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At least 451 records · Page 25

All sources NASA NTRS DOE OSTI

DOE OSTI2022

Atomic Scale Crystal Field Mapping of Polar Vortices in Oxide Superlattices

Polar vortices in oxide superlattices can be utilized as potential candidates for data storage applications due to their unique polarization topologies. The structure and dipole arrangement in polar vortices has been studied via X-ray scattering techniques, (scanning) transmission electron microscopy ((S)/TEM) and computational calculations. However, the fundamental correlation between the atomic structure and the electronic structure (which is manifested in the chemical bonding) has heretofore not been explored. Further, The hybridization between nominally empty $\textit{d}$ orbitals on the B-site with the occupied O 2$\textit{p}$ orbitals favors the condensation of a polar (ferroelectric) state in $\textit{AB}$O 3 perovskite oxides. The complex, continuously rotating local polarization texture of the vortices, in turn, can result in especially intricate $\textit{d}$- orbital interactions. Soft X-ray spectroscopy can probe these interactions at the transition metal $\textit{L}$-edge, but these techniques do not have the spatial resolution to resolve variations within one vortex (~5 nm region). Electron energy loss spectroscopy (EELS) in the STEM mode uses inelastically scattered electrons to probe the core-shell excitations (empty density of states) of transition metals at atomic resolution.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2023

Automated phase segmentation and quantification of high-resolution TEM image for alloy design

In the alloy design and development process, a wealth of atomically resolved structural high-resolution transmission electron microscopy (HRTEM) images are produced. Identifying the different nano-precipitate phases and tracking their evolution under various compositions and during manufacturing or post-processing requires hundreds of HRTEM images and thousands of precipitates. The nanoscopic phase information labeling and analysis purely relies on humans are prohibitively costly and time-consuming, sometimes not reliable because of the lack of authoritative knowledge. Here, in this work, we develop a novel unsupervised machine learning approach coupled with adaptive computer vision techniques with features in the Fourier space to automatically determine the number of phases and segment/quantify the phases with nanoscale resolution, allowing for quantitative correlation between nanostructure formation, processing and functional properties. To automate the phase extraction/quantification and ascertain its applicability, we have applied the developed framework to the HRTEM images from several alloy systems, processing conditions, image magnifications, and phase types and morphologies (precipitates, nano-twins, stacking faults, crystalline matrix, and amorphous structures) for verification. This study paves the road for compression, visualization, and translation of raw image structural data into physically relevant information in real-time with minimal human supervision. It shows the promise of enabling high-throughput materials characterization for the acceleration of alloy manufacturing and design.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Integrating Ultra-Coarse-Grained Protein Models into Accessible Workflows for Multiscale Molecular Dynamics

To capture protein conformational transitions using molecular dynamics (MD), several simulation resolutions covering different spatial and temporal scales are typically needed. All-atom (AA) simulations provide fine resolution, but are computationally infeasible for large systems over longer durations. Coarse-grained (CG) and ultra-coarse-grained (UCG) models have a lower resolution and computational cost while still being able to conserve essential protein features. Prior work on a Multiscale Machinelearned Modeling Infrastructure (MuMMI) combined both AA and CG simulations to study RAS-RAF protein interactions, leveraging CG models for longer time scales and using AA to investigate unusual conformations in greater detail. However, MuMMI is still resource-intensive, and this study aims to maximize exploration of the protein conformational space while reducing computational cost. In this paper, we build on prior work that integrates UCG models based on heterogeneous elastic network modeling (hENM) into the MuMMI workflow. We demonstrate that UCG models enable accurate sampling of protein conformations, focusing on simulating RAS-RAF protein interactions. Using higher-resolution CG Martini simulation data, we can automatically refine intramolecular interactions in UCG models. We present a scalable Python package that uses fluctuations observed in higher-resolution CG Martini simulations to estimate bond coefficients of the UCG model. We built novel machine learning-based backmapping methods to recover more detailed CG Martini structures from UCG structures, using diffusion models to learn the mapping between scales. Finally, we present UCG-mini-MuMMI, an accessible and less compute-intensive version of MuMMI as a resource for the scientific community. Incorporating UCG models into MD studies is applicable to a broad range of systems and proteins, and our study offers insights into the advantages and limitations of these methods.

Chemical structure↗

DOE OSTI2023

Overall protein structure quality assessment using hydrogen-bonding parameters

Atomic model refinement at low resolution is often a challenging task. This is mostly because the experimental data are not sufficiently detailed to be described by atomic models. To make refinement practical and ensure that a refined atomic model is geometrically meaningful, additional information needs to be used such as restraints on Ramachandran plot distributions or residue side-chain rotameric states. However, using Ramachandran plots or rotameric states as refinement targets diminishes the validating power of these tools. Therefore, finding additional model-validation criteria that are not used or are difficult to use as refinement goals is desirable. Hydrogen bonds are one of the important noncovalent interactions that shape and maintain protein structure. These interactions can be characterized by a specific geometry of hydrogen donor and acceptor atoms. Systematic analysis of these geometries performed for quality-filtered high-resolution models of proteins from the Protein Data Bank shows that they have a distinct and a conserved distribution. Here, it is demonstrated how this information can be used for atomic model validation.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Refined views of ancient ocean chemistry: Tracking trace element incorporation in pyrite framboids using atom probe tomography

The trace element chemistry of pyrite can be used to determine the origin, timing, and conditions of formation of ore deposits; as a vectoring tool for mineral exploration; and to determine the evolution of the Earth’s oceanic and atmospheric chemistry. However, little is known about whether trace elements are held with the pyrite structure or within nano-inclusions of other phases. This distinction is important for two primary reasons. First, trace element incorporation into the pyrite structure can affect the partitioning of other trace elements. Second, if trace elements are held within nano-inclusions, the partition coefficient of the mineral phases that make up the nano-inclusion, rather than pyrite, are the critical consideration in related interpretations. Previous studies addressing this topic have used laser ablation inductively coupled plasma mass spectrometry; however, the resulting data do not provide sufficient spatial resolution to delineate trace element distributions unless the inclusions are large. Further, they use these flat element profiles in time resolved laser ablation output graphs to argue that pyrite trace element content provides a direct relationship between trace element content of seawater and pyrite trace element content. To improve resolution, we have used atom probe tomography to characterize trace element distributions in pyrite framboids from the Cariaco Basin and Demerara Rise in three-dimensions at sub-nanometer resolution. Manganese was found to be concentrated in the pyrite nanocrystal part of the original framboid structure. In contrast, Ni was mostly found along the grain boundary, though it still appeared to be contained within the pyrite structure. Copper was concentrated in later pyrite overgrowths, and As varied in its location. These observations suggest that some important trace elements are incorporated into pyrite during early diagenesis, even in euxinic settings dominated by water-column pyrite formation. Statistical analysis was used to determine whether trace elements were incorporated in the lattice or within nanoscale inclusions (referred to here are nano-inclusions). We found that As, Ni, Cu, and Mn were commonly held within the pyrite structure, but As, Ni, and Cu can also be held as nano-inclusions or within grain interfaces. Incorporation of As is known to enhance the incorporation of other trace elements and in this case appears to correlated to elevated Ni and Cu concentrations in the Cariaco Basin samples. Furthermore, understanding these relationships strongly impacts our ability to utilize pyrite trace metal concentrations to analyze and quantify early ocean chemistry and its evolution through time.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

Quantitative Electron Beam‐Single Atom Interactions Enabled by Sub‐20‐pm Precision Targeting

The ability to probe and control matter at the picometer scale is essential for advancing quantum and energy technologies. Scanning transmission electron microscopy offers powerful capabilities for materials analysis and modification, but sample damage, drift, and scan distortions hinder single atom analysis and deterministic manipulation. Materials analysis and modification via electron–solid interactions can be transformed by precise delivery of electrons to a specified atomic location, maintaining the beam position despite drift, and minimizing collateral dose. Here a fast, low-dose, sub-20-pm precision electron beam positioning technique is developed, “atomic lock-on,” (ALO), which offers the ability to position the beam on a specific atomic column without previously irradiating that column. This technique is used to lock onto a single selected atomic location to repeatedly measure its weak electron energy loss signal despite sample drift. Moreover, electron beam-matter interactions in single atomic events are measured with μ s time resolution. This enables observation of single-atom dynamics, such as atomic bistability, revealing partially bonded atomic configurations and recapture phenomena. This opens prospects for using electron microscopy for high-precision measurements and deterministic control of matter for quantum technologies.

2D materials↗

DOE OSTI2023

Real-space inversion and super-resolution of ultrafast scattering

Ultrafast scattering using x-rays or electrons is an emerging method to obtain structure dynamics at the atomic lengthscales and timescales. However, directly resolving in real-space atomic motions is inherently limited by the finite detector range and the probe energy. So, as a result, the time-resolved signal interpretation is mostly done in reciprocal space and relies on modeling and simulations of specific structures and processes. Here, we introduce a model-free approach to directly resolve scattering signals in real space, surpassing the diffraction limit, using scattering kernels and signal priors that naturally arise from the measurement constraints. We demonstrate the approach on simulated and experimental data, recover multiple atomic motions at sub-angstrom resolutions, and discuss the recovery accuracy and resolution limits versus signal fidelity. The approach offers a robust path to obtain high-resolution real-space information of atomic-scale structure dynamics using current time-resolved x-ray or electron scattering sources.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2023

Accelerating Quantum Materials Development with Advances in Transmission Electron Microscopy

Quantum materials are driving a technology revolution in sensing, communication, and computing, while simultaneously testing many core theories of the past century. Materials such as topological insulators, complex oxides, superconductors, quantum dots, color center-hosting semiconductors, and other types of strongly correlated materials can exhibit exotic properties such as edge conductivity, multiferroicity, magnetoresistance, superconductivity, single photon emission, and optical-spin locking. These emergent properties arise and depend strongly on the material’s detailed atomic-scale structure, including atomic defects, dopants, and lattice stacking. In this review, we describe how progress in the field of electron microscopy (EM), including in situ and in operando EM, can accelerate advances in quantum materials and quantum excitations. We begin by describing fundamental EM principles and operation modes. We then discuss various EM methods such as (i) EM spectroscopies, including electron energy loss spectroscopy (EELS), cathodoluminescence (CL), and electron energy gain spectroscopy (EEGS); (ii) four-dimensional scanning transmission electron microscopy (4D-STEM); (iii) dynamic and ultrafast EM (UEM); (iv) complementary ultrafast spectroscopies (UED, XFEL); and (v) atomic electron tomography (AET). We describe how these methods could inform structure–function relations in quantum materials down to the picometer scale and femtosecond time resolution, and how they enable precision positioning of atomic defects and high-resolution manipulation of quantum materials. For each method, we also describe existing limitations to solve open quantum mechanical questions, and how they might be addressed to accelerate progress. Among numerous notable results, our review highlights how EM is enabling identification of the 3D structure of quantum defects; measuring reversible and metastable dynamics of quantum excitations; mapping exciton states and single photon emission; measuring nanoscale thermal transport and coupled excitation dynamics; and measuring the internal electric field and charge density distribution of quantum heterointerfaces- all at the quantum materials’ intrinsic atomic and near atomic-length scale. Finally, we conclude by describing open challenges for the future, including achieving stable sample holders for ultralow temperature (below 10K) atomic-scale spatial resolution, stable spectrometers that enable meV energy resolution, and high-resolution, dynamic mapping of magnetic and spin fields. With atomic manipulation and ultrafast characterization enabled by EM, quantum materials will be poised to integrate into many of the sustainable and energy-efficient technologies needed for the 21st century.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

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↗

NASA NTRS2003

Study of alloy disorder in quantum dots through multi-million atom simulations

A tight binding model which includes s, p, d, s orbitals is used to examine the electronic structures of an ensemble of dome-shaped In0.6 Ga0.4 As quantum dots. Given ensembles of identically sized quantum dots, variations in composition and configuration yield a linewidth broadening of less than 0.35 meV, much smaller than the total broadening determined from photoluminescence experiments. It is also found that the computed disorder-induced broadening is very sensitive to the applied boundary conditions, so that care must be taken to ensure proper convergence of the numerical results. Examination of local eigenenergies as functions of position shows similar convergence problems and indicates that an inaccurate resolution of the equilibrium atomic positions due to truncation of the simulation domain may be the source of the slow ground state convergence.

disorder↗

DOE OSTI2024

Uncovering the three-dimensional structure of upconverting core–shell nanoparticles with multislice electron ptychography

In photon upconverting core–shell nanoparticles, structure strongly dictates performance. Typical imaging in scanning transmission electron microscopy has sufficient resolution to probe the atomic structure of these nanoparticles, but contrast, dose, and projection limitations make conventional methods insufficient for fully characterizing these structures. Phase retrieval techniques provide a promising alternative imaging mode, and, in particular, multislice electron ptychography can recover depth-dependent information. Here, we study beam-sensitive photon upconverting core–shell nanoparticles with a multislice ptychography approach using a low electron dose to avoid damage. Large strain fields arise in these heterostructures due to the mismatch in lattice parameter between the core and the shell. We reconstruct both a nanoparticle that appears defect-free and one that has a large break in the side and map the distribution of strain in 3D by computing distortion fields from high-resolution potential images of each slice. In the defect-free nanoparticle, we observe twisting of the shell, while in the broken nanoparticle, we measure the 3D position of the crack, the core, and dislocations. These results highlight the advantage of multislice electron ptychography to recover 3D information from a single scan, even under strict electron dose requirements from beam-sensitive samples.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2022

Atomic-Level Structure of Mesoporous Hexagonal Boron Nitride Determined by High-Resolution Solid-State Multinuclear Magnetic Resonance Spectroscopy and Density Functional Theory Calculations

Mesoporous hexagonal boron nitride (p-BN) has received significant attention over the last decade as a promising candidate for water cleaning/pollutant removal and hydrogen storage applications. In this work, high-resolution solid-state NMR spectroscopy and plane-wave density-functional theory (DFT) calculations are used to obtain an atomic-level description of p-BN. 1 H– 15 N or 1 H– 14 N heteronuclear (HETCOR) correlation experiments recorded with either conventional NMR at room temperature or dynamic nuclear polarization surface-enhanced spectroscopy (DNP-SENS) at ca. 100 K reveal NB 2 H, NBH 2 , NBH 3 + species residing on the edges of BN sheets. Ultra-high field 35.2 T 11 B NMR spectroscopy was used to resolve 11 B NMR signals from BN 3 , BN 2 O x (OH) 1–x (x = 0–1), BNO x (OH) 2–x (x = 0–2), BO x (OH) 3–x (x = 0–3), and BO x (OH) 4–x – (x = 0–4). Importantly, 2D 11 B dipolar double-quantum–single-quantum homonuclear correlation spectra reveal that many pore/defect sites are composed of boron oxide/hydroxide clusters connected to the BN framework through BN 2 O units. 1D and 2D 11 B{ 15 N} HETCOR NMR experiments, in addition to plane-wave DFT calculations of nine different structural models, further confirm the assignment of all NMR signals. The detailed structure determination of the pore and edge/defect sites within p-BN should further enable the rational design and development of next-generation p-BN-based materials. In addition, the techniques outlined here should be applicable to determine structure within other porous and/or boron-based materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

High-Resolution Three-Dimensional Sculpting of Two-Dimensional Graphene Oxide by E-Beam Direct Write

On demand switchable additive/subtractive patterning of 2D nanomaterials is an essential capability for developing new concepts of functional nanomaterials and their device realizations. Traditionally, this is performed via a multi-step process using photoresist coating and patterning by conventional photo or electron beam lithography, which is followed by bulk dry/wet etch or deposition. This limits the range of functionalities and structural topologies that can be achieved, as well as increases the complexity, cost, and possibility of contamination which are significant barriers to device fabrication from highly sensitive 2D materials. Focused electron beam induced processing (FEBIP) enables a material chemistry/site-specific, high-resolution multi-mode atomic scale processing and provides unprecedented opportunities for direct-write, single-step surface patterning of 2D nanomaterials with an in-situ imaging capability. It allows for realizing a rapid multi-scale/multi-mode approach, ranging from an atomic scale manipulation (e.g., via targeted defect introduction as an active site) to a large-area surface modification on nano and micro scales, including patterned doping and material removal/deposition with 2D (in-plane)/3D (out-of-plane) control. In this work, we report on a new capability of FEBIP for nanoscale patterning of graphene oxide via removal of oxygenated carbon moieties with no use of reactive gas required for etching complemented by carbon atom deposition using focused electron beam. The mechanism of experimentally observed phenomena is explored using the density functional theory (DFT) calculations, revealing that interactions of e-beam liberated reactive oxygen radicals with carbon atoms on graphene basal plane lead to creation of atomic vacancies in the material. The reaction by-products are volatile carbon di-oxides, which are dissociated and volatilized from the graphene oxide surface functional groups by interactions with an energetic focused electron beam. Along with selective “subtractive” patterning of graphene oxide, the same electron beam with increased irradiation doses can deposit out-of-plane 3D carbon nanostructures on top of or around the 2D etched pattern, thus forming a hybrid 2D/3D nanocomposite with feature control down to a few nanometers. Furthermore, this in-operando dual nanofabrication capability of FEBIP is unmatched by any other nanopatterning techniques and opens a new design window for forming 2D/3D complex nanostructures and functional nanodevices.

36 MATERIALS SCIENCE↗

DOE OSTI2025

The Martini 3 Lipidome: Expanded and Refined Parameters Improve Lipid Phase Behavior

Lipid membranes are central to cellular life. Complementing experiments, computational modeling has been essential in unraveling complex lipid-biomolecule interactions, crucial in both academia and industry. The Martini model, a coarse-grained force field for efficient molecular dynamics simulations, is widely used to study membrane phenomena but has faced limitations, particularly in capturing realistic lipid phase behavior. Here, we present refined Martini 3 lipid models with a mapping scheme that distinguishes lipid tails that differ by just two carbon atoms, enhancing the structural resolution and thermodynamic accuracy of model membrane systems including ternary mixtures. The expanded Martini lipid library includes thousands of models, enabling simulations of complex and biologically relevant systems. These advancements establish Martini as a robust platform for lipid-based simulations across diverse fields.

Lipids↗

DOE OSTI2023

Targeting Aspergillus allergen oryzin with a chemical probe at atomic precision

We report the molecular basis of Aspergillus fumigatus oryzin, allergen Asp f 13, or alkaline proteinase ALP1, containing the sequence motif His–Asp–Ser of the subtilisin family, structure, and function at atomic detail. Given the resolution of the data (1.06 Å), we use fragment molecular replacement with ideal polyalanine α-helices to determine the first crystal structure of oryzin. We probe the catalytic serine through formation of an irreversible bond to a small molecule compound, specifically labeling it, describing the amino acid residues performing the catalytic function. Defined by a self-processed pro-peptide, the active site architecture shapes up pocket-like subsites that bind to and unveil the S1′–S4′ substrate binding preferences. We use molecular modeling to dock a model of the pro-peptide in the S1–S4 region and to dock collagen along the active site cleft. Opposite to the face harboring the catalytic serine, the enzyme binds to a calcium ion in a binding site created by backbone flipping. We use thermal unfolding to show that this metal ion provides structural stability. With no known host inhibitor identified thus far, this structure may hasten the progress of developing new therapeutic agents for diseases caused by pathogenic fungi.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2026

Tracking the protein conformational motions driving HIV-1 membrane fusion

HIV-1 Env (trimeric gp120/gp41) is the surface protein responsible for membrane fusion. The Env binds to the receptor proteins, which induces gp120 shedding leading to conformational changes of gp41 from the pre-fusion to post-fusion state, allowing its fusion peptide to embed in the host cell membrane and bringing the viral and host cell membranes together. The gp41 refolding is a target of several peptide inhibitors. Yet, the molecular mechanism of this dynamic process is still not well understood. In this study, we successfully simulate the conformational change of gp41 from pre-fusion to post-fusion state in atomistic resolution using all-atom structure-based models. We reveal that maintaining the directionality of protomer interactions in both pre-fusion and post-fusion states is crucial for gp41 refolding. Additionally, we find that HR1 inherently extends as a three-helical bundle toward the host-cell membrane without any bias. Importantly, we identify native contacts in the pre-fusion state that are critical for the proper refolding of gp41 towards the post-fusion state. Lastly, by incorporating the membrane-fusion inhibitors, T20 and SFT, we identify the most vulnerable stage in the fusion pathway that exhibits the greatest sensitivity to these drugs, which could aid in a better understanding of drug resistance mechanisms.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

A multimodal large language model for materials science

Understanding and predicting the properties of inorganic materials is crucial for accelerating advancements in materials science and driving applications in energy, electronics and beyond. Integrating material structure data with language-based information through multimodal large language models (LLMs) offers great potential to support these efforts by enhancing human–artificial intelligence interaction. However, a key challenge lies in integrating atomic structures at full resolution into LLMs. In this work, we introduce MatterChat, a versatile structure-aware multimodal LLM that unifies material structural data and textual inputs into a single cohesive model. MatterChat uses a bridging module to effectively align a pretrained universal machine learning interatomic potential with a pretrained LLM, reducing training costs and enhancing flexibility. Our results demonstrate that MatterChat greatly improves performance in material property prediction and human–artificial intelligence interaction, surpassing general-purpose LLMs such as GPT-4. We also demonstrate its usefulness in applications such as more advanced scientific reasoning and step-by-step material synthesis.

Tang, Yingheng [Lawrence Berkeley National Laborat↗

DOE OSTI2021

Neutron diffraction study of magnetism in van der Waals layered MnBi 2n Te 3n+1

Two-dimensional van der Waals MnBi 2 n Te 3 n +1 ( n = 1, 2, 3, 4) compounds have been recently found to be intrinsic magnetic topological insulators rendering quantum anomalous Hall effect and diverse topological states. Here, we summarize and compare the crystal and magnetic structures of this family, and discuss the effects of chemical composition on their magnetism. We found that a considerable fraction of Bi occupies at the Mn sites in MnBi 2 n Te 3 n +1 ( n = 1, 2, 3, 4) while there is no detectable Mn at the non-magnetic atomic sites within the resolution of neutron diffraction experiments. The occupancy of Mn monotonically decreases with the increase of n . The polarized neutron diffraction on the representative MnBi 4 Te 7 reveals that its magnetization density is exclusively accumulated at the Mn site, in good agreement with the results from the unpolarized neutron diffraction. The defects of Bi at the Mn site naturally explain the continuously reduced saturated magnetic moments from n = 1 to n = 4. The experimentally estimated critical exponents of all the compounds generally suggest a three-dimensional character of magnetism. Our work provides material-specified structural parameters that may be useful for band structure calculations to understand the observed topological surface states and for designing quantum magnetic materials through chemical doping.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗