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At least 91 records · Page 5
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Quantifying the dislocation content of atomically resolved grain boundary line defects using the Nye tensor

The Nye tensor, which quantifies the density of Burgers vector for a given dislocation line direction, can be effectively used to characterize dislocation content in bulk crystals from atomic-resolution transmission electron microscopy images. The Nye tensor can be calculated from these images, in part because the reference state is simply defined by the lattice of the perfect crystal. The application of the Nye tensor to interfacial line defects, for which the natural reference state is the dichromatic pattern of the two grains in their reference orientation, poses additional challenges. In this work, we present a method that employs the Nye tensor to characterize the edge dislocation content of line defects at grain boundaries from atomic-resolution images. This approach enables us to rapidly characterize all edge dislocation content along a grain boundary. Additionally, the Nye tensor provides information about line defect core structure. Finally, we demonstrate this method on two exemplar defects: a twin boundary disconnection and a facet junction in face-centered cubic Au.

Crystallographic defects↗
DOE OSTI2023

The N‐terminal intrinsically disordered region of Ncb5or docks with the cytochrome b 5 core to form a helical motif that is of ancient origin

Abstract NADH cytochromeb 5 oxidoreductase (Ncb5or) is a cytosolic ferric reductase implicated in diabetes and neurological conditions. Ncb5or comprises cytochromeb 5 (b 5 ) and cytochromeb 5 reductase (b 5 R) domains separated by a CHORD‐Sgt1 (CS) linker domain. Ncb5or redox activity depends on proper inter‐domain interactions to mediate electron transfer from NADH or NADPH via FAD to heme. While full‐length human Ncb5or has proven resistant to crystallization, we have succeeded in obtaining high‐resolution atomic structures of theb 5 domain and a construct containing the CS andb 5 R domains (CS/b 5 R). Ncb5or also contains an N‐terminal intrinsically disordered region of 50 residues that has no homologs in other protein families in animals but features a distinctive, conserved L 34 MDWIRL 40 motif also present in reduced lateral root formation (RLF) protein in rice and increased recombination center 21 in baker's yeast, all attaching to ab 5 domain. After unsuccessful attempts at crystallizing a human Ncb5or construct comprising the N‐terminal region naturally fused to theb 5 domain, we were able to obtain a high‐resolution atomic structure of a recombinant rice RLF construct corresponding to residues 25–129 of human Ncb5or (52% sequence identity; 74% similarity). The structure reveals Trp 120 (corresponding to invariant Trp 37 in Ncb5or) to be part of an 11‐residue α‐helix (S 116 QMDWLKLTRT 126 ) packing against two of the four helices in theb 5 domain that surround heme (α2 and α5). The Trp 120 side chain forms a network of interactions with the side chains of four highly conserved residues corresponding to Tyr 85 and Tyr 88 (α2), Cys 124 (α5), and Leu 47 in Ncb5or. Circular dichroism measurements of human Ncb5or fragments further support a key role of Trp 37 in nucleating the formation of the N‐terminal helix, whose location in the N/b 5 module suggests a role in regulating the function of this multi‐domain redox enzyme. This study revealed for the first time an ancient origin of a helical motif in the N/b 5 module as reflected by its existence in a class of cytochromeb 5 proteins from three kingdoms among eukaryotes.

Biochemistry & Molecular Biology↗
DOE OSTI2024

Secondary-electron imaging of bulk crystalline specimens in an aberration corrected $\text{STEM}$

Atomic-scale electron microscopy traditionally probes thin specimens, with thickness below 100 nm, and its feasibility for bulk samples has not been documented. Here in this study, we explore the practicality of scanning transmission electron microscope (STEM) imaging with secondary electrons (SE), using a silicon-wedge specimen having a maximum thickness of 18 μm. We find that the atomic structure is present in the entire thickness range of the SE images although the background intensity increases moderately with thickness. The consistent intensity of secondary electron (SE) images at atomic positions and the modest increase in intensity in between (background) observed in silicon suggest a limited contribution from SEs generated by backscattered electrons, a conclusion supported by our multislice calculations. We conclude that achieving atomic resolution in SE imaging for bulk specimens is indeed attainable using aberration-corrected STEM and that an aberration-corrected scanning electron microscope (SEM) may have the capacity for atomic-level resolution, holding great promise for future strides in materials research.

25 ENERGY STORAGE↗
DOE OSTI2020

Atomic structures determined from digitally defined nanocrystalline regions

Nanocrystallography has transformed our ability to interrogate the atomic structures of proteins, peptides, organic molecules and materials. By probing atomic level details in ordered sub-10 nm regions of nanocrystals, scanning nanobeam electron diffraction extends the reach of nanocrystallography and in principle obviates the need for diffraction from large portions of one or more crystals. Scanning nanobeam electron diffraction is now applied to determine atomic structures from digitally defined regions of beam-sensitive peptide nanocrystals. Using a direct electron detector, thousands of sparse diffraction patterns over multiple orientations of a given crystal are recorded. Each pattern is assigned to a specific location on a single nanocrystal with axial, lateral and angular coordinates. This approach yields a collection of patterns that represent a tilt series across an angular wedge of reciprocal space: a scanning nanobeam diffraction tomogram. Using this diffraction tomogram, intensities can be digitally extracted from any desired region of a scan in real or diffraction space, exclusive of all other scanned points. Intensities from multiple regions of a crystal or from multiple crystals can be merged to increase data completeness and mitigate missing wedges. It is demonstrated that merged intensities from digitally defined regions of two crystals of a segment from the OsPYL/RCAR5 protein produce fragment-based ab initio solutions that can be refined to atomic resolution, analogous to structures determined by selected-area electron diffraction. In allowing atomic structures to now be determined from digitally outlined regions of a nanocrystal, scanning nanobeam diffraction tomography breaks new ground in nanocrystallography.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Atom Identification in Bilayer Moiré Materials with Gomb-Net

Moiré patterns in van der Waals bilayer materials complicate the analysis of atomic-resolution images, hindering the atomic-scale insight typically attainable with scanning transmission electron microscopy. Here, we report a method to detect the positions and identities of atoms in each of the individual layers that compose twisted bilayer heterostructures. We developed a deep learning model, Gomb-Net, which identifies the coordinates and atomic species in each layer, deconvoluting the moiré pattern. This enables layer-specific mapping of atomic positions and dopant distributions, unlike other commonly used segmentation models which struggle with moiré-induced complexity. Using this approach, we explored the Se atom substitutional site distribution in a twisted fractional Janus WS 2 -WS 2(1–x) Se 2x heterostructure and found that layer-specific implantation sites are unaffected by the moiré pattern’s local energetic or electronic modulation. In conclusion, this advancement enables atom identification within material regimes where it was not possible before, opening new insights into previously inaccessible material physics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

In Situ Observation of Domain Wall Lateral Creeping in a Ferroelectric Capacitor

As a promising candidate for next-generation nonvolatile memory devices, ferroelectric oxide films exhibit many emergent phenomena with functional applications, making understanding polarization switching and domain evolution behaviors of fundamental importance. However, tracking domain wall motion in ferroelectric oxide films with high spatial resolution remains challenging. Here, in this study, an in situ biasing approach for direct atomic-scale observations of domain nucleation and sideways motion is presented. By accurately controlling the applied electric field, the lateral translational speed of the domain wall can decrease to less than 2.2 Å s −1 , which is observable with atomic resolution STEM imaging. In situ observations on a capacitor structured PbZr 0.1 Ti 0.9 O 3 /La 0.7 Sr 0.3 MnO 3 heterojunction demonstrate the unique creeping behavior of a domain wall under a critical electric field, with the atomic structure of the creeping domain wall revealed. Moreover, the evolution of the metastable domain wall forms an elongated morphology, which contains a large proportion of charged segments. Phase-field simulations unveil the competition between gradient, elastic, and electrostatic energies that decide this unique domain wall creeping and morphology variation. This work paves the way toward a complete fundamental understanding of domain wall physics and potential modulations of domain wall properties in real devices.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Multislice Electron Tomography Using Four-Dimensional Scanning Transmission Electron Microscopy

Electron tomography offers useful three-dimensional (3D) structural information, which cannot be observed by two-dimensional imaging. By combining annular dark-field scanning transmission electron microscopy (ADF STEM) with aberration correction, the resolution of electron tomography has reached atomic resolution. However, tomography based on ADF STEM inherently suffers from several issues, including a high electron-dose requirement, poor contrast for light elements, and artifacts from image-contrast nonlinearity. Here, we develop an alternative method called multislice electron tomography (MSET) based on four-dimensional STEM tilt series. In this study, our simulations show that multislice-based 3D reconstruction can effectively reduce undesirable reconstruction artifacts from the nonlinear contrast, allowing precise determination of atomic structures with improved sensitivity for low-Z elements, at considerably low electron-dose conditions. We expect that the MSET method can be applied to a wide variety of materials, including radiation-sensitive samples and materials containing light elements whose 3D atomic structures have never been fully elucidated due to electron-dose limitations or nonlinear imaging contrast.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2023

Oxidized structure and Compositional properties of 1144 phase FBS by analytical electron microscopy

The 1144 phase (Ae1A1Fe4As4) shows a strong advantage of engineering fabrication among Fe Iron)-based superconductor (FBS) family due to the robustness of its superconducting properties with respect to chemical inhomogeneities, granted by its uniform crystalline-layered structure. This regularity is furthermore associated to crystalline defects capable of acting as efficient pinning centers, which high critical currents achieved at high fields for these superconductors. Like other FBS phases, its lossless current-carrying capability can be remarkably degraded by distractions at grain boundaries (GBs). GB oxidation is an issue of upmost importance to the realization of the practical FBS application for high field (> 20T) magnet. In this study, we explore oxidized grain boundary and intrinsic grain structural properties of 1144 polycrystalline samples by applying analytical electron microscopy such as atomic resolution scanning transmission electron microscopy and atom probe tomography. These structural properties of samples produced by a mechanochemically assisted synthesis are evaluated following the degradation of superconducting properties due to oxidation. We observe a strong correlation between the contamination at grain boundaries and the decrease of transport properties of the bulk sample, while the crystallin structure seems to be not affected by the oxidation.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2023

Evidence of Xe-incorporation in the bubble superlattice in irradiated U-Mo fuel

For years, researchers have reported competing ideas on the formation of fission gas bubble super lattices in metallic fuels, which was postulated to be comprised of elemental xenon (Xe) atoms. However, the chemical and physical arrangement of these elements within this gas bubble superlattice has not been verified. In this contribution, Xe was chemically profiled using atomic resolution scanning transmission electron microscopy (STEM) and atom probe tomography (APT) techniques in irradiated uranium-molybdenum (U-Mo) fuels. These complementary techniques provide conclusive evidence of Xe presence in bubble superlattice up to fission densities of 4.5×10 21 fissions/cm 3 and provide quantitative assessment of Xe content within the bubble superlattice. Based on the results of simultaneous imaging and spectroscopy using STEM, the chemical composition of the Xe bubble superlattice present in fission densities less than 4.5x10 21 fissions/cm 3 in U-Mo fuel was measured and found to be up to 8±1.3 atomic %. APT data complements STEM findings on Xe distribution in irradiated U-Mo fuel sample. APT showed a chemical composition of 0.7±0.1 atomic%. Finally, this study concludes by providing conclusive evidence that Xe is not only present within an atomically arranged bubble superlattice but provides fundamental insight the physical state of Xe in low enriched U-Mo monolithic fuel.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Direct growth of crystalline SiGe nanowires on superconducting NbTiN thin films

Novel heterostructures created by coupling one-dimensional semiconductor nanowires with a superconducting thin film show great potential toward next-generation quantum computing. Here, by growing high-crystalline SiGe nanowires on a NbTiN thin film, the resulting heterostructure exhibits Ohmic characteristics as well as a shift of the superconducting transition temperature (T c ). The structure was characterized at atomic resolution showing a sharp SiGe/NbTiN interface without atomic interdiffusion. Lattice spacing, as calculated from large-area x-ray diffraction experiments, suggests a potential preferred d-spacing matching between (200) NbTiN and (110) SiGe grains. The observed out-of-plane compressive strain within the NbTiN films coupled with SiGe nanowires explains the downward shift of the superconductivity behavior. The presented results post scientific insights toward functional heterostructures by coupling multi-dimensional materials, which could enable tunable superconductivity that benefits the quantum science applications.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2020

Atomically precise digital e-beam lithography

Hydrogen Depassivation Lithography (HDL) is a version of electron beam lithography that uses scanning tunneling microscope (STM) instrumentation to expose a self–developing resist that is a monolayer of H chemisorbed to a Si (100) 2x1 H-passivated surface. Developed in the 1990s it has been largely a laboratory tool used in research for nanofabrication. Here, the technique is capable of atomic resolution, the ability to remove single H atoms from the Si surface and has much higher precision than the best conventional e-beam lithography can possibly achieve exposing polymeric resists. However, its most promising attribute is that it can be used as a digital fabrication tool and is the first of a class of nanofabrication techniques that can be considered digital atomic scale fabrication technologies. Digital Atomic Scale Fabrication can be shown to have similar advantages over analog fabrication techniques that digital information technology has over analog information technology.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2023

Cryogenic X-ray crystallographic studies of biomacromolecules at Turkish Light Source " Turkish DeLight "

X-ray crystallography is a robust and powerful structural biology technique that provides high-resolution atomic structures of biomacromolecules. Scientists use this technique to unravel mechanistic and structural details of biological macromolecules (e.g., proteins, nucleic acids, protein complexes, protein-nucleic acid complexes, or large biological compartments). Since its inception, single-crystal cryocrystallography has never been performed in Türkiye due to the lack of a single-crystal X-ray diffractometer. The X-ray diffraction facility recently established at the University of Health Sciences, Istanbul, Türkiye will enable Turkish and international researchers to easily perform high-resolution structural analysis of biomacromolecules from single crystals. Here, we describe the technical and practical outlook of a state-of-the-art home-source X-ray, using lysozyme as a model protein. The methods and practice described in this article can be applied to any biological sample for structural studies. Therefore, this article will be a valuable practical guide from sample preparation to data analysis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Ultra-Microtome for the Preparation of TEM Samples from Battery Cathodes

An ultra-microtome method is developed for the preparation of transmission electron microscopy (TEM) specimens from the cathodes of Li-ion battery. Results indicate that the samples prepared with the ultra-microtome method yield atomic resolution imaging from the core area of particles of hundreds to thousands of nanometers. Analysis of the TEM samples prepared with ultra-microtome indicates that no observable structural damage, such as microcracking, is introduced during the cutting process, and the cathodes cut by ultra-microtome exhibit unchanged micro-morphologies compared with the uncut ones. These results demonstrate that ultra-microtome is a promising method for the preparation of TEM specimens and revealing in-depth microstructures of fragile materials such as battery cathodes.

transmission electron microscopy, Sample Preparati↗
DOE OSTI2020

Structural and spectroscopic characterization of photoactive yellow protein and photoswitchable fluorescent protein constructs containing heavy atoms

Photo-induced structural rearrangements of chromophore-containing proteins are essential for various light-dependent signaling pathways and optogenetic applications. Ultrafast structural and spectroscopic methods have offered insights into these structural rearrangements across many timescales. However, questions still remain about exact mechanistic details, especially regarding photoisomerization of the chromophore within these proteins femtoseconds to picoseconds after photoexcitation. Instrumentation advancements for time-resolved crystallography and ultrafast electron diffraction provide a promising opportunity to study these reactions, but achieving enough signal-to-noise is a constant challenge. In this work, we present four new photoactive yellow protein constructs and one new fluorescent protein construct that contain heavy atoms either within or around the chromophore and can be expressed with high yields. Structural characterization of these constructs, most at atomic resolution, show minimal perturbation caused by the heavy atoms compared to wild-type structures. Spectroscopic studies report the effects of the heavy atom identity and location on the chromophore’s photophysical properties. None of the substitutions prevent photoisomerization, although certain rates within the photocycle may be affected. Overall, these new proteins containing heavy atoms are ideal samples for state-of-the-art time-resolved crystallography and electron diffraction experiments to elucidate crucial mechanistic information of photoisomerization.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Atomically resolved edges and defects in lead halide perovskites

Although edges and defects constitute only a small fraction of crystalline materials, they exert an outsized impact on a material′s properties. Organic–inorganic halide perovskites are promising next-generation semiconductor materials with superior cost effectiveness and interesting optoelectronic properties. However, clear images of their edges have remained challenging to obtain owing to their extreme sensitivity. Using truly high-speed ultralow-dose four-dimensional scanning transmission electron microscopy with dose fractionation, we perform ptychography at, to our knowledge, the lowest-dose atomic resolution to date, revealing not only the detailed atomic structure of the edges of a halide perovskite but also their structural dynamics. Here, a majority methylammonium (MA) and iodine (I) edge termination is observed in methylammonium lead iodide (MAPbI 3 ), and the damage rate of its edges and internal defects is found to depend on the concentration and type of vacancies present, with a preponderance of I vacancies in particular correlating with higher rates of damage.

4D-STEM↗
DOE OSTI2021

Ultranarrow TaS 2 Nanoribbons

Imposing additional confinement in two-dimensional (2D) materials can yield further control over the associated electronic, optical, and topological properties. However, synthesis of ultra-narrow nanoribbons (NRs) remains a challenge, particularly for the transition metal dichalcogenides (TMDs), and synthesizing TMD NRs narrower than 50 nm has remained elusive. In this paper, we report the vapor-phase synthesis of ultra-narrow TaS 2 NRs. The NRs are grown within the hollow cavity of carbon nanotubes, thereby limiting their lateral dimensions and layer number, while simultaneously stabilizing them against the environment. The NRs reach the monolayer (ML) limit and exhibit widths as low as 2.5 nm. Atomic-resolution scanning transmission electron microscopy (STEM) reveals the detailed atomic structure of the ultra-narrow NRs and we observe a hitherto unseen atomic structure supermodulation phenomenon of ordered defect arrays within the NRs. First-principles calculations based on density functional theory (DFT) show the presence of flat bands, as well as edge- and boundary-localized states, and help identify the atomic configuration of the supermodulation. Nanotube-templated synthesis represents a unique, transferable, and broadly deployable route toward ultra-narrow TMD NR growth.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2024

Cryo2StructData: A Large Labeled Cryo-EM Density Map Dataset for AI-based Modeling of Protein Structures

The advent of single-particle cryo-electron microscopy (cryo-EM) has brought forth a new era of structural biology, enabling the routine determination of large biological molecules and their complexes at atomic resolution. The high-resolution structures of biological macromolecules and their complexes significantly expedite biomedical research and drug discovery. However, automatically and accurately building atomic models from high-resolution cryo-EM density maps is still time-consuming and challenging when template-based models are unavailable. Artificial intelligence (AI) methods such as deep learning trained on limited amount of labeled cryo-EM density maps generate inaccurate atomic models. To address this issue, we created a dataset called Cryo2StructData consisting of 7,600 preprocessed cryo-EM density maps whose voxels are labelled according to their corresponding known atomic structures for training and testing AI methods to build atomic models from cryo-EM density maps. Cryo2StructData is larger than existing, publicly available datasets for training AI methods to build atomic protein structures from cryo-EM density maps. We trained and tested deep learning models on Cryo2StructData to validate its quality showing that it is ready for being used to train and test AI methods for building atomic models.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Nanometer Resolution Structure‐Emission Correlation of Individual Quantum Emitters via Enhanced Cathodoluminescence in Twisted Hexagonal Boron Nitride

Understanding the atomic structure of quantum emitters, often originating from point defects or impuritie, is essential for designing and optimizing materials for quantum technologies such as quantum computing, communication, and sensing. Despite the availability of atomic-resolution scanning transmission electron microscopy and nanoscale cathodoluminescence microscopy, experimentally determining the atomic structure of individual emitters is challenging due to the conflicting needs for thick samples to generate strong cathodoluminescence signals and thin samples for structural analysis. To overcome this challenge, significantly enhanced cathodoluminescence at twisted interfaces is leveraged to achieve sub-nanometer localization precision for the first time in mapping individual quantum emitters in carbon-implanted hexagonal boron nitride. This unprecedent spatial sensitivity, together with correlative electron energy loss spectroscopy quantitative scanning transmission electron microscopy imaging, and first principles density functional theory calculations, enables the identification of the atomic structure of the 440 nm blue emitter in hexagonal boron nitride as a substituted vertical carbon dimer. Building on the atomic structure insights, nanoscale spatially precise creation of blue emitters is demonstrated by electron beam irradiation of carbon-coated hexagonal boron nitride. This advancement in correlating atomic structures with optical properties lays the foundation for a deeper understanding and precise engineering of quantum emitters, significantly advancing the development of cutting-edge quantum information technologies.

2D material↗