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At least 1,441 records · Page 80

Applying Two-Dimensional Correlation Spectroscopy and Principal Component Analysis to Understand How Temperature Affects the Neptunium(V) Absorption Spectrum

The visible-near infrared (Vis-NIR) electronic absorption spectrum of neptunium(V) (NpO 2 + ) comprises numerous f-f electronic transitions with mostly undocumented temperature dependencies. The effect of temperature on the absorption spectrum of the pentavalent neptunyl dioxocation (NpO 2 + ) is an important factor to consider with spectrophotometric applications but has often been overlooked. Optical Vis-NIR absorption spectra (400–1700 nm) of Np(V) (0.017–0.89 M) in 1 M nitric acid were evaluated with varying temperatures (T = 10–80 °C). The intensity, position, and overall shape of the bands were sensitive to interactions with the solvent and coordination environment. Numerous temperature-induced isosbestic points were identified resulting from dynamic, overlapping peak shifts. Spectral variations were characterized using principal component analysis (PCA) and 2D correlation spectroscopy (COS). 2D-COS revealed that the absorption band near 1095 nm likely consists of two bands centered near 1087 and 1096 nm, which cannot be explained by current computational methods. 2D-COS analysis also provided an unambiguous assignment of unresolved peaks in the visible region for comparison with computational predictions. PCA was used to identify nonlinearity in the spectral response at elevated Np(V) concentrations ≥ 0.5 M. This unique experimental data and interpretation will foster a deeper understanding of the absorption spectra for complex actinyl ions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Predictions of axisymmetric free turbulent shear flows using a generalized eddy-viscosity approach

The generalized eddy viscosity approach is described and results are presented of test cases which show that predictions obtained by this approach are adequate for most engineering applications. Because of the importance of starting computations from the injection station where experimentally determined mean and turbulence parameters are rarely available, a very simple core model applicable to simple step-type (slug) profiles was developed. Agreement between predicted and experimental mean profiles was generally almost as good for calculations made by using this model throughout the core region and the transition model for all subsequent regions as predictions made by starting from experimental profiles in the transition region. The generalized eddy-viscosity model, which was developed in part through correlation of turbulence parameters, successfully predicted turbulent shear stress, turbulent intensity, and mean velocity profiles for a 0.040-inch-diameter microjet. Therefore, successful scaling by the model was demonstrated since data used in its development was for jet areas up to 90,000 times as large as the microjet and velocities only 1/20th as high.

Morgenthaler, J. H.↗

Constructing an advanced software tool for planetary atmospheric modeling

Scientific model building can be an intensive and painstaking process, often involving the development of large and complex computer programs. Despite the effort involved, scientific models cannot be easily distributed and shared with other scientists. In general, implemented scientific models are complex, idiosyncratic, and difficult for anyone but the original scientist/programmer to understand. We believe that advanced software techniques can facilitate both the model building and model sharing process. In this paper, we describe a prototype for a scientific modeling software tool that serves as an aid to 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. Our prototype has been developed in the domain of planetary atmospheric modeling, and is being used to construct models of Titan's atmosphere.

Keller, Richard M.↗

Vibrational Spectroscopy of Ions and Radicals Present in the Interstellar Medium and in Planetary Atmospheres: A Theoretical Study

Anharmonic vibrational frequencies and intensities are calculated for OH(H2O)n and H(H2O)n radicals (that form on icy particles of the interstellar medium), HCO radical (the main intermediate in the synthesis of organic molecules in space), NH2(-) and C2H(-) anions, H5(+) cation, and other systems relevant to interstellar chemistry. In addition to pure ions and radicals, their complexes with water are studied to assess the effects of water environment on infrared spectra. The calculations are performed using the correlation-corrected vibrational self-consistent field (CC-VSCF) method with ab initio potential surfaces at the MP2 and CCSD(T) levels. Fundamental, overtone, and combination excitations are computed. The results are in good agreement with available experimental data and provide reliable predictions for vibrational excitations not yet measured in laboratory experiments. The data should be useful for interpretation of astronomically observed spectra and identification of ions and radicals present in the interstellar medium and in planetary atmospheres.

Chaban, Galina M.↗

8760-Based Method for Representing Variable Generation Capacity Value in Capacity Expansion Models: Preprint

Capacity expansion models (CEMs) are widely used to evaluate the least-cost portfolio of electricity generators, transmission, and storage needed to reliably serve demand over the evolution of many years or decades. Various CEM formulations are used to evaluate systems ranging in scale from states or utility service territories to national or multi-national systems. CEMs can be computationally complex, and to achieve acceptable solve times, key parameters are often estimated using simplified methods. In this paper, we focus on two of these key parameters associated with the integration of variable generation (VG) resources: capacity value and curtailment. We first discuss common modeling simplifications used in CEMs to estimate capacity value and curtailment, many of which are based on a representative subset of hours that can miss important tail events or which require assumptions about the load and resource distributions that may not match actual distributions. We then present an alternate approach that captures key elements of chronological operation over all hours of the year without the computationally intensive economic dispatch optimization typically employed within more detailed operational models. The updated methodology characterizes the (1) contribution of VG to system capacity during high load and net load hours, (2) the curtailment level of VG, and (3) the potential reductions in curtailments enabled through deployment of storage and more flexible operation of select thermal generators. We apply this alternate methodology to an existing CEM, the Regional Energy Deployment System (ReEDS). Results demonstrate that this alternate approach provides more accurate estimates of capacity value and curtailments by explicitly capturing system interactions across all hours of the year. This approach could be applied more broadly to CEMs at many different scales where hourly resource and load data is available, greatly improving the representation of challenges associate with integration of variable generation resources.

14 SOLAR ENERGY↗

Structural Modification of Graphene on Copper Substrates Irradiated by Nanosecond High-Intensity Ion Beams

Interaction of a nanosecond high-intensity pulsed ion beam with thin graphene films on copper substrates is analyzed. Methods of Raman spectroscopy are used to investigate the degree of graphene degradation depending on the integral implanted dose. The role of the substrate in the structural degradation of graphene irradiated by charged particle beams is demonstrated using the software package SRIM, intended for modeling radiative defect cascades under irradiation by charged particle beams, and the data on radiation resistance of graphene available in the literature.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

On the minimum number of radiation field parameters to specify gas cooling and heating functions

Fast and accurate approximations of gas cooling and heating functions are needed for hydrodynamic galaxy simulations. We use machine learning to analyze atomic gas cooling and heating functions in the presence of a generalized incident local radiation field computed by Cloudy. We characterize the radiation field through binned radiation field intensities instead of the photoionization rates used in our previous work. We find a set of 6 energy bins whose intensities exhibit relatively low correlation. We use these bins as features to train machine learning models to predict Cloudy cooling and heating functions at fixed metallicity. We compare the relative SHapley Additive exPlanation (SHAP) value importance of the features. From the SHAP analysis, we identify a feature subset of 3 energy bins (0.5-1, 1-4, and 13-16Ry) with the largest importance and train additional models on this subset. We compare the mean squared errors and distribution of errors on both the entire training data table and a randomly selected 20% test set withheld from model training. The machine learning models trained with 3 and 6 bins, as well as 3 and 4 photoionization rates, have comparable accuracy everywhere, with errors ≳10 times smaller than for the interpolation table of Gnedin and Hollon (2012). We conclude that 3 energy bins (or 3 analogous photoionization rates: molecular hydrogen photodissociation, neutral hydrogen HI, and fully ionized carbon CVI) are sufficient to characterize the dependence of the gas cooling and heating functions on our assumed incident radiation field model.

79 ASTRONOMY AND ASTROPHYSICS↗

Tokamak-independent Software Analysis Suite for Multi-Spectral Line-Polarization MSE diagnostics

A tokamak-independent analysis suite has been developed to process data from Motional Stark Effect (MSE) diagnostics. The software supports multi-spectral line-polarization MSE diagnostics which simultaneously measure emission at the MSE sigma and pi lines as well as at two `background' wavelengths that are displaced from the MSE spectrum by a few nanometers. This analysis accurately estimates the amplitude of partially-polarized background light at the sigma and pi wavelengths even in situations where the background light changes rapidly in time and space. The signal amplitude at many frequencies is computed using a numerical-beat algorithm which allows the retardance of the MSE photo-elastic modulators (PEMs) to be monitored during routine operation. It also allows the use of summed intensities at multiple frequencies in the calculation of polarization direction, which increases the effective signal strength and reduces sensitivity to PEM retardance drift. The software allows the polarization angles to be corrected for calibration drift using a system that illuminates the MSE diagnostic with polarized light at four known polarization angles within ten seconds of a plasma discharge The software suite is modular, parallelized, and portable to other facilities. (2016-06-06)

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Tokamak-independent Software Analysis Suite for Multi-Spectral Line-Polarization MSE diagnostics

A tokamak-independent analysis suite has been developed to process data from Motional Stark Effect (MSE) diagnostics. The software supports multi-spectral line-polarization MSE diagnostics which simultaneously measure emission at the MSE sigma and pi lines as well as at two `background' wavelengths that are displaced from the MSE spectrum by a few nanometers. This analysis accurately estimates the amplitude of partially-polarized background light at the sigma and pi wavelengths even in situations where the background light changes rapidly in time and space. The signal amplitude at many frequencies is computed using a numerical-beat algorithm which allows the retardance of the MSE photo-elastic modulators (PEMs) to be monitored during routine operation. It also allows the use of summed intensities at multiple frequencies in the calculation of polarization direction, which increases the effective signal strength and reduces sensitivity to PEM retardance drift. The software allows the polarization angles to be corrected for calibration drift using a system that illuminates the MSE diagnostic with polarized light at four known polarization angles within ten seconds of a plasma discharge The software suite is modular, parallelized, and portable to other facilities.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

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.↗