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DOE OSTI2022

Proteome-scale Structure Prediction Data - Pseudodesulfovibrio mercurii

The number of proteins predicted for Pseudodesulfovibrio mercurii is 3,446, each of which have five predicted structures from an AlphaFold run, as well as structural alignment results using the TMscore-based structural alignment method within the APoc program. Specifically, AlphaFold outputs the atoms and coordinates of the protein model in human-readable PDB files and quantitative prediction metrics in Python PICKLE files. The 5 models have been ranked based on the predicted TM-score (pTMS), a quantitative confidence metric output by AlphaFold that reports on protein model quality. The top ranked model has undergone an energy minimization calculation to relax and remove any potential clashes in the atomic coordinates. Structural alignment results are stored in two files for each protein; the top ranked model (as discussed above) is used for all alignment analyses. Both are compressed gzip files that, once unpacked, are human readable. The first file is the TMalign score results and contains the quantitative metrics for the top alignments between the predicted structure and experimental structures from the PDB70, a curated non-redundant database of about 80,000 experimental structures developed by the Soding lab. Each data point in this file is directly associated with one experimental structure; PDB ID and brief meta-data about the protein taken from the PDB70 file are reported alongside the quantitative metrics. The second results file contains the raw results associated with each alignment reported in the score results file. Specifically, the translation and rotation arrays for each alignment are provided so that the structural alignment can be recreated. Additionally, residue-level scores are reported to quantify the closeness of the aligned residues between the predicted and experimental models.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Hyper-Differential Sensitivity Analysis of Uncertain Parameters in PDE-Constrained Optimization

Many problems in engineering and sciences require the solution of large scale optimization constrained by partial differential equations (PDEs). Though PDE-constrained optimization is itself challenging, most applications pose additional complexity, namely, uncertain parameters in the PDEs. Uncertainty quantification (UQ) is necessary to characterize, prioritize, and study the influence of these uncertain parameters. Sensitivity analysis, a classical tool in UQ, is frequently used to study the sensitivity of a model to uncertain parameters. In this article, we introduce "hyper-differential sensitivity analysis" which considers the sensitivity of the solution of a PDE-constrained optimization problem to uncertain parameters. Our approach is a goal-oriented analysis which may be viewed as a tool to complement other UQ methods in the service of decision making and robust design. We formally define hyper-differential sensitivity indices and highlight their relationship to the existing optimization and sensitivity analysis literatures. Assuming the presence of low rank structure in the parameter space, computational efficiency is achieved by leveraging a generalized singular value decomposition in conjunction with a randomized solver which converts the computational bottleneck of the algorithm into an embarrassingly parallel loop. Two multi-physics examples, consisting of nonlinear steady state control and transient linear inversion, demonstrate efficient identification of the uncertain parameters which have the greatest influence on the optimal solution.

97 MATHEMATICS AND COMPUTING↗

NASA NTRS1970

A bibliography of wildlife movements and tracking systems

A bibliography is presented consisting of 1,005 references concerned with animal orientation, homing, navigation, migration, and home range movements, and the various methods of tracking and monitoring such behavior through biotelemetry, radar, and various banding and tagging techniques. A majority of the publications appeared between 1950 and 1970, although the most intensive search was made of the 1965-1970 period. A small number of older articles and books were included because they appeared to have some special or unusual value. The references have been organized in two ways. First, they are grouped in primary categories on the basis of the behavior involved such as orientation, homing, etc., and the methods of tracking. Second, within each of the resulting major areas, the items are arranged in terms of the species of animal. This sequence is maintained throughout the bibliography and in many cases represents a rank order according to the number of publications found.

Werber, M.↗

NASA NTRS1977

Effect of heating rate on toxicity of pyrolysis gases from some elastomers

The effect of heating rate on the toxicity of the pyrolysis gases from six elastomers was investigated, using a screening test method. The elastomers were polyisoprene (natural rubber), styrene-butadiene rubber (SBR), ethylene propylene diene terpolymer (EPDM), acrylonitrile rubber, chlorosulfonated polyethylene rubber, and polychloroprene. The rising temperature and fixed temperature programs produced exactly the same rank order of materials based on time to death. Acrylonitrile rubber exhibited the greatest toxicity under these test conditions, and carbon monoxide was not found in sufficient concentrations to be the primary cause of death.

Hilado, C. J.↗

DOE OSTI2018

Entity Resolution at Large Scale: Benchmarking and Algorithmics

We seek scalable benchmarks for entity resolution problems. Solutions to these problems range from trivial approaches such as string sorting to sophisticated methods such as statistical relational learning. The theoretical and practical complexity of these approaches varies widely, so one of the primary purposes of a benchmark will be to quantify the trade-off between solution quality and runtime. We are motivated by the ubiquitous nature of entity resolution as a fundamental problem faced by any organization that ingests large amounts of noisy text data. A benchmark is typically a rigid specification that provides an objective measure usable for ranking implementations of an algorithm. For example the Top500 and HPCG500 bench- marks rank supercomputers based on their performance of dense and sparse linear algebra problems (respectively). These two benchmarks require participants to report FLOPS counts attainable on various machines. Our purpose is slightly different. Whereas the supercomputing benchmarks mentioned above hold algorithms constant and aim to rank machines, we are primarily interested in ranking algorithms. As mentioned above, entity resolution problems can be approached in completely different ways. We believe that users of our benchmarks must decide what sort of procedure to run before comparing implementations and architectures. Eventually, we also wish to provide a mechanism for ranking machines while holding algorithmic approach constant . Our primary contributions are parallel algorithms for computing solution quality mea- sures per entity. We find in some real datasets that many entities are quite easy to resolve while others are difficult, with a heavy skew toward the former case. Therefore, measures such as global confusion matrices, F measures, etc. do not meet our benchmarking needs. We design methods for computing solution quality at the granularity of a single entity in order to know when proposed solutions do well in difficult situations (perhaps justifying extra computational), or struggling in easy situations. We report on progress toward a viable benchmark for comparing entity resolution algo- rithms. Our work is incomplete, but we have designed and prototyped several algorithms to help evalute the solution quality of competing approaches to these problems. We envision a benchmark in which the objective measure is a ratio of solution quality to runtime.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2016

Delayed Update Algorithms for Quantum Monte Carlo Simulation on GPU: Extended Abstract

QMCPACK is open source scientific software designed to perform Quantum Monte Carlo (QMC) simulation, a first-principles method for describing many-body systems. The evaluation of each Monte Carlo move requires finding the determinant of a dense matrix in the wave functions. This calculation forms a key computational kernel in QMCPACK. After each accepted event, the wave function matrix undergoes a rank-one update to represent a single particle move within the system. The matrix inverse is updated via the Sherman-Morrison formula; occasionally, the explicit inverse must be recomputed to maintain numerical stability.; We propose an alternate approach to this kernel that utilizes QR factorization to maintain stability without refactorization. In addition, algorithms based on a novel delayed update scheme are explored in this effort. This strategy enables probability evaluation for multiple successive Monte Carlo moves, with application of accepted moves to the wave function matrix delayed until an event is denied, or a predetermined limit on acceptances p is reached. Accepted events grouped in this manner are then applied to the matrix en bloc with enhanced arithmetic intensity and computational efficiency. Delayed update Sherman-Morrison probability evaluation algorithms with CPU and GPU-accelerated implementations are tested, profiled, and analyzed. A QR based delayed update algorithm remains in development. Results are evaluated against existing methods for numerical stability and efficiency; emphasis is placed on large systems, for which acceleration is critical.

Computer Science↗

DOE OSTI2017

The impact of intensity-modulated radiation therapy plan normalization in the postprostatectomy settingâ€”does it matter?

The International Commission on Radiation Units & Measurements -83 recommends prescribing intensity-modulated radiation therapy (IMRT) in a dose-volume manner. Despite this, clinical variation still exists in how prostate IMRT plans are prescribed. This study aims to investigate the impact of different plan normalization methods for postprostatectomy IMRT. IMRT treatment plans were created retrospectively for 20 postprostatectomy patients. These were normalized such that the dose received by 98% (D98) of the planning target volume (PTV) was equal to 100% of the prescribed dose. All plans were individually optimized to achieve target coverage and organ at risk (OAR) dose constraints. Each patient's plan was then copied and normalized such that the mean dose (Dmean) received by the PTV was equal to 100% of the prescribed dose. The International Commission on Radiation Units & Measurements -83 recommended dosimetric end points were extracted for targets and Quantitative Analyses of Normal Tissue Effects in the Clinic or Radiation Therapy Oncology Group 0534 end points extracted for OARs. Statistical analysis using the Wilcoxon signed-rank test to measure the difference between data from plans normalized to D98 and Dmean was conducted. Extracted dosimetric end points of the targets and OARs were significantly higher in plans normalized to D98 than Dmean (p Normalization impacts on dosimetric end points of a plan. Hence, reporting the normalization method used is necessary to allow for meaningful interpretation of IMRT dosimetric studies.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

DOE OSTI2016

Assessment of high enthalpy geothermal resources and promising areas of Chile

This work aims to assess geothermal power potential in identified high enthalpy geothermal areas in the Chilean Andes, based on reservoir temperature and volume. In addition, we present a set of highly favorable geothermal areas, but without enough data in order to quantify the resource. Information regarding geothermal systems was gathered and ranked to assess Indicated or Inferred resources, depending on the degree of confidence that a resource may exist as indicated by the geoscientific information available to review. Resources were estimated through the USGS Heat in Place method. A Monte Carlo approach is used to quantify variability in boundary conditions. Estimates of total Indicated resource are confined to 3 geothermal systems; Apacheta, El Tatio and Tolhuaca, yielding a total value of 228 ± 154. MWe. The estimates of the total Inferred resources for Chile include 6 geothermal systems and yield a total value of 431 ± 321. MWe. Standard deviation reflects the high variability of reservoir specific parameters for each system. A set of 65 favorable geothermal areas are proposed as the most likely future development targets. Finally, eight of them have initial exploration results that suggest they are highly favorable targets as potential geothermal resources.

58 GEOSCIENCES↗

DOE OSTI2023

Development of the high energy engineering X-ray (HEX) superconducting wiggler, magnetic measurement, installation, and commissioning

The High energy Engineering X-ray (HEX) diffraction beamline at the National Synchrotron Light Source II (NSLS-II) at Brookhaven National Lab (BNL) is the first high-energy beamline capable of reaching 200 keV for a monochromatic beam. With the 3 GeV electron beam energy for the NSLS-II ring, only the superconducting wiggler (SCW) producing greater than 4 T peak field can cover these ranges with a sufficient number of photons. The 1.2 m-long HEX-SCW has a period length of 70 mm and a field strength on-axis of 4.3 T. It utilizes no liquid helium, and the vertical aperture size of the electron beam vacuum chamber is 8 mm. Unlike regular undulators/wigglers, there is no standard configuration for the magnetic measurement system for superconducting insertion devices. The NSLS-II Insertion Devices group has developed, in collaboration with the vacuum group, a novel in-vacuum Hall mapper with a 1.75 m in-vacuum linear motor and an in-vacuum flip coil system utilizing many commercial-off-the-shelf products. The measurements were conducted at the BNL, and the device was installed in the ring and commissioned. Here, this paper provides a description of the SCW and its magnetic measurement systems, as well as a brief account of the installation and commissioning efforts.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Burden of bacterial bloodstream infections and recent advances for diagnosis

Abstract Bloodstream infections (BSIs) and subsequent organ dysfunction (sepsis and septic shock) are conditions that rank among the top reasons for human mortality and have a great impact on healthcare systems. Their treatment mainly relies on the administration of broad-spectrum antimicrobials since the standard blood culture-based diagnostic methods remain time-consuming for the pathogen's identification. Consequently, the routine use of these antibiotics may lead to downstream antimicrobial resistance and failure in treatment outcomes. Recently, significant advances have been made in improving several methodologies for the identification of pathogens directly in whole blood especially regarding specificity and time to detection. Nevertheless, for the widespread implementation of these novel methods in healthcare facilities, further improvements are still needed concerning the sensitivity and cost-effectiveness to allow a faster and more appropriate antimicrobial therapy. This review is focused on the problem of BSIs and sepsis addressing several aspects like their origin, challenges, and causative agents. Also, it highlights current and emerging diagnostics technologies, discussing their strengths and weaknesses.

Costa, Susana P.↗

DOE OSTI2016

Energy Cost Impact of Non-Residential Energy Code Requirements

The 2012 International Energy Conservation Code contains 396 separate requirements applicable to non-residential buildings; however, there is no systematic analysis of the energy cost impact of each requirement. Consequently, limited code department budgets for plan review, inspection, and training cannot be focused on the most impactful items. An inventory and ranking of code requirements based on their potential energy cost impact is under development. The initial phase focuses on office buildings with simple HVAC systems in climate zone 4C. Prototype building simulations were used to estimate the energy cost impact of varying levels of non-compliance. A preliminary estimate of the probability of occurrence of each level of non-compliance was combined with the estimated lost savings for each level to rank the requirements according to expected savings impact. The methodology to develop and refine further energy cost impacts, specific to building type, system type, and climate location is demonstrated. As results are developed, an innovative alternative method for compliance verification can focus efforts so only the most impactful requirements from an energy cost perspective are verified for every building and a subset of the less impactful requirements are verified on a random basis across a building population. The results can be further applied in prioritizing training material development and specific areas of building official training.

code compliance↗

DOE OSTI2016

Energy Cost Impact of Non-Residential Energy Code Requirements

Energy Codes, code compliance↗

DOE OSTI2014

Calculation of state-to-state differential and integral cross sections for atom-diatom reactions with transition-state wave packets

A recently proposed transition-state wave packet method [R. Welsch, F. Huarte-Larrañaga, and U. Manthe, J. Chem. Phys. 136, 064117 (2012)] provides an efficient and intuitive framework to study reactive quantum scattering at the state-to-state level. It propagates a few transition-state wave packets, defined by the eigenfunctions of the low-rank thermal flux operator located near the transition state, into the asymptotic regions of the reactant and product arrangement channels separately using the corresponding Jacobi coordinates. The entire S-matrix can then be assembled from the corresponding flux-flux cross-correlation functions for all arrangement channels. Since the transition-state wave packets can be defined in a relatively small region, its transformation into either the reactant or product Jacobi coordinates is accurate and efficient. Furthermore, the grid/basis for the propagation, including the maximum helicity quantum number K, is much smaller than that required in conventional wave packet treatments of state-to-state reactive scattering. This approach is implemented for atom-diatom reactions using a time-dependent wave packet method and applied to the H + D{sub 2} reaction with all partial waves. Excellent agreement with benchmark integral and differential cross sections is achieved.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2016

Marine Hydrokinetic Energy Site Identification and Ranking Methodology Part I: Wave Energy

Marine hydrokinetic energy is a promising and growing piece of the renewable energy sector that offers high predictability and additional energy sources for a diversified energy economy. This report investigates the market opportunities for wave energy along the U.S. coastlines. It is part one of a two-part investigation into the United State's two largest marine hydrokinetic resources (wave and tidal). Wave energy technology is still an emerging form of renewable energy for which large-scale, grid-connected project costs are currently poorly defined. Ideally, device designers would like to know the resource conditions at economical project sites so they can optimize device designs. On the other hand, project developers need detailed device cost data to identify sites where projects are economical. That is, device design and siting are, to some extent, a coupled problem. This work describes a methodology for identifying likely deployment locations based on a set of criteria that wave energy experts in industry, academia, and national laboratories agree are likely to be important factors for all technology types. This work groups the data for the six criteria into 'locales' that are defined as the smaller of either the local transmission grid or a state boundary. The former applies to U.S. islands (e.g., Hawaii, American Samoa) and rural villages (e.g., in Alaska); the latter applies to states in the contiguous United States. These data are then scored from 0 to 10 according to scoring functions that were developed with input from wave energy industry and academic experts. The scores are aggregated using a simple product method that includes a weighting factor for each criterion. This work presents two weighting scenarios: a long-term scenario that does not include energy price (weighted zero) and a near term scenario that includes energy price. The aggregated scores are then used to produce ranked lists of likely deployment locales. In both scenarios, Hawaii and the Pacific Northwest (northern California, Oregon, and Washington) rank at the top of the lists. Hawaii ranks highest in the near-term scenario because it has high energy costs. In the long-term scenario, Oregon ranks highest because it has a large market and an energetic resource. Several East Coast states and Puerto Rico are also identified as potential wave energy deployment sites if technological innovations make it possible to efficiently generate electricity from the modest resource there. There are also several small-market sites in Alaska and U.S. Pacific Islands that rank particularly well in the near-term analysis due to their high energy prices. These locations may represent opportunities to demonstrate economical wave energy conversion as a stepping-stone to larger markets. Several factors that will affect wave project costs and siting have not been considered here -- including permitting constraints, conflicting use, seasonal resource variability, extreme event likelihood, and distance to ports -- because consistent data are unavailable or technology-independent scoring could not be identified. As the industry continues to mature and converge around a subset of device archetypes with well-defined costs, more precise investigations of project siting that include these factors will be possible. For now, these results provide a high-level guide pointing to the regions where markets and resource will one day support commercial wave energy projects.

16 TIDAL AND WAVE POWER↗

DOE OSTI2021

Converting tabular data into images for deep learning with convolutional neural networks

Abstract Convolutional neural networks (CNNs) have been successfully used in many applications where important information about data is embedded in the order of features, such as speech and imaging. However, most tabular data do not assume a spatial relationship between features, and thus are unsuitable for modeling using CNNs. To meet this challenge, we develop a novel algorithm, image generator for tabular data (IGTD), to transform tabular data into images by assigning features to pixel positions so that similar features are close to each other in the image. The algorithm searches for an optimized assignment by minimizing the difference between the ranking of distances between features and the ranking of distances between their assigned pixels in the image. We apply IGTD to transform gene expression profiles of cancer cell lines (CCLs) and molecular descriptors of drugs into their respective image representations. Compared with existing transformation methods, IGTD generates compact image representations with better preservation of feature neighborhood structure. Evaluated on benchmark drug screening datasets, CNNs trained on IGTD image representations of CCLs and drugs exhibit a better performance of predicting anti-cancer drug response than both CNNs trained on alternative image representations and prediction models trained on the original tabular data.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

TeraChem: Accelerating electronic structure and ab initio molecular dynamics with graphical processing units

Developed over the past decade, TeraChem is an electronic structure and ab initio molecular dynamics software package designed from the ground up to leverage graphics processing units (GPUs) to perform large-scale ground and excited state quantum chemistry calculations in the gas and the condensed phase. TeraChem’s speed stems from the reformulation of conventional electronic structure theories in terms of a set of individually optimized high-performance electronic structure operations (e.g., Coulomb and exchange matrix builds, one- and two-particle density matrix builds) and rank-reduction techniques (e.g., tensor hypercontraction). Recent efforts have encapsulated these core operations and provided language-agnostic interfaces. Finally, this greatly increases the accessibility and flexibility of TeraChem as a platform to develop new electronic structure methods on GPUs and provides clear optimization targets for emerging parallel computing architectures.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2015

Comparison of HLW Glass Melting Rate Between Frit and Glass Forming Chemicals Using X-Ray Computed Tomography

Efforts are being made to increase the loading of Hanford tank wastes in glass while meeting melter lifetime expectancies, as well as requirements for processing, regulatory compliance, and product quality. To achieve these goals, the Department of Energy – Office of River Protection (DOE-ORP) has requested that the Savannah River National Laboratory (SRNL) support the advancement of glass formulations and process control strategies in various key technical areas, which include melting rate studies. Numerous parameters influence cold cap melting and it is important to identify laboratory test methods to discern changes in melting rate. One of the primary screening tools being used at SRNL for melting rate comparisons is the dry-fed melt rate furnace (MRF). The MRF has been very effective in ranking relative melting rates of candidate frits for the Defense Waste Processing Facility (DWPF) on the laboratory-scale, which has successfully translated to facility operations.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2015

Radiological data consolidation and 3D modeling of a building - 15473

A portion of a building at an industrial facility that conducted monazite sands-processing operations in the 1950's under contract to the Atomic Energy Commission (AEC) became contaminated. Subsequently the U.S. Department of Energy designated the facility for remedial action under the Formerly Used Sites Remedial Action Program (FUSRAP). Remedial investigation, remedial actions and post-remediation surveys have been conducted in portions of the building. Radiological data for the interior of the building were compiled, evaluated and presented in a three dimensional (3-D) model (the model) created by AMEC Foster Wheeler in order to identify areas that meet the Record of Decision (ROD) cleanup criteria, and identity areas that may require remedial action or may require additional investigation due to data gaps. The data from different phases of investigation and remediation cover different portions of the building and in some cases overlap. In addition, the data were collected over a period of more than ten years, for different objectives, and thus the instruments and methods for establishing efficiency were not necessarily consistent. The data consolidation process included determining the relative quality of data points to include in the model and the development of rationale associated with assigning a quality level (i.e. ranking) to each data point. The rationale for ranking data quality included, as the primary determining factors, chronological order of the data (most recent was ranked as more reliable), certainty of the sample locations within the building, and analytical data quality. A 3-D model of the building was created using a laser point cloud scan which was then converted into a 3-D design model. Sample locations were then entered into the model and linked with the analytical database to allow display of the radiological results in the model. The visual model allows both strategic and tactical decisions to be made, depending on the level of detail examined. The evaluation process allowed maximum use of the historical data set, rather than requiring older data to be disregarded, and provided at a minimum a qualitative sense of data quality/confidence in the data. The (authors)process also highlights the importance of collecting high quality data from the very beginning with a consistent locational coordinate system, and the need for a good visualization model in order to assess contaminant locations during remedial action or post-remediation surveys.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗