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DOE OSTI2021

Ultra-Structural Imaging Provides 3D Organization of 46 Chromosomes of a Human Lymphocyte Prophase Nucleus

Three dimensional (3D) ultra-structural imaging is an important tool for unraveling the organizational structure of individual chromosomes at various stages of the cell cycle. Performing hitherto uninvestigated ultra-structural analysis of the human genome at prophase, we used serial block-face scanning electron microscopy (SBFSEM) to understand chromosomal architectural organization within 3D nuclear space. Acquired images allowed us to segment, reconstruct, and extract quantitative 3D structural information about the prophase nucleus and the preserved, intact individual chromosomes within it. Our data demonstrate that each chromosome can be identified with its homolog and classified into respective cytogenetic groups. Thereby, we present the first 3D karyotype built from the compact axial structure seen on the core of all prophase chromosomes. The chromosomes display parallel-aligned sister chromatids with familiar chromosome morphologies with no crossovers. Furthermore, the spatial positions of all 46 chromosomes revealed a pattern showing a gene density-based correlation and a neighborhood map of individual chromosomes based on their relative spatial positioning. A comprehensive picture of 3D chromosomal organization at the nanometer level in a single human lymphocyte cell is presented.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2024

Addressing Experimental Challenges in Probing Dark Energy with Accuracy and Precision with the Rubin Observatory Legacy Survey of Space & Time (LSST)

With support from this award, the Stanford group under the leadership of PI Patricia Burchat focused on pixel-level algorithms that are key to the investigation of dark energy with the Vera C. Rubin Observatory Legacy Survey of Space and Time (LSST). The work was carried out through strong engagement in the DOE-supported LSST Dark Energy Science Collaboration (DESC), for which the PI served as Deputy Spokesperson (07/2019 - 07/2021) and Technical Coordinator (07/2021 - 07/2023). Members of the Burchat group are Full DESC members and are among scientists who have been accepted to join the Rubin Observatory System Integration, Test, and Commissioning (SIT-Com) effort. The specific intellectual focus of the group was the optimization of gravitational lensing as a probe of the evolution of the distribution of dark matter in space and time to learn about the nature of dark energy. The Stanford group pursued an integrated research program to understand in detail, and then remediate or calibrate, systematic effects that could limit the sensitivity of the LSST to cosmic shear as a dark energy probe -- particularly those related to our understanding of the atmospheric point spread function (PSF), challenges associated with blended galaxy images, and impacts of residual camera artifacts. Key to this work was developing, enhancing, and validating the fidelity of simulations that play a key role in the development of our understanding of subtle systematic biases and then using these simulations to develop techniques to characterize and mitigate biases, and associated algorithms for implementation in the LSST or DESC science pipelines. The group’s work included contributions to the open-source GalSim simulation package, which is widely used in the community; simulations and studies of spatial correlations of atmospheric PSFs; studies of temporal correlations of the atmospheric PSF; impacts of chromatic PSFs on cosmic shear calibration; continued studies of anisotropic Gaussian process interpolation of PSF models across the focal plane; and measuring and mitigating impacts of residual camera artifacts on cosmic shear. A primary impact of this work is that it increases the scientific discovery potential of the DOE and NSF investments in the Rubin Observatory Legacy Survey of Space \& Time, by addressing challenges in interpreting astronomical images through more accurate descriptions of the blurring of images due to the atmosphere. Specifically, this work impacts our ability to understand the fundamental nature of dark energy.

Burchat, Patricia Rose↗

DOE OSTI2024

Direct Imaging of Asymmetric Interfaces and Electrostatic Potentials inside a Hafnia–Zirconia Ferroelectric Nanocapacitor

In hafnia-based thin-film ferroelectric devices, chemical phenomena during growth and processing, such as oxygen vacancy formation and interfacial reactions, appear to strongly affect device performance. However, the correlation between the structure, chemistry, and electrical potentials at the nanoscale in these devices is not fully known, making it difficult to understand their influence on device properties. Here, we directly image the composition and electrostatic potential with nanometer resolution in the cross section of a nanocrystalline W/Hf 0.5 Zr 0.5 O 2−δ (HZO)/W ferroelectric capacitor using multimodal electron microscopy. This reveals a 1.4 nm wide tungsten suboxide interfacial layer formed at the bottom interface during fabrication, which introduces a potential dip and leads to asymmetric switching fields. Additionally, we compare the measured potentials to DFT calculations and find it is nearly 3 V lower than expected in the HZO, which appears to be caused by oxygen vacancies and a resulting negative built-in potential. In conclusion, these chemical and electrostatic details are important to characterize and tune to achieve high-performance ferroelectric devices.

Defects in solids↗

DOE OSTI2022

Understanding the Elastic, Plastic, and Damage Features in Fracturing of Self-reinforced Thermoplastic Composites via Non-destructive Digital Imaging Correlation

This work demonstrated the utilization of non-destructive Digital Imaging Correlation (DIC) method to characterize the elastic, plastic, and damage features during the Mode I intra-laminar fracturing process of self-reinforced thermoplastic composites by using a self-reinforced polypropylene (PP) composite as an example. The DIC results clearly showed the development of huge plastic zone (PZ) and non-negligible Fracture Process Zone (FPZ) in front of the notch tip during the fracturing process, and the geometries and sizes of the foregoing zones at the peak load were further quantified. Such an interesting fracturing behavior of self-reinforced thermoplastic composites is way different from brittle materials (e.g., glass, acrylic, etc.), ductile materials (e.g., aluminum, steel, etc.), and even quasi-brittle materials (e.g., concrete, nanoparticle-reinforced composites, tough ceramics, wood, cement, carbon/glass fiber-reinforced polymers, etc.). Thus, understanding the elastic, plastic, and damage features is the first step before better characterizing the material fracture properties of self-reinforced thermoplastic composites through new analytical methods and computational modeling. These efforts are of utmost importance for wide applications of self-reinforced thermoplastic composites in various engineering fields in the future.

Lightweight Composites, Self-reinforced Thermoplas↗

DOE OSTI2023

Design and simulation of multilayer coatings for a multi-channel Wolter-like x-ray imager with large field of view and high resolution

X-ray diagnostics are key instruments for understanding the physics behind inertial confinement fusion experiments. We report on the multilayer design optimization for the Toroidal X-ray Imager (TXI), a hard x-rays microscope instrument designed by Commissariat à l’énergie atomique (CEA) and Laboratoire Charles Fabry (LCF) to be installed on the National Ignition Facility. TXI includes six channels designed for three different energy bands centered on 8.7, 13, and 17.5 keV. Each channel is made up of two toroidal mirrors arranged in a Wolter-like configuration. The required field of view is 800 × 400 µm2, and the resolution should be better than 5 µm. In addition, we seek to estimate the spatial distribution of the temperature, which requires no spectral overlap of the different energy bands and a good spectral homogeneity of the image produced. The development of the multilayer coatings was performed in a two-step method. First, the coatings were optimized to obtain proper energy bands. Then, an x-ray tracing code was used to calculate the integrated optical response of each channel and adjust the response of the mirror to fulfill the requirements. To fulfill all the specifications, we propose an original design using a combination of two aperiodic coatings, one with a narrow bandwidth and the other one with a larger bandwidth.

hard x-rays↗

DOE OSTI2026

Single-shot imaging with randomized structured illumination at a free electron laser

Stroboscopic nanoscale imaging with free electron laser light is revolutionizing our understanding of fast dynamics in heterogeneous systems. The short wavelength of X-ray and extreme ultraviolet radiation makes it possible to achieve nanoscale resolution, while resonance with atomic transitions gives access to electronic and magnetic degrees of freedom. Here, we report on our implementation of a recently developed imaging method, randomized probe imaging, at a free electron laser. The advantage of randomized probe imaging over existing methods is its compatibility with extended and strongly scattering samples. Our implementation delivers robust single-shot reconstructions at up to a full-pitch resolution of 400 nm over a field of view with a 40 µm diameter. We also demonstrate single-shot imaging of magnetic domain structures using circular dichroism at resonance, paving the way to future time-resolved studies of magnetic dynamics, shock physics, and the dynamics of collective electronic phases.

47 OTHER INSTRUMENTATION↗

DOE OSTI2025

In situ atomic-resolution imaging of water vapor–driven multistep oxidation dynamics in strontium cobaltite

Understanding how water vapor interacts with transition metal oxides (TMOs) is critical for tailoring material properties to improve performance and enable new technologies. Despite extensive research efforts, atomic-scale mechanisms underpinning dynamic reactions and reaction-induced phase transitions remain elusive. Here, we use in situ environmental transmission electron microscopy to investigate how water vapor oxidizes vacancy-ordered SrCoO 2.5 at moderately elevated temperatures, demonstrating that water molecules can initiate oxidation more effectively than oxygen under comparable conditions. We discover a distinct “staging” behavior during the oxidation process: A fully ordered intermediate phase, SrCoO 2.75 , forms before transitioning into a near-perovskite SrCoO 3−δ . In addition, antiphase boundaries, originating at step terraces of SrTiO 3 , alleviate strain by creating reversible nanoscale “gaps” during lattice contraction under oxidation, providing a pathway for preserving structural integrity throughout redox cycling. This work provides atomic-level guidance for engineering TMOs by leveraging water vapor to control their redox behavior and tailor functional properties.

Science & Technology - Other Topics↗

DOE OSTI2022

Nano-FTIR Investigation of the CM Chondrite Allan Hills 83100

Mid-infrared (MIR) spectroscopy has been used with great success to quantitatively determine the mineralogy of geologic samples. It has been employed in a variety of contexts from determining bulk composition of powdered samples to spectroscopic imaging of rock thin sections via micro-Fourier transform infrared (micro-FTIR) imaging spectroscopy. Recent advances allow for IR measurements at the nanoscale. Near field nanoscale infrared imaging and spectroscopy with a broadband source (nano-FTIR) enable understanding of the spatial relationships between compositionally distinct materials within a sample. This will be of particular use when analyzing returned samples from Bennu and Ryugu, which are thought to be compositionally like CI or CM1/2 carbonaceous chondrites. Returned samples will likely contain olivine/pyroxene chondrules that have been transformed into hydrous phyllosilicates, sulfides, carbonates, and other alteration phases. The use of near-field infrared techniques to probe the boundaries between once pristine chondrules and alteration phases at the nanoscale is a novel approach to furthering our understanding of the compositional evolution of carbonaceous asteroids and the processes that drive their evolution. Here we report the results of nano-FTIR spectroscopy and imaging measurements performed on the carbonaceous chondrite Allan Hills (ALH) 83100 (CM1/2). We show with nanoscale resolution that spatially resolved Fe-Mg variations exist within the phyllosilicates around a chondrule rim. We also present effects of crystal orientation on the nano-FTIR spectra to account for the spectral differences between the meteorite and mineral spectra.

58 GEOSCIENCES↗

DOE OSTI2023

Let’s Unleash the Network Judgment: A Self-Supervised Approach for Cloud Image Analysis

Accurate cloud type identification and coverage analysis are crucial in understanding the Earth’s radiative budget. Traditional computer vision methods rely on low-level visual features of clouds for estimating cloud coverage or sky conditions. Several handcrafted approaches have been proposed; however, scope for improvement still exists. Newer deep neural networks (DNNs) have demonstrated superior performance for cloud segmentation and categorization. These methods, however, need expert engineering intervention in the preprocessing steps—in the traditional methods—or human assistance in assigning cloud or clear sky labels to a pixel for training DNNs. Such human mediation imposes considerable time and labor costs. We present the application of a new self-supervised learning approach to autonomously extract relevant features from sky images captured by ground-based cameras, for the classification and segmentation of clouds. We evaluate a joint embedding architecture that uses self-knowledge distillation plus regularization. We use two datasets to demonstrate the network’s ability to classify and segment sky images—one with ~85,000 images collected from our ground-based camera and another with 400 labeled images from the WSISEG database. We find that this approach can discriminate full-sky images based on cloud coverage, diurnal variation, and cloud base height. Additionally, it semantically segments the cloud areas without labels. The approach shows competitive performance in all tested tasks, suggesting a new alternative for cloud characterization.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Enhancing Electron Microscopy Image Classification Using Data Augmentation

Manual labeling for machine learning tasks such as image classification is tedious and labor-intensive; as a result, scientific datasets suitable for deep learning applications are scarce and limited. While data augmentation techniques have shown promise for extending image datasets, very little work has been done to understand the impact of combining multiple augmentation methods sequentially or the limits of their effectiveness when combined. Our work addresses this gap by examining how standard and combinatorial data augmentation affects the performance of machine learning models when trained on small datasets for label classification tasks. For our analysis, we generate single, double and quadruple-augmented datasets for a microscopy image classification task using six standard augmentation methods, and compare the resultant improvements observed in binary classification accuracy with three standard image classification models (DenseNet169, MobileNetV2, ResNet101V2). Our experiments show a non-monotonic relationship between the number of simultaneous augmentation methods and classification accuracy, indicating that there is a trade-off between the degree of augmentation and the model performance. These findings suggest that the optimal number of augmentation methods will vary by domain and use case. We also find that the order in which augmentation methods are applied to a limited dataset matters when combining augmentation schemes, with our use case showing performance differences up to 2.6% when the augmentation order is reversed for double-augmented datasets. Our work offers insights to the limits of data augmentation when working on image classification tasks with limited datasets.

Welsman, Jordan A↗

DOE OSTI2020

Three-Dimensional Imaging and Quantification of Gas Storativity in Nanoporous Media via X-rays Computed Tomography

This study provides the engineering science underpinnings for improved characterization and quantification of the interplay of gases with kerogen and minerals in shale. Natural nanoporous media such as shale (i.e., mudstone) often present with low permeability and dual porosity, making them difficult to characterize given the complex structural and chemical features across multiple scales. These structures give nanoporous solids a large surface area for gas to sorb. In oil and gas applications, full understanding of these media and their sorption characteristics are critical for evaluating gas reserves, flow, and storage for enhanced recovery and CO 2 sequestration potential. Other applications include CO 2 capture from industrial plants, hydrogen storage on sorbent surfaces, and heterogeneous catalysis in ammonia synthesis. Therefore, high-resolution experimental procedures are demanded to better understand the gas–solid behavior. In this study, CT imaging was applied on the sub-millimeter scale to shale samples (Eagle Ford and Wolfcamp) to improve quantitative agreement between CT-derived and pulse decay (mass balance) derived results. Improved CT imaging formulations are presented that better match mass balance results, highlighting the significance of gas sorption in complex nanoporous media. The proposed CT routine implemented on the Eagle Ford sample demonstrated a 17% error reduction (22% to 5%) when compared to the conventional CT procedure. These observations are consistent in the Wolfcamp sample, emphasizing the reliability of this technique for broader implementation of digital adsorption studies in nanoporous geomaterials.

42 ENGINEERING↗

DOE OSTI2022

Water Imbibition and Oil Recovery in Shale: Dynamics and Mechanisms Using Integrated Centimeter-to-Nanometer-Scale Imaging

Water imbibition, and the associated oil displacement, is an important process in shale oil reservoirs after hydraulic fracturing and in water-based enhanced oil recovery (EOR). Current techniques for water imbibition measurement are mostly “black-box”-type methods. A more explicit understanding of the water imbibition/oil recovery dynamics and geological controls is in demand. In this paper, a multiscale imaging technique that covers centimeter to nanometer scale (i.e., core to pore scale), integrating neutron radiography, microcomputed tomography (micro-CT), and scanning electron microscope (SEM) is applied to investigate the water imbibition depth and rate and the cause of heterogeneity of imbibition in shale samples. The dynamic processes of water imbibition in the 1-in. (25.4-mm) core sample were explicitly demonstrated, and the imbibition along the matrix and imbibition through microfractures are distinguished through neutron radiography image analysis. The causes of observed imbibition heterogeneity were further investigated through micro-CT and SEM image analysis for 1.5-mm diameter miniplug samples from different laminas of the 1-in. core samples. Imbibition depth and rate were calculated on the basis of image analysis as well. Estimation of oil recovery through water imbibition in shale matrix was performed for an example shale field. Here this innovative and integrated multiscale imaging technique provides a “white/gray-box” method to understand water imbibition and water-oil displacement in shale. The wide span of the length scale (from centimeter to nanometer) of this technique enables a more comprehensive, accurate, and specific understanding of both the core-scale dynamics and pore-scale mechanisms of water imbibition, oil recovery, and matrix-fracture interaction.

04 OIL SHALES AND TAR SANDS↗

DOE OSTI2020

Radar Motion Measurements and Synthetic Aperture Radar Image Geolocation Accuracy

Once a Synthetic Aperture Radar (SAR) image is formed, the natural question then is, "Where is this image?" and/or "Where exactly is this feature displayed in the image?" Thus, geolocation is an important exploitation of the SAR image. Since SAR measures relative location to its own position, it is crucial to understand how the radars position and motion imp acts the ability to geolocate a feature in the SAR image. Furthermore, accuracy and precision of navigation aids like GPS directly impact the goodness of the geolocation solution. These relationships are developed and discussed.

58 GEOSCIENCES↗

DOE OSTI2021

In-situ 4D visualization and analysis of temperature-driven creep in an oil shale propped fracture

Here, the proppant embedment due to creep in shales is a known issue affecting the useable lifetime of wells in unconventional oil and gas recovery. One of the factors influencing creep is the presence of organics, whose properties can be very sensitive to temperature. In this work we investigated for the first time the role of temperature-induced creep increase in proppant embedment in an organics-rich Green River oil shale sample via in-situ synchrotron X-ray micro-computed tomography. We observed that temperatures as low as 75 °C already induce fast creep, with a fracture aperture closing rate of 13 μm/h and a loss of fracture conductivity rate of 8.7%/h, due only to proppant embedment, in the measured interval at the first heating stage. Local displacement data analysis provided evidence for markedly plastic deformation around the proppant-shale contacts, in contrast with the brittle proppant embedment observed on more cemented and less organics-rich shales at room temperature. The results highlight how the problem of temperature-dependent mechanical behavior might be more important than previously thought, in shales with a high content in organics, and that in-situ micro-imaging techniques can play a key role in understanding the underlying mechanisms, contributing to solve creep-related problems associated with hydraulic fracturing in complex scenarios.

02 PETROLEUM↗

DOE OSTI2020

Challenges in Lithium Metal Anodes for Solid-State Batteries

In this Perspective, we highlight recent progress and challenges related to the integration of lithium metal anodes in solid-state batteries. While prior reports have suggested that solid electrolytes may be impermeable to lithium metal, this hypothesis has been disproven under a variety of electrolyte compositions and cycling conditions. Herein, we describe the mechanistic origins and importance of lithium filament growth and interphase formation in inorganic and organic solid electrolytes. Multimodal techniques that combine real and reciprocal space imaging and modeling will be necessary to fully understand nonequilibrium dynamics at these buried interfaces. Currently, most studies on lithium electrode kinetics at solid electrolyte interfaces are completed in symmetric Li–Li configurations. To fully understand the challenges and opportunities afforded by Li-metal anodes, full-cell experiments are necessary. Lastly, the impacts of operating conditions on solid-state batteries are largely unknown with respect to pressure, geometry, and break-in protocols. Given the rapid growth of this community and the diverse portfolio of solid electrolytes, we highlight the need for detailed reporting of experimental conditions and standardization of protocols across the community.

25 ENERGY STORAGE↗

DOE OSTI2025

Operando Neutron Imaging of Reaction Extent and Particle Swelling Informs Limiting Factors for Salt Hydrate Thermochemical Energy Storage

Salt hydrates are a promising thermochemical energy storage medium that stores heat through the reversible uptake (hydration) and release (dehydration) of water vapor. Our study deploys operando neutron imaging to investigate salt hydrate performance with high spatial resolution (42 μm pixels). For flow over a packed bed with diffusion-driven transport, measurements reveal the formation of a solid diffusion layer due to particle swelling for the pure SrBr2 salt. In contrast, the SrBr2–vermiculite composite exhibits significantly less swelling and more than a 2-fold increase in the apparent water vapor diffusivity. For axial flow through a packed bed, neutron imaging confirms theoretically predicted transitions from a moving reaction front to a homogeneous profile with an increase in humid air flow rate. Our study establishes neutron imaging as a powerful technique to advance fundamental understanding of thermochemical systems and help guide composite material design.

Kinzer, Bryan [ORNL] (ORCID:0000000337804910)↗

DOE OSTI2024

Beyond nothingness in the formation and functional relevance of voids in polymer films

Abstract Voids—the nothingness—broadly exist within nanomaterials and impact properties ranging from catalysis to mechanical response. However, understanding nanovoids is challenging due to lack of imaging methods with the needed penetration depth and spatial resolution. Here, we integrate electron tomography, morphometry, graph theory and coarse-grained molecular dynamics simulation to study the formation of interconnected nanovoids in polymer films and their impacts on permeance and nanomechanical behaviour. Using polyamide membranes for molecular separation as a representative system, three-dimensional electron tomography at nanometre resolution reveals nanovoid formation from coalescence of oligomers, supported by coarse-grained molecular dynamics simulations. Void analysis provides otherwise inaccessible inputs for accurate fittings of methanol permeance for polyamide membranes. Three-dimensional structural graphs accounting for the tortuous nanovoids within, measure higher apparent moduli with polyamide membranes of higher graph rigidity. Our study elucidates the significance of nanovoids beyond the nothingness, impacting the synthesis‒morphology‒function relationships of complex nanomaterials.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Analysis of Seismic Signals Generated by Vehicle Traffic with Application to Derivation of Subsurface Q-Values

Correct identification and modeling of anthropogenic sources of ground motion are of considerable importance for many studies, including detection of small earthquakes and imaging seismic properties below the surface. Here, to understand signals generated by common vehicle traffic, we use seismic data recorded by closely spaced geophones normal to roads at two sites on San Jacinto fault zone. To quantify the spatiotemporal and frequency variations of the recorded ground motions, we develop a simple analytical solution accounting for propagation and attenuation of surface waves. The model reproduces well-observed bell-shaped spectrograms of car signals recorded by geophones close to roads, and it can be used to estimate frequency-dependent Q-values of the subsurface materials. The data analysis indicates Q-values of 3–40, for frequencies up to 150 Hz for road-receiver paths at the two examined sites. The derived Q-values are consistent with attenuation factors of surface waves previously obtained with other methods. The analytical results and analysis procedure provide a highly efficient method for deriving Q-values of shallow subsurface materials.

58 GEOSCIENCES↗