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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 703 records · Page 39
All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

Variation in superconducting transition temperature due to tetragonal domains in two-dimensionally doped SrTiO 3

Strontium titanate is a low-temperature, non-Bardeen-Cooper-Schrieffer superconductor that superconducts to carrier concentrations lower than in any other system and exhibits avoided ferroelectricity at low temperatures. Neither the mechanism of superconductivity in strontium titanate nor the importance of the structure and dielectric properties for the superconductivity are well understood. We studied the effects of twin structure on superconductivity in a 5.5-nm-thick layer of niobium-doped SrTiO3 embedded in undoped SrTiO3. We used a scanning superconducting quantum interference device susceptometer to image the local diamagnetic response of the sample as a function of temperature. We observed regions that exhibited a superconducting transition temperature T-c greater than or similar to 10% higher than the temperature at which the sample was fully superconducting. The pattern of these regions varied spatially in a manner characteristic of structural twin domains. Some regions are too wide to originate on twin boundaries; therefore, we propose that the orientation of the tetragonal unit cell with respect to the doped plane affects T-c. Our results suggest that the anisotropic dielectric properties of SrTiO3 are important for its superconductivity and need to be considered in any theory of the mechanism of the superconductivity.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2025

Bounce-averaged theory in arbitrary multi-well plasmas: solution domains and the graph structure of their connections

Bounce-averaged theories provide a framework for simulating relatively slow processes, such as collisional transport and quasilinear diffusion, by averaging these processes over the fast periodic motions of a particle on a closed orbit. This procedure dramatically increases the characteristic time scale and reduces the dimensionality of the modelled system. The natural coordinates for such calculations are the constants of motion (COM) of the fast particle motion, which by definition do not change during an orbit. However, for sufficiently complicated fields – particularly in the presence of local maxima of the electric potential and magnetic field – the COM are not sufficient to specify the particle trajectory. In such cases, multiple domains in COM space must be used to solve the problem, with boundary conditions enforced between the domains to ensure continuity and particle conservation. Previously, these domains have been imposed by hand, or by recognising local maxima in the fields, limiting the flexibility of bounce-averaged simulations. Here, we present a general set of conditions for identifying consistent domains and the boundary condition connections between the domains, allowing the application of bounce-averaged theories in arbitrarily complicated and dynamically evolving electromagnetic field geometries. We also show how the connections between the domains can be represented by a directed graph, which can help to succinctly represent the trajectory bifurcation structure.

fusion plasma↗
DOE OSTI2015

Anisotropic behavior of exchange bias effect in tensile-deformed Pt{sub 3}Fe single crystal

Plastic strain in Pt{sub 3}Fe causes changes in the atomic arrangement around the (111) glide plane and induces ferromagnetism even at room temperature. We have performed detailed magnetization measurements on a Pt{sub 3}Fe single crystal with plastic strains of 11.6% under magnetic fields in various directions with respect to the [100] strain axis in order to elucidate the reversal mechanism of induced ferromagnetic domains. We observed that by decreasing the angle between the magnetization direction and strain axis, hysteresis loops are strongly sheared, which is associated with a large increase in coercivity. We also observed that an exchange bias effect appears for all field orientations, but the exchange field maximizes for an intermediate field direction. On the other hand, both phenomena are insensitive to magnetic fields perpendicular to the [100] strain axis. These observations were explained by a single-domain model with uniaxial anisotropy along the [100] strain axis.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2019

Structures of CENP-C cupin domains at regional centromeres reveal unique patterns of dimerization and recruitment functions for the inner pocket

We discuss the successful assembly and regulation of the kinetochore are critical for the equal and accurate segregation of genetic material during the cell cycle. CENP-C (centromere protein C), a conserved inner kinetochore component, has been broadly characterized as a scaffolding protein and is required for the recruitment of multiple kinetochore proteins to the centromere. At its C terminus, CENP-C harbors a conserved cupin domain that has an established role in protein dimerization. Although the crystal structure of the Saccharomyces cerevisiae Mif2CENP-C cupin domain has been determined, centromeric organization and kinetochore composition vary greatly between S. cerevisiae (point centromere) and other eukaryotes (regional centromere). Therefore, whether the structural and functional role of the cupin domain is conserved throughout evolution requires investigation. Here, we report the crystal structures of the Schizosaccharomyces pombe and Drosophila melanogaster CENP-C cupin domains at 2.52 and 1.81 Å resolutions, respectively. Although the central jelly roll architecture is conserved among the three determined CENP-C cupin domain structures, the cupin domains from organisms with regional centromeres contain additional structural features that aid in dimerization. Moreover, we found that the S. pombe Cnp3CENP-C jelly roll fold harbors an inner binding pocket that is used to recruit the meiosis-specific protein Moa1. In summary, our results unveil the evolutionarily conserved and unique features of the CENP-C cupin domain and uncover the mechanism by which it functions as a recruitment factor.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

A numerical approach for simulating fluid structure interaction of flexible thin shells undergoing arbitrarily large deformations in complex domains

We present a new numerical methodology for simulating fluid–structure interaction (FSI) problems involving thin flexible bodies in an incompressible fluid. The FSI algorithm uses the Dirichlet–Neumann partitioning technique. The curvilinear immersed boundary method (CURVIB) is coupled with a rotation-free finite element (FE) model for thin shells enabling the efficient simulation of FSI problems with arbitrarily large deformation. Turbulent flow problems are handled using large-eddy simulation with the dynamic Smagorinsky model in conjunction with a wall model to reconstruct boundary conditions near immersed boundaries. The CURVIB and FE solvers are coupled together on the flexible solid–fluid interfaces where the structural nodal positions, displacements, velocities and loads are calculated and exchanged between the two solvers. Loose and strong coupling FSI schemes are employed enhanced by the Aitken acceleration technique to ensure robust coupling and fast convergence especially for low mass ratio problems. The coupled CURVIB-FE-FSI method is validated by applying it to simulate two FSI problems involving thin flexible structures: 1) vortex-induced vibrations of a cantilever mounted in the wake of a square cylinder at different mass ratios and at low Reynolds number; and 2) the more challenging high Reynolds number problem involving the oscillation of an inverted elastic flag. For both cases the computed results are in excellent agreement with previous numerical simulations and/or experiential measurements. Grid convergence tests/studies are carried out for both the cantilever and inverted flag problems, which show that the CURVIB-FE-FSI method provides their convergence. Finally, the capability of the new methodology in simulations of complex cardiovascular flows is demonstrated by applying it to simulate the FSI of a tri-leaflet, prosthetic heart valve in an anatomic aorta and under physiologic pulsatile conditions.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2014

Magnetic properties on the surface of FeAl stripes induced by nanosecond pulsed laser irradiation

We demonstrate the formation of magnetic nanostripes on the surface of Fe{sub 52}Al{sub 48} induced by nanosecond pulsed laser irradiation and investigate their magnetic properties. The magnetic stripe consists of a disordered A2 phase of Fe-Al alloys with Al-oxide along the [110] direction on the (111)-oriented plane. According to the focused magneto-optical Kerr effect measurement, the coercive force of the magnetic stripe obeys the 1/cos θ law, where θ is the field rotation angle estimated from the stripe direction. Also, the jump field can be observed in the magnetic hysteresis loop. These results indicate that the magnetization reversal in the magnetic stripe originates from the domain pinning, showing that the magnetization rotates incoherently.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

High-resolution crystal structure of the Borreliella burgdorferi PlzA protein in complex with c-di-GMP: new insights into the interaction of c-di-GMP with the novel xPilZ domain

ABSTRACT In the tick-borne pathogens, Borreliella burgdorferi and Borrelia hermsii, c-di-GMP is produced by a single diguanylate cyclase (Rrp1). In these pathogens, the Plz proteins (PlzA, B and C) are the only c-di-GMP receptors identified to date and PlzA is the sole c-di-GMP receptor found in all Borreliella isolates. Bioinformatic analyses suggest that PlzA has a unique PilZN3-PilZ architecture with the relatively uncommon xPilZ domain. Here, we present the crystal structure of PlzA in complex with c-di-GMP (1.6 Å resolution). This is the first structure of a xPilz domain in complex with c-di-GMP to be determined. PlzA has a two-domain structure, where each domain comprises topologically equivalent PilZ domains with minimal sequence identity but remarkable structural similarity. The c-di-GMP binding site is formed by the linker connecting the two domains. While the structure of apo PlzA could not be determined, previous fluorescence resonance energy transfer data suggest that apo and holo forms of the protein are structurally distinct. The information obtained from this study will facilitate ongoing efforts to identify the molecular mechanisms of PlzA-mediated regulation in ticks and mammals.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1978

Bias structure to efficiently package a magnetic bubble domain device

A single, compact bias structure to efficiently package a plurality of magnetic bubble domain device chips having different bias requirements. The vertical magnetic field distribution within the bias structure air gap is selectively controlled by a magnetically soft field adjusting assembly suitably attached within the bias structure. The size and configuration of the field adjusting assembly tailors local field variations within the air gap to correspond with the bias requirements of the bubble domain chips disposed therein.

Chen, Thomas T.↗
DOE OSTI2018

Water-Mediated Carbon–Oxygen Hydrogen Bonding Facilitates S -Adenosylmethionine Recognition in the Reactivation Domain of Cobalamin-Dependent Methionine Synthase

The C-terminal domain of cobalamin-dependent methionine synthase (MetH) has an essential role in catalyzing the reactivation of the enzyme following the oxidation of its cobalamin cofactor. This reactivation occurs through reductive methylation of the cobalamin using S-adenosylmethionine (AdoMet) as the methyl donor. Here, we examine the molecular recognition of AdoMet by the MetH reactivation domain utilizing structural, biochemical, and computational approaches. Crystal structures of the Escherichia coli MetH reactivation domain in complex with AdoMet, the methyl transfer product S-adenosylhomocysteine (AdoHcy), and the AdoMet analogue inhibitor sinefungin illustrate that the ligands exhibit an analogous conformation within the solvent-exposed substrate binding cleft of the enzyme. AdoMet binding is stabilized by an intramolecular sulfur–oxygen chalcogen bond between the sulfonium and carboxylate groups of the substrate and by water-mediated carbon–oxygen hydrogen bonding between the sulfonium cation and the side chains of Glu1097 and Glu1128 that bracket the substrate binding cleft. AdoMet and sinefungin exhibited similar binding affinities for the MetH reactivation domain, whereas AdoHcy displayed an affinity for the enzyme that was an order of magnitude lower. Mutations of Glu1097 and Glu1128 diminished the AdoMet/AdoHcy binding selectivity ratio to approximately 2-fold, underscoring the role of these residues in enabling the enzyme to discriminate between the substrate and product. Together, these findings indicate that Glu1097 and Glu1128 in MetH promote high-affinity recognition of AdoMet and that sinefungin and potentially other AdoMet-based methyltransferase inhibitors can abrogate MetH reactivation, which would result in off-target effects associated with alterations in methionine homeostasis and one-carbon metabolism.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Structural basis of LAIR1 targeting by polymorphic Plasmodium RIFINs

RIFIN, a large family of Plasmodium variant surface antigens, plays a crucial role in malaria pathogenesis by mediating immune suppression through activation of inhibitory receptors such as LAIR1, and antibodies with LAIR1 inserts have been identified that bind infected erythrocytes through RIFIN. However, details of RIFIN-mediated LAIR1 recognition and receptor activation have been unclear. Here, we use negative-stain EM to define the architecture of LAIR1-inserted antibodies and determine crystal structures of RIFIN-variable 2 (V2) domain in complex with a LAIR1 domain. These structures reveal the LAIR1-binding region of RIFIN to be hydrophobic and membrane-distal, to exhibit extensive structural diversity, and to interact with RIFIN-V2 in a one-to-one fashion. Through structural and sequence analysis of various LAIR1 constructs, we identify essential elements of RIFIN-binding on LAIR1. Furthermore, a structure-derived LAIR1-binding sequence signature ascertained >20 LAIR1-binding RIFINs, including some from P. falciparum field strains and Plasmodium species infecting gorillas and chimpanzees.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Structural and Biochemical Characterization of Human PR70 in Isolation and in Complex with the Scaffolding Subunit of Protein Phosphatase 2A

Protein Phosphatase 2A (PP2A) is a major Ser/Thr phosphatase involved in the regulation of various cellular processes. PP2A assembles into diverse trimeric holoenzymes, which consist of a scaffolding (A) subunit, a catalytic (C) subunit and various regulatory (B) subunits. Here we report a 2.0 A crystal structure of the free B’’/PR70 subunit and a SAXS model of an A/PR70 complex. The crystal structure of B’’/PR70 reveals a two domain elongated structure with two Ca 2+ binding EF-hands. Furthermore, we have characterized the interaction of both binding partner and their calcium dependency using biophysical techniques. Ca 2+ biophysical studies with Circular Dichroism showed that the two EF-hands display different affinities to Ca2+. In the absence of the catalytic C-subunit, the scaffolding A-subunit remains highly mobile and flexible even in the presence of the B’’/PR70 subunit as judged by SAXS. Isothermal Titration Calorimetry studies and SAXS data support that PR70 and the A-subunit have high affinity to each other. This study provides additional knowledge about the structural basis for the function of B’’ containing holoenzymes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Biochemical and Structural Basis for Controlling Chemical Modularity in Fungal Polyketide Biosynthesis

Modular collaboration between iterative fungal polyketide synthases (IPKSs) is an important mechanism for generating structural diversity of polyketide natural products. Inter-PKS communication and substrate channeling are controlled in large by the starter unit acyl carrier protein transacylase (SAT) domain found in the accepting IPKS module. Here in this study, we reconstituted the modular biosynthesis of the benzaldehyde core of the chaetoviridin and chaetomugilin azaphilone natural products using the IPKSs CazF and CazM. Our studies revealed a critical role of CazM’s SAT domain in selectively transferring a highly reduced triketide product from CazF. In contrast, a more oxidized triketide that is also produced by CazF and required in later stages of biosynthesis of the final product is not recognized by the SAT domain. The structural basis for the acyl unit selectivity was uncovered by the first X-ray structure of a fungal SAT domain, highlighted by a covalent hexanoyl thioester intermediate in the SAT active site. Finally, the crystal structure of SAT domain will enable protein engineering efforts aimed at mixing and matching different IPKS modules for the biosynthesis of new compounds.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Cryo-EM structure of OSCA1.2 from Oryza sativa elucidates the mechanical basis of potential membrane hyperosmolality gating

Sensing and responding to environmental water deficiency and osmotic stresses are essential for the growth, development, and survival of plants. Recently, an osmolality-sensing ion channel called OSCA1 was discovered that functions in sensing hyperosmolality in Arabidopsis . In this paper, we report the cryo-electron microscopy (cryo-EM) structure and function of an OSCA1 homolog from rice ( Oryza sativa ; OsOSCA1.2), leading to a model of how it could mediate hyperosmolality sensing and transport pathway gating. The structure reveals a dimer; the molecular architecture of each subunit consists of 11 transmembrane (TM) helices and a cytosolic soluble domain that has homology to RNA recognition proteins. The TM domain is structurally related to the TMEM16 family of calcium-dependent ion channels and lipid scramblases. The cytosolic soluble domain possesses a distinct structural feature in the form of extended intracellular helical arms that are parallel to the plasma membrane. These helical arms are well positioned to potentially sense lateral tension on the inner leaflet of the lipid bilayer caused by changes in turgor pressure. Computational dynamic analysis suggests how this domain couples to the TM portion of the molecule to open a transport pathway. Hydrogen/deuterium exchange mass spectrometry (HDXMS) experimentally confirms the conformational dynamics of these coupled domains. These studies provide a framework to understand the structural basis of proposed hyperosmolality sensing in a staple crop plant, extend our knowledge of the anoctamin superfamily important for plants and fungi, and provide a structural mechanism for potentially translating membrane stress to transport regulation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Structure of the sensory domain of McpX from Sinorhizobium meliloti, the first known bacterial chemotactic sensor for quaternary ammonium compounds

The α-proteobacterium Sinorhizobium meliloti can live freely in the soil or engage in a symbiosis with its legume host. S. meliloti facilitates nitrogen fixation in root nodules, thus providing pivotal, utilizable nitrogen to the host. The organism has eight chemoreceptors, namely McpT to McpZ and IcpA that facilitate chemotaxis. McpX is the first known bacterial sensor of quaternary ammonium compounds (QACs) such as choline and betaines. Because QACs are exuded at chemotaxis-relevant concentrations by germinating alfalfa seeds, McpX has been proposed to contribute to host-specific chemotaxis. We have determined the crystal structure of the McpX periplasmic region (McpX PR ) in complex with the proline betaine at 2.7 Å resolution. In the crystal, the protein forms a symmetric dimer with one proline betaine molecule bound to each monomer of McpX PR within membrane-distal CACHE module. The ligand is bound through cation–π interactions with four aromatic amino acid residues. Mutational analysis in conjunction with binding studies revealed that a conserved aspartate residue is pivotal for ligand binding. We discovered that, in a striking example of convergent evolution, the ligand-binding site of McpX PR resembles that of a group of structurally unrelated betaine-binding proteins including ProX and OpuAC. Through this comparison and docking studies, we rationalized the specificity of McpX PR for this specific group of ligands. Collectively, our structural, biochemical, and molecular docking data have revealed the molecular determinants in McpX that are crucial for its rare ligand specificity for QACs.

Shrestha, Manisha↗
DOE OSTI2024

Periodicity staircase in a centrosymmetric Fe/Gd magnetic thin film system

Abstract The presence of multiple competing periodicities may result in a system to go through states with modulated periodicities, an example of which is the self-similar staircase-like structure called the Devil’s Staircase. Herein we report on a novel staircase structure of domain periodicity in an amorphous and centrosymmetric Fe/Gd magnetic thin film system wherein the reciprocal space wavevector Q due to the ordered stripe domains does not evolve continuously, rather exhibits a staircase structure. Resonant X-ray scattering experiments show jumps in the periodicity of the stripe domains as a function of an external magnetic field. When resolved in components, the length-scale step change along Q x was found to be an integral multiple of a minimum step height of 7 nm, which resembles closely to the exchange length of the system. Modeling the magnetic texture in the Fe/Gd system as an achiral spin arrangement, we have been able to reproduce the steps in the magnetization using a Landau-Lifshitz spin dynamics calculation. Our results indicate that anisotropy and not the dipolar interaction is the dominant cause for the staircase pattern, thereby revealing the effect of achiral magnetism.

36 MATERIALS SCIENCE↗