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At least 1,603 records · Page 89

Invasion of the Giant X-Ray Bubbles

More bizarre news from the bizarre world of neutron stars: They got dozens of giant X-ray bubbles taller than the Empire State Building forming and popping every second. Yet finding evidence of this bubble blowing was no childish endeavor. It took a team of Berkeley scientists just about all they could muster: three days' worth of observational data and 1,200 hours of number-crunching on the slickest of supercomputers at the Lawrence Livermore National Laboratory (LLNL). Mind you, these are the same powerful computers used to model nuclear reactions and calculate Bill Gates' salary. Neutron stars are already known as the bad boys of the cosmic neighborhood. They are the core remains of exploded stars, with a mass greater than our sun condensed into a sphere no bigger than Manhattan, A teaspoon of its densely-packed surface matter, the analogy goes, would weigh three billion tons back on earth. Its 10 trillion gauss magnetic field could wipe your credit card clean at a distance half-way to the moon. Its intense gravity lures gas from nearby stars, spinning the neutron star to speeds of up to a thousand times a second. But giant X-ray bubbles dancing on the surface? That even freaked out the discoverers. "Early on, I tended to disbelieve what the calculations were telling me," said Richard Klein, who splits his time between Berkeley and LLNL. "The bubbles 'appeared' and I wasn't convinced they were real."

Wanjek, Christopher↗

The Transition from Thick to Thin Plate Wake Physics: Whither Vortex Shedding?

The near and very near wake of a flat plate with a circular trailing edge is investigated with data from direct numerical simulations. Computations were performed for six different combinations of the Reynolds numbers based on plate thickness (D) and boundary layer momentum thickness upstream of the trailing edge (theta). Unlike the case of the cylinder, these Reynolds numbers are independent parameters for the flat plate. The separating boundary layers are turbulent in all the cases investigated. One objective of the study is to understand the changes in the wake vortex shedding process as the plate thickness is reduced (increasing theta/D). The value of D varies by a factor of 16 and that of theta by approximately 5 in the computations. Vortex shedding is vigorous in the low theta/D cases with a substantial decrease in shedding intensity in the large theta/D cases. Other shedding characteristics are also significantly altered with increasing theta/D. A visualization of the shedding process in the different cases is provided and discussed. The basic shedding mechanism is explored in depth. The effect of changing theta/D on the time-averaged, near-wake velocity statistics is also discussed. A functional relationship between the shedding frequency and the Reynolds numbers mentioned above is obtained.

CFD↗

Full Integration of Lipidomics Data into Multi-OMIC Functional Enrichment

Lipids have numerous roles critical to living systems. Many of these vital functions are tightly linked or regulated by proteins. Even though the function of many lipid-related enzymes is known, direct links between most individual lipid species and the enzymes that metabolize them are severely lacking. This missing connection impedes biological progress. A resource that allows users to quickly identify protein-lipid relationships will advance our understanding of lipid homeostasis and metabolic perturbed systems. Databases are readily available for mapping small molecule metabolites (i.e., polar metabolites) and specific oxidized fatty acid lipids (e.g., arachidonic acid derivatives) to proteins/enzymes known to be directly involved in metabolism of these molecules (e.g. SMPDB, Reactome, HMDB, BioCyc). This enables the integration of metabolite and protein (as well as transcript) data when performing functional enrichment and metabolic modeling allowing researchers to rapidly examine metabolic pathways from multiple omics sources. Currently, linking lipidomics data with proteomics data is conducted using a time-intensive, user defined, manual process. Here we propose creating a tool that will link lipidomics and proteomics data and also conduct functional enrichment analysis and visualization allowing for full statistical integration. Using text-mining approaches, we will extract lipid references from uniprot and create a database linking lipid species to enzymes directly related to their metabolism. We will also extract directional annotation, which will allow even greater specificity when linking data types and will help eliminate false positives from functional associations.

59 BASIC BIOLOGICAL SCIENCES↗

GlyQ-IQ: Glycomics Quintavariate-Informed Quantification with High-Performance Computing and GlycoGrid 4D Visualization

Dense LC-MS datasets have convoluted extracted ion chromatograms with multiple chromatographic peaks that cloud the differentiation between intact compounds with their overlapping isotopic distributions, peaks due to insource ion fragmentation, and noise. Making this differentiation is critical in glycomics datasets because chromatographic peaks correspond to different intact glycan structural isomers. The GlyQ-IQ software is targeted chromatography centric software designed for chromatogram and mass spectra data processing and subsequent glycan composition annotation. The targeted analysis approach offers several key advantages to LC-MS data processing and annotation over traditional algorithms. A priori information about the individual target’s elemental composition allows for exact isotope profile modeling for improved feature detection and increased sensitivity by focusing chromatogram generation and peak fitting on the isotopic species in the distribution having the highest intensity and data quality. Glycan target annotation is corroborated by glycan family relationships and in source fragmentation detection. The GlyQ-IQ software is developed in this work (Part 1) and was used to profile N-glycan compositions from human serum LC-MS Datasets. The companion manuscript GlyQ-IQ Part 2 discusses developments in human serum N-glycan sample preparation, glycan isomer separation, and glycan electrospray ionization. A case study is presented to demonstrate how GlyQ-IQ identifies and removes confounding chromatographic peaks from high mannose glycan isomers from human blood serum. In addition, GlyQ-IQ was used to generate a broad N-glycan profile from a high resolution (100K/60K) nESI-LS-MS/MS dataset including CID and HCD fragmentation acquired on a Velos Pro Mass spectrometer. 101 glycan compositions and 353 isomer peaks were detected from a single sample. 99% of the GlyQ-IQ glycan-feature assignments passed manual validation and are backed with high resolution mass spectra and mass accuracies less than 7 ppm.

Environmental Molecular Sciences Laboratory↗

Upgrade of the Minos+ Experiment Data Acquisition for the High Energy NuMI Beam Run

The Minos+ experiment is an extension of the Minos experiment at a higher energy and more intense neutrino beam, with the data collection having begun in the fall of 2013. The neutrino beam is provided by the Neutrinos from the Main Injector (NuMI) beam-line at Fermi National Accelerator Laboratory (Fermilab). The detector apparatus consists of two main detectors, one underground at Fermilab and the other in Soudan, Minnesota with the purpose of studying neutrino oscillations at a base line of 735 km. The original data acquisition system has been running for several years collecting data from NuMI, but with the extended run from 2013, parts of the system needed to be replaced due to obsolescence, reliability problems, and data throughput limitations. Specifically, we have replaced the front-end readout controllers, event builder, and data acquisition computing and trigger processing farms with modern, modular and reliable devices with few single points of failure. The new system is based on gigabit Ethernet TCP/IP communication to implement the event building and concatenation of data from many front-end VME readout crates. The simplicity and partitionability of the new system greatly eases the debugging and diagnosing process. As a result, the new system improves throughput by about a factor of three compared to the old system, up to 800 megabits per second, and has proven robust and reliable in the current run.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

The feasibility of head motion tracking in helical CT: A step toward motion correction

Purpose: To establish a practical and accurate motion tracking method for the development of rigid motion correction methods in helical x-ray computed tomography (CT). Methods: A commercially available optical motion tracking system provided 6 degrees of freedom pose measurements at 60 Hz. A 4 Multiplication-Sign 4 calibration matrix was determined to convert raw pose data acquired in tracker coordinates to a fixed CT coordinate system with origin at the isocenter of the scanner. Two calibration methods, absolute orientation (AO), and a new method based on image registration (IR), were compared by means of landmark analysis and correlation coefficient in phantom images coregistered using the derived motion transformations. Results: Transformations calculated using the IR-derived calibration matrix were found to be more accurate, with positional errors less than 0.5 mm (mean RMS), and highly correlated image voxel intensities. The AO-derived calibration matrix yielded larger mean RMS positional errors ( Asymptotically-Equal-To 1.0 mm), and poorer correlation coefficients. Conclusions: The authors have demonstrated the feasibility of accurate motion tracking for retrospective motion correction in helical CT. Their new IR-based calibration method based on image registration and function minimization was simpler to perform and delivered more accurate calibration matrices. This technique is a useful tool for future work on rigid motion correction in helical CT and potentially also other imaging modalities.

60 APPLIED LIFE SCIENCES↗

Precursor Analysis Report: SQL Slammer Worm Infection of Davis-Besse Nuclear Power Plant 2003

The SQL Slammer Worm Infection of Davis-Besse Nuclear Power Plant 2003 Precursor Analysis Report leverages publicly available information about Davis-Besse’s 2003 cyber attack and catalogs anomalous observables for each technique employed in the attack. This analysis is based upon the methodology of the Cybersecurity for the Operational Technology Environment (CyOTE) program. On 25 January 2003, the SQL Slammer worm infected more than 90% of vulnerable hosts and crashed the internet in 10 to 15 minutes, making it one of the fastest spreading worms in history. SQL Slammer is a fileless, memory-resident worm that remotely exploits a stack-based buffer overflow vulnerability on local hosts to intensively scan and rapidly self-propagate across the internet. The worm infected approximately 300,000 unpatched hosts running Microsoft Structured Query Language (SQL) Server 2000 or Microsoft Desktop Engine (MSDE) 2000 with SQL Server Resolution Service. The SQL Slammer worm indirectly infected FirstEnergy’s Davis-Besse nuclear power plant by first infecting a consultant’s company network server and then propagating through an external misconfigured connection into Davis-Besse’s site network. The infection caused major network congestion, slow performance, data overloads, and the inability of local hosts to communicate with each other, which eventually caused a loss of availability and a loss of view when the Safety Parameter Display System (SPDS) and Plant Process Computer (PPC) crashed. At the time of the infection, the plant was already offline, the digital monitoring systems had redundant analog backups, and the plant control and safety functions were not affected, so there were no concerns of a safety breach. However, this incident resulted in many lessons learned and spawned important discussions about cybersecurity’s role in nuclear safety and electric power reliability regulation, policy, and guidance. Researchers and analysts identified 10 unique techniques utilized during the attack with a total of 640 observables using MITRE ATT&CK® for Industrial Control Systems. The CyOTE program assesses observables accompanying techniques used prior to the triggering event to identify opportunities to detect malicious activity. If observables accompanying the attack techniques are perceived and investigated prior to the triggering event, earlier comprehension of malicious activity can take place. Eight of the identified techniques used during Davis-Besse cyber attack were precursors to the triggering event. Analysis identified 596 observables associated with these precursor techniques, 428 of which were assessed to have an increased likelihood of being perceived in the 331 days preceding the triggering event. The response and comprehension time could have been reduced if the observables had been identified earlier. The information gathered in this report contributes to a library of observables tied to a repository of artifacts, data sources, and technique detection references for practitioners and developers to support the comprehension of indicators of attack. Asset owners and operators can use these products if they experience similar observables or to prepare for comparable scenarios.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗

Definition of the unsteady vortex flow over a wing/body configuration

A problem of current interest in computational aerodynamics is the prediction of unsteady vortex flows over aircraft at high angles of attack. A six-month experimental effort was conducted at the John H. Harper Wind Tunnel to acquire qualitative and quantitative information on the unsteady vortex flow over a generic wing-body configuration at high angles of attack. A double-delta flat-plate wing with beveled edges was combined with a slender sharp-nosed body-of-revolution fuselage to form the generic configuration. This configuration produces a strong attached leading edge vortex on the wing, as well as sharply-peaked flow velocity spectra above the wing. While it thus produces flows with several well-defined features of current interest, the model was designed for efficiency of representation in computational codes. A moderate number of surface pressure ports and two unsteady pressure sensors were used to study the pressure distribution over the wing and body surface at high angles of attack; the unsteady pressure sensing did not succeed because of inadequate signal-to-noise ratio. A pulsed copper vapor laser sheet was used to visualize the vortex flow over the model, and vortex trajectories, burst locations, mutual induction of vortex systems from the forebody, strake, and wing, were quantified. Laser Doppler velocimetry was used to quantify all 3 components of the time-average velocity in 3 data planes perpendicular to the freestream direction. Statistics of the instantaneous velocity were used to study intermittency and fluctuation intensity. Hot-film anemometry was used to study the fluctuation energy content in the velocity field, and the spectra of these fluctuations. In addition, a successful attempt was made to measure velocity spectra, component by component, using laser velocimetry, and these were compared with spectra measured by hot-film anemometry at several locations.

Liou, S. G.↗

Artificial intelligence support for scientific model-building

Scientific model-building can be a time-intensive and painstaking process, often involving the development of large and complex computer programs. Despite the effort involved, scientific models cannot easily be distributed and shared with other scientists. In general, implemented scientific models are complex, idiosyncratic, and difficult for anyone but the original scientific development team to understand. We believe that artificial intelligence techniques can facilitate both the model-building and model-sharing process. In this paper, we overview our effort to build a scientific modeling software tool that aids the scientist in developing and using models. This tool includes an interactive intelligent graphical interface, a high-level domain specific modeling language, a library of physics equations and experimental datasets, and a suite of data display facilities.

Keller, Richard M.↗

Sound Diffraction Modeling of Rotorcraft Noise Around Terrain

A new computational technique, Wave Confinement (WC), is extended here to account for sound diffraction around arbitrary terrain. While diffraction around elementary scattering objects, such as a knife edge, single slit, disc, sphere, etc. has been studied for several decades, realistic environments still pose significant problems. This new technique is first validated against Sommerfeld's classical problem of diffraction due to a knife edge. This is followed by comparisons with diffraction over three-dimensional smooth obstacles, such as a disc and Gaussian hill. Finally, comparisons with flight test acoustics data measured behind a hill are also shown. Comparison between experiment and Wave Confinement prediction demonstrates that a Poisson spot occurred behind the isolated hill, resulting in significantly increased sound intensity near the center of the shadowed region.

Stephenson, James H.↗

Modeling Soft X‐Ray Emissions at the Dayside Magnetopause

In this study, we simulate the Solar Wind Charge Exchange (SWCX) soft X-ray emissions at dayside magnetosheath and cusps by using magnetohydrodynamic (MHD) and LAtmos TEst Particle (LaTeP) models. MHD models are unable to resolve the particle kinetic effects, such as the different behaviors of ions with different q/m, or distinguish the magnetospheric plasma from the solar wind plasma. We investigate these effects with the LaTeP model. As the LaTeP model does not self-compute magnetic and electric field, the magnetic and electric field data obtained from Open Geospace General Circulation Model (OpenGGCM) and Lagrangian version of the piecewise parabolic method (PPMLR) MHD model are used as the input to LaTeP model. The soft X-ray emissivity maps simulated from pure OpenGGCM and PPMLR MHD approaches and from LaTeP-OpenGGCM and LaTeP-PPMLR approaches are presented and compared. The results indicate that the LaTeP model can well resolve the kinetic effects and can be used to investigate the individual spectral characteristics. Therefore, the LaTeP model is a complementary approach for simulating the X-ray emissions near the dayside magnetopause. We also calculate the ratio of integrated OVII/OVIII line intensities, produced by charge exchange of O7+ ions and O8+ ions, respectively. We find a relatively higher ratio at the bow shock compared to the surrounding areas, suggesting that this ratio can be an effective parameter to identify the bow shock location.

Qiuyu Xu↗

Improvement in the Accuracy of Flux Measurement of Radio Sources by Exploiting an Arithmetic Pattern in Photon Bunching Noise

A hierarchy of statistics of increasing sophistication and accuracy is proposed to exploit an interesting and fundamental arithmetic structure in the photon bunching noise of incoherent light of large photon occupation number, with the purpose of suppressing the noise and rendering a more reliable and unbiased measurement of the light intensity. The method does not require any new hardware, rather it operates at the software level with the help of high-precision computers to reprocess the intensity time series of the incident light to create a new series with smaller bunching noise coherence length. The ultimate accuracy improvement of this method of flux measurement is limited by the timing resolution of the detector and the photon occupation number of the beam (the higher the photon number the better the performance). The principal application is accuracy improvement in the signal-limited bolometric flux measurement of a radio source.

79 ASTRONOMY AND ASTROPHYSICS↗

Isotopologue Consistency of Semi-Empirically Computed InfraRed Line Lists and Further Improvement for Rare Isotopologues: CO2 and SO2 Case Studies.

The semi-empirical molecular rovibrational IR line lists, such as ExoMol, TheoReTs, and Ames, combine the experimental accuracy and theoretical power to reach better than 0.1 cm-1 accuracy for line positions and better than 80-90% agreement for line intensities. The quality of these existing semi-empirical IR lists allows further improvements of intensity and line positions for those unobserved minor isotopologues. This paper presents our new BTRHE (Best Theory + Reliable High-resolution Experiment) strategy implementation. For line intensity, the isotopologue consistency and the patterns of mass dependence in the Ames-296K SO2 and CO2 IR lists are quantitatively presented along the mass-inverse coordinates. The consistency and patterns are better than those in existing experimental data. The methodology proposed here can be used to identify inconsistencies, outliers, and mistakes in intensities, and help improve Effective Dipole Model (EDM) and molecular IR databases. We call for an experimental study on the 50006 and 60007 bands of CO2 628. For line position predictions, a simple approach combining the variational IR line lists with Effective Hamiltonian (EH) model may refine the effective rotational constants A0/B0/C0 and quartic centrifugal distortion constants of minor isotopologues. The prediction accuracy may be improved by two orders of magnitude, i.e. reaching 0-5 MHz prediction accuracy in the range of J<20-30, Ka<10-20, and 0.01-0.02 MHz accuracy for A0/B0/C0. Several important factors have been systematically investigated and discussed, e.g. convergence, uncertainties, higher order terms, fixing EH parameters, mass coordinates, etc. Amicrowave (MW) line set consisting of 644,636 strong transitions for all 30 isotopologues and corresponding refined EH(Ames) parameters are reported in the supplementary material. This approach may be easily extended to rovibrational bands, hot bands, and other molecular systems.

Xinchuan Huang↗

Star-forming galaxies as the origin of diffuse high-energy backgrounds: gamma-ray and neutrino connections, and implications for starburst history

Star-forming galaxies have been predicted to contribute considerably to the diffuse gamma-ray background as they are guaranteed reservoirs of cosmic rays. Assuming that the hadronic interactions responsible for high-energy gamma rays also produce high-energy neutrinos and that O(100) PeV cosmic rays can be produced and confined in starburst galaxies, we here discuss the possibility that star-forming galaxies are also the main sources of the high-energy neutrinos observed by the IceCube experiment. First, we compute the diffuse gamma-ray background from star-forming galaxies, adopting the latest Herschel PEP/HerMES luminosity function and relying on the correlation between the gamma-ray and infrared luminosities reported by Fermi observations. Then we derive the expected intensity of the diffuse high-energy neutrinos from star-forming galaxies including normal and starburst galaxies. Our results indicate that starbursts, including those with active galactic nuclei and galaxy mergers, could be the main sources of the high-energy neutrinos observed by the IceCube experiment. We find that assuming a cosmic-ray spectral index of 2.1–2.2 for all starburst-like galaxies, our predictions can be consistent with both the Fermi and IceCube data, but larger indices readily fail to explain the observed diffuse neutrino flux. Taking the starburst high-energy spectral index as free parameter, and extrapolating from GeV to PeV energies, we find that the spectra harder than E{sup -2.15} are likely to be excluded by the IceCube data, which can be more constraining than the Fermi data for this population.

79 ASTRONOMY AND ASTROPHYSICS↗

Steepened structures in equatorial spread F. 2: Theory

This paper investigates the properties of a one-dimensional fluid model of plasma convection in the equatorial F region ionosphere. The model equations are similar in form to Burgers equation except for additional higher-order spatial derivatives. Like Burgers equation, solution to the model have the form of propagating, shocklike structures. Numerical simulations of the model closely resemble the steepened structures observed by sounding rocket plasma density probes within equatorial spread F. Simulated denstiy power spectra, like the spectra computed from in situ data, seem to possess power law forms with a break at wavelengths of about 100 m. The precise wavenumber of the spectral break is determined by the ambipolar diffusion coefficient. The model predicts that electric field fluctuations perpendicular to the direction of plasma steepening should be proportional to the plasma density fluctuations. Electric field fluctuations parallel to the steepening will be due primarily to the ambipolar field and have a Boltzmann relationship with density (square of the absolute value of delta E) approximately equal to (K(exp 2))(square of the absolute value of (delta n/n)). At wavelengths less than about 300 m, the ambipolar field should be the dominant component of the total field intensity.

Hysell, D. L↗

The Spectral and Statistical Properties of Turbulence Generated by a Vortex/Blade-Tip Interaction

The perpendicular interaction of a streamwise vortex with the tip of a lifting blade was studied in incompressible flow to provide information useful to the accurate prediction of helicopter rotor noise and the understanding of vortex dominated turbulent flows. The vortex passed 0.3 chord lengths to the suction side of the blade tip, providing a weak interaction. Single and two-point turbulence measurements were made using sub-miniature four sensor hot-wire probes 15 chord lengths downstream of the blade trailing edge; revealing the mean velocity and Reynolds stress tensor distributions of the turbulence, as well as its spanwise length scales as a function of frequency. The single point measurements show the flow downstream of the blade to be dominated by the interaction of the original tip vortex and the vortex shed by the blade. These vortices rotate about each other under their mutual induction, winding up the turbulent wakes of the blades. This interaction between the vortices appears to be the source of new turbulence in their cores and in the region between them. This turbulence appears to be responsible for some decay in the core of the original vortex, not seen when the blade is removed. The region between the vortices is not only a region of comparatively large stresses, but also one of intense turbulence production. Velocity autospectra measured near its center suggests the presence quasi-periodic large eddies with axes roughly parallel to a line joining the vortex cores. Detailed two-point measurements were made on a series of spanwise cuts through the flow so as to reveal the turbulence scales as they would be seen along the span of an intersecting airfoil. The measurements were made over a range of probe separations that enabled them to be analyzed not only in terms of coherence and phase spectra but also in terms of wave-number frequency (kappa-omega) spectra, computed by transforming the measured cross-spectra with respect to the spanwise separation of the probes. These data clearly show the influence of the coherent eddies in the spiral wake and the turbulent region between the cores. These eddies produce distinct peaks in the upwash velocity kappa-omega spectra, and strong anisotropy manifested both in the decay of the kappa-omega spectrum at larger wave-numbers and in differences between the kappa-omega spectra of different components. None of these features are represented in the von Karman spectrum for isotropic turbulence that is often used in broadband noise computations. Wave-number frequency spectra measured in the cores appear to show some evidence that the turbulence outside sets tip core waves, as has previously been hypothesized. These spectra also provide for the first time a truly objective method for distinguishing velocity fluctuations produced by core wandering from other motions.

Devenport, William J.↗

Mid-frequency Band Dynamics of Large Space Structures

High and low intensity dynamic environments experienced by a spacecraft during launch and on-orbit operations, respectively, induce structural loads and motions, which are difficult to reliably predict. Structural dynamics in low- and mid-frequency bands are sensitive to component interface uncertainty and non-linearity as evidenced in laboratory testing and flight operations. Analytical tools for prediction of linear system response are not necessarily adequate for reliable prediction of mid-frequency band dynamics and analysis of measured laboratory and flight data. A new MATLAB toolbox, designed to address the key challenges of mid-frequency band dynamics, is introduced in this paper. Finite-element models of major subassemblies are defined following rational frequency-wavelength guidelines. For computational efficiency, these subassemblies are described as linear, component mode models. The complete structural system model is composed of component mode subassemblies and linear or non-linear joint descriptions. Computation and display of structural dynamic responses are accomplished employing well-established, stable numerical methods, modern signal processing procedures and descriptive graphical tools. Parametric sensitivity and Monte-Carlo based system identification tools are used to reconcile models with experimental data and investigate the effects of uncertainties. Models and dynamic responses are exported for employment in applications, such as detailed structural integrity and mechanical-optical-control performance analyses.

dynamics↗