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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 289 records · Page 16
All sourcesNASA NTRSDOE OSTI
NASA NTRS2006

Relativistic MHD Simulations of Precessed Jets

Relativistic jets are considered to be generated by magnetic fields in a rotating black hole with accretion disk. Consequently, resulting outflows contain magnetic fields in them and control the propagation of jets. We have performed 3D relativistic MHD simulations to investigate the stability and structure of precessed MHD jets with large Lorentz factor by using a newly developed 3D GRMHD code. We have performed simulations of supermagnetosonic jets surrounded by a fast wind. The simulation results reveal complex pressure structure inside the RMHD jet. The structure is produced by a combination of the helical surface and body modes excited by the precession as predicted theoretically. The wavelength of the body mode which occurs in an internal helical twist is much shorter than that of the helical twist surface mode. We will present some comparisons between the RMHD simulations and theoretical predictions, and potential observables and discuss the effect of wind.

Mizuno, Y.↗
NASA NTRS2009

The Structure of Coronal Loops

It is widely believed that the simple coronal loops observed by XUV imagers, such as EIT, TRACE, or XRT, actually have a complex internal structure consisting of many (perhaps hundreds) of unresolved, interwoven "strands". According to the nanoflare model, photospheric motions tangle the strands, causing them to reconnect and release the energy required to produce the observed loop plasma. Although the strands, themselves, are unresolved by present-generation imagers, there is compelling evidence for their existence and for the nanoflare model from analysis of loop intensities and temporal evolution. A problem with this scenario is that, although reconnection can eliminate some of the strand tangles, it cannot destroy helicity, which should eventually build up to observable scales. we consider, therefore, the injection and evolution of helicity by the nanoflare process and its implications for the observed structure of loops and the large-scale corona. we argue that helicity does survive and build up to observable levels, but on spatial and temporal scales larger than those of coronal loops. we discuss the implications of these results for coronal loops and the corona, in general .

Antiochos, Spiro K.↗
DOE OSTI2022

Sas20 is a highly flexible starch-binding protein in the Ruminococcus bromii cell-surface amylosome

Ruminococcus bromii is a keystone species in the human gut that has the rare ability to degrade dietary resistant starch (RS). This bacterium secretes a suite of starch-active proteins that work together within larger complexes called amylosomes that allow R. bromii to bind and degrade RS. Starch adherence system protein 20 (Sas20) is one of the more abundant proteins assembled within amylosomes, but little could be predicted about its molecular features based on amino acid sequence. Here, we performed a structure–function analysis of Sas20 and determined that it features two discrete starch-binding domains separated by a flexible linker. We show that Sas20 domain 1 contains an N-terminal β-sandwich followed by a cluster of α-helices, and the nonreducing end of maltooligosaccharides can be captured between these structural features. Furthermore, the crystal structure of a close homolog of Sas20 domain 2 revealed a unique bilobed starch-binding groove that targets the helical α1,4-linked glycan chains found in amorphous regions of amylopectin and crystalline regions of amylose. Affinity PAGE and isothermal titration calorimetry demonstrated that both domains bind maltoheptaose and soluble starch with relatively high affinity (K d ≤ 20 μM) but exhibit limited or no binding to cyclodextrins. Finally, small-angle X-ray scattering analysis of the individual and combined domains support that these structures are highly flexible, which may allow the protein to adopt conformations that enhance its starch-targeting efficiency. Taken together, we conclude that Sas20 binds distinct features within the starch granule, facilitating the ability of R. bromii to hydrolyze dietary RS.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS2002

A large iris-like expansion of a mechanosensitive channel protein induced by membrane tension

MscL, a bacterial mechanosensitive channel of large conductance, is the first structurally characterized mechanosensor protein. Molecular models of its gating mechanisms are tested here. Disulfide crosslinking shows that M1 transmembrane alpha-helices in MscL of resting Escherichia coli are arranged similarly to those in the crystal structure of MscL from Mycobacterium tuberculosis. An expanded conformation was trapped in osmotically shocked cells by the specific bridging between Cys 20 and Cys 36 of adjacent M1 helices. These bridges stabilized the open channel. Disulfide bonds engineered between the M1 and M2 helices of adjacent subunits (Cys 32-Cys 81) do not prevent channel gating. These findings support gating models in which interactions between M1 and M2 of adjacent subunits remain unaltered while their tilts simultaneously increase. The MscL barrel, therefore, undergoes a large concerted iris-like expansion and flattening when perturbed by membrane tension.

NASA Discipline Cell Biology↗
DOE OSTI2023

De novo designed ice-binding proteins from twist-constrained helices

Attaining molecular-level control over solidification processes is a crucial aspect of materials science. To control ice formation, organisms have evolved bewildering arrays of ice-binding proteins (IBPs), but these have poorly understood structure–activity relationships. We propose that reverse engineering using de novo computational protein design can shed light on structure–activity relationships of IBPs. We hypothesized that the model alpha-helical winter flounder antifreeze protein uses an unusual undertwisting of its alpha-helix to align its putative ice-binding threonine residues in exactly the same direction. We test this hypothesis by designing a series of straight three-helix bundles with an ice-binding helix projecting threonines and two supporting helices constraining the twist of the ice-binding helix. Our findings show that ice-recrystallization inhibition by the designed proteins increases with the degree of designed undertwisting, thus validating our hypothesis, and opening up avenues for the computational design of IBPs.

Science & Technology - Other Topics↗
DOE OSTI2020

Characterizing magnetized plasmas with dynamic mode decomposition

Accurate and efficient plasma models are essential to understand and control experimental devices. Existing magnetohydrodynamic or kinetic models are nonlinear and computationally intensive and can be difficult to interpret, while often only approximating the true dynamics. In this work, data-driven techniques recently developed in the field of fluid dynamics are leveraged to develop interpretable reduced-order models of plasmas that strike a balance between accuracy and efficiency. In particular, dynamic mode decomposition (DMD) is used to extract spatio-temporal magnetic coherent structures from the experimental and simulation datasets of the helicity injected torus with steady inductive (HIT-SI) experiment. Three-dimensional magnetic surface probes from the HIT-SI experiment are analyzed, along with companion simulations with synthetic internal magnetic probes. A number of leading variants of the DMD algorithm are compared, including the sparsity-promoting and optimized DMD. Optimized DMD results in the highest overall prediction accuracy, while sparsity-promoting DMD yields physically interpretable models that avoid overfitting. These DMD algorithms uncover several coherent magnetic modes that provide new physical insights into the inner plasma structure. These modes were subsequently used to discover a previously unobserved three-dimensional structure in the simulation, rotating at the second injector harmonic. Finally, using data from probes at experimentally accessible locations, DMD identifies a resistive kink mode, a ubiquitous instability seen in magnetized plasmas.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2021

Helical magnetic order and Fermi surface nesting in noncentrosymmetric ScFeGe

Here, an investigation of the structural, magnetic, thermodynamic, and charge transport properties of noncentrosymmetric hexagonal ScFeGe reveals it to be an anisotropic metal with a transition to a weak itinerant incommensurate helimagnetic state below T N =36 K. Neutron diffraction measurements discovered a temperature and field independent helical wave vector k = (0 0 0.193) with magnetic moments of 0.53 μ B per Fe confined to the ab-plane. Density functional theory calculations are consistent with these measurements and find several bands that cross the Fermi level along the c-axis with a nearly degenerate set of flat bands just above the Fermi energy. The anisotropy found in the electrical transport is reflected in the calculated Fermi surface, which consists of several warped flat sheets along the c-axis with two regions of significant nesting, one of which has a wave vector that closely matches that found in the neutron diffraction. The electronic structure calculations, along with a strong anomaly in the c-axis conductivity at TN, signal a Fermi surface driven magnetic transition, similar to that found in spin density wave materials. Magnetic fields applied in the ab-plane result in a metamagnetic transition with a threshold field of ≈ 6.7 T along with a sharp, strongly temperature dependent discontinuity and a change in sign of the magnetoresistance for in-plane currents. Thus, ScFeGe is an ideal system to investigate the effect of in-plane magnetic fields on a helimagnet with a c-axis propagation vector, where the relative strength of the magnetic interactions and anisotropies determine the topology and magnetic structure.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

X-ray Crystal Structure of Thorium Tetrahydroborate, Th(BH 4 ) 4 , and Computational Studies of An(BH 4 ) 4 (An = Th, U)

Here the crystal structure of Th(BH 4 ) 4 is described. Two of the four BH 4 – ions are terminal and tridentate (κ 3 ), whereas the other two bridge between neighboring Th IV centers in a κ 2 ,κ 2 (i.e., bis-bidentate) fashion. Thus, each thorium center is bound to six BH 4 – groups by 14 Th–H bonds. The six boron atoms describe a distorted octahedron in which the κ 3 -BH 4 – ions are mutually cis; the 14 ligating hydrogen atoms define a highly distorted bicapped hexagonal antiprism. The thorium centers are linked into a polymer consisting of interconnected helical chains wound about 4-fold screw axes. The structures of An(BH 4 ) 4 (An = Th, U) were also investigated by DFT. The geometries of [An(BH 4 ) 6 ] 2– , [An3(BH 4 ) 16 ] 4– , and [An 5 (BH 4 ) 26 ] 6– fragments of the polymeric structures were optimized at the B3LYP and/or PBE levels. Most calculated geometries are 14-coordinate and agree with the experimental structures, but isolated [Th(BH 4 ) 6 ] 2– units are predicted to feature 16-coordinate Th IV centers.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1998

Helicity, membrane incorporation, orientation and thermal stability of the large conductance mechanosensitive ion channel from E. coli

In this report, we present structural studies on the large conductance mechanosensitive ion channel (MscL) from E. coli in detergent micelles and lipid vesicles. Both transmission Fourier transform infrared spectroscopy and circular dichroism (CD) spectra indicate that the protein is highly helical in detergents as well as liposomes. The secondary structure of the proteins was shown to be highly resistant towards denaturation (25-95 degrees C) based on an ellipticity thermal profile. Amide H+/D+ exchange was shown to be extensive (ca. 66%), implying that two thirds of the protein are water accessible. MscL, reconstituted in oriented lipid bilayers, was shown to possess a net bilayer orientation using dichroic ratios measured by attenuated total-reflection Fourier transform infrared spectroscopy. Here, we present and discuss this initial set of structural data on this new family of ion-channel proteins.

NASA Discipline Cell Biology↗
DOE OSTI2024

Large-eddy simulations of turbulent wake flows behind helical- and straight-bladed vertical axis wind turbines rotating at low tip speed ratios

Turbulent wake flows behind helical- and straight-bladed vertical axis wind turbines (VAWTs) rotating at low tip speed ratios (TSRs) are studied numerically. The turbulent flows are simulated using the large-eddy simulation (LES) model, and the rotating turbine blades are modeled using the actuator line method. The helical VAWT has identical key parameters as the straight VAWT except for the 135° helical twist of the blades over the 0.3m vertical span. A set of LES runs are performed for two TSRs, 0.6 and 0.4, and the results are reported and analyzed. At these low TSRs, the wake behind the straight-bladed VAWT exhibits two-dimensional dominant flow motions (in the horizontal plane perpendicular to the straight blades) in the near-wake region that cause considerable spanwise expansion of the wake as it extends downstream. In contrast, the helical-bladed VAWT generates highly three-dimensional (3D) wake flow structures and upward/downward mean flow motions within the wake that cause the wake to expand mainly in the vertical direction. Turbulence statistical analyses also show that the 3D wake flow features induced by the helical blades accelerate the wake transition to turbulence and enhance the small-scale turbulent dissipation (as shown by the subgrid-scale turbulent dissipation in the LES), which leads to a more rapid decay of the wake turbulence intensity than that in the straight-bladed VAWT case at the same TSR. Finally, compared with the straight-bladed VAWT, the helical-bladed VAWT also exhibits much smaller temporal variations for the torque and power coefficients during the rotation cycle, which can be beneficial for wind power generation.

17 WIND ENERGY↗
DOE OSTI2024

Tertiary folds of the SL5 RNA from the 5 ' proximal region of SARS-CoV-2 and related coronaviruses

Coronavirus genomes sequester their start codons within stem-loop 5 (SL5), a structured, 5' genomic RNA element. In most alpha- and betacoronaviruses, the secondary structure of SL5 is predicted to contain a four-way junction of helical stems, some of which are capped with UUYYGU hexaloops. Here, using cryogenic electron microscopy (cryo-EM) and computational modeling with biochemically determined secondary structures, we present three-dimensional structures of SL5 from six coronaviruses. The SL5 domain of betacoronavirus severe-acute-respiratory-syndrome-related coronavirus 2 (SARS-CoV-2), resolved at 4.7 Å resolution, exhibits a T-shaped structure, with its UUYYGU hexaloops at opposing ends of a coaxial stack, the T’s “arms.” Further analysis of SL5 domains from SARS-CoV-1 and MERS (7.1 and 6.4 to 6.9 Å resolution, respectively) indicate that the junction geometry and inter-hexaloop distances are conserved features across these human-infecting betacoronaviruses. The MERS SL5 domain displays an additional tertiary interaction, which is also observed in the non-human-infecting betacoronavirus BtCoV-HKU5 (5.9 to 8.0 Å resolution). SL5s from human-infecting alphacoronaviruses, HCoV-229E and HCoV-NL63 (6.5 and 8.4 to 9.0 Å resolution, respectively), exhibit the same coaxial stacks, including the UUYYGU-capped arms, but with a phylogenetically distinct crossing angle, an X-shape. As such, all SL5 domains studied herein fold into stable tertiary structures with cross-genus similarities and notable differences, with implications for potential protein-binding modes and therapeutic targets.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1998

Chromatin conformation in living cells: support for a zig-zag model of the 30 nm chromatin fiber

A new method was used to probe the conformation of chromatin in living mammalian cells. The method employs ionizing radiation and is based on the concept that such radiation induces correlated breaks in DNA strands that are in spatial proximity. Human dermal fibroblasts in G0 phase of the cell cycle and Chinese hamster ovary cells in mitosis were irradiated by X-rays or accelerated ions. Following lysis of the cells, DNA fragments induced by correlated breaks were end-labeled and separated according to size on denaturing polyacrylamide gels. A characteristic peak was obtained for a fragment size of 78 bases, which is the size that corresponds to one turn of DNA around the nucleosome. Additional peaks between 175 and 450 bases reflect the relative position of nearest-neighbor nucleosomes. Theoretical calculations that simulate the indirect and direct effect of radiation on DNA demonstrate that the fragment size distributions are closely related to the chromatin structure model used. Comparison of the experimental data with theoretical results support a zig-zag model of the chromatin fiber rather than a simple helical model. Thus, radiation-induced damage analysis can provide information on chromatin structure in the living cell. Copyright 1998 Academic Press.

Non-NASA Center↗
DOE OSTI2023

Structural mechanism of intracellular autoregulation of zinc uptake in ZIP transporters

Abstract Zinc is an essential micronutrient that supports all living organisms through regulating numerous biological processes. However, the mechanism of uptake regulation by intracellular Zn 2+ status remains unclear. Here we report a cryo-electron microscopy structure of a ZIP-family transporter from Bordetella bronchiseptica at 3.05 Å resolution in an inward-facing, inhibited conformation. The transporter forms a homodimer, each protomer containing nine transmembrane helices and three metal ions. Two metal ions form a binuclear pore structure, and the third ion is located at an egress site facing the cytoplasm. The egress site is covered by a loop, and two histidine residues on the loop interact with the egress-site ion and regulate its release. Cell-based Zn 2+ uptake and cell growth viability assays reveal a negative regulation of Zn 2+ uptake through sensing intracellular Zn 2+ status using a built-in sensor. These structural and biochemical analyses provide mechanistic insight into the autoregulation of zinc uptake across membranes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Augmented DNA Nanoarchitectures: A Structural Library of 3D Self-Assembling Tensegrity Triangle Variants

The DNA tensegrity triangle is known to reliably self-assemble into a 3D rhombohedral crystalline lattice via sticky-end cohesion. Here, in this study, the library of accessible motifs is expanded through covalent extensions of intertriangle regions and sticky-end-coordinated linkages of adjacent triangles with double helical segments using both geometrically symmetric and asymmetric configurations. The molecular structures of 18 self-assembled architectures at resolutions of 3.32–9.32 Å are reported; the observed cell dimensions, cavity sizes, and cross-sectional areas agree with theoretical expectations. These data demonstrate that fine control over triclinic and rhombohedral crystal parameters and the customizability of more complex 3D DNA lattices are attainable via rational design. It is anticipated that augmented DNA architectures may be fine-tuned for the self-assembly of designer nanocages, guest–host complexes, and proscriptive 3D nanomaterials, as originally envisioned. Finally, designer asymmetric crystalline building blocks can be seen as a first step toward controlling and encoding information in three dimensions.

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

Structural Characterization and Ligand-Induced Conformational Changes of SenB, a Se-Glycosyltransferase Involved in Selenoneine Biosynthesis

Selenium (Se) is an essential micronutrient that is found naturally in proteins, nucleic acids, and natural products. Unlike selenoproteins and selenonucleic acids, little is known about the structures of biosynthetic enzymes that incorporate Se into small molecules. Here, we report the X-ray crystal structure of SenB, the first known Se-glycosyltransferase that was recently found to be involved in the biosynthesis of the Se-containing metabolite selenoneine. SenB catalyzes C–Se bond formation using selenophosphate and an activated uridine diphosphate sugar as a Se and glycosyl donor, respectively, making it the first known selenosugar synthase and one of only four bona fide C–Se bond-forming enzymes discovered to date. Our crystal structure, determined to 2.25 Å resolution, reveals that SenB is a type B glycosyltransferase, displaying the prototypical fold with two globular Rossmann-like domains and a catalytic interdomain cleft. By employing complementary structural biology techniques, we find that SenB undergoes both local and global substrate-induced conformational changes, demonstrating a significant increase in α-helicity and a transition to a more compact conformation. Our results provide the first structure of SenB and set the stage for further biochemical characterization in the future.

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

Sensor Domain of Histidine Kinase VxrA of Vibrio cholerae : Hairpin-Swapped Dimer and Its Conformational Change

VxrA and VxrB are cognate histidine kinase (HK)-response regulator (RR) pairs of a two-component signaling system (TCS) found in Vibrio cholerae, a bacterial pathogen that causes cholera. The VxrAB TCS positively regulates virulence, the type VI secretion system, biofilm formation, and cell wall homeostasis in V. cholerae, providing protection from environmental stresses and contributing to the transmission and virulence of the pathogen. The VxrA HK has a unique periplasmic sensor domain (SD) and, remarkably, lacks a cytoplasmic linker domain between the second transmembrane helix and the dimerization and histidine phosphotransfer (DHp) domain, indicating that this system may utilize a potentially unique signal sensing and transmission TCS mechanism. Here, we have determined several crystal structures of VxrA-SD and its mutants. These structures reveal a novel structural fold forming an unusual β hairpin-swapped dimer. A conformational change caused by relative rotation of the two monomers in a VxrA-SD dimer could potentially change the association of transmembrane helices and, subsequently, the pairing of cytoplasmic DHp domains. Based on the structural observation, we propose a putative scissor-like closing regulation mechanism for the VxrA HK. IMPORTANCE V. cholerae has a dynamic life cycle, which requires rapid adaptation to changing external conditions. Two-component signal transduction (TCS) systems allow V. cholerae to sense and respond to these environmental changes. The VxrAB TCS positively regulates a number of important V. cholerae phenotypes, including virulence, the type six secretion system, biofilm formation, and cell wall homeostasis. Here, we provide the crystal structures of the VxrA sensor histidine kinase sensing domain and propose a mechanism for signal transduction. The cognate signal for VxrAB remains unknown; however, in this work we couple our structural analysis with functional assessments of key residues to further our understanding of this important TCS.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1998

Identification of Complex Carbon Nanotube Structures

A variety of complex carbon nanotube (CNT) structures have been observed experimentally. These include sharp bends, branches, tori, and helices. They are believed to be formed by using topological defects such as pentagons and heptagons to connect different CNT. The effects of type, number, and arrangement (separation and orientation) of defects on atomic structures and energetics of complex CNT are investigated using topology, quantum mechanics and molecular mechanics calculations. Energetically stable models are derived for identification of observed complex CNT structures.

Han, Jie↗
DOE OSTI2023

Exploration of non-resonant divertor features on the Compact Toroidal Hybrid

Abstract Non-resonant divertors (NRDs) separate the confined plasma from the surrounding plasma facing components (PFCs). The resulting striking field line intersection pattern on these PFCs is insensitive to plasma equilibrium effects. However, a complex scrape-off layer (SOL), created by chaotic magnetic topology in the plasma edge, connects the core plasma to the PFCs through varying magnetic flux tubes. The Compact Toroidal Hybrid (CTH) serves as a test-bed to study this by scanning across its inductive current. Simulations observe a significant change of the chaotic edge structure and an effective distance between the confined plasma and the instrumented wall targets. The intersection pattern is observed to be a narrow helical band, which we claim is a resilient strike line pattern. However, signatures of finger-like structures, defined as heteroclinic tangles in chaotic domains, within the plasma edge connect the island chains to this resilient pattern. The dominant connection length field lines intersecting the targets are observed via heat flux modeling with EMC3-EIRENE. At low inductive current levels, the excursion of the field lines resembles a limited plasma wall scenario. At high currents, a private flux region is created in the area where the helical strike line pattern splits into two bands. These bands are divertor legs with distinct SOL parallel particle flow channels. The results demonstrate the NRD strike line pattern resiliency within CTH, but also show the underlying chaotic edge structure determining if the configuration is diverted or limited. This work supports future design efforts for a mechanical structure for the NRD.

Physics↗