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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix

Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Parameter inference with deep jointly informed neural networks

Abstract A common challenge in modeling inertial confinement fusion (ICF) experiments with computer simulations is that many of the simulation inputs are unknown and cannot be directly measured. Often, parameters that are measured in the experiment are used to infer the unknown inputs by solving the inverse problem: finding the set of simulation inputs that result in outputs consistent with the experimental observations. In ICF, this process is often referred to as a “post‐shot analysis.” Post‐shot analyses are challenging as the inverse problem is often highly degenerate, the input parameter space is vast, and simulations are computationally expensive. In this work, deep neural network models equipped with model uncertainty estimates are used to train inverse models, which map directly from output to input space, to find the distribution of post‐shot simulations that are consistent with experimental observations. The inverse model approach is compared to Markov chain Monte Carlo (MCMC) sampling of the forward model, which maps from input to output space, for parameter inference tasks of varying complexity. The inverse models perform best when searching vast parameter spaces for post‐shot simulations that are consistent with a large number of observables, where MCMC sampling can be prohibitively expensive. We demonstrate how augmenting inverse models with autoencoders enable the inclusion of several dozen observables in the inverse mapping, reducing the degeneracy of the model and improving the accuracy of the post‐shot analysis.

Humbird, Kelli D.↗
DOE OSTI2019

Informative Path Planning for Mapping Radiation

This project involves making measurements of contaminated areas using portable radiation detectors and small robots. Tasks involve operating detectors and small robots, combining data acquisition for the two systems, and automating the systems. The end result is a radiation map of contamination areas. Localization of radioactive sources and mapping of contamination distribution is essential when responding to emergencies, or when dealing with cleanup efforts. Radiation maps are used for situational awareness and for establishing a safe perimeter. However, it may be hazardous or impossible for humans to safely enter the site and survey the area. Informative Path Planning (IPP) is used to design a path for a robotic sensor platform to gather the most information about the radiation distribution while operating under the set of constraints given by the dynamics of the robot and other requirements such as minimizing the overall mission time. The key challenge for IPP is the tight coupling in multiple layers of decisions: Selection of locations to visit; Allocation of sensors to those locations; Processing of information gathered. Given a robot equipped with a basic gamma detector and Lidar sensor, how can we efficiently explore an unknown environment in such a way that we can satisfy the robot's constraints while simultaneously maximizing the accuracy of the map and minimizing the total runtime? This work presents a systematic procedure for IPP and environmental mapping that: Selects the best locations at which to sample; Finds the best path for robots; Estimates the measurement value at unknown locations using a Gaussian Process regression framework. Given a set of points where radiation measurements were taken, we are utilizing a Gaussian Process Regression with a Matern kernel to reconstruct the shape of the underlying ground truth. Mapping is done via the Robot Operating System's OpenSlam Gmapping package, which creates a 2D occupancy grid map. Simulated trials were run with a radiation source placed at random locations, and allowing the robot to select and move towards 20 samples at separate locations, as well as sampling along the path while moving. The simulated sensor model assumed an efficiency of 0.3, collection time of 1 second. Various weighting schemes were tested and compared. Quantitative evaluations often favored exploitation-heavy weighting schemes where μ was emphasized, with the Root Mean Squared Error (RMSE) quickly tending towards 2, whereas qualitative comparisons would favor exploration-biased schemes with greater weight on σ. The difference comes from operators often favoring knowing the general location of a source, rather than the exact properties of a source. Weighting of the path-length π often reduced the quality of the regression as less exploration occurred, however this may be deemed a worthwhile trade-off under certain circumstances, such as with sensitive robots. Successfully developed a methodology for informative path-planning for a robot to efficiently gather information and create a map of radiation. In the future, we would like to focus on: Hardware trials with integration of the robot platform and the IPP software; More refined sensor and environmental modeling; Multiple robot platforms.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2018

Multilevel Semantic Labeling of Mobile Homes from Overhead Imagery

Finding where people live and the vulnerabilities of man-made facilities during natural disasters, is not only critical for rescue efforts, but also essential for damage assessment in the aftermath. Leveraging on the availability of high resolution satellite imagery, advances in machine learning and high performance computing hardware, it is now possible to generate geographical maps for man-made facilities at scale. Mapping from satellite imagery can be a daunting task due to the enormous amount of data to be processed over large areas. In this short paper we take advantage of annotated satellite imagery and automate the semantic labeling of mobile home parks using an efficient framework rooted in patch-based and pixel-level classification. This multilevel labeling effort is a precursor to our future goal for deploying very large scale deep convolutional neural networks toward both broad and finer characterization of man-made structures from one-meter resolution NAIP images.

Lunga, Dalton↗
DOE OSTI2026

Component-Level Inverse Design of Transmon Qubits Using Neural Networks

Designing a superconducting qubit to realize specific Hamiltonian parameters typically requires iterating through a time and compute-intensive forward loop in which the designer chooses a layout geometry, simulates it, extracts circuit parameters such as capacitances, and refines the geometry. We study the inverse version of this task using a neural-network workflow that maps target Hamiltonian parameters directly to component-level layout parameters, which we subsequently demonstrate on a planar transmon layout. During training, we pair the inverse model with a frozen forward surrogate model and evaluate the loss in Hamiltonian space rather than in layout-parameter space. In validation against a conventional EM solver, 97% of generated designs produce usable geometries, and the inverse-plus-surrogate pipeline reaches mean percent errors of 0.73% for qubit frequency and 1.58% for anharmonicity, comparable to or below the fabrication and simulation-to-measurement uncertainty expected for academic-process transmon devices of this type. A single pipeline query takes ~60 ms on CPU, versus ~2 min for a conventional EM capacitance extraction on the same hardware, a speedup of approximately 2,000x. Batching minimizes the AI model inference overhead, reducing the runtime to 3.1 microseconds per sample on CPU and 2.6 microseconds per sample on GPU at a batch size of 2048, resulting in speedups of 3.9 x 10^7 and 4.6 x 10^7, respectively, relative to a single conventional CPU EM extraction. Our results indicate that component-level inverse design usefully extends and complements conventional EM simulation, including for small datasets on the order of 1,000 samples.

Seidel, Olivia [Fermilab; Texas U., Arlington]↗
DOE OSTI2020

Thermochemical Data Fusion Using Graph Representation Learning

Large databases are required for “Big Data” applications in catalysis and materials science. Thermochemical databases can be created by combining data from various sources and by correcting low-fidelity datasets to higher accuracy with minimal computation. To achieve this “data fusion”, thermochemical quantities of interest, calculated at various levels of density functional theory (DFT), need to be mapped to the same, high levels of theory. In this work, a graph theoretical, statistical framework is proposed for such tasks. Subgraph frequencies are shown to provide a natural representation for learning these fusion maps. The maps are linear and are learnt with automated descriptor selection. Using a dataset of as few as ~1% from the QM9 database of 133,885 molecules, these models can predict multiple thermochemical quantities at a higher level of theory with an accuracy of 1 kcal/mol. Here, the method is explainable, generalizable, and provides a diagnostic tool for outlier identification

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Multiview Incomplete Knowledge Graph Integration with application to cross-institutional EHR data harmonization

Objective: The growing availability of electronic health records (EHR) data opens opportunities for integrative analysis of multi-institutional EHR to produce generalizable knowledge. A key barrier to such integrative analyses is the lack of semantic interoperability across different institutions due to coding differences. We propose a Multiview Incomplete Knowledge Graph Integration (MIKGI) algorithm to integrate information from multiple sources with partially overlapping EHR concept codes to enable translations between healthcare systems. Methods: The MIKGI algorithm combines knowledge graph information from (i) embeddings trained from the co-occurrence patterns of medical codes within each EHR system and (ii) semantic embeddings of the textual strings of all medical codes obtained from the Self-Aligning Pretrained BERT (SAPBERT) algorithm. Due to the heterogeneity in the coding across healthcare systems, each EHR source provides partial coverage of the available codes. MIKGI synthesizes the incomplete knowledge graphs derived from these multi-source embeddings by minimizing a spherical loss function that combines the pairwise directional similarities of embeddings computed from all available sources. MIKGI outputs harmonized semantic embedding vectors for all EHR codes, which improves the quality of the embeddings and enables direct assessment of both similarity and relatedness between any pair of codes from multiple healthcare systems. Results: With EHR co-occurrence data from Veteran Affairs (VA) healthcare and Mass General Brigham (MGB), MIKGI algorithm produces high quality embeddings for a variety of downstream tasks including detecting known similar or related entity pairs and mapping VA local codes to the relevant EHR codes used at MGB. Based on the cosine similarity of the MIKGI trained embeddings, the AUC was 0.918 for detecting similar entity pairs and 0.809 for detecting related pairs. For cross-institutional medical code mapping, the top 1 and top 5 accuracy were 91.0% and 97.5% when mapping medication codes at VA to RxNorm medication codes at MGB; 59.1% and 75.8% when mapping VA local laboratory codes to LOINC hierarchy. When trained with 500 labels, the lab code mapping attained top 1 and 5 accuracy at 77.7% and 87.9%. MIKGI also attained best performance in selecting VA local lab codes for desired laboratory tests and COVID-19 related features for COVID EHR studies. Compared to existing methods, MIKGI attained the most robust performance with accuracy the highest or near the highest across all tasks. Conclusions: The proposed MIKGI algorithm can effectively integrate incomplete summary data from biomedical text and EHR data to generate harmonized embeddings for EHR codes for knowledge graph modeling and cross-institutional translation of EHR codes.

Zhou, Doudou↗
DOE OSTI2023

Imaging crossing fibers in mouse, pig, monkey, and human brain using small-angle X-ray scattering

Myelinated axons (nerve fibers) efficiently transmit signals throughout the brain via action potentials. Multiple methods that are sensitive to axon orientations, from microscopy to magnetic resonance imaging, aim to reconstruct the brain's structural connectome. As billions of nerve fibers traverse the brain with various possible geometries at each point, resolving fiber crossings is necessary to generate accurate structural connectivity maps. However, doing so with specificity is a challenging task because signals originating from oriented fibers can be influenced by brain (micro)structures unrelated to myelinated axons. X-ray scattering can specifically probe myelinated axons due to the periodicity of the myelin sheath, which yields distinct peaks in the scattering pattern. Here, in this work, we show that small-angle X-ray scattering (SAXS) can be used to detect myelinated, axon-specific fiber crossings. We first demonstrate the capability using strips of human corpus callosum to create artificial double- and triple-crossing fiber geometries, and we then apply the method in mouse, pig, vervet monkey, and human brains. We compare results to polarized light imaging (3D-PLI), tracer experiments, and to outputs from diffusion MRI that sometimes fails to detect crossings. Given its specificity, capability of 3-dimensional sampling and high resolution, SAXS could serve as a ground truth for validating fiber orientations derived using diffusion MRI as well as microscopy-based methods.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

A Flexible Field Mapping System for Accelerator Magnets

Magnetic field mapping is a fundamental magnetic measurement method that typically uses Hall and NMR sensors. In magnet measurement facilities, such systems are likely used in various configurations suitable for a specific task at hand. To address this diversity, the authors developed a flexible field mapping system capable of being configured and tailored to each particular measurement case. Further, the system needs to address the variability introduced by differences in sensors and their readout systems, probe positioning systems, power supply systems, and required mapping geometry (mapping space and grid, measurement steps and sequences). Although the discussed field mapping systems range from a self-propelled multi-sensor mapper of a large detector magnet to a single 3D Hall sensor system to scan a small permanent magnet, they were all built with the same core mapping system. The variability present in field mapping systems, the measurement system architecture addressing this variability, as well as examples of several field mapping systems built in this architecture are presented.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

A Flexible Field Mapping System for Accelerator Magnets

Magnetic field mapping is a fundamental magnetic measurement method that typically uses Hall and NMR sensors. In magnet measurement facilities, such systems are likely used in various configurations suitable for a specific task at hand. To address this diversity, the authors developed a flexible field mapping system capable of being configured and tailored to each particular measurement case. The system needs to address the variability introduced by differences in sensors and their readout systems, probe positioning systems, power supply systems and in required mapping geometry (mapping space and grid, measurement steps and sequences). Although the discussed field mapping systems range from a self-propelled, multi-sensor mapper of a large detector magnet to a single 3D Hall sensor system to scan a small permanent magnet, they were all built with the same core mapping system. The variability present in field mapping systems and the measurement system architecture addressing this variability, as well as examples of several field mapping systems built in this architecture are presented.

43 PARTICLE ACCELERATORS↗
DOE OSTI2026

Automated tape-target centering based on template matching for construction measurement tasks using robotic total station

Robotic total stations have transformed surveying and construction mapping through precise, efficient, and automated measurements. These instruments integrate a theodolite, which measures horizontal and vertical angles, with an electronic distance measurement (EDM) unit to determine distances, allowing accurate 3D measurement of observable points. Traditionally, users manually aimed the total station at a target. Recent advancements in robotic motor control and integration of cameras now enable automatic rotation and aiming, typically requiring only a single operator to position the target. Automated aiming is commonly performed using retroreflector prisms, which reflect light back to the source with minimal scattering, enabling high-precision measurements over long distances. However, retroreflectors, especially those designed for 360 degree, can be expensive and impractical for certain applications. This paper presents an algorithm for automating the center detection of low-cost disposable tape targets using the total station's onboard camera and a template matching algorithm. The algorithm identifies the target's center pixel in the image, and the instrument is commanded to aim at that location. We evaluated the performance of this template-matching-based centering method under various distances, angles, lighting conditions, and field environments, comparing its results to both manual aiming and conventional automated aiming of tape targets. Manual aiming was used as the baseline operational reference in the absence of an independent ground-truth measurement. The proposed approach achieves target centering results comparable to the manual baseline. This method provides a cost-effective alternative for high-precision applications where retroreflector targets are constrained by budget or logistics.

Harrington, Joshua [ORNL]↗
DOE OSTI2021

Platform Agnostic Streaming Data Application Performance Models

The mapping of computational needs onto execution resources is, by and large, a manual task, and users are frequently guided simply by intuition and past experiences. We present a queueing theory based performance model for streaming data applications that takes steps towards a better understanding of resource mapping decisions, thereby assisting application developers to make good mapping choices. The performance model (and associated cost model) are agnostic to the specific properties of the compute resource and application, simply characterizing them by their achievable data throughput. We illustrate the model with a pair of applications, one chosen from the field of computational biology and the second is a classic machine learning problem.

Faber, Clayton↗
DOE OSTI2022

HYPHY: Deep Generative Conditional Posterior Mapping of Hydrodynamical Physics

Generating large-volume hydrodynamical simulations for cosmological observables is a computationally demanding task necessary for next-generation observations. In this work, we construct a novel fully convolutional variational autoencoder (VAE) to synthesize hydrodynamic fields conditioned on dark matter fields from N -body simulations. After training the model on a single hydrodynamical simulation, we are able to probabilistically map new dark-matter-only simulations to corresponding full hydrodynamical outputs. By sampling over the latent space of our VAE, we can generate posterior samples and study the variance of the mapping. We find that our reconstructed field provides an accurate representation of the target hydrodynamical fields as well as reasonable variance estimates. This approach has promise for the rapid generation of mocks as well as for implementation in a full inverse model of observed data.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

Radioactive Source Localization via Bayesian Particle Filter

In the event of a misplaced radioactive source or other emergency situation, measuring a radiation field, mapping its distribution, and determining a source location are essential tasks to ameliorating the situation. However, radiation fields may be extremely hazardous to human surveyors and minimizing received radiation doses is just as essential. Robots appear to be a potential solution to these problems. Beyond simply measuring radiation, the robot's computer processing capabilities offer a way to apply complex data analysis methods to radiation measurements in real-time. Methods which predict likely source locations can then feed this information into other processes, potentially improving path planning and enabling more efficient measurements. Given a robot mounted with a gamma-ray detector, can we: develop a methodology to account for detector performance across a wide range of source angles, distances, and photon energies? operate an autonomously navigating robot to effectively survey and characterize an area of interest? implement a data analysis method, conventionally used in measurements of motion, for source localization purposes? An open-source TurtleBot 3 robot, running Robot Operating System (ROS) on Ubuntu 16.04 LTS, was fitted with a Kromek GR1{sup R} Cadmium Zinc Telluride (CZT) solid-state gamma-ray detector. As a part of ROS, the packages OpenSlam, gmapping, and amcl were used to perform Simultaneous Localization and Mapping (SLAM), determining the robot's position and mapping the surrounding area. Data was acquired via Lidar mounted on top the TurtleBot 3. Detector Calibration Fit: The equation was fit to 365 counts of various energies, distances, and angles. A MATLAB{sup R} program was written to simulate measurements taken a robot on a random walk, with count data and positions discretized into finite element pixels. Using this program, a sample of 100 runs was performed on a map with a simulated source at the center, with a total of 200 of 2 pixels each. Similarly, multiple runs of the filter were performed on recorded robot measurement data. In both simulation and real tests, when corrected for errors (particles placed outside of bounds or on the robot, and simulation-specific errors), corresponding t-tests of predicted x and y-coordinates were within a 95% confidence interval of the actual position. For the real trial, these positions are slightly skewed right in the x-axis as the robot remained mainly to the left side of the source within the sample area. These simulations demonstrate potential validity for the usage of a particle filter as method of radioactive source localization. In the future, true real-time implementation and data fusion may further augment the performance of the robot to localize lost sources. Additionally, identification of multiple sources, determination of source types, and usage of a collimator are areas to potentially be explored.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2023

A Comparative Study of the Perceptual Sensitivity of Topological Visualizations to Feature Variations

Color maps are a commonly used visualization technique in which data are mapped to optical properties, e.g., color or opacity. Color maps, however, do not explicitly convey structures (e.g., positions and scale of features) within data. Topology-based visualizations reveal and explicitly communicate structures underlying data. Although our understanding of what types of features are captured by topological visualizations is good, our understanding of people's perception of those features is not. Further, this paper evaluates the sensitivity of topology-based isocontour, Reeb graph, and persistence diagram visualizations compared to a reference color map visualization for synthetically generated scalar fields on 2-manifold triangular meshes embedded in 3D. In particular, we built and ran a human-subject study that evaluated the perception of data features characterized by Gaussian signals and measured how effectively each visualization technique portrays variations of data features arising from the position and amplitude variation of a mixture of Gaussians. For positional feature variations, the results showed that only the Reeb graph visualization had high sensitivity. For amplitude feature variations, persistence diagrams and color maps demonstrated the highest sensitivity, whereas isocontours showed only weak sensitivity. These results take an important step toward understanding which topology-based tools are best for various data and task scenarios and their effectiveness in conveying topological variations as compared to conventional color mapping.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Redshift drift cosmography with ELT and SKAO measurements

ABSTRACT Mapping the expansion history of the universe is a compelling task of physical cosmology, especially in the context of the observational evidence for the recent acceleration of the universe, which demonstrates that canonical theories of cosmology and particle physics are incomplete and that there is new physics still to be discovered. Cosmography is a phenomenological approach to cosmology, where (with some caveats) physical quantities are expanded as a Taylor series in the cosmological redshift z, or analogous parameters such as the rescaled redshift y = z/(1 + z) or the logarithmic redshift x = ln (1 + z). Moreover, the redshift drift of objects following cosmological expansion provides a model-independent observable, detectable by facilities currently under construction, viz. the Extremely Large Telescope and the Square Kilometre Array Observatory (at least in its full configuration). Here, we use simulated redshift drift measurements from the two facilities to carry out an assessment of the cosmological impact and model discriminating power of redshift drift cosmography. We find that the combination of measurements from the two facilities can provide a stringent test of the Λ cold dark matter paradigm, and that overall the logarithmic-based expansions of the spectroscopic velocity drift are the most reliable ones, performing better than analogous expansions in the redshift or the rescaled redshift: the former nominally gives the smaller error bars for the cosmographic coefficients but is vulnerable to biases in the higher order terms (in other words, it is only reliable at low redshifts), while the latter always performs poorly.

Rocha, B. A. R.↗
DOE OSTI2025

A continuous calibration of the ATLAS flavour-tagging classifiers via optimal transportation maps

A calibration of the ATLAS flavour-tagging algorithms using a new calibration procedure based on optimal transportation maps is presented. Simultaneous, continuous corrections to the b-jet, c-jet, and light-flavour jet classification probabilities from jet-tagging algorithms in simulation are derived for b-jets using $t\bar{t} \rightarrow e\mu \nu \nu bb$ data. After application of the derived calibration maps, closure between simulation and observation is achieved for jet flavour observables used in ATLAS analyses of Large Hadron Collider (LHC) Run 2 proton-proton collision data. This continuous calibration opens up new possibilities for the future use of jet flavour information in LHC analyses and also serves as a guide for deriving high-dimensional corrections to simulation via transportation maps, an important development for a broad range of inference tasks.

Aad, G. [Aix-Marseille Université] (ORCID:00000002↗