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At least 937 records · Page 52

Monochromatic calculations of atmospheric radiative transfer due to molecular line absorption

Sensitivity studies related to the effects of line cutoff, spectral resolution, and temperature and pressure interpolations in radiative transfer have been performed so that a data set of absorption coefficients for water vapor, CO2, and O3 may be created efficiently. Results show that computations of absorption coefficients are affected only slightly by cutting a line off at a wave number 190 times the Lorentz half width from the center, or equivalently, cutting off 0.33 percent of the line intensity from the wings. To achieve a relative cooling rate error smaller than 2 percent, it is sufficient to precompute the absorption coefficient at three temperatures (210, 250, and 290 K) and 19 pressures with Delta (log 10 p) = 0.2. The absorption coefficient at other conditions can be interpolated linearly with pressure and exponentially with a quadratic in temperature. For the spectral resolution the absorption coefficients can be adequately computed at 0.01, 0.002, 0.005, and 0.025/cm intervals in the thermal water vapor, the CO2 and O3 bands, and the solar water vapor bands, respectively, which limits the error to only a few percent in the cooling and heating rates. Using the precomputed absorption coefficients, repeated monochromatic calculations of atmospheric heating/cooling rates for radiation model developments and for comparison with less detailed calculations are no longer difficult.

Chou, M.-D.↗

The 27-28 October 1986 FIRE IFO cirrus case study: Cirrus parameter relationships derived from satellite and lidar data

Cirrus cloud radiative and physical characteristics are determined using a combination of ground-based, aircraft, and satellite measurements taken as part of the First ISCCP Regional Experiment (FIRE) Cirrus Intensive Field Observations (IFO) during October and November 1986. Lidar backscatter data are used to define cloud base, center, and top heights and the corresponding temperatures. Coincident GOES 4 km visible (0.65 microns) and 8 km infrared window (11.5 microns) radiances are analyzed to determine cloud emittances and reflectances. Infrared optical depth is computed from the emittance results. Visible optical depth is derived from reflectance using a theoretical ice crystal scattering model and an empirical bidirectional reflectance mode. No clouds with visible optical depths greater than 5 or infrared optical depths less than 0.1 were used in the analysis. Average cloud thickness ranged from 0.5 km to 8 km for the 71 scenes. An average visible scattering efficiency of 2.1 was found for this data set. The results reveal a significant dependence of scattering efficiency on cloud temperature.

Minnis, Patrick↗

Cloud spatial structure during the FIRE MS IFO

The fractal properties of clouds observed during the FIRE Marine Stratocumulus Intensive Field Observations (MS IFO) and their effects on the large scale radiative properties of the atmosphere are examined. This involves three states: (1) analysis of LANDSAT Thematic Mapper (TM) cloud data to determine the scaling properties associated with various cloud types; (2) simulation of fractal clouds with realistic scaling properties; and (3) computation of mean radiative properties of fractal clouds as a function of their scaling properties. Thirty-three LANDSAT scenes were acquired as part of the FIRE Marine Stratocumulus IFO in July 1987. They exhibit a wide variety of stratocumulus structures. Analysis has so far focused upon the July 7 scene, in which the NASA ER-2, the BMO C130 and the NCAR Electra repeatedly gathered data across a stratocumulus-fair weather cumulus transition.

Cahalan, Robert F.↗

The 27-28 October 1986 FIRE IFO cirrus case study - Cirrus parameter relationships derived from satellite and lidar data

Cirrus cloud radiative and physical characteristics are determined using a combination of ground-based, aircraft, and satellite measurements taken as part of the First ISCCP Regional Experiment (FIRE) Cirrus Intensive Field Observations (IFO) during October and November 1986. Lidar backscatter data are used to define cloud base, center, and top heights and the corresponding temperatures. Coincident GOES 4 km visible (0.65 microns) and 8 km infrared window (11.5 microns) radiances are analyzed to determine cloud emittances and reflectances. Infrared optical depth is computed from the emittance results. Visible optical depth is derived from reflectance using a theoretical ice crystal scattering model and an empirical bidirectional reflectance mode. No clouds with visible optical depths greater than 5 or infrared optical depths less than 0.1 were used in the analysis. Average cloud thickness ranged from 0.5 km to 8 km for the 71 scenes. An average visible scattering efficiency of 2.1 was found for this data set. The results reveal a significant dependence of scattering efficiency on cloud temperature.

Minnis, Patrick↗

Imaging Sensor Flight and Test Equipment Software

The Lightning Imaging Sensor (LIS) is one of the components onboard the Tropical Rainfall Measuring Mission (TRMM) satellite, and was designed to detect and locate lightning over the tropics. The LIS flight code was developed to run on a single onboard digital signal processor, and has operated the LIS instrument since 1997 when the TRMM satellite was launched. The software provides controller functions to the LIS Real-Time Event Processor (RTEP) and onboard heaters, collects the lightning event data from the RTEP, compresses and formats the data for downlink to the satellite, collects housekeeping data and formats the data for downlink to the satellite, provides command processing and interface to the spacecraft communications and data bus, and provides watchdog functions for error detection. The Special Test Equipment (STE) software was designed to operate specific test equipment used to support the LIS hardware through development, calibration, qualification, and integration with the TRMM spacecraft. The STE software provides the capability to control instrument activation, commanding (including both data formatting and user interfacing), data collection, decompression, and display and image simulation. The LIS STE code was developed for the DOS operating system in the C programming language. Because of the many unique data formats implemented by the flight instrument, the STE software was required to comprehend the same formats, and translate them for the test operator. The hardware interfaces to the LIS instrument using both commercial and custom computer boards, requiring that the STE code integrate this variety into a working system. In addition, the requirement to provide RTEP test capability dictated the need to provide simulations of background image data with short-duration lightning transients superimposed. This led to the development of unique code used to control the location, intensity, and variation above background for simulated lightning strikes at user-selected locations.

Freestone, Kathleen↗

Anomaly Detection in Dynamic Networks

Anomaly detection in dynamic communication networks has many important security applications. These networks can be extremely large and so detecting any changes in their structure can be computationally challenging; hence, computationally fast, parallelisable methods for monitoring the network are paramount. For this reason the methods presented here use independent node and edge based models to detect locally anomalous substructures within communication networks. As a first stage, the aim is to detect changes in the data streams arising from node or edge communications. Throughout the thesis simple, conjugate Bayesian models for counting processes are used to model these data streams. A second stage of analysis can then be performed on a much reduced subset of the network comprising nodes and edges which have been identified as potentially anomalous in the first stage. The first method assumes communications in a network arise from an inhomogeneous Poisson process with piecewise constant intensity. Anomaly detection is then treated as a changepoint problem on the intensities. The changepoint model is extended to incorporate seasonal behavior inherent in communication networks. This seasonal behavior is also viewed as a changepoint problem acting on a piecewise constant Poisson process. In a static time frame, inference is made on this extended model via a Gibbs sampling strategy. In a sequential time frame, where the data arrive as a stream, a novel, fast Sequential Monte Carlo (SMC) algorithm is introduced to sample from the sequence of posterior distributions of the change points over time. A second method is considered for monitoring communications in a large scale computer network. The usage patterns in these types of networks are very bursty in nature and don’t fit a Poisson process model. For tractable inference, discrete time models are considered, where the data are aggregated into discrete time periods and probability models are fitted to the communication counts. In a sequential analysis, anomalous behavior is then identified from outlying behavior with respect to the fitted predictive probability models. Seasonality is again incorporated into the model and is treated as a changepoint model on the transition probabilities of a discrete time Markov process. Second stage analytics are then developed which combine anomalous edges to identify anomalous substructures in the network.

97 MATHEMATICS AND COMPUTING↗

A Model Tree Generator (MTG) Framework for Simulating Hydrologic Systems: Application to Reservoir Routing

Data-driven algorithms have been widely used as effective tools to mimic hydrologic systems. Unlike black-box models, decision tree algorithms offer transparent representations of systems and reveal useful information about the underlying process. A popular class of decision tree models is model tree (MT), which is designed for predicting continuous variables. Most MT algorithms employ an exhaustive search mechanism and a pre-defined splitting criterion to generate a piecewise linear model. However, this approach is computationally intensive, and the selection of the splitting criterion can significantly affect the performance of the generated model. These drawbacks can limit the application of MTs to large datasets. To overcome these shortcomings, a new flexible Model Tree Generator (MTG) framework is introduced here. MTG is equipped with several modules to provide a flexible, efficient, and effective tool for generating MTs. The application of the algorithm is demonstrated through simulation of controlled discharge from several reservoirs across the Contiguous United States (CONUS).

54 ENVIRONMENTAL SCIENCES↗

Coupled Electron-Photon Monte Carlo Radiation Transport for Next-Generation Computing Systems

Traditional Monte Carlo particle transport codes are expected to run inefficiently on next-generation architectures as they are memory-intensive and highly divergent. Since electrons and photons also behave differently, the future for coupled electron-photon radiation transport looks even worse. This project describes preliminary efforts to improve the performance of Monte Carlo particle transport codes when using accelerators like the graphics processing unit (GPU). Two key issues are addressed: how to handle memory-intensive tallies, and how to reduce divergence. Tallying on the GPU can be done efficiently by post-processing particle data, or by using a feature called warp shuffle for summing scores in parallel during the simulation. Reducing divergence is possible by using an event-based algorithm for particle tracking instead of the traditional history-based one. Although performance tests presented in this work show that the history-based algorithm generally outperformed the event-based one for simple problems, this outcome will likely change as the complexity of the code increases.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

WinPSSP : a revamp of the computer program PSSP and its performance solving the crystal structures of small organic compounds and solids of biological and pharmaceutical interest

The direct-space methods software Powder Structure Solution Program ( PSSP ) [Pagola & Stephens (2010). J. Appl. Cryst. 43 , 370–376] has been migrated to the Windows OS and the code has been optimized for fast runs. WinPSSP is a user-friendly graphical user interface that allows the input of preliminary crystal structure information, integrated intensities of the reflections and FWHM, the definition of structural parameters and a simulated annealing schedule, and the visualization of the calculated and experimental diffraction data overlaid for each individual solution. The solutions are reported as filename.cif files, which can be used to analyze packing motifs and chemical bonding, and to input the atomic coordinates into the Rietveld analysis software GSAS. WinPSSP performance in straightforward crystal structure determinations has been evaluated using 18 molecular solids with 6–20 degrees of freedom. The free-distribution program as well as multimedia tutorials can be accessed at http://users.uoi.gr/nkourkou/winpssp/.

60 APPLIED LIFE SCIENCES↗

Aerodynamic Effects of High Turbulence Intensity on a Variable-Speed Power-Turbine Blade With Large Incidence and Reynolds Number Variations

The effects of high inlet turbulence intensity on the aerodynamic performance of a variable speed power turbine blade are examined over large incidence and Reynolds number ranges. These results are compared to previous measurements made in a low turbulence environment. Both high and low turbulence studies were conducted in the NASA Glenn Research Center Transonic Turbine Blade Cascade Facility. The purpose of the low inlet turbulence study was to examine the transitional flow effects that are anticipated at cruise Reynolds numbers. The current study extends this to LPT-relevant turbulence levels while perhaps sacrificing transitional flow effects. Assessing the effects of turbulence at these large incidence and Reynolds number variations complements the existing database. Downstream total pressure and exit angle data were acquired for 10 incidence angles ranging from +15.8deg to −51.0deg. For each incidence angle, data were obtained at five flow conditions with the exit Reynolds number ranging from 2.12×10(exp 5) to 2.12×10(exp 6) and at a design exit Mach number of 0.72. In order to achieve the lowest Reynolds number, the exit Mach number was reduced to 0.35 due to facility constraints. The inlet turbulence intensity, Tu, was measured using a single-wire hotwire located 0.415 axial-chord upstream of the blade row. The inlet turbulence levels ranged from 8 to 15 percent for the current study. Tu measurements were also made farther upstream so that turbulence decay rates could be calculated as needed for computational inlet boundary conditions. Downstream flow field measurements were obtained using a pneumatic five-hole pitch/yaw probe located in a survey plane 7 percent axial chord aft of the blade trailing edge and covering three blade passages. Blade and endwall static pressures were acquired for each flow condition as well. The blade loading data show that the suction surface separation that was evident at many of the low Tu conditions has been eliminated. At the extreme positive and negative incidence angles, the data show substantial differences in the exit flow field. These differences are attributable to both the higher inlet Tu directly and to the thinner inlet endwall boundary layer that the turbulence grid imposes.

Flegel, Ashlie B.↗

Aerodynamic Effects of High Turbulence Intensity on a Variable-Speed Power-Turbine Blade with Large Incidence and Reynolds Number Variations

The effects of high inlet turbulence intensity on the aerodynamic performance of a variable speed power turbine blade are examined over large incidence and Reynolds number ranges. These results are compared to previous measurements made in a low turbulence environment. Both high and low turbulence studies were conducted in the NASA Glenn Research Center Transonic Turbine Blade Cascade Facility. The purpose of the low inlet turbulence study was to examine the transitional flow effects that are anticipated at cruise Reynolds numbers. The current study extends this to LPT-relevant turbulence levels while perhaps sacrificing transitional flow effects. Assessing the effects of turbulence at these large incidence and Reynolds number variations complements the existing database. Downstream total pressure and exit angle data were acquired for 10 incidence angles ranging from +15.8deg to −51.0deg. For each incidence angle, data were obtained at five flow conditions with the exit Reynolds number ranging from 2.12×10(exp 5) to 2.12×10(exp 6) and at a design exit Mach number of 0.72. In order to achieve the lowest Reynolds number, the exit Mach number was reduced to 0.35 due to facility constraints. The inlet turbulence intensity, Tu, was measured using a single-wire hotwire located 0.415 axial-chord upstream of the blade row. The inlet turbulence levels ranged from 8 to 15 percent for the current study. Tu measurements were also made farther upstream so that turbulence decay rates could be calculated as needed for computational inlet boundary conditions. Downstream flow field measurements were obtained using a pneumatic five-hole pitch/yaw probe located in a survey plane 7 percent axial chord aft of the blade trailing edge and covering three blade passages. Blade and endwall static pressures were acquired for each flow condition as well. The blade loading data show that the suction surface separation that was evident at many of the low Tu conditions has been eliminated. At the extreme positive and negative incidence angles, the data show substantial differences in the exit flow field. These differences are attributable to both the higher inlet Tu directly and to the thinner inlet endwall boundary layer that the turbulence grid imposes.

Flegel, Ashlie B.↗

Automation based on knowledge modeling theory and its applications in engine diagnostic systems using Space Shuttle Main Engine vibrational data

Humans can perform many complicated tasks without explicit rules. This inherent and advantageous capability becomes a hurdle when a task is to be automated. Modern computers and numerical calculations require explicit rules and discrete numerical values. In order to bridge the gap between human knowledge and automating tools, a knowledge model is proposed. Knowledge modeling techniques are discussed and utilized to automate a labor and time intensive task of detecting anomalous bearing wear patterns in the Space Shuttle Main Engine (SSME) High Pressure Oxygen Turbopump (HPOTP).

Kim, Jonnathan H.↗

CMed: Crowd Analytics for Medical Imaging Data

In this work, we present a visual analytics framework, CMed, for exploring medical image data annotations acquired from crowdsourcing. CMed can be used to visualize, classify, and filter crowdsourced clinical data based on a number of different metrics such as detection rate, logged events, and clustering of the annotations. CMed provides several interactive linked visualization components to analyze the crowd annotation results for a particular video and the associated workers. Additionally, all results of an individual worker can be inspected using multiple linked views in our CMed framework. We allow a crowdsourcing application analyst to observe patterns and gather insights into the crowdsourced medical data, helping him/her design future crowdsourcing applications for optimal output from the workers. We demonstrate the efficacy of our framework with two medical crowdsourcing studies: polyp detection in virtual colonoscopy videos and lung nodule detection in CT thin-slab maximum intensity projection videos. We also provide experts' feedback to show the effectiveness of our framework. Lastly, we share the lessons we learned from our framework with suggestions for integrating our framework into a clinical workflow.

97 MATHEMATICS AND COMPUTING↗

Robust Machine Learning Inference from X-ray Absorption Near Edge Spectra through Featurization

X-ray absorption spectroscopy (XAS) is a commonly employed technique for characterizing functional materials. In particular, X-ray absorption near edge spectra (XANES) encode local coordination and electronic information, and machine learning approaches to extract this information are of significant interest. To date, most ML approaches for XANES have primarily focused on using the raw spectral intensities as input, overlooking the potential benefits of incorporating spectral transformations and dimensionality reduction techniques into ML predictions. Here, in this work, we focused on systematically comparing the impact of different featurization methods on the performance of ML models for XAS analysis. We evaluated the classification and regression capabilities of these models on computed data sets and validated their performance on previously unseen experimental data sets. Our analysis revealed an intriguing discovery: the cumulative distribution function feature achieves both high prediction accuracy and exceptional transferability. This remarkably robust performance can be attributed to its tolerance to horizontal shifts in the spectra, which is crucial when validating models using experimental data. While this work exclusively focuses on XANES analysis, we anticipate that the methodology presented here will hold promise as a versatile asset to the broader spectroscopy community.

36 MATERIALS SCIENCE↗

Mn IV -Oxo complex of a bis(benzimidazolyl)-containing N5 ligand reveals different reactivity trends for Mn IV -oxo than Fe IV -oxo species

Using the pentadentate ligand (N-bis(1-methyl-2-benzimidazolyl)methyl-N-(bis-2-pyridylmethyl)amine, 2pyN2B), presenting two pyridyl and two (N-methyl)benzimidazolyl donor moieties in addition to a central tertiary amine, new Mn II and Mn IV -oxo complexes were generated and characterized. The [Mn IV (O)(2pyN2B)] 2+ complex showed spectroscopic signatures (i.e., electronic absorption band maxima and intensities, EPR signals, and Mn K-edge X-ray absorption edge and near-edge data) similar to those observed for other MnIV-oxo complexes with neutral, pentadentate N 5 supporting ligands. The near-IR electronic absorption band maximum of [Mn IV (O)(2pyN2B)] 2+ , as well as DFT-computed metric parameters, are consistent with the equatorial (N-methyl)benzimidazolyl ligands being stronger donors to the MnIV center than the pyridyl and quinolinyl ligands found in analogous MnIV-oxo complexes. The hydrogen- and oxygen-atom transfer reactivities of [Mn IV (O)(2pyN2B)] 2+ were assessed through reactions with hydrocarbons and thioanisole, respectively. When compared with related Mn IV -oxo adducts, [Mn IV (O)(2pyN2B)] 2+ showed muted reactivity in hydrogen-atom transfer reactions with hydrocarbons. This result stands in contrast to observations for the analogous Fe IV -oxo complexes, where [Fe IV (O)(2pyN2B)] 2+ was found to be one of the more reactive members of its class.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Constraint methods that accelerate free-energy simulations of biomolecules

Atomistic molecular dynamics simulations of biomolecules are critical for generating narratives about biological mechanisms. The power of atomistic simulations is that these are physics-based methods that satisfy Boltzmann’s law, so they can be used to compute populations, dynamics, and mechanisms. But physical simulations are computationally intensive and do not scale well to the sizes of many important biomolecules. One way to speed up physical simulations is by coarse-graining the potential function. Another way is to harness structural knowledge, often by imposing spring-like restraints. But harnessing external knowledge in physical simulations is problematic because knowledge, data, or hunches have errors, noise, and combinatoric uncertainties. Here, we review recent principled methods for imposing restraints to speed up physics-based molecular simulations that promise to scale to larger biomolecules and motions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

IMG/M: integrated genome and metagenome comparative data analysis system

The Integrated Microbial Genomes with Microbiome Samples (IMG/M: https://img.jgi.doe.gov/m/) system contains annotated DNA and RNA sequence data of (i) archaeal, bacterial, eukaryotic and viral genomes from cultured organisms, (ii) single cell genomes (SCG) and genomes from metagenomes (GFM) from uncultured archaea, bacteria and viruses and (iii) metagenomes from environmental, host associated and engineered microbiome samples. Sequence data are generated by DOE's Joint Genome Institute (JGI), submitted by individual scientists, or collected from public sequence data archives. Structural and functional annotation is carried out by JGI's genome and metagenome annotation pipelines. A variety of analytical and visualization tools provide support for examining and comparing IMG/M's datasets. IMG/M allows open access interactive analysis of publicly available datasets, while manual curation, submission and access to private datasets and computationally intensive workspace-based analysis require login/password access to its expert review(ER) companion system (IMG/M ER: https://img.jgi.doe.gov/ mer/). Since the last report published in the 2014 NAR Database Issue, IMG/M's dataset content has tripled in terms of number of datasets and overall protein coding genes, while its analysis tools have been extended to cope with the rapid growth in the number and size of datasets handled by the system.

59 BASIC BIOLOGICAL SCIENCES↗

SU-D-18A-02: Towards Real-Time On-Board Volumetric Image Reconstruction for Intrafraction Target Verification in Radiation Therapy

Purpose: To expedite on-board volumetric image reconstruction from limited-angle kV—MV projections for intrafraction verification. Methods: A limited-angle intrafraction verification (LIVE) system has recently been developed for real-time volumetric verification of moving targets, using limited-angle kV—MV projections. Currently, it is challenged by the intensive computational load of the prior-knowledge-based reconstruction method. To accelerate LIVE, we restructure the software pipeline to make it adaptable to model and algorithm parameter changes, while enabling efficient utilization of rapidly advancing, modern computer architectures. In particular, an innovative two-level parallelization scheme has been designed: At the macroscopic level, data and operations are adaptively partitioned, taking into account algorithmic parameters and the processing capacity or constraints of underlying hardware. The control and data flows of the pipeline are scheduled in such a way as to maximize operation concurrency and minimize total processing time. At the microscopic level, the partitioned functions act as independent modules, operating on data partitions in parallel. Each module is pre-parallelized and optimized for multi-core processors (CPUs) and graphics processing units (GPUs). Results: We present results from a parallel prototype, where most of the controls and module parallelization are carried out via Matlab and its Parallel Computing Toolbox. The reconstruction is 5 times faster on a data-set of twice the size, compared to recently reported results, without compromising on algorithmic optimization control. Conclusion: The prototype implementation and its results have served to assess the efficacy of our system concept. While a production implementation will yield much higher processing rates by approaching full-capacity utilization of CPUs and GPUs, some mutual constraints between algorithmic flow and architecture specifics remain. Based on a careful analysis of the prototype performance, it will be feasible to resolve such issues through appropriate algorithmic modifications or special-purpose hardware, thus enabling target verification in seconds with the LIVE system. This work was partially supported by a research grant from Varian Medical Systems.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗