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At least 1,153 records · Page 64
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 OSTI2018

Structural, magnetic and impedance spectroscopy analysis of (0.7)CoFe2O4+(0.3)BaTiO3 magnetoelectric composite

Highlights: • Successfully synthesized (0.7)CoFe{sub 2}O{sub 4}+(0.3)BaTiO{sub 3} composite by ball-milling method. • Structural properties confirmed the presence of both constituent phases. • Dielectric properties showed high value of permittivity and diminished dielectric loss at higher frequency. • Electric response of the constituent phases explained the observed relaxation processes. • Small polaron hopping mechanism governed the conduction mechanism. - Abstract: Magnetoelectric composite of particular composition (0.7)CoFe{sub 2}O{sub 4}+(0.3)BaTiO{sub 3} was synthesized by ball-milling method. X-ray diffraction pattern confirmed the presence of cubic spinel phase for CoFe{sub 2}O{sub 4} and the coexistence of tetragonal phase along with a small fraction of hexagonal phase for BaTiO{sub 3} in the prepared composite. The dielectric permittivity increased with increasing temperature (298–373 K); however, it showed relatively high magnitude of permittivity (∼1100) and diminished dielectric loss (∼0.045) at higher frequency. Complex impedance and modulus plots exhibited responses of different electro-active regions which are explained on the basis of coexistence of resistive and comparatively conductive phases in the prepared composite. Small polaronic hopping model was employed to explain the n-type carrier’s mobility as a possible conduction mechanism; whereas the activation energies calculated from the conduction and relaxation processes were found to be comparable. These results indicate that electric/dielectric properties and relaxation phenomenon are associated to the same origin.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2019

Synthesis and pharmacological activity of a silicon—zinc—boron-containing glycerohydrogel

A new pharmacologically active nanostructured silicon—zinc—boron-containing glycerohydrogel was synthesized by the sol—gel method using silicon, zinc, and boron glycerolates as biocompatible precursors. The hydrogel composition and structural features were investigated by transmission electron microscopy, powder X-ray diffraction, IR spectroscopy, atomic emission spectrometry, and elemental analysis; a structural model was proposed. It was found that the 3D framework of the gel is formed by the products of hydrolysis and subsequent (co)condensation of silicon- and boron-containing precursors. Meanwhile, the major part of zinc monoglycerolate does not undergo hydrolytic transformations during gelation, being present in the 3D framework cells as amorphous nano-sized particles. The dispersion medium of the gel is an aqueous glycerol solution of silicon and boron glycerolates, products of their hydrolytic transformations, and water-soluble products of hydrolytic transformations of zinc monoglycerolate. The silicon—zinc—boron gel is nontoxic and possesses wound-healing and antimicrobial activities; it can be considered as a nanostructured dispersed system promising for biomedical applications, which is prepared in a simple and cost-effective way without using catalysts or toxic organic solvents.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
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 OSTI2019

Comprehensive End-To-End Design of Novel High Energy Density Materials: III. Fused Heterocyclic Energetic Compounds

In contrast to synthesis and experimental characterization that are usually expensive and time-consuming, a coupled combination of ab initio and group additive theoretical methods represents a powerful alternative to computationally design and characterize new materials with targeted properties. Heterocyclic energetic materials are considered attractive candidates to replace conventional high explosives, such as PETN, RDX, HMX, and TNT. Heterocycles enable an intriguing opportunity for combinatorial design of new classes of energetic materials with targeted performance and sensitivity properties and offer ways for an accurate analysis of structure–property correlations of the materials. By using a computational strategy that links methods of quantum chemistry and semiempirical statistical analysis, we designed, modeled, and characterized a series of novel linear and fused explosive compounds. Proposed materials with best combinations of performance and sensitivity parameters can be now considered as potential candidates for synthesis and experimental characterization.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
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 OSTI2019

Detection of ratcheting in finite element calculations

The distinction between a ratcheting and non-ratcheting response is critical for many high temperature design methods. Non-ratcheting is generally considered safe deformation remain bounded over the lifetime of the component while ratcheting is undesirable. As a particular example, the elastic perfectly plastic (EPP) design methods described in recent ASME Section III, Division 5 code cases require a designer to distinguish ratcheting from non-ratcheting for finite element analyses using a relatively simple, elastic perfectly-plastic constitutive response. However, it can be quite difficult to distinguish these two deformation regimes using finite element (FE) analysis particularly in the case where the actual ratcheting strain is small. In practice FE analysis of structures that are analytically in either the plastic shakedown or ratcheting regimes will result in small, cycle to -cycle accumulated strains characteristic of ratcheting. Distinguishing false ratcheting the structure is actually in the plastic shakedown regime from true ratcheting can be challenging. We describe the characteristics of nonlinear FE analysis that cause these false ratcheting strains and describe practical methods for distinguishing a ratcheting from a non-ratcheting response.

Messner, M. C.↗
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 OSTI2019

Flow Patterns, Microstructure and Mechanical Properties of AZ31/Al6061 Dissimilar Friction Stir-Welded Joints

Dissimilar joints between die-cast AZ31 and extruded Al6061-T6 were joined using friction stir welding technology at a constant transverse speed (50 mm/min) and rotation rate of 800 or 1000 rpm. The flow patterns, microstructure evolution and intermetallic compounds in dissimilar joints were studied by optical and scanning electron microscopy. The relationship between microstructure and tensile properties was analyzed. The microhardness distribution along the horizontal centerline in cross section was investigated. Local flow without obvious mixing existed between Mg and Al metals in the tool shoulder-affected zone. For the tool-pin-affected zone, two typical zones, namely, the “extrusion zone” and “flow zone” existed because of the different flow modes of the plastic metals. The phase analysis showed that intermetallic compounds, including Al{sub 12}Mg{sub 17} and Al{sub 3}Mg{sub 2} formed in banded structures. Phase analysis showed that a joint with welding parameters of 800 rpm and 50 mm/min (Joint-500) had good mechanical properties because of the more uniform microstructure distribution and fewer intermetallic compounds. Fracture analysis indicated some microvoids and lamellate intermetallic compounds in the fracture surface of the joint with welding parameters of 1000 rpm and 50 mm/min (Joint-1000), which deteriorated its tensile strength significantly.

36 MATERIALS SCIENCE↗
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 OSTI2018

An Efficient Algorithm for Automatic Structure Optimization in X-ray Standing-Wave Experiments

We present that x-ray standing-wave photoemission experiments involving multilayered samples are emerging as unique probes of the buried interfaces that are ubiquitous in current device and materials research. Such data require for their analysis a structure optimization process comparing experiment to theory that is not straightforward. In this work, we present a new computer program for optimizing the analysis of standing-wave data, called SWOPT, that automates this trial-and-error optimization process. The program includes an algorithm that has been developed for computationally expensive problems: so-called black-box simulation optimizations. It also includes a more efficient version of the Yang X-ray Optics Program (YXRO) [Yang, S.-H., Gray, A.X., Kaiser, A.M., Mun, B.S., Sell, B.C., Kortright, J.B., Fadley, C.S., J. Appl. Phys. 113, 1 (2013)] which is about an order of magnitude faster than the original version. Human interaction is not required during optimization. We tested our optimization algorithm on real and hypothetical problems and show that it finds better solutions significantly faster than a random search approach. The total optimization time ranges, depending on the sample structure, from minutes to a few hours on a modern laptop computer, and can be up to 100x faster than a corresponding manual optimization. Finally, these speeds make the SWOPT program a valuable tool for realtime analyses of data during synchrotron experiments.

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↗