Atomic structure datasets for training machine learning interatomic potentials
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Kim, Kwangnam [Lawrence Livermore National Laborat↗
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Doping Metallic Grain Boundaries to Control Atomic Structure and Damage Tolerance
Grain boundaries often act as sites for crack and void nucleation during plastic deformation of metallic materials. While it is known that grain boundary character and structure can greatly influence this damage nucleation process, the current level of control over such details is limited. The objective of this project was to obtain a fundamental understanding of how metallic grain boundary structure can be controlled through intelligent doping, with the idea of inducing planned amorphous grain boundary phases or complexions. The effect of amorphous complexion structure on dislocation accommodation mechanisms was studied, to improve the field’s understanding of damage nucleation at a promising type of interface. Different microstructural descriptors were studied, as grain boundaries can have large variations and complexity of local structure, and influence the mechanical damage resistance of these features was tested. Nanocrystalline systems that contain amorphous grain boundary complexions were prioritized, as these have more extreme variations in interfacial structure and damage tolerance, with an emphasis on isolating the importance of complexion population (type, thickness, etc.), network topology, local structure, and local chemistry. This research used a combination of computational, experimental, and characterization techniques to isolate and understand the importance of nanoscale grain boundary structure and interfacial chemistry. Amorphous grain boundary complexions were found to clearly increase a material’s resistance to mechanical damage, with the local distribution of structural short-range order within the complexions found to be an important descriptor for damage and the proposed focus of future work in this area.
36 MATERIALS SCIENCE↗
Machine-learned relationship between fracture nucleation and local atomic structure in silica glass
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Hardin, Thomas James [Sandia National Laboratories↗
De novo atomic protein structure modeling for cryoEM density maps using 3D transformer and HMM
Accurately building 3D atomic structures from cryo-EM density maps is a crucial step in cryo-EM-based protein structure determination. Converting density maps into 3D atomic structures for proteins lacking accurate homologous or predicted structures as templates remains a significant challenge. Here, we introduce Cryo2Struct, a fully automated de novo cryo-EM structure modeling method. Cryo2Struct utilizes a 3D transformer to identify atoms and amino acid types in cryo-EM density maps, followed by an innovative Hidden Markov Model (HMM) to connect predicted atoms and build protein backbone structures. Cryo2Struct produces substantially more accurate and complete protein structural models than the widely used ab initio method Phenix. Additionally, its performance in building atomic structural models is robust against changes in the resolution of density maps and the size of protein structures.
59 BASIC BIOLOGICAL SCIENCES↗
Generalized representative structures for atomistic systems
A new method is presented to generate atomic structures that reproduce the essential characteristics of arbitrary material systems, phases, or ensembles. Previous methods allow one to reproduce the essential characteristics (e.g. the chemical disorder) of a large random alloy within a small crystal structure. The ability to generate small representations of random alloys, along with the restriction to crystal systems, results from using the fixed-lattice cluster correlations to describe structural characteristics. A more general description of the structural characteristics of atomic systems is obtained using complete sets of atomic environment descriptors. These are used within for generating representative atomic structures without restriction to fixed lattices. A general data-driven approach is provided here utilizing the atomic cluster expansion (ACE) basis. The N-body ACE descriptors are a complete set of atomic environment descriptors that span both chemical and spatial degrees of freedom and are used within for describing atomic structures. The generalized representative structure (GRS) method presented within generates small atomic structures that reproduce ACE descriptor distributions corresponding to arbitrary structural and chemical complexity. It is shown that systematically improvable representations of crystalline systems on fixed parent lattices, amorphous materials, liquids, and ensembles of atomic structures may be produced efficiently through optimization algorithms. With the GRS method, we highlight reduced representations of atomistic machine-learning training datasets that contain similar amounts of information and small 40–72 atom representations of liquid phases. The ability to use GRS methodology as a driver for informed novel structure generation is also demonstrated. The advantages over other data-driven methods and state-of-the-art methods restricted to high-symmetry systems are highlighted.
atomic cluster expansion↗
Polarization-Controlled Structural Modulation in the Single Atomic Layer at the PbZr 0.2 Ti 0.8 O 3 /LaNiO 3 Interface
Conductivity modulation via ferroelectric polarization coupling with LaNiO 3 (LNO) is demonstrated at an epitaxial ferroelectric–LNO interface. Conductivity measurements, varying the thickness of the LNO channel, show that this phenomenon is confined to a few atomic layers at the interface. Combining in situ biasing and off-axis holography, we mapped out electrostatic potentials at the PbZr 0.2 Ti 0.8 O 3 (PZT)/LNO/SrTiO 3 (STO) heterostructure upon polarization switching. Using aberration-corrected STEM, the interfacial atomic structures were investigated for the two different PZT polarization states. Polarization in PZT induces a significant change in the in-plane O–Ni–O bond angles, with a 37° modulation in the topmost 1 or 2 LNO unit cells, driven by strain in the oxygen sublattice for the two opposite polarization directions in PZT. Both oxygen and cation sublattices exhibit strain responses exceeding 10% upon switching. This atomic-layer structural modulation highlights a mechanism for functional oxide heterostructure development, offering pathways for advancements in nonvolatile memory, sensors, and energy-efficient transistors.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
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↗
Spectroscopy-guided discovery of three-dimensional structures of disordered materials with diffusion models
Spectroscopy techniques such as x-ray absorption near edge structure (XANES) provide valuable insights into the atomic structures of materials, yet the inverse prediction of precise structures from spectroscopic data remains a formidable challenge. In this study, we introduce a framework that combines generative artificial intelligence models with XANES spectroscopy to predict three-dimensional atomic structures of disordered systems, using amorphous carbon (a-C) as a model system. In this work, we introduce a new framework based on the diffusion model, a recent generative machine learning method, to predict 3D structures of disordered materials from a target property. For demonstration, we apply the model to identify the atomic structures of a-C as a representative material system from the target XANES spectra. We show that conditional generation guided by XANES spectra reproduces key features of the target structures. Furthermore, we show that our model can steer the generative process to tailor atomic arrangements for a specific XANES spectrum. Finally, our generative model exhibits a remarkable scale-agnostic property, thereby enabling generation of realistic, large-scale structures through learning from a small-scale dataset (i.e. with small unit cells). Our work represents a significant stride in bridging the gap between materials characterization and atomic structure determination; in addition, it can be leveraged for materials discovery in exploring various material properties as targeted.
36 MATERIALS SCIENCE↗
The atomic-level structure and stability of interfaces of Pt nanoparticles in alumina: An experimental and computational evaluation
The atomic-level structure of interfaces between Pt and a transition form of Al2O3 were studied using a combination of electron microscopy and first principles calculations. A model system of Pt nanoprecipitates in Al2O3 were formed in sapphire wafers via high-energy ion implantation of Pt followed by thermal annealing at 1000 °C in air. The Pt nanoparticles took the form of tetrahedra and truncated tetrahedra primarily bound by {111}Pt facets. The high prevalence of these facets motivated the development of density functional theory (DFT) based models of (111)Pt interfaces with six different chemical terminations of ( 2 ¯ 01 ) θ-alumina. The atomic-level structure of the Pt/Al2O3 interfaces was characterized with aberration-corrected scanning transmission electron microscopy (STEM) and the experimental images were compared to STEM image simulations of the DFT models. The model interface with Pt bonded to oxygen-terminated θ-Al2O3, with the Pt located on top of the O and with an underlying layer of octahedral Al, provided the best match to the experimental images. This interfacial termination is also the most stable for the thermal annealing conditions used based on thermodynamic calculations of the interfacial energy as a function of temperature and oxygen partial pressure. This experimentally verified model provides a basis for improving models of Pt/γ-alumina interfaces.
Clauser, A L↗
Electron-impact excitation data for W 2+ in support of tungsten spectroscopy and re-deposition measurements for magnetically-confined plasmas
Abstract To better understand plasma wall interactions involving tungsten, accurate atomic structure and electron-impact driven collisional processes for near-neutral ion stages of tungsten are required. Complementing existing work on neutral and singly ionised tungsten, atomic structure and collisional calculations for W 2+ electron-impact excitation have been completed. These excitation calculations are an important component of S/XB coefficients for near-neutral charge states, which may be used to spectroscopically infer re-deposition of tungsten at the plasma-solid boundary of fusion relevant devices. With W 2+ in particular having emission lines that can be observed at ultraviolet (UV) wavelengths, while higher charge states of tungsten are unlikely to have lines possible to observe outside of the vacuum UV range. The atomic structure was generated using the General-purpose Relativistic Atomic Structure Package (GRASP 0 ), implementing the Multi-configuration Dirac Fock approach. This structure was the basis for a subsequent Dirac R -matrix electron-impact excitation calculation to provide Maxwellian averaged rate coefficients. A synthetic spectrum was generated from this data using a collisional-radiative model to predict the strongest W III spectral lines and these lines were compared to emission from the Compact Toroidal Hybrid (CTH) plasma device. Several of the strongest W III lines are observed in CTH and agree well with the modelled line wavelengths and intensities, a table of these lines is provided that could be observed in other devices.
McCann, M. (ORCID:0000000215321240)↗
Elucidation of a Metastable p(2 × 1) O Atom Adlayer Structure on Cu(111)
Cu-based catalysts are ubiquitous in many industrial reactions, including methanol synthesis. Under partially oxidizing conditions, Cu catalysts can have dynamic surface structures that greatly influence their reactivities. Therefore, elucidating the surface structures that are present on Cu, and looking for metastable structures, aids in the long term goal of understanding and controlling their catalytic behavior. Thin-film copper oxides such as the “29” and “44” structures have been described at length in the literature, but precursors to these thin-film oxides can be challenging to study because they exist only under certain conditions. Using a combination of experimental and computational surface science techniques, we discovered, modeled, and quantified a previously unreported O atom adlayer structure on Cu(111) with a p(2 × 1) unit cell. Here, we used scanning tunneling microscopy to visualize the striped 2 × 1 structure and density functional theory (DFT) structure optimizations to identify the thermodynamically most favorable positions of Cu and O atoms in a p(2 × 1) unit cell. Using X-ray photoelectron spectroscopy and temperature-programmed desorption, we determined the stoichiometry of the structure to be 2:1 for surface Cu atoms to O adatoms, the same stoichiometry as that modeled by DFT. This work reports a new metastable structure formed on Cu(111) at the very initial stages of oxidation and is therefore worth considering in models of catalytically relevant redox processes at Cu surfaces.
36 MATERIALS SCIENCE↗
Insights into Native Single-Atom Electrocatalyst Site Structures
Single-atom electrocatalysts consisting of metal atoms embedded in a carbon matrix are promising next-generation catalysts for green hydrogen production and utilization, CO2 reduction, low-temperature CO oxidation, ammonia production, plastic decomposition, and electrochemical energy storage. The origins of activity and stability for the single-atom sites are still debatable, however, because of constrained insights into their local structure resulting from idealized models and experiments derived from a large number of individual sites. Insights into structural variations around single atomic sites are therefore critical for the continued development of these next-generation catalysts. While electron microscopy commonly provides atomic-scale information about these materials, the beam sensitivity of individual sites makes structural determination by conventional low-voltage (60 keV) techniques challenging. Here, we introduce ultralow-voltage electron ptychography, performed at 30 keV, that enables determination of the lattice structure around individual metal sites in a well-defined single-atom electrocatalyst system while essentially eliminating knock-on structural modifications. Pairing these atomic-scale, site-specific measurements with computational methods will broaden our understanding of the activity and stability of these materials, which will accelerate the development of the next generation of catalysts.
Zachman, Michael [ORNL] (ORCID:0000000319101357)↗
Time-resolved Brownian tomography of single nanocrystals in liquid during oxidative etching
Colloidal nanocrystals inherently undergo structural changes during chemical reactions. The robust structure-property relationships, originating from their nanoscale dimensions, underscore the significance of comprehending the dynamic structural behavior of nanocrystals in reactive chemical media. Moreover, the complexity and heterogeneity inherent in their atomic structures require tracking of structural transitions in individual nanocrystals at three-dimensional (3D) atomic resolution. In this study, we introduce the method of time-resolved Brownian tomography to investigate the temporal evolution of the 3D atomic structures of individual nanocrystals in solution. The methodology is applied to examine the atomic-level structural transformations of Pt nanocrystals during oxidative etching. The time-resolved 3D atomic maps reveal the structural evolution of dissolving Pt nanocrystals, transitioning from a crystalline to a disordered structure. Our study demonstrates the emergence of a phase at the nanometer length scale that has received less attention in bulk thermodynamics.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Atomic-scale identification of active sites of oxygen reduction nanocatalysts
Heterogeneous nanocatalysts play a crucial role in both the chemical and energy industries. Despite substantial advancements in theoretical, computational and experimental studies, identifying their active sites remains a major challenge. Here we utilize atomic electron tomography to determine the three-dimensional atomic structure of PtNi and Mo-doped PtNi nanocatalysts for the electrochemical oxygen reduction reaction. We then employ the experimental atomic structures as input to first-principles-trained machine learning to identify the active sites of the nanocatalysts. Through the analysis of the structure–activity relationships, we formulate an equation termed the local environment descriptor, which balances the strain and ligand effects to provide physical and chemical insights into active sites in the oxygen reduction reaction. The ability to determine the three-dimensional atomic structure and chemical composition of realistic nanoparticles, combined with machine learning, could transform our fundamental understanding of the active sites of catalysts and guide the rational design of optimal nanocatalysts.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Electron Microscopy Approaches to Unraveling the Structure of Amorphous Materials
Determining atomic structures in crystalline materials—where atoms are arranged in rigid, periodic lattices—has been highly successful using probes such as electrons, X-rays, and neutrons. In contrast, amorphous materials, despite their ubiquity and technological importance, remain far more challenging to characterize with comparable accuracy and precision. This review highlights existing, emerging, and potential (scanning) transmission electron microscopy ((S)TEM) techniques for probing short- and medium-range order in amorphous materials. Approaches ranging from high-resolution (S)TEM imaging and selected electron diffraction pattern to four-dimensional STEM (4D-STEM) based pair distribution function, fluctuation electron microscopy, tomography, ptychography, and spectroscopic methods are discussed, emphasizing their ability to provide complementary insights across multiple length scales—from sub-angstrom local environments to nanometer-scale correlations. Here, we further explore the promise of multimodal and correlative strategies, as well as the growing role of machine learning and physics-informed AI in enabling real-time, quantitative interpretation of complex structural signatures. Together, these advances point toward a future where electron microscopy not only reveals the hidden order in amorphous systems but also establishes robust structure–property relationships, paving the way for materials innovation in disordered matter.
77 NANOSCIENCE AND NANOTECHNOLOGY↗
Atomic-scale structure of ZrO 2 : Formation of metastable polymorphs
Metastable phases can exist within local minima in the potential energy landscape when they are kinetically “trapped” by various processing routes, such as thermal treatment, grain size reduction, chemical doping, interfacial stress, or irradiation. Despite the importance of metastable materials for many technological applications, little is known about the underlying structural mechanisms of the stabilization process and atomic-scale nature of the resulting defective metastable phase. Investigating ion-irradiated and nanocrystalline zirconia with neutron total scattering experiments, we show that metastable tetragonal ZrO 2 consists of an underlying structure of ferroelastic, orthorhombic nanoscale domains stabilized by a network of domain walls. The apparent long-range tetragonal structure that can be recovered to ambient conditions is only the configurational ensemble average of the underlying orthorhombic domains. This structural heterogeneity with a distinct short-range order is more broadly applicable to other nonequilibrium materials and provides insight into the synthesis and recovery of functional metastable phases with unique physical and chemical properties.
74 ATOMIC AND MOLECULAR PHYSICS↗
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↗
Atomic-Scale Behavior of Radiation-Resistant ZnO under High-Energy Electron Bombardment
Understanding the atomic structure and defect characteristics of ZnO thin films is crucial for optimizing their electronic properties and performance in advanced applications. Here, we investigate the atomic structure and defect characteristics of atomic layer deposition (ALD)-grown ZnO thin films by using aberration-corrected scanning transmission electron microscopy (STEM). Atomic-resolution imaging identifies prevalent stacking faults, dipole disorder, and various grain boundary types, which are believed to influence the electronic properties of ZnO. Additionally, real-time electron beam exposure experiments demonstrate structural transformations, including crystal growth and surface rearrangements. These findings provide insights into the growth mechanisms of ALD ZnO under high-energy electron irradiation conditions, an important finding for the use of polycrystalline ZnO wide bandgap semiconductors in space-like conditions. In conclusion, our results underscore the capability of STEM in directly visualizing and quantifying atomic-scale defects and beam-induced transformations in radiation-resistant ZnO.
Defects↗