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At least 271 records · Page 15

Defect graph neural networks for materials discovery in high-temperature clean-energy applications

We present a graph neural network approach that fully automates the prediction of defect formation enthalpies for any crystallographic site from the ideal crystal structure, without the need to create defected atomic structure models as input. Here we used density functional theory reference data for vacancy defects in oxides, to train a defect graph neural network (dGNN) model that replaces the density functional theory supercell relaxations otherwise required for each symmetrically unique crystal site. Interfaced with thermodynamic calculations of reduction entropies and associated free energies, the dGNN model is applied to the screening of oxides in the Materials Project database, connecting the zero-kelvin defect enthalpies to high-temperature process conditions relevant for solar thermochemical hydrogen production and other energy applications. The dGNN approach is applicable to arbitrary structures with an accuracy limited principally by the amount and diversity of the training data, and it is generalizable to other defect types and advanced graph convolution architectures. In conclusion, it will help to tackle future materials discovery problems in clean energy and beyond.

97 MATHEMATICS AND COMPUTING↗

Defects in epitaxial Ru(0001) on Al2O3(0001): Dislocations, stacking faults, and deformation twins

In this study, defects in epitaxial Ru(0001) films on c-plane sapphire, with nominal thicknesses of 10–80 nm, deposited at 350 °C and step-annealed to 950 °C, were characterized using transmission electron microscopy. The variation of Ru and sapphire lattice parameters with temperature is such that the misfit strain for the observed 30° rotated-honeycomb epitaxial relationship is essentially constant with temperature at 1.5%, resulting in a biaxial stress of 10.0 GPa and an energy density of 150 MJ m –3 in unrelaxed films. Stress relaxation occurs by the formation of defects. For the 20–80 nm thick films, the defects are a- and c-type dislocations and stacking faults, argued to be of I 2 type. In addition, the films show the surprising presence of $\{11\bar{2}1\}1/3\langle11\bar{2}\bar{6}\rangle$ deformation twins. The 10 nm-thick films were found to be defect free. The critical thickness for misfit strain relaxation via the formation of threading and misfit dislocations is computed as 7±2 nm, depending on the choice of the dislocation core radius. Energetic analysis of twin formation, using both the infinite-matrix and the finite-matrix (Mori–Tanaka) approaches, provides values of the twin aspect ratios, assumed to be ellipsoidal, and shows that the latter but not the former approach can qualitatively explain the formation of the observed twins. In addition to providing the maximum strain relief compared to other potential twin types, $\{11\bar{2}1\}1/3\langle11\bar{2}\bar{6}\rangle$ twins do not require lattice shuffles and have a boundary that is a special boundary, namely, a 35° tilt boundary with a-type dislocations every other {0002} plane, that may also favor their formation.

36 MATERIALS SCIENCE↗

Understanding the phase transformation mechanisms that affect the dynamic response of Fe-based microstructures at the atomic scales

Large-scale molecular dynamics (MD) simulations were carried out to investigate the shock-induced evolution of microstructure in Fe-based systems comprising single-crystal and layered Cu/Fe alloys with a distribution of interfaces. The shock compression of pure single-crystal Fe oriented along [110] above a threshold pressure results in a BCC (α)→HCP (ε) phase transformation behavior that generates a distribution of ε phase variants in the phase transformed region of the microstructure behind the shock front. The propagation of the release wave through a phase transformed ε phase causes a reverse ε→α phase transformation and renders a distribution of twins for the [110] oriented Fe that serve as void nucleation sites during spall failure. The simulations reveal that the α→ε→α transformation-induced twinning for shock loading along the [110] direction is due to a dominant ε phase variant formed during compression that rotates on the arrival of the release wave followed by a reverse phase transformation to twins in the α phase. The modifications in the evolution of the ε phase variants and twins in Fe behavior are also studied for Cu–Fe layered microstructures due to the shock wave interactions with the Cu/Fe interfaces using a newly constructed Cu–Fe alloy potential. Here, the MD simulations suggest that interfaces affect the observed variants during shock compression and, hence, distributions of twins during shock release that affects the void nucleation stresses in the Fe phase of Cu/Fe microstructures.

36 MATERIALS SCIENCE↗

Quantitative measurements of density in shock-compressed silver up to 330 GPa using x-ray diffraction

This work presents a structural study of shock-compressed states in Ag to 331 GPa, accessed via laser shock compression. Structures of the resulting crystalline phases and the average atomic distribution of the liquid state are determined using in situ x-ray diffraction. We employ structure factor analysis, adapted for a non-monochromatic x-ray source, to determine the density of the liquid phase from analysis of x-ray diffraction data for the first time in shock compressed Ag. We also present a detailed analysis of the crystalline phases, which shows good agreement with the phase boundaries reported in previous experimental and theoretical works. We utilize the whole powder pattern fitting approach implemented in the MAUD package to constrain stacking faults in the face centered cubic structure. We observe the ambient fcc structure up to a stress of 146 GPa before a transition to a body-centered cubic structure and liquid phase at 179 GPa, with full melting above 212 GPa.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Proteome-scale Deployment of Protein Structure Prediction Workflows on the Summit Supercomputer

Deep learning has contributed to major advances in the prediction of protein structure from sequence, a fundamental problem in structural bioinformatics. With predictions now approaching the accuracy of crystallographic experiments, and with accelerators like GPUs and TPUs making inference using large models rapid, genome-level structure prediction becomes an obvious aim. Leadership-class computing resources can be used to perform genome-scale protein structure prediction using state-of-the-art deep learning models, providing a wealth of new data for systems biology applications. Here we describe our efforts to efficiently deploy the AlphaFold v.2 program, for full-proteome structure prediction, at scale on the Oak Ridge Leadership Computing Facility's resources, including the Summit supercomputer. We performed inference to produce the predicted structures for 40,526 protein sequences, corresponding to four prokaryotic proteomes and one plant proteome, using under 4,400 total Summit node hours, equivalent to using the majority of the supercomputer for a little over one hour. We also designed an optimized structure refinement that reduced the time for the relaxation stage of the AlphaFold pipeline by over 10X for longer sequences. We demonstrate the types of analyses that can be performed on proteome-scale collections of sequences, including a search for novel quaternary structures and implications for functional annotation.

Gao, Mu↗

Ab initio prediction of rapid kinetics of Fe impurities in δ -Pu

Here, we study the formation energies of iron impurities in δ-Pu within spin–orbital-polarized density functional theory (SOP-DFT). The thermodynamic solubility limit of iron in δ-Pu is calculated, indicating low miscibility. We show that surprisingly, Fe impurities at equilibrium are almost equally likely to occupy octahedral interstitial sites or substitutional sites, with slight preference for the former. In contrast, we find the energy of the tetrahedral interstitial Fe to be nearly 1 eV higher than the octahedral one. We explore the energy landscape for Fe impurity hopping diffusion and conclude that Fe impurities in δ-Pu are divided into two populations: (i) Immobile substitutional Fe impurities and (ii) highly mobile interstitial Fe impurities. The latter, (ii), migrate between octahedral interstitial sites with an energy barrier of around 0.2 eV. The energy barrier for exchange between the two populations is calculated to exceed 0.7 eV. Finally, we discuss the role of magnetic order on the impurity energetics.

Atomic structure↗

High-field superconducting halo in UTe 2

The heavy fermion material UTe 2 is a candidate topological superconductor that exhibits multiple magnetic field–induced superconducting phases. One such phase exists only at fields greater than 40 tesla, a considerable scale given its critical temperature of only 2 K. Here, in this work, we extend measurements of this state with fields outside of the bc crystallographic plane and reveal its core structure: The superconducting phase wraps around the b axis in a halo-like fashion and appears to be stabilized by a field component perpendicular to the magnetic easy axis. This angle dependence points to a multicomponent spin-triplet order parameter with a finite angular momentum of the Cooper pairs. The pairing mechanism remains enigmatic, and UTe 2 ’s specific magnetophilic superconducting tendencies seem incompatible with existing models for field-enhanced superconductivity.

Lewin, Sylvia K. [National Inst. of Standards and ↗

Temperature-dependent angle-resolved photoemission spectroscopy study of the Ce 4f states in a possible topological Kondo insulator CeRhAs

The electronic structure of a possible topological Kondo insulator of CeRhAs has been investigated by employing temperature (T)-dependent angle-resolved photoemission spectroscopy (ARPES). Fermi surfaces (FSs) and band structures are successfully measured for three orthogonal crystallographic planes. The measured Fermi-edge states are found to have a three-dimensional (3D) character, contradictory to the proposed topological surface states of the 2 D character. The measured FSs due to the Ce 4f electrons agree well with those from the density functional theory band structures unfolded into the reduced Ce-only unit cell. The theoretically predicted hourglass-type bulk bands along $\bar{X}\bar{S}\bar{X}$ are not clearly resolved, in spite of the evident existence of those band features. Finally, T -dependent ARPES measurements reveal that the coherent Ce 4f states, having two pseudogap structures of Δ 1 ~ 80 meV and Δ 2 ~ 30 meV, persist to remain above 200 K, in agreement with the high Kondo temperature of CeRhAs.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Evolution of magnetic field induced ordering in the layered quantum Heisenberg triangular-lattice antiferromagnet Ba 3 CoSb 2 O 9

Quantum fluctuations in the effective spin-12 layered triangular-lattice quantum Heisenberg antiferromagnet Ba 3 CoSb 2 O 9 lift the classical degeneracy of the antiferromagnetic ground state in magnetic field, producing a series of novel spin structures for magnetic fields applied within the crystallographic ab plane, including a celebrated collinear “up-up-down” spin ordering with magnetization equal to 1/3 of the saturation magnetization over an extended field range. Theoretically unresolved, however, are the effects of interlayer antiferromagnetic coupling and transverse magnetic fields on the ground states of this system. Additional magnetic field induced phase transitions are theoretically expected and in some cases have been experimentally observed, but details regarding their number, location, and physical character appear inconsistent with the predictions of existing models. Conversely, an absence of experimental measurements as a function of magnetic-field orientation has left other key predictions of these models untested. To address these issues, in this study we have used specific heat, neutron diffraction, thermal conductivity, and magnetic torque measurements to map out the phase diagram as a function of magnetic field intensity and orientation relative to the crystallographic ab plane. For H||ab, we have discovered an additional magnetic field induced phase transition at low temperature and an unexpected tetracritical point in the high-field phase diagram, which coupled with the apparent second-order nature of the phase transitions eliminates several theoretically proposed spin structures for the high-field phases. Our calorimetric measurements as a function of magnetic field orientation are in general agreement with theory for field-orientation angles close to plane parallel (H||a) but diverge at angles near plane perpendicular; a predicted convergence of two phase boundaries at finite angle and a corresponding change in the order of the field induced phase transition are not observed experimentally. Our results emphasize the role of interlayer coupling in selecting and stabilizing field induced phases, provide guidance on the nature of the magnetic order in each phase, and reveal the need for new physics to account for the nature of magnetic ordering in this archetypal two-dimensional spin-12 triangular-lattice quantum Heisenberg antiferromagnet.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Method for the Production of Nanometer Scale Step Height Reference Specimens

Methods are disclosed that provide for structures and techniques for the fabrication of ordered arrangements of crystallographically determined nanometer scale steps on single crystal substrates, particularly Sic. The ordered nanometer scale step structures are produced on the top surfaces of mesas by a combination of growth and etching processes. These structures sometimes referred to herein as artifacts are to enable step-height calibration, particularly suitable for scanning probe microscopes and profilometers, from less than one nanometer (nm) to greater than 10 nm, with substantially no atomic scale roughness of the plateaus on either side of each step.

Phillip B Abel↗

Atom Probe Tomography Analysis of Mica

Laser-assisted atom probe tomography (APT) is a relatively new, powerful technique for sub-nanometric mineral and biomineral analysis. However, the laser-assisted APT analysis of highly anisotropic and chemically diverse minerals, such as phyllosilicates, may prove especially challenging due to the complex interaction between the crystal structure and the laser pulse upon applying a high electric field. Micas are a representative group of nonswelling clay minerals of relevance to a number of scientific and technological fields. In this study, a Mg-rich biotite was analyzed by APT to generate preliminary data on nonisotropic minerals and to investigate the effect of the crystallographic orientation on mica chemical composition and structure estimation. Here, the difference in results obtained for specimens extracted from the (001) and ( hk 0) mica surfaces indicate the importance of both experimental parameters and the crystallography. Anisotropy of mica has a strong influence on the physicochemical properties of the mineral during field evaporation and the interpretation of APT data. The promising results obtained in the present study open the way to future innovative APT applications on mica and clay minerals and contribute to the general discussion on the challenges for the analysis of geomaterials by atom probe tomography.

3D reconstructions↗

Leveraging Polymorphism in YbCuBi to Map Transport and Elastic Properties

AMX Zintl compounds with the hexagonal ZrBeSi structure have gained significant attention for their remarkable vacancy tolerance and low thermal conductivity. Their 2D honeycomb sublattice, composed of M–X covalent bonds, is believed to contribute to high anharmonicity and unusual thermal transport properties. In this study, we explore the temperature-dependent polymorphism of YbCuBi as a model system to investigate the relationship between the structure and elastic and thermal transport properties in AMX Zintls. YbCuBi undergoes a structural transition from the “flat” Cu–Bi layers in the ZrBeSi structure to corrugated layers in the LiGaGe structure below 410 K, resulting in a distortion of its centrosymmetric structure. To probe the effects of this crystallographic transition, we employ inelastic neutron scattering and temperature-dependent resonant ultrasound spectroscopy. These experimental findings, coupled with first-principles calculations and thermal conductivity measurements, allow us to elucidate a direct relationship between corrugation of the honeycomb lattice and the observed changes in elastic and thermal transport properties. These insights can be extended to other Zintl phases with similar structure types, providing a platform for the rational design of functional materials with tailored thermal properties.

Chemical structure↗

Native lattice strain induced structural earthquake in sodium layered oxide cathodes

Abstract High-voltage operation is essential for the energy and power densities of battery cathode materials, but its stabilization remains a universal challenge. To date, the degradation origin has been mostly attributed to cycling-initiated structural deformation while the effect of native crystallographic defects induced during the sophisticated synthesis process has been significantly overlooked. Here, using in situ synchrotron X-ray probes and advanced transmission electron microscopy to probe the solid-state synthesis and charge/discharge process of sodium layered oxide cathodes, we reveal that quenching-induced native lattice strain plays an overwhelming role in the catastrophic capacity degradation of sodium layered cathodes, which runs counter to conventional perception—phase transition and cathode interfacial reactions. We observe that the spontaneous relaxation of native lattice strain is responsible for the structural earthquake (e.g., dislocation, stacking faults and fragmentation) of sodium layered cathodes during cycling, which is unexpectedly not regulated by the voltage window but is strongly coupled with charge/discharge temperature and rate. Our findings resolve the controversial understanding on the degradation origin of cathode materials and highlight the importance of eliminating intrinsic crystallographic defects to guarantee superior cycling stability at high voltages.

25 ENERGY STORAGE↗

Local lattice distortions and electronic orders in strongly correlated systems by resonant total x-ray scattering: A case study of A Pt 2 X 2 intermetallics ( A = U , Ce, or La and X = Si or Ge)

Revealing local lattice distortions in physical systems is nontrivial, largely because such structural features often are not necessarily amenable to traditional crystallographic investigations. This poses limits to our understanding of the underlying physic, particularly in the case of strongly correlated systems where structural, electronic and magnetic degrees of freedom are intertwined. Using resonant total x-ray scattering coupled to differential pair distribution function analysis, we reveal the presence of pronounced local lattice distortions in the square net Pt planes in the prototypical strongly correlated APt 2 X 2 intermetallics (A = U, Ce or La and X = Si or Ge). The distortions are present before charge density wave, magnetic, Kondo lattice coherence and/or superconducting orders emerge in these materials and, as density functional calculations suggest, are likely to affect them. Finally, our study sheds light on the poorly known interactions between electronic orders and structural disorder in strongly correlated systems and also demonstrates an advanced experimental approach to determine it that is relevant to any physical system showing deviations from perfect crystallinity.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Planar, curved and twisted molecular nanographenes: Reduction-induced alkali metal coordination

Planar and curved polycyclic aromatic hydrocarbons (PAHs) attract significant attention as molecular models of fullerenes, carbon nanotubes, and graphene, thus stimulating broad investigation of chemical reactivity and materials applications of designed nanocarbon π-systems. Non-planar molecular nanographenes (NGs) recently emerge as advanced anode materials in energy storage, showing high reduction limits and enhanced alkali metal intercalation levels. However, the lack of direct structure–property correlations in such complex hybrid systems impedes their further development and utilization. With a focus on alkali-metal-induced reduction of selected PAHs, we herein review original metal binding and intercalation trends, site specific coordination, and distinct carbon framework responses to stepwise electron uptake. Small planar graphene fragments, like triphenylene and coronene, are compared to π-expanded hexabenzocoronenes, followed by the discussion of bowl-shaped corannulene, sumanene and other carbon bowls, as well as bent, warped, and twisted molecular nanographenes. The effect of size, symmetry, and framework topology along with the structural deformation of carbon backbones upon reduction are analyzed, using recent crystallographic examples of alkali-metal intercalated products. In conclusion, the revealed insights into the structures, binding, and metal intercalation in molecular nanographenes should stimulate their future applications as new functional materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Dual factors required for cytochrome-P450-mediated hydrocarbon ring contraction in bacterial gibberellin phytohormone biosynthesis

Cytochromes P450 (CYPs) are heme-thiolate monooxygenases that prototypically catalyze the insertion of oxygen into unactivated C–H bonds but are capable of mediating more complex reactions. One of the most remarked-upon alternative reactions occurs during biosynthesis of the gibberellin A (GA) phytohormones, involving hydrocarbon ring contraction with coupled aldehyde extrusion of ent-kaurenoic acid to form the first gibberellin intermediate. While the unusual nature of this reaction has long been noted, its mechanistic basis has remained opaque. Building on identification of the relevant CYP114 from bacterial GA biosynthesis, detailed structure–function studies are reported here, including development of in vitro assays as well as crystallographic analyses both in the absence and presence of substrate. These structures provided insight into enzymatic catalysis of this unusual reaction, as exemplified by identification of a key role for the “missing” acid from an otherwise highly conserved acid–alcohol pair of residues. Notably, the results demonstrate that ring contraction requires dual factors, both the use of a dedicated ferredoxin and absence of the otherwise conserved acidic residue, with exclusion of either limiting turnover to just the initiating and more straightforward hydroxylation. The results provide detailed insight into the enzymatic structure–function relationships underlying this fascinating reaction and support the use of a semipinacol mechanism for the unusual ring contraction reaction.

59 BASIC BIOLOGICAL SCIENCES↗

Structure-property relationships in eutectic composites

The preparation of a composite material of eutectic composition directly from the molten state is investigated. The manufacture of eutectic composites by unidirectional solidification is reviewed, and it is shown how two-phase composite structures of given relative volume fraction can be produced with a range of particle sizes. Crystallographic relationships and the thermal stability of interfaces in controlled eutectic structures are examined, the mechanical behavior of aligned eutectic microstructures is discussed, and characteristics of eutectic composites having mechanical properties of engineering significance are evaluated. Specific properties of the Ni-Nb eutectic alloy are reviewed to demonstrate the effect of structure control (through directional solidification) on the mechanical response of a eutectic composite. It is noted that unidirectionally solidified eutectic composites possess highly aligned and thermally stable microstructures and also exhibit excellent combinations of strength and ductility to very high temperature levels.

Hertzberg, R. W.↗