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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 1,693 records · Page 94
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

The full-length structure of Thermus scotoductus OLD defines the ATP hydrolysis properties and catalytic mechanism of Class 1 OLD family nucleases

Abstract OLD family nucleases contain an N-terminal ATPase domain and a C-terminal Toprim domain. Homologs segregate into two classes based on primary sequence length and the presence/absence of a unique UvrD/PcrA/Rep-like helicase gene immediately downstream in the genome. Although we previously defined the catalytic machinery controlling Class 2 nuclease cleavage, degenerate conservation of the C-termini between classes precludes pinpointing the analogous residues in Class 1 enzymes by sequence alignment alone. Our Class 2 structures also provide no information on ATPase domain architecture and ATP hydrolysis. Here we present the full-length structure of the Class 1 OLD nuclease from Thermus scotoductus (Ts) at 2.20 Å resolution, which reveals a dimerization domain inserted into an N-terminal ABC ATPase fold and a C-terminal Toprim domain. Structural homology with genome maintenance proteins identifies conserved residues responsible for Ts OLD ATPase activity. Ts OLD lacks the C-terminal helical domain present in Class 2 OLD homologs yet preserves the spatial organization of the nuclease active site, arguing that OLD proteins use a conserved catalytic mechanism for DNA cleavage. We also demonstrate that mutants perturbing ATP hydrolysis or DNA cleavage in vitro impair P2 OLD-mediated killing of recBC−Escherichia coli hosts, indicating that both the ATPase and nuclease activities are required for OLD function in vivo.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Oscillating paramagnetic Meissner effect and Berezinskii-Kosterlitz-Thouless transition in underdoped Bi2Sr2CaCu2O8+δ

ABSTRACT Superconducting phase transitions in two dimensions lie beyond the description of the Ginzburg-Landau symmetry-breaking paradigm for three-dimensional superconductors. They are Berezinskii-Kosterlitz-Thouless (BKT) transitions of paired-electron condensate driven by the unbinding of topological excitations, i.e. vortices. The recently discovered monolayers of layered high-transition-temperature (${{{T}}}_{{\rm C}}$) cuprate superconductor Bi2Sr2CaCu2O8+δ (Bi2212) meant that this 2D superconductor promised to be ideal for the study of unconventional superconductivity. But inhomogeneity posed challenges for distinguishing BKT physics from charge correlations in this material. Here, we utilize the phase sensitivity of scanning superconducting quantum interference device microscopy susceptometry to image the local magnetic response of underdoped Bi2212 from the monolayer to the bulk throughout its phase transition. The monolayer segregates into domains with independent phases at elevated temperatures below ${{{T}}}_{{\rm C}}$. Within a single domain, we find that the susceptibility oscillates with flux between diamagnetism and paramagnetism in a Fraunhofer-like pattern up to ${{{T}}}_{{\rm C}}$. The finite modulation period, as well as the broadening of the peaks when approaching ${{{T}}}_{{\rm C}}$ from below, suggests well-defined vortices that are increasingly screened by the dissociation of vortex-antivortex plasma through a BKT transition. In the multilayers, the susceptibility oscillation differs in a small temperature regime below ${{{T}}}_{{\rm C}}$, consistent with a dimensional crossover led by interlayer coupling. Serving as strong evidence for BKT transition in the bulk, we observe a sharp jump in phase stiffness and paramagnetism at small fields just below ${{{T}}}_{{\rm C}}$. These results unify the superconducting phase transitions from the monolayer to the bulk underdoped Bi2212, and can be collectively referred to as the BKT transition with interlayer coupling.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

CO2 response screen in grass Brachypodium reveals the key role of a MAP kinase in CO2-triggered stomatal closure

Abstract Plants respond to increased CO2 concentrations through stomatal closure, which can contribute to increased water use efficiency. Grasses display faster stomatal responses than eudicots due to dumbbell-shaped guard cells flanked by subsidiary cells working in opposition. However, forward genetic screening for stomatal CO2 signal transduction mutants in grasses has yet to be reported. The grass model Brachypodium distachyon is closely related to agronomically important cereal crops, sharing largely collinear genomes. To gain insights into CO2 control mechanisms of stomatal movements in grasses, we developed an unbiased forward genetic screen with an EMS-mutagenized B. distachyon M5 generation population using infrared imaging to identify plants with altered leaf temperatures at elevated CO2. Among isolated mutants, a “chill1” mutant exhibited cooler leaf temperatures than wild-type Bd21-3 parent control plants after exposure to increased CO2. chill1 plants showed strongly impaired high CO2-induced stomatal closure despite retaining a robust abscisic acid-induced stomatal closing response. Through bulked segregant whole-genome sequencing analyses followed by analyses of further backcrossed F4 generation plants and generation and characterization of sodium azide and CRISPR-cas9 mutants, chill1 was mapped to a protein kinase, Mitogen-Activated Protein Kinase 5 (BdMPK5). The chill1 mutation impaired BdMPK5 protein-mediated CO2/HCO3− sensing together with the High Temperature 1 (HT1) Raf-like kinase in vitro. Furthermore, AlphaFold2-directed structural modeling predicted that the identified BdMPK5-D90N chill1 mutant residue is located at the interface of BdMPK5 with the BdHT1 Raf-like kinase. BdMPK5 is a key signaling component that mediates CO2-induced stomatal movements and is proposed to function as a component of the primary CO2 sensor in grasses.

Lopez, Bryn N. K. (ORCID:0009000937288216)↗
DOE OSTI2018

Initially Disordered, Reflectin Assembly Tunably and Reversibly Drives Biophotonic Color

Reflectin proteins are found in the reflective Bragg lamellae in skin cells of certain squids, where they tunably control color for camouflage and communication. Initially disordered in the monomeric form, the reflectins have unusual amino acid compositions and are block copolymers consisting of polyampholytic canonical repeats interspersed with cationic linkers. In vivo, phosphorylation of the cationic linkers induces condensation, secondary folding and hierarchical assembly of the reflectins with concomitant emergence of tunable iridescence. We analyzed the folding and assembly of recombinant phospho‐mimetic and deletion mutants of reflectin, using pH titration as a surrogate for in vivo phosphorylation. Results of dynamic light scattering, transmission electron microscopy, fluorescence, circular dichroism and x‐ray scattering reveal that neutralization of the cationic linkers progressively and reversibly drives the reflectins to form monodisperse spherical assemblies of reproducible size. These analyses reveal a strongly predictive relationship between net charge density and size of the assembled reflectin multimers, with the switch appearing to be equally distributed across the spatially segregated linkers. Accompanying the progressive neutralization of Coulombic repulsion of the linkers, assembly appears to be driven by entropically driven folding of the canonical repeats into amphiphilic secondary structures that are likely to enable hierarchical assembly. These results suggest a model for tunable reflectin assembly and provide insight into the behavior of this unique, initially disordered protein. Support or Funding Information This research was supported by the U.S. Department of Energy, U.S. Army Research Office, and Institute of Collaborative Biotechnologies. This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal .

Levenson, Robert↗
DOE OSTI2018

Moonshot Objectives: Catalyze New Scientific Breakthroughs—Proteogenomics

Breaking down the silos between disciplines to accelerate the pace of cancer research is a key paradigm for the Cancer Moonshot. Molecular analyses of cancer biology have tended to segregate between a focus on nucleic acids – DNA, RNA and their modifications – and a focus on proteins and protein function. Proteogenomics represents a fusion of those two fields, leveraging the strengths of each to provide a more integrated vision of the flow of information from DNA to RNA to protein and eventually function. Proteogenomic studies have been incorporated into multiple activities associated with the cancer moonshot, demonstrating substantial added value. Innovative study designs integrating genomic, transcriptomic and proteomic data, particularly those that use clinically relevant samples and engage clinical trials, are poised to provide new insights regarding cancer risk, progression, and response to therapy,

proteogenomics, proteomics, cancer moonshot, mass ↗
DOE OSTI2017

Reciprocal insulation analysis of Hi-C data shows that TADs represent a functionally but not structurally privileged scale in the hierarchical folding of chromosomes

Understanding how regulatory sequences interact in the context of chromosomal architecture is a central challenge in biology. Chromosome conformation capture revealed that mammalian chromosomes possess a rich hierarchy of structural layers, from multi-megabase compartments to sub-megabase topologically associating domains (TADs) and sub-TAD contact domains. TADs appear to act as regulatory microenvironments by constraining and segregating regulatory interactions across discrete chromosomal regions. However, it is unclear whether other (or all) folding layers share similar properties, or rather TADs constitute a privileged folding scale with maximal impact on the organization of regulatory interactions. Here, we present a novel algorithm named CaTCH that identifies hierarchical trees of chromosomal domains in Hi-C maps, stratified through their reciprocal physical insulation, which is a single and biologically relevant parameter. By applying CaTCH to published Hi-C data sets, we show that previously reported folding layers appear at different insulation levels. We demonstrate that although no structurally privileged folding level exists, TADs emerge as a functionally privileged scale defined by maximal boundary enrichment in CTCF and maximal cell-type conservation. By measuring transcriptional output in embryonic stem cells and neural precursor cells, we show that the likelihood that genes in a domain are coregulated during differentiation is also maximized at the scale of TADs. Finally, we observe that regulatory sequences occur at genomic locations corresponding to optimized mutual interactions at the same scale. Our analysis suggests that the architectural functionality of TADs arises from the interplay between their ability to partition interactions and the specific genomic position of regulatory sequences.

Biochemistry & Molecular Biology↗
DOE OSTI2020

Possible role of grain-boundary and dislocation structure for the magnetic-flux trapping behavior of niobium: A first-principles study

In this work, first-principles methods were used to understand magnetic flux trapping at vacancies, dislocations, and grain boundaries in high-purity superconducting niobium. Full-potential linear augmented plane-wave methods were applied in progressively greater complexity, starting at simple vacancies and extending to screw dislocations and tilt grain boundaries to analyze the effects of magnetic field on the superconducting state surrounding these defects. Density-functional theory calculations identified changes in electronic structure at the dislocation core and different types of symmetric tilt grain boundaries relative to bulk niobium. Electron redistribution enhanced nonparamagnetic effects and thus perturb superconductivity, resulting in local conditions suitable for premature flux penetration and subsequently flux pinning. Since the coherence length of superconducting niobium at 0 K is significantly larger than the lattice parameter, the effects of line and planar defects in niobium are predicted to be stronger for defect clusters than single defects in isolation, which is consistent with recent experimental observations. Controlling accumulation or depletion of charge at the defects, e.g., by segregation of an impurity atom, can mitigate these tendencies thus increasing the quality of superconducting niobium.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Effect of surface steps on chemical ordering in the subsurface of Cu(Au) solid solutions

Atomic steps are typically assumed to only influence surface phenomena of solids. In contrast, in this paper we show, using in-situ atomic-resolution electron microscopy observations and atomistic modeling, the pronounced effect from surface stepsin inducing compositional and structural evolution in the subsurface of a Cu(Au) solid solution. We find that Au surface segregation results in a stacked sequence of Cu-Au ordered phases in the subsurface. The presence of a monatomic step at the surface induces the formation of an anti-phase boundary that extends from the surface step to deeper layers by maintaining the same composition profile associated with each terrace. The bunching of surface steps induces chemical disordering of the Cu-Au ordered phases in the subsurface region of the bunched steps. These results demonstrate the instant propagation of surface dynamics of atomic steps into the subsurface region and can find broader applicability in utilizing surface defects to tune the composition and structure in the subsurface of alloys.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Compositional patterning in irradiated alloys: Effective potentials and effective interfacial energy

Compositional patterning (CP) in binary alloys during energetic particle irradiation is studied using a kinetic model that considers two competing kinetic processes, a thermally activated one promoting macroscopic phase separation (MPS) of the concentration field c(r,t) and a forced one resulting in finite-range random atomic mixing. The forced mixing is modeled by a Gaussian relocation distribution with a characteristic distance R. A series of approximate kinetic models are introduced by expanding the mixing function into a series of n terms, thus replacing the non-local evaluations of the concentration field c(r'-r,t) by local derivatives of c(r,t). This approach makes it possible to obtain exact effective potentials and build steady-state diagrams for each order-n model. Phase field (PF) simulations using these order-n models reveal that near the onset of patterning, phase evolution is accurately described using an order-3 model, which changes smoothly from an extended Cahn-Hilliard free energy in the MPS regime to a one-mode Swift-Hohenberg functional in the CP regime. Deeper into the patterning regime, higher-order models are required to achieve convergence, yielding square-like concentration profiles characteristic of a strong segregation regime. These higher-order effective free energies are analogous to multimodal Swift-Hohenberg functionals. Here, a new definition for the effective interfacial energy is proposed in the CP regime, since the interfacial area is no longer an excess quantity in that regime, precluding the use of the standard thermodynamic definition of interfacial energy.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Tunable competing magnetic anisotropies and spin reconfigurations in ferrimagnetic Fe 100– x Gd x alloy films

Here, we report a comprehensive study of the temperature evolution of in-plane (IP) and out-of-plane (OOP) effective magnetic anisotropies in compensated ferrimagnetic Fe 100– x Gd x alloy films by employing direct current magnetometry and radiofrequency (RF) transverse susceptibility (TS) measurements. We suggest that our Fe 100– x Gd x system is chemically inhomogeneous and phase segregates into Fe- and Gd-enriched regions. Our IP and OOP magnetometry results indicate that the system undergoes a temperature-driven transformation from an IP-spin-configuration-dominated state to an OOP-spin-configuration-dominated state below a certain temperature (spin reorientation temperature). A two-step reversal behavior emerges in the OOP $\textit{M(H)}$ loop near compensation, which we attribute to the sequential magnetization reversals of Fe- and Gd-enriched domains. Field-induced spin-flop transitions were also observed near the compensation. Our RF TS measurements indicate that the effective magnetic anisotropy for the OOP configuration dominates over that for the IP configuration below a certain spin reorientation temperature. Both IP and OOP anisotropy fields determined from our TS measurement exhibit a minimum around the compensation temperature, which has been explained in the framework of the Stoner-Wohlfarth model.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Electronic structure of the honeycomb iridate Cu 2 ⁢IrO 3 at high pressure

Cu 2 IrO 3 has attracted recent interest due to its proximity to the Kitaev quantum spin liquid state and the complex structural response observed at high pressures. We use x-ray spectroscopy and scattering as well as electrical transport techniques to unveil the electronic structure of Cu 2 IrO 3 at ambient and high pressures. Despite featuring a Ir 4+ J eff = 1/2 state at ambient pressure, Ir L 3 -edge resonant inelastic x-ray scattering reveals broadened electronic excitations that point to the importance of Ir 5d-Cu 3d interaction. High pressure first drives an Ir-Ir dimer state with collapsed < L · S > and < L z >/< S z >, signaling the formation of 5d molecular orbitals. A novel Cu → Ir charge transfer is observed above 30 GPa at low temperatures, leading to an approximate Ir 3+ and Cu 1.5+ valence, with persistent insulating electrical transport seemingly driven by charge segregation of Cu 1+ /Cu 2+ ions into distinct sites. Concomitant x-ray spectroscopy and diffraction measurements through different thermodynamic paths demonstrate a strong electron-lattice coupling, with J eff = 1/2 and Ir 3+ /Cu 1.5+ electronic states occurring only in phases 1 and 5, respectively. Remarkably, the charge-transfer state can only be reached if Cu 2 IrO 3 is pressurized at low temperature, suggesting that phonons play an important role in the inhibiting this phase. Furthermore, these results point to the choice of thermodynamic path across interplanar collapse transition as a key parameter to access novel states in intercalated iridates.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2017

Phase stability, ordering tendencies, and magnetism in single-phase fcc Au-Fe nanoalloys

Bulk Au-Fe alloys separate into Au-based fcc and Fe-based bcc phases, but L1 0 and L1 2 orderings were reported in single-phase Au-Fe nanoparticles. Motivated by these observations, we study the structural and ordering energetics in this alloy by combining density functional theory (DFT) calculations with effective Hamiltonian techniques: a cluster expansion with structural filters, and the configuration-dependent lattice deformation model. The phase separation tendency in Au-Fe persists even if the fcc-bcc decomposition is suppressed. The relative stability of disordered bcc and fcc phases observed in nanoparticles is reproduced, but the fully ordered L1 0 AuFe, L1 2 Au 3 Fe, and L1 2 AuFe 3 structures are unstable in DFT. But, a tendency to form concentration waves at the corresponding [001] ordering vector is revealed in nearly-random alloys in a certain range of concentrations. Furthermore, this incipient ordering requires enrichment by Fe relative to the equiatomic composition, which may occur in the core of a nanoparticle due to the segregation of Au to the surface. Effects of magnetism on the chemical ordering are also discussed.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Arrested Phase Separation in Double-Exchange Models: Large-Scale Simulation Enabled by Machine Learning

In this work, we present large-scale dynamical simulations of electronic phase separation in the single-band double-exchange model based on deep-learning neural-network potentials trained from small-size exact diagonalization solutions. We uncover an intriguing correlation-induced freezing behavior as doped holes are segregated from half filled insulating background during equilibration. While the aggregation of holes is stabilized by the formation of ferromagnetic clusters through Hund’s coupling between charge carriers and local magnetic moments, this stabilization also creates confining potentials for holes when antiferromagnetic spin-spin correlation is well developed in the background. The dramatically reduced mobility of the self-trapped holes prematurely disrupts further growth of the ferromagnetic clusters, leading to an arrested phase separation. Implications of our findings for phase separation dynamics in materials that exhibit colossal magnetoresistance effect are discussed.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

Convection-Induced Compositional Patterning at Grain Boundaries in Irradiated Alloys

We consider the stability of precipitates formed at grain boundaries (GBs) by radiation-induced segregation in dilute alloys subjected to irradiation. Here, the effects of grain size and misorientation of symmetric-tilt GBs are quantified using phase field modeling. A novel regime is identified where, at long times, GBs are decorated by precipitate patterns that resist coarsening. Maps of the chemical Péclet number indicate that arrested coarsening takes place when solute advection dominates over thermal diffusion right up to the precipitate/matrix interface, preventing interfacial local equilibrium and overriding capillary effects. This contrasts with liquid-solid mixtures where convection always accelerates coarsening.

36 MATERIALS SCIENCE↗
DOE OSTI2017

Growth and structural characterization of large superconducting crystals of La 2 - x Ca 1 + x Cu 2 O 6

Large crystals of La 2 - x Ca 1 + x Cu 2 O 6 (La-Ca-2126) with x = 0:10 and 0.15 have been grown and converted to bulk superconductors by high-pressure oxygen annealing. The superconducting transition temperature, T c , is as high as 55 K; this can be raised to 60 K by post-annealing in air. Here we present structural and magnetic characterizations of these crystals using neutron scattering and muon spin rotation techniques. While the as-grown, non-superconducting crystals are single phase, we nd that the superconducting crystals contain 3 phases forming coherent domains stacked along the c axis: the dominant La-Ca-2126 phase, very thin (1.5 unit-cell) intergrowths of La 2 CuO 4 , and an antiferromagnetic La 8 Cu 8 O 20 phase. We propose that the formation and segregation of the latter phases increases the Ca concentration of the La-Ca-2126, thus providing the hole-doping that supports superconductivity.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2018

Ta-Nb-Mo-W refractory high-entropy alloys: Anomalous ordering behavior and its intriguing electronic origin

From electronic-structure-based thermodynamic linear response, we establish chemical ordering behavior in complex solid solutions versus how Gibbs' space is traversed—applying it on prototype refractory A2 Ta-Nb-Mo-W high-entropy alloys. Near ideal stoichiometry, this alloy has anomalous, intricate chemical ordering tendencies, with long-ranged chemical interactions that produce competing short-range order (SRO) with a crossover to spinodal segregation. This atypical SRO arises from canonical band behavior that, with alloying, creates features near the Fermi surface (well defined even with disorder) that change to simple commensurate SRO with (un)filling of these states. In conclusion, our results reveal how complexity and competing electronic effects control ordering in these alloys.

36 MATERIALS SCIENCE↗
DOE OSTI2018

Dynamics of interaction between dislocations and point defects in bcc iron

The interaction between dislocations and point defects is crucial for many physical properties and phenomena in materials, such as strengthening mechanisms, dislocation bias and void swelling, creep, and impurity segregation around dislocations. Conventional dislocation-point defect interaction models use approximations based on elasticity theory and/or based on assumptions that transition states energies can be deduced from the binding energies of the defects. In this paper, we present the transport properties of point defects near dislocations based on the actual saddle-point configuration of vacancies and self-interstitial atoms as a function of position with respect to screw and edge dislocations in a model system (bcc iron) using the self-evolving atomistic kinetic Monte Carlo. Here, KMC simulations reveal defect dynamics near dislocations are highly anisotropic and correlated, particularly for dumbbells in the compressive field of the edge dislocation, which could result in zones near dislocation cores where dumbbells are less efficiently absorbed compared with vacancies. This study provides accurate saddle-point configurations and energies required to properly describe the dynamics of point defects around dislocations, allowing fundamental insights on the transport mechanisms which are essential for understanding microstructural evolution and mechanical properties of metallic materials.

36 MATERIALS SCIENCE↗