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At least 559 records · Page 31
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Mott insulators in moiré transition metal dichalcogenides at fractional fillings: Slave-rotor mean-field theory

In this study, we study a slave-rotor mean-field theory of an extended Hubbard model, applicable to transition metal dichalcogenide moiré systems, that captures both the formation of Wigner crystals as well as exotic spin states on top of these charge backgrounds. Phase diagrams are mapped out for different choices of long-range Coulomb repulsion strength, reproducing several experimentally found Wigner crystal states. Assuming unbroken time-reversal symmetry, we find several spin-liquid states as well as dimer states at fractional fillings. While spin dimer states are always found to have the lowest mean-field energy, several spin-liquid states are energetically competitive and may be stabilized by including gauge fluctuations or further interaction terms. We further discuss possible experimental signatures of these states pertinent to two-dimensional moiré heterostructures.

Charge order↗
DOE OSTI2023

Suppressed superexchange interactions in the cuprates by bond-stretching oxygen phonons

We study a multiorbital Hubbard–Su-Schrieffer-Heeger model for the one-dimensional (1D) corner-shared cuprates in the adiabatic and nonadiabatic limits using exact diagonalization and determinant quantum Monte Carlo. At half filling and in the adiabatic limit, lattice dimerization can be achieved only over a narrow range of couplings slightly below a critical coupling g c . Beyond this value, the sign of the effective hopping changes, and the lattice becomes unstable. Strong lattice fluctuations replace the dimerization state in the nonadiabatic case. We also examine the model's temperature-dependent uniform and dynamical magnetic susceptibilities and compare them to the results of an effective spin-1/2 Heisenberg model. In doing so, we demonstrate that lattice fluctuations induced by the e-ph interaction suppress the effective superexchange interaction when g < g c . Furthermore, our results elucidate the effect of bond-stretching phonons in the parent cuprate compounds in general and are particularly relevant to 1D cuprates, where strong e-ph interactions have recently been inferred.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Classical dynamics of the antiferromagnetic Heisenberg spin ladder

We employ a classical limit grounded in SU(4) coherent states to investigate the temperature-dependent dynamical spin structure factor of the S = 1/2 ladder consisting of weakly coupled dimers. By comparing the outcomes of this classical approximation with density matrix renormalization group and exact diagonalization calculations in finite size ladders, we demonstrate that the classical dynamics offers an accurate approximation across the entire temperature range when the interdimer coupling is weak and a good approximation in the high temperature regime even when the interdimer coupling is strong. This agreement is achieved after appropriately rescaling the temperature axis and renormalizing expectation values to satisfy a quantum sum rule. Here, we anticipate the method will be particularly effective when applied to 2D and 3D lattices composed of weakly-coupled dimers, situations that remain challenging for alternative numerical methods.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

Impurity effects on local electronic structure of twisted bilayer cuprates

It has been recently proposed that a fully gapped d-wave superconducting phase emerges in twisted bilayer cuprates when twist angle is in the vicinity of 45°. By considering a twisted bilayer model with a moiré cell, we study the local electronic structure around a single-site impurity and impurity dimer in both topologically trivial and nontrivial superconducting states. Here we find that the topological nontrivial superconducting phase is robust against single scalar-potential impurity scattering but is very sensitive to the interlayer impurity dimer scattering, which avoids and enforces the creation of the subgap quasiparticle state. This behavior is intrinsic to the bilayer structure and topological nature, in contrast to the other types of impurities that inevitably bring subgap quasiparticle states. We expect that our results can contribute to the understanding of electronic properties of twisted bilayer cuprates systems.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2025

High-pressure structural behavior of silicon telluride Si2Te3 nanoplates

The high-pressure behavior of silicon telluride (Si2Te3), a two-dimensional (2D) layered material, was investigated using synchrotron x-ray powder diffraction in a diamond anvil cell to 11.5GPa coupled with first-principles theory. Si2Te3 undergoes a phase transition at <1GPa from a trigonal to a hexagonal crystal structure. At higher pressures (>8.5GPa), x-ray diffraction showed the appearance of new peaks possibly coincident with a new phase transition, though we suspect Si2Te3 retains a hexagonal structure. Density functional theory calculations of the band structure reveal metallization above 9.1GPa consistent with previous measurements of the Raman spectra and disappearance of color and transparency at pressure. The theoretical Raman spectra reproduce the prominent features of the experiment, though a deeper analysis suggests that the orientation of Si dimers dramatically influences the vibrational response. Given the complex structure of Si2Te3, simulation of the resulting high-pressure phase is complicated by disordered vacancies and the initial orientations of Si–Si dimers in the crushed layered phase.

Li, Bohan↗
DOE OSTI2021

Effective interactions between nuclear clusters

In this work, the effective interactions between two nuclear clusters, d + d, t + t, and α + α, are investigated within a cluster model using local nucleon-nucleon (NN) forces. It is shown that the interaction in the spin-aligned d + d system is repulsive for all intercluster distances, whereas the α + α and spin-aligned t + t systems are attractive at intermediate distances. The Pauli blocking between identical-nucleon pairs is responsible for the cluster-cluster repulsion and becomes dominant in the shallow binding limit. We demonstrate that two d clusters could be bound if the NN force has nonzero range and is strong enough to form a deeply bound d cluster, or if the NN force has both even-parity and odd-parity attraction. Effective dimer-dimer interactions for general quantum systems of two-component fermions are also discussed in heavy-light mass limit, where one component is much heavier than the other, and their relation to intercluster interactions in nuclear systems are discussed. Our findings provide a conceptual foundation for conclusions obtained numerically in the literature, that increasing the range or strength of the local part of the attractive nucleon-nucleon interaction results in a more attractive cluster-cluster interaction.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2020

Lifetime of Almost Strong Edge-Mode Operators in One-Dimensional, Interacting, Symmetry Protected Topological Phases

Almost strong edge-mode operators arising at the boundaries of certain interacting one-dimensional symmetry protected topological phases with Z 2 symmetry have infinite temperature lifetimes that are nonperturbatively long in the integrability breaking terms, making them promising as bits for quantum information processing. We extract the lifetime of these edge-mode operators for small system sizes as well as in the thermodynamic limit. For the latter, a Lanczos scheme is employed to map the operator dynamics to a one-dimensional tight-binding model of a single particle in Krylov space. We suggest this model to be that of a spatially inhomogeneous Su-Schrieffer-Heeger model with a hopping amplitude that increases away from the boundary, and a dimerization that decreases away from the boundary. We associate this dimerized or staggered structure with the existence of the almost strong mode. Thus, the short time dynamics of the almost strong mode is that of the edge mode of the Su-Schrieffer-Heeger model, while the long time dynamics involves decay due to tunneling out of that mode, followed by chaotic operator spreading. Furthermore, we show that competing scattering processes can lead to interference effects that can significantly enhance the lifetime.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

Atomistic Mechanism Underlying the Si ( 111 ) - ( 7 × 7 ) Surface Reconstruction Revealed by Artificial Neural-Network Potential

The 7×7 reconstruction of the Si(111) surface represents arguably the most fascinating surface reconstruction so far observed in nature. Yet, the atomistic mechanism underpinning its formation remains unclear after it was discovered sixty years ago. Experimentally, it is observed post priori so that analysis of its formation mechanism can only be carried out in analogy with archaeology. Theoretically, density-functional theory (DFT) correctly predicts the Si(111)-(7×7) ground state but is impractical to simulate its formation process; while empirical potentials failed to produce it as the ground state. Developing an artificial neural-network potential of DFT quality, we carried out accurate large-scale simulations to unravel the formation of the Si(111)-(7×7) surface. We reveal a possible step-mediated atom-pop rate-limiting process that triggers massive nonconserved atomic rearrangements, most remarkably, a critical process of collective vacancy diffusion that mediates a sequence of selective dimer, corner-hole, stacking-fault, and dimer-line pattern formation, to fulfill the 7×7 reconstruction. Our findings may not only solve the long-standing mystery of this famous surface reconstruction but they also illustrate the power of machine learning in studying complex structures.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Dual Orbital Degeneracy Lifting in a Strongly Correlated Electron System

The local structure of NaTiSi 2 O 6 is examined across its Ti-dimerization orbital-assisted Peierls transition at 210 K. An atomic pair distribution function approach evidences local symmetry breaking preexisting far above the transition. The analysis unravels that, on warming, the dimers evolve into a short range orbital degeneracy lifted (ODL) state of dual orbital character, persisting up to at least 490 K. The ODL state is correlated over the length scale spanning ~ 6 sites of the Ti zigzag chains. Results imply that the ODL phenomenology extends to strongly correlated electron systems.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2025

Exploring a New Regime of Molecular Orbital Physics in 4⁢d Cluster Magnets with Resonant Inelastic X-Ray Scattering

Molecular orbital systems with clusters of heavy transition metal (TM) ions are one of the most important classes of model materials for studying the interplay between local physics and effects of itinerancy. Despite a large number of candidates identified in the family of 4⁢d TM materials, an understanding of their physics from competing microscopic energy scales is still missing. Here, we bridge this gap by reporting the first resonant inelastic x-ray scattering (RIXS) measurement on a well-known series of Ru cluster magnets with a 6⁢H-perovskite structure Ba 3 ⁢M⁢Ru 2 ⁢O 9 (M 3+ = In 3+ , Y 3+ , La 3+ ) comprised of Ru dimers. In addition to providing a microscopic explanation for their anomalous magnetic properties, our RIXS measurements combined with theoretical modeling uncover a new regime of molecular orbital physics where the combined effect of large hopping and small spin-orbit coupling results in highly fragile electronic states in the Ru-dimer compounds directly manifested as an abrupt change in the RIXS spectrum accompanying a tiny change in the local structure tuned by the M-site ion. This unique combination of energy scales found only in the 4⁢d but not the 5⁢d cluster magnets highlights the value of these materials as a new platform for studying quantum phase transition involving molecular orbitals.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Multistability of isolated and hydrogenated Ga–O divacancies in β–Ga 2 O 3

This work systematically explores 19 unique configurations of the close-associate Ga–O divacancies (V Ga V O ) in β–Ga 2 O 3 , including their complexes with H impurities, using hybrid functional calculations. Interestingly, most configurations are found to retain the negative-U behavior of V O , as they exhibit a thermodynamic (–/3–) charge-state transition level energetically located in the upper part of the band gap, where the 3– charge state is associated with the formation of a Ga–Ga dimer. The energy positions of the thermodynamic (–/3–) charge-state transition levels divide the divacancy configurations into three different groups, which can be understood from the three possible Ga–Ga dimerizations resulting from the tetrahedral and octahedral Ga sites. The relative formation energies of the different divacancy configurations, and hence the electrical activity of the divacancies, is found to depend on the Fermi-level position, and the energy barriers for transformation between different divacancy configurations are explored from nudged elastic band calculations. Hydrogenation of the divacancies is found to either passivate their negative-U charge-state transition levels or shift them down in Fermi level position, depending on whether the H resides at V O or forms an O–H bond at V Ga , respectively. Finally, the divacancy is discussed as a potential origin of the so-called E$^{*}_{2}$ center previously observed by deep-level transient spectroscopy.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Synthesis and magnetic properties of the Shastry-Sutherland family R 2 Be 2 SiO 7 ( R = Nd , Sm , Gd-Yb )

Compounds forming the quasi-two-dimensional Shastry-Sutherland lattice (SSL) have attracted significant experimental and theoretical attention in the field of frustrated magnetism. This is primarily due to their realization of an exactly soluble J 1 –J 2 orthogonal dimer model capable of hosting magnetic order, dimer singlet, and plaquette singlet phases in zero applied field and their complex magnetic phase diagrams with fractional magnetization plateaus and possible superfluid and supersolid phases found between the plateau states. The discovery and characterization of SSL compounds based on rare-earth magnetic ions provide a direct route to study the stability and properties of these exotic magnetic phases in systems with a variety of different magnetic anisotropies. In this paper, we discuss the synthesis and magnetic characterization of polycrystalline samples of the R 2 ⁢Be 2 ⁢SiO 7 family, where R=Nd, Sm, and Gd-Yb. All family members crystallize in the space group $P\bar{⁢4}⁢2_1⁢m$ (113) and show no signs of long-range magnetic order above 2 K, except for R=Tb which orders antiferromagnetically at 2.6 K.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Cryo-EM visualization of DNA-PKcs structural intermediates in NHEJ

DNA double-strand breaks (DSBs), one of the most cytotoxic forms of DNA damage, can be repaired by the tightly regulated nonhomologous end joining (NHEJ) machinery (Stinson and Loparo and Zhao et al.). Core NHEJ factors form an initial long-range (LR) synaptic complex that transitions into a DNA-PKcs (DNA-dependent protein kinase, catalytic subunit)–free, short-range state to align the DSB ends (Chen et al.). Using single-particle cryo–electron microscopy, we have visualized three additional key NHEJ complexes representing different transition states, with DNA-PKcs adopting distinct dimeric conformations within each of them. Upon DNA-PKcs autophosphorylation, the LR complex undergoes a substantial conformational change, with both Ku and DNA-PKcs rotating outward to promote DNA break exposure and DNA-PKcs dissociation. We also captured a dimeric state of catalytically inactive DNA-PKcs, which resembles structures of other PIKK (Phosphatidylinositol 3-kinase-related kinase) family kinases, revealing a model of the full regulatory cycle of DNA-PKcs during NHEJ.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Structural basis for ATG9A recruitment to the ULK1 complex in mitophagy initiation

The assembly of the autophagy initiation machinery nucleates autophagosome biogenesis, including in the PINK1- and Parkin-dependent mitophagy pathway implicated in Parkinson’s disease. The structural interaction between the sole transmembrane autophagy protein, autophagy-related protein 9A (ATG9A), and components of the Unc-51–like autophagy activating kinase (ULK1) complex is one of the major missing links needed to complete a structural map of autophagy initiation. We determined the 2.4-Å x-ray crystallographic structure of the ternary structure of ATG9A carboxyl-terminal tail bound to the ATG13:ATG101 Hop1/Rev7/Mad2 (HORMA) dimer, which is part of the ULK1 complex. We term the interacting portion of the extreme carboxyl-terminal part of the ATG9A tail the “HORMA dimer–interacting region” (HDIR). This structure shows that the HDIR binds to the HORMA domain of ATG101 by β sheet complementation such that the ATG9A tail resides in a deep cleft at the ATG13:ATG101 interface. Disruption of this complex in cells impairs damage-induced PINK1/Parkin mitophagy mediated by the cargo receptor NDP52.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Structural evidence for a dynamic metallocofactor during N 2 reduction by Mo-nitrogenase

The enzyme nitrogenase uses a suite of complex metallocofactors to reduce dinitrogen (N 2 ) to ammonia. Mechanistic details of this reaction remain sparse. We report a 1.83-angstrom crystal structure of the nitrogenase molybdenum-iron (MoFe) protein captured under physiological N 2 turnover conditions. This structure reveals asymmetric displacements of the cofactor belt sulfurs (S2B or S3A and S5A) with distinct dinitrogen species in the two αβ dimers of the protein. The sulfur-displaced sites are distinct in the ability of protein ligands to donate protons to the bound dinitrogen species, as well as the elongation of either the Mo–O5 (carboxyl) or Mo–O7 (hydroxyl) distance that switches the Mo-homocitrate ligation from bidentate to monodentate. These results highlight the dynamic nature of the cofactor during catalysis and provide evidence for participation of all belt-sulfur sites in this process.

Science & Technology - Other Topics↗
DOE OSTI2023

Stereoinversion via Alcohol Dehydrogenases Enables Complete Catabolism of β-1-Type Lignin-Derived Aromatic Isomers

Sphingobium sp. strain SYK-6 is an efficient aromatic catabolic bacterium that can consume all four stereoisomers of 1,2-diguaiacylpropane-1,3-diol (DGPD), which is a ring-opened β-1-type dimer. Recently, LdpA-mediated catabolism of erythro-DGPD was reported in SYK-6, but the catabolic pathway for threo-DGPD was as yet unknown. Here, in this study, we elucidated the catabolism of threo-DGPD, which proceeds through conversion to erythro-DGPD. When threo-DGPD was incubated with SYK-6, the Cα hydroxy groups of threo-DGPD (DGPD I and II) were initially oxidized to produce the Cα carbonyl form (DGPD-keto I and II). This initial oxidation step is catalyzed by Cα-dehydrogenases, which belong to the short-chain dehydrogenase/reductase (SDR) family and are involved in the catabolism of β-O-4-type dimers. Analysis of seven candidate genes revealed that NAD + -dependent LigD and LigL are mainly involved in the conversion of DGPD I and II, respectively. Next, we found that DGPD-keto I and II were reduced to erythro-DGPD (DGPD III and IV) in the presence of NADPH. Genes involved in this reduction were sought from Cα-dehydrogenase and ldpA-neighboring SDR genes. The gene products of SLG_12690 (ldpC) and SLG_12640 (ldpB) catalyzed the NADPH-dependent conversion of DGPD-keto I to DGPD III and DGPD-keto II to DGPD IV, respectively. Mutational analysis further indicated that ldpC and ldpB are predominantly involved in the reduction of DGPD-keto. Together, these results demonstrate that SYK-6 harbors a comprehensive catabolic enzyme system to utilize all four β-1-type stereoisomers through successive oxidation and reduction reactions of the Cα hydroxy group of threo-DGPD with a net stereoinversion using multiple dehydrogenases.

09 BIOMASS FUELS↗
DOE OSTI2025

Elucidation of a bacterial pathway for catabolism of the β–β-linked dilignol pinoresinol

Monolignol-derived dimers containing β–β linkages are synthesized by vascular plants and can be released during lignin depolymerization. In this work, we isolated a bacterium, Novosphingobium rhizosphaerae LY, that grows with the β–β lignan (+)-pinoresinol as a sole growth substrate. Sequence analysis suggested that this strain encodes a broad range of pathways for assimilation of aromatic monomers as well as one enzyme implicated in pinoresinol catabolism but lacks other known pathways for aromatic dimer catabolism. We constructed a genome-wide barcoded transposon library and identified genes required for pinoresinol catabolism. Using feeding studies, compound isolation, targeted synthesis, and analysis of purified enzymes, we elucidated the biochemical intermediates and reaction pathway involved in pinoresinol catabolism. We demonstrated that the first enzymatic reaction is the reductive cleavage of a furan ring in (±)-pinoresinol with retention of configuration to yield lariciresinol. We additionally confirmed that the final pathway enzyme, PinU, is related to lignostilbene dioxygenases and oxidatively cleaves a diguaiacylbutadiene intermediate to yield vanillin and coniferaldehyde. Finally, based on the enzyme characterization, we demonstrated that the strain can grow with a second β–β lignan, (–)-syringaresinol, as a sole growth substrate. In combination, these results demonstrate a new biocatalytic route for transforming a widely occurring group of plant phenylpropanoid natural products.

Novosphingobium↗
DOE OSTI2022

Pseudomonas aeruginosa C-Terminal Processing Protease CtpA Assembles into a Hexameric Structure That Requires Activation by a Spiral-Shaped Lipoprotein-Binding Partner

Pseudomonas aeruginosa CtpA is a carboxyl-terminal processing protease that partners with the outer membrane lipoprotein LbcA to degrade at least five cell wall-associated proteins, four of which are cell wall hydrolases. This activity plays an important role in supporting P. aeruginosa virulence in a mouse model of acute pneumonia. However, almost nothing is known about the molecular mechanisms underlying CtpA and LbcA function. Here, we used structural analysis to show that CtpA alone assembles into an inactive hexamer comprising a trimer of dimers, which limits its substrate access and prevents nonspecific degradation. The adaptor protein LbcA is a right-handed open spiral with 11 tetratricopeptide repeats, which might wrap around a substrate to deliver it to CtpA for degradation. By structure-guided mutagenesis and functional assays, we also showed that the interfaces of the CtpA trimer of dimers and an N-terminal helix of LbcA are important for LbcA-mediated substrate degradation by CtpA both in vitro and in vivo. This work improves our understanding of the molecular mechanism of the LbcA-CtpA proteolytic system and reveals some striking differences from the arrangements found in some other bacterial CTPs.

structural biology↗