 kpc, seen at frequencies 1.5 GHz and below. We find indication of a possible steepening of the total radio spectrum of the minihalo at high frequencies. Furthermore, a spectral index image shows that the spectrum of the diffuse emission steepens with increasing distance along the tail. A striking spatial correlation is observed between the minihalo emission and two cold fronts visible in the Chandra X-ray image of this cool core. These cold fronts confine the minihalo, as also seen in numerical simulations of minihalo formation by sloshing-induced turbulence. All these observations favor the hypothesis that the radio-emitting electrons in cluster cool cores are produced by turbulent re-acceleration.

79 ASTRONOMY AND ASTROPHYSICS↗

Thermal Hydraulic Modeling of an Advanced Nuclear Reactor using open-source MOOSE tools

The aim of this study is to develop model of a small High Temperature Gas cooled Reactor (HTGR) including the balance of plant. This microreactor produces electricity using the thermal power of the nuclear reaction. This work utilizes the MOOSE Multiphysics simulation tools, which are mainly developed at Idaho National Laboratory (INL, Idaho, United States of America). Its thermal-hydraulics and Heat conduction Modules are used to study the fluids behavior in the primary loop and power conversion system and their interactions with the heating structures. More specifically, one verifies that the temperatures, pressures and mass flow rates of the fluids in both loops are consistent and that, at the same time, all the power transfers occur as expected. Moreover, the various mechanical components characteristics (turbine, compressor, pump) are adapted to the reactor operating conditions. This first analysis is conducted using simplified and one-dimensional model for the core. Ultimately, the obtained results are used to build a higher fidelity core model. This step aims to verify that the initial simplified simulation is consistent with the three-dimensional core modeling. In addition, the calculated material temperatures are checked. This study provides a fairly complete model of the thermal hydraulic phenomena for a particular design of High Temperature Gas cooled Reactor.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

FINDING THE FIRST COSMIC EXPLOSIONS. II. CORE-COLLAPSE SUPERNOVAE

Understanding the properties of Population III (Pop III) stars is prerequisite to elucidating the nature of primeval galaxies, the chemical enrichment and reionization of the early intergalactic medium, and the origin of supermassive black holes. While the primordial initial mass function (IMF) remains unknown, recent evidence from numerical simulations and stellar archaeology suggests that some Pop III stars may have had lower masses than previously thought, 15-50 M{sub Sun} in addition to 50-500 M{sub Sun }. The detection of Pop III supernovae (SNe) by JWST, WFIRST, or the TMT could directly probe the primordial IMF for the first time. We present numerical simulations of 15-40 M{sub Sun} Pop III core-collapse SNe performed with the Los Alamos radiation hydrodynamics code RAGE. We find that they will be visible in the earliest galaxies out to z {approx} 10-15, tracing their star formation rates and in some cases revealing their positions on the sky. Since the central engines of Pop III and solar-metallicity core-collapse SNe are quite similar, future detection of any Type II SNe by next-generation NIR instruments will in general be limited to this epoch.

79 ASTRONOMY AND ASTROPHYSICS↗

Integrated State Estimation and Contingency Analysis Software Implementation using High Performance Computing Techniques

Power system simulation tools are traditionally developed in sequential mode and codes are optimized for single core computing only. However, the increasing complexity in the power grid models requires more intensive computation. The traditional simulation tools will soon not be able to meet the grid operation requirements. Therefore, power system simulation tools need to evolve accordingly to provide faster and better results for grid operations. This paper presents an integrated state estimation and contingency analysis software implementation using high performance computing techniques. The software is able to solve large size state estimation problems within one second and achieve a near-linear speedup of 9,800 with 10,000 cores for contingency analysis application. The performance evaluation is presented to show its effectiveness.

Chen, Yousu↗

Ni-based nanoalloys: Towards thermally stable highly magnetic materials

Molecular dynamics simulations and density functional theory calculations have been used to demonstrate the possibility of preserving high spin states of the magnetic cores within Ni-based core-shell bimetallic nanoalloys over a wide range of temperatures. We show that, unlike the case of Ni–Al clusters, Ni–Ag clusters preserve high spin states (up to 8 μ{sub B} in case of Ni{sub 13}Ag{sub 32} cluster) due to small hybridization between the electronic levels of two species. Intriguingly, such clusters are also able to maintain geometrical and electronic integrity of their cores at temperatures up to 1000 K (e.g., for Ni{sub 7}Ag{sub 27} cluster). Furthermore, we also show the possibility of creating ordered arrays of such magnetic clusters on a suitable support by soft-landing pre-formed clusters on the surface, without introducing much disturbance in geometrical and electronic structure of the cluster. We illustrate this approach with the example of Ni{sub 13}Ag{sub 38} clusters adsorbed on the Si(111)–(7×7) surface, which, having two distinctive halves to the unit cell, acts as a selective template for cluster deposition.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Qutrit and qubit circuits for three-flavor collective neutrino oscillations

We explore the utility of qutrits and qubits for simulating the flavor dynamics of dense neutrino systems. The evolution of such systems impacts some important astrophysical processes, such as core-collapse supernovae and the nucleosynthesis of heavy nuclei. Many-body simulations require classical resources beyond current computing capabilities for physically relevant system sizes. Quantum computers are therefore a promising candidate to efficiently simulate the many-body dynamics of collective neutrino oscillations. Previous quantum simulation efforts have primarily focused on properties of the two-flavor approximation due to their direct mapping to qubits. Furthermore, we present new quantum circuits for simulating three-flavor neutrino systems on qutrit- and qubit-based platforms, and demonstrate their feasibility by simulating systems of two, four, and eight neutrinos on IBM and Quantinuum quantum computers.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

The ADAQ framework: An integrated toolkit for data acquisition and analysis with real and simulated radiation detectors

Here, the ADAQ framework is a collection of software tools that is designed to streamline the acquisition and analysis of radiation detector data produced in modern digital data acquisition (DAQ) systems and in Monte Carlo detector simulations. The purpose of the framework is to maximize user scientific pro-ductivity by minimizing the effort and expertise required to fully utilize radiation detectors in a variety of scientific and engineering disciplines. By using a single set of tools to span the real and simulation domains, the framework eliminates redundancy and provides an integrated workflow for high-fidelity comparison between experimental and simulated detector performance. Built on the ROOT data analysis framework, the core of the ADAQ framework is a set of Cþþ and Python libraries that enable high-level control of digital DAQ systems and detector simulations with data stored into standardized binary ROOT files for further analysis. Two graphical user interface programs utilize the libraries to create powerful tools: ADAQAcquisition handles control and readout of real-world DAQ systems and ADAQAnalysis provides data analysis and visualization methods for experimental and simulated data. At present, the ADAQ framework supports digital DAQ hardware from CAEN S.p.A. and detector simulations performed in Geant4; however, the modular design will facilitate future extension to other manufacturers and simulation platforms.

detector simulation↗

THE EFFECT OF ANISOTROPIC VISCOSITY ON COLD FRONTS IN GALAXY CLUSTERS

Cold fronts—contact discontinuities in the intracluster medium (ICM) of galaxy clusters—should be disrupted by Kelvin-Helmholtz (K-H) instabilities due to the associated shear velocity. However, many observed cold fronts appear stable. This opens the possibility of placing constraints on microphysical mechanisms that stabilize them, such as the ICM viscosity and/or magnetic fields. We performed exploratory high-resolution simulations of cold fronts arising from subsonic gas sloshing in cluster cores using the grid-based Athena MHD code, comparing the effects of isotropic Spitzer and anisotropic Braginskii viscosity (expected in a magnetized plasma). Magnetized simulations with full Braginskii viscosity or isotropic Spitzer viscosity reduced by a factor f ∼ 0.1 are both in qualitative agreement with observations in terms of suppressing K-H instabilities. The rms velocity of turbulence within the sloshing region is only modestly reduced by Braginskii viscosity. We also performed unmagnetized simulations with and without viscosity and find that magnetic fields have a substantial effect on the appearance of the cold fronts, even if the initial field is weak and the viscosity is the same. This suggests that determining the dominant suppression mechanism of a given cold front from X-ray observations (e.g., viscosity or magnetic fields) by comparison with simulations is not straightforward. Finally, we performed simulations including anisotropic thermal conduction, and find that including Braginskii viscosity in these simulations does not significantly affect the evolution of cold fronts; they are rapidly smeared out by thermal conduction, as in the inviscid case.

79 ASTRONOMY AND ASTROPHYSICS↗

Massively parallel X-ray scattering simulations

Although present X-ray scattering techniques can provide tremendous information on the nano-structural properties of materials that are valuable in the design and fabrication of energy-relevant nano-devices, a primary challenge remains in the analyses of such data. In this paper we describe a high-performance, flexible, and scalable Grazing Incidence Small Angle X-ray Scattering simulation algorithm and codes that we have developed on multi-core/CPU and many-core/GPU clusters. We discuss in detail our implementation, optimization and performance on these platforms. Our results show speedups of ~125x on a Fermi-GPU and ~20x on a Cray-XE6 24-core node, compared to a sequential CPU code, with near linear scaling on multi-node clusters. To our knowledge, this is the first GISAXS simulation code that is flexible to compute scattered light intensities in all spatial directions allowing full reconstruction of GISAXS patterns for any complex structures and with highresolutions while reducing simulation times from months to minutes.

Sarje, Abhinav↗

How Does Vertical Wind Shear Influence Updraft Characteristics and Hydrometeor Distributions in Supercell Thunderstorms?

Abstract Vertical wind shear is known to affect supercell thunderstorms by displacing updraft hydrometeor mass downshear, thereby facilitating the storms’ longevity. Shear also impacts the size of supercell updrafts, with stronger shear leading to wider, less dilute, and stronger updrafts with likely greater hydrometeor production. To more clearly define the role of shear across different vertical layers on hydrometeor concentrations and displacements relative to supercell updrafts, a suite of idealized numerical model simulations of supercells was conducted. Shear magnitudes were systematically varied across the 0–1, 1–6, and 6–12 km AGL layers, while the thermodynamic environment was held fixed. Simulations show that as shear magnitude increases, especially from 1 to 6 km, updrafts become wider and less dilute with an increase in hydrometeor loading, along with an increase in the low-level precipitation area/rate and total precipitation accumulation. Even with greater updraft hydrometeor loading amid stronger shear, updrafts are more intense in stronger shear simulations due to larger thermal buoyancy owing to wider, less dilute updraft cores. Furthermore, downshear hydrometeor displacements are larger in environments with stronger 1–6-km shear. In contrast, there is relatively less sensitivity of hydrometeor concentrations and displacements to variations in either 0–1- or 6–12-km shear. Results are consistent across free tropospheric relative humidity sensitivity simulations, which show an increase in updraft size and hydrometeor mass with increasing free tropospheric relative humidity owing to a reduction in entrainment-driven dilution for wider updrafts in moister environments. Significance Statement Rotating thunderstorms, known as supercells, are able to persist for multiple hours. One common explanation is that large changes in wind speed and/or direction with height, or shear, transport rain/hail away from supercell updrafts, supporting their maintenance. The strong shear within supercell environments, however, may also lead to greater rail/hail amounts, thereby leading to weaker storms due to this extra mass of water/ice within updrafts. Furthermore, the impact of shear across different height layers on supercell rain/hail characteristics has not been thoroughly investigated. In this study, computer simulations of supercells were conducted to determine that shear occurring between 1 and 6 km above ground level has a large impact on rain/hail distribution in supercells and that stronger shear in this layer leads to wider/stronger supercells with greater rain/hail accumulations at the surface. Additionally, some of the extra mass of water/ice is transported farther away from updrafts due to the stronger environmental storm-relative winds.

Meteorology & Atmospheric Sciences↗

Shift Verification and Validation

This documentation outlines the verification and validation of Shift for the Consortium for Advanced Simulation of Light Water Reactors (CASL). Five main types of problems were used for validation: small criticality benchmark problems; full-core reactor benchmarks for light water reactors; fixed-source coupled neutron-photon dosimetry benchmarks; depletion/burnup benchmarks; and full-core reactor performance benchmarks. We compared Shift results to measured data and other simulated Monte Carlo radiation transport code results, and found very good agreement in a variety of comparison measures. These include prediction of critical eigenvalue, radial and axial pin power distributions, rod worth, leakage spectra, and nuclide inventories over a burn cycle. Based on this validation of Shift, we are confident in Shift to provide reference results for CASL benchmarking.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Two-dimensional simulations of mixing in classical novae: The effect of white dwarf composition and mass

Context. Classical novae are explosive phenomena that take place in stellar binary systems. They are powered by mass transfer from a low-mass main sequence star onto either a CO or ONe white dwarf. The material accumulates for 104–105 yr until ignition under degenerate conditions, resulting in a thermonuclear runaway. The nuclear energy released produces peak temperatures of ~0.1–0.4 GK. During these events, 10 –7 –10 –3 M ⊙ enriched in intermediate-mass elements, with respect to solar abundances, are ejected into the interstellar medium. Yet, the origin of the large metallicity enhancements and the inhomogeneous distribution of chemical species observed in high-resolution spectra of ejected nova shells is not fully understood. Aims. Recent multidimensional simulations have demonstrated that Kelvin-Helmholtz instabilities that operate at the core-envelope interface can naturally produce self-enrichment of the accreted envelope with material from the underlying white dwarf at levels that agree with observations. Yet, such multidimensional simulations have been performed for a small number of cases and much of the parameter space remains unexplored. Methods. We explored the dredge-up, driven by Kelvin-Helmholtz instabilities, for white dwarf masses in the range 0.8–1.25 M ⊙ and different core compositions, that is, CO-rich and ONe-rich substrates. We present a set of five numerical simulations performed in two dimensions aimed at analyzing the possible impact of the white dwarf mass, and composition, on the metallicity enhancement and explosion characteristics. Results. At the time we stop the simulations, we observe greater mixing (~30% higher when measured in the same conditions) and more energetic outbursts for ONe-rich substrates than for CO-rich substrates and more massive white dwarfs.

79 ASTRONOMY AND ASTROPHYSICS↗

Validation of nonlinear gyrokinetic simulations of L- and I-mode plasmas on Alcator C-Mod

New validation of global, nonlinear, ion-scale gyrokinetic simulations (GYRO) is carried out for L- and I-mode plasmas on Alcator C-Mod, utilizing heat fluxes, profile stiffness, and temperature fluctuations. Previous work at C-Mod found that ITG/TEM-scale GYRO simulations can match both electron and ion heat fluxes within error bars in I-mode [White PoP 2015], suggesting that multi-scale (cross-scale coupling) effects [Howard PoP 2016] may be less important in I-mode than in L-mode. New results presented here, however, show that global, nonlinear, ion-scale GYRO simulations are able to match the experimental ion heat flux, but underpredict electron heat flux (at most radii), electron temperature fluctuations, and perturbative thermal diffusivity in both L- and I-mode. Linear addition of electron heat flux from electron scale runs does not resolve this discrepancy. These results indicate that single-scale simulations do not sufficiently describe the I-mode core transport, and that multi-scale (coupled electron- and ion-scale) transport models are needed. A preliminary investigation with multi-scale TGLF, however, was unable to resolve the discrepancy between ion-scale GYRO and experimental electron heat fluxes and perturbative diffusivity, motivating further work with multi-scale GYRO simulations and a more comprehensive study with multi-scale TGLF.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Quantum information and quantum simulation of neutrino physics

In extreme astrophysical environments such as core-collapse supernovae and binary neutron star mergers, neutrinos play a major role in driving various dynamical and microphysical phenomena, such as baryonic matter outflows, the synthesis of heavy elements, and the supernova explosion mechanism itself. The interactions of neutrinos with matter in these environments are flavor-specific, which makes it of paramount importance to understand the flavor evolution of neutrinos. Flavor evolution in these environments can be a highly nontrivial problem thanks to a multitude of collective effects in flavor space, arising due to neutrino-neutrino ($v$-$v$) interactions in regions with high neutrino densities. A neutrino ensemble undergoing flavor oscillations under the influence of significant $v$-$v$ interactions is somewhat analogous to a system of coupled spins with long-range interactions among themselves and with an external field (‘long-range’ in momentum-space in the case of neutrinos). As a result, it becomes pertinent to consider whether these interactions can give rise to significant quantum correlations among the interacting neutrinos, and whether these correlations have any consequences for the flavor evolution of the ensemble. In particular, one may seek to utilize concepts and tools from quantum information science and quantum computing to deepen our understanding of these phenomena. In this article, we attempt to summarize recent work in this field. In conclusion, we also present some new results in a three-flavor setting, considering complex initial states.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Thermal, Fluid and Neutronic Analysis of an LEU Nuclear Thermal Propulsion Core

This paper describes the use of detailed multidisciplinary fluid/thermal/ structural/neutronic simulations to predict performance of the nuclear fuel elements of a Nuclear Thermal Propulsion rocket reactor. To achieve maximum performance, a rocket reactor's fuel must operate near thermal hydraulic, structural and neutronic limits where multidisciplinary interactions are important. Yet physical testing is expensive, time- consuming and risky. Lower-fidelity correlations (heat transfer) and simulations have always existed for design, and one role of detailed numerical analysis is to confirm correlation validity and accuracy. For complex and subtle issues, detailed numerical simulations may prove their value. The paper gives examples of both of these situations. Limitations of the methods and potential extensions will be explored.

Rocket Engine Design↗