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At least 145 records · Page 8

Advanced Interactive 3D Visualization Tool for Customizable Analyses of Tomography Datasets in Material Science

Current methods for visualizing and analyzing 3D tomography datasets in materials science often lack the interactivity and depth required for detailed structural insights. This limitation restricts a researchers' ability to accurately interpret complex data, which is critical for advancing material innovations and understanding structural properties. To address this issue, we have developed a novel, web-based interactive 3D visualization and analysis tool from the Trame framework that offers customizable features to enhance data interpretability. The tool allows users to adjust parameters such as visible range, slice planes, data rotation, and layering, providing a more detailed and dynamic view of complex structures. Its user-friendly web interface increases the accessibility and ease of use for both novice and experienced researchers, to visualize large volumetric datasets. The tool supports a diverse range of data formats, making it versatile for various research applications. Unique capabilities include real-time data manipulation, automated feature detection, context-sensitive feedback, and real-time volume calculations and distributions per sliced region or layer, alongside the ability to quickly generate high-quality screenshots and videos for presentations and reports. These advancements offer a comprehensive solution for enhanced 3D data exploration, significantly improving the analysis process and communication of results in materials science.

36 - MATERIALS SCIENCE↗

Resolving Triblock Terpolymer Morphologies by Vapor-Phase Infiltration

The spontaneous formation of well-organized three-dimensional (3D) nanostructures from self-assembled block copolymers (BCPs) holds promise for nanofabrication and lithography. The addition of a third block to BCPs provides access to a plethora of 3D geometries, but it remains difficult to resolve the geometry of such “three-color” structures when there is low contrast between the polymeric components at length scales of a few nm. Here, we apply vapor-phase infiltration synthesis to a silicon-containing triblock terpolymer, poly(1,1- dimethyl silacyclobutane-b-styrene-b-lactide) (PDMSB-b-PS-b-PLA or DSL) to distinguish the 3D microdomain morphologies of the two organic blocks, PLA and PS. Selective infiltration of ZnO within the PLA microdomains reveals morphologies consisting of three-color lamellae or lamellae combined with vertically aligned core-shell cylinders, depending on the volume fractions of each block. The infiltration produces ZnO nanoparticles throughout the 260 nm thickness of the DSL film, generating 3D nanocomposites containing ZnO and SiO x . These results provide a strategy for synthesizing multicomponent 3D nanostructures as well as visualizing the phase behavior of multi-block copolymers.

36 MATERIALS SCIENCE↗

Conformational space exploration of cryo-EM structures by variability refinement

Cryo-EM observation of biological samples enables visualization of sample heterogeneity, in the form of discrete states that are separable, or continuous heterogeneity as a result of local protein motion before flash freezing. Variability analysis of this continuous heterogeneity describes the variance between a particle stack and a volume, and results in a map series describing the various steps undertaken by the sample in the particle stack. While this observation is absolutely stunning, it is very hard to pinpoint structural details to elements of the maps. Here, in order to bridge the gap between observation and explanation, we designed a tool that refines an ensemble of structures into all the maps from variability analysis. Using this bundle of structures, it is easy to spot variable parts of the structure, as well as the parts that are not moving. Comparison with molecular dynamics simulations highlights the fact that the movements follow the same directions, albeit with different amplitudes. Ligand can also be investigated using this method. Variability refinement is available in the Phenix software suite, accessible under the program name phenix.varref.

59 BASIC BIOLOGICAL SCIENCES↗

Online Analytics for Remedy Support at DOE Environmental Management Sites

Environmental data is important for managing environmental restoration/waste site remediation, planning of monitoring efforts, addressing climate resilience, and engaging with stakeholders and regulators. A major challenge is how to manage the many different types and the large volume of environmental data in a way that allows practitioners and site managers to understand data implications and support decisions. The Suite Of Comprehensive Rapid Analysis Tools for Environmental Sites (SOCRATES, https://www.pnnl.gov/projects/socrates) is a web application that provides data access, visualization, and rapid analytics to help make sense of environmental data, support remedy decisions, and communicate information. Development of SOCRATES has been funded through the DOE Richland Operations Office (RL) to support communication and decision making for the Hanford Site, thus is only tied into Hanford environmental data. However, the capabilities of SOCRATES are more broadly applicable to DOE-EM sites engaged in environmental remediation and management. This report describes the work to develop mechanisms for bringing non-Hanford data into SOCRATES so that other DOE-EM sites could make use of the visualization and analysis capabilities to support communication and decision making related to managing environmental restoration/waste site remediation, optimization/exit strategies for pump-and-treat systems, planning monitoring efforts, addressing climate resilience, and/or engaging with stakeholders and regulators. The background, approach, data transfer formats, examples, and next steps for this new SOCRATES-EM software are described in this report.

54 ENVIRONMENTAL SCIENCES↗

A quantitative comparison of the fingerprint of twinned microstructures through surface and three-dimensional techniques

Assessing the fingerprint of a material’s microstructure is key for supporting materials design. With the emergence of a wide range of 3D characterization techniques, it is critical to understand the main differences in fingerprints reconstructed from 2D and 3D datasets. To this end, we introduce a graph-based microstructure reconstruction framework that enables structural comparisons of twin domain networks in high purity Ti using 3D and 2D electron backscatter diffraction. Insights into the structure of the twin networks are facilitated by combining statistical analysis of twin crystallography with visual and graphical analysis of the novel graph abstractions of the twins. We demonstrate that compared to 3D reconstructions, conventional 2D views of twinning miss key aspects of the microstructure including the high interconnectivity of domains into networks that span the full reconstruction volume. The reduced cross-grain and in-grain twin connectivity typically observed in 2D has notable implications on our understanding of how twinning mediates the plastic response of microstructures and how twin networks evolve. It is thus clear that 3D characterization is critical for accurately inferring both twin network morphologies as well as the key unit processes facilitating network formation.

36 MATERIALS SCIENCE↗

Development of a Testbed for Pipeline Flushing - 20425

Pipelines which carry high-level waste within the DOE complex should be properly flushed in the cases where stationary or moving beds of solid sediment occur, or lines are prone to hydrogen gas buildup. Present guidelines establish a minimum for the amount of water (flush volume) and flush velocity values used for post-transfer flushing operations to achieve satisfactory cleaning of pipelines. However, further studies are needed to find optimal operating velocity modes/values in order to minimizing the flush volume and consequent downstream waste. These efforts are significantly helpful to DOE waste remediation sites by preserving tank storage, preventing additional waste processing, and minimizing dilution and changes in waste chemistry. An experimental test loop was recently developed for study of non-Newtonian slurry flushing at the Florida International University (FIU). This loop was designed to create sediment beds of various materials and bed heights and investigate parameters that effect the efficiency of flushing operations. The objective is to find flush velocity values/modes which lead to satisfactory cleaning of transport lines with a minimum amount of water usage. A 165 ft experimental test loop made of 3-inch carbon steel pipes was constructed and used in initial testing campaigns. This pipe loop was equipped with real-time monitoring instruments to record variation of pressure, density, mass flow rate, and temperature during testing. Post-flush in-situ no-flow evaluations were performed using ultrasonic, endoscopy, and visual inspection. Additional post-flush evaluations were conducted using filtration and density monitoring of residuals within a designated circulations loop. These provisions enable comparison of pipeline cleanness before the start and after termination of flushing operations for efficiency evaluation. This paper presents efforts associated with flushing of kaolin-water mixtures at different concentrations and with various flush volume and flush velocity values/modes. In initial testing, efforts focused on creating repeatable sediment beds inside the pipeline in both fully-flooded (no pre-flush drainage) and gravity-drained (pre-flush drained) systems. Bed characterization (i.e., measurement of sediment height and solids concentration) was conducted to ensure about consistency of initial conditions between tests. Preliminary results for flushing study of 10% vol. kaolin-water mixtures starting from a fully-flooded initial condition showed that flushing with 1-line volume (65 gallons) could remove up to 72 percent of solids from the pipeline. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Electron tomography unravels new insights into fiber cell wall nanostructure; exploring 3D macromolecular biopolymeric nano-architecture of spruce fiber secondary walls

Lignocellulose biomass has a tremendous potential as renewable biomaterials for fostering the “bio-based society” and circular bioeconomy paradigm. It requires efficient use and breakdown of fiber cell walls containing mainly cellulose, hemicellulose and lignin biopolymers. Despite their great importance, there is an extensive debate on the true structure of fiber walls and knowledge on the macromolecular nano-organization is limited and remains elusive in 3D. We employed dual-axis electron tomography that allows visualization of previously unseen 3D macromolecular organization/biopolymeric nano-architecture of the secondary S2 layer of Norway spruce fiber wall. Unprecedented 3D nano-structural details with novel insights into cellulose microfibrils (~2 nm diameter), macrofibrils, nano-pore network and cell wall chemistry (volume %) across the S2 were explored and quantified including simulation of structure related permeability. Matrix polymer association with cellulose varied between microfibrils and macrofibrils with lignin directly associated with MFs. Simulated bio-nano-mechanical properties revealed stress distribution within the S2 and showed similar properties between the idealized 3D model and the native S2 (actual tomogram). Present work has great potential for significant advancements in lignocellulose research on nano-scale understanding of cell wall assembly/disassembly processes leading to more efficient industrial processes of functionalization, valorization and target modification technologies.

3-D reconstruction↗

COTS Data Analytics Software User Manual: Version 1.0

Large volumes of data are being collected by Sandia National Laboratories as part of an active commercial-off-the-shelf (COTS) part testing and surveillance program. This user manual documents Python-based COTS Data Analytics software that has been developed for standardizing, displaying, visualizing, and analyzing the resulting COTS part testing and surveillance data. It is the objective of these software tools to streamline the analysis of COTS testing and surveillance data and improve the efficiency with which test engineers and data analytics experts can pinpoint possible performance and reliability problems in COTS parts.

42 ENGINEERING↗

Automated pipeline processing X-ray diffraction data from dynamic compression experiments on the Extreme Conditions Beamline of PETRA III

Presented and discussed here is the implementation of a software solution that provides prompt X-ray diffraction data analysis during fast dynamic compression experiments conducted within the dynamic diamond anvil cell technique. It includes efficient data collection, streaming of data and metadata to a high-performance cluster (HPC), fast azimuthal data integration on the cluster, and tools for controlling the data processing steps and visualizing the data using the DIOPTAS software package. This data processing pipeline is invaluable for a great number of studies. The potential of the pipeline is illustrated with two examples of data collected on ammonia–water mixtures and multiphase mineral assemblies under high pressure. The pipeline is designed to be generic in nature and could be readily adapted to provide rapid feedback for many other X-ray diffraction techniques, e.g. large-volume press studies, in situ stress/strain studies, phase transformation studies, chemical reactions studied with high-resolution diffraction etc.

97 MATHEMATICS AND COMPUTING↗

Coil optimization for quasi-helically symmetric stellarator configurations

Filament-based coil optimizations are performed for several quasi-helical stellarator configurations, beginning with the one from Landreman & Paul ( Phys. Rev. Lett. , vol. 128, 2022, 035001), demonstrating that precise quasi-helical symmetry can be achieved with realistic coils. Several constraints are placed on the shape and spacing of the coils, such as low curvature and sufficient plasma–coil distance for neutron shielding. The coils resulting from this optimization have a maximum curvature 0.8 times that of the coils of the Helically Symmetric eXperiment (HSX) and a mean squared curvature 0.4 times that of the HSX coils when scaled to the same plasma minor radius. When scaled up to reactor size and magnetic field strength, no fast particle losses were found in the free-boundary configuration when simulating 5000 alpha particles launched at $3.5\,\mathrm {MeV}$ on the flux surface with a normalized toroidal flux of $s=0.5$ . An analysis of the tolerance of the coils to manufacturing errors is performed using a Gaussian process model, and the coils are found to maintain low particle losses for smooth, large-scale errors up to amplitudes of approximately $0.15\,\mathrm {m}$ . Another coil optimization is performed for the Landreman–Paul configuration with the additional constraint that the coils are purely planar. Visual inspection of the Poincaré plot of the resulting magnetic field-lines reveal that the planar modular coils alone do a poor job of reproducing the target equilibrium. Additional non-planar coil optimizations are performed for the quasi-helical configuration with $5\,\%$ volume-averaged plasma beta from Landreman et al. ( Phys. Plasma , vol. 29, issue 8, 2022, 082501), and a similar configuration also optimized to satisfy the Mercier criterion. The finite beta configurations had larger fast-particle losses, with the free-boundary Mercier-optimized configuration performing the worst, losing approximately $5.5\,\%$ of alpha particles launched at $s=0.5$ .

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

ATDM AD projects to ECP Report (Q3 FY2020)

The SPARC team has completed much of the workflow development needed for the coupled and uncoupled analyses needed to support our flight test validation work. The SPARC team has continued to make progress on development activities to support unsteady, full reentry vehicle aero analysis, which have focused on turbulence modeling, uniform mesh refinement, in-situ visualization (with the Paraview/Catalyst team), and performance analysis. The SPARC team is making solid progress towards our Q4 goal of demonstrating an improved Wall Modeled Large Eddy Simulation (WMLES) capability for standard geometries using high-order finite difference, discontinuous Galerkin, and low-dissipation finite volume methods. The SPARC team has met the minimum completion criteria for parts of the L1, including documenting performance and scaling of SPARC on Trinity, Sierra and Astra, and performing runs for the flight test validation case.

97 MATHEMATICS AND COMPUTING↗

Demonstration of VOC Fenceline Sensors and Canister Grab Sampling near Chemical Facilities in Louisville, Kentucky

Experimental fenceline sensor pods (SPods) fitted with 30 s duration canister grab sampling (CGS) systems were deployed at a site near chemical facilities in Louisville, KY, from 4 June 2018 to 5 January 2020. The objective of the study was to better understand lower cost 10.6 eV photoionization detector (PID)-based volatile organic compound (VOC) sensors and investigate their utility for near-source emissions detection applications. Prototype SPods containing PID sensor elements from two different manufacturers yielded between 78% and 86% valid data over the study, producing a dataset of over 120,000 collocated pair fenceline measurements averaged into 5-min datapoints. Ten-second time-resolved SPod data from an elevated fenceline sensor signal day are presented, illustrating source emission detections from the direction of a facility 500 m west of the monitoring site. An SPod-triggered CGS acquired in the emission plume on this day contained elevated concentrations of 1,3-butadiene and cyclohexane (36 parts per billion by volume (ppbv) and 637 ppbv, respectively), compounds known to be emitted by this facility. Elevated concentrations of these compounds were observed in a subset of the 61 manual and triggered CGS grab samples acquired during the study, with winds from the west. Using novel wind-resolved visualization and normalization approaches described herein, the collocated pair SPod datasets exhibited similarity in emission source signature. With winds from the west, approximately 50% of SPod readings were above our defined theoretical detection limit indicating persistent measurable VOC signal at this site. Overall, this 19-month study demonstrated reasonable prototype SPod operational performance indicating that improved commercial forms of lower cost PID sensors could be useful for select VOC fenceline monitoring applications.

1,3-butadiene↗

Linking void and interphase evolution to electrochemistry in solid-state batteries using operando X-ray tomography

Despite progress in solid-state battery engineering, our understanding of the chemo-mechanical phenomena that govern electrochemical behavior and stability at solid-solid interfaces remains limited compared to solid-liquid interfaces. Here, we use operando synchrotron X-ray computed microtomography to investigate the evolution of lithium/solid-state electrolyte interfaces during battery cycling, revealing how the complex interplay among void formation, interphase growth, and volumetric changes determines cell behavior. Void formation during lithium stripping is directly visualized in symmetric cells, and the loss of contact that drives current constriction at the interface between lithium and the solid-state electrolyte (Li10SnP2S12) is quantified and found to be the primary cause of cell failure. The interphase is found to be redox-active upon charge, and global volume changes occur due to partial molar volume mismatches at either electrode. Finally, these results provide new insight into how chemo-mechanical phenomena can impact cell performance, which is necessary to understand for the development of solid-state batteries.

42 ENGINEERING↗

Three-Dimensional Single-Molecule Localization Microscopy in Whole-Cell and Tissue Specimens

Super-resolution microscopy techniques are versatile and powerful tools for visualizing organelle structures, interactions, and protein functions in biomedical research. However, whole-cell and tissue specimens challenge the achievable resolution and depth of nanoscopy methods. We focus on three-dimensional single-molecule localization microscopy and review some of the major roadblocks and developing solutions to resolving thick volumes of cells and tissues at the nanoscale in three dimensions. These challenges include background fluorescence, system- and sample-induced aberrations, and information carried by photons, as well as drift correction, volume reconstruction, and photobleaching mitigation. We also highlight examples of innovations that have demonstrated significant breakthroughs in addressing the abovementioned challenges together with their core concepts as well as their trade-offs.

59 BASIC BIOLOGICAL SCIENCES↗

Influence of Lake Ice Biases in Reanalysis Data on Downscaled Climate Simulations over the Great Lakes Region

This data package contains observation-based and model-simulated datasets (all provided in NetCDF format) for evaluating how wintertime lake-ice representation affects regional weather and climate over the Laurentian Great Lakes (freshwater lake ecosystem) during the high–ice-cover winter of 2009. The observational component includes: (1) Stage IV gridded precipitation at 4 km, hourly resolution for January–February 2009 over the Great Lakes region (radar–gauge multisensor precipitation analyses); (2) Great Lakes Surface Environmental Analysis (GLSEA) satellite-derived lake-ice coverage at 1.3 km, daily resolution for the 2009 winter months, providing ice coverage over Lakes Superior, Michigan, Huron, Erie, and Ontario; and (3) in situ measurements at the Standard Rock site on Lake Superior from the Great Lakes Evaporation Network (GLEN) at hourly resolution, including near-surface atmospheric variables and sensible and latent heat fluxes (air–lake exchange) at a fixed point location. The modeling component provides corresponding fields from two simulations, both archived at 4 km, hourly resolution: a standalone Weather Research Forecasting model (WRF) run driven by the European Centre for Medium-Range Weather Forecasts (ECMWF) Reanalysis 5 (ERA5), and a two-way coupled model using WRF and the Finite Volume Community Ocean Model (WRF-FVCOM, a 3-D hydrodynamic lake model). These outputs include variables relevant to air–lake interaction and lake-effect processes (e.g., near-surface temperature, humidity, wind, precipitation, and surface turbulent fluxes), enabling direct comparison with the observational datasets. Users can analyze and visualize these NetCDF files with common tools such as Python (e.g., xarray, netCDF4, numpy, pandas), NCO/CDO, Panoply, or ncview; NetCDF variables can also be converted to other formats (e.g., CSV, GeoTIFF) using these utilities.

EARTH SCIENCE > ATMOSPHERE > ATMOSPHERIC TEMPERATU↗

Removable, Sequestration Coatings for Mitigating Hazardous Contaminants Related to Deactivation and Decommissioning Activities

This project is a collaborative effort between InnoSense LLC (ISL) and Oak Ridge National Laboratory (ORNL) aimed at mitigating the mercury (Hg) contamination problem at the Y-12 National Security Complex (NSC). The report summarizes the research and technology development work of the Phase IIB Project, led by Dr. Uma Sampathkumaran at ISL for the period of July 31, 2017–October 31, 2021. The Y-12 site cleanup includes technologies for safe and cost-effective facility demolition, soil remediation, and on-site treatment and disposal of mercury bearing wastes. One of the technology demonstration goals was a reactive strippable coating for targeted pre-demolition and de-contamination to limit Hg mobilization and the volume of debris requiring treatment for disposal. Toward this, ISL has developed a water-based reactive strippable coating (Trap & See-Hg™) to sequester elemental Hg(0) and mercuric Hg(II) species in the coating. The coating provides multiple benefits including (1) Hg vapor suppression, (2) sealing in the hazardous contaminants, (3) visually locating the contaminant through color changes, and (4) remediating the contaminated surfaces upon coating removal. Through collaboration between ORNL and ISL in Phase II work, the team successfully demonstrated the Trap & See-Hg technology to (1) visually locate the presence of Hg on concrete, soil and drywall surfaces, (2) effectively sequester all mercury species (elemental, soluble and insoluble Hg) from lab-generated and ex-situ soil and brick/rubble samples collected from the Y 12 site with 80 to 95% efficiency to capture/reduce Hg vapor concentration, (3) be applied by manual and robotic spray applicators and cure at room ambient, (4) remain a cohesive and peelable coating upon drying, and (5) sequester Hg0 from walls in the alpha-2 building basement at Y-12 during a small scale in-situ field trial. In Phase IIB, ISL’s effort was focused on refining the coating formulations with additives containing passive and reactive sorbents, colorimetric indicator, and thixotropic agents to achieve the desired performance. The paints were then evaluated at ORNL for applicability to metal and concrete surfaces of different sizes and shapes, and soil rubble, Hg-sorption capacity and achieving sag-free coating on surfaces when applied by a manual spray applicator. Ambient cure of the coating resulted in a dry thickness of 16–20 mil. The coatings were removed from smooth or rough surfaces with low to moderate force. Both lab-generated Hg-contaminated samples and soil and brick/rubble samples containing a range of Hg concentrations (collected from the Y-12 site by UCOR) were used in this project. Optimized formulations were applied to these samples and evaluated for ability to suppress Hg vapors, sequester Hg 0 and Hg(II) species and color mapping of mercury species on the test surface. The ORNL team initially identified three to four potential sites at Y-12 and ORNL for potential demonstration. However, the pandemic closed any possible avenues for on-site demonstration of the robotic spray applicator. The metal and concrete samples with low to high Hg content provided by UCOR from an ongoing demolition were subsequently used for ex-situ sample characterization and analysis at ORNL over a period of 25 days. The coatings suppressed Hg vapors with an efficiency of 95–99% from heavily contaminated metal and 60% from concrete substrate. Analysis of total Hg in the peeled paints indicates sorption capacities ranging from 12 µg Hg/g of paint from concrete to 1.2 mg Hg/g of paint from the metal substrates while peeled paints from soil samples could capture a total Hg from 2.3 mg Hg/g to 66 mg/g paint. Toxicity characteristic leaching procedure (TCLP) tests recovered total mercury leached at 0.15±0.0008 µg/L for concrete to 126.81±0.67 µg/L and 377.25±5.67 µg/L for the two metal substrates, to allow for informed decisions on downstream disposal considerations. Together, this Phase IIB demonstrated the potential value of the Trap & See-Hg for Hg uptake, vapor suppression, and color mapping, and may thus be used to enhance worker safety during site cleanup, facility demolition, and downstream waste disposal at Y-12 NSC.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

LBNL Fault Detection and Diagnostics Datasets

These datasets can be used to evaluate and benchmark the performance accuracy of Fault Detection and Diagnostics (FDD) algorithms or tools. It contains operational data from simulation, laboratory experiments, and field measurements from real buildings for seven HVAC systems/equipment (rooftop unit, single-duct air handler unit, dual-duct air handler unit, variable air volume box, fan coil unit, chiller plant, and boiler plant). Each dataset includes a .pdf file to document key information necessary to understand the content and scope, multiple csv files containing all the time-series data for faults at different severity levels and one fault-free case, and a ttl file to visualize the data according to BRICK schema. The dataset was created by LBNL, PNNL, NREL, ORNL and Drexel University.

AC↗

Vortex Flow and Cavitation in Liquid Injection: A Comparison between High-Fidelity CFD Simulations and Experimental Visualizations on Transparent Nozzle Replicas

Experimental instantaneous shadowgraph visualizations on transparent glass nozzle replicas of high-pressure fuel injectors have been used to validate a novel in-house high-fidelity LES-VOF multiphase solver, to study the evolution of vortex flow and fuel cavitation. Both experiments and simulations capture the formation of an unsteady vapor structure inside the nozzle volume, which is referred to as 'string-cavitation'; strings are found at the core of the recirculation zones. Furthermore, high-fidelity simulations provide a very detailed insight into the vortex generation in the injector nozzle; strings appear within the time scales that are relevant for fast injection events (on the order of 0.1 milliseconds) and, for the problem under consideration, their generation seems mostly related to the flow pattern in the sac. It is also shown that vortexes interact, merge till they disrupt and favor the temporary inception of shear cavitation.

3-phase LES-VOF solver↗