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

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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Unravelling Disorder in Aperiodic Crystals – Diffuse Scattering and Atomic Resolution Holography

The atomic–scale disorder of aperiodic crystals, and quasicrystals in particular, is inherently difficult to explore by experimental methods due to their complex atomic arrangements. Two advanced characterization techniques, a revived and an emerging one, offer direct experimental access even to such complex atomic structures: Diffuse Scattering and Atomic Resolution Holography. Finally, in this overview, we introduce their specific application to aperiodic crystals and discuss their merits and difficulties.

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

Quantitative approaches for multiscale structural analysis with atomic resolution electron microscopy

Atomic-resolution imaging with scanning transmission electron microscopy is a powerful tool for characterizing the nanoscale structure of materials, in particular features such as defects, local strains, and symmetry-breaking distortions. In addition to advanced instrumentation, the effectiveness of the technique depends on computational image analysis to extract meaningful features from complex datasets recorded in experiments, which can be complicated by the presence of noise and artifacts, small or overlapping features, and the need to scale analysis over large representative areas. Here, we present image analysis approaches which synergize real and reciprocal space information to efficiently and reliably obtain meaningful structural information with picometer scale precision across hundreds of nanometers of material from atomic-resolution electron microscope images. Damping superstructure peaks in reciprocal space allows symmetry-breaking structural distortions to be disentangled from other sources of inhomogeneity and measured with high precision. Real-space fitting of the wavelike signals resulting from Fourier filtering enables absolute quantification of lattice parameter variations and strain, as well as the uncertainty associated with these measurements. Implementations of these algorithms are made available as an open source python package.

36 MATERIALS SCIENCE↗
DOE OSTI2024

2D Polyhedral Template Matching for Atomic Resolution Microscopy

SAND2024-13879O The 2D Polyhedral Template Matching for Atomic Resolution Microscopy is a suite of functions for analyzing atomic resolution electron microscopy images using the 2D polyhedral template matching (2D-PTM) method. This software analyzes atomic resolution microscopy data from electron microscopic imaging or scanning probe microscopies. The primary application is for identifying different crystal phases, crystal orientations, and defect structures obtained in such atomic resolution images. Written in MATLAB and starting from an atomic resolution image, the code identifies the positions of atomic intensity peaks. It then matches predefined structural templates to the local atomic environments. Outputs include the local structural identification, the template scaling factor and rotation angle, root-mean-squared deviation (RMSD), and centrosymmetry parameter.

Medlin, Douglas↗
DOE OSTI2024

Atomic resolution scanning transmission electron microscopy at liquid helium temperatures for quantum materials

Fundamental quantum phenomena in condensed matter, ranging from correlated electron systems to quantum information processors, manifest their emergent characteristics and behaviors predominantly at low temperatures. This necessitates the use of liquid helium (LHe) cooling for experimental observation. Atomic resolution scanning transmission electron microscopy combined with LHe cooling (cryo-STEM) provides a powerful characterization technique to probe local atomic structural modulations and their coupling with charge, spin and orbital degrees-of-freedom in quantum materials. However, achieving atomic resolution in cryo-STEM is exceptionally challenging, primarily due to sample drifts arising from temperature changes and noises associated with LHe bubbling, turbulent gas flow, etc. In this work, we demonstrate atomic resolution cryo-STEM imaging at LHe temperatures using a commercial side-entry LHe cooling holder. Firstly, we examine STEM imaging performance as a function of He gas flow rate, identifying two primary noise sources: He-gas pulsing and He-gas bubbling. Secondly, we propose two strategies to achieve low noise conditions for atomic resolution STEM imaging: either by temporarily suppressing He gas flow rate using the needle valve or by acquiring images during the natural warming process. Lastly, we show the applications of image acquisition methods and image processing techniques in investigating structural phase transitions in Cr 2 Ge 2 Te 6 , CuIr 2 S 4 , and CrCl 3 . In conclusion, our findings represent an advance in the field of atomic resolution electron microscopy imaging for quantum materials and devices at LHe temperatures, which can be applied to other commercial side-entry LHe cooling TEM holders.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Time-resolved atomic-resolution Brownian tomography of single nanocrystals reveals size-dependent dynamics

Atomic-resolution structure identification of nanocrystals by graphene liquid cell electron microscopy (GLC-EM) has revealed that small, solubilized platinum nanocrystals consist of an ordered crystalline core surrounded by mobile surface atoms, which dissociate during oxidative etching, resulting in distinct temporal structural states. Requirements imposed by the 3D reconstruction algorithm limit the number of structural states that can be resolved. We introduce a regularized 3D reconstruction algorithm that exploits the redundancy inherent in the experimental data, allowing us to improve the time resolution. Our developments provide a comprehensive molecular picture at unprecedented spatial and temporal resolution of the nonlinear, linear, and fluctuating dynamic phenomena that single nanocrystals undergo during the GLC-EM experiment. We determined atomic structures of 66 temporal structural states, extracted from 15 time trajectories of individual nanocrystals. Large (478 to 698 atoms) and small (<300 atoms) nanocrystals show etching that preserves a stable core, whereas mid-sized (351 to 571 atoms) nanocrystals present dynamics that change the coordination of the core.

Meana-Pañeda, Rubén↗
DOE OSTI2024

Atomic resolution coherent x-ray imaging with physics-based phase retrieval

Coherent x-ray imaging and scattering from accelerator based sources such as synchrotrons continue to impact biology, medicine, technology, and materials science. Many synchrotrons around the world are currently undergoing major upgrades to increase their available coherent x-ray flux by approximately two orders of magnitude. The improvement of synchrotrons may enable imaging of materials in operando at the atomic scale which may revolutionize battery and catalysis technologies. Current algorithms used for phase retrieval in coherent x-ray imaging are based on the projection onto sets method. These traditional iterative phase retrieval methods will become more computationally expensive as they push towards atomic resolution and may struggle to converge. Additionally, these methods do not incorporate physical information that may additionally constrain the solution. In this work, we present an algorithm which incorporates molecular dynamics into Bragg coherent diffraction imaging (BCDI). This algorithm, which we call PRAMMol (Phase Retrieval with Atomic Modeling and Molecular Dynamics) combines statistical techniques with molecular dynamics to solve the phase retrieval problem. We present several examples where our algorithm is applied to simulated coherent diffraction from 3D crystals and show convergence to the correct solution at the atomic scale.

47 OTHER INSTRUMENTATION↗
DOE OSTI2025

Solving disorder in (3D) real space: a comparative study of the three-dimensional difference pair distribution function and atomic resolution holography reconstructions

The quantitative analysis of local ordering principles in disordered crystalline systems has gained much attention over the past few years, as it is often considered crucial for optimizing material functionality. This development has been driven by significant advancements in computational and experimental methods, which have led to the establishment and widespread use of various analytical techniques. In this study, we perform model calculations to compare the effectiveness of atomic resolution holography and three-dimensional difference pair distribution function analysis (3D-ΔPDF). Using Cu 3 Au as a model system, we demonstrate an approach to derive local order parameters quantitatively and show that both techniques are well suited to quantifying chemical short-range order correlations and local bond-distance variations. By evaluating the strengths and limitations of both techniques, we advocate for their combined use to solve complex short-range order problems accurately.

3D-ΔPDF↗
DOE OSTI2025

Atomic-resolution structural and spectroscopic evidence for the synthetic realization of two-dimensional copper boride

Since the first realization of borophene on Ag(111), two-dimensional (2D) boron nanomaterials have attracted substantial interest because of their polymorphic diversity and potential for hosting solid-state quantum phenomena. Here, we use atomic-resolution scanning tunneling microscopy (STM) and field-emission resonance (FER) spectroscopy to elucidate the structure and properties of atomically thin boron phases grown on Cu(111). Specifically, FER spectroscopy reveals charge transfer and electronic states that strongly differ from the decoupled borophene phases observed on silver, suggesting that the deposition of boron on copper results in strong covalent bonding characteristic of a 2D copper boride. This conclusion is reinforced by detailed STM characterization of line defects that are consistent with density functional theory calculations for atomically thin Cu8B14. This evidence for 2D copper boride is likely to motivate future synthetic efforts aimed at expanding the relatively unexplored family of atomically thin metal boride materials.

Science & Technology - Other Topics↗
DOE OSTI2025

Atomic-resolution imaging as a mechanistic tool for studying single-site heterogeneous catalysis

Heterogeneous catalysts dominate the chemical industry but typically feature diverse, incompletely defined active sites. Thus, describing structure-activity relationships, unlike homogeneous catalysts, remains challenging. In contrast, molecularly defined single-site heterogeneous catalysts (SSHCs), using appropriate tools, are poised to address these challenges and provide new avenues for catalysis research and development. The present study explores eco-friendly H 2 production mediated by discrete MoO 2 sites supported on carbon nanohorns (CNHs) and active for alcohol dehydrogenation. While informative, detailed ensemble EXAFS/XANES/XPS, kinetic measurements, and DFT analysis alone cannot provide a full molecular picture of the reaction pathway. Here, using single-molecule atomic-resolution time-resolved electron microscopy (SMART-EM), we propose the identification of four key catalytic intermediates anchored to CNHs and uncover a new reaction pathway involving alkoxide/hemiacetal equilibration and acetal oligomerization. Furthermore, these intermediates are inferred through a combination of theory and SMART-EM, showcasing the potential of SMART-EM as a complementary tool for exploring mechanistic hypotheses in catalysis.

36 MATERIALS SCIENCE↗
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 OSTI2025

De novo synthesis and near atomic resolution imaging of host immune receptors critical for pathogen recognition (Abbreviated Final Report)

The innate immune system serves as the body’s first line of defense against invading pathogens, responding rapidly through the deployment of immune cells at common sites of infection, such as the skin and airways. These immune-cell sentinels express a range of highly conserved receptors, including Toll-like receptors (TLRs), which recognize and bind to pathogen-derived components. This recognition event triggers intracellular signaling cascades that initiate and coordinate immune responses. Despite their significance, the complete structural characterization of full-length TLRs, including their extracellular domain (ECD), transmembrane domain (TMD), and Toll/interleukin-1 receptor (TIR) domain, remains incomplete. In this study, we examined the expression and isolation of human TLR4 incorporated into nanodiscs using two approaches: a cell-free synthesis system and a cell-based transfection strategy employing Expi293F cells derived from the human embryonic kidney lineage. Our findings demonstrate that NLP-bound human TLR4 produced via the cell-based method yielded functional protein suitable for time-resolved single-particle cryo-electron microscopy (cryo-EM). This advancement enables structural characterization of full-length TLR4, maintaining the integrity of its extracellular domain, transmembrane domain, and Toll/Interleukin-1 receptor (TIR) domain.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Multi-slice electron ptychographic tomography for three-dimensional phase-contrast microscopy beyond the depth of focus limits

Electron ptychography is a powerful computational method for atomic-resolution imaging with high contrast for weakly and strongly scattering elements. Modern algorithms coupled with fast and efficient detectors allow imaging specimens with tens of nanometers thicknesses with sub-0.5 Ångstrom lateral resolution. However, the axial resolution in these approaches is currently limited to a few nanometers, limiting their ability to solve novel atomic structures ab initio. Here, we experimentally demonstrate multi-slice ptychographic electron tomography, which allows atomic resolution three-dimensional phase-contrast imaging in a volume surpassing the depth of field limits. We reconstruct tilt-series 4D-STEM measurements of a $\mathrm{Co_3O_4}$ nanocube, yielding 2 Å axial and 0.7 Å transverse resolution in a reconstructed volume of $\mathrm{(18.2\,nm)^3}$. Our results demonstrate a 13.5-fold improvement in axial resolution compared to multi-slice ptychography while retaining the atomic lateral resolution and the capability to image volumes beyond the depth of field limit. Multi-slice ptychographic electron tomography significantly expands the volume of materials accessible using high-resolution electron microscopy. We discuss further experimental and algorithmic improvements necessary to also resolve single weakly scattering atoms in 3D.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Hydrogen density mapping in biomolecular crystals through dynamic nuclear polarization

Many fundamental biological processes, including those in photosynthetic reaction centers and enzyme active sites, involve charge and energy transfer, bond cleavage, protonation and hydrogen bonding. Because H atoms play such central roles in these reactions, accurately determining their positions is essential. Yet, conventional X-ray crystallography primarily resolves the heavy atoms in biological structures and provides limited insight into hydrogen, even at atomic resolution. Neutron macromolecular crystallography (NMC) overcomes this limitation by offering exceptional sensitivity to hydrogen and deuterium. Here, we present a theoretical framework for the development of dynamic nuclear polarization NMC (DNP-NMC) techniques, which exploit the alignment of neutron and proton nuclear spins to enhance and tune the hydrogen signal contribution. The DNP-NMC approach advances the resolution of H atoms within biomolecular crystals, whether bound to protein residues or present in solvent. The method establishes key relationships for the coherent structure factor of polarized neutron scattering from hydrogenous matter. It theoretically achieves full accuracy in phase reconstruction and offers a path to improve neutron structure determination, achieving accuracies exceeding ≳80% by incorporating titration states. Using a variant of the hybrid input/output phase-retrieval algorithm, it allows recovery of the hydrogen density with ≳90% phase accuracy. In conclusion, we further discuss sources of experimental uncertainty for the upcoming DNP-enabled, quasi-Laue IMAGINE-X experiment at Oak Ridge National Laboratory's High Flux Isotope Reactor.

dynamic nuclear polarization↗
DOE OSTI2024

CryoTRANS: predicting high-resolution maps of rare conformations from self-supervised trajectories in cryo-EM

Cryogenic electron microscopy (cryo-EM) has revolutionized structural biology, enabling efficient determination of structures at near-atomic resolutions. However, a common challenge arises from the severe imbalance among various conformations of vitrified particles, leading to low-resolution reconstructions in rare conformations due to a lack of particle images in these quasi-stable states. We introduce CryoTRANS, a method that predicts high-resolution maps of rare conformations by constructing a self-supervised pseudo-trajectory between density maps of varying resolutions. This trajectory is represented by an ordinary differential equation parameterized by a deep neural network, ensuring retention of detailed structures from high-resolution density maps. By leveraging a single high-resolution density map, CryoTRANS significantly improves the reconstruction of rare conformations and has been validated on four real-world datasets: alpha-2-macroglobulin, actin-binding protein complexes, SARS-CoV-2 spike glycoprotein, and the 70S ribosome. CryoTRANS can also predict high-resolution structures in cryogenic electron tomography maps using a high-resolution cryo-EM map.Cryogenic electron microscopy (cryo-EM) has revolutionized structural biology, enabling efficient determination of structures at near-atomic resolutions. However, a common challenge arises from the severe imbalance among various conformations of vitrified particles, leading to low-resolution reconstructions in rare conformations due to a lack of particle images in these quasi-stable states. We introduce CryoTRANS, a method that predicts high-resolution maps of rare conformations by constructing a self-supervised pseudo-trajectory between density maps of varying resolutions. This trajectory is represented by an ordinary differential equation parameterized by a deep neural network, ensuring retention of detailed structures from high-resolution density maps. By leveraging a single high-resolution density map, CryoTRANS significantly improves the reconstruction of rare conformations and has been validated on four real-world datasets: alpha-2-macroglobulin, actin-binding protein complexes, SARS-CoV-2 spike glycoprotein, and the 70S ribosome. CryoTRANS can also predict high-resolution structures in cryogenic electron tomography maps using a high-resolution cryo-EM map.

47 OTHER INSTRUMENTATION↗
DOE OSTI2025

Identification of the glassy state in nanoparticles by transmission electron microscopy

Identification of amorphous phases in nanoparticles by atomic-resolution transmission electron microscopy (TEM) requires analyses such as tilt-angle-dependent TEM imaging and single-nanoparticle electron diffraction, rather than relying on a single TEM image. Here, the disordered structures of amorphous nanoparticles offer unique atomic configurations and properties that differ from the properties of their crystalline counterparts. These characteristics have motivated the exploration of such materials for mechanical, sensing and catalytic applications. In addition, the formation of amorphous metal nanoparticles is an important endeavour to understand the process of vitrification and the nature of the glassy state. Atomic-resolution transmission electron microscopy (TEM) is increasingly being used as a tool for characterizing structures of nanoparticles produced by vitrification. In this Comment, we discuss the pitfalls of using TEM for ascertaining whether nanoparticles are amorphous. We also make recommendations of best practices.

Alcorn, Francis M. [Sandia National Laboratories (↗
DOE OSTI2024

Cryogen-free modular scanning tunneling microscope operating at 4-K in high magnetic field on a compact ultra-high vacuum platform

One of the daunting challenges in modern low temperature scanning tunneling microscopy (STM) is the difficulty of combining atomic resolution with cryogen-free cooling. Further functionality needs, such as ultra-high vacuum (UHV), high magnetic field (HF), and compatibility with μm-sized samples, pose additional challenges to an already ambitious build. We present the design, construction, and performance of a cryogen-free, UHV, low temperature, and high magnetic field system for modular STM operation. An internal vibration isolator reduces vibrations in this system, allowing for atomic resolution STM imaging while maintaining a low base temperature of ∼4 K and magnetic fields up to 9 T. Samples and tips can be conditioned in situ utilizing a heating stage, an ion sputtering gun, an e-beam evaporator, a tip treater, and sample exfoliation. In situ sample and tip exchange and alignment are performed in a connected UHV room temperature stage with optical access. Multisite operation without breaking vacuum is enabled by a unique quick-connect STM head design. A novel low-profile vertical transfer mechanism permits transferring the STM between room temperature and the low temperature cryostat.

Instruments & Instrumentation↗
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↗