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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 235 records · Page 13
All sourcesNASA NTRSDOE OSTI
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 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↗
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 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↗
DOE OSTI2022

Interfacial Exchange Phenomena Driven by Ferromagnetic Domains

Abstract Interfacial proximity effects in antiferromagnetic/ferromagnetic (AFM/FM) bilayers control the exchange‐bias (EB) phenomena exploited in most spintronic devices, although still is lack of full understanding. Discordant results, including different exchange‐bias field ( H E ), coercivity ( H C ), or blocking temperature ( T B ) found even in similar systems, are usually ascribed to uncontrolled parameters, namely dissimilar interfacial defects, structure, and thicknesses. Here, it is shown in the very same sample that the magnetic domain structure during the magnetization reversal of the FM layer controls those mentioned effects. Simultaneous transport and vectorial‐resolved magnetic measurements performed in a V 2 O 3 /Co system during warming after different field cooling (FC) procedures exhibit a strong dependence on the FC angle and the domain structure of the FM layer. Remarkably, magnetization reversal analysis reveals 35 K of variation in T B and up to a factor of two in H E . These observations can be explained within the random‐field model for the interfacial exchange coupling with a fixed AFM domain structure in contact with a variable (angle‐dependent) FM domain structure. The results highlight the importance of the domain structure and magnetization reversal of the FM layer (not previously considered) in the EB phenomena, with potential to tailor interfacial effects in future spintronic devices.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Modeling SARS-CoV-2 proteins in the CASP-commons experiment

Critical Assessment of Structure Prediction (CASP) is an organization aimed at advancing the state of the art in computing protein structure from sequence. In the spring of 2020, CASP launched a community project to compute the structures of the most structurally challenging proteins coded for in the SARS-CoV-2 genome. Forty-seven research groups submitted over 3000 three-dimensional models and 700 sets of accuracy estimates on 10 proteins. The resulting models were released to the public. CASP community members also worked together to provide estimates of local and global accuracy and identify structure-based domain boundaries for some proteins. Subsequently, two of these structures (ORF3a and ORF8) have been solved experimentally, allowing assessment of both model quality and the accuracy estimates. Models from the AlphaFold2 group were found to have good agreement with the experimental structures, with main chain GDT_TS accuracy scores ranging from 63 (a correct topology) to 87 (competitive with experiment).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Structural and magnetic properties of CoTeMo⁢O 6

Here, we have conducted a comprehensive investigation into the magnetic properties of the chiral multiferroic material CoTeMo⁢O 6 . In contrast with the previous claim of canted antiferromagnetic order with ferromagnetic components [Y. Doi et al., J. Solid State Chem. 182, 3232 (2009)], our investigation reveals an antiferromagnetic ground state with compensated moments, providing an interesting platform for exploring exotic material properties. Through careful measurements of magnetization under a series of applied fields, we demonstrate that there exist two sequential field-induced magnetic transitions in CoTeMo⁢O 6 , with one occurring at 𝐻 𝑐⁢1 =460 Oe along the 𝑎 axis, and the other at 𝐻 𝑐⁢2 =1.16 T with the field along the 𝑏 axis. The values of 𝐻 𝑐⁢1 and 𝐻 𝑐⁢2 exhibit strong angular dependence and diverge with different rates as the applied field is rotated 90 ° within the 𝑎⁢𝑏 plane. This reflects the distinct nature of these transitions, which is further supported by the different critical behavior of 𝐻 𝑐⁢1 and 𝐻 𝑐⁢2 , characterized by the values of 𝛾, in the function of 𝐻 𝑐 =𝐻 0 ⁡(1−𝑇/𝑇 𝑐 ) 𝛾 . Furthermore, we have demonstrated that there exist structural and magnetic twin domains in CoTeMo⁢O 6 that strongly affect the experimental measurement of their macroscopic properties. Intriguingly, these twin domains can be related to the orthorhombicity/chirality of the crystal structure with the space group 𝑃⁢2 1 ⁢2 1⁢ 2. We further explored the magnetic and structural domains with uniaxial pressure and polarized light microscopy. Our results suggest that CoTeMo⁢O 6 could be used as a unique platform for investigating the intriguing physics involving intertwined degrees of freedom. The tunability of the underlying domain distribution and its strong anisotropy could also be useful for developing functional devices and applications.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

The catalytic domains of Streptococcus mutans glucosyltransferases: a structural analysis

Streptococcus mutans, found in the human oral cavity, is a significant contributor to the pathogenesis of dental caries. This bacterium expresses three genetically distinct types of glucosyltransferases named GtfB (GTF-I), GtfC (GTF-SI) and GtfD (GTF-S) that play critical roles in the development of dental plaque. The catalytic domains of GtfB, GtfC and GtfD contain conserved active-site residues for the overall enzymatic activity that relate to hydrolytic glycosidic cleavage of sucrose to glucose and fructose, release of fructose and generation of a glycosyl-enzyme intermediate in the reducing end. In a subsequent transglycosylation step, the glucosyl moiety is transferred to the nonreducing end of an acceptor to form a growing glucan polymer chain made up of glucose molecules. It has been proposed that both sucrose breakdown and glucan synthesis occur in the same active site of the catalytic domain, although the active site does not appear to be large enough to accommodate both functions. These three enzymes belong to glycoside hydrolase family 70 (GH70), which shows homology to glycoside hydrolase family 13 (GH13). GtfC synthesizes both soluble and insoluble glucans (α-1,3 and α-1,6 glycosidic linkages), while GtfB and GtfD synthesize only insoluble or soluble glucans, respectively. Here, crystal structures of the catalytic domains of GtfB and GtfD are reported. These structures are compared with previously determined structures of the catalytic domain of GtfC. With this work, apo structures and inhibitor-complex structures with acarbose are now available for the catalytic domains of GtfC and GtfB. The structure of GtfC with maltose allows further identification and comparison of active-site residues. A model of sucrose binding to GtfB is also included. The new structure of the catalytic domain of GtfD affords a structural comparison of the three S. mutans glycosyltransferases. Unfortunately, the catalytic domain of GtfD is not complete since crystallization resulted in the structure of a truncated protein lacking approximately 200 N-terminal residues of domain IV.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

The N-terminal domains of NLR immune receptors exhibit structural and functional similarities across divergent plant lineages

Nucleotide-binding domain and leucine-rich repeat (NLR) proteins are a prominent class of intracellular immune receptors in plants. However, our understanding of plant NLR structure and function is limited to the evolutionarily young flowering plant clade. Here, we describe an extended spectrum of NLR diversity across divergent plant lineages and demonstrate the structural and functional similarities of N-terminal domains that trigger immune responses. We show that the broadly distributed coiled-coil (CC) and toll/interleukin-1 receptor (TIR) domain families of nonflowering plants retain immune-related functions through translineage activation of cell death in the angiosperm Nicotiana benthamiana. We further examined a CC subfamily specific to nonflowering lineages and uncovered an essential N-terminal MAEPL motif that is functionally comparable with motifs in resistosome-forming CC-NLRs. Consistent with a conserved role in immunity, the ectopic activation of CC MAEPL in the nonflowering liverwort Marchantia polymorpha led to profound growth inhibition, defense gene activation, and signatures of cell death. Moreover, comparative transcriptomic analyses of CC MAEPL activity delineated a common CC-mediated immune program shared across evolutionarily divergent nonflowering and flowering plants. Collectively, our findings highlight the ancestral nature of NLR-mediated immunity during plant evolution that dates its origin to at least ~500 million years ago.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Disorder-induced time effect in the antiferromagnetic domain state of Fe 1+ y Te

Herein we report on temperature-dependent soft X-ray absorption spectroscopy (XAS) measurements utilizing linearly polarized synchrotron radiation to probe magnetic phase transitions in iron-rich Fe 1+y Te (y ≈ 0.12). X-ray magnetic linear dichroism (XMLD) signals, which sense magnetic ordering processes at surfaces, start to increase monotonically below the Néel temperature T N = 57 K. This increase is due to a progressive bicollinear antiferromagnetic (AFM) alignment of Fe spins of the monoclinic Fe 1+y Te parent phase. This AFM alignment was achieved by a [1 0 0]-oriented biasing field favoring a single-domain state during cooling across T N . Our specific heat and magnetization measurements confirm the bulk character of this AFM phase transition. On longer time scales, however, we observe that the field-biased AFM state is highly unstable even at the lowest temperature of T = 3 K. After switching off the biasing field, the XMLD signal decays exponentially with a time constant τ = 1506 s. The initial XMLD signal is restored only upon repeating a cycle consisting of heating and field-cooling through T N . We explain the time effect by a gradual formation of a multi-domain state with 90° rotated AFM domains, promoted by structural disorder, facilitating the motion of twin-domains. Significant disorder in our Fe 1+y Te sample is evident from our X-ray diffraction and specific heat data. The stability of magnetic phases in Fe-chalcogenides is an important material property, since the Fe(Te 1-x Se x ) phase diagram shows magnetism intimately connected with superconductivity.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Atomic layer epitaxy of kagome magnet Fe 3 Sn 2 and Sn-modulated heterostructures

Magnetic materials with kagome crystal structure exhibit rich physics, such as frustrated magnetism, skyrmion formation, topological flat bands, and Dirac/Weyl points. Until recently, most studies on kagome magnets have been performed on bulk crystals or polycrystalline films. Here, we report the atomic layer molecular beam epitaxy synthesis of high-quality thin films of topological kagome magnet Fe 3 Sn 2 . The structural and magnetic characterization of Fe 3 Sn 2 on epitaxial Pt(111) identifies highly ordered films with c-plane orientation and an in-plane magnetic easy axis. Studies on the local magnetic structure by anomalous Nernst effect imaging reveal in-plane oriented micrometer size domains. Superlattice structures consisting of Fe 3 Sn 2 and Fe 3 Sn are also synthesized by atomic layer molecular beam epitaxy, demonstrating the ability to modulate the sample structure at the atomic level. The realization of high-quality films by atomic layer molecular beam epitaxy opens the door to explore the rich physics of this system and investigate novel spintronic phenomena by interfacing Fe 3 Sn 2 with other materials.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Investigation of the Effect of Temperature on the Structure of SARS-CoV-2 Spike Protein by Molecular Dynamics Simulations

Statistical and epidemiological data imply temperature sensitivity of the SARS-CoV2 coronavirus. However, the molecular level understanding of the virus structure at different temperature is still not clear. Spike protein is the outermost structural protein of the SARS-CoV-2 virus which interacts with the Angiotensin Converting Enzyme 2 (ACE2), a human receptor, and enters the respiratory system. In this study, we performed an all atom molecular dynamics simulation to study the effect of temperature on the structure of the Spike protein. After 200 ns of simulation at different temperatures, we came across some interesting phenomena exhibited by the protein. We found that the solvent exposed domain of Spike protein, namely S1, is more mobile than the transmembrane domain, S2. Structural studies implied the presence of several charged residues on the surface of N-terminal Domain of S1 which are optimally oriented at 10– 30°C. Bioinformatics analyses indicated that it is capable of binding to other human receptors and should not be disregarded. Additionally, we found that receptor binding motif (RBM), present on the receptor binding domain (RBD) of S1, begins to close around temperature of 40°C and attains a completely closed conformation at 50°C. We also found that the presence of glycan moieties did not influence the observed protein dynamics. Nevertheless, the closed conformation disables its ability to bind to ACE2, due to the burying of its receptor binding residues. Our results clearly show that there are active and inactive states of the protein at different temperatures. This would not only prove beneficial for understanding the fundamental nature of the virus, but would be also useful in the development of vaccines and therapeutics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Ferroelectric HfO 2 and the importance of strain

Ferroelectric oxides based on HfO 2 show tremendous promise for the next generation of memory and logic devices. The ferroelectric polymorph is one of several that can be derived from the high symmetry cubic fluorite structure of HfO 2 . A single grain of HfO 2 may consist of a coherent mixture of multiple orientational and translational variants of different polymorphs. Here, we use symmetry-adapted strain-order parameters to elucidate the relationship between the different HfO 2 polymorphs and their symmetrically equivalent variants. We use first-principles electronic structure methods to identify minimum energy pathways and map them in subspaces of the symmetry-adapted strain order parameters. We next investigate the atomic structure of domain boundaries that separate coexisting variants of ferroelectric HfO 2 . Further, we rely on Gibbsian excess quantities and a precise specification of mechanical boundary conditions to describe the thermodynamic properties of domain boundaries. Our first-principles calculations show that the O and Hf shuffle arrangement within a domain boundary is closely related to the intermediate shuffle patterns of the homogeneous pathways between ferroelectric variants. Furthermore, the preferred structure within a boundary is very sensitive to local strain constraints imposed by the adjacent ferroelectric variants, leading to highly anisotropic domain boundary energies.

36 MATERIALS SCIENCE↗