Synthesis and Electrocatalytic Water Oxidation by Electron-Bound Helical Peptide Chromophore – Catalyst Assemblies
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catalysis (homogeneous), catalysis (heterogeneous)↗
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Results for “HELICITY”
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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Two-fluid and finite Larmor radius effects on helicity evolution in a plasma pinch
The evolution of magnetic energy, helicity, and hybrid helicity during nonlinear relaxation of a driven-damped plasma pinch is compared in visco-resistive magnetohydrodynamics and two-fluid models with and without the ion gyroviscous stress tensor. Magnetic energy and helicity are supplied via a boundary electric field which initially balances the resistive dissipation, and the plasma undergoes multiple relaxation events during the nonlinear evolution. The magnetic helicity is well conserved relative to the magnetic energy over each event, which is short compared with the global resistive diffusion time. The magnetic energy decreases by roughly 1.5% of its initial value over a relaxation event, while the magnetic helicity changes by at most 0.2% of the initial value. The hybrid helicity is dominated by magnetic helicity in low-β pinch conditions and is also well conserved. Differences of less than 1% between magnetic helicity and hybrid helicity are observed with two-fluid modeling and result from cross helicity evolution. The cross helicity is found to change appreciably due to the first-order finite Larmor radius effects which have not been included in contemporary relaxation theories. The plasma current evolves towards the flat parallel current state predicted by Taylor relaxation theory but does not achieve it. Plasma flow develops significant structure for two-fluid models, and the flow perpendicular to the magnetic field is much more substantial than the flow along it.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
Evolution of helical perturbations in a thin-shell model of an imploding liner
A thin-shell model of the liner stability has been revisited and applied to the stability of the helical perturbations. Several stages of the implosion have been identified, starting from a long initial “latent” phase of an almost resting liner, continuing to the second stage of a rapid contraction and significant perturbation growth, and then transitioning to the third stage where perturbations become ballistic and highly non-linear. The stage of stagnation and rebound is beyond the scope of this paper. An importance of vorticity conservation during the late stages is emphasized. Nonlinear evolution of perturbations is followed up to the point of the formation of cusp structures. Effects of in-surface flows and of their enhancement due to the vorticity conservation are discussed. It is shown that the pre-machined perturbations created only on the outer surface of the liner grow much slower than one could anticipate. The limitations on the thin-shell description are discussed.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
Effects of Magnetic and Kinetic Helicities on the Growth of Magnetic Fields in Laminar and Turbulent Flows by Helical Fourier Decomposition
We present a numerical and analytical study of incompressible homogeneous conducting fluids using a helical Fourier representation. We analytically study both small- and large-scale dynamo properties, as well as the inverse cascade of magnetic helicity, in the most general minimal subset of interacting velocity and magnetic fields on a closed Fourier triad. We mainly focus on the dependency of magnetic field growth as a function of the distribution of kinetic and magnetic helicities among the three interacting wavenumbers. By combining direct numerical simulations of the full magnetohydrodynamics equations with the helical Fourier decomposition, we numerically confirm that in the kinematic dynamo regime the system develops a large-scale magnetic helicity with opposite sign compared to the small-scale kinetic helicity, a sort of triad-by-triad α -effect in Fourier space. Concerning the small-scale perturbations, we predict theoretically and confirm numerically that the largest instability is achived for the magnetic component with the same helicity of the flow, in agreement with the Stretch–Twist–Fold mechanism. Vice versa, in the presence of Lorentz feedback on the velocity, we find that the inverse cascade of magnetic helicity is mostly local if magnetic and kinetic helicities have opposite signs, while it is more nonlocal and more intense if they have the same sign, as predicted by the analytical approach. Our analytical and numerical results further demonstrate the potential of the helical Fourier decomposition to elucidate the entangled dynamics of magnetic and kinetic helicities both in fully developed turbulence and in laminar flows.
79 ASTRONOMY AND ASTROPHYSICS↗
Relativistic helicity and link in Minkowski space-time
A relativistic helicity has been formulated in the four-dimensional Minkowski space-time. Whereas the relativistic distortion of space-time violates the conservation of the conventional helicity, the newly defined relativistic helicity conserves in a barotropic fluid or plasma, dictating a fundamental topological constraint. The relation between the helicity and the vortex-line topology has been delineated by analyzing the linking number of vortex filaments which are singular differential forms representing the pure states of Banach algebra. While the dimension of space-time is four, vortex filaments link, because vorticities are primarily 2-forms and the corresponding 2-chains link in four dimension; the relativistic helicity measures the linking number of vortex filaments that are proper-time cross-sections of the vorticity 2-chains. A thermodynamic force yields an additional term in the vorticity, by which the vortex filaments on a reference-time plane are no longer pure states. However, the vortex filaments on a proper-time plane remain to be pure states, if the thermodynamic force is exact (barotropic), thus, the linking number of vortex filaments conserves.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
A combined study of photospheric magnetic and current helicities and subsurface kinetic helicities of solar active regions during 2006-2013
We compare the average photospheric current helicity H{sub c} , photospheric twist parameter α (a well-known proxy for the full relative magnetic helicity), and subsurface kinetic helicity H{sub k} for 194 active regions observed between 2006-2013. We use 2440 Hinode photospheric vector magnetograms, and the corresponding subsurface fluid velocity data derived from GONG (2006-2012) and Helioseismic and Magnetic Imager (2010-2013) dopplergrams. We find a significant hemispheric bias in all three parameters. The subsurface kinetic helicity is preferentially positive in the southern hemisphere and negative in the northern hemisphere. The photospheric current helicity and the α parameter have the same bias for strong fields (|B| > 1000 G) and no significant bias for weak fields (100 G <|B| < 500 G). We find no significant region-by-region correlation between the subsurface kinetic helicity and either the strong-field current helicity or α. Subsurface fluid motions of a given handedness correspond to photospheric helicities of both signs in approximately equal numbers. However, common variations appear in annual averages of these quantities over all regions. Furthermore, in a subset of 77 regions, we find significant correlations between the temporal profiles of the subsurface and photospheric helicities. In these cases, the sign of the linear correlation coefficient matches the sign relationship between the helicities, indicating that the photospheric magnetic field twist is sensitive to the twisting motions below the surface.
79 ASTRONOMY AND ASTROPHYSICS↗
Simulation of injector dynamics during steady inductive helicity injection current drive in the HIT-SI experiment
We present simulations of inductive helicity injection in the Helicity Injected Torus with Steady Inductive helicity injection (HIT-SI) device that treats the entire plasma volume in a single dynamic MHD model. A new fully 3D numerical tool, the PSI-center TETrahedral mesh code, was developed that provides the geometric flexibility required for this investigation. Implementation of a zero-β Hall MHD model using PSI-TET will be presented including formulation of a new self-consistent magnetic boundary condition for the wall of the HIT-SI device. Results from simulations of HIT-SI are presented focusing on injector dynamics that are investigated numerically for the first time. Asymmetries in the plasma loading between the two helicity injectors and progression of field reversal in each injector are observed. Analysis indicates cross-coupling between injectors through confinement volume structures. Injector impedance is found to scale with toroidal current at fixed density, consistent with experimental observation. Comparison to experimental data with an injector drive frequency of 14.5 kHz shows good agreement with magnetic diagnostics. Global mode structures from Bi-Orthogonal decomposition agree well with experimental data for the first four modes.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
Quantum spin helices more stable than the ground state: Onset of helical protection
Topological magnetic structures are promising candidates for resilient information storage. An elementary example is spin helices in one-dimensional easy-plane quantum magnets. To quantify their stability, we numerically implement the stochastic Schrödinger equation and time-dependent perturbation theory for spin chains with fluctuating local magnetic fields. Here, we find two classes of quantum spin helices that can reach and even exceed ground-state stability: spin-current-maximizing helices and, for fine-tuned boundary conditions, the recently discovered “phantom helices.” Beyond that, we show that the helicity itself (left or right rotating) is even more stable. We explain these findings by separated helical sectors and connect them to topological sectors in continuous spin systems. The resulting helical protection mechanism is a promising phenomenon for stabilizing helical quantum structures, e.g., in ultracold atoms and solid-state systems. We also identify a third type of phantom helix in the system.
1-dimensional spin chains↗
Energetic particle transport and loss induced by helically-trapped energetic-ion-driven resistive interchange modes in the Large Helical Device
Here, energetic-ion confinement and loss due to energetic-ion driven magnetohydrodynamic modes are studied using comprehensive neutron diagnostics and orbit-following numerical simulations for the Large Helical Device (LHD). The neutron flux monitor is employed in order to obtain global confinement of energetic ions and two installed vertical neutron cameras (VNCs) viewing different poloidal cross-sections are utilized in order to measure the radial profile of energetic ions. A strong helically-trapped energetic-ion-driven resistive interchange mode (EIC) excited in relatively low-density plasma terminated high-temperature state in LHD. Changes in the neutron emission profile due to the EIC excitation are clearly visualized by the VNCs. The reduction in the neutron signal for the helical ripple valley increases with EIC amplitude, which reaches approximately 50%. In addition to the EIC experiment, orbit-following simulations using the DELTA5D code with EIC fluctuations were performed to assess the energetic-ion transport and loss. Two-dimensional temporal evolution results show that the neutron emissivity at the helical ripple decreases significantly due to the EIC. The rapid reduction in neutron emissivity shows that the helically-trapped beam ions immediately escape from the plasma. The reduction in the VNC signals for the helical ripple valley and the total neutron emission rate increase with increasing EIC amplitude, as observed in the experiment. Calculated line-integrated neutron emission results show that the profile measured by VNC1 has one peak, whereas the profile measured by VNC2 has two peaks, as observed in the experiment. Although the neutron emission profile for VNC2 has a relatively wide peak compared with the experimental results, the significant decrease in neutron signal corresponding to the helical ripple valley was successfully reproduced.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
Ambidextrous Helical Nanotubes from Self-Assembly of Designed Helical Hairpin Motifs
Tandem repeat proteins exhibit native designability and represent potentially useful scaffolds for the construction of synthetic biomimetic assemblies. We have designed two synthetic peptides, HEAT R1 and LRV M3Δ1, based on the consensus sequences of single repeats of thermophilic HEAT (PBS HEAT) and Leucine- Rich Variant (LRV) structural motifs, respectively. Self-assembly of the peptides afforded high aspect-ratio helical helical nanotubes. Cryo-electron microscopy with direct electron detection was employed to analyze the structures of the solvated filaments. Three dimensional reconstructions from the cryo-EM maps led to atomic models for the HEAT R1 and LRV M3Δ1 filaments at resolutions of 6.0 Å and 4.4 Å, respectively. Surprisingly, despite sequence similarity at the lateral packing interface, HEAT R1 and LRV M3Δ1 filaments adopt the opposite helical hand and differ significantly in helical geometry, while retaining a local conformation similar to previously characterized repeat proteins of the same class. The differences in the two filaments could be rationalized on the basis of differences in cohesive interactions at the lateral and axial interfaces. These structural data reinforce previous observations regarding the structural plasticity of helical protein assemblies and the need for high resolution structural analysis. Despite these observations, the native designability of tandem repeat proteins offers the opportunity to engineer novel helical nanotubes. Furthermore, the resultant nanotubes have independently addressable and chemically distinguishable interior and exterior surfaces that would facilitate applications in selective recognition, transport, and release.
59 BASIC BIOLOGICAL SCIENCES↗
A field theory approach to the evolution of canonical helicity and energy
A redefinition of the Lagrangian of a multi-particle system in fields reformulates the single-particle, kinetic, and fluid equations governing fluid and plasma dynamics as a single set of generalized Maxwell's equations and Ohm's law for canonical force-fields. The Lagrangian includes new terms representing the coupling between the motion of particle distributions, between distributions and electromagnetic fields, with relativistic contributions. The formulation shows that the concepts of self-organization and canonical helicity transport are applicable across single-particle, kinetic, and fluid regimes, at classical and relativistic scales. The theory gives the basis for comparing canonical helicity change to energy change in general systems. For example, in a fixed, isolated system subject to non-conservative forces, a species' canonical helicity changes less than total energy only if gradients in density or distribution function are shallow.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
High-Fidelity Simulation of Flow-Induced Vibrations in Helical Steam Generators for Small Modular Reactors
Flow-induced vibration (FIV) is a widespread problem in energy systems as they rely on fluid movement for energy conversion. Vibrating structures may be damaged as fatigue or wear occur. Given the importance of reliable components in the nuclear industry, FIV has long been a major concern in the safety and operation of nuclear reactors. In particular, nuclear fuel rods and steam generators have been known to suffer from FIV and related failures. In this paper we discuss the use of the computational fluid dynamics code Nek5000 coupled to the structural code Diablo to simulate the flow in helical coil heat exchangers and associated FIV. In particular, one-way coupled calculations are performed, where pressure and tractions data are loaded into the structural model. The main focus of this paper is on validation of this capability. Fluid-only Nek5000 large eddy simulations are first compared against dedicated high-resolution experiments. Then, one-way coupled calculations are performed with Nek5000 and Diablo for two data sets that provide FIV data for validation. These calculations were aimed at simulating available legacy FIV experiments in helical steam generators in the turbulent buffeting regime. In this regime one-way coupling is judged sufficient since the pressure loads do not cause substantial displacements. It is also the most common source of vibration in helical steam generators at the low flows expected in integral pressurized water reactors. We discuss validation of two-way coupled experiments and benchmarks toward the simulation of fluid elastic instability. We briefly discuss the application of these methods to grid-to-rod fretting.
Flow-Induced Vibration↗
Dimerization of the SP1 Region of HIV-1 Gag Induces a Helical Conformation and Association into Helical Bundles: Implications for Particle Assembly
HIV-1 immature particle (virus-like particle [VLP]) assembly is mediated largely by interactions between the capsid (CA) domains of Gag molecules but is facilitated by binding of the nucleocapsid (NC) domain to nucleic acid. We previously investigated the role of SP1, a “spacer” between CA and NC, in VLP assembly. We found that small changes in SP1 drastically disrupt assembly and that a peptide representing the sequence around the CA-SP1 junction is helical at high but not low concentrations. We suggested that by virtue of such a concentration-dependent change, this region could act as a molecular switch to activate HIV-1 Gag for VLP assembly. A leucine zipper domain can replace NC in Gag and still lead to the efficient assembly of VLPs. We find that SP1 mutants also disrupt assembly by these Gag-Zip proteins and have now studied a small fragment of this Gag-Zip protein, i.e., the CA-SP1 junction region fused to a leucine zipper. Dimerization of the zipper places SP1 at a high local concentration, even at low total concentrations. In this context, the CA-SP1 junction region spontaneously adopts a helical conformation, and the proteins associate into tetramers. Tetramerization requires residues from both CA and SP1. Here, the data suggest that once this region becomes helical, its propensity to self-associate could contribute to Gag-Gag interactions and thus to particle assembly. There is complete congruence between CA/SP1 sequences that promote tetramerization when fused to zippers and those that permit the proper assembly of full-length Gag; thus, equivalent interactions apparently participate in VLP assembly and in SP1-Zip tetramerization. Assembly of HIV-1 Gag into virus-like particles (VLPs) appears to require an interaction with nucleic acid, but replacement of its principal nucleic acid-binding domain with a dimerizing leucine zipper domain leads to the assembly of RNA-free VLPs. It has not been clear how dimerization triggers assembly. Results here show that the SP1 region spontaneously switches to a helical state when fused to a leucine zipper and that these helical molecules further associate into tetramers, mediated by interactions between hydrophobic faces of the helices. Thus, the correct juxtaposition of the SP1 region makes it “association competent.” Residues from both capsid and SP1 contribute to tetramerization, while mutations disrupting proper assembly in Gag also prevent tetramerization. Thus, this region is part of an associating interface within Gag, and its intermolecular interactions evidently help stabilize the immature Gag lattice. These interactions are disrupted by proteolysis of the CA-SP1 junction during virus maturation.
59 BASIC BIOLOGICAL SCIENCES↗
THE EFFECTS OF SPATIAL SMOOTHING ON SOLAR MAGNETIC HELICITY PARAMETERS AND THE HEMISPHERIC HELICITY SIGN RULE
The hemispheric preference for negative/positive helicity to occur in the northern/southern solar hemisphere provides clues to the causes of twisted, flaring magnetic fields. Previous studies on the hemisphere rule may have been affected by seeing from atmospheric turbulence. Using Hinode /SOT-SP data spanning 2006–2013, we studied the effects of two spatial smoothing tests that imitate atmospheric seeing: noise reduction by ignoring pixel values weaker than the estimated noise threshold, and Gaussian spatial smoothing. We studied in detail the effects of atmospheric seeing on the helicity distributions across various field strengths for active regions (ARs) NOAA 11158 and NOAA 11243, in addition to studying the average helicities of 179 ARs with and without smoothing. We found that, rather than changing trends in the helicity distributions, spatial smoothing modified existing trends by reducing random noise and by regressing outliers toward the mean, or removing them altogether. Furthermore, the average helicity parameter values of the 179 ARs did not conform to the hemisphere rule: independent of smoothing, the weak-vertical-field values tended to be negative in both hemispheres, and the strong-vertical-field values tended to be positive, especially in the south. We conclude that spatial smoothing does not significantly affect the overall statistics for space-based data, and thus seeing from atmospheric turbulence seems not to have significantly affected previous studies’ ground-based results on the hemisphere rule.
79 ASTRONOMY AND ASTROPHYSICS↗
Hexagonally Ordered Arrays of α-Helical Bundles Formed from Peptide-Dendron Hybrids
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36 MATERIALS SCIENCE↗
Flow-induced vibration analysis of a helical coil steam generator experiment using large eddy simulation
This paper describes a numerical study of flow-induced vibration in a helical coil steam generator experiment conducted at Argonne National Laboratory in the 1980s. In the experiment, a half-scale sector model of a steam generator helical coil tube bank was subjected to still and flowing air and water, and the vibrational characteristics were recorded. The research detailed in this document utilizes the multi-physics simulation toolkit SHARP developed at Argonne National Laboratory, in cooperation with Lawrence Livermore National Laboratory, to simulate the experiment. SHARP uses the spectral element code Nek5000 for fluid dynamics analysis and the finite element code DIABLO for structural analysis. The flow around the coil tubes is modeled in Nek5000 by using a large eddy simulation turbulence model. Transient pressure data on the tube surfaces is sampled and transferred to DIABLO for the structural simulation. The structural response is simulated in DIABLO via an implicit time-marching algorithm and a combination of continuum elements and structural shells. Tube vibration data (acceleration and frequency) are sampled and compared with the experimental data. Currently, only one-way coupling is used, which means that pressure loads from the fluid simulation are transferred to the structural simulation but the resulting structural displacements are not fed back to the fluid simulation
CFD↗