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At least 145 records · Page 8
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

The 1.3 Å resolution structure of the truncated group Ia type IV pilin from Pseudomonas aeruginosa strain P1

The type IV pilus is a diverse molecular machine capable of conferring a variety of functions and is produced by a wide range of bacterial species. The ability of the pilus to perform host-cell adherence makes it a viable target for the development of vaccines against infection by human pathogens such as Pseudomonas aeruginosa . Here, the 1.3 Å resolution crystal structure of the N-terminally truncated type IV pilin from P. aeruginosa strain P1 (ΔP1) is reported, the first structure of its phylogenetically linked group (group I) to be discussed in the literature. The structure was solved from X-ray diffraction data that were collected 20 years ago with a molecular-replacement search model generated using AlphaFold ; the effectiveness of other search models was analyzed. Examination of the high-resolution ΔP1 structure revealed a solvent network that aids in maintaining the fold of the protein. On comparing the sequence and structure of P1 with a variety of type IV pilins, it was observed that there are cases of higher structural similarities between the phylogenetic groups of P. aeruginosa than there are between the same phylogenetic group, indicating that a structural grouping of pilins may be necessary in developing antivirulence drugs and vaccines. These analyses also identified the α–β loop as the most structurally diverse domain of the pilins, which could allow it to serve a role in pilus recognition. Studies of ΔP1 in vitro polymerization demonstrate that the optimal hydrophobic catalyst for the oligomerization of the pilus from strain K122 is not conducive for pilus formation of ΔP1; a model of a three-start helical assembly using the ΔP1 structure indicates that the α–β loop and the D-loop prevent in vitro polymerization.

Bragagnolo, Nicholas↗
DOE OSTI2024

Solvent organization in the ultrahigh-resolution crystal structure of crambin at room temperature

Ultrahigh-resolution structures provide unprecedented details about protein dynamics, hydrogen bonding and solvent networks. The reported 0.70 Å, room-temperature crystal structure of crambin is the highest-resolution ambient-temperature structure of a protein achieved to date. Sufficient data were collected to enable unrestrained refinement of the protein and associated solvent networks using SHELXL . Dynamic solvent networks resulting from alternative side-chain conformations and shifts in water positions are revealed, demonstrating that polypeptide flexibility and formation of clathrate-type structures at hydrophobic surfaces are the key features endowing crambin crystals with extraordinary diffraction power.

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

The Debye-Waller factor of disordered solids: The case for amorphous silicon

This paper presents a first-principles study of the Debye-Waller factor and the Debye temperature for amorphous silicon (α-Si) from lattice-dynamical calculations and direct molecular-dynamics simulations using density-functional theory (DFT). The effects of temperature and structural disorder on the intensity of the diffraction maxima and the vibrational mean-square displacement (MSD) of Si atoms are studied in the harmonic approximation, with particular emphasis on the bond-length disorder, the presence of coordination defects, and microvoids in α-Si networks. It has been observed that the MSDs associated with tetrahedrally bonded Si atoms are considerably lower than their dangling-bond counterparts—originating from isolated and vacancy-induced clustered defects—and those on the surface of microvoids, leading to an asymmetric non-Gaussian tail in the distribution of atomic displacements. An examination of the effect of anharmonicity on the MSD at high temperatures using direct ab initio molecular-dynamics simulations (without the harmonic approximation) suggests that the vibrational motion in α-Si is practically unaffected by anharmonic effects at temperatures below 400 K, as far as the present DFT calculations are concerned. The Debye temperature of α-Si is found to be in the range of 488–541 K from specific-heat and MSD calculations using first-principles lattice-dynamical calculations in the harmonic approximation, which matches closely with the experimental value of 487–528 K obtained from specific-heat measurements of α-Si at low temperatures.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

Ab initio studies of the impact of the Debye-Waller factor on the structural and dynamical properties of amorphous semiconductors: The case of a-Si

This paper presents a first-principles study of the Debye-Waller factor and the Debye temperature for amorphous silicon (a-Si) from lattice-dynamical calculations and direct molecular-dynamics simulations using density-functional theory (DFT). The effects of temperature and structural disorder on the intensity of the diffraction maxima and the vibrational mean-square displacement (MSD) of Si atoms are studied in the harmonic approximation, with particular emphasis on the bond-length disorder, the presence of coordination defects, and microvoids in a-Si networks. It has been observed that the MSDs associated with tetrahedrally-bonded Si atoms are considerably lower than their dangling-bond counterparts – originating from isolated and vacancy-induced clustered defects – and those on the surface of microvoids, leading to an asymmetric non-gaussian tail in the distribution of atomic displacements. An examination of the effect of anharmonicity on the MSD at high temperatures using direct ab initio molecular-dynamics simulations (without the harmonic approximation) suggests that the vibrational motion in a-Si is practically unaffected by anharmonic effects at temperatures below 400 K, as far as the present DFT calculations are concerned. The Debye temperature of a-Si is found to be in the range of 488–541 K from specific-heat and MSD calculations using first-principles lattice-dynamical calculations in the harmonic approximation, which matches closely with the experimental value of 487–528 K obtained from specific-heat measurements of a-Si at low temperatures.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Capture of Iodine from Nuclear-Fuel-Reprocessing Off-Gas: Influence of Aging on a Reduced Silver Mordenite Adsorbent after Exposure to NO/NO 2

Iodine radioisotopes released during nuclear fuel reprocessing must be removed from the off-gas stream before discharge. One promising material for iodine capture is reduced silver mordenite (Ag 0 Z). Nevertheless, the adsorbent’s capacity will degrade, or age, over time when the material is exposed to other off-gas constituents. Though the overall impact of aging is known, the underlying physical and chemical processes are not. To examine these processes, Ag 0 Z samples were prepared and aged in 2% NO 2 in dry air and in 1% NO in N 2 gas streams at 150 °C for up to six months. Aged samples were then characterized using scanning electron microscopy, X-ray diffraction, Raman spectroscopy, and X-ray absorption spectroscopy. These techniques show that aging involves two overarching processes: (i) oxidation of the silver nanoparticles present in Ag 0 Z and (ii) migration of oxidized silver into the mordenite’s inner network. Silver on the nanoparticle’s surface is oxidized through adsorption of O 2 , NO, and NO 2 . Additionally, Raman spectroscopy and X-ray absorption spectroscopy indicate that nitrates are the primary products of this adsorption. Most of these nitrates migrate into the interior of the mordenite and exchange at framework binding sites, returning silver to its unreduced state (AgZ). The remaining nitrates exist at a persistent concentration without aggregating into bulk-phase AgNO 3 . X-ray absorption spectroscopy results further indicate that iodine adsorption occurs on not just Ag 0 Z but also on AgZ and a portion of the nitrates in the system. AgZ adsorbs a sizable quantity of iodine early in the aging process, but its capacity drops rapidly over time. For well-aged samples, nitrates are responsible for up to 95% of mordenite’s iodine capacity. Overall, these results have enhanced our understanding of the aging process in silver mordenite and are expected to guide the development of superior adsorbents for the capture of radioactive iodine from reprocessing off-gas.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2025

Formation of U(VI) peroxide nanoclusters from cascade reactions with a persulfate radical initiator

Radiolysis of water in high radiation fields generates a variety of reactive oxygen species that influence the chemical behavior and complexation of hexavalent uranium. This study investigates the behavior of interaction of a uranyl cation (UO 2 2+ (VI)) with a series of free radicals that are formed in situ via activation of the free radical initiator persulphate (S 2 O 8 2− ), which releases both SO 4 ˙ − and ˙OH species in the solution. Electron Paramagnetic Resonance (EPR) and Raman spectroscopy were used to evaluate the presence of the hydroperoxyl radical (HO 2 ˙) and superoxide radicals (O 2 ˙ − ) that are formed within the solution through radical cascade reactions. In addition, a uranyl peroxide cluster solid (NaU 24 ) was crystallized and characterized using single crystal X-ray diffraction (SCXRD), vibrational spectroscopy, and EPR spectroscopy. The presence of the hydroperoxyl radical (HO 2 ˙) and superoxide radicals (O 2 ˙ − ) was also observed in the solid-state compound, but spectroscopic evidence suggests that it was associated with the Na + network and not the cluster itself. Density functional theory (DFT) calculations were also utilized to further confirm the radical species produced and determine the potential stabilization of radicals detected within the cluster and lattice.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2020

Multiprincipal Component P2-Na 0.6 (Ti 0.2 Mn 0.2 Co 0.2 Ni 0.2 Ru 0.2 )O 2 as a High-Rate Cathode for Sodium-Ion Batteries

Mixing transition metal cations in nearly equiatomic proportions in layered oxide cathode materials is a new strategy for improving the performances of Na-ion batteries. The mixing of cations not only offers entropic stabilization of the crystal structure but also benefits the diffusion of Na ions with tuned diffusion activation energy barriers. In light of this strategy, a high-rate Na 0.6 (Ti 0.2 Mn 0.2 Co 0.2 Ni 0.2 Ru 0.2 )O 2 cathode was designed, synthesized, and investigated, combining graph-based deep learning calculations and complementary experimental characterizations. This new cathode material delivers high discharge capacities of 164 mA g –1 at 0.1 C and 68 mAh g –1 at a very high rate of 86 C, demonstrating an outstanding high rate capability. Ex situ and operando synchrotron X-ray diffraction were used to reveal the detailed structural evolution of the cathode upon cycling. Using the climbing-image nudged elastic-band calculation and Ab initio molecular dynamics simulations, we show that the optimal transition metal composition enables a percolating network of low barrier pathways for fast, macroscopic Na diffusion, resulting in the observed high rate performance.

25 ENERGY STORAGE↗
DOE OSTI2022

Chemical crystallography by serial femtosecond X-ray diffraction

Abstract Inorganic–organic hybrid materials represent a large share of newly reported structures, owing to their simple synthetic routes and customizable properties 1 . This proliferation has led to a characterization bottleneck: many hybrid materials are obligate microcrystals with low symmetry and severe radiation sensitivity, interfering with the standard techniques of single-crystal X-ray diffraction 2,3 and electron microdiffraction 4–11 . Here we demonstrate small-molecule serial femtosecond X-ray crystallography (smSFX) for the determination of material crystal structures from microcrystals. We subjected microcrystalline suspensions to X-ray free-electron laser radiation 12,13 and obtained thousands of randomly oriented diffraction patterns. We determined unit cells by aggregating spot-finding results into high-resolution powder diffractograms. After indexing the sparse serial patterns by a graph theory approach 14 , the resulting datasets can be solved and refined using standard tools for single-crystal diffraction data 15–17 . We describe the ab initio structure solutions of mithrene (AgSePh) 18–20 , thiorene (AgSPh) and tethrene (AgTePh), of which the latter two were previously unknown structures. In thiorene, we identify a geometric change in the silver–silver bonding network that is linked to its divergent optoelectronic properties 20 . We demonstrate that smSFX can be applied as a general technique for structure determination of beam-sensitive microcrystalline materials at near-ambient temperature and pressure.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Grazing-incidence diffraction reveals cellulose and pectin organization in hydrated plant primary cell wall

Abstract The primary cell wall is highly hydrated in its native state, yet many structural studies have been conducted on dried samples. Here, we use grazing-incidence wide-angle X-ray scattering (GIWAXS) with a humidity chamber, which enhances scattering and the signal-to-noise ratio while keeping outer onion epidermal peels hydrated, to examine cell wall properties. GIWAXS of hydrated and dried onion reveals that the cellulose ( $$110/1\overline{1}0$$ 110 / 1 1 ¯ 0 ) lattice spacing decreases slightly upon drying, while the (200) lattice parameters are unchanged. Additionally, the ( $$110/1\overline{1}0$$ 110 / 1 1 ¯ 0 ) diffraction intensity increases relative to (200). Density functional theory models of hydrated and dry cellulose microfibrils corroborate changes in crystalline properties upon drying. GIWAXS also reveals a peak that we attribute to pectin chain aggregation. We speculate that dehydration perturbs the hydrogen bonding network within cellulose crystals and collapses the pectin network without affecting the lateral distribution of pectin chain aggregates.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Ultrafast perturbation of magnetic domains by optical pumping in a ferromagnetic multilayer

Ultrafast optical pumping of systems with spatially nonuniform magnetic textures is known to cause far-from-equilibrium spin transport effects, such as the broadening of domain-walls. Here, we study the dynamics of labyrinth domain networks in ferromagnetic CoFe/Ni multilayers subject to a femtosecond optical pump and find an ultrafast domain dilation by 6% within 1.6 ps. This surprising result is based on the unambiguous determination of a harmonically-related shift of ultrafast magnetic X-ray diffraction for the first- and third-order rings. Domain dilation is plausible from conservation of momentum arguments, whereby inelastic scattering from a hot, quasi-ballistic, radial current transfers momentum to the magnetic domains. Our results suggest a potentially rich variety of unexpected physical phenomena associated with far-from-equilibrium inelastic electron-magnon scattering processes in the presence of spin textures.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Iodine capture with mechanically robust heat-treated Ag-Al-Si-O xerogel sorbents

Silver-loaded heat-treated aluminosilicate xerogels (Ag-HTX) were evaluated as sorbents for iodine [I2(g)] capture. The heat treatment step was performed to help increase the mechanical integrity of the gels. The synthesized xerogels were characterized using powder X-ray diffraction, scanning electron microscopy, energy-dispersive X-ray spectroscopy, transmission electron microscopy, Brunauer-Emmett-Teller analysis, gravimetric iodine loading, nanoindentation, and dynamic mechanical analysis. The structural and chemical analyses of Ag-HTX showed uniform distribution of Ag throughout the gel network after Ag-exchange. After I2(g) capture, the AgI crystallites were observed in the sorbent verifying chemisorption as the iodine capture mechanism. Iodine loading of this xerogel was 0.43 g g-1 at 150°C over 1 d and 0.52 g g-1 at 22°C over 33 d. The specific surface area of Ag-HTX was 202 m2 g-1 and decreased to 87 m2 g-1 after iodine loading. The hardness of the heat-treated xerogel was 160 times higher than heat-treated aerogel of the same composition. The heat-treatment process increased the modulus value to 40.77 MPa from 6.99 MPa of as-made xerogel, demonstrating the need for this added step in the synthesis process. These results show that Ag-HTX is a promising sorbent for I2(g) capture with good loading capacity and mechanical stability.

xerogels, aerogels, iodine capture, hardness testi↗
DOE OSTI2022

Magnetic structure and spin dynamics of the quasi-two-dimensional antiferromagnet Zn-doped copper pyrovanadate

We report magnetic properties of the antiferromagnet Zn x Cu 2-x V 2 O 7 (ZnCVO) with x ≈ 0.06 have been thoroughly investigated on powder and single-crystal samples. The crystal structure determination using powder x-ray and neutron diffraction confirms that our ZnCVO samples are isostructural with β-Cu 2 V 2 O 7 (β-CVO) with a small deviation in the lattice parameters. Macroscopic magnetic property measurements also confirm the similarity between the two compounds. The Cu 2+ spins were found to align along the crystallographic c axis, antiparallel to their nearest neighbors connected by the leading exchange interaction J 1 . Spin dynamics reveals a typical symmetric spin-wave dispersion with strong interactions in the bc plane and weak interplane coupling. The exchange interaction analysis indicates that the spin network of ZnCVO is topologically consistent with the previous DFT prediction but the values of leading exchange interactions are contradictory. Furthermore, rather than the predicted 2D honeycomb structure, the spin network in ZnCVO could be better described by the anisotropic 2D spin network composed of J 1 , J 5 , and J 6 interactions, four bonds per one spin site, coupled by weak interplane interactions.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2025

Effect of rare earth size on network structure and glass forming ability in binary aluminum garnets

Rare earth aluminate glasses are potentially useful for optical, luminescence, and laser applications. As reluctant glass formers, these materials exhibit unconventional atomic structures. To better understand how their structures correlate with glass formation, we investigate two rare earth aluminum garnet melts, La 3 Al 5 O 12 (LAG) and Yb 3 Al 5 O 12 (YbAG), which represent the relative extremes of good and poor glass forming ability in rare earth aluminates. Structural models have been refined to high-energy X-ray diffraction data over 1340–2740 K. Both melts contain mixtures of AlO 4 , AlO 5 , and AlO 6 polyhedra, with larger fractions of [5] Al and [6] Al in YbAG. Extrapolation of the Al–O coordination distributions to the glass transition match closely with 27 Al nuclear magnetic resonance measurements of (La 1−z Y z ) 3 Al 5 O 12 glasses, z = 0 to 1. During cooling, the mean coordination numbers increase for La–O in LAG from 6.45(8) to 6.98(8) and for Yb–O in YbAG from 6.02(8) to 6.21(8). Linkedness among Al–O polyhedra at ∼2450 K is mostly corner-sharing, with 9% edge-sharing in LAG and 19% in YbAG. Among [4] Al units, both melts have 6% edge-sharing that convert to all corner-sharing upon cooling. Network connectivity is compared using a newly defined metric, K n , that is similar to the Q n distribution but that accounts for the edge-sharing and triply bonded oxygen present in these melts. The lower glass forming ability in YbAG as compared to LAG correlates with more edge-sharing, associated with the larger fractions of [5] Al and [6] Al, and lower connectivity among [4] Al units.

Wilke, Stephen K. [Materials Development, Inc., Ar↗
DOE OSTI2024

Dielectric and magnetic properties of microwave-absorbing FeAl x O y catalysts fabricated via solution combustion synthesis

Iron-based alumina (FeAl x O y ) nanocomposites are microwave-absorbers and catalysts, which makes them promising for emerging microwave-assisted thermocatalytic technologies. Solution combustion synthesis (SCS) has been used to synthesize FeAl x O y powders, and prior work has demonstrated that adjusting SCS parameters significantly changes phase composition and specific surface area of the products. However, it is unclear how synthesis parameters affect their microwave-absorbing properties, which are essential for optimizing microwave-assisted technologies. To address this challenge, in the present work, twelve different FeAl x O y products were synthesized at different combinations of the SCS parameters such as two fuels (citric acid and glycine), two heating modes (hotplate and muffle furnace), and three Fe:Al molar ratios (2:1, 1:1, 1:2). Dielectric and magnetic properties of the products were characterized using a network analyzer and a vibrating sample magnetometer. Based on the measured permittivity and permeability, penetration depth and reflection loss were calculated as a function of frequency and bed thickness. The products were heated by microwaves at 2.45 GHz and then examined with X-ray diffraction (XRD) analysis. For all products, the magnetic saturation was lower than for bulk iron oxides because of the small crystallite size and aluminum substitution. The use of glycine induced high dielectric losses and enabled fast microwave-heating rates compared to citric acid. Higher Fe:Al ratio also led to higher dielectric and magnetic losses. With glycine fuel, SCS in a furnace induced larger penetration depth and lower microwave absorption than SCS on a hotplate. The minimization of reflected power was more sensitive to the thickness of the product bed than to the frequency of the electromagnetic field. Post-heating XRD analysis revealed different phase transformations in the FeAl x O y powders depending on the SCS parameters. As a result, an FeAl x O y material, synthesized via incipient wetness impregnation, lacked magnetic losses and did not heat well as compared to the SCS products.

Combustion synthesis↗
DOE OSTI2020

Automatic Échelle Spectrograph Wavelength Calibration

Time-domain astronomy and the increasing number of exoplanet candidates call for reliable, robust, and automatic wavelength calibration. We present an algorithm for wavelength-calibrating échelle spectrographs that uses order-by-order extracted spectra and a list of laboratory wavelengths. Our approach is fully automatic and does not need the pixel locations of certain spectral features with which to anchor the wavelength solution, nor the true order number of each diffraction order. We use spectral features that are duplicated in adjacent orders to establish the scale-invariant component of the wavelength solution. We then match the central wavelengths of spectral features to laboratory wavelengths to establish the scale and higher-order components of the wavelength solution. We demonstrate our method on the four spectrographs of Las Cumbres Observatory’s Network of Robotic Échelle Spectrographs (NRES), on the High Accuracy Radial Velocity Planet Searcher (HARPS) spectrograph, and on synthetic data. We obtain a velocity-equivalent precision of ∼10 m s{sup −1} on NRES. We achieve ∼1 m s{sup −1} on HARPS, which agrees with the precision reported by the HARPS team. On synthetic data, we achieve the velocity precision set by Gaussian centroiding errors. Our algorithm likely holds for a wide range of spectrographs beyond the five presented here. We provide an open-source Python package, xwavecal, which outputs wavelength-calibrated spectra as well as the wavelengths of spectral features.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

Multi-objective surrogate-assisted calibration of CPFEM models using macroscopic response and in situ EBSD measurements of grain reorientation trajectories

Crystal plasticity finite element method (CPFEM) models are widely used to simulate the deformation behaviour of polycrystalline materials, but their calibration is often limited by their high computational cost and the non-convexity of the optimisation landscape. Here, this study develops a multi-objective surrogate-assisted calibration workflow that couples a multi-objective genetic algorithm (MOGA) with an adaptively trained deep neural network (DNN) surrogate model to efficiently identify CPFEM parameters from experimental data. The workflow is demonstrated on three crystal plasticity (CP) formulations of increasing complexity — Voce hardening (VH), two-coefficient latent hardening (LH2), and six-coefficient latent hardening (LH6) — using in situ electron backscatter diffraction (EBSD) measurements of Alloy 617 under uniaxial tensile loading. The CPFEM models are calibrated against the experimentally observed stress–strain response and reorientation trajectories of eight grains, then validated against eight additional trajectories and overall texture evolution. Across the CP formulations, the macroscopic response was reproduced reliably, while differences emerged in the robustness and accuracy of the grain-scale predictions. Including grain reorientation trajectories in the multi-objective calibration improved texture evolution predictions and filtered out physically inconsistent parameter sets that can arise from calibrating against only the stress–strain data. The workflow also demonstrates good transferability of calibrated parameters from a low- to a high-fidelity microstructural model. These results provide practical guidance for integrating in situ microstructural data into CPFEM through efficient, repeatable, and physically meaningful multi-objective calibration.

Crystal plasticity finite element method↗
DOE OSTI2022

Silver-Loaded Xerogel Nanostructures for Iodine Capture: A Comparison of Thiolated versus Unthiolated Sorbents

Here this paper describes the development and provides comparisons of thiolated (-SH) and unthiolated Ag-Al-Si-O xerogels for iodine gas capture. These xerogels were produced from alkoxides and then heat-treated at 350 °C to provide mechanical strength for subsequent processing steps. Then, a portion of the xerogels was thiolated using (3-mercaptopropyl)trimethoxysilane. Next, thiolated and unthiolated batches were ion-exchanged in AgNO 3 solutions where Ag + replaced Na + in the gel network on a near 1:1 molar basis. Subsamples of the Ag-exchanged xerogels were subjected to a reduction step in H 2 /Ar to convert Ag + to Ag 0 where the rest of the Ag-exchanged (Ag + ) were not reduced. X-ray diffraction, X-ray photoelectron spectroscopy, and transmission electron microscopy revealed nanoscale Ag 0 in the Ag + samples despite no active reduction where actively reduced samples had bimodal Ag 0 distribution of ~2-3 nm hexagonal and ~6-7 nm cubic crystallites. Synchrotron X-ray absorption spectroscopy was used to assess the oxidization states of Ag, S, and I within the different xerogel samples. The specific surface areas of the base xerogels decreased as subsequent treatments were performed on the as-made samples, albeit the decreases were smaller than aerogel equivalents of these samples from a previous study. All iodine-loaded Ag-based samples showed a mixture of β-AgI and γ-AgI. Comparisons of iodine-loading results with other Ag-based iodine sorbents show that the thiolated Ag 0 -xerogels in this work have one of the highest iodine-loading capacities (q e ) reported to date in saturated conditions with the thiolated Ag 0 -xerogel showing 522 mg iodine per g of the sorbent.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗