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At least 1,693 records · Page 94
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

The Milky Way tomography with APOGEE: intrinsic density distribution and structure of mono-abundance populations

ABSTRACT The spatial distribution of mono-abundance populations (MAPs, selected in [Fe/H] and [Mg/Fe]) reflect the chemical and structural evolution in a galaxy and impose strong constraints on galaxy formation models. In this paper, we use APOGEE data to derive the intrinsic density distribution of MAPs in the Milky Way, after carefully considering the survey selection function. We find that a single exponential profile is not a sufficient description of the Milky Way’s disc. Both the individual MAPs and the integrated disc exhibit a broken radial density distribution; densities are relatively constant with radius in the inner Galaxy and rapidly decrease beyond the break radius. We fit the intrinsic density distribution as a function of radius and vertical height with a 2D density model that considers both a broken radial profile and radial variation of scale height (i.e. flaring). There is a large variety of structural parameters between different MAPs, indicative of strong structure evolution of the Milky Way. One surprising result is that high-α MAPs show the strongest flaring. The young, solar-abundance MAPs present the shortest scale height and least flaring, suggesting recent and ongoing star formation confined to the disc plane. Finally we derive the intrinsic density distribution and corresponding structural parameters of the chemically defined thin and thick discs. The chemical thick and thin discs have local surface mass densities of 5.62 ± 0.08 and 15.69 ± 0.32 M⊙pc−2, respectively, suggesting a massive thick disc with a local surface mass density ratio between thick to thin disc of 36 per cent.

79 ASTRONOMY AND ASTROPHYSICS↗
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

Structural basis for cloverleaf RNA-initiated viral genome replication

The genomes of positive-strand RNA viruses serve as a template for both protein translation and genome replication. In enteroviruses, a cloverleaf RNA structure at the 5' end of the genome functions as a switch to transition from viral translation to replication by interacting with host poly(C)-binding protein 2 (PCBP2) and the viral 3CD pro protein. We determined the structures of cloverleaf RNA from coxsackievirus and poliovirus. Cloverleaf RNA folds into an H-type four-way junction and is stabilized by a unique adenosine-cytidine-uridine (A•C-U) base triple involving the conserved pyrimidine mismatch region. The two PCBP2 binding sites are spatially proximal and are located on the opposite end from the 3CD pro binding site on cloverleaf. We determined that the A•C-U base triple restricts the flexibility of the cloverleaf stem–loops resulting in partial occlusion of the PCBP2 binding site, and elimination of the A•C-U base triple increases the binding affinity of PCBP2 to the cloverleaf RNA. Based on the cloverleaf structures and biophysical assays, we propose a new mechanistic model by which enteroviruses use the cloverleaf structure as a molecular switch to transition from viral protein translation to genome replication.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Structure of the Ndc80 complex and its interactions at the yeast kinetochore–microtubule interface

The conserved Ndc80 kinetochore complex, Ndc80c, is the principal link between mitotic spindle microtubules and centromere-associated proteins. We used AlphaFold 2 (AF2) to obtain predictions of the Ndc80 ‘loop’ structure and of the Ndc80 : Nuf2 globular head domains that interact with the Dam1 subunit of the heterodecameric DASH/Dam1 complex (Dam1c). The predictions guided design of crystallizable constructs, with structures close to the predicted ones. The Ndc80 ‘loop’ is a stiff, α-helical ‘switchback’ structure; AF2 predictions and positions of preferential cleavage sites indicate that flexibility within the long Ndc80c rod occurs instead at a hinge closer to the globular head. Conserved stretches of the Dam1 C terminus bind Ndc80c such that phosphorylation of Dam1 serine residues 257, 265 and 292 by the mitotic kinase Ipl1/Aurora B can release this contact during error correction of mis-attached kinetochores. We integrate the structural results presented here into our current molecular model of the kinetochore–microtubule interface. The model illustrates how multiple interactions between Ndc80c, DASH/Dam1c and the microtubule lattice stabilize kinetochore attachments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

From Spin to Pseudospin Symmetry: The Origin of Magic Numbers in Nuclear Structure

Magic numbers lie at the heart of nuclear structure, reflecting enhanced stability in nuclei with closed shells. While the emergence of magic numbers beyond 20 is commonly attributed to strong spin-orbit coupling, the microscopic origin of the spin-orbit potential remains elusive, owing to its dependence on the resolution scale and renormalization scheme of nuclear forces. Here, we investigate the evolution of nuclear shell structure with varying momentum resolution in nuclear interactions derived from chiral effective field theory, using the similarity renormalization group to link different scales. We uncover a novel transition from spin symmetry to pseudospin symmetry as the resolution scale decreases, during which magic numbers emerge naturally. A similar pattern is found in calculations using relativistic one-boson-exchange potentials, underscoring the robustness of the phenomenon. This establishes a direct connection between realistic nuclear forces with a high resolution scale and effective nuclear forces at coarse-grained scales, offering a first-principles explanation for the origin of magic numbers and pseudospin symmetry in nuclear shell structure and new insights into the structure of exotic nuclei far from stability

Energy levels↗
DOE OSTI2026

Crystal structure, compressibility, and thermal expansion of uranium mononitride

The behavior of the uranium mononitride (UN) crystal structure at nonambient conditions is disputed, with studies proposing various mutually exclusive distortions and transformations of the conventional face-centered-cubic structure at extreme temperatures and pressures. Here, in this study, we investigated the UN lattice with diamond anvil cell x-ray diffraction experiments at pressures up to 92 GPa and with density functional theory calculations at temperatures up to 1000 K and pressures up to 90 GPa. We determined that while the UN structure is nearly cubic at ambient conditions, its lattice angle (𝛼) varies as a function of pressure and temperature, meaning its structure can be more precisely described as face-centered-rhombohedral with 𝛼 ≈ 90∘. Over the range of conditions we investigated, UN exhibits a single, isostructural phase transition at ≈ 35 GPa, where 𝛼 collapses to ≈ 86°. Measurements and calculations agree that the compressibility of UN increases significantly beyond this transition, with the bulk modulus falling from ≈ 200 GPa in the low-pressure phase to 121 ± 3 GPa (according to calculations) or 58 ± 4 GPa (according to measurements) in the high-pressure phase. Our measurements also allowed us to constrain the bulk modulus of 𝛼−U 2 ⁢N 3 to 240 ± 10 GPa.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Charge-induced atomic strain as a predictor of structural phase transformation in rare-earth intermetallics

We present a descriptor based on charge-induced atomic strain in crystalline lattices for predicting structural phase transformations in rare-earth intermetallic compounds containing lanthanides and transition metals. The charge-induced local atomic strain was obtained from structural optimization of experimentally known crystalline phases using state of the art density-functional theory methods. The predictive power of the descriptor was evaluated on 𝑅⁢𝐸 2 ⁢In (𝑅𝐸 = rare earth) compounds, a class known for diverse phase transformations. We show that incorporating quantum-mechanical effects—such as local charge distribution, bonding, symmetry, and electronic structure—enhances the robustness of the descriptor. To gain further insight, we analyzed phononic and electronic behavior in Y 2 ⁢In and demonstrated that experimental phase transformations are captured only when atomic strain effects are included. The descriptor was further used to predict structural phase changes in (Y⁢b 1–𝑥 ⁢E⁢r 𝑥 ) 2 ⁢In and G⁡d 2 ⁡(I⁢n 1–𝑥⁢ A⁢l 𝑥 ), with predictions confirmed by x-ray powder diffraction. Here, while the current study is focused on lanthanide-based intermetallics, the underlying principles of the descriptor suggest potential applicability to other closely related classes of rare-earth intermetallics.

Density functional theory↗
DOE OSTI2021

Structural disorder-driven topological phase transition in noncentrosymmetric BiTeI

In this work, we investigate using local structural disorder to induce a topologically nontrivial phase in a solid state system. Using first-principles calculations, we introduce structural disorder in the trivial insulator BiTeI and observe the emergence of a topological insulating phase. By modifying the bonding environments, the crystal-field splitting is enhanced, with spin-orbit interactions producing a band inversion in the bulk electronic structure. Analysis of the Wannier charge centers and the surface electronic structure reveals a strong topological insulator with Dirac surface states. Finally, we propose a prescription for inducing topological states from disorder in crystalline materials. Understanding how local environments produce topological phases is a key step for predicting disordered and amorphous topological materials.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Unoccupied electronic structure of actinide dioxides

Ligand field density functional theory calculations of the dioxides of thorium, uranium, and plutonium have been combined with high-energy-resolution fluorescence detection (HERFD) in x-ray absorption spectroscopy and inverse photoelectron spectroscopy (IPES) measurements to provide powerful insight into the underlying composition of the unoccupied 5f electronic structure in these 5f localized systems. Fine structure in the 5f 5/2 transitions in HERFD can be directly correlated with the fine structure in the leading edge of the IPES. The shapes, intensities, and systematics in HERFD and IPES are explained in a consistent and rigorous fashion in terms of the j-specific 5f electronic structure.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Structural evolution of iodine on approach to the monatomic state

Here, we applied single-crystal x-ray diffraction and Raman spectroscopy in a diamond-anvil cell up to 36 GPa and first-principles theoretical calculations to study the molecular dissociation of solid iodine at high pressure. Unlike previously reported, we find that the familiar Cmce molecular phase transforms to a Cmc2 1 molecular structure at 16 GPa, and then to an incommensurate polymeric Fmmm⁡(00⁢$\gamma$)⁢s⁢00 structure, which can be viewed as a mixture of molecular I 2 and zigzag chains of three iodine atoms, at 20 GPa. The available data are consistent with metallization of iodine at the boundary between the commensurate Cmc⁢2 1 structure and the incommensurate Fmmm⁡(00⁢$\gamma$)s⁢00 structure at 20 GPa.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

Effect of low-temperature compression on superconductivity and crystal structure in strontium metal

The superconducting and structural properties of elemental strontium metal were investigated under pressures up to 60 GPa while maintaining cryogenic conditions during pressure application. Applying pressure at low temperatures reveals differences in superconducting and structural phases compared to previous reports obtained at room temperatures. Notably, the superconducting critical temperature exhibits a twofold increase under compression after cryogenic cooling within the pressure range of 35–42 GPa, compared to cryogenic cooling after room-temperature compression. Subsequently, the transition width becomes significantly sharper above 42 GPa. Low-temperature x-ray diffraction measurements under pressure reveal that this change corresponds to the Sr-III to Sr-IV transition, with no evidence of any metastable structure. Furthermore, the monoclinic Sr-IV structure was observed to remain stable to much higher pressures—at least up to 60 GPa, without the appearance of the incommensurate Sr-V phase present at room temperature. As a result, this implies that thermal activation energy plays an important role in overcoming the presence of a kinetic barrier to the Sr-V phase at room temperature.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2025

Correlation effects on coupled electronic and structural properties of doped rare-earth trihydrides

Rare-earth trihydride (𝑅⁢H 3 ) compounds exhibit intriguing coupled electronic and structural properties as a function of doping, hydrogen vacancies, and thermodynamic conditions. Theoretical studies of these materials typically rely on density functional theory (DFT), including the use of small supercells that may underestimate strong correlation effects and structural distortions which in turn may influence their metallicity. Here, we elucidate the roles of lattice distortions and correlation effects on the electronic properties of pristine and doped 𝑅⁢H 3 compounds by adopting DFT +U and quantum Monte Carlo (QMC) methods. Linear-response constrained DFT (LR-cDFT) methods find Hubbard U ≈ 2 eV for 𝑅 𝑑 orbitals and U ≈ 6 eV for H 𝑠 ⁡/N 𝑝 /O 𝑝 orbitals. The small U on Lu 𝑑 orbitals is consistent with QMC calculations on LuH 3 and LuH 2.875 ⁢N 0.125 . In pure face-centered-cubic (FCC) 𝑅⁢H 3 (𝑅 = Lu,Y) compounds, neither DFT nor DFT +U with the self-consistently determined U is enough to create a band gap, however a supercell with hydrogen distortions creates a small gap whose magnitude increases when performing DFT +U with self-consistently determined U values. Furthermore, correlation effects, in turn, have a moderate influence on the coupled structural and electronic properties of doped 𝑅⁢H 3 compounds and may be important when considering the competition between structural distortions and superconductivity.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

Decay spectroscopy of 160 Eu: Quasiparticle configurations of excited states and structure of K π = 4 + bandheads in 160 Gd

Background: Detailed spectroscopy of neutron-rich, heavy, deformed nuclei is of broad interest for nuclear astrophysics and nuclear structure. Nuclei in the r-process path and following freeze-out region impact the resulting r-process abundance distribution, and the structure of nuclei midshell in both proton and neutron number helps to understand the evolution of subshell gaps and large deformation in these nuclei. Purpose: We aim to improve the understanding of the nuclear structure of 160 Gd, specifically the K π = 4 + bands, as well as study the β decay of 160 Eu into 160 Gd. Methods: High-statistics decay spectroscopy of 160 Gd resulting from the β-decay of 160 Eu was collected using the GRIFFIN spectrometer at the TRIUMF-ISAC facility. Results: Two new excited states and ten new transitions were observed in 160 Gd. The β-decaying half-lives of the low- and high-spin isomers in 160 Eu were determined, and the low-spin state's half-life was measured to be t 1/2 = 26.0 (8) s, ≈ 16% shorter than previous measurements. Lifetimes of the two K π = 4 + bandheads in 160 Gd were measured for the first time, as well as γ – γ angular correlations and mixing ratios of intense transitions out of those bandheads. Conclusions: Lifetimes and mixing ratios suggest that the hexadecapole phonon model of the K π = 4 + bandheads in 160 Gd is preferred over a simple two-state strong mixing scenario, although further theoretical calculations are needed to fully understand these states. Additionally, the 1999.0-keV state in 160 Gd heavily populated in β decay is shown to have positive parity, which raises questions regarding the structure of the high-spin β-decaying state in 160 Eu.

150 ≤ A ≤ 189↗
DOE OSTI2024

Structure and lattice excitations of the copper substituted lead oxyapatite Pb 9.06⁢(7)⁢ Cu 0.94⁢(6)⁢ (PO 3.92⁢(4) ) 6 ⁢O 0.96⁢(3)

The copper substituted lead oxyapatite, Pb 10-x⁢ Cu x (PO 3.92⁢(4) ) 6 ⁢O 0.96⁢(3) [x = 0.94(6)] was studied using neutron and x-ray diffraction and neutron spectroscopy techniques. The crystal structure of the main phase of our sample, which has come to be colloquially known as LK-99, is verified to possess a hexagonal structure with space group P6 3 /m, alongside the presence of impurity phases Cu and Cu 2 ⁢S. We determine the primary substitution location of the Cu as the Pb1 (6⁢ℎ) site, with a small substitution at the Pb2 (4⁢f) site. Consequently, no clear Cu-doping-induced structural distortion was observed in the investigated temperature region between 10 K and 300 K. Specially, we did not observe a reduction of coordinate number at the Pb2 site or a clear tilting of PO 4 tetrahedron. Magnetic characterization reveals a diamagnetic signal in the specimen, accompanied by a very weak ferromagnetic component at 2 K. No long-range magnetic order down to 10 K was detected by the neutron diffraction. Inelastic neutron scattering measurements did not show magnetic excitations for energies up to 350 meV. There is no sign of a superconducting resonance in the excitation spectrum of this material. The measured phonon density of states compares well with density functional theory calculations performed for the main LK-99 phase and its impurity phases. Our study may shed some insight into the role of the favored substitution site of copper in the absence of structural distortion and superconductivity in LK-99.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Electronic structure and exchange interactions in altermagnetic MnGeP 2 in the quasiparticle self-consistent G W approach

The quasiparticle self-consistent 𝐺⁡𝑊 method is used to study the electronic band structure, optical dielectric function, and exchange interactions in chalcopyrite, 𝐼⁢ ‾ 4 ⁢2⁢𝑑, structure MnGeP 2 . The material is found to be an antiferromagnetic semiconductor with a lowest direct gap of 2.44 eV at the Γ point and a lower indirect gap of 1.87 eV from Γ to 𝑀. The material is an altermagnet because the two magnetic atoms of opposite spin are related by a twofold rotation operation perpendicular to the main fourfold rotation inversion axis. The spin splittings along a low symmetry line like 𝑃⁢𝑁 is sizable while at k points on the diagonal mirror planes or on the twofold symmetry axes the spin splitting is zero. The exchange interactions are calculated using a linear response approach. The antiferromagnetic exchange interaction between nearest neighbors in the primitive unit cell is dominating and found to be slightly decreasing upon carrier doping but not sufficiently to change the interaction to become ferromagnetic. The bare (noninteracting) and interacting transverse spin susceptibilities, which provide interatomic site exchange interactions after averaging over the muffin-tin spheres, are calculated from the 𝐺⁡𝑊 band structure and wave functions. From these exchange interactions, the spin wave spectra are obtained along the high symmetry lines and the Néel temperature is calculated using the mean-field and Tyablikov estimations. The dielectric function and the optical absorption spectra are calculated including excitonic effects using the Bethe Salpeter equation. The exchange interactions around Mn Ge defect sites is also studied. While we find it can generate ferromagnetic interactions with neighboring spins, we did not find direct evidence of producing an overall ferromagnetic phase. First, if Mn antisites are introduced by exchanging Mn with a nearby Ge, the interactions stay largely antiferromagnetic. Second, when we add additional Mn, in other words in Mn-rich stoichiometry, the Mn Ge antisites produce a strong ferromagnetic interaction primarily with the Mn in the same basal plane but weaker ferromagnetic interaction with adjacent plane Mn. The interactions between regular lattice Mn stay antiferromagnetic as before and thus favor keeping the antiferromagnetic order along the [001] direction. Adding Mn antisites, however, does lead to a metallic band structure.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Atomic structures determined from digitally defined nanocrystalline regions

Nanocrystallography has transformed our ability to interrogate the atomic structures of proteins, peptides, organic molecules and materials. By probing atomic level details in ordered sub-10 nm regions of nanocrystals, scanning nanobeam electron diffraction extends the reach of nanocrystallography and in principle obviates the need for diffraction from large portions of one or more crystals. Scanning nanobeam electron diffraction is now applied to determine atomic structures from digitally defined regions of beam-sensitive peptide nanocrystals. Using a direct electron detector, thousands of sparse diffraction patterns over multiple orientations of a given crystal are recorded. Each pattern is assigned to a specific location on a single nanocrystal with axial, lateral and angular coordinates. This approach yields a collection of patterns that represent a tilt series across an angular wedge of reciprocal space: a scanning nanobeam diffraction tomogram. Using this diffraction tomogram, intensities can be digitally extracted from any desired region of a scan in real or diffraction space, exclusive of all other scanned points. Intensities from multiple regions of a crystal or from multiple crystals can be merged to increase data completeness and mitigate missing wedges. It is demonstrated that merged intensities from digitally defined regions of two crystals of a segment from the OsPYL/RCAR5 protein produce fragment-based ab initio solutions that can be refined to atomic resolution, analogous to structures determined by selected-area electron diffraction. In allowing atomic structures to now be determined from digitally outlined regions of a nanocrystal, scanning nanobeam diffraction tomography breaks new ground in nanocrystallography.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Toward a quantitative description of solvation structure: a framework for differential solution scattering measurements

Appreciating that the role of the solute–solvent and other outer-sphere interactions is essential for understanding chemistry and chemical dynamics in solution, experimental approaches are needed to address the structural consequences of these interactions, complementing condensed-matter simulations and coarse-grained theories. High-energy X-ray scattering (HEXS) combined with pair distribution function analysis presents the opportunity to probe these structures directly and to develop quantitative, atomistic models of molecular systems in situ in the solution phase. However, at concentrations relevant to solution-phase chemistry, the total scattering signal is dominated by the bulk solvent, prompting researchers to adopt a differential approach to eliminate this unwanted background. Though similar approaches are well established in quantitative structural studies of macromolecules in solution by small- and wide-angle X-ray scattering (SAXS/WAXS), analogous studies in the HEXS regime—where sub-ångström spatial resolution is achieved—remain underdeveloped, in part due to the lack of a rigorous theoretical description of the experiment. To address this, herein we develop a framework for differential solution scattering experiments conducted at high energies, which includes concepts of the solvent-excluded volume introduced to describe SAXS/WAXS data, as well as concepts from the time-resolved X-ray scattering community. Our theory is supported by numerical simulations and experiment and paves the way for establishing quantitative methods to determine the atomic structures of small molecules in solution with resolution approaching that of crystallography.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Li 4 Ru 2 OCl 10 ·10H 2 O: crystal structure, magnetic properties and bonding interactions in ruthenium-oxo complexes

The results of the structural determination, magnetic characterization, and theoretical calculations of a new ruthenium-oxo complex, Li 4 [Ru 2 OCl 10 ]·10H 2 O, are presented. Single crystals were grown using solvent methods and the crystal structure was characterized by single crystal X-ray diffraction. Li 4 [Ru 2 OCl 10 ]·10H 2 O crystallizes into a low-symmetry triclinic structure ($P\bar1$) due to the much smaller Li + cation compared to K + cation in the tetragonal complex K 4 [Ru 2 OCl 10 ]·H 2 O. The X-ray photoelectron spectra confirm only the single valent Ru 4+ in Li 4 [Ru 2 OCl 10 ]·10H 2 O even though two distinct Ru sites exist in the crystal structure. Magnetic measurements reveal the diamagnetic property of Li 4 [Ru 2 OCl 10 ]·10H 2 O with unpaired electrons existing on Ru 4+ . Furthermore, the molecular orbital analysis matches well with the observed UV and magnetic measurements.

36 MATERIALS SCIENCE↗