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At least 37 records · Page 2

Coalescence of two current loops with a kink instability simulated by a three-dimensional electromagnetic particle code

We have studied the dynamics of a coalescence of current loops using three-dimensional electromagnetic (EM) particle simulation code. Our focus is the investigation of such kinetic processes as energy trasnfer, heating particles, and electromagnetic emissions associated with a current loop coalescence which cannot be studied by MHD simulations. First, the two loops undergo a pinching oscillation due to a pressure imbalance between the inside and outside of the current loop. During the pinching oscillation, a kinetic kink instability is excited and electrons in the loops are heated perpendicularly to an ambient magnetic field. Next, the two current loops collide and coalesce, while at the same time a helical structure grows further. Subsequently, the perturbed current, which is due to these helically bunched electrons, can drive a whistler instability. It should be noted in this case that the whistler wave is excited by the kinetic kink instability and not a beam instability. After the coalescence of two helical loops, tilting motions can be observed in the direction of left-hand rotation, and the helical structure will relax resulting in strong plasma heating mostly in the direction perpendicular to the ambient magnetic field. It is also shown that high-frequency electromagnetic waves can be emitted from the region where the two loops coalesce and propagate strongly in the direction of the electron drift velocity. These processes may be important in understanding heating mechansims for coronal loops as well as radio wave emission mechanisms from active regions of solar plasmas.

Nishikawa, K.-I.↗

The Role of Magnetic Helicity in Structuring the Solar Corona

Two of the most widely observed and striking features of the Suns magnetic field are coronal loops, which are smooth and laminar, and prominences or filaments, which are strongly sheared. Loops are puzzling because they show little evidence of tangling or braiding, at least on the quiet Sun, despite the chaotic nature of the solar surface convection. Prominences are mysterious because the origin of their underlying magnetic structure filament channels is poorly understood at best. These two types of features would seem to be quite unrelated and wholly distinct. We argue that, on the contrary, they are inextricably linked and result from a single process: the injection of magnetic helicity into the corona by photospheric motions and the subsequent evolution of this helicity by coronal reconnection. In this paper, we present numerical simulations of the response of a Parker (1972) corona to photospheric driving motions that have varying degrees of helicity preference. We obtain four main conclusions: (1) in agreement with the helicity condensation model of Antiochos (2013), the inverse cascade of helicity by magnetic reconnection in the corona results in the formation of filament channels localized about polarity inversion lines; (2) this same process removes most complex fine structure from the rest of the corona, resulting in smooth and laminar coronal loops; (3) the amount of remnant tangling in coronal loops is inversely dependent on the net helicity injected by the driving motions; and (4) the structure of the solar corona depends only on the helicity preference of the driving motions and not on their detailed time dependence. We discuss the implications of our results for high-resolution observations of the corona.

Knizhnik, K. J.↗

STEREO/SECCHI Stereoscopic Observations Constraining the Initiation of Polar Coronal Jets

We report on the first stereoscopic observations of polar coronal jets made by the EUVI/SECCHI imagers on board the twin STEREO spacecraft. The significantly separated viewpoints (approximately 11 degrees ) allowed us to infer the 3D dynamics and morphology of a well-defined EUV coronal jet for the first time. Triangulations of the jet's location in simultaneous image pairs led to the true 3D position and thereby its kinematics. Initially the jet ascends slowly at approximately equal to 10-20 kilometers per second and then, after an apparent 'jump' takes place, it accelerates impulsively to velocities exceeding 300 kilometers per second with accelerations exceeding the solar gravity. Helical structure is the most important geometrical feature of the jet which shows evidence of untwisting. The jet structure appears strikingly different from each of the two STEREO viewpoints: face-on in the one viewpoint and edge-on in the other. This provides conclusive evidence that the observed helical structure is real and is not resulting from possible projection effects of single viewpoint observations. The clear demonstration of twisted structure in polar jets compares favorably with synthetic images from a recent MHD simulation of jets invoking magnetic untwisting as their driving mechanism. Therefore, the latter can be considered as a viable mechanism for the initiation of polar jets.

Patsourakos, S.↗

Molecular-field-theory fits to magnetic susceptibilities of antiferromagnetic GdCu 2 Si 2 , CuO, LiCrO 2 , and α-CaCr 2 O 4 single crystals below their Néel temperatures

A recently-developed molecular field theory (MFT) has been used to fit single-crystal magnetic susceptibility χ versus temperature T data below the respective antiferromagnetic ordering temperature T N for a variety of collinear and coplanar noncollinear Heisenberg antiferromagnets. The spins in the system are assumed to interact by Heisenberg exchange and to be identical and crystallographically equivalent. The fitting parameters for χ(T ) of collinear antiferromagnets are measurable quantities: the Weiss temperature θ p in the Curie-Weiss law, TN, χ(T N ), and the spin S. For coplanar noncollinear helix and cycloid structures, an additional fitting parameter is the turn angle between layers of ferromagnetically-aligned spins. Here MFT fits to anisotropic χ(T) data from the literature for single crystals of the collinear antiferromagnets GdCu 2 Si 2 and CuO and the noncollinear antiferromagnets LiCrO 2 with a 120° cycloidal structure and α-CaCr 2 O 4 with a 120° helical structure below their respective N´eel temperatures are presented. The MFT fit to the anisotropic χ(T ≤ T N ) data for CuO is poor, whereas the fits to the data for GdCu 2 Si 2 , LiCrO 2 , and α-CaCr 2 O 4 are quite good. The poor fit for CuO is attributed to the influence of strong quantum fluctuations associated with the small Cu spin and the quasi-one-dimensional magnetism that are not taken into account by the MFT. The magnetic contribution to the zero-field heat capacity of the collinear antiferromagnet GdNiGe 3 at T ≤ T N is also fitted by the MFT.

36 MATERIALS SCIENCE↗

Spin dynamics of the centrosymmetric skyrmion material GdRu 2 Si 2

Magnetic skyrmion crystals are traditionally associated with non-centrosymmetric crystal structures; however, it has been demonstrated that skyrmion crystals can be stabilized by competing interactions in centrosymmetric crystals. To understand and optimize the physical responses associated with topologically nontrivial skyrmion textures, it is important to quantify their magnetic interactions by comparing theoretical predictions with spectroscopy data. Here, we present neutron diffraction and spectroscopy data on the centrosymmetric skyrmion material GdRu 2 Si 2 and show that the key spectroscopic features can be explained by magnetic interactions calculated using density functional theory. We further show that the recently proposed 2-q “topological spin stripe” structure yields better agreement with our data than a 1-q helical structure and identify how the magnetic structure evolves with temperature.

36 MATERIALS SCIENCE↗

The [N II] Kinematics of R Aquarii

We report a kinematic study of the symbiotic star system R Aqr derived from [N H]lambda 6584 emission observations with a Fabry-Perot imaging spectrometer. The [N II] spatial structure of the R Aqr jet, first observed circa 1977, and surrounding hourglass-shaped nebulosity, due to an explosion approximately 660 years ago, are derived from 41 velocity planes spaced at approximately 12 km/s intervals. Fabry-Perot imagery shows the elliptical nebulosity comprising the waist of the hourglass shell is consistent with a circular ring expanding radially at 55 km/s as seen at an inclination angle, i approximately 70 deg. Fabry-Perot imagery shows the two-sided R Aqr jet is collimated flow in opposite directions. The intensity-velocity structure of the strong NE jet component is shown in contrast to the amorphous SW jet component. We offer a idealized schematic model for the R Aqr jet motion which results in a small-scale helical structure forming around a larger-scale helical path. The implications of such a jet model are discussed. We present a movie showing a side-by-side comparison of the spatial structure of the model and the data as a function of the 41 velocity planes.

Hollis, J. M.↗

Three-Dimensional Helical-Rotating Plasma Structures in Beam-Generated Partially Magnetized Plasmas

Azimuthal structures emerging in beam-generated partially magnetized plasmas are investigated using three-dimensional particle in cell-Monte Carlo collision simulations. Two distinct instability regimes are identified at low pressures. Furthermore, when the gas pressure is sufficiently high, quasineutrality is attained and 2D spiral-arm structures form as a result of the development of a lower-hybrid instability, resulting in enhanced cross-field transport. At lower pressures, quasineutrality is not achieved and a 3D helical-rotating plasma structure forms due to development of the diocotron instability. Analytical formulas are proposed for the critical threshold pressure between these regimes and for the rotation frequency of the helical structures. Preliminary experimental verification is provided.

Penning discharges↗

Tetragonal Lysozyme, From Monomer to Crystal

The data now leads us to a comprehensive model for the process by which tetragonal lysozyme crystals are nucleated and subsequently grow. Lysozyme is typically desolubilized by addition of ionic salts. The salt anions bind to basic and other sites on the protein and promote protein-protein interactions, i.e., initiate the nucleation self assembly process. Formation of protein-protein interactions occurs at the expense of the protein-anion interactions, with the anions being released to the solution. The association follows a defined pattern, forming the "head to side" interactions of the crystal 4(3) helix. The presence of the high salt also promotes hydrophobic interactions between the protein molecules, further tightening their interaction. The solute assembly process persists after crystal nucleation, and the 4(3) helical structures form the subsequent growth units. AFM measurements show that the growth units follow the dimensions of these helices, and that those on the surface are more compact about the c-axis than in the bulk crystal, with adjacent helices riot being in contact. This further supports the role of hydrophobic interactions, as the surface is still in contact with the bulk solution. Once buried within the crystal the protein:salt ratio radically changes and the hydrophobic interactions relax to those measured crystallographically. Thus the crystal growth process recapitulates the initial stages of the nucleation process, and the two seamlessly merge. Experimental evidence, based upon face growth rate, AFM, and fluorescence energy transfer data, for a postulated model of the nucleation of tetragonal lysozyme crystals and how it transitions into crystal growth will be presented.

Pusey, Marc L.↗

Formation and Shape Changing of Conductive Helical Ribbons via Deposition of Highly Stressed Films on Mechanically Responsive Substrates

Abstract This work demonstrates that the electrodeposition of highly stressed films on compliant ribbons is a robust process to obtain helical structures with excellent mechanical stability and potentially high thermal and electrical conductance. Electrodeposition on end‐tethered ribbons alters their axial and bending stiffness while imparting mechanical stress to drive the formation of a helix with a microscale diameter and pitch in a controlled and scalable manner. The process generates helices with diameters and pitches between 80 and 200 µm and lengths as large as several millimeters. The approach is amenable to parallel processing a large number of 3D structures on any substrate, including large‐area semiconductor wafers. This phenomenon is explained in terms of the change of stress gradients as material is added. Applications of the fabricated helices include antennas, metamaterials, and slow‐wave structures in frequency ranges not previously attainable.

Chemistry↗

Crystal structure of four-stranded Oxytricha telomeric DNA

The sequence d(GGGGTTTTGGGG) from the 3' overhang of the Oxytricha telomere has been crystallized and its three-dimensional structure solved to 2.5 A resolution. The oligonucleotide forms hairpins, two of which join to make a four-stranded helical structure with the loops containing four thymine residues at either end. The guanine residues are held together by cyclic hydrogen bonding and an ion is located in the centre. The four guanine residues in each segment have a glycosyl conformation that alternates between anti and syn. There are two four-stranded molecules in the asymmetric unit showing that the structure has some intrinsic flexibility.

NASA Discipline Exobiology↗

Magnetic order and fluctuations in the quasi-two-dimensional planar magnet Sr( Co 1-x Ni x ) 2 As 2

We use neutron scattering to investigate spin excitations in Sr ( Co 1 - x Ni x ) 2 As 2 , which has a c -axis incommensurate helical structure of the two-dimensional (2D) in-plane ferromagnetic (FM) ordered layers for 0.013 ≤ x ≤ 0.25 . By comparing the wave vector and energy dependent spin excitations in helical ordered Sr ( Co 0.9 Ni 0.1 ) 2 As 2 and paramagnetic SrCo 2 As 2 , we find that Ni doping, while increasing lattice disorder in Sr ( Co 1 - x Ni x ) 2 As 2 , enhances quasi-2D FM spin fluctuations. However, our band structure calculations within the combined density functional theory and dynamic mean field theory ( DFT + DMFT ) failed to generate a correct incommensurate wave vector for the observed helical order from nested Fermi surfaces. Furthermore, since transport measurements reveal increased in-plane and c -axis electrical resistivity with increasing Ni doping and associated lattice disorder, we conclude that the helical magnetic order in Sr ( Co 1 - x Ni x ) 2 As 2 may arise from a quantum order-by-disorder mechanism through the itinerant electron mediated Ruderman-Kittel-Kasuya-Yosida (RKKY) interactions.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Janus skyrmion: Interfacial quasiparticle with two-faced helicity

Janus particles are functional particles with at least two surfaces showing asymmetric properties. Here, we show at the interface between two magnetic regions with different antisymmetric exchange interactions, an alternative species of two-dimensional topological quasiparticles can emerge, in which different helicity structures can coexist. We name such an interfacial quasiparticle a “Janus skyrmion,” in analogy to the Janus particle. As the Janus skyrmion shows helicity asymmetry, its size could vary with both the in-plane and out-of-plane magnetic fields. A vertical spin current could drive the Janus skyrmion into one-dimensional motion along the interface without showing the skyrmion Hall effect, at a speed which depends on both the in-plane spin-polarization direction and current density. Thermal fluctuations could also lead to one-dimensional random walk of a Brownian Janus skyrmion. This work uncovers unique dynamics intrinsic to interfacial quasiparticles with exotic helicity, which may be realized in interface-engineered magnetic layers.

36 MATERIALS SCIENCE↗

A human antibody reveals a conserved site on beta-coronavirus spike proteins and confers protection against SARS-CoV-2 infection

Broadly neutralizing antibodies (bnAbs) to coronaviruses (CoVs) are valuable in their own right as prophylactic and therapeutic reagents to treat diverse CoVs and as templates for rational pan-CoV vaccine design. We recently described a bnAb, CC40.8, from a CoV disease 2019 (COVID-19) convalescent donor that exhibits broad reactivity with human β-CoVs. Here, we showed that CC40.8 targets the conserved S2 stem helix region of the CoV spike fusion machinery. We determined a crystal structure of CC40.8 Fab with a SARS-CoV-2 S2 stem peptide at 1.6-Å resolution and found that the peptide adopted a mainly helical structure. Conserved residues in β-CoVs interacted with CC40.8 antibody, thereby providing a molecular basis for its broad reactivity. CC40.8 exhibited in vivo protective efficacy against SARS-CoV-2 challenge in two animal models. In both models, CC40.8-treated animals exhibited less weight loss and reduced lung viral titers compared to controls. Furthermore, we noted that CC40.8-like bnAbs are relatively rare in human COVID-19 infection, and therefore, their elicitation may require rational structure-based vaccine design strategies. Overall, our study describes a target on β-CoV spike proteins for protective antibodies that may facilitate the development of pan–β-CoV vaccines.

60 APPLIED LIFE SCIENCES↗

The three-way junction structure of the HIV-1 PBS-segment binds host enzyme important for viral infectivity

HIV-1 reverse transcription initiates at the primer binding site (PBS) in the viral genomic RNA (gRNA). Although the structure of the PBS-segment undergoes substantial rearrangement upon tRNALys3 annealing, the proper folding of the PBS-segment during gRNA packaging is important as it ensures loading of beneficial host factors. DHX9/RNA helicase A (RHA) is recruited to gRNA to enhance the processivity of reverse transcriptase. Because the molecular details of the interactions have yet to be defined, we solved the solution structure of the PBS-segment preferentially bound by RHA. Evidence is provided that PBS-segment adopts a previously undefined adenosine-rich three-way junction structure encompassing the primer activation stem (PAS), tRNA-like element (TLE) and tRNA annealing arm. Disruption of the PBS-segment three-way junction structure diminished reverse transcription products and led to reduced viral infectivity. Because of the existence of the tRNA annealing arm, the TLE and PAS form a bent helical structure that undergoes shape-dependent recognition by RHA double-stranded RNA binding domain 1 (dsRBD1). Mutagenesis and phylogenetic analyses provide evidence for conservation of the PBS-segment three-way junction structure that is preferentially bound by RHA in support of efficient reverse transcription, the hallmark step of HIV-1 replication.

59 BASIC BIOLOGICAL SCIENCES↗

Distinct Secondary Structures of the Leucine-Rich Repeat Proteoglycans Decorin and Biglycan: Glycosylation-Dependent Conformational Stability

Biglycan and decorin, closely related small leucine-rich repeat proteoglycans, have been overexpressed in eukaryotic cers and two major glycoforms isolated under native conditions: a proteoglycan substituted with glycosaminoglycan chains; and a core protein form secreted devoid of glycosaminoglycans. A comparative biophysical study of these glycoforms has revealed that the overall secondary structures of biglycan and decorin are different. Far-UV Circular Dichroism (CD) spectroscopy of decorin and biglycan proteoglycans indicates that, although they are predominantly Beta-sheet, biglycan has a significantly higher content of alpha-helical structure. Decorin proteoglycan and core protein are very similar, whereas the biglycan core protein exhibits closer similarity to the decorin glycoforms than to. the biglycan proteoglycan form. However, enzymatic removal of the chondroitin sulfate chains from biglycan proteoglycan does not induce a shift to the core protein structure, suggesting that the fmal form is influenced by polysaccharide addition only during biosynthesis. Fluorescence emission spectroscopy demonstrated that the single tryptophan residue, which is at a conserved position at the C-terminal domain of both biglycan and decorin, is found in similar microenvironments. This indicates that at least in this specific domain, the different glycoforms do exhibit apparent conservation of structure. Exposure of decorin and biglycan to 10 M urea resulted in an increase in fluorescent intensity, which indicates that the emission from tryptophan in the native state is quenched. Comparison of urea-induced protein unfolding curves provided further evidence that decorin and biglycan assume different structures in solution. Decorin proteoglycan and core protein unfold in a manner similar to a classic two-state model, in which there is a steep transition to an unfolded state between 1-2 M urea. The biglycan core protein also shows a similar steep transition. However, biglycan proteoglycan shows a broad unfolding transition between 1-6 M urea, probably indicating the presence of stable unfolding intermediates.

Krishnan, Priya↗

Nucleic acid duplexes incorporating a dissociable covalent base pair

We have used molecular modeling techniques to design a dissociable covalently bonded base pair that can replace a Watson-Crick base pair in a nucleic acid with minimal distortion of the structure of the double helix. We introduced this base pair into a potential precursor of a nucleic acid double helix by chemical synthesis and have demonstrated efficient nonenzymatic template-directed ligation of the free hydroxyl groups of the base pair with appropriate short oligonucleotides. The nonenzymatic ligation reactions, which are characteristic of base paired nucleic acid structures, are abolished when the covalent base pair is reduced and becomes noncoplanar. This suggests that the covalent base pair linking the two strands in the duplex is compatible with a minimally distorted nucleic acid double-helical structure.

Non-NASA Center↗