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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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All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

RCSB Protein Data Bank: supporting research and education worldwide through explorations of experimentally determined and computationally predicted atomic level 3D biostructures

The Protein Data Bank (PDB) was established as the first open-access digital data resource in biology and medicine in 1971 with seven X-ray crystal structures of proteins. Today, the PDB houses >210 000 experimentally determined, atomic level, 3D structures of proteins and nucleic acids as well as their complexes with one another and small molecules ( e.g. approved drugs, enzyme cofactors). These data provide insights into fundamental biology, biomedicine, bioenergy and biotechnology. They proved particularly important for understanding the SARS-CoV-2 global pandemic. The US-funded Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) and other members of the Worldwide Protein Data Bank (wwPDB) partnership jointly manage the PDB archive and support >60 000 `data depositors' (structural biologists) around the world. wwPDB ensures the quality and integrity of the data in the ever-expanding PDB archive and supports global open access without limitations on data usage. The RCSB PDB research-focused web portal at https://www.rcsb.org/ (RCSB.org) supports millions of users worldwide, representing a broad range of expertise and interests. In addition to retrieving 3D structure data, PDB `data consumers' access comparative data and external annotations, such as information about disease-causing point mutations and genetic variations. RCSB.org also provides access to >1 000 000 computed structure models (CSMs) generated using artificial intelligence/machine-learning methods. To avoid doubt, the provenance and reliability of experimentally determined PDB structures and CSMs are identified. Related training materials are available to support users in their RCSB.org explorations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Atomic-scale 3D imaging of individual dopant atoms in an oxide semiconductor

The physical properties of semiconductors are controlled by chemical doping. In oxide semiconductors, small variations in the density of dopant atoms can completely change the local electric and magnetic responses caused by their strongly correlated electrons. In lightly doped systems, however, such variations are difficult to determine as quantitative 3D imaging of individual dopant atoms is a major challenge. We apply atom probe tomography to resolve the atomic sites that donors occupy in the small band gap semiconductor Er(Mn,Ti)O 3 with a nominal Ti concentration of 0.04 at. %, map their 3D lattice positions, and quantify spatial variations. Our work enables atomic-level 3D studies of structure-property relations in lightly doped complex oxides, which is crucial to understand and control emergent dopant-driven quantum phenomena.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Correlation between thickness dependent nanoscale structural chemistry and superconducting properties of ultrathin epitaxial NbN films

NbN-based superconductors have attracted interest for superconducting circuits, quantum computation and high frequency devices. The superconducting properties of NbN films are predominately reliant on the microstructure, therefore, an atomic-level understanding of the structure-chemistry is required to achieve high quality epitaxial NbN films. Here, in this study, the thickness-dependent superconducting properties of NbN films (5, 10, and 50 nm) within NbN/AlN/Al 2 O 3 heterostructures are investigated. NbN and AlN were epitaxially grown by an industrial scale physical vapor deposition technique. The role of nanoscale chemistry on the ultrathin NbN superconducting film is investigated at the atomic level for the first time via atom probe tomography, providing three-dimensional atomic distribution, chemical homogeneity, effect of impurities, specially, in secondary phase formations and interfacial abruptness. The NbN film with 5 nm of thickness demonstrates a superconducting transition temperature of 11.2 K as compared to 50 nm NbN films with a transition temperature of 15.3 K. These thickness dependent variation of superconducting properties are associated with the chemical inhomogeneity in terms of in-plane N:Nb distribution, secondary phase formations and NbN/AlN interfacial abruptness as a function of the NbN films thicknesses. The analysis depicts the interplay between the surface/interface and the superconducting properties of ultrathin NbN films. These results provide insights on material design and growth that will enable the development of optimized superconducting NbN films for quantum devices.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Strain release by 3D atomic misfit in fivefold twinned icosahedral nanoparticles with amorphization and dislocations

Multiple twinning to form fivefold twinned nanoparticles in crystal growth is common and has attracted broad attention ranging from crystallography research to physical chemistry and materials science. Lattice-misfit strain and defects in multiple twinned nanoparticles (MTP) are key to understand and tailor their electronic properties. However, the structural defects and related strain distributions in MTPs are poorly understood in three dimensions (3D). Here, we show the 3D atomic misfit and strain relief mechanism in fivefold twinned icosahedral nanoparticles with amorphization and dislocations by using atomic resolution electron tomography. We discover a two-sided heterogeneity in variety of structural characteristics. A nearly ideal crystallographic fivefold face is always found opposite to a less ordered face, forming Janus-like icosahedral nanoparticles with two distinct hemispheres. The disordered amorphous domains release a large amount of strain. Molecular dynamics simulations further reveal the Janus-like icosahedral nanoparticles are prevalent in the MTPs formed in liquid-solid phase transition. This work provides insights on the atomistic models for the modelling of formation mechanisms of fivefold twinned structures and computational simulations of lattice distortions and defects. We anticipate it will inspire future studies on fundamental problems such as twin boundary migration and kinetics of structures in 3D at atomic level.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

PDB‐101: Molecular Explorations through Biology and Medicine

PDB‐101 is an online portal for teachers, students, and the general public to promote exploration of the structural biology of proteins and nucleic acids ( pdb101.rcsb.org ). Learning about the diverse shapes and functions of these biological macromolecules helps to understand all aspects of biomedicine and agriculture, from protein synthesis to health and disease to biological energy. Why PDB‐101? Researchers around the world are studying these molecules at the atomic level. These 3D structures are freely available at the Protein Data Bank (PDB), the central storehouse of biomolecular structures. This website builds introductory materials to help beginners get started in the basics of biomolecular structure and function (“101”, as in an entry level course) as well as resources for extended learning. Since 2011, PDB‐101 has been developed by the RCSB PDB , a global resource for the advancement of research and education in biology and medicine. Along with our Worldwide PDB collaborators, RCSB PDB curates, annotates, and makes publicly available the PDB data deposited by scientists around the globe. The RCSB PDB then provides a window to these data through a rich online resource with powerful searching, reporting, and visualization tools for researchers. This information is then streamlined for students and teachers at PDB‐101. Features include the ongoing Molecule of the Month series, educational materials such as paper models, posters, molecular animations, educational curricula and more. The section “Guide to Understanding PDB Data” is a primer for detailed PDB‐specific information: PDB Data, Visualizing Structures, Reading Coordinate Files, scientific methods for structure determination, and more. PDB‐101 also runs annual Video Challenges for high school students. Participants create short videos that tell molecular stories that connect structural biology and medicine. Previous topics have included HIV/AIDS, diabetes, and antimicrobial resistance. The 2022 challenge will focus on Molecular Mechanisms of Cancer. PDB‐101 activities are evaluated using user surveys, feedback from in‐person activities, and website analytics. In 2020, PDB‐101 hosted >850,000 users and >2.6 million page views.

Zardecki, Christine↗
DOE OSTI2021

PDB ‐101: Educational resources supporting molecular explorations through biology and medicine

Abstract The Protein Data Bank (PDB) archive is a rich source of information in the form of atomic‐level three‐dimensional (3D) structures of biomolecules experimentally determined using macromolecular crystallography, nuclear magnetic resonance (NMR) spectroscopy, and electron microscopy (3DEM). Originally established in 1971 as a resource for protein crystallographers to freely exchange data, today PDB data drive research and education across scientific disciplines. In 2011, the online portal PDB‐101 was launched to support teachers, students, and the general public in PDB archive exploration ( pdb101.rcsb.org ). Maintained by the Research Collaboratory for Structural Bioinformatics PDB, PDB‐101 aims to help train the next generation of PDB users and to promote the overall importance of structural biology and protein science to nonexperts. Regularly published features include the highly popular Molecule of the Month series, 3D model activities, molecular animation videos, and educational curricula. Materials are organized into various categories (Health and Disease, Molecules of Life, Biotech and Nanotech, and Structures and Structure Determination) and searchable by keyword. A biennial health focus frames new resource creation and provides topics for annual video challenges for high school students. Web analytics document that PDB‐101 materials relating to fundamental topics (e.g., hemoglobin, catalase) are highly accessed year‐on‐year. In addition, PDB‐101 materials created in response to topical health matters (e.g., Zika, measles, coronavirus) are well received. PDB‐101 shows how learning about the diverse shapes and functions of PDB structures promotes understanding of all aspects of biology, from the central dogma of biology to health and disease to biological energy.

Zardecki, Christine↗
DOE OSTI2024

Updated resources for exploring experimentally-determined PDB structures and Computed Structure Models at the RCSB Protein Data Bank

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB, RCSB.org), the US Worldwide Protein Data Bank (wwPDB, wwPDB.org) data center for the global PDB archive, provides access to the PDB data via its RCSB.org research-focused web portal. We report substantial additions to the tools and visualization features available at RCSB.org, which now delivers more than 227000 experimentally determined atomic-level three-dimensional (3D) biostructures stored in the global PDB archive alongside more than 1 million Computed Structure Models (CSMs) of proteins (including models for human, model organisms, select human pathogens, crop plants and organisms important for addressing climate change). In addition to providing support for 3D structure motif searches with user-provided coordinates, new features highlighted herein include query results organized by redundancy-reduced Groups and summary pages that facilitate exploration of groups of similar proteins. Newly released programmatic tools are also described, as are enhanced training opportunities.

Burley, Stephen K.↗
DOE OSTI2025

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↗
DOE OSTI2024

Atomic-Scale Interface for Pt Nanoparticles on SrTiO 3 (001)

The interfacial structure formed by Pt nanoparticles grown epitaxially on a SrTiO 3 (001) surface by pulsed laser deposition was studied by X-ray standing-wave (XSW) excited core-level photoelectron emission. The XSW-generated 3D atomic map of the Pt and interfacial oxygens for the oxidized Pt/SrTiO 3 interface differs significantly from that of the as-deposited interface. After oxidation, the Pt atoms shifted upward and their atomic occupation at fcc-like sites evolved as the oxidation temperature increased. Interfacial oxygen atoms were differentiated from bulk O atoms by the chemical shift in the binding energy of their 1s electrons. After oxidation, the interfacial oxygen atoms rearranged to form a TiO 2 bilayer at the interface. Furthermore, these results provide a more complete description of the strong metal–support interaction process at the interface.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Deformation mechanisms in single crystal Ni-based concentrated solid solution alloys by nanoindentation

Nanoindentation is a critical technique to probe mechanical properties at the micrometer and sub-micrometer scales, accompanied by challenges from indentation size effect, pile-up/sink-in effect, and strain rate sensitivity. In this work, different nanoindentation techniques have been employed to explore Ni-based concentrated solid solution alloys (CSAs) with the addition of 3d transition metal elements including Co, Cr, Mn, and Fe, including unique single-crystal Ni, NiCo, NiFe, Ni 80 Cr 20 , and NiCoFeCr samples with (100) surfaces. A procedure of nanoindentation tests and data analysis/correction have been developed, and a data set of hardness, elastic modulus, strain rate sensitivity, and activation volume for Ni-based CSAs are provided, including the less explored binary alloys such as Ni 80 Cr 20 and Ni 80 Mn 20 . The results show that the type of alloying elements is more critical than the number of elements in strengthening: Co does not provide strengthening in NiCo, while Cr, Mn, and Fe are effective strengthening elements. Cr is the most effective among all the 3d transition metal elements. Furthermore, atomic-level lattice distortion is responsible for the strengthening and the role of stacking fault energy is insignificant in Ni-based CSAs at room temperature. In summary, nanoindentation shows increasing promise as a reliable and fast tool to provide comprehensive mechanical information for new alloy design and development.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Atomic Three-Dimensional Investigations of Pd Nanocatalysts for Acetylene Semi-hydrogenation

Deciphering the three-dimensional (3D) insight into nanocatalyst surfaces at the atomic level is crucial to understanding catalytic reaction mechanisms and developing high-performance catalysts. Nevertheless, better understanding the inherent insufficiency of a long-range ordered lattice in nanocatalysts is a big challenge. Here, in this work, we report the local structure of Pd nanocatalysts, which is beneficial for demonstrating the shape-structure-adsorption relationship in acetylene hydrogenation. The 5.27 nm spherical Pd catalyst (Pd sph ) shows an ethylene selectivity of 88% at complete acetylene conversion, which is much higher than those of the Pd octahedron and Pd cube and superior to other reported monometallic Pd nanocatalysts so far. By virtue of the local structure revelation combined with the atomic pair distribution function (PDF) and reverse Monte Carlo (RMC) simulation, the atomic surface distribution of the unique compressed strain of Pd-Pd pairs in Pd sph was revealed. Density functional theory calculations verified the obvious weakening of the ethylene adsorption energy on account of the surface strain of Pd sph . It is the main factor to avoid the over-hydrogenation of acetylene. The present work, entailing shape-induced surface strain manipulation and atomic 3D insight, opens a new path to understand and optimize chemical activity and selectivity in the heterogeneous catalysis process.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Direct strain correlations at the single-atom level in three-dimensional core-shell interface structures

Abstract Nanomaterials with core-shell architectures are prominent examples of strain-engineered materials. The lattice mismatch between the core and shell materials can cause strong interface strain, which affects the surface structures. Therefore, surface functional properties such as catalytic activities can be designed by fine-tuning the misfit strain at the interface. To precisely control the core-shell effect, it is essential to understand how the surface and interface strains are related at the atomic scale. Here, we elucidate the surface-interface strain relations by determining the full 3D atomic structure of Pd@Pt core-shell nanoparticles at the single-atom level via atomic electron tomography. Full 3D displacement fields and strain profiles of core-shell nanoparticles were obtained, which revealed a direct correlation between the surface and interface strain. The strain distributions show a strong shape-dependent anisotropy, whose nature was further corroborated by molecular statics simulations. From the observed surface strains, the surface oxygen reduction reaction activities were predicted. These findings give a deep understanding of structure-property relationships in strain-engineerable core-shell systems, which can lead to direct control over the resulting catalytic properties.

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

Extending Interfaces in 3D to Achieve Superior Nanoscale Strength in Ti/Nb Nanolaminates

Tuning the atomic-level structure of nanolaminates enables high strength, increased deformability, and the ability to absorb and mitigate damage due to varied crystalline defects, including dislocations. Here, we present the enhanced strength of Ti/Nb nanolaminates containing thick 3D interfaces (3DIs), relative to their chemically abrupt 2D counterparts. We examine the effects of crystallographic alignment and compositional gradients on mechanical behavior via experiments and phase-field-dislocation dynamics (PFDD) modeling. Mechanical testing reveals that nanolaminates containing thicker 3DIs demonstrate a 28% hardness enhancement compared with sharp-interface nanolaminates. PFDD modeling shows that the critical resolved shear stress (CRSS) increases with the 3DI thickness. Gradual compositional transitions in 3DIs were confirmed via scanning transmission electron microscopy and high-resolution transmission electron microscopy, showing sharp crystallographic transitions and a heightened interface topography. The findings establish a positive function between the 3DI thickness and mechanical robustness for hexagonal-closest-packed-containing composites, emphasizing the role of defect–interface interactions in tailoring the mechanical performance and providing a foundation for future interfacial engineering.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Understanding the Origin of Structural Diversity of DNA Double Helix

Deciphering the contribution of DNA subunits to the variability of its 3D structure represents an important step toward the elucidation of DNA functions at the atomic level. In the pursuit of that goal, our previous studies revealed that the essential conformational characteristics of the most populated “canonic” BI and AI conformational families of Watson–Crick duplexes, including the sequence dependence of their 3D structure, preexist in the local energy minima of the elemental single-chain fragments, deoxydinucleoside monophosphates (dDMPs). Those computations have uncovered important sequence-dependent regularity in the superposition of neighbor bases. The present work expands our studies to new minimal fragments of DNA with Watson–Crick nucleoside pairs that differ from canonic families in the torsion angles of the sugar-phosphate backbone (SPB). To address this objective, computations have been performed on dDMPs, cdDMPs (complementary dDMPs), and minimal fragments of SPBs of respective systems by using methods of molecular and quantum mechanics. These computations reveal that the conformations of dDMPs and cdDMPs having torsion angles of SPB corresponding to the local energy minima of separate minimal units of SPB exhibit sequence-dependent characteristics representative of canonic families. In contrast, conformations of dDMP and cdDMP with SPB torsions being far from the local minima of separate SPB units exhibit more complex sequence dependence.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Discovery of orbital ordering in Bi 2 Sr 2 CaCu 2 O 8+x

The primordial ingredient of cuprate superconductivity is the CuO 2 unit cell. Theories usually concentrate on the intra-atom Coulombic interactions dominating the 3d 9 and 3d 10 configurations of each copper ion. However, if Coulombic interactions also occur between electrons of the 2p 6 orbitals of each planar oxygen atom, spontaneous orbital ordering may split their energy levels. This long-predicted intra-unit-cell symmetry breaking should generate an orbitally ordered phase, for which the charge transfer energy ε separating the 2p 6 and 3d 10 orbitals is distinct for the two oxygen atoms. Here we introduce sublattice-resolved ε(r) imaging to CuO 2 studies and discover intra-unit-cell rotational symmetry breaking of ε(r). Spatially, this state is arranged in disordered Ising domains of orthogonally oriented orbital order bounded by dopant ions, and within whose domain walls low-energy electronic quadrupolar two-level systems occur. Overall, these data reveal a Q = 0 orbitally ordered state that splits the oxygen energy levels by ~50 meV, in underdoped CuO 2 .

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2025

Visualizing and analyzing 3D biomolecular structures using Mol* at RCSB.org: Influenza A H5N1 virus proteome case study

The easiest and often most useful way to work with experimentally determined or computationally predicted structures of biomolecules is by viewing their three-dimensional (3D) shapes using a molecular visualization tool. Mol* was collaboratively developed by RCSB Protein Data Bank (RCSB PDB, RCSB.org) and Protein Data Bank in Europe (PDBe, PDBe.org) as an open-source, web-based, 3D visualization software suite for examination and analyses of biostructures. It is capable of displaying atomic coordinates and related experimental data of biomolecular structures together with a variety of annotations, facilitating basic and applied research, training, education, and information dissemination. Across RCSB.org, the RCSB PDB research-focused web portal, Mol* has been implemented to support single-mouse-click atomic-level visualization of biomolecules (e.g., proteins, nucleic acids, carbohydrates) with bound cofactors, small-molecule ligands, ions, water molecules, or other macromolecules. RCSB.org Mol* can seamlessly display 3D structures from various sources, allowing structure interrogation, superimposition, and comparison. Using influenza A H5N1 virus as a topical case study of an important pathogen, we exemplify how Mol* has been embedded within various RCSB.org tools—allowing users to view polymer sequence and structure-based annotations integrated from trusted bioinformatics data resources, assess patterns and trends in groups of structures, and view structures of any size and compositional complexity. In addition to being linked to every experimentally determined biostructure and Computed Structure Model made available at RCSB.org, Standalone Mol* is freely available for visualizing any atomic-level or multi-scale biostructure at rcsb.org/3d-view.

3D biostructure↗
DOE OSTI2022

RCSB Protein Data Bank 1D3D module: displaying positional features on macromolecular assemblies

Mapping positional features from one-dimensional (1D) sequences onto three-dimensional (3D) structures of biological macromolecules is a powerful tool to show geometric patterns of biochemical annotations and provide a better understanding of the mechanisms underpinning protein and nucleic acid function at the atomic level. We present a new library designed to display fully customizable interactive views between 1D positional features of protein and/or nucleic acid sequences and their 3D structures as isolated chains or components of macromolecular assemblies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Probing the atomically diffuse interfaces in Pd@Pt core-shell nanoparticles in three dimensions

Deciphering the three-dimensional atomic structure of solid-solid interfaces in core-shell nanomaterials is the key to understand their catalytical, optical and electronic properties. Here, we probe the three-dimensional atomic structures of palladium-platinum core-shell nanoparticles at the single-atom level using atomic resolution electron tomography. We quantify the rich structural variety of core-shell nanoparticles with heteroepitaxy in 3D at atomic resolution. Instead of forming an atomically-sharp boundary, the core-shell interface is found to be atomically diffuse with an average thickness of 4.2 Å, irrespective of the particle’s morphology or crystallographic texture. The high concentration of Pd in the diffusive interface is highly related to the free Pd atoms dissolved from the Pd seeds, which is confirmed by atomic images of Pd and Pt single atoms and sub-nanometer clusters using cryogenic electron microscopy. These results advance our understanding of core-shell structures at the fundamental level, providing potential strategies into precise nanomaterial manipulation and chemical property regulation.

74 ATOMIC AND MOLECULAR PHYSICS↗