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At least 271 records · Page 15

All sources NASA NTRS DOE OSTI

DOE OSTI2023

Exploration of non-resonant divertor features on the Compact Toroidal Hybrid

Abstract Non-resonant divertors (NRDs) separate the confined plasma from the surrounding plasma facing components (PFCs). The resulting striking field line intersection pattern on these PFCs is insensitive to plasma equilibrium effects. However, a complex scrape-off layer (SOL), created by chaotic magnetic topology in the plasma edge, connects the core plasma to the PFCs through varying magnetic flux tubes. The Compact Toroidal Hybrid (CTH) serves as a test-bed to study this by scanning across its inductive current. Simulations observe a significant change of the chaotic edge structure and an effective distance between the confined plasma and the instrumented wall targets. The intersection pattern is observed to be a narrow helical band, which we claim is a resilient strike line pattern. However, signatures of finger-like structures, defined as heteroclinic tangles in chaotic domains, within the plasma edge connect the island chains to this resilient pattern. The dominant connection length field lines intersecting the targets are observed via heat flux modeling with EMC3-EIRENE. At low inductive current levels, the excursion of the field lines resembles a limited plasma wall scenario. At high currents, a private flux region is created in the area where the helical strike line pattern splits into two bands. These bands are divertor legs with distinct SOL parallel particle flow channels. The results demonstrate the NRD strike line pattern resiliency within CTH, but also show the underlying chaotic edge structure determining if the configuration is diverted or limited. This work supports future design efforts for a mechanical structure for the NRD.

Physics↗

DOE OSTI2023

Synthesis and Crystal Structure of the Zintl Phases NaSrSb, NaBaSb and NaEuSb

This work details the synthesis and the crystal structures of the ternary compounds NaSrSb, NaBaSb and NaEuSb. They are isostructural and adopt the hexagonal ZrNiAl-type structure (space group P6¯2m; Pearson code hP9). The structure determination in all three cases was performed using single-crystal X-ray diffraction methods. The structure features isolated Sb3– anions arranged in layers stacked along the crystallographic c-axis. In the interstices, alkali and alkaline-earth metal cations are found in tetrahedral and square pyramidal coordination environments, respectively. The formal partitioning of the valence electrons adheres to the valence rules, i.e., Na+Sr2+Sb3–, Na+Ba2+Sb3– and Na+Eu2+Sb3– can be considered as Zintl phases with intrinsic semiconductor behavior. Electronic band structure calculations conducted for NaBaSb are consistent with this notion and show a direct gap of approx. 0.9 eV. Additionally, the calculations hint at possible inverted Dirac cones, a feature that is reminiscent of topological quantum materials.

36 MATERIALS SCIENCE↗

NASA NTRS1991

Model correlation and damage location for large space truss structures: Secant method development and evaluation

On-orbit testing of a large space structure will be required to complete the certification of any mathematical model for the structure dynamic response. The process of establishing a mathematical model that matches measured structure response is referred to as model correlation. Most model correlation approaches have an identification technique to determine structural characteristics from the measurements of the structure response. This problem is approached with one particular class of identification techniques - matrix adjustment methods - which use measured data to produce an optimal update of the structure property matrix, often the stiffness matrix. New methods were developed for identification to handle problems of the size and complexity expected for large space structures. Further development and refinement of these secant-method identification algorithms were undertaken. Also, evaluation of these techniques is an approach for model correlation and damage location was initiated.

Smith, Suzanne Weaver↗

DOE OSTI2020

Finite-Temperature Structures of Supported Subnanometer Catalysts Inferred via Statistical Learning and Genetic Algorithm-Based Optimization

Single-atom catalysts (SACs) minimize noble metal utilization and can alter the activity and selectivity of supported metal nanoparticles. However, the morphology of active centers, including single atoms and subnanometer clusters of a few atoms, remains elusive due to experimental challenges. The computational cost to describe numerous cluster shapes and sizes makes direct first-principles calculations impractical. We present a computational framework to enable structure determination for single-atom and subnanometer cluster catalysts. As a case study, we obtained the low energy structures of Pd n (n = 1-21) clusters supported on CeO 2 (111), which are critical components of automobile three-way catalysts. Trained on density functional theory data, a three-dimensional cluster expansion is established using statistical learning to describe the Hamiltonian and predict energies of supported Pdn clusters of any structure. Low energy stable and metastable structures are identified using a Metropolis Monte Carlo-based genetic algorithm in the canonical ensemble at 300 K. We observe that supported single atoms sinter to form bilayer clusters and large cluster isomers share similarities in both shape and energy, and elucidate the significance of the support and microstructure on cluster stability. We discovered a simple surrogate structure-energy model, where the energy per atom scales with the square root of the average first coordination number, which can be used to estimate energies and compare the stability of clusters. Our framework, applicable to any metal/support system, fills an important methodological gap to predict the stability of supported metal catalysts in the subnanometer regime.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Resolution of Virtual Depth Sectioning from Four-Dimensional Scanning Transmission Electron Microscopy

Abstract One approach to three-dimensional structure determination using the wealth of scattering data in four-dimensional (4D) scanning transmission electron microscopy (STEM) is the parallax method proposed by Ophus et al. (2019. Advanced phase reconstruction methods enabled by 4D scanning transmission electron microscopy, Microsc Microanal25, 10–11), which determines the scattering matrix and uses it to synthesize a virtual depth-sectioning reconstruction of the sample structure. Drawing on an equivalence with a hypothetical confocal imaging mode, we derive contrast transfer and point spread functions for this parallax method applied to weakly scattering objects, showing them identical to earlier depth-sectioning STEM modes when only bright field signal is used, but that improved depth resolution is possible if dark field signal can be used. Through a simulation-based study of doped Si, we show that this depth resolution is preserved for thicker samples, explore the impact of shot noise on the parallax reconstructions, discuss challenges to making use of dark field signal, and identify cases where the interpretation of the parallax reconstruction breaks down.

3D imaging↗

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↗

NASA NTRS1964

The structure of c2b5h7

Microwave spectroscopic methods for molecular structure determination of 2,4-dicarbaheptaborane

MOLECULAR STRUCTURE↗

DOE OSTI2020

BinaryCIF and CIFTools—Lightweight, efficient and extensible macromolecular data management

3D macromolecular structural data is growing ever more complex and plentiful in the wake of substantive advances in experimental and computational structure determination methods including macromolecular crystallography, cryo-electron microscopy, and integrative methods. Efficient means of working with 3D macromolecular structural data for archiving, analyses, and visualization are central to facilitating interoperability and reusability in compliance with the FAIR Principles. We address two challenges posed by growth in data size and complexity. First, data size is reduced by bespoke compression techniques. Second, complexity is managed through improved software tooling and fully leveraging available data dictionary schemas. To this end, we introduce BinaryCIF, a serialization of Crystallographic Information File (CIF) format files that maintains full compatibility to related data schemas, such as PDBx/mmCIF, while reducing file sizes by more than a factor of two versus gzip compressed CIF files. Moreover, for the largest structures, BinaryCIF provides even better compression—factor ten and four versus CIF files and gzipped CIF files, respectively. Herein, we describe CIFTools, a set of libraries in Java and TypeScript for generic and typed handling of CIF and BinaryCIF files. Together, BinaryCIF and CIFTools enable lightweight, efficient, and extensible handling of 3D macromolecular structural data.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Li 2 GeS 3 : Lithium Ionic Conductor with an Unprecedented Structural Type

Lithium-ion batteries (LIBs) are widely used in electric vehicles, mobile electronic devices, and large-scale stationary energy storage systems. However, their liquid electrolytes present significant safety concerns due to their inherent flammability. To address this, the focus has shifted toward all-solid-state batteries (ASSBs) utilizing inorganic solid electrolytes that promise enhanced safety. In this work, we report the discovery of a new crystal structural type of Li-ion conductor, Li 2 GeS 3 , with a unique structure, synthesized by a solid-state reaction from Li 2 S and GeS 2 . It was first reported in 2000 with an orthorhombic unit cell, but its detailed crystal structure remains veiled. Here, we have unveiled its structure for the first time, employing an ab initio structure determination technique from powder X-ray and time-of-flight neutron diffraction data. The compound has an unprecedented crystal structural type with a hexagonal $P6_1$ symmetry and a unit cell of α = 6.79364(4) Å and c = 17.90724(14) Å. Its structure is comprised of a distorted hexagonal close-packed arrangement of sulfur anions with three asymmetric metal atoms: Li1, Li2, and Ge are in tetrahedral cavities surrounded by sulfur atoms. The ionic conductivity of Li 2 GeS 3 was measured to be 1.63 × 10 –8 S cm –1 at 303 K and 2.45 × 10 –7 S cm –1 at 383 K. Bond valence energy landscape calculations revealed three-dimensional lithium diffusion pathways within the structure. This novel crystal structure in Li 2 GeS 3 holds the potential for developing high-performance ionic conductors through suitable chemical substitution and offers valuable insights into designing new ionic conductors for ASSBs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Structural Characterization of the Human Cytosolic Malate Dehydrogenase I

The first crystal structure of the human cytosolic malate dehydrogenase I (MDH1) is described. Structure determination at a high resolution (1.65 Å) followed production, isolation, and purification of human MDH1 using a bacterial expression system. The structure is a binary complex of MDH1 with only a bound malonate molecule in the substrate binding site. Comparisons of this structure with malate dehydrogenase enzymes from other species confirm that the human enzyme adopts similar secondary, tertiary, and quaternary structures and that the enzyme retains a similar conformation even when nicotinamide adenine dinucleotide (NAD + ) is not bound. A comparison to the highly homologous porcine (sus scrofa) MDH1 ternary structures leads to the conclusion that only small conformational differences are needed to accommodate binding by NAD + or other NAD + mimetics. Conformational differences observed in the second subunit show that the NAD + binding elements are nevertheless quite flexible. Comparison of hMDH1 to the human mitochondrial malate dehydrogenase (hMDH2) reveals some key differences in the α7–α8 loop, which lies directly beneath the substrate binding pocket. These differences might be exploited in the structure-assisted design of selective small molecule inhibitors of hMDH1, an emerging target for the development of anticancer therapeutics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS1994

Surface Passivation for 3-5 Semiconductor Processing: Stable Gallium Sulphide Films by MOCVD

Gallium sulphide (GaS) has been deposited on GaAs to form stable, insulating, passivating layers. Spectrally resolved photoluminescence and surface recombination velocity measurements indicate that the GaS itself can contribute a significant fraction of the photoluminescence in GaS/GaAs structures. Determination of surface recombination velocity by photoluminescence is therefore difficult. By using C-V analysis of metal-insulator-semiconductor structures, passivation of the GaAs with GaS films is quantified.

Macinnes, Andrew N.↗

DOE OSTI2025

Predicting receptor-ligand pairing preferences in plant-microbe interfaces via molecular dynamics and machine learning

Microbiome assembly, structure, and dynamics significantly influence plant health. Secreted microbial signaling molecules initiate and mediate symbiosis by binding to structurally compatible plant receptors. For example, lipo-chitooligosaccharides (LCOs), produced by nitrogen-fixing rhizobial bacteria and various fungi, are recognized by plant lysin motif receptor-like kinases (LysM-RLKs), which activate the common symbiotic pathway. Accurately predicting these molecular interactions could reveal complementary signatures underlying the initial stages of endosymbiosis. Despite the breakthrough in protein-ligand structure prediction with deep learning-based tools, such as AlphaFold3, the large size and highly flexible nature of signaling compounds like LCOs present major challenges for detailed structural characterization and binding-affinity prediction. Typical structure-/physics-based methods of ligand virtual screening are designed for small, drug-like molecules, often rely on high-resolution, experimentally determined structures of the protein receptors, and rarely achieve sufficient sampling to obtain converged thermodynamic quantities with large ligands. In this study, we developed a hybrid molecular dynamics/machine learning (MD/ML) approach capable of predicting binding affinity rankings with high accuracy in systems involving large, flexible ligands, despite limited experimental structural information. Using coarse initial structural models, the predictions using the MD/ML workflow achieved strong alignment with experimental trends, particularly in the top-affinity tier for four legume LysM-RLKs (LYR3) binding to LCOs and a chitooligosaccharide. Furthermore, the MD-based conformation selection protocol provided critical structural insights into substrate specificity and binding mechanisms. This study demonstrates a powerful method to screen for challenging cognate ligand-receptors and advance our understanding of the molecular basis of microbial colonization in plants.

Lipo-chitooligosaccharides↗

DOE OSTI2023

Distinct Conformations of SARS-CoV-2 Omicron Spike Protein and Its Interaction with ACE2 and Antibody

Since November 2021, Omicron has been the dominant severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant that causes the coronavirus disease 2019 (COVID-19) and has continuously impacted human health. Omicron sublineages are still increasing and cause increased transmission and infection rates. The additional 15 mutations on the receptor binding domain (RBD) of Omicron spike proteins change the protein conformation, enabling the Omicron variant to evade neutralizing antibodies. For this reason, many efforts have been made to design new antigenic variants to induce effective antibodies in SARS-CoV-2 vaccine development. However, understanding the different states of Omicron spike proteins with and without external molecules has not yet been addressed. In this review, we analyze the structures of the spike protein in the presence and absence of angiotensin-converting enzyme 2 (ACE2) and antibodies. Compared to previously determined structures for the wildtype spike protein and other variants such as alpha, beta, delta, and gamma, the Omicron spike protein adopts a partially open form. The open-form spike protein with one RBD up is dominant, followed by the open-form spike protein with two RBD up, and the closed-form spike protein with the RBD down. It is suggested that the competition between antibodies and ACE2 induces interactions between adjacent RBDs of the spike protein, which lead to a partially open form of the Omicron spike protein. The comprehensive structural information of Omicron spike proteins could be helpful for the efficient design of vaccines against the Omicron variant.

60 APPLIED LIFE SCIENCES↗

NASA NTRS1985

Advances and trends in structures and dynamics; Proceedings of the Symposium, Washington, DC, October 22-25, 1984

Among the topics discussed are developments in structural engineering hardware and software, computation for fracture mechanics, trends in numerical analysis and parallel algorithms, mechanics of materials, advances in finite element methods, composite materials and structures, determinations of random motion and dynamic response, optimization theory, automotive tire modeling methods and contact problems, the damping and control of aircraft structures, and advanced structural applications. Specific topics covered include structural design expert systems, the evaluation of finite element system architectures, systolic arrays for finite element analyses, nonlinear finite element computations, hierarchical boundary elements, adaptive substructuring techniques in elastoplastic finite element analyses, automatic tracking of crack propagation, a theory of rate-dependent plasticity, the torsional stability of nonlinear eccentric structures, a computation method for fluid-structure interaction, the seismic analysis of three-dimensional soil-structure interaction, a stress analysis for a composite sandwich panel, toughness criterion identification for unidirectional composite laminates, the modeling of submerged cable dynamics, and damping synthesis for flexible spacecraft structures.

Noor, A. K.↗

NASA NTRS1985

Prediction of wing aeroelastic effects on aircraft lift and pitching moment characteristics

The distribution of flight loads on an aircraft structure determines the lift and pitching moment characteristics of the aircraft. When the load distribution changes due to the aeroelastic response of the structure, the lift and pitching moment characteristics also change. Some estimate of the effect of aeroelasticity on stability and control characteristics, particularly lift and pitching moment, is required for use in aircraft simulation models for evaluation of flight characteristics. This presentation outlines a procedure to incorporate aeroelastic effects into lift and pitching moment data from wind tunnel tests. Results are presented which were obtained from applying this procedure to an aircraft with a very flexible transport-type research wing. The procedure described is generally applicable to all types of aircraft.

Eckstrom, C. V.↗

NASA NTRS1986

Prediction of wing aeroelastic effects on aircraft lift and pitching moment characteristics

The distribution of flight loads on an aircraft structure determine the lift and pitching moment characteristics of the aircraft. When the load distribution changes due to the aeroelastic response of the structure, the lift and pitching moment characteristics also change. An estimate of the effect of aeroelasticity on stability and control characteristics is often required for the development of aircraft simulation models of evaluation of flight characteristics. This presentation outlines a procedure for incorporating calculated linear aeroelastic effects into measured nonlinear lift and pitching moment data from wind tunnel tests. Results are presented which were obtained from applying this procedure to data for an aircraft with a very flexible transport type research wing. The procedure described is generally applicable to all types of aircraft.

Eckstrom, Clinton V.↗

NASA NTRS1987

Prediction of wing aeroelastic effects on aircraft life and pitching moment characteristics

Eckstrom, Clinton V.↗

NASA NTRS2012

Mars Sample Return: The Next Step Required to Revolutionize Knowledge of Martian Geological and Climatological History

The capability of scientific instrumentation flown on planetary orbiters and landers has made great advances since the signature Viking mission of the seventies. At some point, however, the science return from orbital remote sensing, and even in situ measurements, becomes incremental, rather than revolutionary. This is primarily caused by the low spatial resolution of such measurements, even for landed instrumentation, the incomplete mineralogical record derived from such measurements, the inability to do the detailed textural, mineralogical and compositional characterization needed to demonstrate equilibrium or reaction paths, and the lack of chronological characterization. For the foreseeable future, flight instruments will suffer from this limitation. In order to make the next revolutionary breakthrough in understanding the early geological and climatological history of Mars, samples must be available for interrogation using the full panoply of laboratory-housed analytical instrumentation. Laboratory studies of samples allow for determination of parageneses of rocks through microscopic identification of mineral assemblages, evaluation of equilibrium through electron microbeam analyses of mineral compositions and structures, determination of formation temperatures through secondary ion or thermal ionization mass spectrometry (SIMS or TIMS) analyses of stable isotope compositions. Such details are poorly constrained by orbital data (e.g. phyllosilicate formation at Mawrth Vallis), and incompletely described by in situ measurements (e.g. genesis of Burns formation sediments at Meridiani Planum). Laboratory studies can determine formation, metamorphism and/or alteration ages of samples through SIMS or TIMS of radiogenic isotope systems; a capability well-beyond flight instrumentation. Ideally, sample return should be from a location first scouted by landers such that fairly mature hypotheses have been formulated that can be tested. However, samples from clastic sediments derived from an extensive region of Mars can provide important, detailed understanding of early martian geological and climatological history. Interrogating clastic "sediments" from the Earth, Moon and asteroids has allowed discovery of new crustal units, identification of now-vanished crust, and determination of the geological history of extensive, remote regions. Returned sample of martian fluvial and/or aeolian sediments, for example from Gale crater, could be "read like a book" in terrestrial laboratories to provide truly revolutionary new insights into early martian geological and climatological evolution.

Mittlefehldt, D. W.↗