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At least 1,099 records · Page 61
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Semimetallicity and electron-hole liquid in two-dimensional C and BN based compounds

Insulating-metallic transition mediated by substitutional atoms is predicted in a series of two-dimensional carbon-based structures. Introducing Si atoms in selected sites of tetrahexcarbon [Carbon 137 (2018) 266] according to rational chemical rules, metallicity by trivial band inversion without band gap opening is induced. Additional substitution of remaining C atoms by BN dimers introduces no changes in the metallic properties. A series of isomorphous two-dimensional materials with isoelectronic structures derived by exchanging group IV elements exhibiting various band gaps is obtained. Dynamical stability is verified with phonon analysis and beyond the harmonic approximation with molecular dynamics up to room temperature. The semi-metallic compounds have well-nested pockets of carriers and are good candidates for the formation of an excitonic insulator.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Structure, electronic and magnetic characterization, and calculated electronic structures of two oxyhalide hexagonal perovskites

Herein we report the crystal structures, initial magnetic and charge transport characterization, and calculated electronic structures of the hexagonal oxyhalide perovskites, Ba 7 Ru 4 O 15 Cl 2 and Ba 7 Ru 4 O 15 Br 2 . The experimental information is obtained through the study of single crystals. Face-sharing Ru O 6 octahedra form Ru 2 O 9 dimers in a layered triangular geometry in these materials; minor amounts of off-magnetic-site structural disorder are present in our crystals. Both are magnetically isotropic, with 2.5 μB/mol-Ru, Curie-Weiss theta –185 K, and 2.9 μB/mol-Ru, Curie-Weiss theta –168 K, respectively. Broad features in the magnetic susceptibility and heat capacity associated with magnetic ordering (at 35 and 37 K, respectively) are observed. The charge transport band gaps are 0.03 eV for the oxychloride and 0.006 eV for the oxybromide. There is no gap at the Fermi level for either of these compounds in density-functional theory electronic structure calculations.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Insulating band gaps both below and above the Néel temperature in d -electron LaTi O 3 , LaV O 3 , SrMn O 3 , and LaMn O 3 perovskites as a symmetry-breaking event

Metal d-electron oxides having an odd number of electrons per cell should exhibit band degeneracy at the Fermi energy, making them, in band theory, formally metallic. In many cases, however, these are “false metals”, as evidenced by the observation that many ABO 3 oxide perovskites with a magnetic 3d B-atom are observed to be insulators both below and above the Néel temperature. These inconsistencies between experimental observation and expectation have historically been resolved by invoking degeneracy-breaking physics, based largely on -pure electron effects, such as strong interelectronic correlation for d-electron compounds (the Mott mechanism). Such explanations generally consider microscopic lattice or magnetic degrees of freedom (m-DOF) as largely passive spectators, not a cause of the formally metallic being an insulator. Yet, it has long been known that ABO 3 perovskites can manifest an arrangement of m-DOFs in the form of octahedral tilting, bond dimerization, Jahn-Teller distortions, and ordering of local magnetic moments. It appears reasonable that such structural and magnetic local degrees of freedom need to be allowed to compete with purely electronic strong correlation. To answer this question, we explored a range of d-electron oxide perovskites exemplified by the archetypes LaTiO 3 , LaVO 3 , SrMnO 3 , and LaMnO 3 with 1, 2, 3, or 4 d -electrons, respectively. Using a mean-field-like electronic structure method (here, density functional theory), we find that a combination of magnetic symmetry breaking with structural distortions can account for insulating band gaps in this series while at the same time correctly predicting for the control case an intrinsic paramagnetic metal in SrVO 3 as symmetry-breaking is insufficiently strong to remove the degeneracy. Finally, this indicates that calculating quantitatively local magnetic and positional symmetry-breaking motifs in unit cells that avoid averaging at the outset over the low symmetry motifs can provide consistent trends in a Mott transition without Mott U.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Anisotropic magnetism of the Shastry-Sutherland lattice material BaNd 2 PtO 5

For this work, single crystals were grown and characterized to investigate the physical properties and magnetic ground state of BaNd 2 PtO 5 , a candidate to host physics of the Shastry-Sutherland model. Analysis of single crystal x-ray diffraction data yields an updated crystal structure, similar to the prior report but now in space group P4/mbm. Magnetization and specific heat measurements reveal an antiferromagnetic transition at T N =1.9K and a large magnetic anisotropy with in-plane magnetization much larger than out-of-plane magnetization. Single crystal neutron diffraction at zero field reveals a propagation vector of ($\frac{1}{2}$$\frac{1}{2}$$\frac{1}{2}$) for the magnetic ground state as compared to the ($\frac{1}{2}$$\frac{1}{2}$0) wave vector observed in the related body-centered material BaNd 2 ZnO 5 . The ground state is found to be a fully compensated antiferromagnet with diffraction data well fitted within the magnetic space group P S –1 (BNS setting #2.7). The ordered moment is mostly in the basal plane with nearest neighbors forming ferromagnetic dimers, however it also has a finite out-of-plane component unlike the related easy-plane materials BaNd 2 ZnO 5 and BaNd 2 ZnS 5 . Field-induced transitions are observed below T N when the field is applied within the basal plane, and in-plane anisotropy of the associated critical fields is observed. The magnetization is strongly impacted by misalignment of the field away from high symmetry directions. These results suggest complex magnetic structures may arise in the field-induced states, and they highlight the need for extreme care when studying this and related Shastry-Sutherland materials.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Enhancement of vibrationally assisted energy transfer by proximity to exceptional points, probed by fluorescence-detected vibrational spectroscopy

Emulation of energy transfer processes in natural systems on quantum platforms can further our understanding of complex dynamics in nature. One notable example is the demonstration of vibrationally assisted energy transfer (VAET) on a trapped-ion quantum emulator, which offers insights for the energetics of light harvesting. In this work, we expand the study of VAET simulation with trapped ions to a non-Hermitian quantum system comprising a 𝒫⁢𝑇-symmetric chromophore dimer weakly coupled to a vibrational mode. We first characterize exceptional points (EPs) and non-Hermitian features of the excitation energy transfer processes in the absence of the vibration, finding a degenerate pair of second-order EPs. Exploring the non-Hermitian dynamics of the whole system including vibrations, we find that energy transfer accompanied by absorption of phonons from a vibrational mode can be significantly enhanced near such a degenerate EP. Our calculations reveal a unique spectral feature accompanying the coalescing of eigenstates and eigenenergies that provides a unique approach to probe the degenerate EP by fluorescence-detected vibrational spectroscopy. Enhancement of the VAET process near the EP is found to be due to maximal favorability of phonon absorption at the degenerate EP, enabling multiple simultaneous excitations. Our work on improving VAET processes in non-Hermitian quantum systems paves the way for leveraging non-Hermiticity in quantum dynamics related to excitation energy transfer.

Non-Hermitian systems↗
DOE OSTI2025

Spin-strain interactions under hydrostatic pressure in α-RuCl 3

We investigate the effects of hydrostatic pressure on 𝛼−RuCl 3 , a prototypical material for the Kitaev spin model on a honeycomb lattice with a possible spin-liquid ground state. Using ultrasound measurements at pressures up to 1.16 GPa, we reveal significant modifications of the acoustic properties and the 𝐻−𝑇 phase diagram of this material. Hydrostatic pressure suppresses the three-dimensional magnetic order and induces a dimerization transition at higher pressures. At low pressures, the sound attenuation exhibits a linear temperature dependence, while above 0.28 GPa, it becomes nearly temperature independent, suggesting a shift in the phonon scattering regime dominated by Majorana fermions. These findings provide new insights into spin-strain interactions in Kitaev magnets and deliver a detailed characterization of the 𝐻−𝑇 phase diagram of 𝛼−RuCl 3 under hydrostatic pressure.

Focused ion beam↗
DOE OSTI2025

Topological phase diagram of generalized Su-Schrieffer-Heeger models with interactions

We investigate interacting Su-Schrieffer-Heeger (SSH) chains with two- and three-site unit cells using density matrix renormalization group (DMRG) simulations. By selecting appropriate filling fractions and sweeping across interaction strength 𝐽 𝑧 and dimerization 𝛿, we map out their phase diagrams and identify transition lines via entanglement entropy and magnetization measurements. In the two-site model, we observe the emergence of an interaction-induced antiferromagnetic intermediate phase between the topologically trivial and nontrivial regimes, as well as a critical region at negative 𝐽 𝑧 with suppressed magnetization and finite-size scaling of entanglement entropy. In contrast, the three-site model lacks an intermediate phase and exhibits asymmetric edge localization and antiferromagnetic ordering in both positive and negative 𝐽 𝑧 regimes. We further examine the response of edge states to Ising perturbations. In the two-site model, zero-energy edge modes are topologically protected and remain robust up to a finite interaction strength. However, in the three-site model, where the edge states reside at finite energy, this protection breaks down. Despite this, the edge-localized nature of these states survives in the form of polarized modes whose spatial profiles reflect the noninteracting limit.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

Seedling Chloroplast Responses Induced by N-Linolenoylethanolamine Require Intact G-Protein Complexes

In animals, several long-chain N-acylethanolamines (NAEs) have been identified as endocannabinoids and are autocrine signals that operate through cell surface G-protein coupled, cannabinoid receptors. Despite the occurrence of N-acylethanolamines in land plants, including non-vascular plants, their precise signaling properties and molecular targets are not well defined. Here we show that the activity of N-linolenoylethanolamine (NAE 18:3) requires an intact G-protein complex. Specifically, genetic ablation of the Gβγ dimer or loss of the full set of atypical Gα subunits strongly attenuates an NAE 18:3-induced de-greening of cotyledons in Arabidopsis seedlings. This effect involves, at least in part, transcriptional regulation of chlorophyll biosynthesis and catabolism genes. In addition, there is feedforward transcriptional control of G-protein signaling components and G-protein interactors. These results are consistent with NAE 18:3 being a lipid signaling molecule in plants with a requirement for G-proteins to mediate signal transduction, a situation similar, but not identical, to the action of NAE endocannabinoids in animal systems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Hydroxyl radical mediated damage of proteins in low oxygen solution investigated using X-ray footprinting mass spectrometry

In the method of X-ray footprinting mass spectrometry (XFMS), proteins at micromolar concentration in solution are irradiated with a broadband X-ray source, and the resulting hydroxyl radical modifications are characterized using liquid chromatography mass spectrometry to determine sites of solvent accessibility. These data are used to infer structural changes in proteins upon interaction with other proteins, folding, or ligand binding. XFMS is typically performed under aerobic conditions; dissolved molecular oxygen in solution is necessary in many, if not all, the hydroxyl radical modifications that are generally reported. In this study we investigated the result of X-ray induced modifications to three different proteins under aerobic versus low oxygen conditions, and correlated the extent of damage with dose calculations. We observed a concentration-dependent protecting effect at higher protein concentration for a given X-ray dose. For the typical doses used in XFMS experiments there was minimal X-ray induced aggregation and fragmentation, but for higher doses we observed formation of covalent higher molecular weight oligomers, as well as fragmentation, which was affected by the amount of dissolved oxygen in solution. The higher molecular weight products in the form of dimers, trimers, and tetramers were present in all sample preparations, and, upon X-ray irradiation, these oligomers became non-reducible as seen in SDS-PAGE. The results provide an important contribution to the large body of X-ray radiation damage literature in structural biology research, and will specifically help inform the future planning of XFMS, and well as X-ray crystallography and small-angle X-ray scattering experiments.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

The temperature-dependent conformational ensemble of SARS-CoV-2 main protease (M pro )

The COVID-19 pandemic, instigated by the SARS-CoV-2 coronavirus, continues to plague the globe. The SARS-CoV-2 main protease, or M pro , is a promising target for the development of novel antiviral therapeutics. Previous X-ray crystal structures of M pro were obtained at cryogenic temperature or room temperature only. Here we report a series of high-resolution crystal structures of unliganded M pro across multiple temperatures from cryogenic to physiological, and another at high humidity. We interrogate these data sets with parsimonious multiconformer models, multi-copy ensemble models, and isomorphous difference density maps. Our analysis reveals a perturbation-dependent conformational landscape for M pro , including a mobile zinc ion interleaved between the catalytic dyad, mercurial conformational heterogeneity at various sites including a key substrate-binding loop, and a far-reaching intramolecular network bridging the active site and dimer interface. Our results may inspire new strategies for antiviral drug development to aid preparation for future coronavirus pandemics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Application of sulfur SAD to small crystals with a large asymmetric unit and anomalous substructure

The application of sulfur single-wavelength anomalous dispersion (S-SAD) to determine the crystal structures of macromolecules can be challenging if the asymmetric unit is large, the crystals are small, the size of the anomalously scattering sulfur structure is large and the resolution at which the anomalous signals can be accurately measured is modest. Here, as a study of such a case, approaches to the SAD phasing of orthorhombic Ric-8A crystals are described. The structure of Ric-8A was published with only a brief description of the phasing process [Zeng et al. (2019), Structure , 27 , 1137–1141]. Here, alternative approaches to determining the 40-atom sulfur substructure of the 103 kDa Ric-8A dimer that composes the asymmetric unit are explored. At the data-collection wavelength of 1.77 Å measured at the Frontier micro-focusing Macromolecular Crystallography (FMX) beamline at National Synchrotron Light Source II, the sulfur anomalous signal strength, |Δ ano |/σΔ ano ( d ′′/sig), approaches 1.4 at 3.4 Å resolution. The highly redundant, 11 000 000-reflection data set measured from 18 crystals was segmented into isomorphous clusters using BLEND in the CCP 4 program suite. Data sets within clusters or sets of clusters were scaled and merged using AIMLESS from CCP 4 or, alternatively, the phenix.scale_and_merge tool from the Phenix suite. The latter proved to be the more effective in extracting anomalous signals. The HySS tool in Phenix , SHELXC / D and PRASA as implemented in the CRANK 2 program suite were each employed to determine the sulfur substructure. All of these approaches were effective, although HySS , as a component of the phenix.autosol tool, required data from all crystals to find the positions of the sulfur atoms. Critical contributors in this case study to successful phase determination by SAD included (i) the high-flux FMX beamline, featuring helical-mode data collection and a helium-filled beam path, (ii) as recognized by many authors, a very highly redundant, multiple-crystal data set and (iii) the inclusion within that data set of data from crystals that were scanned over large ω ranges, yielding highly isomorphous and highly redundant intensity measurements.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Bacterial and fungal growth on fungal necromass and its diverse components: Shared profiles and divergent constraints revealed by high‐throughput phenotyping

1. While fungal necromass is increasingly recognized as a major source of persistent carbon (C) in soils, the relative functional roles of bacteria and fungi in decomposing necromass are not fully resolved, and the processes that select for necromass decomposer communities from the broader soil microbial community are an emerging area of interest. 2. In this study, we characterized the growth of 52 bacterial and 83 fungal strains isolated from necromass and soil on 22 C substrates, including different necromass phenotypes, fungal cell wall polymers, dimers and monomers. 3. We found that the isolation habitat of the strains used in this experiment (necromass vs. soil) had no effect on the substrates they were able to use. Isolates from both microbial domains were able to grow on different labile carbon substrates, polymers and necromass phenotypes. However, fungal growth was most limited by necromass melanin content, while bacterial growth was more limited by the abundance of cell wall polysaccharides. Additionally, overall differences in substrate use between bacteria and fungi were most pronounced on polymer substrates. 4. Collectively, our results suggest that there is substantial functional overlap in necromass substrate use across microbial domains, but some notable differences in bacterial and fungal utilization of cell wall polymers, which can function as a direct energy source or a means of accessing other compounds within necromass. Future studies assessing bacteria and fungi decomposing necromass together rather than in isolation will help to uncover potential physical and chemical interactions within and between these two domains during the decay of this important source of persistent soil C.

dead fungal biomass↗
DOE OSTI2020

The Potential of Low Molecular Weight Heparin to Mitigate Cytokine Storm in Severe COVID‐19 Patients: A Retrospective Cohort Study

On March 11, 2020, the World Health Organization declared its assessment of coronavirus disease 2019 (COVID‐19) as a global pandemic. However, specific anti‐severe acute respiratory syndrome‐coronavirus 2 (SARS‐CoV‐2) drugs are still under development, and patients are managed by multiple complementary treatments. We performed a retrospective analysis to compare and evaluate the effect of low molecular weight heparin (LMWH) treatment on disease progression. For this purpose, the clinical records and laboratory indicators were extracted from electronic medical records of 42 patients with COVID‐19 (21 of whom were treated with LMWH, and 21 without LMWH) hospitalized (Union Hospital of Huazhong University of Science and Technology) from February 1 to March 15, 2020. Changes in the percentage of lymphocytes before and after LMWH treatment were significantly different from those in the control group ( P = 0.011). Likewise, changes in the levels of D‐dimer and fibrinogen degradation products in the LMWH group before and after treatment were significantly different from those in the control group ( P = 0.035). Remarkably, IL‐6 levels were significantly reduced after LMWH treatment ( P = 0.006), indicating that, besides other beneficial properties, LMWH may exert an anti‐inflammatory effect and attenuate in part the “cytokine storm” induced by the virus. Our results support the use of LMWH as a potential therapeutic drug for the treatment of COVID‐19, paving the way for a subsequent well‐controlled clinical study.

Shi, Chen↗
DOE OSTI2023

Structural insights into hydrolytic defluorination of difluoroacetate by microbial fluoroacetate dehalogenases

Fluorine forms the strongest single bond to carbon with the highest bond dissociation energy among natural products. However, fluoroacetate dehalogenases (FADs) have been shown to hydrolyze this bond in fluoroacetate under mild reaction conditions. Furthermore, two recent studies demonstrated that the FAD RPA1163 fromRhodopseudomonas palustriscan also accept bulkier substrates. In this study, we explored the substrate promiscuity of microbial FADs and their ability to defluorinate polyfluorinated organic acids. Enzymatic screening of eight purified dehalogenases with reported fluoroacetate defluorination activity revealed significant hydrolytic activity against difluoroacetate in three proteins. Product analysis using liquid chromatography‐mass spectrometry identified glyoxylic acid as the final product of enzymatic DFA defluorination. The crystal structures of DAR3835 fromDechloromonas aromaticaand NOS0089 fromNostocsp. were determined in the apo‐state along with the DAR3835 H274N glycolyl intermediate. Structure‐based site‐directed mutagenesis of DAR3835 demonstrated a key role for the catalytic triad and other active site residues in the defluorination of both fluoroacetate and difluoroacetate. Computational analysis of the dimer structures of DAR3835, NOS0089, and RPA1163 indicated the presence of one substrate access tunnel in each protomer. Moreover, protein‐ligand docking simulations suggested similar catalytic mechanisms for the defluorination of both fluoroacetate and difluoroacetate, with difluoroacetate being defluorinated via two consecutive defluorination reactions producing glyoxylate as the final product. Thus, our findings provide molecular insights into substrate promiscuity and catalytic mechanism of FADs, which are promising biocatalysts for applications in synthetic chemistry and bioremediation of fluorochemicals.

Biochemistry & Molecular Biology↗
DOE OSTI2020

Structure and stability of alkali gallates structurally reminiscent of hollandite

Abstract Single crystals of CsGa 7 O 11 , RbGa 7 O 11 , and RbGa 4 In 5 O 14 were grown from alkali halide melts and their structures were characterized by single crystal and powder X‐ray diffraction. CsGa 7 O 11 and RbGa 7 O 11 adopt the same structure type, reminiscent of the hollandite structure type, as it contains nearly rectangular channels made up of two dimers of edge‐sharing GaO 6 octahedra, and two corner‐sharing octahedron/tetrahedron pairs. The structure of RbGa 4 In 5 O 14 is more complex and is comprised of indium octahedra, gallium trigonal bipyramids, and gallium tetrahedra, and contains similar sized tunnels as CsGa 7 O 11 and RbGa 7 O 11 . CsGa 7 O 11 and RbGa 4 In 5 O 14 were further characterized by TGA, ion exchange experiments, and DFT studies revealing that both structures are thermodynamically stable up to 850°C; however, CsGa 7 O 11 decomposes to GaO(OH) xH 2 O when heated in warm aqueous solutions. CsGa 7 O 11 undergoes ion exchange in both an aqueous solution of RbCl and a RbNO 3 melt, as predicted by DFT studies, where the ion exchange is more extensive in the RbNO 3 melt.

Juillerat, Christian A.↗
DOE OSTI2022

Hole in one: Pathways to deterministic single-acceptor incorporation in Si(100)-2 x 1

We report that stochastic incorporation kinetics can be a limiting factor in the scalability of semiconductor fabrication technologies using atomic-precision techniques. While these technologies have recently been extended from donors to acceptors, the extent to which kinetics will impact single-acceptor incorporation has yet to be assessed. To identify the precursor molecule and dosing conditions that are promising for deterministic incorporation, we develop and apply an atomistic model for the single-acceptor incorporation rates of several recently demonstrated molecules: diborane (B 2 H 6 ), boron trichloride (BCl 3 ), and aluminum trichloride in both monomer (AlCl 3 ) and dimer forms (Al 2 Cl 6 ). While all three precursors can realize single-acceptor incorporation, we predict that diborane is unlikely to realize deterministic incorporation, boron trichloride can realize deterministic incorporation with modest heating (50 °C), and aluminum trichloride can realize deterministic incorporation at room temperature. We conclude that both boron and aluminum trichloride are promising precursors for atomic-precision single-acceptor applications, with the potential to enable the reliable production of large arrays of single-atom quantum devices.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

A new approach to removing H atoms in hydrogen depassivation lithography

Hydrogen deppasivation lithography (HDL) carried out by a scanning tunneling microscope (STM) is used to make patterns of Si dimers on a hydrogen passivated silicon surface. In this paper we discuss a new STM mode of operation that is highly suitable for removing single H atoms from the surface. This is made possible by changes we have made to the STM feedback control system that allows the STM to remove hydrogen atoms without switching the operational mode from imaging to lithography. Employing this method can potentially reduce the chance of tip-sample crash and increase the lithography precision.

Moheimani, S. O. Reza↗
DOE OSTI2021

Structural basis for heme-dependent NCoR binding to the transcriptional repressor REV-ERBβ

Heme is the endogenous ligand for the constitutively repressive REV-ERB nuclear receptors, REV-ERBα (NR1D1) and REV-ERBβ (NR1D2), but how heme regulates REV-ERB activity remains unclear. Cellular studies indicate that heme is required for the REV-ERBs to bind the corepressor NCoR and repress transcription. However, fluorescence-based biochemical assays suggest that heme displaces NCoR; here, we show that this is due to a heme-dependent artifact. Using ITC and NMR spectroscopy, we show that heme binding remodels the thermodynamic interaction profile of NCoR receptor interaction domain (RID) binding to REV-ERBβ ligand-binding domain (LBD). We solved two crystal structures of REV-ERBβ LBD cobound to heme and NCoR peptides, revealing the heme-dependent NCoR binding mode. ITC and chemical cross-linking mass spectrometry reveals a 2:1 LBD:RID stoichiometry, consistent with cellular studies showing that NCoR-dependent repression of REV-ERB transcription occurs on dimeric DNA response elements. Our findings should facilitate renewed progress toward understanding heme-dependent REV-ERB activity.

59 BASIC BIOLOGICAL SCIENCES↗