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At least 1,351 records · Page 75
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Structural and biochemical insights into NEIL2’s preference for abasic sites

Cellular DNA is subject to damage from a multitude of sources and repair or bypass of sites of damage utilize an array of context or cell cycle dependent systems. The recognition and removal of oxidatively damaged bases is the task of DNA glycosylases from the base excision repair pathway utilizing two structural families that excise base lesions in a wide range of DNA contexts including duplex, single-stranded and bubble structures arising during transcription. The mammalian NEIL2 glycosylase of the Fpg/Nei family excises lesions from each of these DNA contexts favoring the latter two with a preference for oxidized cytosine products and abasic sites. We have determined the first liganded crystal structure of mammalian NEIL2 in complex with an abasic site analog containing DNA duplex at 2.08 Å resolution. Comparison to the unliganded structure revealed a large interdomain conformational shift upon binding the DNA substrate accompanied by local conformational changes in the C-terminal domain zinc finger and N-terminal domain void-filling loop necessary to position the enzyme on the DNA. The detailed biochemical analysis of NEIL2 with an array of oxidized base lesions indicates a significant preference for its lyase activity likely to be paramount when interpreting the biological consequences of variants.

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

Structures, activity and mechanism of the Type IIS restriction endonuclease PaqCI

Abstract Type IIS restriction endonucleases contain separate DNA recognition and catalytic domains and cleave their substrates at well-defined distances outside their target sequences. They are employed in biotechnology for a variety of purposes, including the creation of gene-targeting zinc finger and TAL effector nucleases and DNA synthesis applications such as Golden Gate assembly. The most thoroughly studied Type IIS enzyme, FokI, has been shown to require multimerization and engagement with multiple DNA targets for optimal cleavage activity; however, details of how it or similar enzymes forms a DNA-bound reaction complex have not been described at atomic resolution. Here we describe biochemical analyses of DNA cleavage by the Type IIS PaqCI restriction endonuclease and a series of molecular structures in the presence and absence of multiple bound DNA targets. The enzyme displays a similar tetrameric organization of target recognition domains in the absence or presence of bound substrate, with a significant repositioning of endonuclease domains in a trapped DNA-bound complex that is poised to deliver the first of a series of double-strand breaks. PaqCI and FokI share similar structural mechanisms of DNA cleavage, but considerable differences in their domain organization and quaternary architecture, facilitating comparisons between distinct Type IIS enzymes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Transporters and ascorbate–glutathione metabolism for differential cadmium accumulation and tolerance in two contrasting willow genotypes

Salix matsudana Koidz is a low cadmium (Cd)-accumulating willow, whereas its cultivated variety, Salix matsudana var. matsudana f. umbraculifera Rehd., is a high Cd-accumulating and tolerant willow (HCW). The physiological and molecular mechanisms underlying differential Cd accumulation and tolerance in the two Salix species are poorly understood. In this study, we confirmed that the differential Cd translocation capacity from roots to the shoots leads to the differential Cd accumulation in their aboveground parts between these two willow genotypes. Cadmium accumulation happens preferentially in the transport pathway, and Cd is mainly located in the vacuolar, cell wall and intercellular space in HCW bark by cadmium location analysis at tissue and subcellular levels. Comparative transcriptome analysis revealed that higher expressions of several metal transporter genes (ATP-binding cassette transporters, K + transporters/channels, yellow stripe-like proteins, zinc-regulated transporter/iron-regulated transporter-like proteins, etc.) are involved in root uptake and translocation capacity in HCW; meanwhile, ascorbate–glutathione metabolic pathways play essential roles in Cd detoxification and higher tolerance of the Cd-accumulator HCW. These results lay the foundation for further understanding the molecular mechanisms of Cd accumulation in woody plants and provide new insights into molecular-assisted-screening woody plant varieties for phytoremediation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Analysis of putative quadruplex-forming sequences in fungal genomes: novel antifungal targets?

Fungal infections cause >1 million deaths annually and the emergence of antifungal resistance has prompted the exploration for novel antifungal targets. Quadruplexes are four-stranded nucleic acid secondary structures, which can regulate processes such as transcription, translation, replication and recombination. They are also found in genes linked to virulence in microbes, and ligands that bind to quadruplexes can eliminate drug-resistant pathogens. Using a computational approach, we quantified putative quadruplex-forming sequences (PQS) in 1359 genomes across the fungal kingdom and explored their presence in genes related to virulence, drug resistance and biological processes associated with pathogenicity in Aspergillus fumigatus. Here we present the largest analysis of PQS in fungi and identify significant heterogeneity of these sequences throughout phyla, genera and species. PQS were genetically conserved in Aspergillus spp. and frequently pathogenic species appeared to contain fewer PQS than their lesser/non-pathogenic counterparts. GO-term analysis identified that PQS-containing genes were involved in processes linked with virulence such as zinc ion binding, the biosynthesis of secondary metabolites and regulation of transcription in A. fumigatus. Although the genome frequency of PQS was lower in A. fumigatus, PQS could be found enriched in genes involved in virulence, and genes upregulated during germination and hypoxia. Moreover, PQS were found in genes involved in drug resistance. Quadruplexes could have important roles within fungal biology and virulence, but their roles require further elucidation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Charge Transport and Space-Charge Formation in Cd 1 - x Zn x Te 1 - y Se y Radiation Detectors

The electron- and hole-transport properties in cadmium zinc telluride selenide (CZTS) crystals are studied using a laser-induced transient-current technique with pulsed and dc bias. The internal electric field profile and velocity of surface recombination are determined by Monte Carlo simulations of electron and hole transient currents combined with a numerical solution of the drift-diffusion equation coupled with Poisson’s equation. Electron and hole drift mobilities of μe = 830 cm 2 /Vs and μh = 40 cm 2 /Vs, respectively, are determined. We also develop a simple technique for evaluating surface recombination directly from measured current waveforms without the need for numerical simulation. The good quality of the prepared detector at pulsed bias, with electron- and hole-mobility-lifetime products of (μτ)e = 1.9 × 10 -3 cm 2 /V and (μτ)h = 1.4 × 10 -4 cm 2 /V, respectively, are observed. The formation of a positive space charge, originating from hole injection combined with a recombination level, is found. We observe a significant position dependence of the lifetime of electrons and holes in dc bias due to hole injection. The experiment is successfully fitted by a simple model dominated by a single deep recombination level with an energy of E t =E C -0.73eV; concentration of 7.3 × 10 11 cm -3 ; and electron- and hole-capture cross sections of 3.5 × 10 -14 cm 2 and 6.5 × 10 -14 cm 2 , respectively.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Polarization Selectivity of Aloof-Beam Electron Energy-Loss Spectroscopy in One-Dimensional ZnO Nanorods

Orientation-dependent electronic properties of wurtzite zinc oxide nanorods are characterized by aloof-beam electron energy-loss spectroscopy (EELS) carried out in a scanning transmission electron microscope (STEM). The two key crystal orientation differentiating transitions specific to the in-plane (13.0 eV) and out-of-plane (11.2 eV) directions with respect to the wurtzite structure are examined by first-principles density-functional theory calculations. We note some degree of orientation dependence at the onset of direct band gap transition near 3.4 eV. We demonstrate that good polarization selectivity can be achieved by placing the electron probe at different locations around the specimen with increasing impact parameter while keeping the beam-specimen orientation fixed. The observed results are qualitatively elucidated in terms of the perpendicular electric fields generated by the fast electron (60 kV) used in the microscope. The fact that good polarization selectivity can be achieved by aloof-beam EELS without the requirement of sample reorientation is an attractive aspect from the characterization method point of view in the STEM-EELS community.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

Characterization of rattling in relation to thermal conductivity: Ordered half-Heusler semiconductors

We report that the factors that affect the thermal conductivity of semiconductors is a topic of great scientific interest, especially in relation to thermoelectrics. Key developments have been the concept of the phonon-glass-electron-crystal (PGEC) and the related idea of rattling to achieve this. We use first-principles phonon and thermal conductivity calculations to explore the concept of rattling for stoichiometric-ordered half-Heusler compounds. These compounds can be regarded as filled zinc blende materials, and the filling atom could be viewed as a rattler if it is weakly bound. We use two simple metrics, one related to the frequency and the other to bond frustration and anharmonicity. We find that both measures correlate with thermal conductivity. Lastly, this suggests that both may be useful in screening materials for low thermal conductivity.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Discrete quantum geometry and intrinsic spin Hall effect

We show that the quantum geometry of the Fermi surface can be numerically described by a three-dimensional discrete quantum manifold. This approach not only avoids singularities in the Fermi sea, but it also enables the precise computation of the intrinsic Hall conductivity resolved in spin, as well as any other local properties of the Fermi surface. The method assures numerical accuracy when the Fermi level is arbitrarily close to singularities, and it remains robust when Kramers degeneracy is protected by symmetry. Furthermore, the approach is demonstrated by calculating the anomalous Hall and spin Hall conductivities of a two-band lattice model of a Weyl semimetal and a full-band ab initio model of zinc-blende GaAs.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Anisotropy of the magnetic and transport properties of EuZn 2 As 2

Several recent studies have shown that the anisotropy in the magnetic structure of EuCd 2 As 2 plays a significant role in stabilizing the Weyl nodes. Therefore, to investigate the relationship between magnetic anisotropy and Weyl physics, we present a comparative study between EuZn 2 As 2 and EuCd 2 As 2 that are isostructural but with different magnetic anisotropy. We performed structural analysis, electronic transport, and magnetization experiments on millimeter-sized single crystals of EuZn 2 As 2 , and compared the results to those of EuCd 2 As 2 . By combining the first principle calculations and neutron diffraction experiment, we identify the magnetic ground state of EuZn 2 As 2 as A-type antiferromagnetic order with a transition temperature (T_N = 19.6 K) twice that of EuCd 2 As 2 . Like EuCd 2 As 2 , the negative magnetoresistance of EuZn 2 As 2 is observed after suppressing the resistivity peak at T_N with increasing fields. However, the anisotropy in both transport and magnetization are much reduced in EuZn 2 As 2 . The difference could be ascribed to the weaker spin-orbit coupling, more localized d orbitals, and a larger contribution from the Eu s orbitals in the zinc compound, as suggested by the electronic band calculations. The same band structure effect could be also responsible for the observation of a smaller nonlinear anomalous Hall effect in EuZn 2 As 2 compared to EuCd 2 As 2 .

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Electronic structure of intrinsic defects in c -gallium nitride: Density functional theory study without the jellium approximation

Here, we report the first nonjellium, systematic, density functional theory (DFT) study of intrinsic and extrinsic defects and defect levels in zinc-blende (cubic) gallium nitride. We use the local moment counter charge (LMCC) method, the standard Perdew-Becke-Ernzerhoff (PBE) exchange-correlation potential, and two pseudopotentials, where the Ga 3$\textit{d}$ orbitals are either in the core ($d^0$) or explicitly in the valence set ($d^{10}$). We studied 64, 216, 512, and 1000 atom supercells, and demonstrated convergence to the infinite limit, crucial for delineating deep from shallow states near band edges, and for demonstrating the elimination of finite cell-size errors. Contrary to common claims, we find that exact exchange is not required to obtain defect levels across the experimental band gap. As was true in silicon, silicon carbide, and gallium arsenide, the extremal LMCC defect levels of the aggregate of defects yield an effective LMCC defect band gap that is within 10% of the experimental gap (3.3 eV) for both pseudopotentials. We demonstrate that the gallium vacancy is more complicated than previously reported. There is dramatic metastability–a nearest-neighbor nitrogen atom shifts into the gallium site, forming an antisite, nitrogen vacancy pair, which is more stable than the simple vacancy for positive charge states. Our assessment of the $d^0$ and $d^{10}$ pseudopotentials yields minimal differences in defect structures and defect levels. The better agreement of the $d^0$ lattice constant with experiment suggests that the more computationally economical $d^0$ pseudopotentials are sufficient to achieve the fidelity possible within the physical accuracy of DFT, and thereby enable calculations in larger supercells necessary to demonstrate convergence with respect to finite size supercell errors.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

Symmetry-driven persistent spin texture for the two-dimensional nonsymmorphic CdTe and ZnTe crystal structures

In this paper, two nonsymmorphic two-dimensional structures of CdTe and ZnTe are modeled, and using state-of-the-art density functional theory with the group theory of solids, their symmetry-enforced electronic properties are studied. The in-plane ferroelectricity coupled with strong spin-orbit coupling induces a unidirectional out-of-plane Rashba spin-orbit field that can host a momentum-independent uniform spin configuration known as persistent spin texture (PST) at the Brillouin zone center. PST in these structures is found to be robust against external perturbations such as strain, structural distortion, and independent of layer thickness. These unprecedented intrinsic spin transport properties hold utmost importance in spintronics, as the experimental stringent condition of equal Rashba and Dresselhaus constants [Phys. Rev. Lett. 90, 146801 (2003)] is eliminated. The calculated persistent spin helix wavelength of <~5 nm paves the way for developing next-generation nanosized nonballistic spin field-effect transistors compared with micrometer-sized GaAs/AlGaAs quantum wells. Further, these materials exhibit finite spin Hall conductivity at the band edges and hence can be used in ferromagnet-free spin Hall transistors. Although CdTe and ZnTe systems have been widely studied for photocatalysis and solar cell applications over the past few decades, their potential application in spintronic devices has not been explored. Mono/few layers of CdTe and ZnTe synthesized from (110) facets of bulk zinc-blende crystals [Nat. Commun. 3, 1057 (2012)] satisfy all symmetry operations of the nonsymmorphic space group and hence can be considered ideal materials to verify our theoretical results experimentally.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2025

Phonon dynamics in quantum spin liquid and valence bond crystal states in the barlowite family of kagome magnets

The barlowite [Cu 4 ⁢(OD) 6⁢ FBr] family of materials is characterized by antiferromagnetic spin-1/2 kagome layers and are believed to host interesting ground states of quantum magnetism. Substituting the interlayer sites with zinc ions yields Zn-barlowite (Zn 𝑥 ⁢Cu 4−𝑥 ⁢(OD) 6 ⁢FBr, 𝑥 ≈ 0.80) which is a strong candidate to have a quantum spin liquid (QSL) state. Experimentally distinguishing between valence bond crystal (VBC) and QSL states in the absence of magnetic ordering can prove challenging as both states exhibit similar average spin-spin correlations. Using high-resolution inelastic x-ray scattering with 1.4 meV energy resolution, we probe acoustic phonons in these structurally similar materials at various temperatures. Our measurements uncover robust differences possibly driven by different spin-phonon physics in VBC and QSL states, particularly at the 𝑀-point Brillouin zone boundary. Over a large 𝑇=[15,200]⁢ K temperature range, where neither material undergoes magnetic ordering nor a structural transition, we observe phonon softening in Zn-barlowite in contrast to a hardening of the same phonon in barlowite. Further, these results indicate that acoustic phonons in the barlowite system can be used to study and possibly distinguish between QSL and disordered VBC states in quantum magnets.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Universal trend of charge radii of even-even Ca–Zn nuclei

Radii of nuclear charge distributions carry information about the strong and electromagnetic forces acting inside the atomic nucleus. Whereas the global behavior of nuclear charge radii is governed by the bulk properties of nuclear matter, their local trends are affected by quantum motion of proton and neutron nuclear constituents. The measured differential charge radii δ$\langle$$r^{2}_{c}$$\rangle$ between neutron numbers N = 28 and N = 40 exhibit a universal pattern as a function of n = N – 28 that is independent of the atomic number. In this work, we analyze this remarkable behavior in even-even nuclei from calcium to zinc using two state-of-the-art theories based on quantified nuclear interactions: the ab initio coupled cluster theory and nuclear density functional theory. Both theories reproduce the smooth rise of differential charge radii and their weak dependence on the atomic number. By considering a large set of isotopic chains, we show that this trend can be captured by just two parameters: the slope and curvature of δ$\langle$$r^{2}_{c}$$\rangle$(n). We demonstrate that these parameters show appreciable model dependence, and the statistical analysis indicates that they are not correlated with any single model property, i.e., they are impacted by both bulk nuclear properties as well as shell structure.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2024

Isolation of Single Donors in ZnO

The shallow donor in zinc oxide (ZnO) is a promising semiconductor spin qubit with optical access. Single indium donors are isolated in a commercial ZnO substrate using plasma focused ion beam (PFIB) milling. Quantum emitters are identified optically by spatial and frequency filtering. The indium donor assignment is based on the optical bound exciton transition energy and magnetic dependence. The emission stability of these single donors in terms of both intensity and frequency, alongside their transition linewidths less than twice the lifetime limit, highlight the promise of single In donors as optically accessible spin qubits. Here, the optical stability of single donors after FIB fabrication is promising for optical device integration required for scalable quantum technologies based on single donors in direct band gap semiconductors.

42 ENGINEERING↗
DOE OSTI2021

Structural, electronic, and polarization properties of YN and LaN

ScN has attracted great attention for its electronic properties and its ability to enhance polarization of AlN; however, its sister compounds, YN and LaN, remain much less studied. Here, we use first-principles calculations to evaluate YN and LaN in their cubic and hexagonal phases. Rocksalt YN and LaN are semiconductors, although we show that LaN differs from ScN and YN in having a direct band gap, which we attribute to its weaker p-p coupling. Both have low electron effective masses. In addition to their rocksalt structures, we evaluate the layered hexagonal and wurtzite phases of YN and LaN. For YN, the wurtzite phase cannot be stabilized, and hexagonal YN is higher in energy than rocksalt YN. In contrast, for LaN, the wurtzite phase is favored, and it is comparable in energy to rocksalt LaN. Wurtzite LaN has a polarization of 0.608 C/m 2 (referenced to the centrosymmetric layered hexagonal phase), and a high piezoelectric coefficient e 33 = 1.78 C/m 2 . Interestingly, we find that the polarization of wurtzite LaN may be reversible; we find a relatively small switching barrier of 0.06 eV per formula unit, offering the potential for its use as a ferroelectric. Since wurtzite LaN is closely lattice matched to InP, we investigate a heterostructure between (0001) wurtzite LaN and (111) zinc-blende InP, and find the polarization discontinuity would yield a bound charge of 1.3 × 10 14 e/cm 2 , offering the potential for novel electronic applications such as tunnel junctions. Furthermore, our results compare and contrast ScN, YN, and LaN, and highlight the potential of these materials for adoption in electronic and ferroelectric devices.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Accurate point defect energy levels from non-empirical screened range-separated hybrid functionals: The case of native vacancies in ZnO

We use density functional theory (DFT) with non-empirically tuned screened range-separated hybrid (SRSH) functionals to calculate the electronic properties of native zinc and oxygen vacancy point defects in ZnO, and we predict their defect levels for thermal and optical transitions in excellent agreement with available experiments and prior calculations that use empirical hybrid functionals. Furthermore, the ability of this non-empirical first-principles framework to accurately predict quantities of relevance to both bulk- and defect-level spectroscopy enables high-accuracy DFT calculations with non-empirical hybrid functionals for defect physics, at a reduced computational cost.

Defects↗
DOE OSTI2026

Gepta-EX: a multi-channel germanium detector for X-ray absorption fine structure

Fluorescence-mode X-ray absorption spectroscopy (XAS) at high photon energies requires detectors with high stopping power and excellent energy resolution to measure weak element-specific signals. Traditional silicon-based detectors suffer from poor efficiency above ∼20 keV, while most high-Z materials such as cadmium telluride, cadmium zinc telluride, and gallium arsenide have focused predominantly on imaging applications with limited spectroscopic resolution. In contrast, germanium combines excellent stopping power with superior intrinsic energy resolution due to its low Fano factor and favorable charge transport properties, making it ideal for high-resolution spectroscopy in the 15 keV to 100 keV range. To address these requirements, we report on the development, fabrication, and performance evaluation of Gepta-EX, a compact multi-channel high-purity germanium (HPGe) detector system for fluorescence-mode XAS. The Gepta-EX system features a monolithic seven-channel HPGe pixel array integrated with low-noise CUBE charge-sensitive preamplifiers, housed within a thermally isolated compact cryostat operating near 90 K. The detector achieves energy resolutions of 218 eV at 5.9 keV (from a 55 Fe source) and 373 eV at 59.5 keV (from a 241 Am source), with uniform performance across all channels. By avoiding the escape peak interference commonly associated with silicon detectors and providing stable, high-resolution performance, Gepta-EX represents a powerful tool for high-energy X-ray spectroscopy.

36 MATERIALS SCIENCE↗