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

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At least 793 records · Page 44
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Identifying Topological Defects in Lamellar Phases through Contour Analysis of Complex Wave Fields

Lamellar phases frequently contain structural imperfections that significantly affect their behaviors and properties. Our previous research successfully reconstructed real-space configurations of defective lamellar phases from diffuse scattering patterns, indicating the presence of phase vortices as a potential method for identifying topological defects disrupting the smectic ordering. Here, this report presents a mathematical framework using regularized wave fields to represent defective lamellar structures in real space. Phase singularities, resulting from the interference of random waves and indicating lamellar order disruption, are identified through a contour integral. These wave fields, derived from coherent scattering in reciprocal space, were validated via computational benchmarks analyzing small-angle neutron scattering data from AOT surfactant solutions, facilitating further statistical analysis of the defects. Our study highlights the potential to extract meaningful information about topological defects in lyotropic phases by inversely analyzing experimentally measured two-point static correlations. Our method allows for detailed structural analysis of various lyotropic phases, both particulate and nonparticulate, in their quiescent states and facilitates quantitative investigation of defects’ role in phase transitions. By integrating small-angle scattering, deep learning, and vortex tangle analysis, our comprehensive approach shows promise in addressing complex challenges in the structural analysis of soft matter systems.

36 MATERIALS SCIENCE↗
DOE OSTI2021

New Insights into Structural Evolution of LiNiO 2 Revealed by Operando Neutron Diffraction

LiNiO 2 (LNO) represents the end member in the compositional space of the LiNi 1-x-y Mn x Co y O 2 (as x and y approach zero) cathode system. Despite its high theoretical specific capacity (275 mAh/g), LNO suffers from phase transitions with large volume change and unfavorable reactions upon electrochemical cycling, which restricts its practical use in the application of lithium-ion batteries. While the contributing factor to the structural instability is commonly linked to the undesired volume collapse associated with the H2-H3 phase transition, detailed analysis of structural evolution following the entire route of phase transitions (H1-M-H2-H3) in real time under battery operating conditions remains a challenging task. In this work, we employ operando neutron diffraction to study the structural changes (crystal lattice, Li/Ni–O bond length, O–Ni–O bond angles, and LiO 2 /NiO 2 layer thickness) of LNO cathode in a home-built Li x NiO 2 || graphite full cell during Li + de-/intercalation. In particular, the anomalous increase(decrease) of Ni–O(Li–O) bond length at high SOC (>~85 %) in the H3 phase is discussed in the context of O 2- (2p)→Ni 4+ (3d) negative charge transfer.

25 ENERGY STORAGE↗
DOE OSTI2025

Solving the “Coloring Problem” in InPd 3– x Ag x ( x = 0–0.7) by Phase Diagrams Modeling and Diffraction Experiments

Here, a series of InPd 3–x Ag x (x = 0–1) compositions were synthesized by conventional high-temperature synthesis, and as-synthesized samples were characterized by powder X-ray diffraction experiments. Up to x = 0.7, InPd 3–x Ag x adopts the ternary substitutional variant of the InPd 3 structure (TiAl 3 -type), when x > 0.7, elemental Ag starts to segregate along with the main phase. Accurate structural characterization in InPd 3–x Ag x faces a critical challenge due to the narrow X-ray scattering contrast among constituents In, Pd, and Ag and nearly identical neutron scattering lengths of Pd and Ag. To overcome this “coloring problem”, a combination of calculation of phase diagrams modeling (CALPHAD) and diffraction techniques (X-ray and neutron) was employed. In the compositional range 0 ≤ x ≤ 0.7, InPd 3–x Ag x presents a ternary variant of the TiAl 3 -type structure, where Ag atoms selectively substitute one (the 2b Wyckoff site) of the two Pd sites in InPd 3 . Notably, in contrast to the isologous InPd 3–x Cu x (x = 0–1) system, Ag substitution does not form an ordered VRh 2 Sn-type structure at the limiting composition. The distinct site preference in InPd 3–x Ag x is elucidated by charge population analysis, electronic structure calculations, and orbital-resolved chemical bonding investigations, and the extent of substitution is supported by formation free energy calculations.

36 MATERIALS SCIENCE↗
DOE OSTI2020

A glycoprotein B-neutralizing antibody structure at 2.8 Å uncovers a critical domain for herpesvirus fusion initiation

Members of the Herpesviridae, including the medically important alphaherpesvirus varicella-zoster virus (VZV), induce fusion of the virion envelope with cell membranes during entry, and between cells to form polykaryocytes in infected tissues. The conserved glycoproteins, gB, gH and gL, are the core functional proteins of the herpesvirus fusion complex. gB serves as the primary fusogen via its fusion loops, but functions for the remaining gB domains remain unexplained. As a pathway for biological discovery of domain function, our approach used structure-based analysis of the viral fusogen together with a neutralizing antibody. We report here a 2.8 Å cryogenic-electron microscopy structure of native gB recovered from VZV-infected cells, in complex with a human monoclonal antibody, 93k. This high-resolution structure guided targeted mutagenesis at the gB-93k interface, providing compelling evidence that a domain spatially distant from the gB fusion loops is critical for herpesvirus fusion, revealing a potential new target for antiviral therapies. Herpesvirus virions have an outer lipid membrane dotted with glycoproteins that enable fusion with cell membranes to initiate entry and establish infection. Here the authors elucidate the structural mechanism of a neutralizing antibody derived from a patient infected by the herpesvirus varicella-zoster virus and targeted to its fusogen, glycoprotein-B.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Understanding the Mn dissolution mechanism in rock salt-type Li 4 Mn 2 O 5 cathodes

For the first time, a detailed exploration of Mn dissolution in disordered rock salt (DRX) Li 4 Mn 2 O 5 is presented. Herein, we apply a suite of synchrotron and lab scale X-ray techniques to both the cathode and the separator harvested from pristine, charged, or cycled lithium half-cells containing the disordered rock salt (DRX) material Li 4 Mn 2 O 5 , in order to understand Mn dissolution processes throughout charging and discharging. Previous research has hypothesized two concurrent effects that may drive Mn dissolution in cells during cycling: acid-induced disproportionation of Jahn–Teller active Mn 3+ and structural rearrangement of the cathode lattice. Through depth probing of the Mn oxidation state in both the cathode and separator via soft X-ray absorption spectroscopy (XAS), hard XAS, and X-ray photoelectron spectroscopy (XPS) in progressive states-of-charge, as well as extended X-ray absorption fine structure (EXAFS) analysis of the local Mn environment, the primary driving force of Mn dissolution is determined to be high-voltage structural rearrangement above 4.2 V. Mn dissolution is, additionally, a main source of capacity fade in Li 4 Mn 2 O 5 DRX cells, which retain only 59% capacity after 20 cycles.

Theibault, Monica↗
DOE OSTI2020

Amino acid interacting network in the receptor-binding domain of SARS-CoV-2 spike protein

The relation between amino acid (AA) sequence and biologically active conformation controls the process of polypeptide chains folding into three-dimensional (3d) protein structures. The recent achievements in the resolution achieved in cryo-electron microscopy coupled with improvements in computational methodologies have accelerated the analysis of structures and properties of proteins. However, the detailed interaction between AAs has not been fully elucidated. Herein, we present a de novo method to evaluate inter-amino acid interactions based on the concept of accurately evaluating the amino acid bond pairs (AABP). The results obtained enabled the identification of complex 3d long-range interconnected AA interacting network in proteins. The method is applied to the receptor binding domain (RBD) of the SARS-CoV-2 spike protein. We show that although nearest-neighbor AAs in the primary sequence have large AABP, other nonlocal AAs make substantial contribution to AABP with significant participation of both covalent and hydrogen bonding. Detailed analysis of AABP in RBD reveals the pivotal role they play in sequence conservation with profound implications on residue mutations and for therapeutic drug design. This approach could be easily applied to many other proteins of biomedical interest in life sciences.

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

PyLRO: A Python calculator for analyzing long-range structural order

We present PyLRO, an open-source Python calculator designed to detect, quantify, and display long-range order in periodic structures. The program’s design methodology, workflow, and approach to order quantification are described and demonstrated using a simple toy model. Additionally, we apply PyLRO to a series of metastable AlPO 4 structural intermediates from a prior high-pressure study, demonstrating how to compute and visualize structural order in all directions on a Miller sphere. We further highlight the program’s capabilities through a high-throughput analysis of structural patterns in the pressure-induced amorphization of AlPO 4 , revealing atomistic insights into specific energy regions of massive amorphous structures. These results suggest that PyLRO can be a valuable tool for investigating crystal–amorphous transition in materials research.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Sas20 is a highly flexible starch-binding protein in the Ruminococcus bromii cell-surface amylosome

Ruminococcus bromii is a keystone species in the human gut that has the rare ability to degrade dietary resistant starch (RS). This bacterium secretes a suite of starch-active proteins that work together within larger complexes called amylosomes that allow R. bromii to bind and degrade RS. Starch adherence system protein 20 (Sas20) is one of the more abundant proteins assembled within amylosomes, but little could be predicted about its molecular features based on amino acid sequence. Here, we performed a structure–function analysis of Sas20 and determined that it features two discrete starch-binding domains separated by a flexible linker. We show that Sas20 domain 1 contains an N-terminal β-sandwich followed by a cluster of α-helices, and the nonreducing end of maltooligosaccharides can be captured between these structural features. Furthermore, the crystal structure of a close homolog of Sas20 domain 2 revealed a unique bilobed starch-binding groove that targets the helical α1,4-linked glycan chains found in amorphous regions of amylopectin and crystalline regions of amylose. Affinity PAGE and isothermal titration calorimetry demonstrated that both domains bind maltoheptaose and soluble starch with relatively high affinity (K d ≤ 20 μM) but exhibit limited or no binding to cyclodextrins. Finally, small-angle X-ray scattering analysis of the individual and combined domains support that these structures are highly flexible, which may allow the protein to adopt conformations that enhance its starch-targeting efficiency. Taken together, we conclude that Sas20 binds distinct features within the starch granule, facilitating the ability of R. bromii to hydrolyze dietary RS.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Adsorption of rare earth elements in carboxylated mesoporous carbon

The separation of Rare Earth Elements (REEs) from various non-conventional sources is critically important to maintain the supply–demand balance of REEs in the western world. Here, in this research, we have investigated coal Fly Ash (CFA) as the non-conventional source of REEs. In order to recover REEs, we have synthesized carboxylate-functionalized mesoporous carbon (CMC) to harness the chelation-induced adsorption of REEs. These adsorbents were characterized with pore textural properties, FTIR spectroscopy, and SEM-EDX mapping. In the initial study with single-component La(III) Dy(III) and Lu(III), it was revealed that CMC can adsorb those REEs 2–4 times more than that of pristine mesoporous carbon confirming the effective role of the carboxylate group in the REE separation. Furthermore, the affiliation of the carboxylate group towards heavier REEs (Lu>Dy>La, when present is equal amounts) provides an added benefit of this adsorbent owing to the high demand for heavier REEs in the technology sectors. The leachate solution produced from CFA contained sixteen REEs in the range of 50–200 ppb for most of the REEs. It was revealed that CMC can extract 80–90% of all the REEs thereby further confirming the success of the CMC as an effective REE sorbent. Three successive cycles of adsorption and desorption of REEs with the same CMC revealed the consistent adsorption capacity of REEs. In-situ X-ray Absorption Near Edge Spectroscopy (XANES) analysis confirmed the +3 oxidation states of La, Dy, and Lu within CMC. In-situ Extended X-ray Absorption Fine Structure (EXAFS) analysis revealed the shortening of mean La-O, Dy-O, and Lu-O bond distance by 0.03–0.05 Å thereby confirming the coordination of these REEs with carboxylate groups present on CMC.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Cannabis monoterpene synthases: evaluating structure–function relationships

Terpene synthases catalyze the first committed step in the biosynthesis of terpenes, a structurally diverse class of natural products that also encompasses volatiles derived from precursors in the C10 to C15 range (termed monoterpenes and sesquiterpenes, respectively). In the review section of this article, we are providing information about all functionally characterized monoterpene synthases (MTSs) and sesquiterpene synthases (STSs) of Cannabis sativa L. We are also exploring the locations of MTSs and STSs in the chromosome-level assembly of the reference chemovar CBDRx. A follow-up computational structure–function analysis focuses on MTSs, as there is already a rich literature available on the topic. More specifically, by employing sequence comparisons and homology structural modeling, we infer which amino acid residues are likely to constrain the available space in the active site of cannabis MTSs. The emphasis of these studies was to investigate why some MTSs accept only a C10 diphosphate as substrate, while mixed MTS/STS enzymes also accommodate a C15 diphosphate. Here, by combining a literature review and computational analyses in a hybrid format, we are laying the foundation for future studies to better understand the determinants of substrate and product specificity in these fascinating enzymes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Amplicon Sequencing Assessment to Measure Microbial Community Response from Heavy Metal Contaminated Soils in Savannah River site, Tims Branch watershed

Long-term presence of heavy metal contamination in soils is correlated with changes in microbial community structures and can lead to the reduction of indigenous species. Tolerance to soil heavy metal toxicity varies among different microbial communities. It remains unclear whether long term effects caused by metal perturbations are associated with soil microbial community dysregulation in Tims Branch watershed. Research Questions: Does heavy metal contamination in Tims Branch soils decrease microbial species diversity significantly compared to non-contaminated soils? Does the species richness decrease in contaminated samples? between samples? Is diversity in low, mid and high contamination soils significantly different compared to control samples? Hypothesis: The relative abundance and diversity of species are significantly altered in soils which are contaminated with heavy metals in the Tims Branch watershed. Objectives: Use amplicon sequencing technology along with bioinformatics to compare bacterial communities between four sites in Tims Branch watershed. Evaluate the percent relative abundance and diversity across the site. Conclusions: All bacterial communities exposed to different heavy metal concentrations were dominated by four major groups (Proteobacteria, Acidobacteria, Chloroflexi and Verrucomicrobia). The dominant phyla Proteobacteria, Acidobacteria and Chloroflexi accounted for 61 % of the relative abundance. Soil bacterial α-diversity, expressed as observed species richness metric and Shannon's diversity index, was the highest in sample location four (high contamination). The lowest observed was at the control location. Species richness increased when concentrations of heavy metals were localized, inferring that the metals can alter microbial community structure. PERMANOVA analysis between contaminated groups tested significant using the Adonis (F (4,29) =1.9712; p < 0.001). There is a 20 percent variation explained between groups (R2 = 0.214). This analysis proves to be beneficial in detecting microbial communities altered by contaminated soils. Moreover, certain concentrations of heavy metals can alter microbial community structures.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2023

Spectroscopic Characterization of Highly Active Fe–N–C Oxygen Reduction Catalysts and Discovery of Strong Interaction with Nafion Ionomer

Scaling up clean-energy applications necessitates the development of platinum group metal (PGM)-free fuel cell electrocatalysts with high activity, stability, and low cost. Here, X-ray absorption (XAS) at the Fe K-edge and Fe K β X-ray emission (XES) spectroscopies were used to study the electronic structure of Fe centers in highly active Fe–N–C oxygen reduction catalysts with significant commercial potential. X-ray absorption near-edge structure (XANES) analysis has shown that the majority (>95%) of Fe centers are in the Fe 3+ oxidation state, while extended X-ray absorption fine structure (EXAFS) detected a mixture of single site Fe–N 4 centers (>95%) and centers with short (~2.5 Å) Fe–Fe interactions of Fe metal and/or Fe-carbide nanoparticles (<5%) featuring the Fe o oxidation state. Surprisingly, addition of Nafion, the most widely used ionomer, resulted in pronounced changes in the XAS spectra, consistent with a strong catalyst–ionomer interaction where long Fe–Fe interactions at ~3.1 Å were shown to be a feature of Fe 3+ ions bound with the Nafion. We conclude that exposure to Nafion during the device formulation has a different effect from the aggressive acid leaching typically used in the preparation of Fe–N–C catalysts. Furthermore, it was hypothesized that the polymer interacts with single sites’ Fe 3+ centers, as well as with graphene layers protecting the Fe o nanoparticles, and extracts some Fe ions into the Nafion matrix.

25 ENERGY STORAGE↗
DOE OSTI2021

X-ray absorption spectroscopy of trivalent Eu, Gd, Tb, and Dy chlorides and oxychlorides

Growing interest in next generation molten salt nuclear reactors necessitates a fundamental understanding of the chemical and physico-chemical properties of fission products, including elements of the lanthanide series. In this study, we probed coordination environment of Eu, Gd, Tb, and Dy in their chloride salts with both laboratory and synchrotron scale X-ray absorption spectroscopy (XAS). Here the aerobic melting was carried out with LnCl 3 ·nH 2 O, where Ln is Eu, Gd, Tb, and Dy, and yielded predominant formation of oxychlorides (LnOCl), that was confirmed by extended X-ray absorption fine structure (EXAFS) analysis and X-ray diffraction (XRD). Density functional theory (DFT) and time-dependent density functional theory (TDDFT) computations were performed to obtain ground state structures, lattice parameters, and to simulate L 3 -edge XANES (X-ray absorption near edge structure) spectra of the LnCl 3 ·nH 2 O and LnOCl. A blue shift, initially predicted by our calculations, was also observed for the experimental Ln L 3 -edge XANES spectra of the hydrated trichlorides vs oxychlorides, highlighting the power of combining the predictive ability of theory with experiment to elucidate the properties of the compounds of interest. The blue shift is indicative of structural stabilization of LnCl 3 ·nH 2 O due to higher symmetry compared with LnOCl. To the best of knowledge, this is a first study providing the framework for fundamental insights into the structure of Ln trichlorides and oxychlorides in support of future characterization of lanthanides in the molten salt environment.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Affinity propagation clustering of full-field, high-spatial-dimensional measurements for robust output-only modal identification: A proof-of-concept study

Determination of the model order is a challenging problem in system identification, especially in output-only or operational modal identification where some modes are weakly excited. While existing methods such as the stabilization diagram method (spectral information) are effective, they do not scale to high-dimensional data, which is usually needed for high-fidelity characterization of structural dynamics and has been made available in the emerging full-field measurement techniques using optical methods such as photogrammetry and laser vibrometers. In this proof-of-concept study we present a new non-parametric, data-driven approach for robust output-only identification of high-spatial-dimensional modal parameters of basic structures by efficiently processing and interactively exploiting the full-field measurement (i.e., very dense spatial measurement points). Specifically, we first over-estimate the system model once, producing a pool of candidate modes associated with their modal frequencies and full-field, high-spatial-dimensional mode shapes. This is accomplished by a data-driven method termed affinity propagation clustering (APC), where the active clusters, which are the active modes in our formulations, emerge from the "message-passing" procedure and does not require a pre-determination of the cluster number (mode or model order). Next, rather than using the spectral information to distinguish the physical and spurious modes in the stabilization diagram method, we exploit and visualize the spatial, full-field mode shape associated with each candidate mode to do so. We conduct extensive experiments on basic structural models with comparisons to a few existing methods. The results indicate that the new method is computationally efficient for identifying high-spatial-dimensional modal parameters, and robust to identify weak modes by exploiting the full-field measurement. We also discuss its applicability and limitations for structures with complex geometry (shapes).

42 ENGINEERING↗
DOE OSTI2020

Magnetic domain engineering in SrRuO3 thin films

Abstract Magnetic domain engineering in ferromagnetic thin films is a very important route toward the rational design of spintronics and memory devices. Although the magnetic domain formation has been extensively studied, artificial control of magnetic domain remains challenging. Here, we present the control of magnetic domain formation in paradigmatic SrRuO 3 /SrTiO 3 heterostructures via structural domain engineering. The formation of structural twin domains in SrRuO 3 films can be well controlled by breaking the SrTiO 3 substrate symmetry through engineering miscut direction. The combination of x-ray diffraction analysis of structural twin domains and magnetic imaging of reversal process demonstrates a one-to-one correspondence between structural domains and magnetic domains, which results in multi-step magnetization switching and anomalous Hall effect in films with twin domains. Our work sheds light on the control of the magnetic domain formation via structural domain engineering, which will pave a path toward desired properties and devices applications.

Materials Science↗
DOE OSTI2023

Resolving Atomic-Scale Structure and Chemical Coordination in High-Entropy Alloy Electrocatalysts for Structure–Function Relationship Elucidation

The recent breakthrough in confining five or more atomic species in nanocatalysts, referred to as high-entropy alloy nanocatalysts (HEAs), has revealed the possibilities of multielemental interactions that can surpass the limitations of binary and ternary electrocatalysts. The wide range of potential surface configurations in HEAs, however, presents a significant challenge in resolving active structural motifs, preventing the establishment of structure-function relationships for rational catalyst design and optimization. Here, we present a methodology for creating sub-5 nm HEAs using an aqueous-based peptide-directed route. Using a combination of pair distribution function and X-ray absorption spectroscopy, HEA structure models are constructed from reverse Monte Carlo modeling of experimental data sets and showcase a clear peptide-induced influence on atomic-structure and chemical miscibility. Coordination analysis of our structure models facilitated the construction of structure-function correlations applied to electrochemical methanol oxidation reactions, revealing the complex interplay between multiple metals that leads to improved catalytic properties. Our results showcase a viable strategy for elucidating structure-function relationships in HEAs, prospectively providing a pathway for future materials design.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Bacterial hemophilin homologs and their specific type eleven secretor proteins have conserved roles in heme capture and are diversifying as a family

Cellular life relies on enzymes that require metals, which must be acquired from extracellular sources. Bacteria utilize surface and secreted proteins to acquire such valuable nutrients from their environment. These include the cargo proteins of the type eleven secretion system (T11SS), which have been connected to host specificity, metal homeostasis, and nutritional immunity evasion. This Sec-dependent, Gram-negative secretion system is encoded by organisms throughout the phylum Proteobacteria, including human pathogens Neisseria meningitidis, Proteus mirabilis, Acinetobacter baumannii, and Haemophilus influenzae. Experimentally verified T11SS-dependent cargo include transferrin-binding protein B (TbpB), the hemophilin homologs heme receptor protein C (HrpC), hemophilin A (HphA), the immune evasion protein factor-H binding protein (fHbp), and the host symbiosis factor nematode intestinal localization protein C (NilC). Here, we examined the specificity of T11SS systems for their cognate cargo proteins using taxonomically distributed homolog pairs of T11SS and hemophilin cargo and explored the ligand binding ability of those hemophilin cargo homologs. In vivo expression in Escherichia coli of hemophilin homologs revealed that each is secreted in a specific manner by its cognate T11SS protein. Sequence analysis and structural modeling suggest that all hemophilin homologs share an N-terminal ligand-binding domain with the same topology as the ligand-binding domains of the Haemophilus haemolyticus heme binding protein (Hpl) and HphA. We term this signature feature of this group of proteins the hemophilin ligand-binding domain. Network analysis of hemophilin homologs revealed five subclusters and representatives from four of these showed variable heme-binding activities, which, combined with sequence-structure variation, suggests that hemophilins are diversifying in function.

59 BASIC BIOLOGICAL SCIENCES↗