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All sources NASA NTRS DOE OSTI

DOE OSTI2023

The Model Assessment Wizard (MAW): A Visualization System for Ontology Constraint Violations

Validation and verification of engineering models is important to understand potential weaknesses and issues in the model. This is accomplished through the application of constraint logic to the model. These models and the constraints put upon them can be represented through a graph structure. Here we give a visualization system to aid users understanding, locating, and fixing constraint violations in their systems. We give users several ways to narrow down on the specific errors and parts of the graph they’re interested in. Users have the opportunity to choose the types of errors that will be shown in the graph. Clustering is applied to the graph to help users narrow down their searches. Several other graph interactions are given to support discovery of constraint violations.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

Dynamic compressed sensing for real-time tomographic reconstruction

Electron tomography has achieved higher resolution and quality at reduced doses with recent advances in compressed sensing. Compressed sensing (CS) exploits the inherent sparse signal structure to efficiently reconstruct three-dimensional (3D) volumes at the nanoscale from undersampled measurements. However, the process bottlenecks 3D reconstruction with computation times that run from hours to days. Here we demonstrate a framework for dynamic compressed sensing that produces a 3D specimen structure that updates in real-time as new specimen projections are collected. Researchers can begin interpreting 3D specimens as data is collected to facilitate high-throughput and interactive analysis. Using scanning transmission electron microscopy (STEM), we show that dynamic compressed sensing accelerates the convergence speed by ~3-fold while also reducing its error by 27% for a Au/SrTiO 3 nanoparticle specimen. Before a tomography experiment is completed, the 3D tomogram has interpretable structure within ~33% of completion and fine details are visible as early as ~66%. Upon completion of an experiment, a high-fidelity 3D visualization is produced without further delay. Additionally, we report reconstruction parameters that tune data fidelity can be manipulated throughout the computation without re-running the entire process.

47 OTHER INSTRUMENTATION↗

DOE OSTI2022

The His-tag as a decoy modulating preferred orientation in cryoEM

The His-tag is a widely used affinity tag that facilitates purification by means of affinity chromatography of recombinant proteins for functional and structural studies. We show here that His-tag presence affects how coproheme decarboxylase interacts with the air-water interface during grid preparation for cryoEM. Depending on His-tag presence or absence, we observe significant changes in patterns of preferred orientation. Our analysis of particle orientations suggests that His-tag presence can mask the hydrophobic and hydrophilic patches on a protein’s surface that mediate the interactions with the air-water interface, while the hydrophobic linker between a His-tag and the coding sequence of the protein may enhance other interactions with the air-water interface. Our observations suggest that tagging, including rational design of the linkers between an affinity tag and a protein of interest, offer a promising approach to modulating interactions with the air-water interface.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

PySIDT: Subgraph Isomorphic Decision Trees for Molecular Property Prediction

Accurate molecular property prediction is important across all fields of chemistry. Deep neural networks (DNNs) have become increasingly popular due to their ability to train automatically, avoiding the incredibly tedious process of constructing and extending traditional property estimation schemes. However, DNNs require large amounts of training data, are challenging to interpret, require large amounts of memory to load even during inference, and have severe difficulties incorporating qualitative chemical knowledge, which are often desired for molecular property prediction tasks. Here, in this study, we present PySIDT (https://github.com/zadorlab/PySIDT), a software for training and running inference on Subgraph Isomorphic Decision Trees (SIDTs). SIDTs are graph-based decision trees made of nodes associated with molecular substructures. Inference is done by descending target molecular structures down the decision tree to nodes with matching subgraph isomorphic substructures and making predictions based on the final (most specific) nodes matched. SIDTs scale down well to dataset sizes much smaller than is feasible for DNNs. As trees of molecular substructures, SIDTs are inherently readable and easy to visualize, making them easy to analyze. They are also straightforward to extend and retrain, facilitate uncertainty estimation, and enable easy integration of expert knowledge. We demonstrate the SIDT approach discussing its application to a diverse range of molecular prediction tasks: rate coefficient estimation, diffusion coefficient estimation, thermochemistry estimation, transition state bond stretch prediction, p K a prediction, stability of molecular structures, stability of surface structures, and prediction of surface lateral interaction energetics. Additionally, we demonstrate the power of the SIDT algorithms in two direct learning curve vanilla comparisons with the popular DNN-based software Chemprop and the popular gradient boosted trees-based software XGBoost on enthalpy of formation and rate coefficient prediction tasks. In particular, in the enthalpy of formation case, vanilla PySIDT is able to outperform vanilla Chemprop and XGBoost across the full range of training/validation set sizes out to 11,560 data points.

Johnson, Matthew Sean [Sandia National Laboratorie↗

DOE OSTI2026

Rasterization with Data-Parallel Primitives

Parallel rasterization can suffer from race conditions during fragment generation, which is traditionally addressed by using specialized hardware accessible via vendor graphics APIs. Unfortunately, graphics APIs are increasingly problematic on high-performance computers, either because they are not provided or because of concerns about dependencies with in situ visualization. In response, we present a hardware-agnostic rasterization algorithm that handles race conditions using only data-parallel primitives (DPPs), enabling efficient rendering on HPC systems without graphics API dependencies and aligning with recent efforts to deliver visualization software with DPPs. Our evaluation consists of three phases: (1) evaluating portability across different CPU and GPU architectures, (2) evaluating competitiveness with a community standard, and (3) evaluating performance across varying workloads and available parallelism. The supporting experiments run on both AMD and NVIDIA GPUs, considering data sets as large as 460 million triangles and 160 million pixels. While performance generally falls short of graphics API baselines, it achieves interactive frame rates on most workloads. As a result, we conclude our approach is a viable solution for rasterization on high-performance computers since our approach is portably performant across different architectures without the need for specialized vendor support.

Buckley, Makani [University of Oregon] (ORCID:0009↗

DOE OSTI2023

High-speed mapping of surface charge dynamics using sparse scanning Kelvin probe force microscopy

Unraveling local dynamic charge processes is vital for progress in diverse fields, from microelectronics to energy storage. This relies on the ability to map charge carrier motion across multiple length- and timescales and understanding how these processes interact with the inherent material heterogeneities. Towards addressing this challenge, we introduce high-speed sparse scanning Kelvin probe force microscopy, which combines sparse scanning and image reconstruction. This approach is shown to enable sub-second imaging (>3 frames per second) of nanoscale charge dynamics, representing several orders of magnitude improvement over traditional Kelvin probe force microscopy imaging rates. Bridging this improved spatiotemporal resolution with macroscale device measurements, we successfully visualize electrochemically mediated diffusion of mobile surface ions on a LaAlO 3 /SrTiO 3 planar device. Such processes are known to impact band-alignment and charge-transfer dynamics at these heterointerfaces. Furthermore, we monitor the diffusion of oxygen vacancies at the single grain level in polycrystalline TiO 2 . Through temperature-dependent measurements, we identify a charge diffusion activation energy of 0.18 eV, in good agreement with previously reported values and confirmed by DFT calculations. Together, these findings highlight the effectiveness and versatility of our method in understanding ionic charge carrier motion in microelectronics or nanoscale material systems.

25 ENERGY STORAGE↗

DOE OSTI2024

Imaging moiré excited states with photocurrent tunnelling microscopy

Moiré superlattices provide a highly tuneable and versatile platform to explore novel quantum phases and exotic excited states ranging from correlated insulators to moiré excitons. Scanning tunnelling microscopy has played a key role in probing microscopic behaviours of the moiré correlated ground states at the atomic scale. However, imaging of quantum excited states in moiré heterostructures remains an outstanding challenge. In this report we develop a photocurrent tunnelling microscopy technique that combines laser excitation and scanning tunnelling spectroscopy to directly visualize the electron and hole distribution within the photoexcited moiré exciton in twisted bilayer WS 2 . The tunnelling photocurrent alternates between positive and negative polarities at different locations within a single moiré unit cell. This alternating photocurrent originates from the in-plane charge transfer moiré exciton in twisted bilayer WS 2 , predicted by our GW-Bethe–Salpeter equation calculations, that emerges from the competition between the electron–hole Coulomb interaction and the moiré potential landscape. Our technique enables the exploration of photoexcited non-equilibrium moiré phenomena at the atomic scale.

36 MATERIALS SCIENCE↗

DOE OSTI2024

An ontology-based knowledge graph for representing interactions involving RNA molecules

The "RNA world" represents a novel frontier for the study of fundamental biological processes and human diseases and is paving the way for the development of new drugs tailored to each patient's biomolecular characteristics. Although scientific data about coding and non-coding RNA molecules are constantly produced and available from public repositories, they are scattered across different databases and a centralized, uniform, and semantically consistent representation of the "RNA world" is still lacking. We propose RNA-KG, a knowledge graph (KG) encompassing biological knowledge about RNAs gathered from more than 60 public databases, integrating functional relationships with genes, proteins, and chemicals and ontologically grounded biomedical concepts. To develop RNA-KG, we first identified, pre-processed, and characterized each data source; next, we built a meta-graph that provides an ontological description of the KG by representing all the bio-molecular entities and medical concepts of interest in this domain, as well as the types of interactions connecting them. Finally, we leveraged an instance-based semantically abstracted knowledge model to specify the ontological alignment according to which RNA-KG was generated. RNA-KG can be downloaded in different formats and also queried by a SPARQL endpoint. A thorough topological analysis of the resulting heterogeneous graph provides further insights into the characteristics of the "RNA world". RNA-KG can be both directly explored and visualized, and/or analyzed by applying computational methods to infer bio-medical knowledge from its heterogeneous nodes and edges. The resource can be easily updated with new experimental data, and specific views of the overall KG can be extracted according to the bio-medical problem to be studied.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Characterization and visualization of grain boundary disconnections

We introduce a method to visualize dislocations along grain boundaries at the atomic level. It uses an atomic-level Nye tensor, representing the dislocation density. To calculate the Nye tensor at grain boundaries, we extend the Hartley-Mishin strain gradient calculation to the displacement shift complete lattice. We show that the method is effective in visualizing disconnections and the dislocation content of grain boundary phase junctions in body-centered cubic tungsten, as well as face-centered cubic copper. In addition, we use the method to characterize the morphology of a two-dimensional grain boundary phase nucleus in a symmetric tilt grain boundary in tungsten. This method can be applied to both bulk dislocations and grain boundary disconnections, which makes it ideal for studying the interactions and reactions of bulk dislocations with grain boundaries, and grain boundary disconnections.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Spatially co-registered wide-field nonlinear optical imaging of living and complex biosystems in a total internal reflection geometry

Nonlinear optical microscopy that leverages an objective based total internal reflection (TIR) excitation scheme is an attractive means for rapid, wide-field imaging with enhanced surface sensitivity. Through select combinations of distinct modalities, one can, in principle, access complementary chemical and structural information for various chemical species near interfaces. Here, we report a successful implementation of such a wide-field nonlinear optical microscope system, which combines coherent anti-Stokes Raman scattering (CARS), two-photon fluorescence (TPF), second harmonic generation (SHG), and sum frequency generation (SFG) modalities on the same platform. The intense optical fields needed to drive these high order nonlinear optical processes are achieved through the use of femtosecond pulsed light in combination with the intrinsic field confinement induced by TIR over a large field of view. The performance of our multimodal microscope was first assessed through the experimental determination of its chemical fidelity, intensity and polarization dependences, and spatial resolution using a set of well-defined model systems. Subsequently, its unique capabilities were validated through imaging complex biological systems, including Hydrangea quercifolia pollen grains and Pantoea sp. YR343 bacterial cells. Specifically, the spatial distribution of different molecular groups in the former was visualized via vibrational contrast mechanisms of CARS, whereas co-registered TPF imaging allowed the identification of spatially localized intrinsic fluorophores. We further demonstrate the feasibility of our microscope for wide-field CARS imaging on live cells through independent characterization of cell viability using spatially co-registered TPF imaging. Overall, this approach to TIR enabled wide-field imaging is expected to provide new insights into bacterial strains and their interactions with other species in the rhizosphere in a time-resolved and chemically selective manner.

47 OTHER INSTRUMENTATION↗

DOE OSTI2023

Real-time imaging of acoustic waves in bulk materials with X-ray microscopy

The dynamics of lattice vibrations govern many material processes, such as acoustic wave propagation, displacive phase transitions, and ballistic thermal transport. The maximum velocity of these processes and their effects is determined by the speed of sound, which therefore defines the temporal resolution (picoseconds) needed to resolve these phenomena on their characteristic length scales (nanometers). Here, we present an X-ray microscope capable of imaging acoustic waves with subpicosecond resolution within mm-sized crystals. We directly visualize the generation, propagation, branching, and energy dissipation of longitudinal and transverse acoustic waves in diamond, demonstrating how mechanical energy thermalizes from picosecond to microsecond timescales. Bulk characterization techniques capable of resolving this level of structural detail have previously been available on millisecond time scales—orders of magnitude too slow to capture these fundamental phenomena in solid-state physics and geoscience. As such, the reported results provide broad insights into the interaction of acoustic waves with the structure of materials, and the availability of ultrafast time-resolved dark-field X-ray microscopy opens a vista of new opportunities for 3D imaging of materials dynamics on their intrinsic submicrosecond time scales.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Λ Baryon Production in ν¯µ Interactions in the MicroBooNE Detector

The Cabibbo suppressed production of $\Lambda$ baryons in anti-neutrino interactions with nuclei is a rare process that is yet to be measured with a modern neutrino detector with automated reconstruction. The cross section for this process is sensitive to a number of unique nuclear effects, most notably the secondary interactions of the produced hyperon while attempting to escape from the nucleus. Other interactions within the nuclear remnant can impact the estimation of neutrino energy in oscillation measurements, and thus an accurate description of the nuclear environment is required. The strangeness violating hyperon production process is only available to anti-neutrinos. The model of this interaction is implemented into the NuWro neutrino interaction Monte Carlo simulation, and some predictions are presented, focusing on the role of nuclear effects. This model introduces a hyperon-nucleus potential, which calculations from hypernuclear theory permit to be strongly repulsive in th e case of $\Sigma$ baryons. The presence of this potential is found to sculpt the shape of the differential cross section in some variables. The MicroBooNE detector will be described, followed by a description of a measurement of the flux averaged, restricted phase space cross section of Cabibbo suppressed $\Lambda$ baryon production. A sophisticated event selection is employed, as a very large quantity of background neutrino interactions must be removed to perform the measurement with any sensitivity. This selection introduces some novel techniques such as the island finding method, and achieves a background reduction of $\sim 10^6$, with an efficiency of around 7\%. The calculation of the systematic uncertainties will be explained, including two procedures explored to handle sources of background with extremely poor simulation statistics: an in-situ constraint using data from sidebands, and a visual inspection of the data and simulation to remove the troublesome background events. The sensitivity to the $\Lambda$ baryon production cross section is calculated in the form of Bayesian posterior probability distributions, combining the systematic uncertainties with data and simulation statistical uncertainties. As a rare process, the statistical uncertainties are highly non-Gaussian, and the Bayesian approach is applied to include the full shapes of these uncertainties. Data corresponding to $2.2 \times 10^{20}$ protons on target of neutrino mode running and $4.9 \times 10^{20}$ protons on target of anti-neutrino running is analysed. When the data was unblinded, five $\Lambda$ production candidates were selected from the data, consistent with the MC simulation prediction of $5.3 \pm 1.1$ events. The final estimated cross section is $1.8^{+2.0}_{-1.6} \times 10^{-40}$cm$^2/$Ar when employing the sideband constraint procedure. A similar result of $2.0^{+2.2}_{-1.8} \times 10^{-40}$cm$^2/$Ar is obtained when performing the visual scan instead. The methods used in t his analysis are intended to be easily exported to other LArTPC detectors such as the Short Baseline Near Detector.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2024

Offshore Geologic Carbon Storage Data Collection and International Project Inventory

We present an interactive data collection to aggregate, understand, and disseminate the data that are publicly available to support offshore GCS which can be leveraged by stakeholders to understand where GCS may be viable offshore, create GCS project analogs, and address challenges to GCS in offshore environments. The Offshore Geologic Carbon Storage Data Collection is an Experience Builder web application of multiple web mapping applications, aggregated into a single tool for each data type for access, visualization, and exploration. We also present a spatial inventory of global offshore GCS efforts to visualize the scale and locations of actualized and potential offshore GCS. It includes project location, project type and stage, CO2 storage resource potential, injection rate, reservoir and seal geology, and key literature references. Quantitative and qualitative comparisons of the distribution and magnitude of projects by their attributes lends spatial insight into the status of global GCS operations and storage resource potential, thereby enabling comparative assessments and cross-cutting knowledge transfer for projects in development. These datasets illuminate trends in ongoing offshore projects and can be leveraged by stakeholders to estimate storage resources, identify subsurface analogs, review regulations, and address challenges to offshore GCS. Additionally, opportunities for concurrent decarbonization strategies can be identified.

Mulhern, Julia↗

DOE OSTI2024

International Offshore Geologic Carbon Storage Project Inventory and Data Collection

Mulhern, Julia↗

DOE OSTI2024

International Offshore Geologic Carbon Storage Inventory and Data Collection

Mulhern, Julia↗

DOE OSTI2022

Visualizing the unusual spectral weight transfer in DyBa2Cu3O7–δ thin film

Abstract We report a Spectroscopic Imaging Scanning Tunneling Microscopy (SI-STM) study of a DyBa 2 Cu 3 O 7-δ (DBCO) thin film ( T c ~ 79 K) synthesized by the molecular beam epitaxy (MBE). We observed an unusual transfer of spectral weight in the local density of states (LDOS) spectra occurring only within the superconducting gap. By a systematic control of the tip-sample distance and the junction resistance, we demonstrate that the spectral weight transfer can be switched at a nano-meter length scale. These results suggest that an interaction between the STM tip and the sample alters the electronic configurations in the film. This probably originates from a combination of an intrinsic band bending at the interface between the surface and the bulk, and a tip-induced band bending. These results may open a new avenue for band engineering and applications of thin films of high- T c cuprates.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2022

Star formation characteristics of CNN-identified post-mergers in the Ultraviolet Near Infrared Optical Northern Survey (UNIONS)

ABSTRACT The importance of the post-merger epoch in galaxy evolution has been well documented, but post-mergers are notoriously difficult to identify. While the features induced by mergers can sometimes be distinctive, they are frequently missed by visual inspection. In addition, visual classification efforts are highly inefficient because of the inherent rarity of post-mergers (~1 per cent in the low-redshift Universe), and non-parametric statistical merger selection methods do not account for the diversity of post-mergers or the environments in which they appear. To address these issues, we deploy a convolutional neural network (CNN) that has been trained and evaluated on realistic mock observations of simulated galaxies from the IllustrisTNG simulations, to galaxy images from the Canada France Imaging Survey, which is part of the Ultraviolet Near Infrared Optical Northern Survey. We present the characteristics of the galaxies with the highest CNN-predicted post-merger certainties, as well as a visually confirmed subset of 699 post-mergers. We find that post-mergers with high CNN merger probabilities [p(x) > 0.8] have an average star formation rate that is 0.1 dex higher than a mass- and redshift-matched control sample. The SFR enhancement is even greater in the visually confirmed post-merger sample, a factor of 2 higher than the control sample.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2021

Real-Time Omnidirectional Stereo Rendering: Generating 360° Surround-View Panoramic Images for Comfortable Immersive Viewing

Surround-view panoramic images and videos have become a popular form of media for interactive viewing on mobile devices and virtual reality headsets. Viewing such media provides a sense of immersion by allowing users to control their view direction and experience an entire environment. When using a virtual reality headset, the level of immersion can be improved by leveraging stereoscopic capabilities. Stereoscopic images are generated in pairs, one for the left eye and one for the right eye, and result in providing an important depth cue for the human visual system. For computer generated imagery, rendering proper stereo pairs is well known for a fixed view. However, it is much more difficult to create omnidirectional stereo pairs for a surround-view projection that work well when looking in any direction. One major drawback of traditional omnidirectional stereo images is that they suffer from binocular misalignment in the peripheral vision as a user's view direction approaches the zenith / nadir (north / south pole) of the projection sphere. This paper presents a real-time geometry-based approach for omnidirectional stereo rendering that fits into the standard rendering pipeline. Our approach includes tunable parameters that enable pole merging - a reduction in the stereo effect near the poles that can minimize binocular misalignment. Results from a user study indicate that pole merging reduces visual fatigue and discomfort associated with binocular misalignment without inhibiting depth perception.

360° panorama↗