Magnetic field generation by pointwise zero-helicity three-dimensional steady flow of an incompressible electrically conducting fluid

NASA Astrophysics Data System (ADS)

Rasskazov, Andrey; Chertovskih, Roman; Zheligovsky, Vladislav

2018-04-01

We introduce six families of three-dimensional space-periodic steady solenoidal flows, whose kinetic helicity density is zero at any point. Four families are analytically defined. Flows in four families have zero helicity spectrum. Sample flows from five families are used to demonstrate numerically that neither zero kinetic helicity density nor zero helicity spectrum prohibit generation of large-scale magnetic field by the two most prominent dynamo mechanisms: the magnetic α -effect and negative eddy diffusivity. Our computations also attest that such flows often generate small-scale field for sufficiently small magnetic molecular diffusivity. These findings indicate that kinetic helicity and helicity spectrum are not the quantities controlling the dynamo properties of a flow regardless of whether scale separation is present or not.

Inhomogeneous helicity effect in the solar angular-momentum transport

NASA Astrophysics Data System (ADS)

Yokoi, Nobumitsu

2017-04-01

Coupled with mean absolute vorticity Ω∗ (rotation and mean relative vorticity), inhomogeneous turbulent helicity is expected to contribute to the generation of global flow structure against the linear and angular momentum mixing due to turbulent or eddy viscosity. This inhomogeneous helicity effect was originally derived in Yokoi & Yoshizawa (1993) [1], and recently has been validated by direct numerical simulations (DNSs) of rotating helical turbulence [2]. Turbulence effect enters the mean-vorticity equation through the turbulent vortexmotive force ⟨u'×ω'⟩ [u': velocity fluctuation, ω'(= ∇× u'): vorticity fluctuation], which is the vorticity counterpart of the electromotive force ⟨u'× b'⟩ (b': magnetic fluctuation) in the mean magnetic-field induction. The mean velocity induction δU is proportional to the vortexmotive force. According to the theoretical result [1,2], it is expressed as δU = -νT∇×Ω∗-ηT(∇2H)Ω∗, where ηT is the transport coefficient, H = ⟨u'ṡω'⟩ the turbulent helicity, and Ω∗ the mean absolute vorticity. The first term corresponds to the enhanced diffusion due to turbulent viscosity νT. The second term expresses the large-scale flow generation due to inhomogeneous helicity. Since helicity is self-generated in rotating stratified turbulence [3], an inhomogeneous helicity distribution is expected to exist in the solar convection zone. A rising flow with expansion near the surface of the Sun generates a strongly negative helicity there [4]. This spatial distribution of helicity would lead to a positive Laplacian of turbulent helicity (∇2H > 0) in the subsurface layer of the Sun. In the combination with the large-scale vorticity associated with the meridional circulation, the inhomogeneous helicity effect works for accelerating the mean velocity in the azimuthal direction. The relevance of this inhomogeneous helicity effect in the solar convection zone is discussed further. References [1] Yokoi, N. and Yoshizawa, A., "Statistical analysis of the effects of helicity in inhomogeneous turbulence," Phys. Fluids A, 5, 464-477 (1993). [2] Yokoi, N. and Brandenburg, A., "Large-scale flow generation by inhomogeneous helicity," Phys. Rev. E, 93, 033125-1-14 (2016). [3] Marino, R., Mininni, P., Rosenberg, D., and Pouquet, A., "Emergence of helicity in rotating stratified turbulence," Phys. Rev. E, 87, 033016-1-9 (2013). [4] Duarte, L. D. V., Wicht, J., Browning, M. K., and Gastine, T., "Helicity inversion in spherical convection as a means for equatorward dynamo wave propagation," Mon. Not. Roy. Astron. Soc. 456, 1708-1722 (2016).

Bacterial flagellar microhydrodynamics: Laminar flow over complex flagellar filaments, analog archimedean screws and cylinders, and its perturbations.

PubMed

Trachtenberg, Shlomo; Fishelov, Dalia; Ben-Artzi, Matania

2003-09-01

The flagellar filament, the bacterial organelle of motility, is the smallest rotary propeller known. It consists of 1), a basal body (part of which is the proton driven rotary motor), 2), a hook (universal joint-allowing for off-axial transmission of rotary motion), and 3), a filament (propeller-a long, rigid, supercoiled helical assembly allowing for the conversion of rotary motion into linear thrust). Helically perturbed (so-called "complex") filaments have a coarse surface composed of deep grooves and ridges following the three-start helical lines. These surface structures, reminiscent of a turbine or Archimedean screw, originate from symmetry reduction along the six-start helical lines due to dimerization of the flagellin monomers from which the filament self assembles. Using high-resolution electron microscopy and helical image reconstruction methods, we calculated three-dimensional density maps of the complex filament of Rhizobium lupini H13-3 and determined its surface pattern and boundaries. The helical symmetry of the filament allows viewing it as a stack of identical slices spaced axially and rotated by constant increments. Here we use the closed outlines of these slices to explore, in two dimensions, the hydrodynamic effect of the turbine-like boundaries of the flagellar filament. In particular, we try to determine if, and under what conditions, transitions from laminar to turbulent flow (or perturbations of the laminar flow) may occur on or near the surface of the bacterial propeller. To address these questions, we apply the boundary element method in a manner allowing the handling of convoluted boundaries. We tested the method on several simple, well-characterized cylindrical structures before applying it to real, highly convoluted biological surfaces and to simplified mechanical analogs. Our results indicate that under extreme structural and functional conditions, and at low Reynolds numbers, a deviation from laminar flow might occur on the flagellar surface. These transitions, and the conditions enabling them, may affect flagellar polymorphism and the formation and dispersion of flagellar bundles-factors important in the chemotactic response.

Nonlinear MHD simulation of current drive by multi-pulsed coaxial helicity injection in spherical torus

NASA Astrophysics Data System (ADS)

Kanki, Takashi; Nagata, Masayoshi; Kagei, Yasuhiro

2011-10-01

The dynamics of structures of magnetic field, current density, and plasma flow generated during multi-pulsed coaxial helicity injection in spherical torus is investigated by 3-D nonlinear MHD simulations. During the driven phase, the flux and current amplifications occur due to the merging and magnetic reconnection between the preexisting plasma in the confinement region and the ejected plasma from the gun region involving the n = 1 helical kink distortion of the central open flux column (COFC). Interestingly, the diamagnetic poloidal flow which tends toward the gun region is then observed due to the steep pressure gradients of the COFC generated by ohmic heating through an injection current winding around the inboard field lines, resulting in the formation of the strong poloidal flow shear at the interface between the COFC and the core region. This result is consistent with the flow shear observed in the HIST. During the decay phase, the configuration approaches the axisymmetric MHD equilibrium state without flow because of the dissipation of magnetic fluctuation energy to increase the closed flux surfaces, suggesting the generation of ordered magnetic field structure. The parallel current density λ concentrated in the COFC then diffuses to the core region so as to reduce the gradient in λ, relaxing in the direction of the Taylor state.

Dynamics of zonal flows in helical systems.

PubMed

Sugama, H; Watanabe, T-H

2005-03-25

A theory for describing collisionless long-time behavior of zonal flows in helical systems is presented and its validity is verified by gyrokinetic-Vlasov simulation. It is shown that, under the influence of particles trapped in helical ripples, the response of zonal flows to a given source becomes weaker for lower radial wave numbers and deeper helical ripples while a high-level zonal-flow response, which is not affected by helical-ripple-trapped particles, can be maintained for a longer time by reducing their bounce-averaged radial drift velocity. This implies a possibility that helical configurations optimized for reducing neoclassical ripple transport can simultaneously enhance zonal flows which lower anomalous transport.

Helical vortices generated by flapping wings of bumblebees

NASA Astrophysics Data System (ADS)

Farge, Marie; Engels, Thomas; Kolomenskiy, Dmitry; Schneider, Kai; Lehmann, Fritz; Sesterhenn, Jörn

2016-11-01

We analyze high resolution numerical simulation data of a bumblebee with fixed body and prescribed wing motion, flying in a numerical wind tunnel, presented in. The inflow condition of the tunnel varies from unperturbed laminar to strongly turbulent. The flow generated by the flapping wings indicates the important role of the leading edge vortex (LEV), responsible for elevated lift production and which is not significantly altered by the inflow turbulence. The LEV has a conical structure due to the three-dimensional motion of the wings. This flow configuration produces strong vorticity on the sharp leading edge and the outwards velocity (from the root to the tip of the wing) in the spanwise direction. Flow visualizations show that the generated vortical structures are characterized by a strong helicity. We study the evolution of the mean helicity for each wing and analyze the impact of turbulent inflow. We thankfully acknowledge financial support from the French-German AIFIT project funded by DFG and ANR (Grant 15-CE40-0019). DK gratefully acknowledges financial support from the JSPS postdoctoral fellowship.

Epi-Two-Dimensional Fluid Flow: A New Topological Paradigm for Dimensionality

NASA Astrophysics Data System (ADS)

Yoshida, Z.; Morrison, P. J.

2017-12-01

While a variety of fundamental differences are known to separate two-dimensional (2D) and three-dimensional (3D) fluid flows, it is not well understood how they are related. Conventionally, dimensional reduction is justified by an a priori geometrical framework; i.e., 2D flows occur under some geometrical constraint such as shallowness. However, deeper inquiry into 3D flow often finds the presence of local 2D-like structures without such a constraint, where 2D-like behavior may be identified by the integrability of vortex lines or vanishing local helicity. Here we propose a new paradigm of flow structure by introducing an intermediate class, termed epi-two-dimensional flow, and thereby build a topological bridge between 2D and 3D flows. The epi-2D property is local and is preserved in fluid elements obeying ideal (inviscid and barotropic) mechanics; a local epi-2D flow may be regarded as a "particle" carrying a generalized enstrophy as its charge. A finite viscosity may cause "fusion" of two epi-2D particles, generating helicity from their charges giving rise to 3D flow.

Three-dimensional prominence-hosting magnetic configurations: Creating a helical magnetic flux rope

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xia, C.; Keppens, R.; Guo, Y.

2014-01-10

The magnetic configuration hosting prominences and their surrounding coronal structure is a key research topic in solar physics. Recent theoretical and observational studies strongly suggest that a helical magnetic flux rope is an essential ingredient to fulfill most of the theoretical and observational requirements for hosting prominences. To understand flux rope formation details and obtain magnetic configurations suitable for future prominence formation studies, we here report on three-dimensional isothermal magnetohydrodynamic simulations including finite gas pressure and gravity. Starting from a magnetohydrostatic corona with a linear force-free bipolar magnetic field, we follow its evolution when introducing vortex flows around the mainmore » polarities and converging flows toward the polarity inversion line near the bottom of the corona. The converging flows bring the feet of different loops together at the polarity inversion line, where magnetic reconnection and flux cancellation happen. Inflow and outflow signatures of the magnetic reconnection process are identified, and thereby the newly formed helical loops wind around preexisting ones so that a complete flux rope grows and ascends. When a macroscopic flux rope is formed, we switch off the driving flows and find that the system relaxes to a stable state containing a helical magnetic flux rope embedded in an overlying arcade structure. A major part of the formed flux rope is threaded by dipped field lines that can stably support prominence matter, while the total mass of the flux rope is in the order of 4-5× 10{sup 14} g.« less

Evaluation of CFD Methods for Simulation of Two-Phase Boiling Flow Phenomena in a Helical Coil Steam Generator

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pointer, William David; Shaver, Dillon; Liu, Yang

The U.S. Department of Energy, Office of Nuclear Energy charges participants in the Nuclear Energy Advanced Modeling and Simulation (NEAMS) program with the development of advanced modeling and simulation capabilities that can be used to address design, performance and safety challenges in the development and deployment of advanced reactor technology. The NEAMS has established a high impact problem (HIP) team to demonstrate the applicability of these tools to identification and mitigation of sources of steam generator flow induced vibration (SGFIV). The SGFIV HIP team is working to evaluate vibration sources in an advanced helical coil steam generator using computational fluidmore » dynamics (CFD) simulations of the turbulent primary coolant flow over the outside of the tubes and CFD simulations of the turbulent multiphase boiling secondary coolant flow inside the tubes integrated with high resolution finite element method assessments of the tubes and their associated structural supports. This report summarizes the demonstration of a methodology for the multiphase boiling flow analysis inside the helical coil steam generator tube. A helical coil steam generator configuration has been defined based on the experiments completed by Polytecnico di Milano in the SIET helical coil steam generator tube facility. Simulations of the defined problem have been completed using the Eulerian-Eulerian multi-fluid modeling capabilities of the commercial CFD code STAR-CCM+. Simulations suggest that the two phases will quickly stratify in the slightly inclined pipe of the helical coil steam generator. These results have been successfully benchmarked against both empirical correlations for pressure drop and simulations using an alternate CFD methodology, the dispersed phase mixture modeling capabilities of the open source CFD code Nek5000.« less

Aortic Valve Stenosis Increases Helical Flow and Flow Complexity: A Study of Intra-Operative Cardiac Vector Flow Imaging.

PubMed

Hansen, Kristoffer Lindskov; Møller-Sørensen, Hasse; Kjaergaard, Jesper; Jensen, Maiken Brit; Jensen, Jørgen Arendt; Nielsen, Michael Bachmann

2017-08-01

Aortic valve stenosis alters blood flow in the ascending aorta. Using intra-operative vector flow imaging on the ascending aorta, secondary helical flow during peak systole and diastole, as well as flow complexity of primary flow during systole, were investigated in patients with normal, stenotic and replaced aortic valves. Peak systolic helical flow, diastolic helical flow and flow complexity during systole differed between the groups (p < 0.0001), and correlated to peak systolic velocity (R = 0.94, 0.87 and 0.88, respectively). The study indicates that aortic valve stenosis increases helical flow and flow complexity, which are measurable with vector flow imaging. For assessment of aortic stenosis and optimization of valve surgery, vector flow imaging may be useful. Copyright © 2017 World Federation for Ultrasound in Medicine & Biology. Published by Elsevier Inc. All rights reserved.

Finite element analysis of helical flows in human aortic arch: A novel index

PubMed Central

Lee, Cheng-Hung; Liu, Kuo-Sheng; Jhong, Guan-Heng; Liu, Shih-Jung; Hsu, Ming-Yi; Wang, Chao-Jan; Hung, Kuo-Chun

2014-01-01

This study investigates the helical secondary flows in the aortic arch using finite element analysis. The relationship between helical flow and the configuration of the aorta in patients of whose three-dimensional images constructed from computed tomography scans was examined. A finite element model of the pressurized root, arch, and supra-aortic vessels was developed to simulate the pattern of helical secondary flows. Calculations indicate that most of the helical secondary flow was formed in the ascending aorta. Angle α between the zero reference point and the aortic ostium (correlation coefficient (r) = −0.851, P = 0.001), the dispersion index of the cross section of the ascending (r = 0.683, P = 0.021) and descending aorta (r = 0.732, P = 0.010), all correlated closely with the presence of helical flow (P < 0.05). Stepwise multiple linear regression analysis confirmed angel α to be independently associated with the helical flow pattern in therein (standardized coefficients = −0.721, P = 0.023). The presence of helical fluid motion based on the atherosclerotic risks of patients, including those associated with diabetes, hypertension, hyperlipidemia, or renal insufficiency, was also evaluated. Numerical simulation of the flow patterns in aortas incorporating the atherosclerotic risks may better explain the mechanism of formation of helical flows and provide insight into causative factors that underlie them. PMID:24803960

Effect of helicity on the correlation time of large scales in turbulent flows

NASA Astrophysics Data System (ADS)

Cameron, Alexandre; Alexakis, Alexandros; Brachet, Marc-Étienne

2017-11-01

Solutions of the forced Navier-Stokes equation have been conjectured to thermalize at scales larger than the forcing scale, similar to an absolute equilibrium obtained for the spectrally truncated Euler equation. Using direct numeric simulations of Taylor-Green flows and general-periodic helical flows, we present results on the probability density function, energy spectrum, autocorrelation function, and correlation time that compare the two systems. In the case of highly helical flows, we derive an analytic expression describing the correlation time for the absolute equilibrium of helical flows that is different from the E-1 /2k-1 scaling law of weakly helical flows. This model predicts a new helicity-based scaling law for the correlation time as τ (k ) ˜H-1 /2k-1 /2 . This scaling law is verified in simulations of the truncated Euler equation. In simulations of the Navier-Stokes equations the large-scale modes of forced Taylor-Green symmetric flows (with zero total helicity and large separation of scales) follow the same properties as absolute equilibrium including a τ (k ) ˜E-1 /2k-1 scaling for the correlation time. General-periodic helical flows also show similarities between the two systems; however, the largest scales of the forced flows deviate from the absolute equilibrium solutions.

SHEAR-DRIVEN DYNAMO WAVES IN THE FULLY NONLINEAR REGIME

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pongkitiwanichakul, P.; Nigro, G.; Cattaneo, F.

2016-07-01

Large-scale dynamo action is well understood when the magnetic Reynolds number ( Rm ) is small, but becomes problematic in the astrophysically relevant large Rm limit since the fluctuations may control the operation of the dynamo, obscuring the large-scale behavior. Recent works by Tobias and Cattaneo demonstrated numerically the existence of large-scale dynamo action in the form of dynamo waves driven by strongly helical turbulence and shear. Their calculations were carried out in the kinematic regime in which the back-reaction of the Lorentz force on the flow is neglected. Here, we have undertaken a systematic extension of their work tomore » the fully nonlinear regime. Helical turbulence and large-scale shear are produced self-consistently by prescribing body forces that, in the kinematic regime, drive flows that resemble the original velocity used by Tobias and Cattaneo. We have found four different solution types in the nonlinear regime for various ratios of the fluctuating velocity to the shear and Reynolds numbers. Some of the solutions are in the form of propagating waves. Some solutions show large-scale helical magnetic structure. Both waves and structures are permanent only when the kinetic helicity is non-zero on average.« less

A SOLAR TORNADO OBSERVED BY AIA/SDO: ROTATIONAL FLOW AND EVOLUTION OF MAGNETIC HELICITY IN A PROMINENCE AND CAVITY

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Xing; Morgan, Huw; Leonard, Drew

During 2011 September 24, as observed by the Atmospheric Imaging Assembly instrument of the Solar Dynamic Observatory and ground-based H{alpha} telescopes, a prominence and associated cavity appeared above the southwest limb. On 2011 September 25 8:00 UT, material flows upward from the prominence core along a narrow loop-like structure, accompanied by a rise ({>=}50,000 km) of the prominence core and the loop. As the loop fades by 10:00, small blobs and streaks of varying brightness rotate around the top part of the prominence and cavity, mimicking a cyclone. The most intense and coherent rotation lasts for over three hours, withmore » emission in both hot ({approx}1 MK) and cold (hydrogen and helium) lines. We suggest that the cyclonic appearance and overall evolution of the structure can be interpreted in terms of the expansion of helical structures into the cavity, and the movement of plasma along helical structures which appears as a rotation when viewed along the helix axis. The coordinated movement of material between prominence and cavity suggests that they are structurally linked. Complexity is great due to the combined effect of these actions and the line-of-sight integration through the structure which contains tangled fields.« less

Flow through triple helical microchannel

NASA Astrophysics Data System (ADS)

Rajbanshi, Pravat; Ghatak, Animangsu

2018-02-01

Flow through helical tubes and channels have been examined in different contexts, for facilitating heat and mass transfer at low Reynolds number flow, for generating plug flow to minimize reactor volume for many reactions. The curvature and torsion of the helices have been shown to engender secondary flow in addition to the primary axial flow, which enhances passive in-plane mixing between different fluid streams. Most of these studies, however, involve a single spiral with circular cross-section, which in essence is symmetric. It is not known, however, how the coupled effect of asymmetry of cross-section and the curvature and torsion of channel would affect the flow profile inside such tubes or channels. In this context, we have presented here the analysis of fluid flow at low Reynolds number inside a novel triple helical channel that consists of three helical flow paths joined along their contour length forming a single channel. We have carried out both microparticle image velocimetry (micro-PIV) and 3D simulation in FLUENT of flow of a Newtonian fluid through such channels. Our analysis shows that whereas in conventional single helices, the secondary flow is characterized by two counter-rotating vortices, in the case of triple helical channels, number of such vortices increases with the helix angle. Such flow profile is expected to enhance possibility of mixing between the liquids, yet diminish the pressure drop.

Effect of Swirl on Turbulent Structures in Supersonic Jets

NASA Technical Reports Server (NTRS)

Rao, Ram Mohan; Lundgren, Thomas S.

1998-01-01

Direct Numerical Simulation (DNS) is used to study the mechanism of generation and evolution of turbulence structures in a temporally evolving supersonic swirling round jet and also to examine the resulting acoustic radiations. Fourier spectral expansions are used in the streamwise and azimuthal directions and a 1-D b-spline Galerkin representation is used in the radial direction. Spectral-like accuracy is achieved using this numerical scheme. Direct numerical simulations, using the b-spline spectral method, are carried out starting from mean flow initial conditions which are perturbed by the most unstable linear stability eigenfunctions. It is observed that the initial helical instability waves evolve into helical vortices which eventually breakdown into smaller scales of turbulence. 'Rib' structures similar to those seen in incompressible mixing layer flow of Rogers and Moserl are observed. The jet core breakdown stage exhibits increased acoustic radiations.

Scaling laws and reduced-order models for mixing and reactive-transport in heterogeneous anisotropic porous media

NASA Astrophysics Data System (ADS)

Mudunuru, M. K.; Karra, S.; Nakshatrala, K. B.

2016-12-01

Fundamental to enhancement and control of the macroscopic spreading, mixing, and dilution of solute plumes in porous media structures is the topology of flow field and underlying heterogeneity and anisotropy contrast of porous media. Traditionally, in literature, the main focus was limited to the shearing effects of flow field (i.e., flow has zero helical density, meaning that flow is always perpendicular to vorticity vector) on scalar mixing [2]. However, the combined effect of anisotropy of the porous media and the helical structure (or chaotic nature) of the flow field on the species reactive-transport and mixing has been rarely studied. Recently, it has been experimentally shown that there is an irrefutable evidence that chaotic advection and helical flows are inherent in porous media flows [1,2]. In this poster presentation, we present a non-intrusive physics-based model-order reduction framework to quantify the effects of species mixing in-terms of reduced-order models (ROMs) and scaling laws. The ROM framework is constructed based on the recent advancements in non-negative formulations for reactive-transport in heterogeneous anisotropic porous media [3] and non-intrusive ROM methods [4]. The objective is to generate computationally efficient and accurate ROMs for species mixing for different values of input data and reactive-transport model parameters. This is achieved by using multiple ROMs, which is a way to determine the robustness of the proposed framework. Sensitivity analysis is performed to identify the important parameters. Representative numerical examples from reactive-transport are presented to illustrate the importance of the proposed ROMs to accurately describe mixing process in porous media. [1] Lester, Metcalfe, and Trefry, "Is chaotic advection inherent to porous media flow?," PRL, 2013. [2] Ye, Chiogna, Cirpka, Grathwohl, and Rolle, "Experimental evidence of helical flow in porous media," PRL, 2015. [3] Mudunuru, and Nakshatrala, "On enforcing maximum principles and achieving element-wise species balance for advection-diffusion-reaction equations under the finite element method," JCP, 2016. [4] Quarteroni, Manzoni, and Negri. "Reduced Basis Methods for Partial Differential Equations: An Introduction," Springer, 2016.

Numerical simulation of helical flow in a cylindrical channel

NASA Astrophysics Data System (ADS)

Vasiliev, A.; Sukhanovskii, A.; Stepanov, R.

2017-06-01

Numerical simulation of the helical flow in a cylindrical channel with diverter was carried out using open-source software OpenFOAM Extend 4.0. The velocity, vorticity and helicity density distributions were analyzed. It was shown that azimithal contribution of helicity is negative near the wall and positive in the center. In opposite axial helicity contribution is negative in the center and positive near the wall. Analysis of helicity of non-axisymmetric part of the flow showed that it has substantial values near the diverter but than rapidly decreases with y (axial coordinate) and further downstream it can be neglected. Dependencies of integrated values of azimuthal Hϕ and axial Hy contributions of helicity density on y show a remarkable quantitative similarity. It was found that integral values of Hϕ and Hy are negative for all y. Magnitudes of Hϕ and Hy decrease after the diverter up to y ≈ 70 mm and after that monotonically increase. The flow behind the diverter is characterized by substantial amount of helicity and can be used as a helicity generator.

A factor involved in efficient breakdown of supersonic streamwise vortices

NASA Astrophysics Data System (ADS)

Hiejima, Toshihiko

2015-03-01

Spatially developing processes in supersonic streamwise vortices were numerically simulated at Mach number 5.0. The vortex evolution largely depended on the azimuthal vorticity thickness of the vortices, which governs the negative helicity profile. Large vorticity thickness greatly enhanced the centrifugal instability, with consequent development of perturbations with competing wavenumbers outside the vortex core. During the transition process, supersonic streamwise vortices could generate large-scale spiral structures and a number of hairpin like vortices. Remarkably, the transition caused a dramatic increase in the total fluctuation energy of hypersonic flows, because the negative helicity profile destabilizes the flows due to helicity instability. Unstable growth might also relate to the correlation length between the axial and azimuthal vorticities of the streamwise vortices. The knowledge gained in this study is important for realizing effective fuel-oxidizer mixing in supersonic combustion engines.

In Vitro MRV-based Hemodynamic Study of Complex Helical Flow in a Patient-specific Jugular Model

NASA Astrophysics Data System (ADS)

Kefayati, Sarah; Acevedo-Bolton, Gabriel; Haraldsson, Henrik; Saloner, David

2014-11-01

Neurointerventional Radiologists are frequently requested to evaluate the venous side of the intracranial circulation for a variety of conditions including: Chronic Cerebrospinal Venous Insufficiency thought to play a role in the development of multiple sclerosis; sigmoid sinus diverticulum which has been linked to the presence of pulsatile tinnitus; and jugular vein distension which is related to cardiac dysfunction. Most approaches to evaluating these conditions rely on structural assessment or two dimensional flow analyses. This study was designed to investigate the highly complex jugular flow conditions using magnetic resonance velocimetry (MRV). A jugular phantom was fabricated based on the geometry of the dominant jugular in a tinnitus patient. Volumetric three-component time-resolved velocity fields were obtained using 4D PC-MRI -with the protocol enabling turbulence acquisition- and the patient-specific pulsatile waveform. Flow was highly complex exhibiting regions of jet, high swirling strength, and strong helical pattern with the core originating from the focal point of the jugular bulb. Specifically, flow was analyzed for helicity and the level of turbulence kinetic energy elevated in the core of helix and distally, in the post-narrowing region.

Comparison of magnetic helicity close to the sun and in magnetic clouds

NASA Astrophysics Data System (ADS)

Rust, D.

Magnetic helicity is present in the solar atmosphere - as inferred from vector magnetograph measurements, solar filaments, S-shaped coronal structures known as sigmoids, and sunspot whorls. I will survey the possible solar sources of this magnetic helicity. Included are fieldline footpoint motions, effects of Coriolis forces, effects of convection, shear associated with differential rotation, and, of course, the internal dynamo. Besides the survey of possible local mechanisms for helicity generation, I will consider the global view of the flow of helicity from the sun into interplanetary space. The principal agents by which the sun sheds helicity are coronal mass ejections (CMEs). They are often associated with interplanetary magnetic clouds (MCs), whose fields are regularly probed with sensitive spacecraft magnetometers. MCs yield more direct measurements of helicity. They show that each MC carries helicity away from the sun. A major issue in solar-heliospheric research is whether the amount of helicity that MCs carry away in a solar cycle can be accounted for by the helicity generation mechanisms proposed so far. The NASA Solar and Heliospheric Physics Program supports this work under grants NAG5- 7921 and NAG 5-11584.

Cascades of energy and helicity in axisymmetric turbulence

NASA Astrophysics Data System (ADS)

Qu, Bo; Naso, Aurore; Bos, Wouter J. T.

2018-01-01

A spectral analysis of strictly axisymmetric turbulence is performed. Both freely decaying and statistically steady flows are considered. In helical flows we identify a dual cascade, where energy is transferred towards the large scales and helicity to the smallest ones. It is shown that even in the absence of net helicity, a dual cascade persists, transferring energy backward and positively and negatively polarized helicity fluctuations forward.

The influence of the aortic valve angle on the hemodynamic features of the thoracic aorta

NASA Astrophysics Data System (ADS)

Ha, Hojin; Kim, Guk Bae; Kweon, Jihoon; Lee, Sang Joon; Kim, Young-Hak; Kim, Namkug; Yang, Dong Hyun

2016-08-01

Since the first observation of a helical flow pattern in aortic blood flow, the existence of helical blood flow has been found to be associated with various pathological conditions such as bicuspid aortic valve, aortic stenosis, and aortic dilatation. However, an understanding of the development of helical blood flow and its clinical implications are still lacking. In our present study, we hypothesized that the direction and angle of aortic inflow can influence helical flow patterns and related hemodynamic features in the thoracic aorta. Therefore, we investigated the hemodynamic features in the thoracic aorta and various aortic inflow angles using patient-specific vascular phantoms that were generated using a 3D printer and time-resolved, 3D, phase-contrast magnetic resonance imaging (PC-MRI). The results show that the rotational direction and strength of helical blood flow in the thoracic aorta largely vary according to the inflow direction of the aorta, and a higher helical velocity results in higher wall shear stress distributions. In addition, right-handed rotational flow conditions with higher rotational velocities imply a larger total kinetic energy than left-handed rotational flow conditions with lower rotational velocities.

The influence of the aortic valve angle on the hemodynamic features of the thoracic aorta.

PubMed

Ha, Hojin; Kim, Guk Bae; Kweon, Jihoon; Lee, Sang Joon; Kim, Young-Hak; Kim, Namkug; Yang, Dong Hyun

2016-08-26

Since the first observation of a helical flow pattern in aortic blood flow, the existence of helical blood flow has been found to be associated with various pathological conditions such as bicuspid aortic valve, aortic stenosis, and aortic dilatation. However, an understanding of the development of helical blood flow and its clinical implications are still lacking. In our present study, we hypothesized that the direction and angle of aortic inflow can influence helical flow patterns and related hemodynamic features in the thoracic aorta. Therefore, we investigated the hemodynamic features in the thoracic aorta and various aortic inflow angles using patient-specific vascular phantoms that were generated using a 3D printer and time-resolved, 3D, phase-contrast magnetic resonance imaging (PC-MRI). The results show that the rotational direction and strength of helical blood flow in the thoracic aorta largely vary according to the inflow direction of the aorta, and a higher helical velocity results in higher wall shear stress distributions. In addition, right-handed rotational flow conditions with higher rotational velocities imply a larger total kinetic energy than left-handed rotational flow conditions with lower rotational velocities.

The influence of the aortic valve angle on the hemodynamic features of the thoracic aorta

PubMed Central

Ha, Hojin; Kim, Guk Bae; Kweon, Jihoon; Lee, Sang Joon; Kim, Young-Hak; Kim, Namkug; Yang, Dong Hyun

2016-01-01

Since the first observation of a helical flow pattern in aortic blood flow, the existence of helical blood flow has been found to be associated with various pathological conditions such as bicuspid aortic valve, aortic stenosis, and aortic dilatation. However, an understanding of the development of helical blood flow and its clinical implications are still lacking. In our present study, we hypothesized that the direction and angle of aortic inflow can influence helical flow patterns and related hemodynamic features in the thoracic aorta. Therefore, we investigated the hemodynamic features in the thoracic aorta and various aortic inflow angles using patient-specific vascular phantoms that were generated using a 3D printer and time-resolved, 3D, phase-contrast magnetic resonance imaging (PC-MRI). The results show that the rotational direction and strength of helical blood flow in the thoracic aorta largely vary according to the inflow direction of the aorta, and a higher helical velocity results in higher wall shear stress distributions. In addition, right-handed rotational flow conditions with higher rotational velocities imply a larger total kinetic energy than left-handed rotational flow conditions with lower rotational velocities. PMID:27561388

A generalised model of secondary circulation for a wide range of geophysical flows from direct observations of natural turbidity currents

NASA Astrophysics Data System (ADS)

Azpiroz, M.; Cartigny, M.; Sumner, E. J.; Talling, P.; Parsons, D. R.; Clare, M. A.; Cooper, C.

2017-12-01

Turbidity currents transport sediment through submarine channel systems for hundreds of kilometres to form vast deposits of sediment in the deep sea called submarine fans. The largest submarine fans are fed by meandering channels suggesting that bends may enhance sediment transport distances. The interaction between meander bends and turbidity currents has been a topic of intense debate. Due to the absence of observations of deep-sea turbidity currents flowing through meander bends, our understanding has been based on experimental and numerical models. Measurements of geophysical flows demonstrate a common helical flow structure around meanders. Previous work has demonstrated that helical circulation in rivers is dominated by a single helix that rotates towards the inner bend at near-bed depths. In contrast, initial numerical and experimental models for turbidity currents found both river-like and river-reversed circulations. Saline flows in well-mixed estuaries show a river-like basal helical circulation, while stratified estuaries and saline flows are river-reversed. The existence of lateral stratification in stratified flows is thought to be the key factor in the change of direction of rotation. Stratification causes lateral pressure gradients that can govern the rotation of the flow helix. Turbidity currents are stratified due to their upwards-decreasing sediment load. It has therefore been proposed that stratified turbidity currents behave like stratified saline flow, but this hypothesis remains so far untested. Here we present the first observations of the helical flow in turbidity currents, which occurred within the deep-sea Congo Canyon. The measurements show a consistent river-reversed pattern downstream of the bend apex. Those results lead us to develop a new generalised model for a wide range of flows around meanders. Our conclusions have implications for understanding the flow erosional and depositional patterns, the evolution of channel systems and the architecture of the depositional record.

Biot-Savart helicity versus physical helicity: A topological description of ideal flows

NASA Astrophysics Data System (ADS)

Sahihi, Taliya; Eshraghi, Homayoon

2014-08-01

For an isentropic (thus compressible) flow, fluid trajectories are considered as orbits of a family of one parameter, smooth, orientation-preserving, and nonsingular diffeomorphisms on a compact and smooth-boundary domain in the Euclidian 3-space which necessarily preserve a finite measure, later interpreted as the fluid mass. Under such diffeomorphisms the Biot-Savart helicity of the pushforward of a divergence-free and tangent to the boundary vector field is proved to be conserved and since these circumstances present an isentropic flow, the conservation of the "Biot-Savart helicity" is established for such flows. On the other hand, the well known helicity conservation in ideal flows which here we call it "physical helicity" is found to be an independent constant with respect to the Biot-Savart helicity. The difference between these two helicities reflects some topological features of the domain as well as the velocity and vorticity fields which is discussed and is shown for simply connected domains the two helicities coincide. The energy variation of the vorticity field is shown to be formally the same as for the incompressible flow obtained before. For fluid domains consisting of several disjoint solid tori, at each time, the harmonic knot subspace of smooth vector fields on the fluid domain is found to have two independent base sets with a special type of orthogonality between these two bases by which a topological description of the vortex and velocity fields depending on the helicity difference is achieved since this difference is shown to depend only on the harmonic knot parts of velocity, vorticity, and its Biot-Savart vector field. For an ideal magnetohydrodynamics (MHD) flow three independent constant helicities are reviewed while the helicity of magnetic potential is generalized for non-simply connected domains by inserting a special harmonic knot field in the dynamics of the magnetic potential. It is proved that the harmonic knot part of the vorticity in hydrodynamics and the magnetic field in MHD is presented by constant coefficients (fluxes) when expanded in terms of one of the time dependent base functions.

Hydrogen bonds and heat diffusion in α-helices: a computational study.

PubMed

Miño, German; Barriga, Raul; Gutierrez, Gonzalo

2014-08-28

Recent evidence has shown a correlation between the heat diffusion pathways and the known allosteric communication pathways in proteins. Allosteric communication in proteins is a central, yet unsolved, problem in biochemistry, and the study and characterization of the structural determinants that mediate energy transfer among different parts of proteins is of major importance. In this work, we characterized the role of hydrogen bonds in diffusivity of thermal energy for two sets of α-helices with different abilities to form hydrogen bonds. These hydrogen bonds can be a constitutive part of the α-helices or can arise from the lateral chains. In our in vacuo simulations, it was observed that α-helices with a higher possibility of forming hydrogen bonds also had higher rates of thermalization. Our simulations also revealed that heat readily flowed through atoms involved in hydrogen bonds. As a general conclusion, according to our simulations, hydrogen bonds fulfilled an important role in heat diffusion in structural patters of proteins.

ANATOMY OF HELICAL EXTRAGALACTIC JETS: THE CASE OF S5 0836+710

DOE Office of Scientific and Technical Information (OSTI.GOV)

Perucho, M.; Kovalev, Y. Y.; Lobanov, A. P.

Helical structures are common in extragalactic jets. They are usually attributed in the literature to periodical phenomena in the source (e.g., precession). In this work, we use very long baseline interferometry data of the radio jet in the quasar S5 0836+710 and hypothesize that the ridgeline of helical jets like this corresponds to a pressure maximum in the jet and assume that the helically twisted pressure maximum is the result of a helical wave pattern. For our study, we use observations of the jet in S5 0836+710 at different frequencies and epochs. The results show that the structures observed aremore » physical and not generated artificially by the observing arrays. Our hypothesis that the observed intensity ridgeline can correspond to a helically twisted pressure maximum is confirmed by our observational tests. This interpretation allows us to explain jet misalignment between parsec and kiloparsec scales when the viewing angle is small, and also brings us to the conclusion that high-frequency observations may show only a small region of the jet flow concentrated around the maximum pressure ridgeline observed at low frequencies. Our work provides a potential explanation for the apparent transversal superluminal speeds observed in several extragalactic jets by means of transversal shift of an apparent core position with time.« less

Non-Native α-Helices in the Initial Folding Intermediate Facilitate the Ordered Assembly of the β-Barrel in β-Lactoglobulin.

PubMed

Sakurai, Kazumasa; Yagi, Masanori; Konuma, Tsuyoshi; Takahashi, Satoshi; Nishimura, Chiaki; Goto, Yuji

2017-09-12

The roles of non-native α-helices frequently observed in the initial folding stage of β-sheet proteins have been examined for many years. We herein investigated the residue-level structures of several mutants of bovine β-lactoglobulin (βLG) in quenched-flow pH-pulse labeling experiments. βLG assumes a collapsed intermediate with a non-native α-helical structure (I 0 ) in the early stage of folding, although its native form is predominantly composed of β-structures. The protection profile in I 0 of pseudo-wild type (WT*) βLG was found to deviate from the pattern of the "average area buried upon folding" (AABUF). In particular, the level of protection at the region of strand A, at which non-native α-helices form in the I 0 state, was significantly low compared to AABUF. G17E, the mutant with an increased helical propensity, showed a similar protection pattern. In contrast, the protection pattern for I 0 of E44L, the mutant with an increased β-sheet propensity, was distinct from that of WT* and resembled the AABUF pattern. Transverse relaxation measurements demonstrated that the positions of the residual structures in the unfolded states of these mutants were consistent with those of the protected residues in the respective I 0 states. On the basis of the slower conversion of I 0 to the native state for E44L to that for WT*, non-native α-helices facilitate the ordered assembly of the β-barrel by preventing interactions that trap folding.

Theoretical model of chirality-induced helical self-propulsion

NASA Astrophysics Data System (ADS)

Yamamoto, Takaki; Sano, Masaki

2018-01-01

We recently reported the experimental realization of a chiral artificial microswimmer exhibiting helical self-propulsion [T. Yamamoto and M. Sano, Soft Matter 13, 3328 (2017), 10.1039/C7SM00337D]. In the experiment, cholesteric liquid crystal (CLC) droplets dispersed in surfactant solutions swam spontaneously, driven by the Marangoni flow, in helical paths whose handedness is determined by the chirality of the component molecules of CLC. To study the mechanism of the emergence of the helical self-propelled motion, we propose a phenomenological model of the self-propelled helical motion of the CLC droplets. Our model is constructed by symmetry argument in chiral systems, and it describes the dynamics of CLC droplets with coupled time-evolution equations in terms of a velocity, an angular velocity, and a tensor variable representing the symmetry of the helical director field of the droplet. We found that helical motions as well as other chiral motions appear in our model. By investigating bifurcation behaviors between each chiral motion, we found that the chiral coupling terms between the velocity and the angular velocity, the structural anisotropy of the CLC droplet, and the nonlinearity of model equations play a crucial role in the emergence of the helical motion of the CLC droplet.

Shear sensitive monomer-polymer laminate structure and method of using same

NASA Technical Reports Server (NTRS)

Singh, Jag J. (Inventor); Eftekhari, Abe (Inventor); Parmar, Devendra S. (Inventor)

1993-01-01

Monomer cholesteric liquid crystals have helical structures which result in a phenomenon known as selective reflection, wherein incident white light is reflected in such a way that its wavelength is governed by the instantaneous pitch of the helix structure. The pitch is dependent on temperature and external stress fields. It is possible to use such monomers in flow visualization and temperature measurement. However, the required thin layers of these monomers are quickly washed away by a flow, making their application time dependent for a given flow rate. The laminate structure according to the present invention comprises a liquid crystal polymer substrate attached to a test surface of an article. A light absorbing coating is applied to the substrate and is thin enough to permit bonding steric interaction between the liquid crystal polymer substrate and an overlying liquid crystal monomer thin film. Light is directed through and reflected by the liquid crystal monomer thin film and unreflected light is absorbed by the underlying coating. The wavelength of the reflected light is indicative of the shear stress experienced by the test surface. Novel aspects of the invention include its firm bonding of a liquid crystal monomer to a model and its use of a coating to reduce interference from light unreflected by the monomer helical structure.

A Novel Class of Helical Nanostructures: Paradigms for their Design and Synthesis Using Imprint Lithography and Carbon Nanotubes

NASA Astrophysics Data System (ADS)

Smalling, David

2006-03-01

This research focuses on the use of solenoid-like configurations which are both microscopic and macroscopic, to make energy conversions between electrical energy and other forms. Numerous conceptual models are to be evaluated for the construction of an environment in which a charged particle could be allowed travel along a helical path of extremely small pitch and comparatively large large radius. The two main types of solenoid designs discussed, are lithographically synthesized solenoids and coiled carbon nano tube solenoids. For future identification the family of structures described will be referred to as Zeta (ζ) Structures. In the case of a ζ solenoid, the objective would be to create a solenoid whose general structure is macroscopic but comprises a conductive trace which is on the nano-scale, In the case of such a solenoid the current flowing I and the magnetic flux B would be related approximately by B 1.256x10^3I. Such a situation gives rise to a very fascinating relationship between B and I. This means that if a current of say 1 ampere was made to flow through the solenoid, a magnetic flux of 1250 Tesla would be generated. The defining characteristic of ζ structures is their overall macroscopic dimensions which comprise high level nano-scale repetition. This research discusses theoretical propositions for the development of a class sub micron structures defined by a unique helical foundation, to be used for the generation of magnetic fields.

Helicity, geostrophic balance and mixing in rotating stratified turbulence: a multi-scale problem

NASA Astrophysics Data System (ADS)

Pouquet, A.; Marino, R.; Mininni, P.; Rorai, C.; Rosenberg, D. L.

2012-12-01

Helicity, geostrophic balance and mixing in rotating stratified turbulence: a multi-scale problem A. Pouquet, R. Marino, P. D. Mininni, C. Rorai & D. Rosenberg, NCAR Interactions between winds and waves have important roles in planetary and oceanic boundary layers, affecting momentum, heat and CO2 transport. Within the Abyssal Southern Ocean at Mid latitude, this may result in a mixed layer which is too shallow in climate models thereby affecting the overall evolution because of poor handling of wave breaking as in Kelvin-Helmoltz instabilities: gravity waves couple nonlinearly on slow time scales and undergo steepening through resonant interactions, or due to the presence of shear. In the oceans, sub-mesoscale frontogenesis and significant departure from quasi-geostrophy can be seen as turbulence intensifies. The ensuing anomalous vertical dispersion may not be simply modeled by a random walk, due to intermittent structures, wave propagation and to their interactions. Conversely, the energy and seeds required for such intermittent events to occur, say in the stable planetary boundary layer, may come from the wave field that is perturbed, or from winds and the effect of topography. Under the assumption of stationarity, weak nonlinearities, dissipation and forcing, one obtains large-scale geostrophic balance linking pressure gradient, gravity and Coriolis force. The role of helicity (velocity-vorticity correlations) has not received as much attention, outside the realm of astrophysics when considering the growth of large-scale magnetic fields. However, it is measured routinely in the atmosphere in order to gauge the likelihood of supercell convective storms to strengthen, and it may be a factor to consider in the formation of hurricanes. In this context, we examine the transition from a wave-dominated regime to an isotropic small-scale turbulent one in rotating flows with helical forcing. Using a direct numerical simulation (DNS) on a 3072^3 grid with Rossby and Reynolds numbers of 0.07 and 27000, one can resolve both the Zeman scale at which the inertial and eddy turn-over times equalize, and the dissipation scale. We show that fully helical vertical columns dominate at intermediate scales, presumably self-similar and shrouded by a sea of small-scale vortex filaments as in Kolmogorov turbulence. Helicity has a profound effect on the structures of the flow, and a previously developed model that includes a helical component in its eddy viscosity and eddy noise shows a measurable improvement. Indeed, if dimensionless parameters for inertial and gravity waves are reachable numerically, the Reynolds number is too low in DNS for geophysics unless one uses parametrizations of small scale interactions. For spin-down stably-stratified flows, energy and helicity undergo a substantially slower decay than in the unstratified case, and a type of large-scale cyclostrophic balance is invoked to explain this behavior. The decay rate is similar to that occurring in the unstratified rotating case, as modeled by taking into account the quasi-conservation of helicity. We finally mention helicity production when rotation and stratification are both combined. In conclusion, much remains to be done, e.g. examining transport properties of rotating stratified turbulence, such as the effect of helicity on mixing in geophysical flows that can be studied with high-performance computing allowing multi-scale interactions and intermittency to develop.

Godbillon Vey Helicity and Magnetic Helicity in Magnetohydrodynamics

NASA Astrophysics Data System (ADS)

Webb, G. M.; Hu, Q.; Anco, S.; Zank, G. P.

2017-12-01

The Godbillon-Vey invariant arises in homology theory, and algebraic topology, where conditions for a layered family of 2D surfaces forms a 3D manifold were elucidated. The magnetic Godbillon-Vey helicity invariant in magnetohydrodynamics (MHD) is a helicity invariant that occurs for flows, in which the magnetic helicity density hm= A\\cdotB=0 where A is the magnetic vector potential and B is the magnetic induction. Our purpose is to elucidate the evolution of the magnetic Godbillon-Vey field η =A×B/|A|2 and the Godbillon-Vey helicity hgv}= η \\cdot∇ × η in general MHD flows in which the magnetic helicity hm≠q 0. It is shown that hm acts as a source term in the Godbillon-Vey helicity transport equation, in which hm is coupled to hgv via the shear tensor of the background flow. The transport equation for hgv depends on the electric field potential ψ , which is related to the gauge for A, which takes its simplest form for the advected A gauge in which ψ =A\\cdot u where u is the fluid velocity.

Vorticity and helicity decompositions and dynamics with real Schur form of the velocity gradient

NASA Astrophysics Data System (ADS)

Zhu, Jian-Zhou

2018-03-01

The real Schur form (RSF) of a generic velocity gradient field ∇u is exploited to expose the structures of flows, in particular, our field decomposition resulting in two vorticities with only mutual linkage as the topological content of the global helicity (accordingly decomposed into two equal parts). The local transformation to the RSF may indicate alternative (co)rotating frame(s) for specifying the objective argument(s) of the constitutive equation. When ∇u is uniformly of RSF in a fixed Cartesian coordinate frame, i.e., ux = ux(x, y) and uy = uy(x, y), but uz = uz(x, y, z), the model, with the decomposed vorticities both frozen-in to u, is for two-component-two-dimensional-coupled-with-one-component-three-dimensional flows in between two-dimensional-three-component (2D3C) and fully three-dimensional-three-component ones and may help curing the pathology in the helical 2D3C absolute equilibrium, making the latter effectively work in more realistic situations.

Hydrodynamic characteristics of viscous fluid flow in screw channels formed by two ribs

NASA Astrophysics Data System (ADS)

Kadyirov, A. I.; Abaydullin, B. R.; Vachagina, E. K.

2018-03-01

The mathematical model of laminar viscous flows in screw channels, formed by two ribs, is developed using the helical coordinates. The numerical results of the flow with helical symmetry are presented.

CFD analysis of the two-phase bubbly flow characteristics in helically coiled rectangular and circular tube heat exchangers

NASA Astrophysics Data System (ADS)

Hussain, Alamin; Fsadni, Andrew M.

2016-03-01

Due to their ease of manufacture, high heat transfer efficiency and compact design, helically coiled heat exchangers are increasingly being adopted in a number of industries. The higher heat transfer efficiency over straight pipes is due to the secondary flow that develops as a result of the centrifugal force. In spite of the widespread use of helically coiled heat exchangers, and the presence of bubbly two-phase flow in a number of systems, very few studies have investigated the resultant flow characteristics. This paper will therefore present the results of CFD simulations for the two-phase bubbly flow in helically coiled heat exchangers as a function of the volumetric void fraction and the tube cross-section design. The CFD results are compared to the scarce flow visualisation experimental results available in the open literature.

Large-scale vortex structures and local heat release in lean turbulent swirling jet-flames under vortex breakdown conditions

NASA Astrophysics Data System (ADS)

Chikishev, Leonid; Lobasov, Aleksei; Sharaborin, Dmitriy; Markovich, Dmitriy; Dulin, Vladimir; Hanjalic, Kemal

2017-11-01

We investigate flame-flow interactions in an atmospheric turbulent high-swirl methane/air lean jet-flame at Re from 5,000 to 10,000 and equivalence ratio below 0.75 at the conditions of vortex breakdown. The focus is on the spatial correlation between the propagation of large-scale vortex structures, including precessing vortex core, and the variations of the local heat release. The measurements are performed by planar laser-induced fluorescence of hydroxyl and formaldehyde, applied simultaneously with the stereoscopic particle image velocimetry technique. The data are processed by the proper orthogonal decomposition. The swirl rate exceeded critical value for the vortex breakdown resulting in the formation of a processing vortex core and secondary helical vortex filaments that dominate the unsteady flow dynamics both of the non-reacting and reacting jet flows. The flame front is located in the inner mixing layer between the recirculation zone and the annular swirling jet. A pair of helical vortex structures, surrounding the flame, stretch it and cause local flame extinction before the flame is blown away. This work is supported by Russian Science Foundation (Grant No 16-19-10566).

Free-fall dynamics of a pair of rigidly linked disks

NASA Astrophysics Data System (ADS)

Kim, Taehyun; Chang, Jaehyeock; Kim, Daegyoum

2018-03-01

We investigate experimentally the free-fall motion of a pair of identical disks rigidly connected to each other. The three-dimensional coordinates of the pair of falling disks were constructed to quantitatively describe its trajectory, and the flow structure formed by the disk pair was identified by using dye visualization. The rigidly linked disk pair exhibits a novel falling pattern that creates a helical path with a conical configuration in which the lower disk rotates in a wider radius than the upper disk with respect to a vertical axis. The helical motion occurs consistently for the range of disk separation examined in this study. The dye visualization reveals that a strong, noticeable helical vortex core is generated from the outer tip of the lower disk during the helical motion. With an increasing length ratio, which is the ratio of the disk separation to the diameter of the disks, the nutation angle and the rate of change in the precession angle that characterize the combined helical and conical kinematics decrease linearly, whereas the pitch of the helical path increases linearly. Although all disk pairs undergo this helical motion, the horizontal-drift patterns of the disk pair depend on the length ratio.

Pseudo-invariants contributing to inverse energy cascades in three-dimensional turbulence

NASA Astrophysics Data System (ADS)

Rathmann, Nicholas M.; Ditlevsen, Peter D.

2017-05-01

Three-dimensional (3D) turbulence is characterized by a dual forward cascade of both kinetic energy and helicity, a second inviscid flow invariant besides energy, from the integral scale of motion to the viscous dissipative scale. In helical flows, however, such as strongly rotating flows with broken mirror symmetry, an inverse (reversed) energy cascade can be observed analogous to that of two-dimensional turbulence (2D) where enstrophy, a second positive-definite flow invariant, unlike helicity in 3D, effectively blocks the forward cascade of energy. In the spectral-helical decomposition of the Navier-Stokes equation, it has previously been shown that a subset of three-wave (triad) interactions conserve helicity in 3D in a fashion similar to enstrophy in 2D, thus leading to a 2D-like inverse energy cascade in 3D. In this work, we show, both theoretically and numerically, that an additional subset of interactions exist, conserving a new pseudo-invariant in addition to energy and helicity, which contributes either to a forward or an inverse energy cascade depending on the specific triad interaction geometry.

Deformation of a soft helical filament in an axial flow at low Reynolds number.

PubMed

Jawed, Mohammad K; Reis, Pedro M

2016-02-14

We perform a numerical investigation of the deformation of a rotating helical filament subjected to an axial flow, under low Reynolds number conditions, motivated by the propulsion of bacteria using helical flagella. Given its slenderness, the helical rod is intrinsically soft and deforms due to the interplay between elastic forces and hydrodynamic loading. We make use of a previously developed and experimentally validated computational tool framework that models the elasticity of the filament using the discrete elastic rod method and the fluid forces are treated using Lighthill's slender body theory. Under axial flow, and in the absence of rotation, the initially helical rod is extended. Above a critical flow speed its configuration comprises a straight portion connected to a localized helix near the free end. When the rod is also rotated about its helical axis, propulsion is only possible in a finite range of angular velocity, with an upper bound that is limited by buckling of the soft helix arising due to viscous stresses. A systematic exploration of the parameter space allows us to quantify regimes for successful propulsion for a number of specific bacteria.

High regression rate hybrid rocket fuel grains with helical port structures

NASA Astrophysics Data System (ADS)

Walker, Sean D.

Hybrid rockets are popular in the aerospace industry due to their storage safety, simplicity, and controllability during rocket motor burn. However, they produce fuel regression rates typically 25% lower than solid fuel motors of the same thrust level. These lowered regression rates produce unacceptably high oxidizer-to-fuel (O/F) ratios that produce a potential for motor instability, nozzle erosion, and reduced motor duty cycles. To achieve O/F ratios that produce acceptable combustion characteristics, traditional cylindrical fuel ports are fabricated with very long length-to-diameter ratios to increase the total burning area. These high aspect ratios produce further reduced fuel regression rate and thrust levels, poor volumetric efficiency, and a potential for lateral structural loading issues during high thrust burns. In place of traditional cylindrical fuel ports, it is proposed that by researching the effects of centrifugal flow patterns introduced by embedded helical fuel port structures, a significant increase in fuel regression rates can be observed. The benefits of increasing volumetric efficiencies by lengthening the internal flow path will also be observed. The mechanisms of this increased fuel regression rate are driven by enhancing surface skin friction and reducing the effect of boundary layer "blowing" to enhance convective heat transfer to the fuel surface. Preliminary results using additive manufacturing to fabricate hybrid rocket fuel grains from acrylonitrile-butadiene-styrene (ABS) with embedded helical fuel port structures have been obtained, with burn-rate amplifications up to 3.0x than that of cylindrical fuel ports.

Effects of Magnetic and Kinetic Helicities on the Growth of Magnetic Fields in Laminar and Turbulent Flows by Helical Fourier Decomposition

DOE Office of Scientific and Technical Information (OSTI.GOV)

Linkmann, Moritz; Sahoo, Ganapati; Biferale, Luca

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 kinematicmore » 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.« less

Magnet design with 100-kA HTS STARS conductors for the helical fusion reactor

NASA Astrophysics Data System (ADS)

Yanagi, N.; Terazaki, Y.; Ito, S.; Tamura, H.; Hamaguchi, S.; Mito, T.; Hashizume, H.; Sagara, A.

2016-12-01

The high-temperature superconducting (HTS) option is employed for the conceptual design of the LHD-type helical fusion reactor FFHR-d1. The 100-kA-class STARS (Stacked Tapes Assembled in Rigid Structure) conductor is used for the magnet system including the continuously wound helical coils. Protection of the magnet system in case of a quench is a crucial issue and the hot-spot temperature during an emergency discharge is estimated based on the zero-dimensional and one-dimensional analyses. The number of division of the coil winding package is examined to limit the voltage generation. For cooling the HTS magnet, helium gas flow is considered and its feasibility is examined by simple analysis as a first step.

Measurements of the Canonical Helicity Evolution of a Gyrating Kinked Flux Rope

NASA Astrophysics Data System (ADS)

von der Linden, J.; Sears, J.; Intrator, T.; You, S.

2017-12-01

Magnetic structures in the solar corona and planetary magnetospheres are often modelled as magnetic flux ropes governed by magnetohydrodynamics (MHD); however, inside these structures, as exhibited in reconnection, conversions between magnetic and kinetic energies occur over a wide range of scales. Flux ropes based on the flux of canonical momentum circulation extend the flux rope concept to include effects of finite particle momentum and present the distinct advantage of reconciling all plasma regimes - e.g. kinetic, two-fluid, and MHD - with the topological concept of helicity: twists, writhes, and linkages. This presentation shows the first visualization and analysis of the 3D dynamics of canonical flux ropes and their relative helicity evolution from laboratory measurements. Ion and electron canonical flux ropes are visualized from a dataset of Mach, triple, and Ḃ probe measurements at over 10,000 spatial locations of a gyrating kinked flux rope. The flux ropes co-gyrate with the peak density and electron temperature in and out of a measurement volume. The electron and ion canonical flux ropes twist with opposite handedness and the ion flux ropes writhe around the electron flux ropes. The relative cross helicity between the magnetic and ion flow vorticity flux ropes dominates the relative ion canonical helicity and is anti-correlated with the relative magnetic helicity. The 3D nature of the kink and a reverse eddy current affect the helicity evolution. This work is supported by DOE Grant DE-SC0010340 and the DOE Office of Science Graduate Student Research Program and prepared in part by LLNL under Contract DE-AC52-07NA27344. LLNL-ABS-735426

Chirality-specific lift forces of helix under shear flows: Helix perpendicular to shear plane.

PubMed

Zhang, Qi-Yi

2017-02-01

Chiral objects in shear flow experience a chirality-specific lift force. Shear flows past helices in a low Reynolds number regime were studied using slender-body theory. The chirality-specific lift forces in the vorticity direction experienced by helices are dominated by a set of helix geometry parameters: helix radius, pitch length, number of turns, and helix phase angle. Its analytical formula is given. The chirality-specific forces are the physical reasons for the chiral separation of helices in shear flow. Our results are well supported by the latest experimental observations. © 2016 Wiley Periodicals, Inc.

Sharp magnetic structures from dynamos with density stratification

NASA Astrophysics Data System (ADS)

Jabbari, Sarah; Brandenburg, Axel; Kleeorin, Nathan; Rogachevskii, Igor

2017-05-01

Recent direct numerical simulations (DNS) of large-scale turbulent dynamos in strongly stratified layers have resulted in surprisingly sharp bipolar structures at the surface. Here, we present new DNS of helically and non-helically forced turbulence with and without rotation and compare with corresponding mean-field simulations (MFS) to show that these structures are a generic outcome of a broader class of dynamos in density-stratified layers. The MFS agree qualitatively with the DNS, but the period of oscillations tends to be longer in the DNS. In both DNS and MFS, the sharp structures are produced by converging flows at the surface and might be driven in non-linear stage of evolution by the Lorentz force associated with the large-scale dynamo-driven magnetic field if the dynamo number is at least 2.5 times supercritical.

Numerical simulation of mechanical mixing in high solid anaerobic digester.

PubMed

Yu, Liang; Ma, Jingwei; Chen, Shulin

2011-01-01

Computational fluid dynamics (CFD) was employed to study mixing performance in high solid anaerobic digester (HSAD) with A-310 impeller and helical ribbon. A mathematical model was constructed to assess flow fields. Good agreement of the model results with experimental data was obtained for the A-310 impeller. A systematic comparison for the interrelationship of power number, flow number and Reynolds number was simulated in a digester with less than 5% TS and 10% TS (total solids). The simulation results suggested a great potential for using the helical ribbon mixer in the mixing of high solids digester. The results also provided quantitative confirmation for minimum power consumption in HSAD and the effect of share rate on bio-structure. Copyright © 2010 Elsevier Ltd. All rights reserved.

Spheromak plasma flow injection into a torus chamber and the HIST plasmas

NASA Astrophysics Data System (ADS)

Hatuzaki, Akinori

2005-10-01

The importance of plasma flow or two-fluid effect is recognized in understanding the relaxed states of high-beta torus plasmas, start-up and current drive by non-coaxial helicity injection, magnetic reconnection and plasma dynamo in fusion, laboratory and space plasmas. As a new approach to create a flowing two-fluid plasma equilibrium, we have tried to inject tangentially the plasma flow with spheromak-type magnetic configurations into a torus vacuum chamber with an external toroidal magnetic field (TF) coil. In the initial experiments, the RFP-like configuration with helical magnetic structures was realized in the torus vessel. The ion flow measurement with Mach probes showed that the ion flow keeps the same direction despite the reversal of the toroidal current and the axial electric field. The ion fluid comes to flow in the opposite direction to the electron fluid by the reversal of TF. This result suggests that not only electron but also ion flow contributes significantly on the reversed toroidal current. In this case, the ratio of ui to the electron flow velocity ue is estimated as ui/ue ˜ 1/2. We also will inject the spheromak flow into the HIST spherical torus plasmas to examine the possibilities to embedding the two-fluid effect in the ST plasmas.

Two-phase pressure drop in a helical coil flow boiling system

NASA Astrophysics Data System (ADS)

Hardik, B. K.; Prabhu, S. V.

2018-05-01

The objective of the present work is to study the two-phase pressure drop in helical coils. Literature on the two-phase pressure drop in a helical coil suggests the complexity in flow boiling inside a helical coil due to secondary flow. Most of correlations reported in the literature on the two-phase pressure drop in a helical coil are limited to a specific operating range. No general correlation is available for a helical coil which is applicable for all fluids. In the present study, an experimental databank collected containing a total of 832 data points includes the data from the present study and from the literature. The data includes diabatic pressure drop of two fluids namely water and R123. Data covers a range of parameters namely a mass flux of 120-2058 kg/m2 s, a heat flux of 18-2831 kW/m2, an exit quality of 0.03-1, a density ratio of 32-1404 and a coil to tube diameter ratio of 14-58. The databank is compared with eighteen empirical correlations which include well referred correlations of straight tubes and the available correlations of helical coils. The straight tube correlations are not working well for the present data set. The helical coil correlations work reasonably well for the present databank. A correlation is suggested to predict the two-phase pressure drop in helical coils. The present study suggests that the influence of a helical coil is completely included in the single phase pressure drop correlation for helical coils.

Two-Phase Annular Flow in Helical Coil Flow Channels in a Reduced Gravity Environment

NASA Technical Reports Server (NTRS)

Keshock, Edward G.; Lin, Chin S.

1996-01-01

A brief review of both single- and two-phase flow studies in curved and coiled flow geometries is first presented. Some of the complexities of two-phase liquid-vapor flow in curved and coiled geometries are discussed, and serve as an introduction to the advantages of observing such flows under a low-gravity environment. The studies proposed -- annular two-phase air-water flow in helical coil flow channels are described. Objectives of the studies are summarized.

Numerical Simulations of Helicity Condensation in the Solar Corona

NASA Technical Reports Server (NTRS)

Zhao, L.; DeVore, C. R.; Antiochos, S. K.; Zurbuchen, T. H.

2015-01-01

The helicity condensation model has been proposed by Antiochos (2013) to explain the observed smoothness of coronal loops and the observed buildup of magnetic shear at filament channels. The basic hypothesis of the model is that magnetic reconnection in the corona causes the magnetic stress injected by photospheric motions to collect only at those special locations where prominences form. In this work we present the first detailed quantitative MHD simulations of the reconnection evolution proposed by the helicity condensation model. We use the well-known ansatz of modeling the closed corona as an initially uniform field between two horizontal photospheric plates. The system is driven by applying photospheric rotational flows that inject magnetic helicity into the system. The flows are confined to a finite region on the photosphere so as to mimic the finite flux system of, for example, a bipolar active region. The calculations demonstrate that, contrary to common belief, coronal loops having opposite helicity do not reconnect, whereas loops having the same sense of helicity do reconnect. Furthermore, we find that for a given amount of helicity injected into the corona, the evolution of the magnetic shear is insensitive to whether the pattern of driving photospheric motions is fixed or quasi-random. In all cases, the shear propagates via reconnection to the boundary of the flow region while the total magnetic helicity is conserved, as predicted by the model. We discuss the implications of our results for solar observations and for future, more realistic simulations of the helicity condensation process.

Passive scalars: Mixing, diffusion, and intermittency in helical and nonhelical rotating turbulence

NASA Astrophysics Data System (ADS)

Imazio, P. Rodriguez; Mininni, P. D.

2017-03-01

We use direct numerical simulations to compute structure functions, scaling exponents, probability density functions, and effective transport coefficients of passive scalars in turbulent rotating helical and nonhelical flows. We show that helicity affects the inertial range scaling of the velocity and of the passive scalar when rotation is present, with a spectral law consistent with ˜k⊥-1.4 for the passive scalar variance spectrum. This scaling law is consistent with a phenomenological argument [P. Rodriguez Imazio and P. D. Mininni, Phys. Rev. E 83, 066309 (2011), 10.1103/PhysRevE.83.066309] for rotating nonhelical flows, which follows directly from Kolmogorov-Obukhov scaling and states that if energy follows a E (k ) ˜k-n law, then the passive scalar variance follows a law V (k ) ˜k-nθ with nθ=(5 -n ) /2 . With the second-order scaling exponent obtained from this law, and using the Kraichnan model, we obtain anomalous scaling exponents for the passive scalar that are in good agreement with the numerical results. Multifractal intermittency models are also considered. Intermittency of the passive scalar is stronger than in the nonhelical rotating case, a result that is also confirmed by stronger non-Gaussian tails in the probability density functions of field increments. Finally, Fick's law is used to compute the effective diffusion coefficients in the directions parallel and perpendicular to rotation. Calculations indicate that horizontal diffusion decreases in the presence of helicity in rotating flows, while vertical diffusion increases. A simple mean field argument explains this behavior in terms of the amplitude of velocity fluctuations.

The vorticity of Solar photospheric flows on the scale of granulation

NASA Astrophysics Data System (ADS)

Pevtsov, A. A.

2016-12-01

We employ time sequences of images observed with a G-band filter (λ4305Å) by the Solar Optical Telescope (SOT) on board of Hinode spacecraft at different latitude along solar central meridian to study vorticity of granular flows in quiet Sun areas during deep minimum of solar activity. Using a feature correlation tracking (FCT) technique, we calculate the vorticity of granular-scale flows. Assuming the known pattern of vertical flows (upward in granules and downward in intergranular lanes), we infer the sign of kinetic helicity of these flows. We show that the kinetic helicity of granular flows and intergranular vortices exhibits a weak hemispheric preference, which is in agreement with the action of the Coriolis force. This slight hemispheric sign asymmetry, however, is not statistically significant given large scatter in the average vorticity. The sign of the current helicity density of network magnetic fields computed using full disk vector magnetograms from the Synoptic Optical Long-term Investigations of the Sun (SOLIS) does not show any hemispheric preference. The combination of these two findings suggests that the photospheric dynamo operating on the scale of granular flows is non-helical in nature.

Turbulent structure of three-dimensional flow behind a model car: 1. Exposed to uniform approach flow

NASA Astrophysics Data System (ADS)

Kozaka, Orçun E.; Özkan, Gökhan; Özdemir, Bedii I.

2004-01-01

Turbulent structure of flow behind a model car is investigated with local velocity measurements with emphasis on large structures and their relevance to aerodynamic forces. Results show that two counter-rotating helical vortices, which are formed within the inner wake region, play a key role in determining the flux of kinetic energy. The turbulence is generated within the outermost shear layers due to the instabilities, which also seem to be the basic drive for these relatively organized structures. The measured terms of the turbulent kinetic energy production, which are only part of the full expression, indicate that vortex centres act similar to the manifolds draining the energy in the streamwise direction. As the approach velocity increases, the streamwise convection becomes the dominant means of turbulent transport and, thus, the acquisition of turbulence by relatively non-turbulent flow around the wake region is suppressed.

Cryo-EM Structure Determination Using Segmented Helical Image Reconstruction.

PubMed

Fromm, S A; Sachse, C

2016-01-01

Treating helices as single-particle-like segments followed by helical image reconstruction has become the method of choice for high-resolution structure determination of well-ordered helical viruses as well as flexible filaments. In this review, we will illustrate how the combination of latest hardware developments with optimized image processing routines have led to a series of near-atomic resolution structures of helical assemblies. Originally, the treatment of helices as a sequence of segments followed by Fourier-Bessel reconstruction revealed the potential to determine near-atomic resolution structures from helical specimens. In the meantime, real-space image processing of helices in a stack of single particles was developed and enabled the structure determination of specimens that resisted classical Fourier helical reconstruction and also facilitated high-resolution structure determination. Despite the progress in real-space analysis, the combination of Fourier and real-space processing is still commonly used to better estimate the symmetry parameters as the imposition of the correct helical symmetry is essential for high-resolution structure determination. Recent hardware advancement by the introduction of direct electron detectors has significantly enhanced the image quality and together with improved image processing procedures has made segmented helical reconstruction a very productive cryo-EM structure determination method. © 2016 Elsevier Inc. All rights reserved.

Experimental investigation of in-cylinder air flow to optimize number of helical guide vanes to enhance DI diesel engine performance using mamey sapote biodiesel

NASA Astrophysics Data System (ADS)

Kumar, A. Raj; Janardhana Raju, G.; Hemachandra Reddy, K.

2018-03-01

The current research work investigates the influence of helical guide vanes in to the intake runner of a D.I diesel engine operating by the high viscous Mamey Sapote biodiesel to enhance in-cylinder suction air flow features. Helical guide vanes of different number of vanes are produced from 3D printing and placed in the intake manifold to examine the air flow characteristics. Four different helical guide vane devices namely 3, 4, 5 and 6 vanes of the same dimensions are tested in a D.I diesel engine operating with Mamey Sapote biodiesel blend. As per the experimental results of engine performance and emission characteristics, it is found that 5 vanes helical guide vane swirl device exhibited in addition number of increased improvements such as the brake power and bake thermal efficiency by 2.4% and 8.63% respectively and the HC, NOx, Carbon monoxide and, Smoke densities are reduced by 15.62%, 4.23%, 14.27% and 9.6% at peak load operating conditions as collate with normal engine at the same load. Hence this investigation concluded that Helical Guide Vane Devices successfully enhanced the in-cylinder air flow to improve better addition of Mamey Sapote biodiesel with air leading in better performance of the engine than without vanes.

NUMERICAL SIMULATIONS OF HELICITY CONDENSATION IN THE SOLAR CORONA

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhao, L.; Zurbuchen, T. H.; DeVore, C. R.

The helicity condensation model has been proposed by Antiochos to explain the observed smoothness of coronal loops and the observed buildup of magnetic shear at filament channels. The basic hypothesis of the model is that magnetic reconnection in the corona causes the magnetic stress injected by photospheric motions to collect only at those special locations where prominences are observed to form. In this work we present the first detailed quantitative MHD simulations of the reconnection evolution proposed by the helicity condensation model. We use the well-known ansatz of modeling the closed corona as an initially uniform field between two horizontalmore » photospheric plates. The system is driven by applying photospheric rotational flows that inject magnetic helicity into the corona. The flows are confined to a finite region on the photosphere so as to mimic the finite flux system of a bipolar active region, for example. The calculations demonstrate that, contrary to common belief, opposite helicity twists do not lead to significant reconnection in such a coronal system, whereas twists with the same sense of helicity do produce substantial reconnection. Furthermore, we find that for a given amount of helicity injected into the corona, the evolution of the magnetic shear is insensitive to whether the pattern of driving photospheric motions is fixed or quasi-random. In all cases, the shear propagates via reconnection to the boundary of the flow region while the total magnetic helicity is conserved, as predicted by the model. We discuss the implications of our results for solar observations and for future, more realistic simulations of the helicity condensation process.« less

An experimental study of the flow of LPG as refrigerant inside an adiabatic helical coiled capillary tube in vapour compression refrigeration system

NASA Astrophysics Data System (ADS)

Punia, Sanjeev Singh; Singh, Jagdev

2015-11-01

This paper presents an experimental investigation for the flow of liquefied petroleum gas (LPG) as a refrigerant inside an adiabatic helically coiled capillary tube in vapour compression refrigeration system. The effect of various geometric parameters and operating conditions like capillary tube inner diameter, length of capillary tube, coil diameter and different inlet subcoolings on the mass flow rate of LPG through the helical coiled capillary tube geometry has been investigated. It has been established that the coil diameter significantly influences the mass flow rate of LPG through the adiabatic helical capillary tube. It has been concluded that the effect of coiling of capillary tube reduces the mass flow rate by 5-12 % as compared to those of the straight capillary tube operating under similar conditions. The data obtained from the experiments are analyzed and a dimensionless correlation has been developed. The proposed correlation predicts that more than 90 % of experimental data which is in agreement with measured data in an error band of ±10 %.

Evolution of sausage and helical modes in magnetized thin-foil cylindrical liners driven by a Z-pinch

NASA Astrophysics Data System (ADS)

Yager-Elorriaga, D. A.; Lau, Y. Y.; Zhang, P.; Campbell, P. C.; Steiner, A. M.; Jordan, N. M.; McBride, R. D.; Gilgenbach, R. M.

2018-05-01

In this paper, we present experimental results on axially magnetized (Bz = 0.5 - 2.0 T), thin-foil (400 nm-thick) cylindrical liner-plasmas driven with ˜600 kA by the Michigan Accelerator for Inductive Z-Pinch Experiments, which is a linear transformer driver at the University of Michigan. We show that: (1) the applied axial magnetic field, irrespective of its direction (e.g., parallel or anti-parallel to the flow of current), reduces the instability amplitude for pure magnetohydrodynamic (MHD) modes [defined as modes devoid of the acceleration-driven magneto-Rayleigh-Taylor (MRT) instability]; (2) axially magnetized, imploding liners (where MHD modes couple to MRT) generate m = 1 or m = 2 helical modes that persist from the implosion to the subsequent explosion stage; (3) the merging of instability structures is a mechanism that enables the appearance of an exponential instability growth rate for a longer than expected time-period; and (4) an inverse cascade in both the axial and azimuthal wavenumbers, k and m, may be responsible for the final m = 2 helical structure observed in our experiments. These experiments are particularly relevant to the magnetized liner inertial fusion program pursued at Sandia National Laboratories, where helical instabilities have been observed.

An Amino Acid Packing Code for α-helical Structure and Protein Design

PubMed Central

Joo, Hyun; Chavan, Archana G.; Phan, Jamie; Day, Ryan; Tsai, Jerry

2012-01-01

This work demonstrates that all packing in α-helices can be simplified to repetitive patterns of a single motif: the knob-socket. Using the precision of Voronoi Polyhedra/Deluaney Tessellations to identify contacts, the knob-socket is a 4 residue tetrahedral motif: a knob residue on one α-helix packs into the 3 residue socket on another α-helix. The principle of the knob-socket model relates the packing between levels of protein structure: the intra-helical packing arrangements within secondary structure that permit inter-helix tertiary packing interactions. Within an α-helix, the 3 residue sockets arrange residues into a uniform packing lattice. Inter-helix packing results from a definable pattern of interdigitated knob-socket motifs between 2 α-helices. Furthermore, the knob-socket model classifies 3 types of sockets: 1) free: favoring only intra-helical packing, 2) filled: favoring inter-helical interactions and 3) non: disfavoring α-helical structure. The amino acid propensities in these 3 socket classes essentially represent an amino acid code for structure in α-helical packing. Using this code, a novel yet straightforward approach for the design of α-helical structure was used to validate the knob-socket model. Unique sequences for 3 peptides were created to produce a predicted amount of α-helical structure: mostly helical, some helical, and no-helix. These 3 peptides were synthesized and helical content assessed using CD spectroscopy. The measured α-helicity of each peptide was consistent with the expected predictions. These results and analysis demonstrate that the knob-socket motif functions as the basic unit of packing and presents an intuitive tool to decipher the rules governing packing in protein structure. PMID:22426125

Helical flow in RFX-mod tokamak plasmas

NASA Astrophysics Data System (ADS)

Piron, L.; Zaniol, B.; Bonfiglio, D.; Carraro, L.; Kirk, A.; Marrelli, L.; Martin, R.; Piron, C.; Piovesan, P.; Zuin, M.

2017-05-01

This work presents the first evidence of helical flow in RFX-mod q(a)  <  2 tokamak plasmas. The flow pattern is characterized by the presence of convective cells with m  =  1 and n  =  1 periodicity in the poloidal and toroidal directions, respectively. A similar helical flow deformation has been observed in the same device when operated as a reversed field pinch (RFP). In RFP plasmas, the flow dynamic is tailored by the innermost resonant m  =  1, n  =  7 tearing mode, which sustains the magnetic field configuration through the dynamo mechanism (Bonomo et al 2011 Nucl. Fusion 51 123007). By contrast, in the tokamak experiments presented here, it is strongly correlated with the m  =  1, n  =  1 MHD activity. A helical deformation of the flow pattern, associated with the deformation of the magnetic flux surfaces, is predicted by several codes, such as Specyl (Bonfiglio et al 2005 Phys. Rev. Lett. 94 145001), PIXIE3D (Chacón et al 2008 Phys. Plasmas 15 056103), NIMROD (King et al 2012 Phys. Plasmas 19 055905) and M3D-C1 (Jardin et al 2015 Phys. Rev. Lett. 115 215001). Among them, the 3D fully non-linear PIXIE3D has been used to calculate synthetic flow measurements, using a 2D flow modelling code. Inputs to the code are the PIXIE3D flow maps, the ion emission profiles as calculated by a 1D collisional radiative impurity transport code (Carraro et al 2000 Plasma Phys. Control. Fusion 42 731) and a synthetic diagnostic with the same geometry installed in RFX-mod. Good agreement between the synthetic and the experimental flow behaviour has been obtained, confirming that the flow oscillations observed with the associated convective cells are a signature of helical flow.

Statistical analyses and computational prediction of helical kinks in membrane proteins

NASA Astrophysics Data System (ADS)

Huang, Y.-H.; Chen, C.-M.

2012-10-01

We have carried out statistical analyses and computer simulations of helical kinks for TM helices in the PDBTM database. About 59 % of 1562 TM helices showed a significant kink, and 38 % of these kinks are associated with prolines in a range of ±4 residues. Our analyses show that helical kinks are more populated in the central region of helices, particularly in the range of 1-3 residues away from the helix center. Among 1,053 helical kinks analyzed, 88 % of kinks are bends (change in helix axis without loss of helical character) and 12 % are disruptions (change in helix axis and loss of helical character). It is found that proline residues tend to cause larger kink angles in helical bends, while this effect is not observed in helical disruptions. A further analysis of these kinked helices suggests that a kinked helix usually has 1-2 broken backbone hydrogen bonds with the corresponding N-O distance in the range of 4.2-8.7 Å, whose distribution is sharply peaked at 4.9 Å followed by an exponential decay with increasing distance. Our main aims of this study are to understand the formation of helical kinks and to predict their structural features. Therefore we further performed molecular dynamics (MD) simulations under four simulation scenarios to investigate kink formation in 37 kinked TM helices and 5 unkinked TM helices. The representative models of these kinked helices are predicted by a clustering algorithm, SPICKER, from numerous decoy structures possessing the above generic features of kinked helices. Our results show an accuracy of 95 % in predicting the kink position of kinked TM helices and an error less than 10° in the angle prediction of 71.4 % kinked helices. For unkinked helices, based on various structure similarity tests, our predicted models are highly consistent with their crystal structure. These results provide strong supports for the validity of our method in predicting the structure of TM helices.

Structures of the transmembrane helices of the G-protein coupled receptor, rhodopsin.

PubMed

Katragadda, M; Chopra, A; Bennett, M; Alderfer, J L; Yeagle, P L; Albert, A D

2001-07-01

An hypothesis is tested that individual peptides corresponding to the transmembrane helices of the membrane protein, rhodopsin, would form helices in solution similar to those in the native protein. Peptides containing the sequences of helices 1, 4 and 5 of rhodopsin were synthesized. Two peptides, with overlapping sequences at their termini, were synthesized to cover each of the helices. The peptides from helix 1 and helix 4 were helical throughout most of their length. The N- and C-termini of all the peptides were disordered and proline caused opening of the helical structure in both helix 1 and helix 4. The peptides from helix 5 were helical in the middle segment of each peptide, with larger disordered regions in the N- and C-termini than for helices 1 and 4. These observations show that there is a strong helical propensity in the amino acid sequences corresponding to the transmembrane domain of this G-protein coupled receptor. In the case of the peptides from helix 4, it was possible to superimpose the structures of the overlapping sequences to produce a construct covering the whole of the sequence of helix 4 of rhodopsin. As similar superposition for the peptides from helix 1 also produced a construct, but somewhat less successfully because of the disordering in the region of sequence overlap. This latter problem was more severe for helix 5 and therefore a single peptide was synthesized for the entire sequence of this helix, and its structure determined. It proved to be helical throughout. Comparison of all these structures with the recent crystal structure of rhodopsin revealed that the peptide structures mimicked the structures seen in the whole protein. Thus similar studies of peptides may provide useful information on the secondary structure of other transmembrane proteins built around helical bundles.

ON ASYMMETRY OF MAGNETIC HELICITY IN EMERGING ACTIVE REGIONS: HIGH-RESOLUTION OBSERVATIONS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tian Lirong; Alexander, David; Zhu Chunming

We employ the DAVE (differential affine velocity estimator) tracking technique on a time series of Michelson Doppler Imager (MDI)/1 minute high spatial resolution line-of-sight magnetograms to measure the photospheric flow velocity for three newly emerging bipolar active regions (ARs). We separately calculate the magnetic helicity injection rate of the leading and following polarities to confirm or refute the magnetic helicity asymmetry, found by Tian and Alexander using MDI/96 minute low spatial resolution magnetograms. Our results demonstrate that the magnetic helicity asymmetry is robust, being present in the three ARs studied, two of which have an observed balance of the magneticmore » flux. The magnetic helicity injection rate measured is found to depend little on the window size selected, but does depend on the time interval used between the two successive magnetograms being tracked. It is found that the measurement of the magnetic helicity injection rate performs well for a window size between 12 x 10 and 18 x 15 pixels and at a time interval {Delta}t = 10 minutes. Moreover, the short-lived magnetic structures, 10-60 minutes, are found to contribute 30%-50% of the magnetic helicity injection rate. Comparing with the results calculated by MDI/96 minute data, we find that the MDI/96 minute data, in general, can outline the main trend of the magnetic properties, but they significantly underestimate the magnetic flux in strong field regions and are not appropriate for quantitative tracking studies, so provide a poor estimate of the amount of magnetic helicity injected into the corona.« less

Effects of Helicity on Lagrangian and Eulerian Time Correlations in Turbulence

NASA Technical Reports Server (NTRS)

Rubinstein, Robert; Zhou, Ye

1998-01-01

Taylor series expansions of turbulent time correlation functions are applied to show that helicity influences Eulerian time correlations more strongly than Lagrangian time correlations: to second order in time, the helicity effect on Lagrangian time correlations vanishes, but the helicity effect on Eulerian time correlations is nonzero. Fourier analysis shows that the helicity effect on Eulerian time correlations is confined to the largest inertial range scales. Some implications for sound radiation by swirling flows are discussed.

The Cryoelectron Microscopy Structure of the Type 1 Chaperone-Usher Pilus Rod.

PubMed

Hospenthal, Manuela K; Zyla, Dawid; Costa, Tiago R D; Redzej, Adam; Giese, Christoph; Lillington, James; Glockshuber, Rudi; Waksman, Gabriel

2017-12-05

Adhesive chaperone-usher pili are long, supramolecular protein fibers displayed on the surface of many bacterial pathogens. The type 1 and P pili of uropathogenic Escherichia coli (UPEC) play important roles during urinary tract colonization, mediating attachment to the bladder and kidney, respectively. The biomechanical properties of the helical pilus rods allow them to reversibly uncoil in response to flow-induced forces, allowing UPEC to retain a foothold in the unique and hostile environment of the urinary tract. Here we provide the 4.2-Å resolution cryo-EM structure of the type 1 pilus rod, which together with the previous P pilus rod structure rationalizes the remarkable "spring-like" properties of chaperone-usher pili. The cryo-EM structure of the type 1 pilus rod differs in its helical parameters from the structure determined previously by a hybrid approach. We provide evidence that these structural differences originate from different quaternary structures of pili assembled in vivo and in vitro. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Effects of multi-pulsed coaxial helicity injection on dynamics of spherical torus

NASA Astrophysics Data System (ADS)

Kanki, T.; Nagata, M.; Kagei, Y.

2012-10-01

The mechanism to rebuild the magnetic fields and to amplify the currents in the high-q spherical torus (ST) by the multi-pulsed coaxial helicity injection is investigated using the resistive nonlinear 3D-MHD simulations. During the driven phase, the dynamics is almost axisymmetric because the magnetic fluctuation level of n=0 mode compared with other higher modes is much larger. The toroidal current It is effectively amplified due to the merging of plasmoid ejected from the gun region with the pre-existing ST in the confinement region. The poloidal flux is not significantly amplified because the current sheet generated by the merging process does not rapidly decay. The negative toroidal flow vt is then induced in the direction of It around the central open flux column (OFC) region by inductive toroidal electric field Et (=-vzBr) because of the plasmoid ejection. The strong poloidal flow vz (=ErBt) is also driven from the gun to confinement region due to the Lorentz force. As the result of vz, the flow vortices associated with the dynamo effect are caused around the upper confinement region. During the decay phase, the closed field lines are regenerated due to the dissipation of magnetic fluctuations. The helical distortion of the OFC becomes small, and then ordered magnetic field structures without flows are built. Just after turning off the external electric field, the poloidal flow from the confinement to gun region is caused by the pressure gradients. The parallel current density λ concentrated in the OFC diffuses to the core region, but does not relax in the direction of the Taylor state due to the pressure gradients.

Hydrodynamic studies of CNT nanofluids in helical coil heat exchanger

NASA Astrophysics Data System (ADS)

Babita; Sharma, S. K.; Mital Gupta, Shipra; Kumar, Arinjay

2017-12-01

Helical coils are extensively used in several industrial processes such as refrigeration systems, chemical reactors, recovery processes etc to accommodate a large heat transfer area within a smaller space. Nanofluids are getting great attention due to their enhanced heat transfer capability. In heat transfer equipments, pressure drop is one of the major factors of consideration for pumping power calculations. So, the present work is aimed to study hydrodynamics of CNT nanofluids in helical coils. In this study, pressure drop characteristics of CNT nanofluid flowing inside horizontal helical coils are investigated experimentally. The helical coil to tube diameter was varied from 11.71 to 27.34 keeping pitch of the helical coil constant. Double distilled water was used as basefluid. SDBS and GA surfactants were added to stablilize CNT nanofluids. The volumetric fraction of CNT nanofluid was varied from 0.003 vol% to 0.051 vol%. From the experimental data, it was analyzed that the friction factor in helical coils is greater than that of straight tubes. Concentration of CNT in nanofluids also has a significant influence on the pressure drop/friction factor of helical coils. At a constant concentration of CNT, decreasing helical coil to tube diameter from 27.24 to 11.71, fanning friction factor of helical coil; f c increases for a constant value of p/d t. This increase in the value of fanning friction factor can be attributed to the secondary flow of CNT nanofluid in helical coils.

High temperature helical tubular receiver for concentrating solar power system

NASA Astrophysics Data System (ADS)

Hossain, Nazmul

In the field of conventional cleaner power generation technology, concentrating solar power systems have introduced remarkable opportunity. In a solar power tower, solar energy concentrated by the heliostats at a single point produces very high temperature. Falling solid particles or heat transfer fluid passing through that high temperature region absorbs heat to generate electricity. Increasing the residence time will result in more heat gain and increase efficiency. A novel design of solar receiver for both fluid and solid particle is approached in this paper which can increase residence time resulting in higher temperature gain in one cycle compared to conventional receivers. The helical tubular solar receiver placed at the focused sunlight region meets the higher outlet temperature and efficiency. A vertical tubular receiver is modeled and analyzed for single phase flow with molten salt as heat transfer fluid and alloy625 as heat transfer material. The result is compared to a journal paper of similar numerical and experimental setup for validating our modeling. New types of helical tubular solar receivers are modeled and analyzed with heat transfer fluid turbulent flow in single phase, and granular particle and air plug flow in multiphase to observe the temperature rise in one cyclic operation. The Discrete Ordinate radiation model is used for numerical analysis with simulation software Ansys Fluent 15.0. The Eulerian granular multiphase model is used for multiphase flow. Applying the same modeling parameters and boundary conditions, the results of vertical and helical receivers are compared. With a helical receiver, higher temperature gain of heat transfer fluid is achieved in one cycle for both single phase and multiphase flow compared to the vertical receiver. Performance is also observed by varying dimension of helical receiver.

Inverse energy cascade in three-dimensional isotropic turbulence.

PubMed

Biferale, Luca; Musacchio, Stefano; Toschi, Federico

2012-04-20

We study the statistical properties of homogeneous and isotropic three-dimensional (3D) turbulent flows. By introducing a novel way to make numerical investigations of Navier-Stokes equations, we show that all 3D flows in nature possess a subset of nonlinear evolution leading to a reverse energy transfer: from small to large scales. Up to now, such an inverse cascade was only observed in flows under strong rotation and in quasi-two-dimensional geometries under strong confinement. We show here that energy flux is always reversed when mirror symmetry is broken, leading to a distribution of helicity in the system with a well-defined sign at all wave numbers. Our findings broaden the range of flows where the inverse energy cascade may be detected and rationalize the role played by helicity in the energy transfer process, showing that both 2D and 3D properties naturally coexist in all flows in nature. The unconventional numerical methodology here proposed, based on a Galerkin decimation of helical Fourier modes, paves the road for future studies on the influence of helicity on small-scale intermittency and the nature of the nonlinear interaction in magnetohydrodynamics.

Computational prediction of kink properties of helices in membrane proteins

NASA Astrophysics Data System (ADS)

Mai, T.-L.; Chen, C.-M.

2014-02-01

We have combined molecular dynamics simulations and fold identification procedures to investigate the structure of 696 kinked and 120 unkinked transmembrane (TM) helices in the PDBTM database. Our main aim of this study is to understand the formation of helical kinks by simulating their quasi-equilibrium heating processes, which might be relevant to the prediction of their structural features. The simulated structural features of these TM helices, including the position and the angle of helical kinks, were analyzed and compared with statistical data from PDBTM. From quasi-equilibrium heating processes of TM helices with four very different relaxation time constants, we found that these processes gave comparable predictions of the structural features of TM helices. Overall, 95 % of our best kink position predictions have an error of no more than two residues and 75 % of our best angle predictions have an error of less than 15°. Various structure assessments have been carried out to assess our predicted models of TM helices in PDBTM. Our results show that, in 696 predicted kinked helices, 70 % have a RMSD less than 2 Å, 71 % have a TM-score greater than 0.5, 69 % have a MaxSub score greater than 0.8, 60 % have a GDT-TS score greater than 85, and 58 % have a GDT-HA score greater than 70. For unkinked helices, our predicted models are also highly consistent with their crystal structure. These results provide strong supports for our assumption that kink formation of TM helices in quasi-equilibrium heating processes is relevant to predicting the structure of TM helices.

On the Conservation of Cross Helicity and Wave Action in Solar-wind Models with Non-WKB Alfvén Wave Reflection

NASA Astrophysics Data System (ADS)

Chandran, Benjamin D. G.; Perez, Jean C.; Verscharen, Daniel; Klein, Kristopher G.; Mallet, Alfred

2015-09-01

The interaction between Alfvén-wave turbulence and the background solar wind affects the cross helicity (\\int {d}3x {\\boldsymbol{v}}\\cdot {\\boldsymbol{B}}) in two ways. Non-WKB reflection converts outward-propagating Alfvén waves into inward-propagating Alfvén waves and vice versa, and the turbulence transfers momentum to the background flow. When both effects are accounted for, the total cross helicity is conserved. In the special case that the background density and flow speed are independent of time, the equations of cross-helicity conservation and total-energy conservation can be combined to recover a well-known equation derived by Heinemann and Olbert that has been interpreted as a non-WKB generalization of wave-action conservation. This latter equation (in contrast to cross-helicity and energy conservation) does not hold when the background varies in time.

Self-assembly of a double-helical complex of sodium.

PubMed

Bell, T W; Jousselin, H

1994-02-03

Spontaneous self-organization of helical and multiple-helical molecular structures occurs on several levels in living organisms. Key examples are alpha-helical polypeptides, double-helical nucleic acids and helical protein structures, including F-actin, microtubules and the protein sheath of the tobacco mosaic virus. Although the self-assembly of double-helical transition-metal complexes bears some resemblance to the molecular organization of double-stranded DNA, selection between monohelical, double-helical and triple-helical structures is determined largely by the size and geometrical preference of the tightly bound metal. Here we present an example of double-helical assembly induced by the weaker and non-directional interactions of an alkali-metal ion with an organic ligand that is pre-organized into a coil. We have characterized the resulting complex by two-dimensional NMR and fast-atom-bombardment mass spectrometry. These results provide a step toward the creation of molecular tubes or ion channels consisting of intertwined coils.

A unified convention for biological assemblies with helical symmetry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tsai, Chung-Jung, E-mail: tsaic@mail.nih.gov; Nussinov, Ruth; Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978

A new representation of helical structure by four parameters, [n{sub 1}, n{sub 2}, twist, rise], is able to generate an entire helical construct from asymmetric units, including cases of helical assembly with a seam. Assemblies with helical symmetry can be conveniently formulated in many distinct ways. Here, a new convention is presented which unifies the two most commonly used helical systems for generating helical assemblies from asymmetric units determined by X-ray fibre diffraction and EM imaging. A helical assembly is viewed as being composed of identical repetitive units in a one- or two-dimensional lattice, named 1-D and 2-D helical systems,more » respectively. The unification suggests that a new helical description with only four parameters [n{sub 1}, n{sub 2}, twist, rise], which is called the augmented 1-D helical system, can generate the complete set of helical arrangements, including coverage of helical discontinuities (seams). A unified four-parameter characterization implies similar parameters for similar assemblies, can eliminate errors in reproducing structures of helical assemblies and facilitates the generation of polymorphic ensembles from helical atomic models or EM density maps. Further, guidelines are provided for such a unique description that reflects the structural signature of an assembly, as well as rules for manipulating the helical symmetry presentation.« less

Real-space processing of helical filaments in SPARX

PubMed Central

Behrmann, Elmar; Tao, Guozhi; Stokes, David L.; Egelman, Edward H.; Raunser, Stefan; Penczek, Pawel A.

2012-01-01

We present a major revision of the iterative helical real-space refinement (IHRSR) procedure and its implementation in the SPARX single particle image processing environment. We built on over a decade of experience with IHRSR helical structure determination and we took advantage of the flexible SPARX infrastructure to arrive at an implementation that offers ease of use, flexibility in designing helical structure determination strategy, and high computational efficiency. We introduced the 3D projection matching code which now is able to work with non-cubic volumes, the geometry better suited for long helical filaments, we enhanced procedures for establishing helical symmetry parameters, and we parallelized the code using distributed memory paradigm. Additional feature includes a graphical user interface that facilitates entering and editing of parameters controlling the structure determination strategy of the program. In addition, we present a novel approach to detect and evaluate structural heterogeneity due to conformer mixtures that takes advantage of helical structure redundancy. PMID:22248449

Measurements of the Structure of the Plasma Rotation in Slowly Rotating Tearing Modes in DIII-D

NASA Astrophysics Data System (ADS)

Taylor, N. Z.; Ferraro, N. M.; La Haye, R. J.; Petty, C. C.; Bowman, C.

2014-10-01

A helically modified ion flow by an island can lead to helical ion polarization currents which can affect tearing mode stability. This issue is of particular importance to ITER where large inertia and relatively low torque will likely result in low rotation. In DIII-D cases either (1) a m/n = 2/1 mode is slowed down to ~1 kHz (faster than the inverse wall time) by near balanced neutral beams or (2) an island is entrained by applied rotating n = 1 magnetic field at 10 Hz (slower than the inverse wall time). The n = 1 island structure is measured with electron cyclotron emission radiometry. The ion rotation and temperature are measured by fast resolution (274 μ s) charge exchange recombination (CER) spectroscopy in the 1 kHz freely rotating case and by standard CER (5 ms) in the 10 Hz entrainment. Tangential and vertical CER arrays allow for the radial profile of the helically perturbed rotation to be determined. A comparison of the measured nonlinear island structures with that from the linear resistive stability code M3D-C1 will be presented. Work supported in part by the US Department of Energy under DE-FG02-95ER54309 and DE-FC02-04ER54698.

An Algorithm for Protein Helix Assignment Using Helix Geometry

PubMed Central

Cao, Chen; Xu, Shutan; Wang, Lincong

2015-01-01

Helices are one of the most common and were among the earliest recognized secondary structure elements in proteins. The assignment of helices in a protein underlies the analysis of its structure and function. Though the mathematical expression for a helical curve is simple, no previous assignment programs have used a genuine helical curve as a model for helix assignment. In this paper we present a two-step assignment algorithm. The first step searches for a series of bona fide helical curves each one best fits the coordinates of four successive backbone Cα atoms. The second step uses the best fit helical curves as input to make helix assignment. The application to the protein structures in the PDB (protein data bank) proves that the algorithm is able to assign accurately not only regular α-helix but also 310 and π helices as well as their left-handed versions. One salient feature of the algorithm is that the assigned helices are structurally more uniform than those by the previous programs. The structural uniformity should be useful for protein structure classification and prediction while the accurate assignment of a helix to a particular type underlies structure-function relationship in proteins. PMID:26132394

Approaches to ab initio molecular replacement of α-helical transmembrane proteins.

PubMed

Thomas, Jens M H; Simkovic, Felix; Keegan, Ronan; Mayans, Olga; Zhang, Chengxin; Zhang, Yang; Rigden, Daniel J

2017-12-01

α-Helical transmembrane proteins are a ubiquitous and important class of proteins, but present difficulties for crystallographic structure solution. Here, the effectiveness of the AMPLE molecular replacement pipeline in solving α-helical transmembrane-protein structures is assessed using a small library of eight ideal helices, as well as search models derived from ab initio models generated both with and without evolutionary contact information. The ideal helices prove to be surprisingly effective at solving higher resolution structures, but ab initio-derived search models are able to solve structures that could not be solved with the ideal helices. The addition of evolutionary contact information results in a marked improvement in the modelling and makes additional solutions possible.

Modeling the Structure of Helical Assemblies with Experimental Constraints in Rosetta.

PubMed

André, Ingemar

2018-01-01

Determining high-resolution structures of proteins with helical symmetry can be challenging due to limitations in experimental data. In such instances, structure-based protein simulations driven by experimental data can provide a valuable approach for building models of helical assemblies. This chapter describes how the Rosetta macromolecular package can be used to model homomeric protein assemblies with helical symmetry in a range of modeling scenarios including energy refinement, symmetrical docking, comparative modeling, and de novo structure prediction. Data-guided structure modeling of helical assemblies with experimental information from electron density, X-ray fiber diffraction, solid-state NMR, and chemical cross-linking mass spectrometry is also described.

Turbulent Helicity in the Atmospheric Boundary Layer

NASA Astrophysics Data System (ADS)

Chkhetiani, Otto G.; Kurgansky, Michael V.; Vazaeva, Natalia V.

2018-05-01

We consider the assumption postulated by Deusebio and Lindborg (J Fluid Mech 755:654-671, 2014) that the helicity injected into the Ekman boundary layer undergoes a cascade, with preservation of its sign (right- or alternatively left-handedness), which is a signature of the system rotation, from large to small scales, down to the Kolmogorov microscale of turbulence. At the same time, recent direct field measurements of turbulent helicity in the steppe region of southern Russia near Tsimlyansk Reservoir show the opposite sign of helicity from that expected. A possible explanation for this phenomenon may be the joint action of different scales of atmospheric flows within the boundary layer, including the sea-breeze circulation over the test site. In this regard, we consider a superposition of the classic Ekman spiral solution and Prandtl's jet-like slope-wind profile to describe the planetary boundary-layer wind structure. The latter solution mimics a hydrostatic shallow breeze circulation over a non-uniformly heated surface. A 180°-wide sector on the hodograph plane exists, within which the relative orientation of the Ekman and Prandtl velocity profiles favours the left rotation with height of the resulting wind velocity vector in the lowermost part of the boundary layer. This explains the negative (left-handed) helicity cascade toward small-scale turbulent motions, which agrees with the direct field measurements of turbulent helicity in Tsimlyansk. A simple turbulent relaxation model is proposed that explains the measured positive values of the relatively minor contribution to turbulent helicity from the vertical components of velocity and vorticity.

Flow-through polymerase chain reaction inside a seamless 3D helical microreactor fabricated utilizing a silicone tube and a paraffin mold.

PubMed

Wu, Wenming; Trinh, Kieu The Loan; Lee, Nae Yoon

2015-03-07

We introduce a new strategy for fabricating a seamless three-dimensional (3D) helical microreactor utilizing a silicone tube and a paraffin mold. With this method, various shapes and sizes of 3D helical microreactors were fabricated, and a complicated and laborious photolithographic process, or 3D printing, was eliminated. With dramatically enhanced portability at a significantly reduced fabrication cost, such a device can be considered to be the simplest microreactor, developed to date, for performing the flow-through polymerase chain reaction (PCR).

Local invariants in non-ideal flows of neutral fluids and two-fluid plasmas

NASA Astrophysics Data System (ADS)

Zhu, Jian-Zhou

2018-03-01

The main objective is the locally invariant geometric object of any (magneto-)fluid dynamics with forcing and damping (nonideal), while more attention is paid to the untouched dynamical properties of two-fluid fashion. Specifically, local structures, beyond the well-known "frozen-in" to the barotropic flows of the generalized vorticities, of the two-fluid model of plasma flows are presented. More general non-barotropic situations are also considered. A modified Euler equation [T. Tao, "Finite time blowup for Lagrangian modifications of the three-dimensional Euler equation," Ann. PDE 2, 9 (2016)] is also accordingly analyzed and remarked from the angle of view of the two-fluid model, with emphasis on the local structures. The local constraints of high-order differential forms such as helicity, among others, find simple formulation for possible practices in modeling the dynamics. Thus, the Cauchy invariants equation [N. Besse and U. Frisch, "Geometric formulation of the Cauchy invariants for incompressible Euler flow in flat and curved spaces," J. Fluid Mech. 825, 412 (2017)] may be enabled to find applications in non-ideal flows. Some formal examples are offered to demonstrate the calculations, and particularly interestingly the two-dimensional-three-component (2D3C) or the 2D passive scalar problem presents that a locally invariant Θ = 2θζ, with θ and ζ being, respectively, the scalar value of the "vertical velocity" (or the passive scalar) and the "vertical vorticity," may be used as if it were the spatial density of the globally invariant helicity, providing a Lagrangian prescription to control the latter in some situations of studying its physical effects in rapidly rotating flows (ubiquitous in atmosphere of astrophysical objects) with marked 2D3C vortical modes or in purely 2D passive scalars.

Roles of effective helical ripple rates in nonlinear stability of externally induced magnetic islands

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nishimura, Seiya, E-mail: n-seiya@kobe-kosen.ac.jp

Magnetic islands are externally produced by resonant magnetic perturbations (RMPs) in toroidal plasmas. Spontaneous annihilation of RMP-induced magnetic islands called self-healing has been observed in helical systems. A possible mechanism of the self-healing is shielding of RMP penetration by helical ripple-induced neoclassical flows, which give rise to neoclassical viscous torques. In this study, effective helical ripple rates in multi-helicity helical systems are revisited, and a multi-helicity effect on the self-healing is investigated, based on a theoretical model of rotating magnetic islands. It is confirmed that effective helical ripple rates are sensitive to magnetic axis positions. It is newly found thatmore » self-healing thresholds also strongly depend on magnetic axis positions, which is due to dependence of neoclassical viscous torques on effective helical ripple rates.« less

Axial flow positive displacement worm compressor

NASA Technical Reports Server (NTRS)

Murrow, Kurt David (Inventor); Giffin, Rollin George (Inventor); Fakunle, Oladapo (Inventor)

2010-01-01

An axial flow positive displacement compressor has an inlet axially spaced apart and upstream from an outlet. Inner and outer bodies have offset inner and outer axes extend from the inlet to the outlet through first and second sections of a compressor assembly in serial downstream flow relationship. At least one of the bodies is rotatable about its axis. The inner and outer bodies have intermeshed inner and outer helical blades wound about the inner and outer axes respectively. The inner and outer helical blades extend radially outwardly and inwardly respectively. The helical blades have first and second twist slopes in the first and second sections respectively. The first twist slopes are less than the second twist slopes. An engine including the compressor has in downstream serial flow relationship from the compressor a combustor and a high pressure turbine drivingly connected to the compressor by a high pressure shaft.

Theory of formation of helical structures in a perfectly conducting, premagnetized Z-pinch liner

NASA Astrophysics Data System (ADS)

Yu, Edmund; Velikovich, Alexander; Peterson, Kyle

2014-10-01

The magnetized liner inertial fusion (MagLIF) concept uses an azimuthal magnetic field to collapse a thick metallic liner containing preheated fusion fuel. A critical component of the concept is an axial magnetic field, permeating both the fuel and surrounding liner, which reduces the compression necessary to achieve fusion conditions. Recent experiments demonstrate that a liner premagnetized with a 10 T axial field develops helical structures with a pitch significantly larger than an estimate of Bz /Bθ would suggest. The cause of the helical perturbations is still not understood. In this work, we present an analytic, linear theory in which we model the liner as a perfectly conducting metal, and study how bumps and divots on its surface redirect current flow, resulting in perturbations to B as well as j × B . We show that in the presence of axial and azimuthal magnetic field, the theory predicts divots will grow and deform at an angle determined by the magnetic field. We compare theoretical results with three dimensional, resistive MHD simulations. Sandia is a multiprogram laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the National Nuclear Security Administration under DE-AC04-94AL85000.

Deformation of a helical filament by flow and electric or magnetic fields

NASA Astrophysics Data System (ADS)

Kim, Munju; Powers, Thomas R.

2005-02-01

Motivated by recent advances in the real-time imaging of fluorescent flagellar filaments in living bacteria [Turner, Ryu, and Berg, J. Bacteriol. 82, 2793 (2000)], we compute the deformation of a helical elastic filament due to flow and external magnetic or high-frequency electric fields. Two cases of deformation due to hydrodynamic drag are considered: the compression of a filament rotated by a stationary motor and the extension of a stationary filament due to flow along the helical axis. We use Kirchhoff rod theory for the filament, and work to linear order in the deflection. Hydrodynamic forces are described first by resistive-force theory, and then for comparison by the more accurate slender-body theory. For helices with a short pitch, the deflection in axial flow predicted by slender-body theory is significantly smaller than that computed with resistive-force theory. Therefore, our estimate of the bending stiffness of a flagellar filament is smaller than that of previous workers. In our calculation of the deformation of a polarizable helix in an external field, we show that the problem is equivalent to the classical case of a helix deformed by forces applied only at the ends.

Secondary Structural Changes of Intact and Disulfide Bridges-Cleaved Human Serum Albumins in Thermal Denaturation up to 130°C - Additive Effects of Sodium Dodecyl Sulfate on the Changes.

PubMed

Moriyama, Yoshiko; Takeda, Kunio

2017-05-01

The secondary structural changes of human serum albumin with the intact 17 disulfide bridges (HSA) and the disulfide bridges-cleaved human serum albumin (RCM-HSA) in thermal denaturation were examined. Most of the helical structures of HSA, whose original helicity was 66%, were sharply disrupted between 50 and 100°C. However, 14% helicity remained even at 130°C. The temperature dependence of the degree of disrupted helical structures of HSA was discussed in connection with questions about a general protein denaturation model. When HSA lost the disulfide bridges, about two-thirds of the original helices were disrupted. Although the helices of RCM-HSA remaining after the cleavage of the disulfide bridges were relatively resistant against the heat treatment, the helicity changed from 22% at 25°C to 14% at 130℃. The helicity of RCM-HSA at 130°C agreed with the helicity of HSA at the same temperature, indicating that the same helical moieties of the polypeptides remained unaffected at this high temperature. The additive effects of sodium dodecyl sulfate (SDS) on the structural changes of HSA and RCM-HSA in thermal denaturation were also examined. A slight amount of SDS protected the helical structures of HSA from thermal denaturation below 80°C. Upon cooling to 25°C after heat treatment at temperatures below 70°C with the coexistence of SDS of low concentrations, the helical structures of HSA were reformed to the original level at 25°C before heating. A similar tendency was also observed after heat treatment at 80°C. In contrast, the helical structures of the RCM-HSA complexes with SDS are completely recovered upon cooling to 25°C even after heat treatment up to 100°C. Similar investigations were also carried out on bovine serum albumins which had the intact 17 disulfide bridges and lost all of the bridges.

A current-driven resistive instability and its nonlinear effects in simulations of coaxial helicity injection in a tokamak

DOE PAGES

Hooper, E. B.; Sovinec, C. R.

2016-10-06

An instability observed in whole-device, resistive magnetohydrodynamic simulations of the driven phase of coaxial helicity injection in the National Spherical Torus eXperiment is identified as a current-driven resistive mode in an unusual geometry that transiently generates a current sheet. The mode consists of plasma flow velocity and magnetic field eddies in a tube aligned with the magnetic field at the surface of the injected magnetic flux. At low plasma temperatures (~10–20 eV), the mode is benign, but at high temperatures (~100 eV) its amplitude undergoes relaxation oscillations, broadening the layer of injected current and flow at the surface of themore » injected toroidal flux and background plasma. The poloidal-field structure is affected and the magnetic surface closure is generally prevented while the mode undergoes relaxation oscillations during injection. Furthermore, this study describes the mode and uses linearized numerical computations and an analytic slab model to identify the unstable mode.« less

Instability mechanisms and transition scenarios of spiral turbulence in Taylor-Couette flow.

PubMed

Meseguer, Alvaro; Mellibovsky, Fernando; Avila, Marc; Marques, Francisco

2009-10-01

Alternating laminar and turbulent helical bands appearing in shear flows between counterrotating cylinders are accurately computed and the near-wall instability phenomena responsible for their generation identified. The computations show that this intermittent regime can only exist within large domains and that its spiral coherence is not dictated by endwall boundary conditions. A supercritical transition route, consisting of a progressive helical alignment of localized turbulent spots, is carefully studied. Subcritical routes disconnected from secondary laminar flows have also been identified.

Implementation of dispersion-free slow acoustic wave propagation and phase engineering with helical-structured metamaterials

PubMed Central

Zhu, Xuefeng; Li, Kun; Zhang, Peng; Zhu, Jie; Zhang, Jintao; Tian, Chao; Liu, Shengchun

2016-01-01

The ability to slow down wave propagation in materials has attracted significant research interest. A successful solution will give rise to manageable enhanced wave–matter interaction, freewheeling phase engineering and spatial compression of wave signals. The existing methods are typically associated with constructing dispersive materials or structures with local resonators, thus resulting in unavoidable distortion of waveforms. Here we show that, with helical-structured acoustic metamaterials, it is now possible to implement dispersion-free sound deceleration. The helical-structured metamaterials present a non-dispersive high effective refractive index that is tunable through adjusting the helicity of structures, while the wavefront revolution plays a dominant role in reducing the group velocity. Finally, we numerically and experimentally demonstrate that the helical-structured metamaterials with designed inhomogeneous unit cells can turn a normally incident plane wave into a self-accelerating beam on the prescribed parabolic trajectory. The helical-structured metamaterials will have profound impact to applications in explorations of slow wave physics. PMID:27198887

Helical vortices: Quasiequilibrium states and their time evolution

NASA Astrophysics Data System (ADS)

Selçuk, Can; Delbende, Ivan; Rossi, Maurice

2017-08-01

The time evolution of a viscous helical vortex is investigated by direct numerical simulations of the Navier-Stokes equations where helical symmetry is enforced. Using conservation laws in the framework of helical symmetry, we elaborate an initial condition consisting in a finite core vortex, the time evolution of which leads to a generic quasiequilibrium state independent of the initial core size. Numerical results at different helical pitch values provide an accurate characterization in time for such helical states, for which specific techniques have been introduced: helix radius, angular velocity, stream function-velocity-vorticity relationships, and core properties (size, self-similarity, and ellipticity). Viscosity is shown to be at the origin of a small helical velocity component, which we relate to the helical vorticity component. Finally, changes in time of the flow topology are studied using the helical stream function and three-dimensional Lagrangian orbits.

Theory for nanoparticle retention time in the helical channel of quadrupole magnetic field-flow fractionation

NASA Astrophysics Data System (ADS)

Williams, P. Stephen; Carpino, Francesca; Zborowski, Maciej

2009-05-01

Quadrupole magnetic field-flow fractionation (QMgFFF) is a separation and characterization technique for magnetic nanoparticles such as those used for cell labeling and for targeted drug therapy. A helical separation channel is used to efficiently exploit the quadrupole magnetic field. The fluid and sample components therefore have angular and longitudinal components to their motion in the thin annular space occupied by the helical channel. The retention ratio is defined as the ratio of the times for non-retained and a retained material to pass through the channel. Equations are derived for the respective angular and longitudinal components to retention ratio.

Magnetic helical micromachines.

PubMed

Peyer, Kathrin E; Tottori, Soichiro; Qiu, Famin; Zhang, Li; Nelson, Bradley J

2013-01-02

Helical microrobots have the potential to be used in a variety of application areas, such as in medical procedures, cell biology, or lab-on-a-chip. They are powered and steered wirelessly using low-strength rotating magnetic fields. The helical shape of the device allows propulsion through numerous types of materials and fluids, from tissue to different types of bodily fluids. Helical propulsion is suitable for pipe flow conditions or for 3D swimming in open fluidic environments. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Numerical Assessment of Novel Helical/Spiral Grafts with Improved Hemodynamics for Distal Graft Anastomoses

PubMed Central

Kabinejadian, Foad; McElroy, Michael; Ruiz-Soler, Andres; Leo, Hwa Liang; Slevin, Mark A.; Badimon, Lina

2016-01-01

In the present work, numerical simulations were conducted for a typical end-to-side distal graft anastomosis to assess the effects of inducing secondary flow, which is believed to remove unfavourable flow environment. Simulations were carried out for four models, generated based on two main features of 'out-of-plane helicity' and 'spiral ridge' in the grafts as well as their combination. Following a qualitative comparison against in vitro data, various mean flow and hemodynamic parameters were compared and the results showed that helicity is significantly more effective in inducing swirling flow in comparison to a spiral ridge, while their combination could be even more effective. In addition, the induced swirling flow was generally found to be increasing the wall shear stress and reducing the flow stagnation and particle residence time within the anastomotic region and the host artery, which may be beneficial to the graft longevity and patency rates. Finally, a parametric study on the spiral ridge geometrical features was conducted, which showed that the ridge height and the number of spiral ridges have significant effects on inducing swirling flow, and revealed the potential of improving the efficiency of such designs. PMID:27861485

Numerical simulation of a cross flow Marine Hydrokinetic turbine.

NASA Astrophysics Data System (ADS)

Hall, Taylor; Aliseda, Alberto

2011-11-01

In the search for alternative sources of energy, the kinetic energy of water currents in oceans, rivers and estuaries is being explored as predictable and environmentally benign. We are investigating the flow past a cross flow turbine in which a helical blade under hydrodynamic forces turns around a shaft perpendicular to the free stream. This type of turbine, while very different from the classical horizontal axis turbine commonly used in the wind energy field, presents advantages for stacking in very narrow constricted channels where the water currents are consistently high and therefore turbine installation may be economically feasible. We use a model of a helical four-bladed turbine in cross flow to investigate the efficiency of the energy capture and the dynamics of the turbulent wake. Scale model experiments in a flume are used to validate the numerical results on a stationary configuration as an initial step towards creating an accurate numerical model of the turbine. The simulation of the rotating turbine provides a full perspective on the effect of angular position on flow detachment and vortex shedding from the blade, as well as on the fluctuations of the shaft torque produced (a problematic feature of this type of turbine). The results are analyzed in terms of hydrodynamic optimization of the blade and its structural loading. Supported by DOE through the Northwest National Marine Renewable Energy Center.

Laboratory Experiments of Helicity or Vortex Generation in an Electric Quadrupole: Simulation of Tonadoes with and without Lightning

NASA Astrophysics Data System (ADS)

Kikuchi, H.

2007-05-01

Laboratory Experiments of Helicity or Vortex Generation in an Electric Quadrupole: Simulation of Tornadoes with and without Lightning H. Kikuchi Institute for Environmental Electromagnetics 3-8-18, Komagome, Toshima-ku, Tokyo 170, Japan e-mail: hkikuchi@mars.dti.ne.jp Abstract Usually the source-origins of helicity or vortex generation have been considered to be thermohydrodynamic in the hydrodynamic (HD) regime and/or magnetohydrodynamic in the magnetohydrodynamic (MHD) regime. It has been shown, however, by the present author that an electric quadrupole is also capable for helicity or vortex generation and a new electric helic- ity defined as hE= v·E (v: flow velocity; E: electric field) has been introduced. Accordingly, we have now three kinds of helicity, namely fluid, magnetic, and electric helicity. In many cases of atmospheric and space electricity phenomena in nature, electric helicity or vortex generation of electric origin is involved as typically seen in tornadic thunderstorms. Conventional theory of tornadoes, however, space- charge and electric fields have never been considered properly so far, surprisingly in spite of their effects of significance, because of no theorv for such cases, although those effects have been recognized implicitly by field experiments. This paper fills up these demands by newly introducing the concept of 'Electric Helicity' based on 'Electrohydrodynamics' (EHD) established and developed over the last more than two decades and such a whole theory is applied to tornadioes with and without lightning. Further, experimental evidence of this theory is presented for the first time by using a 'universal electric-cusp type plasma reactor' designed more than a decade ago [1]. This device is composed of two positive and negative electrodes of lead spheres 1.5 cm in diameter suspended 2~5 cm above a copper plane on which a semispherical lead 1.25 cm in diameter or its modified object is placed. A whole setup is arranged in a wooden box whose back and both sides are covered by black papers to prevent scattered and reflected light while its front side is open. We are particularly focusing on 'significance of electric quadrupole(s) in helicity and vortex generation',taking photos of wind flows with the use of a bunch of incense sticks burned and placed on the semispherical lead at the cusp center in the reactor. With increasing both electrode voltages from zero to a certain kV, ascending straight wind flows turn to be cyclonic separately toward the both electrodes. As soon as electric discharge from both electrodes to object starts at a certain breakdown voltage, typically 20~30 kV, wind flows suddenly turn to be violent and wind flows toward negative electrode are still cyclonic but wind flows toward positive electrode become anticyclonic. These results are shown by a number of photos taken and provide at the same time 'laboratory simulation of tonadoes with and without lightning'. [1] Kikuchi, H. Electrohydrodynamics in Dusty and Dirty Plasmas, Kluwer Academic Publishers, Dordrecht/The Netherlands, 2001, pp.93-94.

Simulation of Helical Flow Hydrodynamics in Meanders and Advection-Turbulent Diffusion Using Smoothed Particle Hydrodynamics

NASA Astrophysics Data System (ADS)

Gusti, T. P.; Hertanti, D. R.; Bahsan, E.; Soeryantono, H.

2013-12-01

Particle-based numerical methods, such as Smoothed Particle Hydrodynamics (SPH), may be able to simulate some hydrodynamic and morphodynamic behaviors better than grid-based numerical methods. This study simulates hydrodynamics in meanders and advection and turbulent diffusion in straight river channels using Microsoft Excel and Visual Basic. The simulators generate three-dimensional data for hydrodynamics and one-dimensional data for advection-turbulent diffusion. Fluid at rest, sloshing, and helical flow are simulated in the river meanders. Spill loading and step loading are done to simulate concentration patterns associated with advection-turbulent diffusion. Results indicate that helical flow is formed due to disturbance in morphology and particle velocity in the stream and the number of particles does not have a significant effect on the pattern of advection-turbulent diffusion concentration.

On the Construction and Dynamics of Knotted Fields

NASA Astrophysics Data System (ADS)

Kedia, Hridesh

Representing a physical field in terms of its field lines has often enabled a deeper understanding of complex physical phenomena, from Faraday's law of magnetic induction, to the Helmholtz laws of vortex motion, to the free energy density of liquid crystals in terms of the distortions of the lines of the director field. At the same time, the application of ideas from topology--the study of properties that are invariant under continuous deformations--has led to robust insights into the nature of complex physical systems from defects in crystal structures, to the earth's magnetic field, to topological conservation laws. The study of knotted fields, physical fields in which the field lines encode knots, emerges naturally from the application of topological ideas to the investigation of the physical phenomena best understood in terms of the lines of a field. A knot--a closed loop tangled with itself which can not be untangled without cutting the loop--is the simplest topologically non-trivial object constructed from a line. Remarkably, knots in the vortex (magnetic field) lines of a dissipationless fluid (plasma), persist forever as they are transported by the flow, stretching and rotating as they evolve. Moreover, deeply entwined with the topology-preserving dynamics of dissipationless fluids and plasmas, is an additional conserved quantity--helicity, a measure of the average linking of the vortex (magnetic field) lines in a fluid (plasma)--which has had far-reaching consequences for fluids and plasmas. Inspired by the persistence of knots in dissipationless flows, and their far-reaching physical consequences, we seek to understand the interplay between the dynamics of a field and the topology of its field lines in a variety of systems. While it is easy to tie a knot in a shoelace, tying a knot in the the lines of a space-filling field requires contorting the lines everywhere to match the knotted region. The challenge of analytically constructing knotted field configurations has impeded a deeper understanding of the interplay between topology and dynamics in fluids and plasmas. We begin by analytically constructing knotted field configurations which encode a desired knot in the lines of the field, and show that their helicity can be tuned independently of the encoded knot. The nonlinear nature of the physical systems in which these knotted field configurations arise, makes their analytical study challenging. We ask if a linear theory such as electromagnetism can allow knotted field configurations to persist with time. We find analytical expressions for an infinite family of knotted solutions to Maxwell's equations in vacuum and elucidate their connections to dissipationless flows. We present a design rule for constructing such persistently knotted electromagnetic fields, which could possibly be used to transfer knottedness to matter such as quantum fluids and plasmas. An important consequence of the persistence of knots in classical dissipationless flows is the existence of an additional conserved quantity, helicity, which has had far-reaching implications. To understand the existence of analogous conserved quantities, we ask if superfluids, which flow without dissipation just like classical dissipationless flows, have an additional conserved quantity akin to helicity. We address this question using an analytical approach based on defining the particle relabeling symmetry--the symmetry underlying helicity conservation--in superfluids, and find that an analogous conserved quantity exists but vanishes identically owing to the intrinsic geometry of complex scalar fields. Furthermore, to address the question of a ``classical limit'' of superfluid vortices which recovers classical helicity conservation, we perform numerical simulations of \\emph{bundles} of superfluid vortices, and find behavior akin to classical viscous flows.

The supernova-regulated ISM. III. Generation of vorticity, helicity, and mean flows

NASA Astrophysics Data System (ADS)

Käpylä, M. J.; Gent, F. A.; Väisälä, M. S.; Sarson, G. R.

2018-03-01

Context. The forcing of interstellar turbulence, driven mainly by supernova (SN) explosions, is irrotational in nature, but the development of significant amounts of vorticity and helicity, accompanied by large-scale dynamo action, has been reported. Aim. Several earlier investigations examined vorticity production in simpler systems; here all the relevant processes can be considered simultaneously. We also investigate the mechanisms for the generation of net helicity and large-scale flow in the system. Methods: We use a three-dimensional, stratified, rotating and shearing local simulation domain of the size 1 × 1 × 2 kpc3, forced with SN explosions occurring at a rate typical of the solar neighbourhood in the Milky Way. In addition to the nominal simulation run with realistic Milky Way parameters, we vary the rotation and shear rates, but keep the absolute value of their ratio fixed. Reversing the sign of shear vs. rotation allows us to separate the rotation- and shear-generated contributions. Results: As in earlier studies, we find the generation of significant amounts of vorticity, the rotational flow comprising on average 65% of the total flow. The vorticity production can be related to the baroclinicity of the flow, especially in the regions of hot, dilute clustered supernova bubbles. In these regions, the vortex stretching acts as a sink of vorticity. In denser, compressed regions, the vortex stretching amplifies vorticity, but remains sub-dominant to baroclinicity. The net helicities produced by rotation and shear are of opposite signs for physically motivated rotation laws, with the solar neighbourhood parameters resulting in the near cancellation of the total net helicity. We also find the excitation of oscillatory mean flows, the strength and oscillation period of which depend on the Coriolis and shear parameters; we interpret these as signatures of the anisotropic-kinetic-α (AKA) effect. We use the method of moments to fit for the turbulent transport coefficients, and find αAKA values of the order 3-5 km s-1. Conclusions: Even in a weakly rotationally and shear-influenced system, small-scale anisotropies can lead to significant effects at large scales. Here we report on two consequences of such effects, namely on the generation of net helicity and on the emergence of large-scale flows by the AKA effect, the latter detected for the first time in a direct numerical simulation of a realistic astrophysical system.

Properties of two-fluid flowing equilibria observed in double-pulsing coaxial helicity injection on HIST

NASA Astrophysics Data System (ADS)

Kanki, T.; Nagata, M.

2013-10-01

Multi-pulsing coaxial helicity injection (M-CHI) method which aims to achieve both quasi-steady sustainment and good confinement has been proposed as a refluxing scenario of the CHI. To explore the usefulness of the M-CHI for spherical torus (ST) configurations, the double-pulsing operations have been carried out in the HIST, verifying the flux amplification and the formation of the closed flux surfaces after the second CHI pulse. The purpose of this study is to investigate the properties of the magnetic field and plasma flow structures during the sustainment by comparing the results of plasma flow, density, and magnetic fields measurements with those of two-fluid equilibrium calculations. The two-fluid flowing equilibrium model which is described by a pair of generalized Grad-Shafranov equations for ion and electron surface variables and Bernoulli equations for density is applied to reconstruct the ST configuration with poloidal flow shear observed in the HIST. Due to the negative steep density gradient in high field side, the toroidal field has a diamagnetic profile (volume average beta, < β > = 68 %) in the central open flux column region. The ion flow velocity with strong flow shear from the separatrix in the inboard side to the core region is the opposite direction to the electron flow velocity due to the diamagentic drift through the density gradient. The electric field is relatively small in the whole region, and thus the Lorentz force nearly balances with the two-fluid effect which is particularly significant in a region with the steep density gradient due to the ion and electron diamagnetic drifts.

Magnetic structure in Mn1 -xCoxGe compounds

NASA Astrophysics Data System (ADS)

Altynbaev, E.; Siegfried, S.-A.; Strauß, P.; Menzel, D.; Heinemann, A.; Fomicheva, L.; Tsvyashchenko, A.; Grigoriev, S.

2018-04-01

The magnetic system of the pseudobinary compound Mn1 -xCoxGe has been studied using small-angle neutron scattering and susceptibility measurements. It is found that Mn1 -xCoxGe orders magnetically at low temperatures in the whole concentration range of x ∈[0 /0.9 ] . Four different states of the magnetic structure have been found at low temperatures: the long-range-ordered (LRO) short-period helical magnetic structure at x

Flow directing means for air-cooled transformers

DOEpatents

Jallouk, Philip A.

1977-01-01

This invention relates to improvements in systems for force-cooling transformers of the kind in which an outer helical winding and an insulation barrier nested therein form an axially extending annular passage for cooling-fluid flow. In one form of the invention a tubular shroud is positioned about the helical winding to define an axially extending annular chamber for cooling-fluid flow. The chamber has a width in the range of from about 4 to 25 times that of the axially extending passage. Two baffles extend inward from the shroud to define with the helical winding two annular flow channels having hydraulic diameters smaller than that of the chamber. The inlet to the chamber is designed with a hydraulic diameter approximating that of the coolant-entrance end of the above-mentioned annular passage. As so modified, transformers of the kind described can be operated at significantly higher load levels without exceeding safe operating temperatures. In some instances the invention permits continuous operation at 200% of the nameplate rating.

Optimization of Operation Parameters for Helical Flow Cleanout with Supercritical CO2 in Horizontal Wells Using Back-Propagation Artificial Neural Network.

PubMed

Song, Xianzhi; Peng, Chi; Li, Gensheng; He, Zhenguo; Wang, Haizhu

2016-01-01

Sand production and blockage are common during the drilling and production of horizontal oil and gas wells as a result of formation breakdown. The use of high-pressure rotating jets and annular helical flow is an effective way to enhance horizontal wellbore cleanout. In this paper, we propose the idea of using supercritical CO2 (SC-CO2) as washing fluid in water-sensitive formation. SC-CO2 is manifested to be effective in preventing formation damage and enhancing production rate as drilling fluid, which justifies tis potential in wellbore cleanout. In order to investigate the effectiveness of SC-CO2 helical flow cleanout, we perform the numerical study on the annular flow field, which significantly affects sand cleanout efficiency, of SC-CO2 jets in horizontal wellbore. Based on the field data, the geometry model and mathematical models were built. Then a numerical simulation of the annular helical flow field by SC-CO2 jets was accomplished. The influences of several key parameters were investigated, and SC-CO2 jets were compared to conventional water jets. The results show that flow rate, ambient temperature, jet temperature, and nozzle assemblies play the most important roles on wellbore flow field. Once the difference between ambient temperatures and jet temperatures is kept constant, the wellbore velocity distributions will not change. With increasing lateral nozzle size or decreasing rear/forward nozzle size, suspending ability of SC-CO2 flow improves obviously. A back-propagation artificial neural network (BP-ANN) was successfully employed to match the operation parameters and SC-CO2 flow velocities. A comprehensive model was achieved to optimize the operation parameters according to two strategies: cost-saving strategy and local optimal strategy. This paper can help to understand the distinct characteristics of SC-CO2 flow. And it is the first time that the BP-ANN is introduced to analyze the flow field during wellbore cleanout in horizontal wells.

Optimization of Operation Parameters for Helical Flow Cleanout with Supercritical CO2 in Horizontal Wells Using Back-Propagation Artificial Neural Network

PubMed Central

Song, Xianzhi; Peng, Chi; Li, Gensheng

2016-01-01

Sand production and blockage are common during the drilling and production of horizontal oil and gas wells as a result of formation breakdown. The use of high-pressure rotating jets and annular helical flow is an effective way to enhance horizontal wellbore cleanout. In this paper, we propose the idea of using supercritical CO2 (SC-CO2) as washing fluid in water-sensitive formation. SC-CO2 is manifested to be effective in preventing formation damage and enhancing production rate as drilling fluid, which justifies tis potential in wellbore cleanout. In order to investigate the effectiveness of SC-CO2 helical flow cleanout, we perform the numerical study on the annular flow field, which significantly affects sand cleanout efficiency, of SC-CO2 jets in horizontal wellbore. Based on the field data, the geometry model and mathematical models were built. Then a numerical simulation of the annular helical flow field by SC-CO2 jets was accomplished. The influences of several key parameters were investigated, and SC-CO2 jets were compared to conventional water jets. The results show that flow rate, ambient temperature, jet temperature, and nozzle assemblies play the most important roles on wellbore flow field. Once the difference between ambient temperatures and jet temperatures is kept constant, the wellbore velocity distributions will not change. With increasing lateral nozzle size or decreasing rear/forward nozzle size, suspending ability of SC-CO2 flow improves obviously. A back-propagation artificial neural network (BP-ANN) was successfully employed to match the operation parameters and SC-CO2 flow velocities. A comprehensive model was achieved to optimize the operation parameters according to two strategies: cost-saving strategy and local optimal strategy. This paper can help to understand the distinct characteristics of SC-CO2 flow. And it is the first time that the BP-ANN is introduced to analyze the flow field during wellbore cleanout in horizontal wells. PMID:27249026

The Weakly Nonlinear Magnetorotational Instability in a Global, Cylindrical Taylor–Couette Flow

DOE Office of Scientific and Technical Information (OSTI.GOV)

Clark, S. E.; Oishi, Jeffrey S., E-mail: seclark@astro.columbia.edu

We conduct a global, weakly nonlinear analysis of the magnetorotational instability (MRI) in a Taylor–Couette flow. This is a multiscale, perturbative treatment of the nonideal, axisymmetric MRI near threshold, subject to realistic radial boundary conditions and cylindrical geometry. We analyze both the standard MRI, initialized by a constant vertical background magnetic field, and the helical MRI, with an azimuthal background field component. This is the first weakly nonlinear analysis of the MRI in a global Taylor–Couette geometry, as well as the first weakly nonlinear analysis of the helical MRI. We find that the evolution of the amplitude of the standardmore » MRI is described by a real Ginzburg–Landau equation (GLE), whereas the amplitude of the helical MRI takes the form of a complex GLE. This suggests that the saturated state of the helical MRI may itself be unstable on long spatial and temporal scales.« less

Torsion effect on fully developed flow in a helical pipe

NASA Technical Reports Server (NTRS)

Kao, Hsiao C.

1987-01-01

Two techniques, a series expansion method of perturbed Poiseuille flow valid for low Dean numbers and a solution of the complete Navier-Stokes equation applicable to intermediate Dean values, are used to investigate the torsion effect on the fully developed laminar flow in a helical pipe of constant circular cross section. For the secondary flow patterns, the results show that the presence of torsion can produce a significant effect if the ratio of the curvature to the torsion is of order unity. The secondary flow is distorted in these cases. It is noted that the torsion effect is, however, usually small, and that the secondary flow has the usual pattern of a pair of counter-rotating vortices of nearly equal strength.

Evaluation of helicity generation in the tropical storm Gonu

NASA Astrophysics Data System (ADS)

Farahani, Majid M.; Khansalari, Sakineh; Azadi, Majid

2017-06-01

Helicity is a valuable dynamical concept for the study of rotating flows. Consequently helicity flux, indicative of the source or sink of helicity, owns comparable importance. In this study, while reviewing the existing methods, a mathematical relation between helicity and helicity-flux is introduced, discussed and examined. The computed values of helicity and helicity fluxes in an actual case, using the classical and this proposed method are compared. The down-stream helicity flux including sources and sinks of helicity is considered for the tropical storm Gonu that occurred over the coasts of Oman and Iran on June 2-7, 2007. Results show that the buoyancy, through the upper troposphere down to a height within boundary layer, is the main source in producing helicity, and surface friction from earth surface up to a height within boundary layer, is the main dissipating element of helicity. The dominance of buoyancy forcing over the dissipative friction forcing results in generation of vortex or enhancement of it after bouncing the land. Furthermore, the increase (decrease) of helicity results in an increase (decrease) in the height of the level in which maximum helicity flux occurs. It is suggested that the maximum helicity flux occurs at the top of the turbulent boundary layer, so that the height of boundary layer could be obtained.

Structure and interactions of biological helices

NASA Astrophysics Data System (ADS)

Kornyshev, Alexei A.; Lee, Dominic J.; Leikin, Sergey; Wynveen, Aaron

2007-07-01

Helices are essential building blocks of living organisms, be they molecular fragments of proteins ( α -helices), macromolecules (DNA and collagen), or multimolecular assemblies (microtubules and viruses). Their interactions are involved in packing of meters of genetic material within cells and phage heads, recognition of homologous genes in recombination and DNA repair, stability of tissues, and many other processes. Helical molecules form a variety of mesophases in vivo and in vitro. Recent structural studies, direct measurements of intermolecular forces, single-molecule manipulations, and other experiments have accumulated a wealth of information and revealed many puzzling physical phenomena. It is becoming increasingly clear that in many cases the physics of biological helices cannot be described by theories that treat them as simple, unstructured polyelectrolytes. The present article focuses on the most important and interesting aspects of the physics of structured macromolecules, highlighting various manifestations of the helical motif in their structure, elasticity, interactions with counterions, aggregation, and poly- and mesomorphic transitions.

Enhanced performance of core-shell structured polyaniline at helical carbon nanotube hybrids for ammonia gas sensor

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tian, Xin; Wang, Qiang; Chen, Xiangnan

2014-11-17

A core-shell structured hybrid of polyaniline at helical carbon nanotubes was synthesized using in situ polymerization, which the helical carbon nanotubes were uniformly surrounded by a layer of polyaniline nanorods array. More interestingly, repeatable responses were experimentally observed that the sensitivity to ammonia gas of the as-prepared helical shaped core-shell hybrid displays an enhancement of more than two times compared to those of only polyaniline or helical carbon nanotubes sensors because of the peculiar structures with high surface area. This kind of hybrid comprising nanorod arrays of conductive polymers covering carbon nanotubes and related structures provide a potential in sensorsmore » of trace gas detection for environmental monitoring and safety forecasting.« less

Gyrokinetic-Vlasov simulations of the ion temperature gradient turbulence in tokamak and helical systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Watanabe, T.-H.; Sugama, H.; Graduate University for Advanced Studies

2006-11-30

Recent progress of the gyrokinetic-Vlasov simulations on the ion temperature gradient (ITG) turbulence in tokamak and helical systems is reported, where the entropy balance is checked as a reference for the numerical accuracy. The tokamak ITG turbulence simulation carried out on the Earth Simulator clearly captures a nonlinear generation process of zonal flows. The tera-flops and tera-bytes scale simulation is also applied to a helical system with the same poloidal and toroidal periodicities of L = 2 and M = 10 as in the Large Helical Device.

Axial flow positive displacement worm gas generator

NASA Technical Reports Server (NTRS)

Giffin, Rollin George (Inventor); Fakunle, Oladapo (Inventor); Murrow, Kurt David (Inventor)

2010-01-01

An axial flow positive displacement engine has an inlet axially spaced apart and upstream from an outlet. Inner and outer bodies have offset inner and outer axes extend from the inlet to the outlet through first, second, and third sections of a core assembly in serial downstream flow relationship. At least one of the bodies is rotatable about its axis. The inner and outer bodies have intermeshed inner and outer helical blades wound about the inner and outer axes respectively. The inner and outer helical blades extend radially outwardly and inwardly respectively. The helical blades have first, second, and third twist slopes in the first, second, and third sections respectively. The first twist slopes are less than the second twist slopes and the third twist slopes are less than the second twist slopes. A combustor section extends axially downstream through at least a portion of the second section.

Mathematical Simulation of Convective Processes in the Liquid Core of the Earth and Implications for the Interpretation of Geomagnetic Field Variations in Polar Latitudes

NASA Astrophysics Data System (ADS)

Abakumov, M. V.; Chechetkin, V. M.; Shalimov, S. L.

2018-05-01

The flow structure induced by thermal convection in a rotating spherical shell with viscous boundary conditions is considered under the assumption that the differential rotation of the core relative to the mantle is absent. The radial, azimuthal, and meridional components of the flow's velocity and helicity are studied. With the magnetic field assumed to be frozen into a liquid (frozen-flux hypothesis), it is shown that the numerical results fit the observations of the geomagnetic field variations close to the pole.

Dispersion Characteristics of a Helix Loaded Waveguide.

DTIC Science & Technology

1985-09-01

be employed to increase the bandwidth of gyroton amplifiers. The structure consists of helical wires contained concentrially 6. in a cylindrical...bandwidth of gyroton amplifiers. The structure consists of helical wires contained concentrially in a cylindrical conductor. The helical wires are close

Membrane-spanning α-helical barrels as tractable protein-design targets.

PubMed

Niitsu, Ai; Heal, Jack W; Fauland, Kerstin; Thomson, Andrew R; Woolfson, Derek N

2017-08-05

The rational ( de novo ) design of membrane-spanning proteins lags behind that for water-soluble globular proteins. This is due to gaps in our knowledge of membrane-protein structure, and experimental difficulties in studying such proteins compared to water-soluble counterparts. One limiting factor is the small number of experimentally determined three-dimensional structures for transmembrane proteins. By contrast, many tens of thousands of globular protein structures provide a rich source of 'scaffolds' for protein design, and the means to garner sequence-to-structure relationships to guide the design process. The α-helical coiled coil is a protein-structure element found in both globular and membrane proteins, where it cements a variety of helix-helix interactions and helical bundles. Our deep understanding of coiled coils has enabled a large number of successful de novo designs. For one class, the α-helical barrels-that is, symmetric bundles of five or more helices with central accessible channels-there are both water-soluble and membrane-spanning examples. Recent computational designs of water-soluble α-helical barrels with five to seven helices have advanced the design field considerably. Here we identify and classify analogous and more complicated membrane-spanning α-helical barrels from the Protein Data Bank. These provide tantalizing but tractable targets for protein engineering and de novo protein design.This article is part of the themed issue 'Membrane pores: from structure and assembly, to medicine and technology'. © 2017 The Author(s).

Blood flow characteristics in the ascending aorta after TAVI compared to surgical aortic valve replacement.

PubMed

Trauzeddel, Ralf Felix; Löbe, Ulrike; Barker, Alex J; Gelsinger, Carmen; Butter, Christian; Markl, Michael; Schulz-Menger, Jeanette; von Knobelsdorff-Brenkenhoff, Florian

2016-03-01

Ascending aortic blood flow characteristics are altered after aortic valve surgery, but the effect of transcatheter aortic valve implantation (TAVI) is unknown. Abnormal flow may be associated with aortic and cardiac remodeling. We analyzed blood flow characteristics in the ascending aorta after TAVI in comparison to conventional stented aortic bioprostheses (AVR) and healthy subjects using time-resolved three-dimensional flow-sensitive cardiovascular magnetic resonance imaging (4D-flow MRI). Seventeen patients with TAVI (Edwards Sapien XT), 12 with AVR and 9 healthy controls underwent 4D-flow MRI of the ascending aorta. Target parameters were: severity of vortical and helical flow pattern (semiquantitative grading from 0 = none to 3 = severe) and the local distribution of systolic wall shear stress (WSSsystole). AVR revealed significantly more extensive vortical and helical flow pattern than TAVI (p = 0.042 and p = 0.002) and controls (p < 0.001 and p = 0.001). TAVI showed significantly more extensive vortical flow than controls (p < 0.001). Both TAVI and AVR revealed marked blood flow eccentricity (64.7 and 66.7%, respectively), whereas controls showed central blood flow (88.9%). TAVI and AVR exhibited an asymmetric distribution of WSSsystole in the mid-ascending aorta with local maxima at the right anterior aortic wall and local minima at the left posterior wall. In contrast, controls showed a symmetric distribution of WSSsystole along the aortic circumference. Blood flow was significantly altered in the ascending aorta after TAVI and AVR. Changes were similar regarding WSSsystole distribution, while TAVI resulted in less helical and vortical blood flow.

Structure-activity relationship of HP (2-20) analog peptide: enhanced antimicrobial activity by N-terminal random coil region deletion.

PubMed

Park, Yoonkyung; Park, Seong-Cheol; Park, Hae-Kyun; Shin, Song Yub; Kim, Yangmee; Hahm, Kyung-Soo

2007-01-01

HP (2-20) (AKKVFKRLEKLFSKIQNDK) is a 19-aa antimicrobial peptide derived from N-terminus of Helicobacter pylori Ribosomal protein L1 (RpL1). In the previous study, several analogs with amino acid substitutions were designed to increase or decrease only the net hydrophobicity. In particular, substitutions of Gln(16) and Asp(18) with Trp (Anal 3) for hydrophobic amino acid caused a dramatic increase in antibiotic activity without a hemolytic effect. HP-A3 is a potent antimicrobial peptide that forms, in a hydrophobic medium, an amphipathic structure consisting of an N-terminal random coil region (residues 2-5) and extended C-terminal regular alpha-helical region (residues 6-20). To obtain the short and potent alpha-helical antimicrobial peptide, we synthesized a N-terminal random coil deleted HP-A3 (A3-NT) and examined their antimicrobial activity and mechanism of action. The resulting 15mer peptide showed increased antibacterial and antifungal activity to 2- and 4-fold, respectively, without hemolysis. Confocal fluorescence microscopy studies showed that A3-NT was accumulated in the plasma membrane. Flow cytometric analysis revealed that A3-NT acted in salt- and energy-independent manner. Furthermore, A3-NT causes significant morphological alterations of the bacterial surfaces as shown by scanning electron microscopy. Circular dichroism (CD) analysis revealed that A3-NT showed higher alpha-helical contents than the HP-A3 peptide in 50% TFE solution. Therefore, the cell-lytic efficiency of HP-A3, which depended on the alpha-helical content of peptide, correlated linearly with their antimicrobial potency.

Tubular Crystals and Helical Arrays: Structural Determination of HIV-1 Capsid Assemblies Using Iterative Helical Real-Space Reconstruction

PubMed Central

Zhang, Peijun; Meng, Xin; Zhao, Gongpu

2013-01-01

Helical structures are important in many different life forms and are well-suited for structural studies by cryo-EM. A unique feature of helical objects is that a single projection image contains all the views needed to perform a three-dimensional (3D) crystallographic reconstruction. Here, we use HIV-1 capsid assemblies to illustrate the detailed approaches to obtain 3D density maps from helical objects. Mature HIV-1 particles contain a conical- or tubular-shaped capsid that encloses the viral RNA genome and performs essential functions in the virus life cycle. The capsid is composed of capsid protein (CA) oligomers which are helically arranged on the surface. The N-terminal domain (NTD) of CA is connected to its C-terminal domain (CTD) through a flexible hinge. Structural analysis of two- and three-dimensional crystals provided molecular models of the capsid protein (CA) and its oligomer forms. We determined the 3D density map of helically assembled HIV-1 CA hexamers at 16 Å resolution using an iterative helical real-space reconstruction method. Docking of atomic models of CA-NTD and CA-CTD dimer into the electron density map indicated that the CTD dimer interface is retained in the assembled CA. Furthermore, molecular docking revealed an additional, novel CTD trimer interface. PMID:23132072

A proline-hinge alters the characteristics of the amphipathic α-helical AMPs.

PubMed

Lee, Jong Kook; Gopal, Ramamourthy; Park, Seong-Cheol; Ko, Hyun Sook; Kim, Yangmee; Hahm, Kyung-Soo; Park, Yoonkyung

2013-01-01

HP (2-20) is a 19-aa, amphipathic, α-helical peptide with antimicrobial properties that was derived from the N-terminus of Helicobacter pylori ribosomal protein L1. We previously showed that increasing the net hydrophobicity of HP (2-20) by substituting Trp for Gln(17) and Asp(19) (Anal 3) increased the peptide's antimicrobial activity. In hydrophobic medium, Anal 3 forms an amphipathic structure consisting of an N-terminal random coil region (residues 2-5) and an extended helical region (residues 6-20). To investigate the structure-activity relationship of Anal 3, we substituted Pro for Glu(9) (Anal 3-Pro) and then examined the new peptide's three-dimensional structure, antimicrobial activity and mechanism of action. Anal 3-Pro had an α-helical structure in the presence of trifluoroethanol (TFE) and sodium dodecyl sulfate (SDS). NMR spectroscopic analysis of Anal 3-Pro's tertiary structure in SDS micelles confirmed that the kink potential introduced by Pro(10) was responsible for the helix distortion. We also found that Anal 3-Pro exhibited about 4 times greater antimicrobial activity than Anal 3. Fluorescence activated flow cytometry and confocal fluorescence microscopy showed that incorporating a Pro-hinge into Anal 3 markedly reduced its membrane permeability so that it accumulated in the cytoplasm without remaining in the cell membrane. To investigate the translocation mechanism, we assessed its ability to release of FITC-dextran. The result showed Anal 3-Pro created a pore <1.8 nm in diameter, which is similar to buforin II. Notably, scanning electron microscopic observation of Candida albicans revealed that Anal 3-Pro and buforin II exert similar effects on cell membranes, whereas magainin 2 exerts a different, more damaging, effect. In addition, Anal 3-Pro assumed a helix-hinge-helix structure in the presence of biological membranes and formed micropores in both bacterial and fungal membranes, through which it entered the cytoplasm and tightly bound to DNA. These results indicate that the bending region of Anal 3- Pro peptide is prerequisite for effective antibiotic activity and may facilitate easy penetration of the lipid bilayers of the cell membrane.

Time-dependent behavior in a transport-barrier model for the quasi-single helcity state

NASA Astrophysics Data System (ADS)

Terry, P. W.; Whelan, G. G.

2014-09-01

Time-dependent behavior that follows from a recent theory of the quasi-single-helicity (QSH) state of the reversed field pinch is considered. The theory (Kim and Terry 2012 Phys. Plasmas 19 122304) treats QSH as a core fluctuation structure tied to a tearing mode of the same helicity, and shows that strong magnetic and velocity shears in the structure suppress the nonlinear interaction with other fluctuations. By summing the multiple helicity fluctuation energies over wavenumber, we reduce the theory to a predator-prey model. The suppression of the nonlinear interaction is governed by the single helicity energy, which, for fixed radial structure, controls the magnetic and velocity shearing rates. It is also controlled by plasma current which, in the theory, sets the shearing threshold for suppression. The model shows a limit cycle oscillation in which the system toggles between QSH and multiple helicity states, with the single helicity phase becoming increasingly long-lived relative to the multiple helicity phase as plasma current increases.

Free Energy and Structure of Helix-forming Peptides: A Theoretical Investigation

NASA Astrophysics Data System (ADS)

Karpusenka, Vadzim

This thesis focuses on the structure and free energy of helical secondary structures of short peptides in a variety of experimental settings. Specifically, the formation of alpha-, pi- and 310-helices was investigated using large-scale classical molecular dynamics simulations with state-of-the-art force fields. In addition, the recently developed Adaptively Biased Molecular Dynamics (ABMD) and Steered Molecular Dynamics (SMD) methods were used to calculate the corresponding free energies. The most important results are as follows. For the examined peptide homopolymers, the observed minima on the free energy landscapes (based on suitable collective variables such as the radius of gyration, number of hydrogen bonds, and handedness) were associated with alpha-helices and "globular" or "knot-like" configurations only. No evidence was found to indicate that 310- or pi-helices represent equilibrium structures for these systems. In addition, the free energy landscape of short peptide chains formed by mixing two different amino acids were also examined. These results too indicate that the alpha-helix is only equilibrium helical secondary structure, and that the mixing of different amino acids does not result in the introduction of any significant new minima into the free energy landscapes. These results are in agreement with experimental observations insofar as these indicate that helical structural motifs are primary based on alpha-helices, with 310- and pi-helices being observed only rarely. Although pi- and 310-helices represent nonequilibrium structures, we were still able to estimate their free energies by means of SMD simulations. The helical secondary structure of the examined polypeptide chains is due to the formation of hydrogen bonds. However, there are other mechanisms that may allow for the additional stabilization of these structures. Specifically, in the so-called AK-(4,7) protein, the possible presence of disulfide bonds connecting cysteine residues may significantly alter the free energy landscapes and therefore the stability of different helical structures. We therefore examined this issue with ABMD simulations. However, our results show that while the free energy landscapes are indeed significantly altered only the formation of alpha-helices is favored as a secondary structural motif. Since all the results indicate that alpha-helix formation dominates, it is natural to think in terms of an alpha-helix forming propensity for different amino acids. To address this question, we carried out an extensive residue-by-residue population analysis of different amino acid guests in an alanine-based host setting. Such an analysis allows us to rank the different amino acid guests based on whether they increased or decreased the population in the alpha-helix region of the corresponding Ramachandran plots. Our ranking of the different guest amino acids is in reasonable correspondence with the experimental results, although some differences are observed. Finally, using a four-beads coarse-grained model were have investigated the stability of GA88 and GB88 proteins, which are quite similar in terms of their amino acid sequence, by means of 10mus simulations. The results indicate that while the three alpha-helix bundle of the GA88 protein remains stable, the 2beta--alpha--2beta configuration of the GB88 protein does not: the latter rapidly converts to a structure consisting mostly of helices similar to the GA88 protein design. These results indicate that this particular four-bead coarse-grained model is not able to properly grasp the dynamics of the beta-sheet secondary structure and overstabilizes the corresponding helical content.

PROMINENCE FORMATION ASSOCIATED WITH AN EMERGING HELICAL FLUX ROPE

DOE Office of Scientific and Technical Information (OSTI.GOV)

Okamoto, Takenori J.; Tsuneta, Saku; Katsukawa, Yukio

2009-05-20

The formation and evolution process and magnetic configuration of solar prominences remain unclear. In order to study the formation process of prominences, we examine continuous observations of a prominence in NOAA AR 10953 with the Solar Optical Telescope on the Hinode satellite. As reported in our previous Letter, we find a signature suggesting that a helical flux rope emerges from below the photosphere under a pre-existing prominence. Here we investigate more detailed properties and photospheric indications of the emerging helical flux rope, and discuss their relationship to the formation of the prominence. Our main conclusions are: (1) a dark regionmore » with absence of strong vertical magnetic fields broadens and then narrows in Ca II H-line filtergrams. This phenomenon is consistent with the emergence of the helical flux rope as photospheric counterparts. The size of the flux rope is roughly 30,000 km long and 10,000 km wide. The width is larger than that of the prominence. (2) No shear motion or converging flows are detected, but we find diverging flows such as mesogranules along the polarity inversion line. The presence of mesogranules may be related to the emergence of the helical flux rope. (3) The emerging helical flux rope reconnects with magnetic fields of the pre-existing prominence to stabilize the prominence for the next several days. We thus conjecture that prominence coronal magnetic fields emerge in the form of helical flux ropes that contribute to the formation and maintenance of the prominence.« less

Topological characteristics of helical repeat proteins.

PubMed

Groves, M R; Barford, D

1999-06-01

The recent elucidation of protein structures based upon repeating amino acid motifs, including the armadillo motif, the HEAT motif and tetratricopeptide repeats, reveals that they belong to the class of helical repeat proteins. These proteins share the common property of being assembled from tandem repeats of an alpha-helical structural unit, creating extended superhelical structures that are ideally suited to create a protein recognition interface.

The [N II] Kinematics of R Aquarii

NASA Technical Reports Server (NTRS)

Hollis, J. M.; Vogel, S. N.; VanBuren, D.; Strong, J. P.; Lyon, R. G.; Dorband, J. E.

1998-01-01

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.

Molecular dynamics of individual alpha-helices of bacteriorhodopsin in dimyristol phosphatidylocholine. I. Structure and dynamics.

PubMed

Woolf, T B

1997-11-01

Understanding the role of the lipid bilayer in membrane protein structure and dynamics is needed for tertiary structure determination methods. However, the molecular details are not well understood. Molecular dynamics computer calculations can provide insight into these molecular details of protein:lipid interactions. This paper reports on 10 simulations of individual alpha-helices in explicit lipid bilayers. The 10 helices were selected from the bacteriorhodopsin structure as representative alpha-helical membrane folding components. The bilayer is constructed of dimyristoyl phosphatidylcholine molecules. The only major difference between simulations is the primary sequence of the alpha-helix. The results show dramatic differences in motional behavior between alpha-helices. For example, helix A has much smaller root-mean-squared deviations than does helix D. This can be understood in terms of the presence of aromatic residues at the interface for helix A that are not present in helix D. Additional motions are possible for the helices that contain proline side chains relative to other amino acids. The results thus provide insight into the types of motion and the average structures possible for helices within the bilayer setting and demonstrate the strength of molecular simulations in providing molecular details that are not directly visualized in experiments.

Structural details (kinks and non-alpha conformations) in transmembrane helices are intrahelically determined and can be predicted by sequence pattern descriptors.

PubMed

Rigoutsos, Isidore; Riek, Peter; Graham, Robert M; Novotny, Jiri

2003-08-01

One of the promising methods of protein structure prediction involves the use of amino acid sequence-derived patterns. Here we report on the creation of non-degenerate motif descriptors derived through data mining of training sets of residues taken from the transmembrane-spanning segments of polytopic proteins. These residues correspond to short regions in which there is a deviation from the regular alpha-helical character (i.e. pi-helices, 3(10)-helices and kinks). A 'search engine' derived from these motif descriptors correctly identifies, and discriminates amongst instances of the above 'non-canonical' helical motifs contained in the SwissProt/TrEMBL database of protein primary structures. Our results suggest that deviations from alpha-helicity are encoded locally in sequence patterns only about 7-9 residues long and can be determined in silico directly from the amino acid sequence. Delineation of such variations in helical habit is critical to understanding the complex structure-function relationships of polytopic proteins and for drug discovery. The success of our current methodology foretells development of similar prediction tools capable of identifying other structural motifs from sequence alone. The method described here has been implemented and is available on the World Wide Web at http://cbcsrv.watson.ibm.com/Ttkw.html.

A predictor-corrector technique for visualizing unsteady flow

NASA Technical Reports Server (NTRS)

Banks, David C.; Singer, Bart A.

1995-01-01

We present a method for visualizing unsteady flow by displaying its vortices. The vortices are identified by using a vorticity-predictor pressure-corrector scheme that follows vortex cores. The cross-sections of a vortex at each point along the core can be represented by a Fourier series. A vortex can be faithfully reconstructed from the series as a simple quadrilateral mesh, or its reconstruction can be enhanced to indicate helical motion. The mesh can reduce the representation of the flow features by a factor of one thousand or more compared with the volumetric dataset. With this amount of reduction it is possible to implement an interactive system on a graphics workstation to permit a viewer to examine, in three dimensions, the evolution of the vortical structures in a complex, unsteady flow.

Flow around a helically twisted elliptic cylinder

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kim, Woojin; Lee, Jungil; Choi, Haecheon, E-mail: choi@snu.ac.kr

In the present study, we conduct unsteady three-dimensional simulations of flows around a helically twisted elliptic (HTE) cylinder at the Reynolds numbers of 100 and 3900, based on the free-stream velocity and square root of the product of the lengths of its major and minor axes. A parametric study is conducted for Re = 100 by varying the aspect ratio (AR) of the elliptic cross section and the helical spanwise wavelength (λ). Depending on the values of AR and λ, the flow in the wake contains the characteristic wavelengths of λ, 2λ, 6λ, or even longer than 60λ, showing amore » wide diversity of flows in the wake due to the shape change. The drag on the optimal (i.e., having lowest drag) HTE cylinder (AR = 1.3 and λ = 3.5d) is lower by 18% than that of the circular cylinder, and its lift fluctuations are zero owing to complete suppression of vortex shedding in the wake. This optimal HTE configuration reduces the drag by 23% for Re = 3900 where the wake is turbulent, showing that the HTE cylinder reduces the mean drag and lift fluctuations for both laminar and turbulent flows.« less

Noncovalent Interactions in the Asymmetric Synthesis of Rigid, Conjugated Helical Structures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Miyasaka, Makoto; Pink, Maren; Rajca, Suchada

Tetrakis({beta}-trithiophene) 1 folds into a helical conformation (RRR) that facilitates double ring annelation, with high diastereoselectivity and modest enantioselectivity, to provide bis[7]helicene 2 (MRM). This rigid, helically locked structure has enhanced chiroptical properties similar to the corresponding [15]helicene.

Transmembrane Helices Tilt, Bend, Slide, Torque, and Unwind between Functional States of Rhodopsin

PubMed Central

Ren, Zhong; Ren, Peter X.; Balusu, Rohith; Yang, Xiaojing

2016-01-01

The seven-helical bundle of rhodopsin and other G-protein coupled receptors undergoes structural rearrangements as the transmembrane receptor protein is activated. These structural changes are known to involve tilting and bending of various transmembrane helices. However, the cause and effect relationship among structural events leading to a cytoplasmic crevasse for G-protein binding is less well defined. Here we present a mathematical model of the protein helix and a simple procedure to determine multiple parameters that offer precise depiction of a helical conformation. A comprehensive survey of bovine rhodopsin structures shows that the helical rearrangements during the activation of rhodopsin involve a variety of angular and linear motions such as torsion, unwinding, and sliding in addition to the previously reported tilting and bending. These hitherto undefined motion components unify the results obtained from different experimental approaches, and demonstrate conformational similarity between the active opsin structure and the photoactivated structures in crystallo near the retinal anchor despite their marked differences. PMID:27658480

Computational design of water-soluble α-helical barrels.

PubMed

Thomson, Andrew R; Wood, Christopher W; Burton, Antony J; Bartlett, Gail J; Sessions, Richard B; Brady, R Leo; Woolfson, Derek N

2014-10-24

The design of protein sequences that fold into prescribed de novo structures is challenging. General solutions to this problem require geometric descriptions of protein folds and methods to fit sequences to these. The α-helical coiled coils present a promising class of protein for this and offer considerable scope for exploring hitherto unseen structures. For α-helical barrels, which have more than four helices and accessible central channels, many of the possible structures remain unobserved. Here, we combine geometrical considerations, knowledge-based scoring, and atomistic modeling to facilitate the design of new channel-containing α-helical barrels. X-ray crystal structures of the resulting designs match predicted in silico models. Furthermore, the observed channels are chemically defined and have diameters related to oligomer state, which present routes to design protein function. Copyright © 2014, American Association for the Advancement of Science.

Depicting mass flow rate of R134a /LPG refrigerant through straight and helical coiled adiabatic capillary tubes of vapor compression refrigeration system using artificial neural network approach

NASA Astrophysics Data System (ADS)

Gill, Jatinder; Singh, Jagdev

2018-07-01

In this work, an experimental investigation is carried out with R134a and LPG refrigerant mixture for depicting mass flow rate through straight and helical coil adiabatic capillary tubes in a vapor compression refrigeration system. Various experiments were conducted under steady-state conditions, by changing capillary tube length, inner diameter, coil diameter and degree of subcooling. The results showed that mass flow rate through helical coil capillary tube was found lower than straight capillary tube by about 5-16%. Dimensionless correlation and Artificial Neural Network (ANN) models were developed to predict mass flow rate. It was found that dimensionless correlation and ANN model predictions agreed well with experimental results and brought out an absolute fraction of variance of 0.961 and 0.988, root mean square error of 0.489 and 0.275 and mean absolute percentage error of 4.75% and 2.31% respectively. The results suggested that ANN model shows better statistical prediction than dimensionless correlation model.

Pumping Characteristics of a Helical Screw Agitator with a Draught Tube

NASA Astrophysics Data System (ADS)

Hwang, Jung-Hoon; Kim, Youn-Jea

In the use of helical type agitator, the mixing process is usually restricted to the laminar flow regime. Common examples of laminar mixing are found where the fluid has a very high viscosity, i.e., pseudoplastic fluids. It can be indicated that a helical type agitator is sufficiently suited to the creeping flow mixing. The pumping characteristic of a Helical Screw Agitator with a draught tube (HSA) is required to evaluate its capacity for the optimal configuration of the mixing chamber. It could be executed by changing some parameters such as the number of helix, the angular velocity and the rotating direction and so on. In this study, the numerical simulation was carried out with the Eulerian multiphase mixture model and the moving mesh approximation. Some of the optimum design parameters have been developed with the aid of numerical data from the Computational Fluid Dynamics (CFD) analysis. Using the commercial code, Fluent, the pumping characteristics in the HSA are investigated from the rheological properties, and the results are graphically depicted.

Homooligomeric β3 (R)-valine peptides: Transformation between C14 and C12 helical structures induced by a guest Aib residue.

PubMed

Vasantha, Basavalingappa; George, Gijo; Raghothama, Srinivasarao; Balaram, Padmanabhan

2017-01-01

Novel helical, structures unprecedented in the chemistry of α-polypeptides, may be found in polypeptides containing β and γ amino acids. The structural characterization of C 12 and C 14 -helices in oligo β-peptides was originally achieved using conformationally constrained cyclic β-residues. This study explores the conformational characteristics of proteinogenic β 3 residues in homooligomeric sequences and addresses the issue of inducing a transition between C 14 and C 12 helices by the introduction of a guest α-residue. Folded C 14 -helical structures are demonstrated for the nonapeptide Boc-[β 3 (R)Val] 9 -OMe by NMR methods in CDCl 3 -DMSO mixtures, while the peptide was found to be aggregated in CDCl 3 . The insertion of a guest Aib residue into an oligo-β-valine sequence in the octapeptide model Boc-[(β 3 (R)Val) 3 -Aib-(β 3 (R)Val] 4 -OMe results in well dispersed NH region in the NMR spectrum indicating folded structures in CDCl 3 . Structure calculations for both the peptides using NOE distance constraints support a C 14 helical structure in the homooligomer which transform into a C 12 helix on introduction of the guest Aib residue. © 2016 Wiley Periodicals, Inc.

Magnetic Energy and Helicity in Two Emerging Active Regions in the Sun

NASA Technical Reports Server (NTRS)

Liu, Y.; Schuck, P. W.

2012-01-01

The magnetic energy and relative magnetic helicity in two emerging solar active regions, AR 11072 and AR 11158,are studied. They are computed by integrating over time the energy and relative helicity fluxes across the photosphere. The fluxes consist of two components: one from photospheric tangential flows that shear and braid field lines (shear term), the other from normal flows that advect magnetic flux into the corona (emergence term). For these active regions: (1) relative magnetic helicity in the active-region corona is mainly contributed by the shear term,(2) helicity fluxes from the emergence and the shear terms have the same sign, (3) magnetic energy in the corona (including both potential energy and free energy) is mainly contributed by the emergence term, and(4) energy fluxes from the emergence term and the shear term evolved consistently in phase during the entire flux emergence course.We also examine the apparent tangential velocity derived by tracking field-line footpoints using a simple tracking method. It is found that this velocity is more consistent with tangential plasma velocity than with the flux transport velocity, which agrees with the conclusion by Schuck.

A Novel Method for Sampling Alpha-Helical Protein Backbones

DOE R&D Accomplishments Database

Fain, Boris; Levitt, Michael

2001-01-01

We present a novel technique of sampling the configurations of helical proteins. Assuming knowledge of native secondary structure, we employ assembly rules gathered from a database of existing structures to enumerate the geometrically possible 3-D arrangements of the constituent helices. We produce a library of possible folds for 25 helical protein cores. In each case the method finds significant numbers of conformations close to the native structure. In addition we assign coordinates to all atoms for 4 of the 25 proteins. In the context of database driven exhaustive enumeration our method performs extremely well, yielding significant percentages of structures (0.02%--82%) within 6A of the native structure. The method's speed and efficiency make it a valuable contribution towards the goal of predicting protein structure.

Helical flow couplets in submarine gravity underflows

NASA Astrophysics Data System (ADS)

Imran, Jasim; Ashraful Islam, Mohammad; Huang, Heqing; Kassem, Ahmed; Dickerson, John; Pirmez, Carlos; Parker, Gary

2007-07-01

Active and relic meandering channels are common on the seafloor adjacent to continental margins. These channels and their associated submarine fan deposits are products of the density-driven gravity flows known as turbidity currents. The tie between channel curvature and its effects on these gravity flows has been an enigma. This paper records the results of both large-scale laboratory measurements and a numerical simulation that captures the three-dimensional flow field of a gravity underflow at a channel bend. These findings reveal that channel curvature drives two helical flow cells, one stacked upon the other. The lower cell forms near the channel bed surface and has a circulation pattern similar to that observed in fluvial channels, i.e., with a near-bed flow directed inward. The other circulation cell forms in the upper part of the gravity flow and has a streamwise vorticity with the opposite sense of the lower cell.

Contribution of proline to the pre-structuring tendency of transient helical secondary structure elements in intrinsically disordered proteins.

PubMed

Lee, Chewook; Kalmar, Lajos; Xue, Bin; Tompa, Peter; Daughdrill, Gary W; Uversky, Vladimir N; Han, Kyou-Hoon

2014-03-01

IDPs function without relying on three-dimensional structures. No clear rationale for such a behavior is available yet. PreSMos are transient secondary structures observed in the target-free IDPs and serve as the target-binding "active" motifs in IDPs. Prolines are frequently found in the flanking regions of PreSMos. Contribution of prolines to the conformational stability of the helical PreSMos in IDPs is investigated. MD simulations are performed for several IDP segments containing a helical PreSMo and the flanking prolines. To measure the influence of flanking-prolines on the structural content of a helical PreSMo calculations were done for wild type as well as for mutant segments with Pro→Asp, His, Lys, or Ala. The change in the helicity due to removal of a proline was measured both for the PreSMo region and for the flanking regions. The α-helical content in ~70% of the helical PreSMos at the early stage of simulation decreases due to replacement of an N-terminal flanking proline by other residues whereas the helix content in nearly all PreSMos increases when the same replacements occur at the C-terminal flanking region. The helix destabilizing/terminating role of the C-terminal flanking prolines is more pronounced than the helix promoting effect of the N-terminal flanking prolines. This work represents a novel example demonstrating that a proline is encoded in an IDP with a defined purpose. The helical PreSMos presage their target-bound conformations. As they most likely mediate IDP-target binding via conformational selection their helical content can be an important feature for IDP function. Copyright © 2013 Elsevier B.V. All rights reserved.

Fluid Mechanics and Heat Transfer Spirally Fluted Tubing,

DTIC Science & Technology

1981-08-01

Condensation of Helically Fluted Tubes in a Vertical Configuration 7 2. EXPERIMENTAL PROGRAM 2.1 Water Flow Facility 13 2.2 Test Section Construction...transfer on the outside of the tube is achieved. In a vertical orientation with fluid condensing on the outside of the helically fluted tube, the...transfer performance on the inside of helically fluted tubes as indicated by the Nusselt modulus, Nu/Pr0 .4 . as a function of the Reynolds number is

Evaluation of Aortic Blood Flow and Wall Shear Stress in Aortic Stenosis and Its Association With Left Ventricular Remodeling

PubMed Central

von Knobelsdorff-Brenkenhoff, Florian; Karunaharamoorthy, Achudhan; Trauzeddel, Ralf Felix; Barker, Alex J; Blaszczyk, Edyta; Markl, Michael; Schulz-Menger, Jeanette

2016-01-01

Background Aortic stenosis (AS) leads to variable stress for the left ventricle (LV) and consequently a broad range of LV remodeling. Study aim was to describe blood flow patterns in the ascending aorta of AS patients and determine their association with remodeling. Methods and Results Thirty-seven patients with AS (14 mild, 8 moderate, 15 severe; age 63±13 years) and 37 healthy controls (age 60±10 years) underwent 4D-flow MRI. Helical and vortical flow formations and flow eccentricity were assessed in the ascending aorta. Normalized flow displacement from the vessel center and peak systolic wall shear stress (WSSpeak) in the ascending aorta were quantified. LV remodeling was assessed based on LV mass index (LVMI-I) and the ratio of LV mass to enddiastolic volume (relative wall mass; RWM). Marked helical and vortical flow formation and eccentricity were more prevalent in patients with AS than in healthy subjects, and AS patients exhibited an asymmetric and elevated distribution of WSSpeak. In AS, aortic orifice area was strongly negatively associated with vortical flow formation (p=0.0274), eccentricity (p=0.0070) and flow displacement (p=0.0021). Bicuspid aortic valve was associated with more intense helical (p=0.0098) and vortical flow formation (p=0.0536), higher flow displacement (p=0.11) and higher WSSpeak (p=0.0926). LVM-I and RWM were significantly associated with aortic orifice area (p=0.0611, p=0.0058) and flow displacement (p=0.0058, p=0.0283). Conclusions In this pilot study, AS leads to abnormal blood flow pattern and WSSpeak in the ascending aorta. In addition to aortic orifice area, normalized flow displacement was significantly associated with LV remodeling. PMID:26917824

Structure determination of helical filaments by solid-state NMR spectroscopy

PubMed Central

Ahmed, Mumdooh; Spehr, Johannes; König, Renate; Lünsdorf, Heinrich; Rand, Ulfert; Lührs, Thorsten; Ritter, Christiane

2016-01-01

The controlled formation of filamentous protein complexes plays a crucial role in many biological systems and represents an emerging paradigm in signal transduction. The mitochondrial antiviral signaling protein (MAVS) is a central signal transduction hub in innate immunity that is activated by a receptor-induced conversion into helical superstructures (filaments) assembled from its globular caspase activation and recruitment domain. Solid-state NMR (ssNMR) spectroscopy has become one of the most powerful techniques for atomic resolution structures of protein fibrils. However, for helical filaments, the determination of the correct symmetry parameters has remained a significant hurdle for any structural technique and could thus far not be precisely derived from ssNMR data. Here, we solved the atomic resolution structure of helical MAVSCARD filaments exclusively from ssNMR data. We present a generally applicable approach that systematically explores the helical symmetry space by efficient modeling of the helical structure restrained by interprotomer ssNMR distance restraints. Together with classical automated NMR structure calculation, this allowed us to faithfully determine the symmetry that defines the entire assembly. To validate our structure, we probed the protomer arrangement by solvent paramagnetic resonance enhancement, analysis of chemical shift differences relative to the solution NMR structure of the monomer, and mutagenesis. We provide detailed information on the atomic contacts that determine filament stability and describe mechanistic details on the formation of signaling-competent MAVS filaments from inactive monomers. PMID:26733681

Structure stability of lytic peptides during their interactions with lipid bilayers.

PubMed

Chen, H M; Lee, C H

2001-10-01

In this work, molecular dynamics simulations were used to examine the consequences of a variety of analogs of cecropin A on lipid bilayers. Analog sequences were constructed by replacing either the N- or C-terminal helix with the other helix in native or reverse sequence order, by making palindromic peptides based on both the N- and C-terminal helices, and by deleting the hinge region. The structure of the peptides was monitored throughout the simulation. The hinge region appeared not to assist in maintaining helical structure but help in motion flexibility. In general, the N-terminal helix of peptides was less stable than the C-terminal one during the interaction with anionic lipid bilayers. Sequences with hydrophobic helices tended to regain helical structure after an initial loss while sequences with amphipathic helices were less able to do this. The results suggests that hydrophobic design peptides have a high structural stability in an anionic membrane and are the candidates for experimental investigation.

Radial electric field and ion parallel flow in the quasi-symmetric and Mirror configurations of HSX

NASA Astrophysics Data System (ADS)

Kumar, S. T. A.; Dobbins, T. J.; Talmadge, J. N.; Wilcox, R. S.; Anderson, D. T.

2018-05-01

The radial electric field and the ion mean parallel flow are obtained in the helically symmetric experiment stellarator from toroidal flow measurements of C+6 ion at two locations on a flux surface, using the Pfirsch–Schlüter effect. Results from the standard quasi-helically symmetric magnetic configuration are compared with those from the Mirror configuration where the quasi-symmetry is deliberately degraded using auxiliary coils. For similar injected power, the quasi-symmetric configuration is observed to have significantly lower flows while the experimental observations from the Mirror geometry are in better agreement with neoclassical calculations. Indications are that the radial electric field near the core of the quasi-symmetric configuration may be governed by non-neoclassical processes.

Enhanced heat transfer with full circumferential ribs in helical pipe

NASA Astrophysics Data System (ADS)

Chang, S. W.; Su, L. M.; Yang, T. L.

2002-08-01

This paper describes an experimental study of heat transfers in the smooth-walled and rib-roughened helical pipes with reference to the design of enhanced cooling passages in the cylinder head and liner of a marine propulsive diesel engine. The manner in which the repeated ribs modify the forced heat convection in the helical pipe is considered for the case where the flow is turbulent upon entering the coil but laminar in further downstream. A selection of experimental results illustrates the individual and interactive effects of Dean vortices and rib-flows on heat transfer along the inner and outer helixes of coils. The experimental-based observations reveal that the centrifugal force modifies the heat transfer in a manner to generate circumferential heat transfer variation with better cooling performance on the outer edge relative to its inner counterpart even with the agitated flow field caused by the repeated ribs. Heat transfer augmentation factor in the range of 1.3 - 3 times of the smooth-walled level is achieved using the present ribbing geometry. A set of empirical correlations based on the experimental data has been developed to permit the evaluation of heat transfers along the inner and outer helixes of the smooth-walled and rib-roughened helical pipes.

Hierarchical Nanostructures Self-Assembled from a Mixture System Containing Rod-Coil Block Copolymers and Rigid Homopolymers

PubMed Central

Li, Yongliang; Jiang, Tao; Lin, Shaoliang; Lin, Jiaping; Cai, Chunhua; Zhu, Xingyu

2015-01-01

Self-assembly behavior of a mixture system containing rod-coil block copolymers and rigid homopolymers was investigated by using Brownian dynamics simulations. The morphologies of formed hierarchical self-assemblies were found to be dependent on the Lennard-Jones (LJ) interaction εRR between rod blocks, lengths of rod and coil blocks in copolymer, and mixture ratio of block copolymers to homopolymers. As the εRR value decreases, the self-assembled structures of mixtures are transformed from an abacus-like structure to a helical structure, to a plain fiber, and finally are broken into unimers. The order parameter of rod blocks was calculated to confirm the structure transition. Through varying the length of rod and coil blocks, the regions of thermodynamic stability of abacus, helix, plain fiber, and unimers were mapped. Moreover, it was discovered that two levels of rod block ordering exist in the helices. The block copolymers are helically wrapped on the homopolymer bundles to form helical string, while the rod blocks are twistingly packed inside the string. In addition, the simulation results are in good agreement with experimental observations. The present work reveals the mechanism behind the formation of helical (experimentally super-helical) structures and may provide useful information for design and preparation of the complex structures. PMID:25965726

Pore Helices Play a Dynamic Role as Integrators of Domain Motion during Kv11.1 Channel Inactivation Gating*

PubMed Central

Perry, Matthew D.; Ng, Chai Ann; Vandenberg, Jamie I.

2013-01-01

Proteins that form ion-selective pores in the membrane of cells are integral to many rapid signaling processes, including regulating the rhythm of the heartbeat. In potassium channels, the selectivity filter is critical for both endowing an exquisite selectivity for potassium ions, as well as for controlling the flow of ions through the pore. Subtle rearrangements in the complex hydrogen-bond network that link the selectivity filter to the surrounding pore helices differentiate conducting (open) from nonconducting (inactivated) conformations of the channel. Recent studies suggest that beyond the selectivity filter, inactivation involves widespread rearrangements of the channel protein. Here, we use rate equilibrium free energy relationship analysis to probe the structural changes that occur during selectivity filter gating in Kv11.1 channels, at near atomic resolution. We show that the pore helix plays a crucial dynamic role as a bidirectional interface during selectivity filter gating. We also define the molecular bases of the energetic coupling between the pore helix and outer helix of the pore domain that occurs early in the transition from open to inactivated states, as well as the coupling between the pore helix and inner helix late in the transition. Our data demonstrate that the pore helices are more than just static structural elements supporting the integrity of the selectivity filter; instead they play a crucial dynamic role during selectivity filter gating. PMID:23471968

Numerical study of the influence of geometrical characteristics of a vertical helical coil on a bubbly flow

NASA Astrophysics Data System (ADS)

Saffari, H.; Moosavi, R.

2014-11-01

In this article, turbulent single-phase and two-phase (air-water) bubbly fluid flows in a vertical helical coil are analyzed by using computational fluid dynamics (CFD). The effects of the pipe diameter, coil diameter, coil pitch, Reynolds number, and void fraction on the pressure loss, friction coefficient, and flow characteristics are investigated. The Eulerian-Eulerian model is used in this work to simulate the two-phase fluid flow. Three-dimensional governing equations of continuity, momentum, and energy are solved by using the finite volume method. The k- ɛ turbulence model is used to calculate turbulence fluctuations. The SIMPLE algorithm is employed to solve the velocity and pressure fields. Due to the effect of a secondary force in helical pipes, the friction coefficient is found to be higher in helical pipes than in straight pipes. The friction coefficient increases with an increase in the curvature, pipe diameter, and coil pitch and decreases with an increase in the coil diameter and void fraction. The close correlation between the numerical results obtained in this study and the numerical and empirical results of other researchers confirm the accuracy of the applied method. For void fractions up to 0.1, the numerical results indicate that the friction coefficient increases with increasing the pipe diameter and keeping the coil pitch and diameter constant and decreases with increasing the coil diameter. Finally, with an increase in the Reynolds number, the friction coefficient decreases, while the void fraction increases.

A new simple dynamo model for solar activity cycle

NASA Astrophysics Data System (ADS)

Yokoi, Nobumitsu; Schmitt, Dieter

2015-04-01

The solar magnetic activity cycle has been investigated in an elaborated manner with several types of dynamo models [1]. In most of the current mean-field approaches, the inhomogeneity of the large-scale flow is treated as an essential ingredient in the mean magnetic field equation whereas it is completely neglected in the turbulence equation. In this work, a new simple model for the solar activity cycle is proposed. The present model differs from the previous ones mainly in two points. First, in addition to the helicity coefficient α, we consider a term related to the cross helicity, which represents the effect of the inhomogeneous mean flow, in the turbulent electromotive force [2, 3]. Second, this transport coefficient (γ) is not treated as an adjustable parameter, but the evolution equation for γ is simultaneously solved. The basic scenario for the solar activity cycle in this approach is as follows: The toroidal field is induced by the toroidal rotation in mediation by the turbulent cross helicity. Then due to the α or helicity effect, the poloidal field is generated from the toroidal field. The poloidal field induced by the α effect produces a turbulent cross helicity whose sign is opposite to the original one (negative cross-helicity production). The cross helicity with this opposite sign induces a reversed toroidal field. Results of the eigenvalue analysis of the model equations are shown, which confirm the above scenario. References [1] Charbonneau, Living Rev. Solar Phys. 7, 3 (2010). [2] Yoshizawa, A. Phys. Fluids B 2, 1589 (1990). [3] Yokoi, N. Geophys. Astrophys. Fluid Dyn. 107, 114 (2013).

Measurement of Two-Phase Flow Characteristics Under Microgravity Conditions

NASA Technical Reports Server (NTRS)

Keshock, E. G.; Lin, C. S.; Edwards, L. G.; Knapp, J.; Harrison, M. E.; Xhang, X.

1999-01-01

This paper describes the technical approach and initial results of a test program for studying two-phase annular flow under the simulated microgravity conditions of KC-135 aircraft flights. A helical coil flow channel orientation was utilized in order to circumvent the restrictions normally associated with drop tower or aircraft flight tests with respect to two-phase flow, namely spatial restrictions preventing channel lengths of sufficient size to accurately measure pressure drops. Additionally, the helical coil geometry is of interest in itself, considering that operating in a microgravity environment vastly simplifies the two-phase flows occurring in coiled flow channels under 1-g conditions for virtually any orientation. Pressure drop measurements were made across four stainless steel coil test sections, having a range of inside tube diameters (0.95 to 1.9 cm), coil diameters (25 - 50 cm), and length-to-diameter ratios (380 - 720). High-speed video photographic flow observations were made in the transparent straight sections immediately preceding and following the coil test sections. A transparent coil of tygon tubing of 1.9 cm inside diameter was also used to obtain flow visualization information within the coil itself. Initial test data has been obtained from one set of KC-135 flight tests, along with benchmark ground tests. Preliminary results appear to indicate that accurate pressure drop data is obtainable using a helical coil geometry that may be related to straight channel flow behavior. Also, video photographic results appear to indicate that the observed slug-annular flow regime transitions agree quite reasonably with the Dukler microgravity map.

Numerical Simulation of Subsonic and Transonic Propeller Flow. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Snyder, Aaron

1988-01-01

The numerical simulation of 3-D transonic flow about a system of propeller blades is investigated. In particular, it is shown that the use of helical coordinates significantly simplifies the form of the governing equation when the propeller system is assumed to be surrounded by an irrotational flow field of an inviscid fluid. The unsteady small disturbance equation, valid for lightly loaded blades and expressed in helical coordinates, is derived from the general blade-fixed potential equation, given for an arbitrary coordinate system. The use of a coordinate system which inherently adapts to the mean flow results in a disturbance equation requiring relatively few terms to accurately model the physics of the flow. Furthermore, the helical coordinate system presented here is novel in that it is periodic in the circumferential direction while, simultaneously, maintaining orthogonal properties at the mean blade locations. The periodic characteristic allows a complete cascade of blades to be treated, and the orthogonality property affords straightforward treatment of blade boundary conditions. An ADI numerical scheme is used to compute the solution of the steady flow as an asymptotic limit of an unsteady flow. As an example of the method, solutions are presented for subsonic and transonic flow about a 5 percent thick bicircular arc blade of an 8-bladed cascade. Both high and low advance ratio cases are computed and include a lifting as well as nonlifting cases. The nonlifting solutions obtained are compared to solutions from a Euler code.

The SSME seal test program: Leakage tests for helically-grooved seals

NASA Technical Reports Server (NTRS)

Childs, D. W.

1983-01-01

Helically grooved annular seal configurations were tested in highly turbulent flow to determine if reduced leakage and enhanced stability would result from the pumping action of the seal. It was found that: (1) leakage of a helically grooved seals decreases with running speed; (2) leakage reduction due to increased running speed is greater at lower values of R sub a; (3) an asymptote for leakage reduction is indicated with increasing running speed; (4) leakage is reduced by reducing the ridge (minimum) and average clearances; (5) leakage increases with increasing pitch angles and with increasing groove depth. Plain seals with smooth rotors and stators will leak more than a helically grooved seal. It was also found that plain seals with a rough rotor and a rough stator leak less than a properly designed helically grooved seal. A properly designed helically grooved seal consumes at least twice as much power as a conventional annular seal.

Sequence and conformational preferences at termini of α-helices in membrane proteins: role of the helix environment.

PubMed

Shelar, Ashish; Bansal, Manju

2014-12-01

α-Helices are amongst the most common secondary structural elements seen in membrane proteins and are packed in the form of helix bundles. These α-helices encounter varying external environments (hydrophobic, hydrophilic) that may influence the sequence preferences at their N and C-termini. The role of the external environment in stabilization of the helix termini in membrane proteins is still unknown. Here we analyze α-helices in a high-resolution dataset of integral α-helical membrane proteins and establish that their sequence and conformational preferences differ from those in globular proteins. We specifically examine these preferences at the N and C-termini in helices initiating/terminating inside the membrane core as well as in linkers connecting these transmembrane helices. We find that the sequence preferences and structural motifs at capping (Ncap and Ccap) and near-helical (N' and C') positions are influenced by a combination of features including the membrane environment and the innate helix initiation and termination property of residues forming structural motifs. We also find that a large number of helix termini which do not form any particular capping motif are stabilized by formation of hydrogen bonds and hydrophobic interactions contributed from the neighboring helices in the membrane protein. We further validate the sequence preferences obtained from our analysis with data from an ultradeep sequencing study that identifies evolutionarily conserved amino acids in the rat neurotensin receptor. The results from our analysis provide insights for the secondary structure prediction, modeling and design of membrane proteins. © 2014 Wiley Periodicals, Inc.

Helicity conservation by flow across scales in reconnecting vortex links and knots

PubMed Central

Scheeler, Martin W.; Kleckner, Dustin; Kindlmann, Gordon L.; Irvine, William T. M.

2014-01-01

The conjecture that helicity (or knottedness) is a fundamental conserved quantity has a rich history in fluid mechanics, but the nature of this conservation in the presence of dissipation has proven difficult to resolve. Making use of recent advances, we create vortex knots and links in viscous fluids and simulated superfluids and track their geometry through topology-changing reconnections. We find that the reassociation of vortex lines through a reconnection enables the transfer of helicity from links and knots to helical coils. This process is remarkably efficient, owing to the antiparallel orientation spontaneously adopted by the reconnecting vortices. Using a new method for quantifying the spatial helicity spectrum, we find that the reconnection process can be viewed as transferring helicity between scales, rather than dissipating it. We also infer the presence of geometric deformations that convert helical coils into even smaller scale twist, where it may ultimately be dissipated. Our results suggest that helicity conservation plays an important role in fluids and related fields, even in the presence of dissipation. PMID:25326419

Three New Structures of Left-Handed RadA Helical Filaments: Structural Flexibility of N-Terminal Domain Is Critical for Recombinase Activity

PubMed Central

Chang, Yu-Wei; Ko, Tzu-Ping; Lee, Chien-Der; Chang, Yuan-Chih; Lin, Kuei-Ann; Chang, Chia-Seng; Wang, Andrew H.-J.; Wang, Ting-Fang

2009-01-01

RecA family proteins, including bacterial RecA, archaeal RadA, and eukaryotic Dmc1 and Rad51, mediate homologous recombination, a reaction essential for maintaining genome integrity. In the presence of ATP, these proteins bind a single-strand DNA to form a right-handed nucleoprotein filament, which catalyzes pairing and strand exchange with a homologous double-stranded DNA (dsDNA), by as-yet unknown mechanisms. We recently reported a structure of RadA left-handed helical filament, and here present three new structures of RadA left-handed helical filaments. Comparative structural analysis between different RadA/Rad51 helical filaments reveals that the N-terminal domain (NTD) of RadA/Rad51, implicated in dsDNA binding, is highly flexible. We identify a hinge region between NTD and polymerization motif as responsible for rigid body movement of NTD. Mutant analysis further confirms that structural flexibility of NTD is essential for RadA's recombinase activity. These results support our previous hypothesis that ATP-dependent axial rotation of RadA nucleoprotein helical filament promotes homologous recombination. PMID:19295907

Tire

NASA Technical Reports Server (NTRS)

Benzing, II, James Alfred (Inventor); Kish, James Christopher (Inventor); Asnani, Vivake Manohar (Inventor)

2012-01-01

A tire includes a plurality of helical springs. Each helical spring includes a first end portion, a second end portion, and an arching middle portion. Each helical spring is interlaced with at least one other helical spring thereby forming a laced toroidal structure extending about an entire circumference of the tire.

Structural details (kinks and non-α conformations) in transmembrane helices are intrahelically determined and can be predicted by sequence pattern descriptors

PubMed Central

Rigoutsos, Isidore; Riek, Peter; Graham, Robert M.; Novotny, Jiri

2003-01-01

One of the promising methods of protein structure prediction involves the use of amino acid sequence-derived patterns. Here we report on the creation of non-degenerate motif descriptors derived through data mining of training sets of residues taken from the transmembrane-spanning segments of polytopic proteins. These residues correspond to short regions in which there is a deviation from the regular α-helical character (i.e. π-helices, 310-helices and kinks). A ‘search engine’ derived from these motif descriptors correctly identifies, and discriminates amongst instances of the above ‘non-canonical’ helical motifs contained in the SwissProt/TrEMBL database of protein primary structures. Our results suggest that deviations from α-helicity are encoded locally in sequence patterns only about 7–9 residues long and can be determined in silico directly from the amino acid sequence. Delineation of such variations in helical habit is critical to understanding the complex structure–function relationships of polytopic proteins and for drug discovery. The success of our current methodology foretells development of similar prediction tools capable of identifying other structural motifs from sequence alone. The method described here has been implemented and is available on the World Wide Web at http://cbcsrv.watson.ibm.com/Ttkw.html. PMID:12888523

On the helical arrangements of protein molecules.

PubMed

Dauter, Zbigniew; Jaskolski, Mariusz

2018-03-01

Helical structures are prevalent in biology. In the PDB, there are many examples where protein molecules are helically arranged, not only according to strict crystallographic screw axes but also according to approximate noncrystallographic screws. The preponderance of such screws is rather striking as helical arrangements in crystals must preserve an integer number of subunits per turn, while intuition and simple packing arguments would seem to favor fractional helices. The article provides insights into such questions, based on stereochemistry, trigonometry, and topology, and illustrates the findings with concrete PDB structures. Updated statistics of Sohncke space groups in the PDB are also presented. © 2017 The Protein Society.

Ruby-Helix: an implementation of helical image processing based on object-oriented scripting language.

PubMed

Metlagel, Zoltan; Kikkawa, Yayoi S; Kikkawa, Masahide

2007-01-01

Helical image analysis in combination with electron microscopy has been used to study three-dimensional structures of various biological filaments or tubes, such as microtubules, actin filaments, and bacterial flagella. A number of packages have been developed to carry out helical image analysis. Some biological specimens, however, have a symmetry break (seam) in their three-dimensional structure, even though their subunits are mostly arranged in a helical manner. We refer to these objects as "asymmetric helices". All the existing packages are designed for helically symmetric specimens, and do not allow analysis of asymmetric helical objects, such as microtubules with seams. Here, we describe Ruby-Helix, a new set of programs for the analysis of "helical" objects with or without a seam. Ruby-Helix is built on top of the Ruby programming language and is the first implementation of asymmetric helical reconstruction for practical image analysis. It also allows easier and semi-automated analysis, performing iterative unbending and accurate determination of the repeat length. As a result, Ruby-Helix enables us to analyze motor-microtubule complexes with higher throughput to higher resolution.

Collective Modes of Dust Helical Clusters

NASA Astrophysics Data System (ADS)

Tsytovich, V. N.; Gousein-Zade, N. G.; Morfill, G. E.

2005-10-01

The helical structures are the simplest 3D crystal-like cylindrical structures with radius R being a system of 2D clusters equally separated along the cylindrical axis with a relative rotation on constant angle φ0. For mean free path for grain charging much larger than the separation of the grains, the total energy of grain interaction is a sum of all pair grain interactions. The helical structures have been found experimentally for ions in laser traps in cylindrical gas discharges at very low temperatures (in both case as ``warms''). The equilibrium criterion and the criteria of stability including the absence of saddle points show that in the plane ρ, φ the bifurcation points are often present with new branches appearing (stable and unstable). Numerical MD simulations show that for cylindrical symmetry any random distributions of grains is developing into helical structures. The theory of collective modes of helical structures is developed for arbitrary grain interactions. The dispersion relation for frequencies of the collective modes for different branches of helical structures is derived and solved numerically for interaction including different type of screened grain potentials including the grain attraction. The dispersion relation in the first Brillouin zone for the square of the frequency ω2 is shown to be a be-cubic equation and gives the square of frequency ω2 > 0 for stable modes and the square of the growth rates for the unstable modes ω2 < 0. Modes for helical structures in parabolic external confining potential well perpendicular to cylindrical axis are found. Stabile self-confined structures without external confinement are discovered in presence of both non-collective and collective grain attractions.

Characterizing optical chirality

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bliokh, Konstantin Y.; Advanced Science Institute, RIKEN, Wako-shi, Saitama 351-0198; Nori, Franco

We examine the recently introduced measure of chirality of a monochromatic optical field [Y. Tang and A. E. Cohen, Phys. Rev. Lett. 104, 163901 (2010)] using the momentum (plane-wave) representation and helicity basis. Our analysis clarifies the physical meaning of the measure of chirality and unveils its close relation to the polarization helicity, spin angular momentum, energy density, and Poynting energy flow. We derive the operators of the optical chirality and of the corresponding chiral momentum, which acquire remarkably simple forms in the helicity representation.

The Writhe of Helical Structures in the Solar Corona

NASA Technical Reports Server (NTRS)

Toeroek, T.; Berger, M. A.; Kliem, B.

2010-01-01

Context. Helicity is a fundamental property of magnetic fields, conserved in ideal MHD. In flux rope topology, it consists of twist and writhe helicity. Despite the common occurrence of helical structures in the solar atmosphere, little is known about how their shape relates to the writhe, which fraction of helicity is contained in writhe, and how much helicity is exchanged between twist and writhe when they erupt. Aims. Here we perform a quantitative investigation of these questions relevant for coronal flux ropes. Methods. The decomposition of the writhe of a curve into local and nonlocal components greatly facilitates its computation. We use it to study the relation between writhe and projected S shape of helical curves and to measure writhe and twist in numerical simulations of flux rope instabilities. The results are discussed with regard to filament eruptions and coronal mass ejections (CMEs). Results. (1) We demonstrate that the relation between writhe and projected S shape is not unique in principle, but that the ambiguity does not affect low-lying structures, thus supporting the established empirical rule which associates stable forward (reverse) S shaped structures low in the corona with positive (negative) helicity. (2) Kink-unstable erupting flux ropes are found to transform a far smaller fraction of their twist helicity into writhe helicity than often assumed. (3) Confined flux rope eruptions tend to show stronger writhe at low heights than ejective eruptions (CMEs). This argues against suggestions that the writhing facilitates the rise of the rope through the overlying field. (4) Erupting filaments which are S shaped already before the eruption and keep the sign of their axis writhe (which is expected if field of one chirality dominates the source volume of the eruption), must reverse their S shape in the course of the rise. Implications for the occurrence of the helical kink instability in such events are discussed.

Fuel injection and mixing systems and methods of using the same

DOEpatents

Mao, Chien-Pei; Short, John

2010-08-03

A fuel injection and mixing system is provided. The system includes an injector body having a fuel inlet and a fuel outlet, and defines a fuel flow path between the inlet and outlet. The fuel flow path may include a generally helical flow passage having an inlet end portion disposed proximate the fuel inlet of the injector body. The flow path also may include an expansion chamber downstream from and in fluid communication with the helical flow passage, as well as a fuel delivery device in fluid communication with the expansion chamber for delivering fuel. Heating means is also provided in thermal communication with the injector body. The heating means may be adapted and configured for maintaining the injector body at a predetermined temperature to heat fuel traversing the flow path. A method of preheating and delivering fuel is also provided.

Molecular Structure of a Helical ribbon in a Peptide Self-Assembly

NASA Astrophysics Data System (ADS)

Hwang, Wonmuk; Marini, Davide; Kamm, Roger D.; Zhang, Shuguang

2002-03-01

We have studied the molecular structure of nanometer scale helical ribbons observed during self-assembly of the peptide KFE8 (amino acid sequence: FKFEFKFE) (NanoLetters (2002, in press)). By analyzing the hydrogen bonding patterns between neighboring peptide backbones, we constructed a number of possible β-sheets. Using all possible combinations of these, we built helical ribbons with dimensions close to those found experimentally and performed molecular dynamics simulations to identify the most stable structure. Solvation effects were implemented by the analytic continuum electrostatics (ACE) model developed by Schaefer and Karplus (J. Phys. Chem. 100, 1578 (1996)). By applying electrostatic double layer theory, we incorporated the effect of pH by scaling the amount of charge on the sidechains. Our results suggest that the helical ribbon is comprised of a double β-sheet where the inner and the outer helices have distinct hydrogen bonding patterns. Our approach has general applicability to the study of helices formed by the self-assembly of β-sheet forming peptides with various amino acid sequences.

Three-phase flow? Consider helical-coil heat exchangers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Haraburda, S.S.

1995-07-01

In recent years, chemical process plants are increasingly encountering processes that require heat exchange in three-phase fluids. A typical application, for example, is heating liquids containing solid catalyst particles and non-condensable gases. Heat exchangers designed for three-phase flow generally have tubes with large diameters (typically greater than two inches), because solids can build-up inside the tube and lead to plugging. At the same time, in order to keep heat-transfer coefficients high, the velocity of the process fluid within the tube should also be high. As a result, heat exchangers for three-phase flow may require less than five tubes -- eachmore » having a required linear length that could exceed several hundred feet. Given these limitations, it is obvious that a basic shell-and-tube heat exchanger is not the most practical solution for this purpose. An alternative for three-phase flow is a helical-coil heat exchanger. The helical-coil units offer a number of advantages, including perpendicular, counter-current flow and flexible overall dimensions for the exchanger itself. The paper presents equations for: calculating the tube-side heat-transfer coefficient; calculating the shell-side heat-transfer coefficient; calculating the heat-exchanger size; calculating the tube-side pressure drop; and calculating shell-side pressure-drop.« less

Increasing Helicity to Achieve a Dynamo State on the Three-Meter Model of the Earth's Core

NASA Astrophysics Data System (ADS)

Rojas, R.; Perevalov, A.; Lathrop, D. P.

2017-12-01

Dynamo theory describes the generation of magnetic fields in the flows of conducting fluids, for example, in stars and planetary cores. Spherical Couette flows, which are flows between two concentric and independently rotating spheres, is one of the experimental models for achieving this task in the laboratory. We have performed dynamo state search in our three-meter spherical-Couette model reaching up to Reynolds number near 108 with amplifications of the field between 10-30% but without a self-sustained dynamo magnetic field. A recent numerical work [K. Finke and A. Tilgner. Phys. Rev. E, 86:016310, Jul 2012] suggested that a roughened inner core reduces the threshold for dynamo action. The mean flow would have more poloidal component than the one we are generating with our current smooth sphere setup. With baffles flow would be expelled radially outward on the equatorial plane and returned at the poles, with opposite helicities in the two hemispheres. Baffles welded on our smooth inner sphere are proposed to achieve this task. We are working to perform experiments on a scaled water model of our experimental setup with Reynolds number near 105 to measure the helicity improvements of different baffle designs in support of upcoming Three-Meter modifications. We gratefully acknowledge support from NSF EAR-1417148.

Effect of the amyloid β hairpin's structure on the handedness of helices formed by its aggregates

DOE PAGES

GhattyVenkataKrishna, Pavan K.; Uberbacher, Edward C.; Cheng, Xiaolin

2013-07-08

Various structural models for amyloid β fibrils have been derived from a variety of experimental techniques. However, these models cannot differentiate between the relative position of the two arms of the β hairpin called the stagger. Amyloid fibrils of various hierarchical levels form left-handed helices composed of β sheets. However it is unclear if positive, negative and zero staggers all form the macroscopic left-handed helices. To address this issue we have conducted extensive molecular dynamics simulations of amyloid β sheets of various staggers and shown that only negative staggers lead to the experimentally observed left-handed helices while positive staggers generatemore » the incorrect right-handed helices. In conclusion, this result suggests that the negative staggers are physiologically relevant structure of the amyloid β fibrils.« less

Control of Helical Chirality of Ferrocene-Dipeptide Conjugates by the Secondary Structure of Dipeptide Chains.

PubMed

Moriuchi, Toshiyuki; Nishiyama, Taiki; Nobu, Masaki; Hirao, Toshikazu

2017-09-18

Controlling helical chirality and creating protein secondary structures in cyclic/acyclic ferrocene-dipeptide bioorganometallic conjugates were achieved by adjusting the conformational flexibility of the dipeptide chains. In systems reported to date, the helical chirality of a conjugate was determined by the absolute configuration of the adjacent amino acid reside. In contrast, it was possible to induce both M- and P-helical chirality, even when the configuration of the adjacent amino acid was the same. It is particularly interesting to note that M-helical chirality was produced in a cyclic ferrocene-dipeptide conjugate composed of the l-Ala-d-Pro-cystamine-d-Pro-l-Ala dipeptide sequence (1), in which a type II β-turn-like secondary structure was established. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

ICPP: Beltrami fields in plasmas -- H-mode boundary layers and high beta equilibria

NASA Astrophysics Data System (ADS)

Yoshida, Zensho

2000-10-01

The Beltrami fields, eigenfunctions of the curl operator, represent essential characteristics of twisted, spiral, chiral or helical structures in various vector fields. Amongst diverse applications of the theory of Beltrami fields, the present paper focuses on the self-organized states of plasmas. The Taylor relaxed state is the principal example of self-organized Beltrami fields. Suppose that a plasma is produced in an external magnetic field (harmonic field). If we do not apply any drive, the plasma will disappear and the system will relax into the harmonic magnetic field. When we drive a current and sustain the total helicity, the plasma relaxes into the Taylor state and achieves the Beltrami magnetic field. When a strong flow is implemented to a plasma, self-organized states becomes qualitatively different from the conventional relaxed stats. The two-fluid effect induces a coupling among the flow, magnetic field, electric field and the pressure, resulting in a "singular perturbation" to the MHD system. To invoke this effect, one must supply a driving force to sustain a strong flow. It is equivalent to giving an internal electric field or applying a steep gradient in pressure, because these fields are tightly coupled. In the two-fluid model, the Beltrami condition demands that the vorticity parallels the flow in both electron and ion fluids. We find that a superposition of two Beltrami magnetic fields (and also two Beltrami flows) solves the simultaneous two-fluid Beltrami conditions [1]. Despite this simple mathematical structure, the set of solutions contains field configurations that are far richer than the conventional theory. The hydrodynamic pressure of a shear flow yields a diamagnetic state that is suitable for confining a high-beta plasma. The H-mode boundary layer is an example, which is spontaneously generated by the core plasma pressure [2]. Active control of shear flow will significantly extend the scope of such self-organized states [3]. [1] S. M. Mahajan and Z. Yoshida, Phys. Rev. Lett. 81, 4863 (1998). [2] S. M. Mahajan and Z. Yoshida, Phys. Plasmas 7, 635 (2000). [3] Z. Yoshida et al., in Non-Neutral Plasma Physics III (ed. J.J. Bollinger, AIP, 1999), 397.

Observation of the magnetic flux and three-dimensional structure of skyrmion lattices by electron holography.

PubMed

Park, Hyun Soon; Yu, Xiuzhen; Aizawa, Shinji; Tanigaki, Toshiaki; Akashi, Tetsuya; Takahashi, Yoshio; Matsuda, Tsuyoshi; Kanazawa, Naoya; Onose, Yoshinori; Shindo, Daisuke; Tonomura, Akira; Tokura, Yoshinori

2014-05-01

Skyrmions are nanoscale spin textures that are viewed as promising candidates as information carriers in future spintronic devices. Skyrmions have been observed using neutron scattering and microscopy techniques. Real-space imaging using electrons is a straightforward way to interpret spin configurations by detecting the phase shifts due to electromagnetic fields. Here, we report the first observation by electron holography of the magnetic flux and the three-dimensional spin configuration of a skyrmion lattice in Fe(0.5)Co(0.5)Si thin samples. The magnetic flux inside and outside a skyrmion was directly visualized and the handedness of the magnetic flux flow was found to be dependent on the direction of the applied magnetic field. The electron phase shifts φ in the helical and skyrmion phases were determined using samples with a stepped thickness t (from 55 nm to 510 nm), revealing a linear relationship (φ = 0.00173 t). The phase measurements were used to estimate the three-dimensional structures of both the helical and skyrmion phases, demonstrating that electron holography is a useful tool for studying complex magnetic structures and for three-dimensional, real-space mapping of magnetic fields.

Mean-field dynamo action in renovating shearing flows.

PubMed

Kolekar, Sanved; Subramanian, Kandaswamy; Sridhar, S

2012-08-01

We study mean-field dynamo action in renovating flows with finite and nonzero correlation time (τ) in the presence of shear. Previous results obtained when shear was absent are generalized to the case with shear. The question of whether the mean magnetic field can grow in the presence of shear and nonhelical turbulence, as seen in numerical simulations, is examined. We show in a general manner that, if the motions are strictly nonhelical, then such mean-field dynamo action is not possible. This result is not limited to low (fluid or magnetic) Reynolds numbers nor does it use any closure approximation; it only assumes that the flow renovates itself after each time interval τ. Specifying to a particular form of the renovating flow with helicity, we recover the standard dispersion relation of the α(2)Ω dynamo, in the small τ or large wavelength limit. Thus mean fields grow even in the presence of rapidly growing fluctuations, surprisingly, in a manner predicted by the standard quasilinear closure, even though such a closure is not strictly justified. Our work also suggests the possibility of obtaining mean-field dynamo growth in the presence of helicity fluctuations, although having a coherent helicity will be more efficient.

An energy-harvesting power supply for underwater bridge scour monitoring sensors

NASA Astrophysics Data System (ADS)

Wang, Yuli; Li, Yingjie; He, Longzhuang; Shamsi, Pourya; Zheng, Yahong R.

2018-03-01

The natural force of scouring has become one of the most critical risk endangering the endurance of bridges, thus leading to the necessity of deploying underwater monitoring sensors to actively detect potential scour holes under bridges. Due to the difficulty in re-charging batteries for underwater sensors, super capacitors with energy harvesting (EH) means are exploited to prolong the sustainability of underwater sensors. In this paper, an energy harvesting power supply based on a helical turbine is proposed to power underwater monitoring sensors. A small helical turbine is designed to convert water flow energy to electrical energy with favorable environmental robustness. A 3-inch diameter, 2.5-inch length and 3-bladed helical turbine was designed with two types of waterproof coupling with the sensor housing. Both designs were prototyped and tested under different flow conditions and we get valid voltage around 0.91 V which is enough to power monitoring sensor. The alternating current (AC) electrical energy generated by the helical turbine is then rectified and boosted to drive a DC charger for efficiently charging one super capacitor. The charging circuit was designed, prototyped and tested thoroughly with the helical turbine harvester. The results were promising, that the overall power supply can power an underwater sensor node with wireless transceivers for long-term operations

Performance of Upgraded Cooling System for Lhd Helical Coils

NASA Astrophysics Data System (ADS)

Hamaguchi, S.; Imagawa, S.; Obana, T.; Yanagi, N.; Moriuchi, S.; Sekiguchi, H.; Oba, K.; Mito, T.; Motojima, O.; Okamura, T.; Semba, T.; Yoshinaga, S.; Wakisaka, H.

2008-03-01

Helical coils of the Large Helical Device (LHD) are large scale superconducting magnets for heliotron plasma experiments. The helical coils had been cooled by saturated helium at 4.4 K, 120 kPa until 2005. An upgrade of the cooling system was carried out in 2006 in order to improve the cryogenic stability of the helical coils and then it has been possible to supply the coils with subcooled helium at 3.2 K, 120 kPa. A designed mass flow of the supplied subcooled helium is 50 g/s. The subcooled helium is generated at a heat exchanger in a saturated helium bath. A series of two centrifugal cold compressors with gas foil bearing is utilized to lower the helium pressure in the bath. The supplied helium temperature is regulated by rotational speed of the cold compressors and power of a heater in the bath. The mass flow of the supplied helium is also controlled manually by a supply valve and its surplus is evaporated by ten heaters at the outlet above the coils. In the present study, the performance of the cooling system has been investigated and a stable operating method has also developed. As the result, it was confirmed that the performance of the upgraded cooling system satisfies the requirements.

Non-linearity of the collagen triple helix in solution and implications for collagen function.

PubMed

Walker, Kenneth T; Nan, Ruodan; Wright, David W; Gor, Jayesh; Bishop, Anthony C; Makhatadze, George I; Brodsky, Barbara; Perkins, Stephen J

2017-06-16

Collagen adopts a characteristic supercoiled triple helical conformation which requires a repeating (Xaa-Yaa-Gly) n sequence. Despite the abundance of collagen, a combined experimental and atomistic modelling approach has not so far quantitated the degree of flexibility seen experimentally in the solution structures of collagen triple helices. To address this question, we report an experimental study on the flexibility of varying lengths of collagen triple helical peptides, composed of six, eight, ten and twelve repeats of the most stable Pro-Hyp-Gly (POG) units. In addition, one unblocked peptide, (POG) 10unblocked , was compared with the blocked (POG) 10 as a control for the significance of end effects. Complementary analytical ultracentrifugation and synchrotron small angle X-ray scattering data showed that the conformations of the longer triple helical peptides were not well explained by a linear structure derived from crystallography. To interpret these data, molecular dynamics simulations were used to generate 50 000 physically realistic collagen structures for each of the helices. These structures were fitted against their respective scattering data to reveal the best fitting structures from this large ensemble of possible helix structures. This curve fitting confirmed a small degree of non-linearity to exist in these best fit triple helices, with the degree of bending approximated as 4-17° from linearity. Our results open the way for further studies of other collagen triple helices with different sequences and stabilities in order to clarify the role of molecular rigidity and flexibility in collagen extracellular and immune function and disease. © 2017 The Author(s).

Tensile properties of helical auxetic structures: A numerical study

NASA Astrophysics Data System (ADS)

Wright, J. R.; Sloan, M. R.; Evans, K. E.

2010-08-01

This paper discusses a helical auxetic structure which has a diverse range of practical applications. The mechanical properties of the system can be determined by particular combinations of geometry and component material properties; finite element analysis is used to investigate the static behavior of these structures under tension. Modeling criteria are determined and design issues are discussed. A description of the different strain-dependent mechanical phases is provided. It is shown that the stiffnesses of the component fibers and the initial helical wrap angle are critical design parameters, and that strain-dependent changes in cross-section must be taken into consideration: we observe that the structures exhibit nonlinear behavior due to nonzero component Poisson's ratios. Negative Poisson's ratios for the helical structures as low as -5 are shown. While we focus here on the structure as a yarn our findings are, in principle, scaleable.

Peptide crystal simulations reveal hidden dynamics

PubMed Central

Janowski, Pawel A.; Cerutti, David S.; Holton, James; Case, David A.

2013-01-01

Molecular dynamics simulations of biomolecular crystals at atomic resolution have the potential to recover information on dynamics and heterogeneity hidden in the X-ray diffraction data. We present here 9.6 microseconds of dynamics in a small helical peptide crystal with 36 independent copies of the unit cell. The average simulation structure agrees with experiment to within 0.28 Å backbone and 0.42 Å all-atom rmsd; a model refined against the average simulation density agrees with the experimental structure to within 0.20 Å backbone and 0.33 Å all-atom rmsd. The R-factor between the experimental structure factors and those derived from this unrestrained simulation is 23% to 1.0 Å resolution. The B-factors for most heavy atoms agree well with experiment (Pearson correlation of 0.90), but B-factors obtained by refinement against the average simulation density underestimate the coordinate fluctuations in the underlying simulation where the simulation samples alternate conformations. A dynamic flow of water molecules through channels within the crystal lattice is observed, yet the average water density is in remarkable agreement with experiment. A minor population of unit cells is characterized by reduced water content, 310 helical propensity and a gauche(−) side-chain rotamer for one of the valine residues. Careful examination of the experimental data suggests that transitions of the helices are a simulation artifact, although there is indeed evidence for alternate valine conformers and variable water content. This study highlights the potential for crystal simulations to detect dynamics and heterogeneity in experimental diffraction data, as well as to validate computational chemistry methods. PMID:23631449

Decay of helical and nonhelical magnetic knots

NASA Astrophysics Data System (ADS)

Candelaresi, Simon; Brandenburg, Axel

2011-07-01

We present calculations of the relaxation of magnetic field structures that have the shape of particular knots and links. A set of helical magnetic flux configurations is considered, which we call n-foil knots of which the trefoil knot is the most primitive member. We also consider two nonhelical knots; namely, the Borromean rings as well as a single interlocked flux rope that also serves as the logo of the Inter-University Centre for Astronomy and Astrophysics in Pune, India. The field decay characteristics of both configurations is investigated and compared with previous calculations of helical and nonhelical triple-ring configurations. Unlike earlier nonhelical configurations, the present ones cannot trivially be reduced via flux annihilation to a single ring. For the n-foil knots the decay is described by power laws that range form t-2/3 to t-1/3, which can be as slow as the t-1/3 behavior for helical triple-ring structures that were seen in earlier work. The two nonhelical configurations decay like t-1, which is somewhat slower than the previously obtained t-3/2 behavior in the decay of interlocked rings with zero magnetic helicity. We attribute the difference to the creation of local structures that contain magnetic helicity which inhibits the field decay due to the existence of a lower bound imposed by the realizability condition. We show that net magnetic helicity can be produced resistively as a result of a slight imbalance between mutually canceling helical pieces as they are being driven apart. We speculate that higher order topological invariants beyond magnetic helicity may also be responsible for slowing down the decay of the two more complicated nonhelical structures mentioned above.

Chaotic coordinates for the Large Helical Device

NASA Astrophysics Data System (ADS)

Hudson, Stuart; Suzuki, Yasuhiro

2014-10-01

The study of dynamical systems is facilitated by a coordinate framework with coordinate surfaces that coincide with invariant structures of the dynamical flow. For axisymmetric systems, a continuous family of invariant surfaces is guaranteed and straight-fieldline coordinates may be constructed. For non-integrable systems, e.g. stellarators, perturbed tokamaks, this continuous family is broken. Nevertheless, coordinates can still be constructed that simplify the description of the dynamics. The Poincare-Birkhoff theorem, the Aubry-Mather theorem, and the KAM theorem show that there are important structures that are invariant under the perturbed dynamics; namely the periodic orbits, the cantori, and the irrational flux surfaces. Coordinates adapted to these invariant sets, which we call chaotic coordinates, provide substantial advantages. The regular motion becomes straight, and the irregular motion is bounded by, and dissected by, coordinate surfaces that coincide with surfaces of locally-minimal magnetic-fieldline flux. The chaotic edge of the magnetic field, as calculated by HINT2 code, in the Large Helical Device (LHD) is examined, and a coordinate system is constructed so that the flux surfaces are ``straight'' and the islands become ``square.''

A MAGNETOHYDRODYNAMIC MODEL OF THE M87 JET. I. SUPERLUMINAL KNOT EJECTIONS FROM HST-1 AS TRAILS OF QUAD RELATIVISTIC MHD SHOCKS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nakamura, Masanori; Garofalo, David; Meier, David L., E-mail: nakamura@stsci.ed, E-mail: david.a.garofalo@jpl.nasa.go, E-mail: david.l.meier@jpl.nasa.go

2010-10-01

This is the first in a series of papers that introduces a new paradigm for understanding the jet in M87: a collimated relativistic flow in which strong magnetic fields play a dominant dynamical role. Here, we focus on the flow downstream of HST-1-an essentially stationary flaring feature that ejects trails of superluminal components. We propose that these components are quad relativistic magnetohydrodynamic shock fronts (forward/reverse fast and slow modes) in a narrow jet with a helically twisted magnetic structure. And we demonstrate the properties of such shocks with simple one-dimensional numerical simulations. Quasi-periodic ejections of similar component trails may bemore » responsible for the M87 jet substructures observed further downstream on 10{sup 2}-10{sup 3} pc scales. This new paradigm requires the assimilation of some new concepts into the astrophysical jet community, particularly the behavior of slow/fast-mode waves/shocks and of current-driven helical kink instabilities. However, the prospects of these ideas applying to a large number of other jet systems may make this worth the effort.« less

Nonlinear generation of large-scale magnetic fields in forced spherical shell dynamos

DOE Office of Scientific and Technical Information (OSTI.GOV)

Livermore, P. W.; Hughes, D. W.; Tobias, S. M.

2010-03-15

In an earlier paper [P. W. Livermore, D. W. Hughes, and S. M. Tobias, ''The role of helicity and stretching in forced kinematic dynamos in a spherical shell'', Phys. Fluids 19, 057101 (2007)], we considered the kinematic dynamo action resulting from a forced helical flow in a spherical shell. Although mean field electrodynamics suggests that the resulting magnetic field should have a significant mean (axisymmetric) component, we found no evidence for this; the dynamo action was distinctly small scale. Here we extend our investigation into the nonlinear regime in which the magnetic field reacts back on the velocity via themore » Lorentz force. Our main result is somewhat surprising, namely, that nonlinear effects lead to a considerable change in the structure of the magnetic field, its final state having a significant mean component. By investigating the dominant flow-field interactions, we isolate the dynamo mechanism and show schematically how the generation process differs between the kinematic and nonlinear regimes. In addition, we are able to calculate some components of the transport coefficient {alpha} and thus discuss our results within the context of mean field electrodynamics.« less

Internally bridging water molecule in transmembrane alpha-helical kink.

PubMed

Miyano, Masashi; Ago, Hideo; Saino, Hiromichi; Hori, Tetsuya; Ida, Koh

2010-08-01

There are hundreds of membrane protein atomic coordinates in the Protein Data Bank (PDB), and high-resolution structures of better than 2.5 A enable the visualization of a sizable number of amphiphiles (lipid and/or detergent) and bound water molecules as essential parts of the structure. Upon scrutinizing these high-resolution structures, water molecules were found to 'wedge' and stabilize large kink angle (30-40 degrees) in a simple cylindrical model at the transmembrane helical kinks so as to form an inter-helical cavity to accommodate a ligand binding or active site as a crucial structural feature in alpha-helical integral membrane proteins. Furthermore, some of these water molecules are proposed to play a pivotal role of their conformational change to exert their functional regulation. Copyright (c) 2010 Elsevier Ltd. All rights reserved.

Stability of plasma cylinder with current in a helical plasma flow

NASA Astrophysics Data System (ADS)

Leonovich, Anatoly S.; Kozlov, Daniil A.; Zong, Qiugang

2018-04-01

Stability of a plasma cylinder with a current wrapped by a helical plasma flow is studied. Unstable surface modes of magnetohydrodynamic (MHD) oscillations develop at the boundary of the cylinder enwrapped by the plasma flow. Unstable eigenmodes can also develop for which the plasma cylinder is a waveguide. The growth rate of the surface modes is much higher than that for the eigenmodes. It is shown that the asymmetric MHD modes in the plasma cylinder are stable if the velocity of the plasma flow is below a certain threshold. Such a plasma flow velocity threshold is absent for the symmetric modes. They are unstable in any arbitrarily slow plasma flows. For all surface modes there is an upper threshold for the flow velocity above which they are stable. The helicity index of the flow around the plasma cylinder significantly affects both the Mach number dependence of the surface wave growth rate and the velocity threshold values. The higher the index, the lower the upper threshold of the velocity jump above which the surface waves become stable. Calculations have been carried out for the growth rates of unstable oscillations in an equilibrium plasma cylinder with current serving as a model of the low-latitude boundary layer (LLBL) of the Earth's magnetic tail. A tangential discontinuity model is used to simulate the geomagnetic tail boundary. It is shown that the magnetopause in the geotail LLBL is unstable to a surface wave (having the highest growth rate) in low- and medium-speed solar wind flows, but becomes stable to this wave in high-speed flows. However, it can remain weakly unstable to the radiative modes of MHD oscillations.

Helical Structure Determines Different Susceptibilities of dsDNA, dsRNA, and tsDNA to Counterion-Induced Condensation

PubMed Central

Kornyshev, Alexei A.; Leikin, Sergey

2013-01-01

Recent studies of counterion-induced condensation of nucleic acid helices into aggregates produced several puzzling observations. For instance, trivalent cobalt hexamine ions condensed double-stranded (ds) DNA oligomers but not their more highly charged dsRNA counterparts. Divalent alkaline earth metal ions condensed triple-stranded (ts) DNA oligomers but not dsDNA. Here we show that these counterintuitive experimental results can be rationalized within the electrostatic zipper model of interactions between molecules with helical charge motifs. We report statistical mechanical calculations that reveal dramatic and nontrivial interplay between the effects of helical structure and thermal fluctuations on electrostatic interaction between oligomeric nucleic acids. Combining predictions for oligomeric and much longer helices, we also interpret recent experimental studies of the role of counterion charge, structure, and chemistry. We argue that an electrostatic zipper attraction might be a major or even dominant force in nucleic acid condensation. PMID:23663846

Helicity transformation under the collision and merging of two magnetic flux ropes

NASA Astrophysics Data System (ADS)

DeHaas, Timothy; Gekelman, Walter

2017-07-01

Magnetic helicity has become a useful tool in the analysis of astrophysical plasmas. Its conservation in the magnetohydrodynamic limit (and other fluid approaches) constrains the global behavior of large plasma structures. One such astrophysical structure is a magnetic flux rope: a tube-like, current-carrying plasma embedded in an external magnetic field. Bundles of these ropes are commonly observed in the near-earth environment and solar atmosphere. In this well-diagnosed experiment (three-dimensional measurements of ne, Te, Vp, B, J, E, and uflow), two magnetic flux ropes are generated in the Large Plasma Device at UCLA. These ropes are driven kink-unstable to trigger complex motion. As they interact, helicity conservation is examined in regions of reconnection. We examine (1) the transport of helicity and (2) the dissipation of the helicity. As the ropes move and the topology of the field lines diverge, a quasi-separatrix layer (QSL) is formed. As the QSL forms, magnetic helicity is dissipated within this region. At the same time, there is an influx of canonical helicity into the region such that the temporal derivative of magnetic helicity is zero.

Right-Handed Helical Foldamers Consisting of De Novo d -AApeptides

DOE Office of Scientific and Technical Information (OSTI.GOV)

Teng, Peng; Ma, Ning; Cerrato, Darrell Cole

New types of foldamer scaffolds are formidably challenging to design and synthesize, yet highly desirable as structural mimics of peptides/proteins with a wide repertoire of functions. In particular, the development of peptidomimetic helical foldamers holds promise for new biomaterials, catalysts, and drug molecules. Unnatural l-sulfono-γ-AApeptides were recently developed and shown to have potential applications in both biomedical and material sciences. However, d-sulfono-γ-AApeptides, the enantiomers of l-sulfono-γ-AApeptides, have never been studied due to the lack of high-resolution three-dimensional structures to guide structure-based design. Herein, we report the first synthesis and X-ray crystal structures of a series of 2:1 l-amino acid/d-sulfono-γ-AApeptide hybridmore » foldamers, and elucidate their folded conformation at the atomic level. Single-crystal X-ray crystallography indicates that this class of oligomers folds into well-defined right-handed helices with unique helical parameters. The helical structures were consistent with data obtained from solution 2D NMR, CD studies, and molecular dynamics simulations. Our findings are expected to inspire the structure-based design of this type of unique folding biopolymers for biomaterials and biomedical applications.« less

Deceleration of arginine kinase refolding by induced helical structures.

PubMed

Li, Hai-Long; Zhou, Sheng-Mei; Park, Daeui; Jeong, Hyoung Oh; Chung, Hae Young; Yang, Jun-Mo; Meng, Fan-Guo; Hu, Wei-Jiang

2012-04-01

Arginine kinase (AK) is a key metabolic enzyme for keeping energy balance in invertebrates. Therefore, regulation of the enzymatic activity and the folding studies of AK from the various invertebrates have been the focus of investigation. We studied the effects of helical structures by using hexafluoroisopropanol (HFIP) on AK folding. Folding kinetic studies showed that the folding rates of the urea-denatured AKs were significantly decelerated after being induced in various concentrations of HFIP. AK lost its activity completely at concentrations greater than 60%. The results indicated that the HFIP-induced helical structures in the denatured state play a negative role in protein folding, and the helical structures induced in 5% (v/v) HFIP act as the most effective barrier against AK taking its native structure. The computational docking simulations (binding energies for -2.19 kcal/mol for AutoDock4.2 and -20.47 kcal/mol for Dock6.3) suggested that HFIP interacts with the several important residues that are predicted by both programs. The excessively pre-organized helical structures not only hampered the folding process, but also ultimately brought about changes in the three-dimensional conformation and biological function of AK.

Thrust Augmented Nozzle for a Hybrid Rocket with a Helical Fuel Port

NASA Astrophysics Data System (ADS)

Marshall, Joel H.

A thrust augmented nozzle for hybrid rocket systems is investigated. The design lever-ages 3-D additive manufacturing to embed a helical fuel port into the thrust chamber of a hybrid rocket burning gaseous oxygen and ABS plastic as propellants. The helical port significantly increases how quickly the fuel burns, resulting in a fuel-rich exhaust exiting the nozzle. When a secondary gaseous oxygen flow is injected into the nozzle downstream of the throat, all of the remaining unburned fuel in the plume spontaneously ignites. This secondary reaction produces additional high pressure gases that are captured by the nozzle and significantly increases the motor's performance. Secondary injection and combustion allows a high expansion ratio (area of the nozzle exit divided by area of the throat) to be effective at low altitudes where there would normally be significantly flow separation and possibly an embedded shock wave due. The result is a 15 percent increase in produced thrust level with no loss in engine efficiency due to secondary injection. Core flow efficiency was increased significantly. Control tests performed using cylindrical fuel ports with secondary injection, and helical fuel ports without secondary injection did not exhibit this performance increase. Clearly, both the fuel-rich plume and secondary injection are essential features allowing the hybrid thrust augmentation to occur. Techniques for better design optimization are discussed.

Studies on convective heat transfer through helical coils

NASA Astrophysics Data System (ADS)

Pawar, S. S.; Sunnapwar, Vivek K.

2013-12-01

An experimental investigation on steady state convection heat transfer from vertical helical coiled tubes in water was performed for laminar flow regime. Three coils with curvature ratios as 0.0757, 0.064, 0.055 and range of Prandtl number from 3.81 to 4.8, Reynolds number from 3,166 to 9,658 were considered in this work. The heat transfer data were generated from 30 experiments conducted at constant water bath temperature (60 °C) for different cold water flow rates in helical coils. For the first time, an innovative approach of correlating Nusselt number with ‘M’ number is proposed which is not available in the literature and the developed correlations are found to be in good agreement with the work of earlier researchers. Thus, dimensionless number ‘M’ was found to be significant to characterize the hydrodynamics of fluid flow and heat transfer correlations in helical coils. Several other correlations based on experimental data are developed. To cover wide range of industrial applications, suitable generalized correlations based on extended parameters beyond the range of present experimental work are also developed. All these correlations are developed by using least-squares power law fit and multiple-regression analysis of MATLAB software. Correlations so developed were compared with published correlations and were found to be in good agreement. Comparison of heat transfer coefficients, friction factor and Nusselt number for different geometrical conditions is presented in this paper.

Dynamics of Single Flux Rope in the Reconnection Scaling Experiment

NASA Astrophysics Data System (ADS)

Feng, Y.; Sears, J.; Intrator, T.; Weber, T.; Swan, H.; Dunn, J. P.; Gao, K.; Chapdelaine, L.

2013-12-01

A magnetic flux tube threaded by current is a flux rope with helically twisted field lines. In the Reconnection Scaling Experiment (RSX) we use a plasma gun to generate a single flux rope with a choice of axial boundary conditions. If this flux rope is driven hard enough, i.e., when J●B /B2 is larger than the kink instability threshold, we measure a helically distorted kinked structure. Rather than exploding in an Alfvén time, this kink appears to saturate to a steady amplitude, helical, gyrating flux rope, which persists as long as the plasma gun sources the current. To understand it, we have experimentally measured three-dimensional (3D) profiles of various quantities of this flux rope. These quantities include magnetic field B, plasma density n and potential φ, ion flow velocity vi, so that current density J, electron flow velocity ve and electron pressure Pe can also be derived. Consequently we can analyze the single flux rope dynamics systematically in 3D. Besides gyrating (writhe), we also find the flux rope has a spin (twist) center, around which the J×B - ▽Pe ≠ 0 suggesting that there should be other forces for the radial balance. We also find that there is a reverse current moving around with the flux rope at some locations, i.e. there are local induced currents that are not at all apparent from measurements outside the 3D volume. Work supported by LANL-DOE, DOE Fusion Energy Sciences DE-AC52-06NA25396, NASA Geospace NNHIOA044I Basic, CMSO, SULI, NUF.

Mutational Analysis of the Stability of the H2A and H2B Histone Monomers

PubMed Central

Stump, Matthew R.; Gloss, Lisa M.

2008-01-01

The eukaryotic histone heterodimer H2A-H2B folds through an obligatory dimeric intermediate that forms in a nearly diffusion-limited association reaction in the stopped-flow dead time. It is unclear whether there is partial folding of the isolated monomers before association. To address the possible contributions of structure in the monomers to the rapid association, we characterized H2A and H2B monomers in the absence of their heterodimeric partner. By far-UV circular dichroism, the H2A and H2B monomers are 15% and 31% helical, respectively—significantly less than observed in X-ray crystal structures. Acrylamide quenching of the intrinsic Tyr fluorescence was indicative of tertiary structure. The H2A and H2B monomers exhibit free energies of unfolding of 2.5 and 2.9 kcal mol−1, respectively; at 10 μM, the sum of the stability of the monomers is ~60% of the stability of the native dimer. The helical content, stability and m values indicate that H2B has a more stable, compact structure than H2A. The monomer m values are larger than expected for the extended histone fold motif, suggesting that the monomers adopt an overly-collapsed structure. Stopped-flow refolding—initiated from urea-denatured monomers or the partially folded monomers populated at low denaturant concentrations—yielded essentially identical rates, indicating that monomer folding is productive in the rapid association and folding of the heterodimer. A series of Ala and Gly mutations were introduced into H2A and H2B to probe the importance of helix propensity on the structure and stability of the monomers. The mutational studies show that the central α-helix of the histone fold, which makes extensive inter-monomer contacts, is structured in H2B but only partially folded in H2A. PMID:18976667

INVESTIGATION OF HELICITY AND ENERGY FLUX TRANSPORT IN THREE EMERGING SOLAR ACTIVE REGIONS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vemareddy, P., E-mail: vemareddy@iiap.res.in

We report the results of an investigation of helicity and energy flux transport from three emerging solar active regions (ARs). Using time sequence vector magnetic field observations obtained from the Helioseismic Magnetic Imager, the velocity field of plasma flows is derived by the differential affine velocity estimator for vector magnetograms. In three cases, the magnetic fluxes evolve to pump net positive, negative, and mixed-sign helicity flux into the corona. The coronal helicity flux is dominantly coming from the shear term that is related to horizontal flux motions, whereas energy flux is dominantly contributed by the emergence term. The shear helicity fluxmore » has a phase delay of 5–14 hr with respect to absolute magnetic flux. The nonlinear curve of coronal energy versus relative helicity identifies the configuration of coronal magnetic fields, which is approximated by a fit of linear force-free fields. The nature of coronal helicity related to the particular pattern of evolving magnetic fluxes at the photosphere has implications for the generation mechanism of two kinds of observed activity in the ARs.« less

The L49F mutation in alpha erythroid spectrin induces local disorder in the tetramer association region: Fluorescence and molecular dynamics studies of free and bound alpha spectrin

PubMed Central

Song, Yuanli; Pipalia, Nina H; Fung, L W-M

2009-01-01

The bundling of the N-terminal, partial domain helix (Helix C′) of human erythroid α-spectrin (αI) with the C-terminal, partial domain helices (Helices A′ and B′) of erythroid β-spectrin (βI) to give a spectrin pseudo structural domain (triple helical bundle A′B′C′) has long been recognized as a crucial step in forming functional spectrin tetramers in erythrocytes. We have used apparent polarity and Stern–Volmer quenching constants of Helix C′ of αI bound to Helices A′ and B′ of βI, along with previous NMR and EPR results, to propose a model for the triple helical bundle. This model was used as the input structure for molecular dynamics simulations for both wild type (WT) and αI mutant L49F. The simulation output structures show a stable helical bundle for WT, but not for L49F. In WT, four critical interactions were identified: two hydrophobic clusters and two salt bridges. However, in L49F, the region downstream of Helix C′ was unable to assume a helical conformation and one critical hydrophobic cluster was disrupted. Other molecular interactions critical to the WT helical bundle were also weakened in L49F, possibly leading to the lower tetramer levels observed in patients with this mutation-induced blood disorder. PMID:19593814

Formation of Helically Structured Chitin/CaCO3 Hybrids through an Approach Inspired by the Biomineralization Processes of Crustacean Cuticles.

PubMed

Matsumura, Shunichi; Kajiyama, Satoshi; Nishimura, Tatsuya; Kato, Takashi

2015-10-01

Chitin/CaCO3 hybrids with helical structures are formed through a biomineralization-inspired crystallization process under ambient conditions. Liquid-crystalline chitin whiskers are used as helically ordered templates. The liquid-crystalline structures are stabilized by acidic polymer networks which interact with the chitin templates. The crystallization of CaCO3 is conducted by soaking the templates in the colloidal suspension of amorphous CaCO3 (ACC) at room temperature. At the initial stage of crystallization, ACC particles are introduced inside the templates, and they crystallize to CaCO3 nanocrystals. The acidic polymer networks induce CaCO3 crystallization. The characterization of the resultant hybrids reveals that they possess helical order and homogeneous hybrid structures of chitin and CaCO3 , which resemble the structure and composition of the exoskeleton of crustaceans. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The helical structure of DNA facilitates binding

NASA Astrophysics Data System (ADS)

Berg, Otto G.; Mahmutovic, Anel; Marklund, Emil; Elf, Johan

2016-09-01

The helical structure of DNA imposes constraints on the rate of diffusion-limited protein binding. Here we solve the reaction-diffusion equations for DNA-like geometries and extend with simulations when necessary. We find that the helical structure can make binding to the DNA more than twice as fast compared to a case where DNA would be reactive only along one side. We also find that this rate advantage remains when the contributions from steric constraints and rotational diffusion of the DNA-binding protein are included. Furthermore, we find that the association rate is insensitive to changes in the steric constraints on the DNA in the helix geometry, while it is much more dependent on the steric constraints on the DNA-binding protein. We conclude that the helical structure of DNA facilitates the nonspecific binding of transcription factors and structural DNA-binding proteins in general.

3D nanomolding and fluid mixing in micromixers with micro-patterned microchannel walls

NASA Astrophysics Data System (ADS)

Farshchian, Bahador; Amirsadeghi, Alborz; Choi, Junseo; Park, Daniel S.; Kim, Namwon; Park, Sunggook

2017-03-01

Microfluidic devices where the microchannel walls were decorated with micro and nanostructures were fabricated using 3D nanomolding. Using 3D molded microfluidic devices with microchannel walls decorated with microscale gratings, the fluid mixing behavior was investigated through experiments and numerical simulation. The use of microscale gratings in the micromixer was predicated by the fact that large obstacles in a microchannel enhances the mixing performance. Slanted ratchet gratings on the channel walls resulted in a helical flow along the microchannel, thus increasing the interfacial area between fluids and cutting down the diffusion length. Increasing the number of walls decorated with continuous ratchet gratings intensified the strength of the helical flow, enhancing mixing further. When ratchet gratings on the surface of the top cover plate were aligned in a direction to break the continuity of gratings from the other three walls, a stack of two helical flows was formed one above each other. This work concludes that the 3D nanomolding process can be a cost-effective tool for scaling-up the fabrication of microfluidic mixers with improved mixing efficiencies.[Figure not available: see fulltext.

Effect of Torsion on the Friction Factor of Helical Pipe Flow

NASA Astrophysics Data System (ADS)

Kumer Datta, Anup; Yanase, Shinichiro; Hayamizu, Yasutaka; Kouchi, Toshinori; Nagata, Yasunori; Yamamoto, Kyoji

2017-06-01

Three-dimensional direct numerical simulations of a viscous incompressible fluid flow through a helical pipe with a circular cross section were conducted for three Reynolds numbers, Re (= 80, 300, and 1000), and two nondimensional curvatures, δ (= 0.1 and 0.05), over a wide range of torsion parameters, β (= nondimensional torsion/√{2δ } ), from 0.02 to 2.8. Well-developed axially invariant regions were obtained where the friction factors were calculated, in good agreement with the experimental data obtained by Yamamoto et al. [https://doi.org/10.1016/0169-5983(95)00022-6, Fluid Dyn. Res. 16, 237 (1995)]. It was found that the friction factor sharply increases as β increases from zero, then decreases after taking a maximum, and finally slowly approaches that of a straight pipe when β tends to infinity. It is interesting that a peak of the friction factor exists in the region 0.2 ≤ β ≤ 0.3 for all the Reynolds numbers and curvatures studied in the present paper, which manifests the importance of the torsion parameter in helical pipe flow.

Controllable rotational inversion in nanostructures with dual chirality.

PubMed

Dai, Lu; Zhu, Ka-Di; Shen, Wenzhong; Huang, Xiaojiang; Zhang, Li; Goriely, Alain

2018-04-05

Chiral structures play an important role in natural sciences due to their great variety and potential applications. A perversion connecting two helices with opposite chirality creates a dual-chirality helical structure. In this paper, we develop a novel model to explore quantitatively the mechanical behavior of normal, binormal and transversely isotropic helical structures with dual chirality and apply these ideas to known nanostructures. It is found that both direction and amplitude of rotation can be finely controlled by designing the cross-sectional shape. A peculiar rotational inversion of overwinding followed by unwinding, observed in some gourd and cucumber tendril perversions, not only exists in transversely isotropic dual-chirality helical nanobelts, but also in the binormal/normal ones when the cross-sectional aspect ratio is close to 1. Beyond this rotational inversion region, the binormal and normal dual-chirality helical nanobelts exhibit a fixed directional rotation of unwinding and overwinding, respectively. Moreover, in the binormal case, the rotation of these helical nanobelts is nearly linear, which is promising as a possible design for linear-to-rotary motion converters. The present work suggests new designs for nanoscale devices.

Aperiodic pressure pulsation under non optimal hydraulic turbine regimes at low swirl number

NASA Astrophysics Data System (ADS)

Skripkin, S. G.; Tsoy, M. A.; Kuibin, P. A.; Shtork, S. I.

2017-09-01

Off-design operating conditions of hydraulic turbines is hindered by pressure fluctuations in the draft tube of the turbine. A precessing helical vortex rope develops, which imperils the mechanical structure and limits the operation flexibility of hydropower station. Understanding of the underlying instabilities of precessing vortex rope at low swirl number is incomplete. In this paper flow regimes with different residual swirl is analysed, particular attention is paid to the regime with a small swirl parameter. Study defines upper and low boundaries of regime where aperiodic pressure surge is observed. Flow field at the runner exit is investigated by Laser Doppler Velocimetry and high-speed visualizations, which are complemented draft tube wall pressure measurements.

Common and divergent structural features of a series of corticotropin releasing factor-related peptides.

PubMed

Grace, Christy Rani R; Perrin, Marilyn H; Cantle, Jeffrey P; Vale, Wylie W; Rivier, Jean E; Riek, Roland

2007-12-26

Members of the corticoliberin family include the corticotropin releasing factors (CRFs), sauvagine, the urotensins, and urocortin 1 (Ucn1), which bind to both the CRF receptors CRF-R1 and CRF-R2, and the urocortins 2 (Ucn2) and 3 (Ucn3), which are selective agonists of CRF-R2. Structure activity relationship studies led to several potent and long-acting analogues with selective binding to either one of the receptors. NMR structures of six ligands of this family (the antagonists astressin B and astressin2-B, the agonists stressin1, and the natural ligands human Ucn1, Ucn2, and Ucn3) were determined in DMSO. These six peptides show differences in binding affinities, receptor-selectivity, and NMR structure. Overall, their backbones are alpha-helical, with a small kink or a turn around residues 25-27, resulting in a helix-loop-helix motif. The C-terminal helices are of amphipathic nature, whereas the N-terminal helices vary in their amphipathicity. The C-terminal helices thereby assume a conformation very similar to that of astressin bound to the ECD1 of CRF-R2 recently reported by our group.1 On the basis of an analysis of the observed 3D structures and relative potencies of [Ala]-substituted analogues, it is proposed that both helices could play a crucial role in receptor binding and selectivity. In conclusion, the C-terminal helices may interact along their hydrophobic faces with the ECD1, whereas the entire N-terminal helical surface may be involved in receptor activation. On the basis of the common and divergent features observed in the 3D structures of these ligands, multiple binding models are proposed that may explain their plurality of actions.

Extended MHD Modeling of Tearing-Driven Magnetic Relaxation

NASA Astrophysics Data System (ADS)

Sauppe, Joshua

2016-10-01

Driven plasma pinch configurations are characterized by the gradual accumulation and episodic release of free energy in discrete relaxation events. The hallmark of this relaxation in a reversed-field pinch (RFP) plasma is flattening of the parallel current density profile effected by a fluctuation-induced dynamo emf in Ohm's law. Nonlinear two-fluid modeling of macroscopic RFP dynamics has shown appreciable coupling of magnetic relaxation and the evolution of plasma flow. Accurate modeling of RFP dynamics requires the Hall effect in Ohm's law as well as first order ion finite Larmor radius (FLR) effects, represented by the Braginskii ion gyroviscous stress tensor. New results find that the Hall dynamo effect from < J × B > / ne can counter the MHD effect from - < V × B > in some of the relaxation events. The MHD effect dominates these events and relaxes the current profile toward the Taylor state, but the opposition of the two dynamos generates plasma flow in the direction of equilibrium current density, consistent with experimental measurements. Detailed experimental measurements of the MHD and Hall emf terms are compared to these extended MHD predictions. Tracking the evolution of magnetic energy, helicity, and hybrid helicity during relaxation identifies the most important contributions in single-fluid and two-fluid models. Magnetic helicity is well conserved relative to the magnetic energy during relaxation. The hybrid helicity is dominated by magnetic helicity in realistic low-beta 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 through ion FLR effects, which have not been included in contemporary relaxation theories. The kinetic energy driven by relaxation in the computations is dominated by velocity components perpendicular to the magnetic field, an effect that had not been predicted. Work performed at University of Wisconsin-Madison. LA-UR-16-24727.

Ultrasound SIV measurement of helical valvular flow behind the great saphenous vein

NASA Astrophysics Data System (ADS)

Park, Jun Hong; Kim, Jeong Ju; Lee, Sang Joon; Yeom, Eunseop; Experimental Fluid Mechanics Laboratory Team; LaboratoryMicrothermal; Microfluidic Measurements Collaboration

2017-11-01

Dysfunction of venous valve and induced secondary abnormal flow are closely associated with venous diseases. Thus, detailed analysis of venous valvular flow is invaluable from biological and medical perspectives. However, most previous studies on venous perivalvular flows were based on qualitative analyses. On the contrary, quantitative analysis on the perivalvular flows has not been fully understood yet. In this study, 3D valvular flows under in vitro and in vivo conditions were experimentally investigated using ultrasound speckle image velocimetry (SIV) for analyzing their flow characteristics. The results for in vitro model obtained by the SIV technique were compared with those derived by numerical simulation and color Doppler method to validate its measurement accuracy. Then blood flow in the human great saphenous vein was measured using the SIV with respect to the dimensionless index, helical intensity. The results obtained by the SIV method are well matched well with those obtained by the numerical simulation and color Doppler method. The hemodynamic characteristics of 3D valvular flows measured by the validated SIV method would be helpful in diagnosis of valve-related venous diseases. None.

Evaluation of Aortic Blood Flow and Wall Shear Stress in Aortic Stenosis and Its Association With Left Ventricular Remodeling.

PubMed

von Knobelsdorff-Brenkenhoff, Florian; Karunaharamoorthy, Achudhan; Trauzeddel, Ralf Felix; Barker, Alex J; Blaszczyk, Edyta; Markl, Michael; Schulz-Menger, Jeanette

2016-03-01

Aortic stenosis (AS) leads to variable stress for the left ventricle (LV) and consequently a broad range of LV remodeling. The aim of this study was to describe blood flow patterns in the ascending aorta of patients with AS and determine their association with remodeling. Thirty-seven patients with AS (14 mild, 8 moderate, 15 severe; age, 63±13 years) and 37 healthy controls (age, 60±10 years) underwent 4-dimensional-flow magnetic resonance imaging. Helical and vortical flow formations and flow eccentricity were assessed in the ascending aorta. Normalized flow displacement from the vessel center and peak systolic wall shear stress in the ascending aorta were quantified. LV remodeling was assessed based on LV mass index and the ratio of LV mass:end-diastolic volume (relative wall mass). Marked helical and vortical flow formation and eccentricity were more prevalent in patients with AS than in healthy subjects, and patients with AS exhibited an asymmetrical and elevated distribution of peak systolic wall shear stress. In AS, aortic orifice area was strongly negatively associated with vortical flow formation (P=0.0274), eccentricity (P=0.0070), and flow displacement (P=0.0021). Bicuspid aortic valve was associated with more intense helical (P=0.0098) and vortical flow formation (P=0.0536), higher flow displacement (P=0.11), and higher peak systolic wall shear stress (P=0.0926). LV mass index and relative wall mass were significantly associated with aortic orifice area (P=0.0611, P=0.0058) and flow displacement (P=0.0058, P=0.0283). In this pilot study, AS leads to abnormal blood flow pattern and peak systolic wall shear stress in the ascending aorta. In addition to aortic orifice area, normalized flow displacement was significantly associated with LV remodeling. © 2016 American Heart Association, Inc.

Propulsion by a helical flagellum in a capillary tube

NASA Astrophysics Data System (ADS)

Liu, Bin; Breuer, Kenneth S.; Powers, Thomas R.

2014-01-01

We study the microscale propulsion of a rotating helical filament confined by a cylindrical tube, using a boundary-element method for Stokes flow that accounts for helical symmetry. We determine the effect of confinement on swimming speed and power consumption. Except for a small range of tube radii at the tightest confinements, the swimming speed at fixed rotation rate increases monotonically as the confinement becomes tighter. At fixed torque, the swimming speed and power consumption depend only on the geometry of the filament centerline, except at the smallest pitch angles for which the filament thickness plays a role. We find that the "normal" geometry of Escherichia coli flagella is optimized for swimming efficiency, independent of the degree of confinement. The efficiency peaks when the arc length of the helix within a pitch matches the circumference of the cylindrical wall. We also show that a swimming helix in a tube induces a net flow of fluid along the tube.

alpha-helical structural elements within the voltage-sensing domains of a K(+) channel.

PubMed

Li-Smerin, Y; Hackos, D H; Swartz, K J

2000-01-01

Voltage-gated K(+) channels are tetramers with each subunit containing six (S1-S6) putative membrane spanning segments. The fifth through sixth transmembrane segments (S5-S6) from each of four subunits assemble to form a central pore domain. A growing body of evidence suggests that the first four segments (S1-S4) comprise a domain-like voltage-sensing structure. While the topology of this region is reasonably well defined, the secondary and tertiary structures of these transmembrane segments are not. To explore the secondary structure of the voltage-sensing domains, we used alanine-scanning mutagenesis through the region encompassing the first four transmembrane segments in the drk1 voltage-gated K(+) channel. We examined the mutation-induced perturbation in gating free energy for periodicity characteristic of alpha-helices. Our results are consistent with at least portions of S1, S2, S3, and S4 adopting alpha-helical secondary structure. In addition, both the S1-S2 and S3-S4 linkers exhibited substantial helical character. The distribution of gating perturbations for S1 and S2 suggest that these two helices interact primarily with two environments. In contrast, the distribution of perturbations for S3 and S4 were more complex, suggesting that the latter two helices make more extensive protein contacts, possibly interfacing directly with the shell of the pore domain.

Enhanced heat transfer and frictional losses in heat exchanger tube with modified helical coiled inserts

NASA Astrophysics Data System (ADS)

Verma, Aditya; Kumar, Manoj; Patil, Anil Kumar

2018-04-01

The application of compact heat exchangers in any thermal system improves overall performance with a considerable reduction in size and weight. Inserts of different geometrical features have been used as turbulence promoting devices to increase the heat transfer rates. The present study deals with the experimental investigation of heat transfer and fluid flow characteristics of a tubular heat exchanger fitted with modified helical coiled inserts. Experiments have been carried out for a smooth tube without insert, tube fitted with helical coiled inserts, and modified helical coiled inserts. The helical coiled inserts are tested by varying the pitch ratio and wire diameter ratio from 0.5-1.5, and 0.063-0.125, respectively for the Reynolds number range of 1400 to 11,000. Experimental data have also been collected for the modified helical coiled inserts with gradually increasing pitch (GIP) and gradually decreasing pitch (GDP) configurations. The Nusselt number and friction factor values for helical coiled inserts are enhanced in the range of 1.42-2.62, 3.4-27.4, relative to smooth tube, respectively. The modified helical coiled insert showed enhancements in Nusselt number and friction factor values in the range of 1.49-3.14, 11.2-19.9, relative to smooth tube, respectively. The helical coiled and modified helical coiled inserts have thermo-hydraulic performance factor in the range of 0.59-1.29, 0.6-1.39, respectively. The empirical correlations of Nusselt number and friction factor for helical coiled inserts are proposed.

Chiral Organic Cages with a Triple-Stranded Helical Structure Derived from Helicene.

PubMed

Malik, Abaid Ullah; Gan, Fuwei; Shen, Chengshuo; Yu, Na; Wang, Ruibin; Crassous, Jeanne; Shu, Mouhai; Qiu, Huibin

2018-02-28

We report the use of helicene with an intrinsic helical molecular structure to prepare covalent organic cages via imine condensation. The organic cages revealed a [3+2]-type architecture containing a triple-stranded helical structure with three helicene units arranged in a propeller-like fashion with the framework integrally twisted. Such structural chirality was retained upon dissolution in organic solvents, as indicated by a strong diastereotopy effect in proton NMR and unique Cotton effects in circular dichroism spectra. Further study on chiral adsorption showed that the chiral organic cages possess considerable enantioselectivity toward a series of aromatic racemates.

Two-fluid flowing equilibria of spherical torus sustained by coaxial helicity injection

NASA Astrophysics Data System (ADS)

Kanki, Takashi; Steinhauer, Loren; Nagata, Masayoshi

2007-11-01

Two-dimensional equilibria in helicity-driven systems using two-fluid model were previously computed, showing the existence of an ultra-low-q spherical torus (ST) configuration with diamagnetism and higher beta. However, this computation assumed purely toroidal ion flow and uniform density. The purpose of the present study is to apply the two-fluid model to the two-dimensional equilibria of helicity-driven ST with non-uniform density and both toroidal and poloidal flows for each species by means of the nearby-fluids procedure, and to explore their properties. We focus our attention on the equilibria relevant to the HIST device, which are characterized by either driven or decaying λ profiles. The equilibrium for the driven λ profile has a diamagnetic toroidal field, high-β (βt = 32%), and centrally broad density. By contrast, the decaying equilibrium has a paramagnetic toroidal field, low-β (βt = 10%), and centrally peaked density with a steep gradient in the outer edge region. In the driven case, the toroidal ion and electron flows are in the same direction, and two-fluid effects are less important since the ExB drift is dominant. In the decaying case, the toroidal ion and electron flows are opposite in the outer edge region, and two-fluid effects are significant locally in the edge due to the ion diamagnetic drift.

Radial electric field and ion parallel flow in the quasi-symmetric and Mirror configurations of HSX

DOE PAGES

Kumar, S. T. A.; Dobbins, T. J.; Talmadge, J. N.; ...

2018-03-07

In this paper, the radial electric field and the ion mean parallel flow are obtained in the helically symmetric experiment stellarator from toroidal flow measurements of C +6 ion at two locations on a flux surface, using the Pfirsch–Schlüter effect. Results from the standard quasi-helically symmetric magnetic configuration are compared with those from the Mirror configuration where the quasi-symmetry is deliberately degraded using auxiliary coils. For similar injected power, the quasi-symmetric configuration is observed to have significantly lower flows while the experimental observations from the Mirror geometry are in better agreement with neoclassical calculations. Finally, indications are that the radialmore » electric field near the core of the quasi-symmetric configuration may be governed by non-neoclassical processes.« less

Radial electric field and ion parallel flow in the quasi-symmetric and Mirror configurations of HSX

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kumar, S. T. A.; Dobbins, T. J.; Talmadge, J. N.

In this paper, the radial electric field and the ion mean parallel flow are obtained in the helically symmetric experiment stellarator from toroidal flow measurements of C +6 ion at two locations on a flux surface, using the Pfirsch–Schlüter effect. Results from the standard quasi-helically symmetric magnetic configuration are compared with those from the Mirror configuration where the quasi-symmetry is deliberately degraded using auxiliary coils. For similar injected power, the quasi-symmetric configuration is observed to have significantly lower flows while the experimental observations from the Mirror geometry are in better agreement with neoclassical calculations. Finally, indications are that the radialmore » electric field near the core of the quasi-symmetric configuration may be governed by non-neoclassical processes.« less

Experimental and predicted cavitation performance of an 80.6 deg helical inducer in high temperature water

NASA Technical Reports Server (NTRS)

Kovich, G.

1972-01-01

The cavitating performance of a stainless steel 80.6 degree flat-plate helical inducer was investigated in water over a range of liquid temperatures and flow coefficients. A semi-empirical prediction method was used to compare predicted values of required net positive suction head in water with experimental values obtained in water. Good agreement was obtained between predicted and experimental data in water. The required net positive suction head in water decreased with increasing temperature and increased with flow coefficient, similar to that observed for a like inducer in liquid hydrogen.

Role of coherent structures in supersonic impinging jetsa)

NASA Astrophysics Data System (ADS)

Kumar, Rajan; Wiley, Alex; Venkatakrishnan, L.; Alvi, Farrukh

2013-07-01

This paper describes the results of a study examining the flow field and acoustic characteristics of a Mach 1.5 ideally expanded supersonic jet impinging on a flat surface and its control using steady microjets. Emphasis is placed on two conditions of nozzle to plate distances (h/d), of which one corresponds to where the microjet based active flow control is very effective in reducing flow unsteadiness and near-field acoustics and the other has minimal effectiveness. Measurements include unsteady pressures, nearfield acoustics using microphone and particle image velocimetry. The nearfield noise and unsteady pressure spectra at both h/d show discrete high amplitude impinging tones, which in one case (h/d = 4) are significantly reduced with control but in the other case (h/d = 4.5) remain unaffected. The particle image velocimetry measurements, both time-averaged and phase-averaged, were used to better understand the basic characteristics of the impinging jet flow field especially the role of coherent vortical structures in the noise generation and control. The results show that the flow field corresponding to the case of least control effectiveness comprise well defined, coherent, and symmetrical vortical structures and may require higher levels of microjet pressure supply for noise suppression when compared to the flow field more responsive to control (h/d = 4) which shows less organized, competing (symmetrical and helical) instabilities.

Coulomb double helical structure

NASA Astrophysics Data System (ADS)

Kamimura, Tetsuo; Ishihara, Osamu

2012-01-01

Structures of Coulomb clusters formed by dust particles in a plasma are studied by numerical simulation. Our study reveals the presence of various types of self-organized structures of a cluster confined in a prolate spheroidal electrostatic potential. The stable configurations depend on a prolateness parameter for the confining potential as well as on the number of dust particles in a cluster. One-dimensional string, two-dimensional zigzag structure and three-dimensional double helical structure are found as a result of the transition controlled by the prolateness parameter. The formation of stable double helical structures resulted from the transition associated with the instability of angular perturbations on double strings. Analytical perturbation study supports the findings of numerical simulations.

Identifying intrinsically disordered protein regions likely to undergo binding-induced helical transitions.

PubMed

Glover, Karen; Mei, Yang; Sinha, Sangita C

2016-10-01

Many proteins contain intrinsically disordered regions (IDRs) lacking stable secondary and ordered tertiary structure. IDRs are often implicated in macromolecular interactions, and may undergo structural transitions upon binding to interaction partners. However, as binding partners of many protein IDRs are unknown, these structural transitions are difficult to verify and often are poorly understood. In this study we describe a method to identify IDRs that are likely to undergo helical transitions upon binding. This method combines bioinformatics analyses followed by circular dichroism spectroscopy to monitor 2,2,2-trifluoroethanol (TFE)-induced changes in secondary structure content of these IDRs. Our results demonstrate that there is no significant change in the helicity of IDRs that are not predicted to fold upon binding. IDRs that are predicted to fold fall into two groups: one group does not become helical in the presence of TFE and includes examples of IDRs that form β-strands upon binding, while the other group becomes more helical and includes examples that are known to fold into helices upon binding. Therefore, we propose that bioinformatics analyses combined with experimental evaluation using TFE may provide a general method to identify IDRs that undergo binding-induced disorder-to-helix transitions. Copyright © 2016 Elsevier B.V. All rights reserved.

4D Magnetic Resonance Velocimetry in a 3D printed brain aneurysm

NASA Astrophysics Data System (ADS)

Amili, Omid; Schiavazzi, Daniele; Coletti, Filippo

2016-11-01

Cerebral aneurysms are of great clinical importance. It is believed that hemodynamics play a critical role in the development, growth, and rupture of brain arteries with such condition. The flow structure in the aneurysm sac is complex, unsteady, and three-dimensional. Therefore the time-resolved measurement of the three-dimensional three-component velocity field is crucial to predict the clinical outcome. In this study magnetic resonance velocimetry is used to assess the fluid dynamics inside a 3D printed model of a giant intracranial aneurysm. We reach sub-millimeter resolution while resolving sixteen instances within the cardiac cycle. The physiological flow waveform is imposed using an in-house built pump in a flow circuit where the cardiovascular impedance is matched. The flow evolution over time is reconstructed in detail. The complex flow structure is characterized by vortical and helical motions that reside in the aneurysm for most part of the cycle. The 4D pressured distribution is also reconstructed from the velocity field. The present case study was used in a previous CFD challenge, therefore these results may provide useful experimental comparison for simulations performed by other research groups.

Magnetic helicity generation in the frame of Kazantsev model

NASA Astrophysics Data System (ADS)

Yushkov, Egor V.; Lukin, Alexander S.

2017-11-01

Using a magnetic dynamo model, suggested by Kazantsev (J. Exp. Theor. Phys. 1968, vol. 26, p. 1031), we study the small-scale helicity generation in a turbulent electrically conducting fluid. We obtain the asymptotic dependencies of dynamo growth rate and magnetic correlation functions on magnetic Reynolds numbers. Special attention is devoted to the comparison of a longitudinal correlation function and a function of magnetic helicity for various conditions of asymmetric turbulent flows. We compare the analytical solutions on small scales with numerical results, calculated by an iterative algorithm on non-uniform grids. We show that the exponential growth of current helicity is simultaneous with the magnetic energy for Reynolds numbers larger than some critical value and estimate this value for various types of asymmetry.

Measurements of Magnetic Helicity within Two Interacting Flux Ropes

NASA Astrophysics Data System (ADS)

Dehaas, Timothy; Gekelman, Walter

2016-10-01

Magnetic helicity (HM) has become a useful tool in the exploration of astrophysical plasmas. Its conservation in the MHD limit (and even some fluid approaches) constrains the global behavior of large plasma structures. One such astrophysical structure is a magnetic flux rope: a rope-like, current-carrying plasma embedded in an external magnetic field. Bundles of these ropes are commonly observed extending from the solar surface and can be found in the near-earth environment. In this well-diagnosed experiment (3D measurements of ne, Te, Vp, B, J, E, uflow) , two magnetic flux ropes were generated in the Large Plasma Device at UCLA. These ropes were driven kink-unstable, commencing complex motion. As they interact, helicity conservation is broken in regions of reconnection, turbulence, and instabilities. The changes in helicity can be visualized as 1) the transport of helicity (ϕB +E × A) and 2) the dissipation of the helicity (-2EB). Magnetic helicity is observed to have a negative sign and its counterpart, cross helicity, a positive one. These qualities oscillate 8% peak-to-peak. As the ropes move and the topology of the field lines change, a quasi-separatrix layer (QSL) is formed. The volume averaged HM and the largest value of Q both oscillate but not in phase. In addition to magnetic helicity, similar quantities such as self-helicity, mutual-helicity, vorticity, and canonical helicity are derived and will be presented. This work is supported by LANL-UC research Grant and done at the Basic Plasma Science Facility, which is funded by DOE and NSF.

3D nanomolding and fluid mixing in micromixers with micro-patterned microchannel walls.

PubMed

Farshchian, Bahador; Amirsadeghi, Alborz; Choi, Junseo; Park, Daniel S; Kim, Namwon; Park, Sunggook

2017-01-01

Microfluidic devices where the microchannel walls were decorated with micro and nanostructures were fabricated using 3D nanomolding. Using 3D molded microfluidic devices with microchannel walls decorated with microscale gratings, the fluid mixing behavior was investigated through experiments and numerical simulation. The use of microscale gratings in the micromixer was predicated by the fact that large obstacles in a microchannel enhances the mixing performance. Slanted ratchet gratings on the channel walls resulted in a helical flow along the microchannel, thus increasing the interfacial area between fluids and cutting down the diffusion length. Increasing the number of walls decorated with continuous ratchet gratings intensified the strength of the helical flow, enhancing mixing further. When ratchet gratings on the surface of the top cover plate were aligned in a direction to break the continuity of gratings from the other three walls, a stack of two helical flows was formed one above each other. This work concludes that the 3D nanomolding process can be a cost-effective tool for scaling-up the fabrication of microfluidic mixers with improved mixing efficiencies.Graphical abstractIn this paper we show that a micromixer with patterned walls can be fabricated using 3D nanomolding and solvent-assisted bonding to manipulate the flow patterns to improve mixing.

The Role of Magnetic Helicity in Structuring the Solar Corona

NASA Technical Reports Server (NTRS)

Knizhnik, K. J.; Antiochos, S. K.; DeVore, C. R.

2017-01-01

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.

Maintenance of electrostatic stabilization in altered tubulin lateral contacts may facilitate formation of helical filaments in foraminifera.

PubMed

Bassen, David M; Hou, Yubo; Bowser, Samuel S; Banavali, Nilesh K

2016-08-19

Microtubules in foraminiferan protists (forams) can convert into helical filament structures, in which longitudinal intraprotofilament interactions between tubulin heterodimers are thought to be lost, while lateral contacts across protofilaments are still maintained. The coarse geometric features of helical filaments are known through low-resolution negative stain electron microscopy (EM). In this study, geometric restraints derived from these experimental data were used to generate an average atomic-scale helical filament model, which anticipated a modest reorientation in the lateral tubulin heterodimer interface. Restrained molecular dynamics (MD) simulations of the nearest neighbor interactions combined with a Genalized Born implicit solvent model were used to assess the lateral, longitudinal, and seam contacts in 13-3 microtubules and the reoriented lateral contacts in the helical filament model. This electrostatic analysis suggests that the change in the lateral interface in the helical filament does not greatly diminish the lateral electrostatic interaction. After longitudinal dissociation, the 13-3 seam interaction is much weaker than the reoriented lateral interface in the helical filament model, providing a plausible atomic-detail explanation for seam-to-lateral contact transition that enables the transition to a helical filament structure.

Maintenance of electrostatic stabilization in altered tubulin lateral contacts may facilitate formation of helical filaments in foraminifera

NASA Astrophysics Data System (ADS)

Bassen, David M.; Hou, Yubo; Bowser, Samuel S.; Banavali, Nilesh K.

2016-08-01

Microtubules in foraminiferan protists (forams) can convert into helical filament structures, in which longitudinal intraprotofilament interactions between tubulin heterodimers are thought to be lost, while lateral contacts across protofilaments are still maintained. The coarse geometric features of helical filaments are known through low-resolution negative stain electron microscopy (EM). In this study, geometric restraints derived from these experimental data were used to generate an average atomic-scale helical filament model, which anticipated a modest reorientation in the lateral tubulin heterodimer interface. Restrained molecular dynamics (MD) simulations of the nearest neighbor interactions combined with a Genalized Born implicit solvent model were used to assess the lateral, longitudinal, and seam contacts in 13-3 microtubules and the reoriented lateral contacts in the helical filament model. This electrostatic analysis suggests that the change in the lateral interface in the helical filament does not greatly diminish the lateral electrostatic interaction. After longitudinal dissociation, the 13-3 seam interaction is much weaker than the reoriented lateral interface in the helical filament model, providing a plausible atomic-detail explanation for seam-to-lateral contact transition that enables the transition to a helical filament structure.

Self-Assembly of an α-Helical Peptide into a Crystalline Two-Dimensional Nanoporous Framework

DOE Office of Scientific and Technical Information (OSTI.GOV)

Magnotti, Elizabeth L.; Hughes, Spencer A.; Dillard, Rebecca S.

Sequence-specific peptides have been demonstrated to self-assemble into structurally defined nanoscale objects including nanofibers, nanotubes, and nanosheets. The latter structures display significant promise for the construction of hybrid materials for functional devices due to their extended planar geometry. Realization of this objective necessitates the ability to control the structural features of the resultant assemblies through the peptide sequence. The design of a amphiphilic peptide, 3FD-IL, is described that comprises two repeats of a canonical 18 amino acid sequence associated with straight α-helical structures. Peptide 3FD-IL displays 3-fold screw symmetry in a helical conformation and self-assembles into nanosheets based on hexagonalmore » packing of helices. Biophysical evidence from TEM, cryo-TEM, SAXS, AFM, and STEM measurements on the 3FD-IL nanosheets support a structural model based on a honeycomb lattice, in which the length of the peptide determines the thickness of the nanosheet and the packing of helices defines the presence of nanoscale channels that permeate the sheet. The honeycomb structure can be rationalized on the basis of geometrical packing frustration in which the channels occupy defect sites that define a periodic superlattice. In conclusion, the resultant 2D materials may have potential as materials for nanoscale transport and controlled release applications.« less

Self-Assembly of an α-Helical Peptide into a Crystalline Two-Dimensional Nanoporous Framework

DOE PAGES

Magnotti, Elizabeth L.; Hughes, Spencer A.; Dillard, Rebecca S.; ...

2016-11-22

Sequence-specific peptides have been demonstrated to self-assemble into structurally defined nanoscale objects including nanofibers, nanotubes, and nanosheets. The latter structures display significant promise for the construction of hybrid materials for functional devices due to their extended planar geometry. Realization of this objective necessitates the ability to control the structural features of the resultant assemblies through the peptide sequence. The design of a amphiphilic peptide, 3FD-IL, is described that comprises two repeats of a canonical 18 amino acid sequence associated with straight α-helical structures. Peptide 3FD-IL displays 3-fold screw symmetry in a helical conformation and self-assembles into nanosheets based on hexagonalmore » packing of helices. Biophysical evidence from TEM, cryo-TEM, SAXS, AFM, and STEM measurements on the 3FD-IL nanosheets support a structural model based on a honeycomb lattice, in which the length of the peptide determines the thickness of the nanosheet and the packing of helices defines the presence of nanoscale channels that permeate the sheet. The honeycomb structure can be rationalized on the basis of geometrical packing frustration in which the channels occupy defect sites that define a periodic superlattice. In conclusion, the resultant 2D materials may have potential as materials for nanoscale transport and controlled release applications.« less

Role of helicity in triad interactions in three-dimensional turbulence investigated by a new shell model

NASA Astrophysics Data System (ADS)

Rathmann, Nicholas M.; Ditlevsen, Peter D.

2016-09-01

Fully developed homogeneous isotropic turbulence in two dimensions is fundamentally different from that in three dimensions. In two dimensions, the simultaneous inviscid conservation of both kinetic energy and enstrophy within the inertial range of scales leads to a forward cascade of enstrophy and a reverse cascade of energy. In three dimensions, helicity, the integral of the scalar product of velocity and vorticity, is also an inviscid flow invariant along with the energy. Unlike the enstrophy, however, the helicity does not block the forward cascade of energy to small scales. Energy and helicity are conserved not only globally but also within each nonlinear triadic interaction between three plane waves in the spectral form of the Navier-Stokes equation (NSE). By decomposing each plane wave into two helical modes of opposite helicities, each triadic interaction is split into a set of eight helical triadic interactions between helical modes [F. Waleffe, Phys. Fluids A 4, 350 (1992), 10.1063/1.858309]. Recently it was found that a subset of these helical interactions, which render both signs of helicity separately conserved (enstrophy-like), leads to an inverse cascade of (part of) the energy [L. Biferale et al., Phys. Rev. Lett. 108, 164501 (2012), 10.1103/PhysRevLett.108.164501]. Motivated by this finding we introduce a new shell model, obtained from the NSE expressed in the helical basis, allowing the eight helical interactions to be coupled as in the NSE and their relative contributions evaluated as a function of both the net helicity input and triad geometry. By numerically integrating the new model, we find that the intermittency of the energy cascade decreases with the net helicity input. Studying the partitioning of the energy cascade between the eight helical interactions, we find that the decrease in intermittency is related to a shift in the dominating helical interactions when helically forced, two of which exhibit a larger cascade intermittency than the other six interactions. Among the relatively local triad geometries considered here, the partitioning of the energy and helicity cascades between the eight helical interactions shows no sign of change with triad geometry.

An Evolutionarily Conserved Family of Virion Tail Needles Related to Bacteriophage P22 gp26: Correlation between Structural Stability and Length of the -Helical Trimeric Coiled Coil

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bhardwaj, A.; Walker-Kopp, N; Casjens, S

2009-01-01

Bacteriophages of the Podoviridae family use short noncontractile tails to inject their genetic material into Gram-negative bacteria. In phage P22, the tail contains a thin needle, encoded by the phage gene 26, which is essential both for stabilization and for ejection of the packaged viral genome. Bioinformatic analysis of the N-terminal domain of gp26 (residues 1-60) led us to identify a family of genes encoding putative homologues of the tail needle gp26. To validate this idea experimentally and to explore their diversity, we cloned the gp26-like gene from phages HK620, Sf6 and HS1, and characterized these gene products in solution.more » All gp26-like factors contain an elongated {alpha}-helical coiled-coil core consisting of repeating, adjacent trimerization heptads and form trimeric fibers with length ranging between about 240 to 300 {angstrom}. gp26 tail needles display a high level of structural stability in solution, with Tm (temperature of melting) between 85 and 95 C. To determine how the structural stability of these phage fibers correlates with the length of the {alpha}-helical core, we investigated the effect of insertions and deletions in the helical core. In the P22 tail needle, we identified an 85-residue-long helical domain, termed MiCRU (minimal coiled-coil repeat unit), that can be inserted in-frame inside the gp26 helical core, preserving the straight morphology of the fiber. Likewise, we were able to remove three quarters of the helical core of the HS1 tail needle, minimally decreasing the stability of the fiber. We conclude that in the gp26 family of tail needles, structural stability increases nonlinearly with the length of the {alpha}-helical core. Thus, the overall stability of these bacteriophage fibers is not solely dependent on the number of trimerization repeats in the {alpha}-helical core.« less

Triangular prism-shaped β-peptoid helices as unique biomimetic scaffolds

NASA Astrophysics Data System (ADS)

Laursen, Jonas S.; Harris, Pernille; Fristrup, Peter; Olsen, Christian A.

2015-05-01

β-Peptoids are peptidomimetics based on N-alkylated β-aminopropionic acid residues (or N-alkyl-β-alanines). This type of peptide mimic has previously been incorporated in biologically active ligands and has been hypothesized to be able to exhibit foldamer properties. Here we show, for the first time, that β-peptoids can be tuned to fold into stable helical structures. We provide high-resolution X-ray crystal structures of homomeric β-peptoid hexamers, which reveal right-handed helical conformations with exactly three residues per turn and a helical pitch of 9.6-9.8 Å between turns. The presence of folded conformations in solution is supported by circular dichroism spectroscopy showing length- and solvent dependency, and molecular dynamics simulations provide further support for a stabilized helical secondary structure in organic solvent. We thus outline a framework for future design of novel biomimetics that display functional groups with high accuracy in three dimensions, which has potential for development of new functional materials.

Mechanics of tunable helices and geometric frustration in biomimetic seashells

NASA Astrophysics Data System (ADS)

Guo, Qiaohang; Chen, Zi; Li, Wei; Dai, Pinqiang; Ren, Kun; Lin, Junjie; Taber, Larry A.; Chen, Wenzhe

2014-03-01

Helical structures are ubiquitous in nature and engineering, ranging from DNA molecules to plant tendrils, from sea snail shells to nanoribbons. While the helical shapes in natural and engineered systems often exhibit nearly uniform radius and pitch, helical shell structures with changing radius and pitch, such as seashells and some plant tendrils, add to the variety of this family of aesthetic beauty. Here we develop a comprehensive theoretical framework for tunable helical morphologies, and report the first biomimetic seashell-like structure resulting from mechanics of geometric frustration. In previous studies, the total potential energy is everywhere minimized when the system achieves equilibrium. In this work, however, the local energy minimization cannot be realized because of the geometric incompatibility, and hence the whole system deforms into a shape with a global energy minimum whereby the energy in each segment may not necessarily be locally optimized. This novel approach can be applied to develop materials and devices of tunable geometries with a range of applications in nano/biotechnology.

Modeling helical proteins using residual dipolar couplings, sparse long-range distance constraints and a simple residue-based force field

PubMed Central

Eggimann, Becky L.; Vostrikov, Vitaly V.; Veglia, Gianluigi; Siepmann, J. Ilja

2013-01-01

We present a fast and simple protocol to obtain moderate-resolution backbone structures of helical proteins. This approach utilizes a combination of sparse backbone NMR data (residual dipolar couplings and paramagnetic relaxation enhancements) or EPR data with a residue-based force field and Monte Carlo/simulated annealing protocol to explore the folding energy landscape of helical proteins. By using only backbone NMR data, which are relatively easy to collect and analyze, and strategically placed spin relaxation probes, we show that it is possible to obtain protein structures with correct helical topology and backbone RMS deviations well below 4 Å. This approach offers promising alternatives for the structural determination of proteins in which nuclear Overha-user effect data are difficult or impossible to assign and produces initial models that will speed up the high-resolution structure determination by NMR spectroscopy. PMID:24639619

Hydrodynamics of the double-wave structure of insect spermatozoa flagella

PubMed Central

Pak, On Shun; Spagnolie, Saverio E.; Lauga, Eric

2012-01-01

In addition to conventional planar and helical flagellar waves, insect sperm flagella have also been observed to display a double-wave structure characterized by the presence of two superimposed helical waves. In this paper, we present a hydrodynamic investigation of the locomotion of insect spermatozoa exhibiting the double-wave structure, idealized here as superhelical waves. Resolving the hydrodynamic interactions with a non-local slender body theory, we predict the swimming kinematics of these superhelical swimmers based on experimentally collected geometric and kinematic data. Our consideration provides insight into the relative contributions of the major and minor helical waves to swimming; namely, propulsion is owing primarily to the minor wave, with negligible contribution from the major wave. We also explore the dependence of the propulsion speed on geometric and kinematic parameters, revealing counterintuitive results, particularly for the case when the minor and major helical structures are of opposite chirality. PMID:22298815

Structural virology. Near-atomic cryo-EM structure of the helical measles virus nucleocapsid.

PubMed

Gutsche, Irina; Desfosses, Ambroise; Effantin, Grégory; Ling, Wai Li; Haupt, Melina; Ruigrok, Rob W H; Sachse, Carsten; Schoehn, Guy

2015-05-08

Measles is a highly contagious human disease. We used cryo-electron microscopy and single particle-based helical image analysis to determine the structure of the helical nucleocapsid formed by the folded domain of the measles virus nucleoprotein encapsidating an RNA at a resolution of 4.3 angstroms. The resulting pseudoatomic model of the measles virus nucleocapsid offers important insights into the mechanism of the helical polymerization of nucleocapsids of negative-strand RNA viruses, in particular via the exchange subdomains of the nucleoprotein. The structure reveals the mode of the nucleoprotein-RNA interaction and explains why each nucleoprotein of measles virus binds six nucleotides, whereas the respiratory syncytial virus nucleoprotein binds seven. It provides a rational basis for further analysis of measles virus replication and transcription, and reveals potential targets for drug design. Copyright © 2015, American Association for the Advancement of Science.

High-speed imaging of submerged jet: visualization analysis using proper orthogonality decomposition

NASA Astrophysics Data System (ADS)

Liu, Yingzheng; He, Chuangxin

2016-11-01

In the present study, the submerged jet at low Reynolds numbers was visualized using laser induced fluoresce and high-speed imaging in a water tank. Well-controlled calibration was made to determine linear dependency region of the fluoresce intensity on its concentration. Subsequently, the jet fluid issuing from a circular pipe was visualized using a high-speed camera. The animation sequence of the visualized jet flow field was supplied for the snapshot proper orthogonality decomposition (POD) analysis. Spatio-temporally varying structures superimposed in the unsteady fluid flow were identified, e.g., the axisymmetric mode and the helical mode, which were reflected from the dominant POD modes. The coefficients of the POD modes give strong indication of temporal and spectral features of the corresponding unsteady events. The reconstruction using the time-mean visualization and the selected POD modes was conducted to reveal the convective motion of the buried vortical structures. National Natural Science Foundation of China.

The phosphorylation site in double helical amylopectin as investigated by a combined approach using chemical synthesis, crystallography and molecular modeling.

PubMed

Engelsen, Søren Balling; Madsen, Anders Østergaard; Blennow, Andreas; Motawia, Mohammed Saddik; Møller, Birger Lindberg; Larsen, Sine

2003-04-24

The only known in planta substitution of starch is phosphorylation. Whereas the function of starch phosphorylation is poorly understood, phosphorylated starch possesses improved functionality in vitro. Molecular models of native crystalline starch are currently being developed and the starch phosphorylating enzyme has recently been discovered. Accordingly, it is desirable to obtain a more exact description of the molecular structures of phosphorylated starch. We have determined the crystal structure of methyl alpha-D-glucopyranoside 6-O-phosphate as its potassium salt which is thought to be the starch phosphate counterion in vivo. From this structure and previously known glucophosphate structures we describe the possible 6-O-phosphate geometries and through modeling extrapolate the results to the double helical structure of the crystalline part of amylopectin. The geometries of the existing crystal structures of 6-O-phosphate groups were found to belong to two main adiabatic valleys. One of these conformations could be fitted into the double helical amylopectin part without perturbing the double helical amylopectin structure and without creating steric problems for the hexagonal chain-chain packing.

Alternating phenylene and furan/pyrrole/thiophene units-based oligomers: A computational study of the structures and optoelectronic properties

NASA Astrophysics Data System (ADS)

Sahu, Harikrishna; Shukla, Rishabh; Goswami, Juri; Gaur, Priyank; Panda, Aditya N.

2018-01-01

Structural and optoelectronic properties of phenylene-furan, phenylene-pyrrole and phenylene-thiophene oligomers are reported using density functional theory methods. Studies reveal that stabilities of conformers change with increasing chain length, and helical conformers are energetically feasible for large oligomers of the studied systems, due to stacking interactions between adjacent helical turns. Absorption spectra of helices are dominated by multiple number of electronic transitions other than the S0 →S1 , involving orbitals other than the HOMO/LUMO. All studied helices are optically active having similar pattern of negative and positive peaks in the CD spectra.

Chiral Sulfoxide-Induced Single Turn Peptide α-Helicity

PubMed Central

Zhang, Qingzhou; Jiang, Fan; Zhao, Bingchuan; Lin, Huacan; Tian, Yuan; Xie, Mingsheng; Bai, Guoyun; Gilbert, Adam M.; Goetz, Gilles H.; Liras, Spiros; Mathiowetz, Alan A.; Price, David A.; Song, Kun; Tu, Meihua; Wu, Yujie; Wang, Tao; Flanagan, Mark E.; Wu, Yun-Dong; Li, Zigang

2016-01-01

Inducing α-helicity through side-chain cross-linking is a strategy that has been pursued to improve peptide conformational rigidity and bio-availability. Here we describe the preparation of small peptides tethered to chiral sulfoxide-containing macrocyclic rings. Furthermore, a study of structure-activity relationships (SARs) disclosed properties with respect to ring size, sulfur position, oxidation state, and stereochemistry that show a propensity to induce α-helicity. Supporting data include circular dichroism spectroscopy (CD), NMR spectroscopy, and a single crystal X-ray structure for one such stabilized peptide. Finally, theoretical studies are presented to elucidate the effect of chiral sulfoxides in inducing backbone α-helicity. PMID:27934919

Experimental Study of the Influence of Speed and Load on Thermal Behavior of High-Speed Helical Gear Trains

NASA Technical Reports Server (NTRS)

Handschuh, R.; Kilmain, C.

2005-01-01

An experimental effort has been conducted on an aerospace-quality helical gear train to investigate the thermal behavior of the gear system as speed, load, and lubricant flow rate were varied. Temperature test data from a helical gear train at varying speeds and loads (to 5000 hp and 15000 rpm) was collected using thermocouple rakes and axial arrays. The instrumentation was able to capture the radial and axial expelled lubricant-air environment (fling-off lubricant) that is expelled during the gear meshing process. Effects of operational characteristics are presented.

Structure and Dynamics of Helical Protein Fragments Investigated by Theory and Experiment

NASA Astrophysics Data System (ADS)

Karimi, Afshin

This work addresses the conformation and dynamics of model peptides using spectroscopy and molecular dynamics simulations. Experimentally, we investigate the structure and dynamics of peptide fragments taken from coiled coil and three helical bundle motifs of bacterial coat proteins. Theoretically, we use molecular dynamics simulations of isolated helices with explicit water molecules to derive trajectories which reveal features about picosecond dynamics and local unfolding events. The assignment of the ^1H, ^{15}N, and ^ {13}C resonances, secondary structure, backbone dynamics, hydration and other biophysical parameters of a 30 residue recombinant peptide corresponding to an immunogenic site on the coiled coil region of Streptococcus pyogenes 24M protein are reported. Our results suggest that this peptide is a symmetric parallel dimeric alpha-helical coiled coil with local defects within the helix and fraying at the termini. The ^1H and ^ {15}N assignments, the hydration, the overall fold, and other biophysical parameters of a recombinant B domain of Staphylococcal protein A (FB) are reported. Our results indicate FB is a highly stable monomeric three helical bundle. A symmetric two domain construct was used to probe the modular assembly of two B domains. Here, spectroscopic results suggest weak interactions between the two domains. The folding pathway of FB was investigated using amide exchange data of the native protein and peptide models. We propose that the helical hairpin consisting of helices II and III is an on-pathway intermediate in the folding of FB. Two 1 ns molecular dynamics simulations (MD) on two mainly helical peptides--an 18 residue peptide corresponding to a portion of the H helix of myoglobin (MBH) and a 14 residue analogue of the C-peptide of ribonuclease A (CRNA) --were carried out in water using the united atom AMBER/OPLS force-field. In the case of MBH, the initial helical conformation progressively frays to a more disordered structure. A common motif in the unfolding mechanism involves the formation of transient turn structures involving several water molecules. In contrast to the MBH simulation, the CRNA trajectory was characterized by the presence of fairly stable i ... i+4 (alpha-helical) hydrogen bonds throughout the simulation, except at the N-terminus where some fraying was observed.

Study of two-phase flow in helical and spiral coils

NASA Technical Reports Server (NTRS)

Keshock, Edward G.; Yan, AN; Omrani, Adel

1990-01-01

The principal purposes of the present study were to: (1) observe and develop a fundamental understanding of the flow regimes and their transitions occurring in helical and spiral coils; and (2) obtain pressure drop measurements of such flows, and, if possible, develop a method for predicting pressure drop in these flow geometries. Elaborating upon the above, the general intent is to develop criteria (preferably generalized) for establishing the nature of the flow dynamics (e.g. flow patterns) and the magnitude of the pressure drop in such configurations over a range of flow rates and fluid properties. Additionally, the visualization and identification of flow patterns were a fundamental objective of the study. From a practical standpoint, the conditions under which an annular flow pattern exists is of particular practical importance. In the possible practical applications which would implement these geometries, the working fluids are likely to be refrigerant fluids. In the present study the working fluids were an air-water mixture, and refrigerant 113 (R-113). In order to obtain records of flow patterns and their transitions, video photography was employed extensively. Pressure drop measurements were made using pressure differential transducers connected across pressure taps in lines immediately preceding and following the various test sections.

Studying the Transfer of Magnetic Helicity in Solar Active Regions with the Connectivity-based Helicity Flux Density Method

NASA Astrophysics Data System (ADS)

Dalmasse, K.; Pariat, É.; Valori, G.; Jing, J.; Démoulin, P.

2018-01-01

In the solar corona, magnetic helicity slowly and continuously accumulates in response to plasma flows tangential to the photosphere and magnetic flux emergence through it. Analyzing this transfer of magnetic helicity is key for identifying its role in the dynamics of active regions (ARs). The connectivity-based helicity flux density method was recently developed for studying the 2D and 3D transfer of magnetic helicity in ARs. The method takes into account the 3D nature of magnetic helicity by explicitly using knowledge of the magnetic field connectivity, which allows it to faithfully track the photospheric flux of magnetic helicity. Because the magnetic field is not measured in the solar corona, modeled 3D solutions obtained from force-free magnetic field extrapolations must be used to derive the magnetic connectivity. Different extrapolation methods can lead to markedly different 3D magnetic field connectivities, thus questioning the reliability of the connectivity-based approach in observational applications. We address these concerns by applying this method to the isolated and internally complex AR 11158 with different magnetic field extrapolation models. We show that the connectivity-based calculations are robust to different extrapolation methods, in particular with regard to identifying regions of opposite magnetic helicity flux. We conclude that the connectivity-based approach can be reliably used in observational analyses and is a promising tool for studying the transfer of magnetic helicity in ARs and relating it to their flaring activity.

α-Helical Structural Elements within the Voltage-Sensing Domains of a K+ Channel

PubMed Central

Li-Smerin, Yingying; Hackos, David H.; Swartz, Kenton J.

2000-01-01

Voltage-gated K+ channels are tetramers with each subunit containing six (S1–S6) putative membrane spanning segments. The fifth through sixth transmembrane segments (S5–S6) from each of four subunits assemble to form a central pore domain. A growing body of evidence suggests that the first four segments (S1–S4) comprise a domain-like voltage-sensing structure. While the topology of this region is reasonably well defined, the secondary and tertiary structures of these transmembrane segments are not. To explore the secondary structure of the voltage-sensing domains, we used alanine-scanning mutagenesis through the region encompassing the first four transmembrane segments in the drk1 voltage-gated K+ channel. We examined the mutation-induced perturbation in gating free energy for periodicity characteristic of α-helices. Our results are consistent with at least portions of S1, S2, S3, and S4 adopting α-helical secondary structure. In addition, both the S1–S2 and S3–S4 linkers exhibited substantial helical character. The distribution of gating perturbations for S1 and S2 suggest that these two helices interact primarily with two environments. In contrast, the distribution of perturbations for S3 and S4 were more complex, suggesting that the latter two helices make more extensive protein contacts, possibly interfacing directly with the shell of the pore domain. PMID:10613917

Heliconical smectic phases formed by achiral molecules

DOE PAGES

Abberley, Jordan P.; Killah, Ross; Walker, Rebecca; ...

2018-01-15

Chiral symmetry breaking in soft matter is a hot topic of current research. Recently, such a phenomenon was found in a fluidic phase showing orientational order of molecules - the nematic phase; although built of achiral molecules, the phase can exhibit structural chirality - average molecular direction follows a short-pitch helix. Here in this paper, we report a series of achiral asymmetric dimers with an odd number of atoms in the spacer, which form twisted structures in nematic as well as in lamellar phases. The tight pitch heliconical nematic (N TB) phase and heliconical tilted smectic C (SmC TB) phasemore » are formed. The formation of a variety of helical structures is accompanied by a gradual freezing of molecular rotation. In the lowest temperature smectic phase, HexI, the twist is expressed through the formation of hierarchical structure: nanoscale helices and mesoscopic helical filaments. The short-pitch helical structure in the smectic phases is confirmed by resonant X-ray measurements.« less

Heliconical smectic phases formed by achiral molecules

DOE Office of Scientific and Technical Information (OSTI.GOV)

Abberley, Jordan P.; Killah, Ross; Walker, Rebecca

Chiral symmetry breaking in soft matter is a hot topic of current research. Recently, such a phenomenon was found in a fluidic phase showing orientational order of molecules - the nematic phase; although built of achiral molecules, the phase can exhibit structural chirality - average molecular direction follows a short-pitch helix. Here in this paper, we report a series of achiral asymmetric dimers with an odd number of atoms in the spacer, which form twisted structures in nematic as well as in lamellar phases. The tight pitch heliconical nematic (N TB) phase and heliconical tilted smectic C (SmC TB) phasemore » are formed. The formation of a variety of helical structures is accompanied by a gradual freezing of molecular rotation. In the lowest temperature smectic phase, HexI, the twist is expressed through the formation of hierarchical structure: nanoscale helices and mesoscopic helical filaments. The short-pitch helical structure in the smectic phases is confirmed by resonant X-ray measurements.« less

Probing RNA tertiary structure: interhelical crosslinking of the hammerhead ribozyme.

PubMed Central

Sigurdsson, S T; Tuschl, T; Eckstein, F

1995-01-01

Distinct structural models for the hammerhead ribozyme derived from single-crystal X-ray diffraction and fluorescence resonance energy transfer (FRET) measurements have been compared. Both models predict the same overall geometry, a wishbone shape with helices II and III nearly colinear and helix I positioned close to helix II. However, the relative orientations of helices I and II are different. To establish whether one of the models represents a kinetically active structure, a new crosslinking procedure was developed in which helices I and II of hammerhead ribozymes were disulfide-crosslinked via the 2' positions of specific sugar residues. Crosslinking residues on helices I and II that are close according to the X-ray structure did not appreciably reduce the catalytic efficiency. In contrast, crosslinking residues closely situated according to the FRET model dramatically reduced the cleavage rate by at least three orders of magnitude. These correlations between catalytic efficiencies and spatial proximities are consistent with the X-ray structure. PMID:7489517

Mode switching and linear stability analysis of resonant acoustic flows

NASA Astrophysics Data System (ADS)

Panickar, Praveen

Resonant acoustic flows occur in a wide variety of practical, aerospace-related applications and are a rich source of complex flow-physics. The primary concern associated with these types of flows is the high-amplitude fluctuating pressures associated with the resonant tones that could lead to sonic fatigue failure of sensitive components in the vicinity of such flows. However, before attempting to devise methods to suppress the resonant tones, it is imperative to understand the physics governing these flows in the hope that such an understanding will lead to more robust and effective suppression techniques. To this end, an in-depth study of various resonant acoustic flows was undertaken in this thesis, the main aim being to bring about a better understanding of such flows by revealing physically relevant information. Starting with the resonant acoustic mechanism in underexpanded jets from two-dimensional nozzles, it was shown that, for a variety of flow situations (geometries, shock-cell structures and orientations) in such jets, the nonlinear interaction density acted as a faithful precursor to a, hitherto unpredictable, spanwise instability mode switch. Following this, a study of the occurrence of, previously undocumented and theoretically unexpected, helical instabilities in subsonic impinging jets was undertaken. Using metrics from linear stability analysis, it was shown that the presence of the helical modes was justified. The results from this study on impinging jets are directly applicable to modern Stationary Take-Off and Vertical Landing (STOVL) aircraft that have twin, closely spaced exhausts. Finally, a novel technique that yielded dramatic suppression of resonant acoustic tones using high frequency excitation, in subsonic flows over open cavities, was investigated. Linear stability calculations of the experimentally measured baseline and excited velocity profiles showed that the instability of the high frequency excitation corresponded to a spatially decaying mode, which in turn lead to the resonance suppression associated with this mechanism. The experimental results showed good agreement with linear stability calculations for the measured mean velocity profiles. It is hoped that the work presented in this thesis will further the understanding of resonant acoustic flows and provide insights that can lead to better control techniques in the future.

High speed variable delivery helical screw compressor/expander automotive air conditioning and waste heat energy recovery system

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gagnon, J.A.; Schaefer, D.D.; Shaw, D.N.

1980-09-02

A compact, helical screw compressor/expander unit is described that is mounted in a vehicle and connected to the vehicle engine driven drive shaft has inlet and outlet ports and a capacity control slide valve and a pressure matching or volume ratio slide valve, respectively, for said ports. A refrigerant loop includes the compressor, a condenser mounted in the path of air flow over the engine and an evaporator mounted in a fresh air/cab return air flow duct for the occupant. Heat pipes thermally connect the cab air flow duct to the engine exhaust system which also bears the vapor boiler.more » Selectively operated damper valves control the fresh air/cab return air for passage selectively over the evaporator coil and the heat pipes as well as the exhaust gas flow over opposite ends of the heat pipes and the vapor boiler.« less

Plasma Flow During RF Discharges in VASIMR

NASA Technical Reports Server (NTRS)

Jacobson, V. T.; Chang Diaz, F. R.; Squire, J. P.; Ilin, A. V.; Bengtson, R. D.; Carter, M. D.; Goulding, R. H.

1999-01-01

The Variable Specific Impulse Magnetoplasma Rocket (VASIMR) plasma source consists of a helical antenna, driven at frequencies of 4 to 19 MHz with powers up to 1 kW, in a magnetic field up to 3 kG. Helium is the current test gas, and future experiments with hydrogen are planned. Plasma density and temperature profiles were measured by a reciprocating Langmuir probe, and plasma flow profiles were measured with a reciprocating Mach probe. Both probes were located about 0.5 m downstream from the helical antenna. The plasma source operated in capacitive and inductive modes in addition to a helicon mode. During capacitive and inductive modes, densities were low and plasma flow was < 0.5 Cs. When the plasma operated in a helicon mode, the densities measured downstream from the source were higher [10(exp 12) / cubic cm ] and plasma flow along the magnetic field was of the order Mach 1. Details of the measurements will be shown.

Experimental evidence of a helical, supercritical instability in pipe flow of shear thinning fluids

NASA Astrophysics Data System (ADS)

Picaut, L.; Ronsin, O.; Caroli, C.; Baumberger, T.

2017-08-01

We study experimentally the flow stability of entangled polymer solutions extruded through glass capillaries. We show that the pipe flow becomes linearly unstable beyond a critical value (Wic≃5 ) of the Weissenberg number, via a supercritical bifurcation which results in a helical distortion of the extrudate. We find that the amplitude of the undulation vanishes as the aspect ratio L /R of the capillary tends to zero, and saturates for large L /R , indicating that the instability affects the whole pipe flow, rather than the contraction or exit regions. These results, when compared to previous theoretical and experimental works, lead us to argue that the nature of the instability is controlled by the level of shear thinning of the fluids. In addition, we provide strong hints that the nonlinear development of the instabiilty is mitigated, in our system, by the gradual emergence of gross wall slip.

Conversion from mutual helicity to self-helicity observed with IRIS

NASA Astrophysics Data System (ADS)

Li, L. P.; Peter, H.; Chen, F.; Zhang, J.

2014-10-01

Context. In the upper atmosphere of the Sun observations show convincing evidence for crossing and twisted structures, which are interpreted as mutual helicity and self-helicity. Aims: We use observations with the new Interface Region Imaging Spectrograph (IRIS) to show the conversion of mutual helicity into self-helicity in coronal structures on the Sun. Methods: Using far UV spectra and slit-jaw images from IRIS and coronal images and magnetograms from SDO, we investigated the evolution of two crossing loops in an active region, in particular, the properties of the Si IV line profile in cool loops. Results: In the early stage two cool loops cross each other and accordingly have mutual helicity. The Doppler shifts in the loops indicate that they wind around each other. As a consequence, near the crossing point of the loops (interchange) reconnection sets in, which heats the plasma. This is consistent with the observed increase of the line width and of the appearance of the loops at higher temperatures. After this interaction, the two new loops run in parallel, and in one of them shows a clear spectral tilt of the Si IV line profile. This is indicative of a helical (twisting) motion, which is the same as to say that the loop has self-helicity. Conclusions: The high spatial and spectral resolution of IRIS allowed us to see the conversion of mutual helicity to self-helicity in the (interchange) reconnection of two loops. This is observational evidence for earlier theoretical speculations. Movie associated with Fig. 1 and Appendix A are available in electronic form at http://www.aanda.org

CURRENT AND KINETIC HELICITY OF LONG-LIVED ACTIVITY COMPLEXES

DOE Office of Scientific and Technical Information (OSTI.GOV)

Komm, Rudolf; Gosain, Sanjay, E-mail: komm@nso.edu

2015-01-01

We study long-lived activity complexes and their current helicity at the solar surface and their kinetic helicity below the surface. The current helicity has been determined from synoptic vector magnetograms from the NSO/SOLIS facility, and the kinetic helicity of subsurface flows has been determined with ring-diagram analysis applied to full-disk Dopplergrams from NSO/GONG and SDO/HMI. Current and kinetic helicity of activity complexes follow the hemispheric helicity rule with mainly positive values (78%; 78%, respectively, with a 95% confidence level of 31%) in the southern hemisphere and negative ones (80%; 93%, respectively, with a 95% confidence level of 22% and 14%,more » respectively) in the northern hemisphere. The locations with the dominant sign of kinetic helicity derived from Global Oscillation Network Group (GONG) and SDO/HMI data are more organized than those of the secondary sign even if they are not part of an activity complex, while locations with the secondary sign are more fragmented. This is the case for both hemispheres even for the northern one where it is not as obvious visually due to the large amount of magnetic activity present as compared to the southern hemisphere. The current helicity shows a similar behavior. The dominant sign of current helicity is the same as that of kinetic helicity for the majority of the activity complexes (83% with a 95% confidence level of 15%). During the 24 Carrington rotations analyzed here, there is at least one longitude in each hemisphere where activity complexes occur repeatedly throughout the epoch. These ''active'' longitudes are identifiable as locations of strong current and kinetic helicity of the same sign.« less

Propagation dynamics of Helical Hermite-Gaussian beams

NASA Astrophysics Data System (ADS)

López-Mariscal, Carlos; Gutiérrez-Vega, Julio C.

2007-09-01

We investigate theoretically and experimentally the propagation characteristics of the Helical Hermite-Gauss beams corresponding to the helical Ince-Gauss beams in the limit of infinite ellipticity. Particular attention is paid to the transverse irradiance structure, the orbital angular momentum density, and the vortex distribution.

Gyrotactic suppression and emergence of chaotic trajectories of swimming particles in three-dimensional flows

NASA Astrophysics Data System (ADS)

Richardson, S. I. Heath; Baggaley, A. W.; Hill, N. A.

2018-02-01

We study the effects of imposed three-dimensional flows on the trajectories and mixing of gyrotactic swimming microorganisms and identify phenomena not seen in flows restricted to two dimensions. Through numerical simulation of Taylor-Green and Arnold-Beltrami-Childress (ABC) flows, we explore the role that the flow and the cell shape play in determining the long-term configuration of the cells' trajectories, which often take the form of multiple sinuous and helical "plumelike" structures, even in the chaotic ABC flow. This gyrotactic suppression of Lagrangian chaos persists even in the presence of random noise. Analytical solutions for a number of cases reveal the how plumes form and the nature of the competition between torques acting on individual cells. Furthermore, studies of Lyapunov exponents reveal that, as the ratio of cell swimming speed relative to the flow speed increases from zero, the initial chaotic trajectories are first suppressed and then give way to a second unexpected window of chaotic trajectories at speeds greater than unity, before suppression of chaos at high relative swimming speeds.

Linear and nonlinear stability criteria for compressible MHD flows in a gravitational field

NASA Astrophysics Data System (ADS)

Moawad, S. M.; Moawad

2013-10-01

The equilibrium and stability properties of ideal magnetohydrodynamics (MHD) of compressible flow in a gravitational field with a translational symmetry are investigated. Variational principles for the steady-state equations are formulated. The MHD equilibrium equations are obtained as critical points of a conserved Lyapunov functional. This functional consists of the sum of the total energy, the mass, the circulation along field lines (cross helicity), the momentum, and the magnetic helicity. In the unperturbed case, the equilibrium states satisfy a nonlinear second-order partial differential equation (PDE) associated with hydrodynamic Bernoulli law. The PDE can be an elliptic or a parabolic equation depending on increasing the poloidal flow speed. Linear and nonlinear Lyapunov stability conditions under translational symmetric perturbations are established for the equilibrium states.

Effect of the helicity injection rate and the Lundquist number on spheromak sustainment

NASA Astrophysics Data System (ADS)

García-Martínez, Pablo Luis; Lampugnani, Leandro Gabriel; Farengo, Ricardo

2014-12-01

The dynamics of the magnetic relaxation process during the sustainment of spheromak configurations at different helicity injection rates is studied. The three-dimensional activity is recovered using time-dependent resistive magnetohydrodynamic simulations. A cylindrical flux conserver with concentric electrodes is used to model configurations driven by a magnetized coaxial gun. Magnetic helicity is injected by tangential boundary flows. Different regimes of sustainment are identified and characterized in terms of the safety factor profile. The spatial and temporal behavior of fluctuations is described. The dynamo action is shown to be in close agreement with existing experimental data. These results are relevant to the design and operation of helicity injected devices, as well as to basic understanding of the plasma relaxation mechanism in quasi-steady state.

Solid state NMR: The essential technology for helical membrane protein structural characterization

PubMed Central

Cross, Timothy A.; Ekanayake, Vindana; Paulino, Joana; Wright, Anna

2014-01-01

NMR spectroscopy of helical membrane proteins has been very challenging on multiple fronts. The expression and purification of these proteins while maintaining functionality has consumed countless graduate student hours. Sample preparations have depended on whether solution or solid-state NMR spectroscopy was to be performed – neither have been easy. In recent years it has become increasingly apparent that membrane mimic environments influence the structural result. Indeed, in these recent years we have rediscovered that Nobel laureate, Christian Anfinsen, did not say that protein structure was exclusively dictated by the amino acid sequence, but rather by the sequence in a given environment (Anfinsen, 1973) [106]. The environment matters, molecular interactions with the membrane environment are significant and many examples of distorted, non-native membrane protein structures have recently been documented in the literature. However, solid-state NMR structures of helical membrane proteins in proteoliposomes and bilayers are proving to be native structures that permit a high resolution characterization of their functional states. Indeed, solid-state NMR is uniquely able to characterize helical membrane protein structures in lipid environments without detergents. Recent progress in expression, purification, reconstitution, sample preparation and in the solid-state NMR spectroscopy of both oriented samples and magic angle spinning samples has demonstrated that helical membrane protein structures can be achieved in a timely fashion. Indeed, this is a spectacular opportunity for the NMR community to have a major impact on biomedical research through the solid-state NMR spectroscopy of these proteins. PMID:24412099

Solid state NMR: The essential technology for helical membrane protein structural characterization

NASA Astrophysics Data System (ADS)

Cross, Timothy A.; Ekanayake, Vindana; Paulino, Joana; Wright, Anna

2014-02-01

NMR spectroscopy of helical membrane proteins has been very challenging on multiple fronts. The expression and purification of these proteins while maintaining functionality has consumed countless graduate student hours. Sample preparations have depended on whether solution or solid-state NMR spectroscopy was to be performed - neither have been easy. In recent years it has become increasingly apparent that membrane mimic environments influence the structural result. Indeed, in these recent years we have rediscovered that Nobel laureate, Christian Anfinsen, did not say that protein structure was exclusively dictated by the amino acid sequence, but rather by the sequence in a given environment (Anfinsen, 1973) [106]. The environment matters, molecular interactions with the membrane environment are significant and many examples of distorted, non-native membrane protein structures have recently been documented in the literature. However, solid-state NMR structures of helical membrane proteins in proteoliposomes and bilayers are proving to be native structures that permit a high resolution characterization of their functional states. Indeed, solid-state NMR is uniquely able to characterize helical membrane protein structures in lipid environments without detergents. Recent progress in expression, purification, reconstitution, sample preparation and in the solid-state NMR spectroscopy of both oriented samples and magic angle spinning samples has demonstrated that helical membrane protein structures can be achieved in a timely fashion. Indeed, this is a spectacular opportunity for the NMR community to have a major impact on biomedical research through the solid-state NMR spectroscopy of these proteins.

A Helical Structural Nucleus Is the Primary Elongating Unit of Insulin Amyloid Fibrils

PubMed Central

Roessle, Manfred; Kastrup, Jette S; van de Weert, Marco; Flink, James M; Frokjaer, Sven; Gajhede, Michael; Svergun, Dmitri I

2007-01-01

Although amyloid fibrillation is generally believed to be a nucleation-dependent process, the nuclei are largely structurally uncharacterized. This is in part due to the inherent experimental challenge associated with structural descriptions of individual components in a dynamic multi-component equilibrium. There are indications that oligomeric aggregated precursors of fibrillation, and not mature fibrils, are the main cause of cytotoxicity in amyloid disease. This further emphasizes the importance of characterizing early fibrillation events. Here we present a kinetic x-ray solution scattering study of insulin fibrillation, revealing three major components: insulin monomers, mature fibrils, and an oligomeric species. Low-resolution three-dimensional structures are determined for the fibril repeating unit and for the oligomer, the latter being a helical unit composed of five to six insulin monomers. This helical oligomer is likely to be a structural nucleus, which accumulates above the supercritical concentration used in our experiments. The growth rate of the fibrils is proportional to the amount of the helical oligomer present in solution, suggesting that these oligomers elongate the fibrils. Hence, the structural nucleus and elongating unit in insulin amyloid fibrillation may be the same structural component above supercritical concentrations. A novel elongation pathway of insulin amyloid fibrils is proposed, based on the shape and size of the fibrillation precursor. The distinct helical oligomer described in this study defines a conceptually new basis of structure-based drug design against amyloid diseases. PMID:17472440

Chiral self-assembly of helical particles.

PubMed

Kolli, Hima Bindu; Cinacchi, Giorgio; Ferrarini, Alberta; Giacometti, Achille

2016-01-01

The shape of the building blocks plays a crucial role in directing self-assembly towards desired architectures. Out of the many different shapes, the helix has a unique position. Helical structures are ubiquitous in nature and a helical shape is exhibited by the most important biopolymers like polynucleotides, polypeptides and polysaccharides as well as by cellular organelles like flagella. Helical particles can self-assemble into chiral superstructures, which may have a variety of applications, e.g. as photonic (meta)materials. However, a clear and definite understanding of these structures has not been entirely achieved yet. We have recently undertaken an extensive investigation on the phase behaviour of hard helical particles, using numerical simulations and classical density functional theory. Here we present a detailed study of the phase diagram of hard helices as a function of their morphology. This includes a variety of liquid-crystal phases, with different degrees of orientational and positional ordering. We show how, by tuning the helix parameters, it is possible to control the organization of the system. Starting from slender helices, whose phase behaviour is similar to that of rodlike particles, an increase in curliness leads to the onset of azimuthal correlations between the particles and the formation of phases specific to helices. These phases feature a new kind of screw order, of which there is experimental evidence in colloidal suspensions of helical flagella.

The effects of the stellar wind and orbital motion on the jets of high-mass microquasars

NASA Astrophysics Data System (ADS)

Bosch-Ramon, V.; Barkov, M. V.

2016-05-01

Context. High-mass microquasar jets propagate under the effect of the wind from the companion star, and the orbital motion of the binary system. The stellar wind and the orbit may be dominant factors determining the jet properties beyond the binary scales. Aims: This is an analytical study, performed to characterise the effects of the stellar wind and the orbital motion on the jet properties. Methods: Accounting for the wind thrust transferred to the jet, we derive analytical estimates to characterise the jet evolution under the impact of the stellar wind. We include the Coriolis force effect, induced by orbital motion and enhanced by the wind's presence. Large-scale evolution of the jet is sketched, accounting for wind-to-jet thrust transfer, total energy conservation, and wind-jet flow mixing. Results: If the angle of the wind-induced jet bending is larger than its half-opening angle, the following is expected: (I) a strong recollimation shock; (II) bending against orbital motion, caused by Coriolis forces and enhanced by the wind presence; and (III) non-ballistic helical propagation further away. Even if disrupted, the jet can re-accelerate due to ambient pressure gradients, but wind entrainment can weaken this acceleration. On large scales, the opening angle of the helical structure is determined by the wind-jet thrust relation, and the wind-loaded jet flow can be rather slow. Conclusions: The impact of stellar winds on high-mass microquasar jets can yield non-ballistic helical jet trajectories, jet partial disruption and wind mixing, shocks, and possibly non-thermal emission. Among other observational diagnostics, such as radiation variability at any band, the radio morphology on milliarcsecond scales can be informative on the wind-jet interaction.

Solution conformation of a peptide fragment representing a proposed RNA-binding site of a viral coat protein studied by two-dimensional NMR

DOE Office of Scientific and Technical Information (OSTI.GOV)

van der Graaf, M.; van Mierlo, C.P.M.; Hemminga, M.A.

1991-06-11

The first 25 amino acids of the coat protein of cowpea chlorotic mottle virus are essential for binding the encapsidated RNA. Although an {alpha}-helical conformation has been predicted for this highly positively charged N-terminal region. No experimental evidence for this conformation has been presented so far. In this study, two-dimensional proton NMR experiments were performed on a chemically synthesized pentacosapeptide containing the first 25 amino acids of this coat protein. All resonances could be assigned by a combined use of two-dimensional correlated spectroscopy and nuclear Overhauser enhancement spectroscopy carried out at four different temperatures. Various NMR parameters indicate the presencemore » of a conformational ensemble consisting of helical structures rapidly converting into more extended states. Differences in chemical shifts and nuclear Overhauser effects indicate that lowering the temperature induces a shift of the dynamic equilibrium toward more helical structures. At 10{degrees}C, a perceptible fraction of the conformational ensemble consists of structures with an {alpha}-helical conformation between residues 9 and 17, likely starting with a turnlike structure around Thr9 and Arg10. Both the conformation and the position of this helical region agree well with the secondary structure predictions mentioned above.« less

High-Resolution Crystal Structures of Protein Helices Reconciled with Three-Centered Hydrogen Bonds and Multipole Electrostatics

PubMed Central

Kuster, Daniel J.; Liu, Chengyu; Fang, Zheng; Ponder, Jay W.; Marshall, Garland R.

2015-01-01

Theoretical and experimental evidence for non-linear hydrogen bonds in protein helices is ubiquitous. In particular, amide three-centered hydrogen bonds are common features of helices in high-resolution crystal structures of proteins. These high-resolution structures (1.0 to 1.5 Å nominal crystallographic resolution) position backbone atoms without significant bias from modeling constraints and identify Φ = -62°, ψ = -43 as the consensus backbone torsional angles of protein helices. These torsional angles preserve the atomic positions of α-β carbons of the classic Pauling α-helix while allowing the amide carbonyls to form bifurcated hydrogen bonds as first suggested by Némethy et al. in 1967. Molecular dynamics simulations of a capped 12-residue oligoalanine in water with AMOEBA (Atomic Multipole Optimized Energetics for Biomolecular Applications), a second-generation force field that includes multipole electrostatics and polarizability, reproduces the experimentally observed high-resolution helical conformation and correctly reorients the amide-bond carbonyls into bifurcated hydrogen bonds. This simple modification of backbone torsional angles reconciles experimental and theoretical views to provide a unified view of amide three-centered hydrogen bonds as crucial components of protein helices. The reason why they have been overlooked by structural biologists depends on the small crankshaft-like changes in orientation of the amide bond that allows maintenance of the overall helical parameters (helix pitch (p) and residues per turn (n)). The Pauling 3.613 α-helix fits the high-resolution experimental data with the minor exception of the amide-carbonyl electron density, but the previously associated backbone torsional angles (Φ, Ψ) needed slight modification to be reconciled with three-atom centered H-bonds and multipole electrostatics. Thus, a new standard helix, the 3.613/10-, Némethy- or N-helix, is proposed. Due to the use of constraints from monopole force fields and assumed secondary structures used in low-resolution refinement of electron density of proteins, such structures in the PDB often show linear hydrogen bonding. PMID:25894612

High-resolution crystal structures of protein helices reconciled with three-centered hydrogen bonds and multipole electrostatics.

PubMed

Kuster, Daniel J; Liu, Chengyu; Fang, Zheng; Ponder, Jay W; Marshall, Garland R

2015-01-01

Theoretical and experimental evidence for non-linear hydrogen bonds in protein helices is ubiquitous. In particular, amide three-centered hydrogen bonds are common features of helices in high-resolution crystal structures of proteins. These high-resolution structures (1.0 to 1.5 Å nominal crystallographic resolution) position backbone atoms without significant bias from modeling constraints and identify Φ = -62°, ψ = -43 as the consensus backbone torsional angles of protein helices. These torsional angles preserve the atomic positions of α-β carbons of the classic Pauling α-helix while allowing the amide carbonyls to form bifurcated hydrogen bonds as first suggested by Némethy et al. in 1967. Molecular dynamics simulations of a capped 12-residue oligoalanine in water with AMOEBA (Atomic Multipole Optimized Energetics for Biomolecular Applications), a second-generation force field that includes multipole electrostatics and polarizability, reproduces the experimentally observed high-resolution helical conformation and correctly reorients the amide-bond carbonyls into bifurcated hydrogen bonds. This simple modification of backbone torsional angles reconciles experimental and theoretical views to provide a unified view of amide three-centered hydrogen bonds as crucial components of protein helices. The reason why they have been overlooked by structural biologists depends on the small crankshaft-like changes in orientation of the amide bond that allows maintenance of the overall helical parameters (helix pitch (p) and residues per turn (n)). The Pauling 3.6(13) α-helix fits the high-resolution experimental data with the minor exception of the amide-carbonyl electron density, but the previously associated backbone torsional angles (Φ, Ψ) needed slight modification to be reconciled with three-atom centered H-bonds and multipole electrostatics. Thus, a new standard helix, the 3.6(13/10)-, Némethy- or N-helix, is proposed. Due to the use of constraints from monopole force fields and assumed secondary structures used in low-resolution refinement of electron density of proteins, such structures in the PDB often show linear hydrogen bonding.

HIGH TEMPERATURE REACTOR

DOEpatents

Kulsrud, R.M.; Spitzer, L. Jr.

1961-12-12

An apparatus of the stellarator type for heating a plasma to high temperatures is designed. Circularizers at the end of then helical windings produce a circular magnetic surface and provide improved confining and heating of the plasma. Reverse curvature sections formed in the end loops of the reaction tube provide increased plasma pressure for a given magnetic field pressure and thereby minimize the current flow in the helical windings. (AEC)

Structure and mechanism of maximum stability of isolated alpha-helical protein domains at a critical length scale.

PubMed

Qin, Zhao; Fabre, Andrea; Buehler, Markus J

2013-05-01

The stability of alpha helices is important in protein folding, bioinspired materials design, and controls many biological properties under physiological and disease conditions. Here we show that a naturally favored alpha helix length of 9 to 17 amino acids exists at which the propensity towards the formation of this secondary structure is maximized. We use a combination of thermodynamical analysis, well-tempered metadynamics molecular simulation and statistical analyses of experimental alpha helix length distributions and find that the favored alpha helix length is caused by a competition between alpha helix folding, unfolding into a random coil and formation of higher-order tertiary structures. The theoretical result is suggested to be used to explain the statistical distribution of the length of alpha helices observed in natural protein structures. Our study provides mechanistic insight into fundamental controlling parameters in alpha helix structure formation and potentially other biopolymers or synthetic materials. The result advances our fundamental understanding of size effects in the stability of protein structures and may enable the design of de novo alpha-helical protein materials.

Computational prediction of atomic structures of helical membrane proteins aided by EM maps.

PubMed

Kovacs, Julio A; Yeager, Mark; Abagyan, Ruben

2007-09-15

Integral membrane proteins pose a major challenge for protein-structure prediction because only approximately 100 high-resolution structures are available currently, thereby impeding the development of rules or empirical potentials to predict the packing of transmembrane alpha-helices. However, when an intermediate-resolution electron microscopy (EM) map is available, it can be used to provide restraints which, in combination with a suitable computational protocol, make structure prediction feasible. In this work we present such a protocol, which proceeds in three stages: 1), generation of an ensemble of alpha-helices by flexible fitting into each of the density rods in the low-resolution EM map, spanning a range of rotational angles around the main helical axes and translational shifts along the density rods; 2), fast optimization of side chains and scoring of the resulting conformations; and 3), refinement of the lowest-scoring conformations with internal coordinate mechanics, by optimizing the van der Waals, electrostatics, hydrogen bonding, torsional, and solvation energy contributions. In addition, our method implements a penalty term through a so-called tethering map, derived from the EM map, which restrains the positions of the alpha-helices. The protocol was validated on three test cases: GpA, KcsA, and MscL.

Large-Scale Flow Structure in Turbulent Nonpremixed Flames under Normal- And Low-Gravity Conditions

NASA Technical Reports Server (NTRS)

Clemens, N. T.; Idicheria, C. A.; Boxx, I. G.

2001-01-01

It is well known that buoyancy has a major influence on the flow structure of turbulent nonpremixed jet flames. Buoyancy acts by inducing baroclinic torques, which generate large-scale vortical structures that can significantly modify the flow field. Furthermore, some suggest that buoyancy can substantially influence the large-scale structure of even nominally momentum-dominated flames, since the low velocity flow outside of the flame will be more susceptible to buoyancy effects. Even subtle buoyancy effects may be important because changes in the large-scale structure affects the local entrainment and fluctuating strain rate, and hence the structure of the flame. Previous studies that have compared the structure of normal- and micro-gravity nonpremixed jet flames note that flames in microgravity are longer and wider than in normal-gravity. This trend was observed for jet flames ranging from laminar to turbulent regimes. Furthermore, imaging of the flames has shown possible evidence of helical instabilities and disturbances starting from the base of the flame in microgravity. In contrast, these characteristics were not observed in normal-gravity. The objective of the present study is to further advance our knowledge of the effects of weak levels of buoyancy on the structure of transitional and turbulent nonpremixed jet flames. In later studies we will utilize the drop tower facilities at NASA Glenn Research Center (GRC), but the preliminary work described in this paper was conducted using the 1.25-second drop tower located at the University of Texas at Austin. A more detailed description of these experiments can be found in Idicheria et al.

Accurate Cold-Test Model of Helical TWT Slow-Wave Circuits

NASA Technical Reports Server (NTRS)

Kory, Carol L.; Dayton, James A., Jr.

1997-01-01

Recently, a method has been established to accurately calculate cold-test data for helical slow-wave structures using the three-dimensional electromagnetic computer code, MAFIA. Cold-test parameters have been calculated for several helical traveling-wave tube (TWT) slow-wave circuits possessing various support rod configurations, and results are presented here showing excellent agreement with experiment. The helical models include tape thickness, dielectric support shapes and material properties consistent with the actual circuits. The cold-test data from this helical model can be used as input into large-signal helical TWT interaction codes making it possible, for the first time, to design a complete TWT via computer simulation.

ISEE 3 observations of low-energy proton bidirectional events and their relation to isolated interplanetary magnetic structures

NASA Technical Reports Server (NTRS)

Marsden, R. G.; Sanderson, T. R.; Tranquille, C.; Wenzel, K.-P.; Smith, E. J.

1987-01-01

The paper represents the results of a comprehensive survey of low-energy proton bidirectional anisotropies and associated transient magnetic structures as observed in the 35-1600 keV energy range on ISEE-3 during the last solar maximum. The majority of observed bidirectional flow (BDF) events (more than 70 percent) are associated with isolated magnetic structures which are postulated to be an interplanetary manifestation of coronal mass ejection (CME) events. The observed BDF events can be qualitatively grouped into five classes depending on the field signature of the related magnetic structure and the association (or lack of association) with an interplanetary shock. Concerning the topology of the CME-related magnetic structures, the observations are interpreted as being consistent with a detached bubble, comprising closed loops or tightly wound helices.

Fabrication of a magnetic helical mesostructured silica rod

NASA Astrophysics Data System (ADS)

Zhang, Lei; Zhang Qiao, Shi; Cheng, Lina; Yan, Zifeng; Qing Lu, Gao Max

2008-10-01

We report a one-step synthesis of magnetic helical mesostructured silica (MHMS) by self-assembly of an achiral surfactant, magnetic nanocrystals with stearic acid ligands and silicate. This core-shell structured material consists of an Fe3O4 superparamagnetic nanocrystal core and a highly ordered periodic helical mesoporous silica shell. We propose that the formation of the helical structure is induced by the interaction between the surfactant and dissociated stearic acid ligands. The MHMS obtained possesses superparamagnetism, uniform mesostructure, narrow pore size distribution, high surface area, and large pore volume. Furthermore, the drug release process is demonstrated using aspirin as a drug model and MHMS as a drug carrier in a sodium phosphate buffer solution.

Salt-bridging effects on short amphiphilic helical structure and introducing sequence-based short beta-turn motifs.

PubMed

Guarracino, Danielle A; Gentile, Kayla; Grossman, Alec; Li, Evan; Refai, Nader; Mohnot, Joy; King, Daniel

2018-02-01

Determining the minimal sequence necessary to induce protein folding is beneficial in understanding the role of protein-protein interactions in biological systems, as their three-dimensional structures often dictate their activity. Proteins are generally comprised of discrete secondary structures, from α-helices to β-turns and larger β-sheets, each of which is influenced by its primary structure. Manipulating the sequence of short, moderately helical peptides can help elucidate the influences on folding. We created two new scaffolds based on a modestly helical eight-residue peptide, PT3, we previously published. Using circular dichroism (CD) spectroscopy and changing the possible salt-bridging residues to new combinations of Lys, Arg, Glu, and Asp, we found that our most helical improvements came from the Arg-Glu combination, whereas the Lys-Asp was not significantly different from the Lys-Glu of the parent scaffold, PT3. The marked 3 10 -helical contributions in PT3 were lessened in the Arg-Glu-containing peptide with the beginning of cooperative unfolding seen through a thermal denaturation. However, a unique and unexpected signature was seen for the denaturation of the Lys-Asp peptide which could help elucidate the stages of folding between the 3 10 and α-helix. In addition, we developed a short six-residue peptide with β-turn/sheet CD signature, again to help study minimal sequences needed for folding. Overall, the results indicate that improvements made to short peptide scaffolds by fine-tuning the salt-bridging residues can enhance scaffold structure. Likewise, with the results from the new, short β-turn motif, these can help impact future peptidomimetic designs in creating biologically useful, short, structured β-sheet-forming peptides.

Evidence for α-helices in the gas phase: a case study using Melittin from honey bee venom.

PubMed

Florance, Hannah V; Stopford, Andrew P; Kalapothakis, Jason M; McCullough, Bryan J; Bretherick, Andrew; Barran, Perdita E

2011-09-07

Gas phase methodologies are increasingly used to study the structure of proteins and peptides. A challenge to the mass spectrometrist is to preserve the structure of the system of interest intact and unaltered from solution into the gas phase. Small peptides are very flexible and can present a number of conformations in solution. In this work we examine Melittin a 26 amino acid peptide that forms the active component of honey bee venom. Melittin is haemolytic and has been shown to form an α-helical tetrameric structure by X-ray crystallography [M. Gribskov et al., The RCSB Protein Data Bank, 1990] and to be helical in high concentrations of methanol. Here we use ion mobility mass spectrometry, molecular dynamics and gas-phase HDX to probe its structure in the gas phase and specifically interrogate whether the helical form can be preserved. All low energy calculated structures possess some helicity. In our experiments we examine the peptide following nano-ESI from solutions with varying methanol content. Ion mobility gives collision cross sections (CCS) that compare well with values found from molecular modelling and from other reported structures, but with inconclusive results regarding the effect of solvent. There is only a slight increase in CCS with charge, showing minimal coloumbically driven unfolding. HDX supports preservation of some helical content into the gas phase and again shows little difference in the exchange rates of species sprayed from different solvents. The [M + 3H](3+) species has two exchanging populations both of which exhibit faster exchange rates than observed for the [M + 2H](2+) species. One interpretation for these results is that the time spent being analysed is sufficient for this peptide to form a helix in the 'ultimate' hydrophobic environment of a vacuum.

Recognizing asymmetry in pseudo-symmetry; structural insights into the interaction between amphipathic α-helices and X-bundle proteins.

PubMed

Haddad, John Faissal; Yang, Yidai; Yeung, Sylvain; Couture, Jean-François

2017-11-01

An α-helix bundle is a small and compact protein fold always composed of more than 2 α-helices that typically run nearly parallel or antiparallel to each other. The repertoire of arrangements of α-helix bundle is such that these domains bind to a myriad of molecular entities including DNA, RNA, proteins and small molecules. A special instance of α-helical bundle is the X-type in which the arrangement of two α-helices interact at 45° to form an X. Among those, some X-helix bundle proteins bind to the hydrophobic section of an amphipathic α-helix in a seemingly orientation and sequence specific manner. In this review, we will compare the binding mode of amphipathic α-helices to X-helix bundle and α-helical bundle proteins. From these structures, we will highlight potential regulatory paradigms that may control the specific interactions of X-helix bundle proteins to amphipathic α-helices. This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman. Copyright © 2017 Elsevier B.V. All rights reserved.

Biomimetic Hierarchical Assembly of Helical Supraparticles from Chiral Nanoparticles

DOE PAGES

Zhou, Yunlong; Marson, Ryan L.; van Anders, Greg; ...

2016-02-22

Chiroptical materials found in butterflies, beetles, stomatopod crustaceans, and other creatures are attributed to biocomposites with helical motifs and multiscale hierarchical organization. These structurally sophisticated materials self-assemble from primitive nanoscale building blocks, a process that is simpler and more energy efficient than many top-down methods currently used to produce similarly sized three-dimensional materials. In this paper, we report that molecular-scale chirality of a CdTe nanoparticle surface can be translated to nanoscale helical assemblies, leading to chiroptical activity in the visible electromagnetic range. Chiral CdTe nanoparticles coated with cysteine self-organize around Te cores to produce helical supraparticles. D-/L-Form of the aminomore » acid determines the dominant left/right helicity of the supraparticles. Coarse-grained molecular dynamics simulations with a helical pair-potential confirm the assembly mechanism and the origin of its enantioselectivity, providing a framework for engineering three-dimensional chiral materials by self-assembly. Finally, the helical supraparticles further self-organize into lamellar crystals with liquid crystalline order, demonstrating the possibility of hierarchical organization and with multiple structural motifs and length scales determined by molecular-scale asymmetry of nanoparticle interactions.« less

Screening Libraries of Semifluorinated Arylene Bisimides to Discover and Predict Thermodynamically Controlled Helical Crystallization.

PubMed

Ho, Ming-Shou; Partridge, Benjamin E; Sun, Hao-Jan; Sahoo, Dipankar; Leowanawat, Pawaret; Peterca, Mihai; Graf, Robert; Spiess, Hans W; Zeng, Xiangbing; Ungar, Goran; Heiney, Paul A; Hsu, Chain-Shu; Percec, Virgil

2016-12-12

Synthesis, structural, and retrostructural analysis of a library containing 16 self-assembling perylene (PBI), 1,6,7,12-tetrachloroperylene (Cl 4 PBI), naphthalene (NBI), and pyromellitic (PMBI) bisimides functionalized with environmentally friendly AB 3 chiral racemic semifluorinated minidendrons at their imide groups via m = 0, 1, 2, and 3 methylene units is reported. These semifluorinated compounds melt at lower temperatures than homologous hydrogenated compounds, permitting screening of all their thermotropic phases via structural analysis to discover thermodynamically controlled helical crystallization from propeller-like, cogwheel, and tilted molecules as well as lamellar-like structures. Thermodynamically controlled helical crystallization was discovered for propeller-like PBI, Cl 4 PBI and NBI with m = 0. Unexpectedly, assemblies of twisted Cl 4 PBIs exhibit higher order than those of planar PBIs. PBI with m = 1, 2, and 3 form a thermodynamically controlled columnar hexagonal 2D lattice of tilted helical columns with intracolumnar order. PBI and Cl 4 PBI with m = 1 crystallize via a recently discovered helical cogwheel mechanism, while NBI and PMBI with m = 1 form tilted helical columns. PBI, NBI and PMBI with m = 2 generate lamellar-like structures. 3D and 2D assemblies of PBI with m = 1, 2, and 3, NBI with m = 1 and PMBI with m = 2 exhibit 3.4 Å π-π stacking. The library approach applied here and in previous work enabled the discovery of six assemblies which self-organize via thermodynamic control into 3D and 2D periodic arrays, and provides molecular principles to predict the supramolecular structure of electronically active components.

Evolution of helical perturbations in a thin-shell model of an imploding liner

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ryutov, D. D.; Dorf, M. A.

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 pointmore » 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.« less

Simulation of confined magnetohydrodynamic flows with Dirichlet boundary conditions using a pseudo-spectral method with volume penalization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Morales, Jorge A.; Leroy, Matthieu; Bos, Wouter J.T.

A volume penalization approach to simulate magnetohydrodynamic (MHD) flows in confined domains is presented. Here the incompressible visco-resistive MHD equations are solved using parallel pseudo-spectral solvers in Cartesian geometries. The volume penalization technique is an immersed boundary method which is characterized by a high flexibility for the geometry of the considered flow. In the present case, it allows to use other than periodic boundary conditions in a Fourier pseudo-spectral approach. The numerical method is validated and its convergence is assessed for two- and three-dimensional hydrodynamic (HD) and MHD flows, by comparing the numerical results with results from literature and analyticalmore » solutions. The test cases considered are two-dimensional Taylor–Couette flow, the z-pinch configuration, three dimensional Orszag–Tang flow, Ohmic-decay in a periodic cylinder, three-dimensional Taylor–Couette flow with and without axial magnetic field and three-dimensional Hartmann-instabilities in a cylinder with an imposed helical magnetic field. Finally, we present a magnetohydrodynamic flow simulation in toroidal geometry with non-symmetric cross section and imposing a helical magnetic field to illustrate the potential of the method.« less

Macroscopic ordering of helical pores for arraying guest molecules noncentrosymmetrically

PubMed Central

Li, Chunji; Cho, Joonil; Yamada, Kuniyo; Hashizume, Daisuke; Araoka, Fumito; Takezoe, Hideo; Aida, Takuzo; Ishida, Yasuhiro

2015-01-01

Helical nanostructures have attracted continuous attention, not only as media for chiral recognition and synthesis, but also as motifs for studying intriguing physical phenomena that never occur in centrosymmetric systems. To improve the quality of signals from these phenomena, which is a key issue for their further exploration, the most straightforward is the macroscopic orientation of helices. Here as a versatile scaffold to rationally construct this hardly accessible structure, we report a polymer framework with helical pores that unidirectionally orient over a large area (∼10 cm2). The framework, prepared by crosslinking a supramolecular liquid crystal preorganized in a magnetic field, is chemically robust, functionalized with carboxyl groups and capable of incorporating various basic or cationic guest molecules. When a nonlinear optical chromophore is incorporated in the framework, the resultant complex displays a markedly efficient nonlinear optical output, owing to the coherence of signals ensured by the macroscopically oriented helical structure. PMID:26416086

Turbomachinery Laboratory Texas A and M University research progress on annular gas seals

NASA Technical Reports Server (NTRS)

Childs, Dara W.

1994-01-01

Three helically-grooved seals were tested and the results were compared to the MTI code SPIRALG. A smooth annular seal was tested at six eccentricity ratios from 0 to 0.5. The following are concluded in this viewgraph presentation: (1) Helical-grooved seals provide a substantial reduction in cross-coupled stiffness coefficients. Negative k(sub xy) values are obtained for no-swirl or low-swirl cases. (2) SPIRALG is completely unsuitable for the type of seal tested, namely, turbulent flow, wide grooves and lands, etc. (3) A good analysis code is needed to guide the design of helically-grooved annular seals including groove and smooth sections.

Flow Structure and Channel Morphology at a Confluent-Meander Bend

NASA Astrophysics Data System (ADS)

Riley, J. D.; Rhoads, B. L.

2009-12-01

Flow structure and channel morphology in meander bends have been well documented. Channel curvature subjects flow through a bend to centrifugal acceleration, inducing a counterbalancing pressure-gradient force that initiates secondary circulation. Transverse variations in boundary shear stress and bedload transport parallel cross-stream movement of high velocity flow and determine spatial patterns of erosion along the outer bank and deposition along the inner bank. Laboratory experiments and numerical modeling of confluent-meander bends, a junction planform that develops when a tributary joins a meandering river along the outer bank of a bend, suggest that flow and channel morphology in such bends deviate from typical patterns. The purpose of this study is to examine three-dimensional (3-D) flow structure and channel morphology at a natural confluent-meander bend. Field data were collected in southeastern Illinois where Big Muddy Creek joins the Little Wabash River near a local maximum of curvature along an elongated meander loop. Measurements of 3-D velocity components were obtained with an acoustic Doppler current profiler (ADCP) for two flow events with differing momentum ratios. Channel bathymetry was also resolved from the four-beam depths of the ADCP. Analysis of velocity data reveals a distinct shear layer flanked by dual helical cells within the bend immediately downstream of the confluence. Flow from the tributary confines flow from the main channel along the inner part of the channel cross section, displacing the thalweg inward, limiting the downstream extent of the point bar, protecting the outer bank from erosion and enabling bar-building along this bank. Overall, this pattern of flow and channel morphology is quite different from typical patterns in meander bends, but is consistent with a conceptual model derived from laboratory experiments and numerical modeling.

Emergent perversions in the buckling of heterogeneous elastic strips

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Shuangping; Yao, Zhenwei; Chiou, Kevin

A perversion in an otherwise uniform helical structure, such as a climbing plant tendril, refers to a kink that connects two helices with opposite chiralities. Such singularity structures are widely seen in natural and artificial mechanical systems, and they provide the fundamental mechanism of helical symmetry breaking. However, it is still not clear how perversions arise in various helical structures and which universal principles govern them. As such, a heterogeneous elastic bistrip system provides an excellent model to address these questions. In this paper, we investigate intrinsic perversion properties which are independent of strip shapes. This study reveals the richmore » physics of perversions in the 3D elastic system, including the condensation of strain energy over perversions during their formation, the repulsive nature of the perversion–perversion interaction, and the coalescence of perversions that finally leads to a linear defect structure. Finally, this study may have implications for understanding relevant biological motifs and for use of perversions as energy storers in the design of micromuscles and soft robotics.« less

Emergent perversions in the buckling of heterogeneous elastic strips

DOE PAGES

Liu, Shuangping; Yao, Zhenwei; Chiou, Kevin; ...

2016-06-14

A perversion in an otherwise uniform helical structure, such as a climbing plant tendril, refers to a kink that connects two helices with opposite chiralities. Such singularity structures are widely seen in natural and artificial mechanical systems, and they provide the fundamental mechanism of helical symmetry breaking. However, it is still not clear how perversions arise in various helical structures and which universal principles govern them. As such, a heterogeneous elastic bistrip system provides an excellent model to address these questions. In this paper, we investigate intrinsic perversion properties which are independent of strip shapes. This study reveals the richmore » physics of perversions in the 3D elastic system, including the condensation of strain energy over perversions during their formation, the repulsive nature of the perversion–perversion interaction, and the coalescence of perversions that finally leads to a linear defect structure. Finally, this study may have implications for understanding relevant biological motifs and for use of perversions as energy storers in the design of micromuscles and soft robotics.« less

Transmembrane helix prediction: a comparative evaluation and analysis.

PubMed

Cuthbertson, Jonathan M; Doyle, Declan A; Sansom, Mark S P

2005-06-01

The prediction of transmembrane (TM) helices plays an important role in the study of membrane proteins, given the relatively small number (approximately 0.5% of the PDB) of high-resolution structures for such proteins. We used two datasets (one redundant and one non-redundant) of high-resolution structures of membrane proteins to evaluate and analyse TM helix prediction. The redundant (non-redundant) dataset contains structure of 434 (268) TM helices, from 112 (73) polypeptide chains. Of the 434 helices in the dataset, 20 may be classified as 'half-TM' as they are too short to span a lipid bilayer. We compared 13 TM helix prediction methods, evaluating each method using per segment, per residue and termini scores. Four methods consistently performed well: SPLIT4, TMHMM2, HMMTOP2 and TMAP. However, even the best methods were in error by, on average, about two turns of helix at the TM helix termini. The best and worst case predictions for individual proteins were analysed. In particular, the performance of the various methods and of a consensus prediction method, were compared for a number of proteins (e.g. SecY, ClC, KvAP) containing half-TM helices. The difficulties of predicting half-TM helices suggests that current prediction methods successfully embody the two-state model of membrane protein folding, but do not accommodate a third stage in which, e.g., short helices and re-entrant loops fold within a bundle of stable TM helices.

AFM Studies of Salt Concentration Effects on the (110) Surface Structure of Tetragonal Lysozyme Crystals

NASA Technical Reports Server (NTRS)

Pusey, Marc Lee; Gorti, Sridhar; Forsythe, Elizabeth; Konnert, John

2002-01-01

Previous high resolution AFM studies of the (110) surface of tetragonal chicken egg white lysozyme crystals had shown that only one of two possible molecular surfaces is present, those constituting the completed 43 helices. These suggested that the crystal growth process was by the solution-phase assembly of the growth units, which then attach to the surface. However, the best fit for the imaged surfaces, vs. those predicted based upon the bulk crystallographic coordinates, were obtained when the packing about the 43 helices was "tightened up", while maintaining the underlying crystallographic unit cell spacing. This results in a widening of the gap between adjacent helices, and the top- most layer(s) may no longer be in contact. We postulated that the tightened packing about the helices is a result of the high salt concentrations in the bulk solution, used to crystallize the protein, driving hydrophobic interactions. Once the crystal surface is sufficiently buried by subsequent growth layers the ratio of salt to protein molecules decreases and the helices relax to their bulk crystallographic coordinates. The crystal surface helix structure is thus a reflection of the solution structure, and the tightness of the packing about the 43 helices would be a function of the bulk salt concentration. AFM images of the (110) surface of tetragonal lysozyme crystals grown under low (2%) and high (5%) NaCl concentrations reveal differences in the packing about the 43 helices consistent with the above proposal.

On random pressure pulses in the turbine draft tube

NASA Astrophysics Data System (ADS)

Kuibin, P. A.; Shtork, S. I.; Skripkin, S. G.; Tsoy, M. A.

2017-04-01

The flow in the conical part of the hydroturbine draft tube undergoes various instabilities due to deceleration and flow swirling at off-design operation points. In particular, the precessing vortex rope develops at part-load regimes in the draft tube. This rope induces periodical low-frequency pressure oscillations in the draft tube. Interaction of rotational (asynchronous) mode of disturbances with the elbow can bring to strong oscillations in the whole hydrodynamical system. Recent researches on flow structure in the discharge cone in a regime of free runner had revealed that helical-like vortex rope can be unstable itself. Some coils of helix close to each other and reconnection appears with generation of a vortex ring. The vortex ring moves toward the draft tube wall and downstream. The present research is focused on interaction of vortex ring with wall and generation of pressure pulses.

Absolute versus convective helical magnetorotational instability in a Taylor-Couette flow.

PubMed

Priede, Jānis; Gerbeth, Gunter

2009-04-01

We analyze numerically the magnetorotational instability of a Taylor-Couette flow in a helical magnetic field [helical magnetorotational instability (HMRI)] using the inductionless approximation defined by a zero magnetic Prandtl number (Pr_{m}=0) . The Chebyshev collocation method is used to calculate the eigenvalue spectrum for small-amplitude perturbations. First, we carry out a detailed conventional linear stability analysis with respect to perturbations in the form of Fourier modes that corresponds to the convective instability which is not in general self-sustained. The helical magnetic field is found to extend the instability to a relatively narrow range beyond its purely hydrodynamic limit defined by the Rayleigh line. There is not only a lower critical threshold at which HMRI appears but also an upper one at which it disappears again. The latter distinguishes the HMRI from a magnetically modified Taylor vortex flow. Second, we find an absolute instability threshold as well. In the hydrodynamically unstable regime before the Rayleigh line, the threshold of absolute instability is just slightly above the convective one although the critical wavelength of the former is noticeably shorter than that of the latter. Beyond the Rayleigh line the lower threshold of absolute instability rises significantly above the corresponding convective one while the upper one descends significantly below its convective counterpart. As a result, the extension of the absolute HMRI beyond the Rayleigh line is considerably shorter than that of the convective instability. The absolute HMRI is supposed to be self-sustained and, thus, experimentally observable without any external excitation in a system of sufficiently large axial extension.

Synthesis of Norbornene Derived Helical Copolymer by Simple Molecular Marriage Approach to Produce Smart Nanocarrier

NASA Astrophysics Data System (ADS)

Mane, Shivshankar R.; Sathyan, Ashlin; Shunmugam, Raja

2017-03-01

A novel library of norbornene derived helical copolymer has been synthesized through the coupling of two homopolymers via Molecular Marriage Approach. The helicity is governed by the non-covalent interactions like hydrogen bonding, π-π stacking and the influence of hydrophobic and hydrophilic motifs. The detailed characterization of the copolymer (Copoly 1) has been provided and the super structures are confirmed through dynamic light scattering (DLS), scanning electron microscopy (SEM) and transmission electron microscopy (TEM). The observed size of the aggregates was about 200 nm. The density functional theory (DFT) is favorably supported for the formation of proposed structure of Copoly 1. Circular dichroism (CD) measurement has confirmed the one handed helical structure of the copolymer. Reservoir capability of this pH responsive polymer (Copoly 1) to encapsulate anti-cancer drug doxorubicin (DOX) warrants its potential applications in the field of bio-medical sciences.

Counteranion Driven Homochiral Assembly of a Cationic C3-Symmetric Gelator through Ion-Pair Assisted Hydrogen Bond.

PubMed

Maity, Arunava; Gangopadhyay, Monalisa; Basu, Arghya; Aute, Sunil; Babu, Sukumaran Santhosh; Das, Amitava

2016-09-07

The helical handedness in achiral self-assemblies is mostly complex due to spontaneous symmetry breaking or kinetically controlled random assembly formation. Here an attempt has been made to address this issue through chiral anion exchange. A new class of cationic achiral C3-symmetric gelator devoid of any conventional gelation assisting functional units is found to form both right- and left-handed helical structures. A chiral counteranion exchange-assisted approach is successfully introduced to control the chirality sign and thereby to obtain preferred homochiral assemblies. Formation of anion-assisted chiral assembly was confirmed by circular dichroism (CD) spectroscopy, microscopic images, and crystal structure. The X-ray crystal structure reveals the construction of helical assemblies with opposite handedness for (+)- and (-)-chiral anion reformed gelators. The appropriate counteranion driven ion-pair-assisted hydrogen-bonding interactions are found responsible for the helical bias control in this C3-symmetric gelator.

Contribution of Long-Range Interactions to the Secondary Structure of an Unfolded Globin

PubMed Central

Fedyukina, Daria V.; Rajagopalan, Senapathy; Sekhar, Ashok; Fulmer, Eric C.; Eun, Ye-Jin; Cavagnero, Silvia

2010-01-01

This work explores the effect of long-range tertiary contacts on the distribution of residual secondary structure in the unfolded state of an α-helical protein. N-terminal fragments of increasing length, in conjunction with multidimensional nuclear magnetic resonance, were employed. A protein representative of the ubiquitous globin fold was chosen as the model system. We found that, while most of the detectable α-helical population in the unfolded ensemble does not depend on the presence of the C-terminal region (corresponding to the native G and H helices), specific N-to-C long-range contacts between the H and A-B-C regions enhance the helical secondary structure content of the N terminus (A-B-C regions). The simple approach introduced here, based on the evaluation of N-terminal polypeptide fragments of increasing length, is of general applicability to identify the influence of long-range interactions in unfolded proteins. PMID:20816043

Synthesis of Norbornene Derived Helical Copolymer by Simple Molecular Marriage Approach to Produce Smart Nanocarrier.

PubMed

Mane, Shivshankar R; Sathyan, Ashlin; Shunmugam, Raja

2017-03-22

A novel library of norbornene derived helical copolymer has been synthesized through the coupling of two homopolymers via Molecular Marriage Approach. The helicity is governed by the non-covalent interactions like hydrogen bonding, π-π stacking and the influence of hydrophobic and hydrophilic motifs. The detailed characterization of the copolymer (Copoly 1) has been provided and the super structures are confirmed through dynamic light scattering (DLS), scanning electron microscopy (SEM) and transmission electron microscopy (TEM). The observed size of the aggregates was about 200 nm. The density functional theory (DFT) is favorably supported for the formation of proposed structure of Copoly 1. Circular dichroism (CD) measurement has confirmed the one handed helical structure of the copolymer. Reservoir capability of this pH responsive polymer (Copoly 1) to encapsulate anti-cancer drug doxorubicin (DOX) warrants its potential applications in the field of bio-medical sciences.

Twisted ribbon structure of paired helical filaments revealed by atomic force microscopy.

PubMed Central

Pollanen, M. S.; Markiewicz, P.; Bergeron, C.; Goh, M. C.

1994-01-01

Progressive deposition of phosphorylated tau into the paired helical filaments (PHF) that compose neurofibrillary tangles, dystrophic neurites, and neuropil threads is an obligate feature of Alzheimer's disease. The standard model of PHF structure, derived from electron microscopic studies, suggests that two 8- to 10-nm filaments each composed of three to four protofilaments are wound into a helix with a maximal diameter of -20 nm and a half period of 65 to 80 nm. However, recent vertical platinum-carbon replicas of PHF more closely resemble a thin helical ribbon without constitutive protofilaments. Here we report that native PHF imaged with an atomic force microscope appear as twisted ribbons rather than the generally accepted structure derived from electron microscopic studies. These data imply that the assembly of PHF is not due to the twisting of pair-wise filaments but rather the helical winding of self-associated tau molecules arranged into a flattened structure. Future structural models of PHF should be based on quantitative data obtained from imaging techniques, such as scanning probe microscopy, which do not require harsh specimen preparation procedures. Images Figure 1 PMID:8178938

Twisted ribbon structure of paired helical filaments revealed by atomic force microscopy.

PubMed

Pollanen, M S; Markiewicz, P; Bergeron, C; Goh, M C

1994-05-01

Progressive deposition of phosphorylated tau into the paired helical filaments (PHF) that compose neurofibrillary tangles, dystrophic neurites, and neuropil threads is an obligate feature of Alzheimer's disease. The standard model of PHF structure, derived from electron microscopic studies, suggests that two 8- to 10-nm filaments each composed of three to four protofilaments are wound into a helix with a maximal diameter of -20 nm and a half period of 65 to 80 nm. However, recent vertical platinum-carbon replicas of PHF more closely resemble a thin helical ribbon without constitutive protofilaments. Here we report that native PHF imaged with an atomic force microscope appear as twisted ribbons rather than the generally accepted structure derived from electron microscopic studies. These data imply that the assembly of PHF is not due to the twisting of pair-wise filaments but rather the helical winding of self-associated tau molecules arranged into a flattened structure. Future structural models of PHF should be based on quantitative data obtained from imaging techniques, such as scanning probe microscopy, which do not require harsh specimen preparation procedures.

Formation of insulin amyloid fibrils followed by FTIR simultaneously with CD and electron microscopy.

PubMed Central

Bouchard, M.; Zurdo, J.; Nettleton, E. J.; Dobson, C. M.; Robinson, C. V.

2000-01-01

Fourier transform infrared spectroscopy (FTIR), circular dichroism (CD), and electron microscopy (EM) have been used simultaneously to follow the temperature-induced formation of amyloid fibrils by bovine insulin at acidic pH. The FTIR and CD data confirm that, before heating, insulin molecules in solution at pH 2.3 have a predominantly native-like alpha-helical structure. On heating to 70 degrees C, partial unfolding occurs and results initially in aggregates that are shown by CD and FT-IR spectra to retain a predominantly helical structure. Following this step, changes in the CD and FTIR spectra occur that are indicative of the extensive conversion of the molecular conformation from alpha-helical to beta-sheet structure. At later stages, EM shows the development of fibrils with well-defined repetitive morphologies including structures with a periodic helical twist of approximately 450 A. The results indicate that formation of fibrils by insulin requires substantial unfolding of the native protein, and that the most highly ordered structures result from a slow evolution of the morphology of the initially formed fibrillar species. PMID:11106169

THE ROLE OF MAGNETIC HELICITY IN STRUCTURING THE SOLAR CORONA

DOE Office of Scientific and Technical Information (OSTI.GOV)

Knizhnik, K. J.; Antiochos, S. K.; DeVore, C. R.

Two of the most widely observed and striking features of the Sun's 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 frommore » 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.« less

Autonomously folded α-helical lockers promote RNAi*

NASA Astrophysics Data System (ADS)

Guyader, Christian P. E.; Lamarre, Baptiste; de Santis, Emiliana; Noble, James E.; Slater, Nigel K.; Ryadnov, Maxim G.

2016-10-01

RNAi is an indispensable research tool with a substantial therapeutic potential. However, the complete transition of the approach to an applied capability remains hampered due to poorly understood relationships between siRNA delivery and gene suppression. Here we propose that interfacial tertiary contacts between α-helices can regulate siRNA cytoplasmic delivery and RNAi. We introduce a rationale of helical amphipathic lockers that differentiates autonomously folded helices, which promote gene silencing, from helices folded with siRNA, which do not. Each of the helical designs can deliver siRNA into cells via energy-dependent endocytosis, while only autonomously folded helices with pre-locked hydrophobic interfaces were able to promote statistically appreciable gene silencing. We propose that it is the amphipathic locking of interfacing helices prior to binding to siRNA that enables RNAi. The rationale offers structurally balanced amphipathic scaffolds to advance the exploitation of functional RNAi.

Autonomously folded α-helical lockers promote RNAi*

PubMed Central

Guyader, Christian P. E.; Lamarre, Baptiste; De Santis, Emiliana; Noble, James E.; Slater, Nigel K.; Ryadnov, Maxim G.

2016-01-01

RNAi is an indispensable research tool with a substantial therapeutic potential. However, the complete transition of the approach to an applied capability remains hampered due to poorly understood relationships between siRNA delivery and gene suppression. Here we propose that interfacial tertiary contacts between α-helices can regulate siRNA cytoplasmic delivery and RNAi. We introduce a rationale of helical amphipathic lockers that differentiates autonomously folded helices, which promote gene silencing, from helices folded with siRNA, which do not. Each of the helical designs can deliver siRNA into cells via energy-dependent endocytosis, while only autonomously folded helices with pre-locked hydrophobic interfaces were able to promote statistically appreciable gene silencing. We propose that it is the amphipathic locking of interfacing helices prior to binding to siRNA that enables RNAi. The rationale offers structurally balanced amphipathic scaffolds to advance the exploitation of functional RNAi. PMID:27721465

Autonomously folded α-helical lockers promote RNAi.

PubMed

Guyader, Christian P E; Lamarre, Baptiste; De Santis, Emiliana; Noble, James E; Slater, Nigel K; Ryadnov, Maxim G

2016-10-10

RNAi is an indispensable research tool with a substantial therapeutic potential. However, the complete transition of the approach to an applied capability remains hampered due to poorly understood relationships between siRNA delivery and gene suppression. Here we propose that interfacial tertiary contacts between α-helices can regulate siRNA cytoplasmic delivery and RNAi. We introduce a rationale of helical amphipathic lockers that differentiates autonomously folded helices, which promote gene silencing, from helices folded with siRNA, which do not. Each of the helical designs can deliver siRNA into cells via energy-dependent endocytosis, while only autonomously folded helices with pre-locked hydrophobic interfaces were able to promote statistically appreciable gene silencing. We propose that it is the amphipathic locking of interfacing helices prior to binding to siRNA that enables RNAi. The rationale offers structurally balanced amphipathic scaffolds to advance the exploitation of functional RNAi.

Zn(II) coordination polymers with flexible V-shaped dicarboxylate ligand: Syntheses, helical structures and properties

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Lin; Liu, Chong-Bo, E-mail: cbliu@nchu.edu.cn; Yang, Gao-Shan

2015-11-15

Hydrothermal reactions of 2,2′-[hexafluoroisopropylidenebis(p-phenyleneoxy)]diacetic acid (H{sub 2}L) and zinc ions in the presence of N-donor ancillary ligands afford four novel coordination polymers, namely, [Zn{sub 2}(μ{sub 2}-OH)(μ{sub 4}-O){sub 0.5}(L)]·0.5H{sub 2}O (1), [Zn(L)(2,2′-bipy)(H{sub 2}O)] (2), [Zn{sub 3}(L){sub 3}(phen){sub 2}]·H{sub 2}O (3) and [Zn{sub 2}(L){sub 2}(4,4′-bipy)] (4) (2,2′-bipy=2,2′-bipyridine; 4,4′-bipy=4,4′-bipyridine; phen=1,10-phenanthroline). Their structures have been determined by single-crystal X-ray diffraction analyses, elemental analyses, IR spectra, powder X-ray diffraction (PXRD), and thermogravimetric (TG) analyses. Complex 1 shows a 3-D clover framework consisting of [Zn{sub 4}(µ{sub 4}-O)(µ{sub 2}-OH){sub 2}]{sup 4+} clusters, and exhibits a novel (3,8)-connected topological net with the Schläfli symbol of {3·4·5}{sub 2}{3"4·4"4·5"2·6"6·7"1"0·8"2}, andmore » contains double-stranded and two kinds of meso-helices. 2 displays a helical chain structure, which is further extended via hydrogen bonds into a 3-D supramolecular structure with meso-helix chains. 3 displays a 2-D {4"4·6"2} parallelogram structure, which is further extended via hydrogen bonds into a 3-D supramolecular structure with single-stranded helical chains. 4 shows a 2-D {4"4·6"2} square structure with left- and right-handed helical chains. Moreover, the luminescent properties of 1–4 have been investigated. - Graphical abstract: Four new Zn(II) coordination polymers with helical structures based on flexible V-shaped dicarboxylate ligand have been synthesized and structurally characterized. Photoluminescent properties have been investigated. - Highlights: • Four novel Zn(II) coordination polymers with V-shaped ligand were characterized. • Complexes 1–4 show diverse intriguing helical characters. • Fluorescence properties of complexes 1–4 were investigated.« less

Structure-activity relationship study of Aib-containing amphipathic helical peptide-cyclic RGD conjugates as carriers for siRNA delivery.

PubMed

Wada, Shun-Ichi; Takesada, Anna; Nagamura, Yurie; Sogabe, Eri; Ohki, Rieko; Hayashi, Junsuke; Urata, Hidehito

2017-12-15

The conjugation of Aib-containing amphipathic helical peptide with cyclo(-Arg-Gly-Asp-d-Phe-Cys-) (cRGDfC) at the C-terminus of the helix peptide (PI) has been reported to be useful for constructing a carrier for targeted siRNA delivery into cells. In order to explore structure-activity relationships for the development of potential carriers for siRNA delivery, we synthesized conjugates of Aib-containing amphipathic helical peptide with cRGDfC at the N-terminus (PII) and both the N- and C-termini (PIII) of the helical peptide. Furthermore, to examine the influence of PI helical chain length on siRNA delivery, truncated peptides containing 16 (PIV), 12 (PV), and 8 (PVI) amino acid residues at the N-terminus of the helical chain were synthesized. PII and PIII, as well as PI, could deliver anti-luciferase siRNA into cells to induce the knockdown of luciferase stably expressed in cells. In contrast, all of the truncated peptides were unlikely to transport siRNA into cells. Copyright © 2017 Elsevier Ltd. All rights reserved.

Helicity conservation under quantum reconnection of vortex rings.

PubMed

Zuccher, Simone; Ricca, Renzo L

2015-12-01

Here we show that under quantum reconnection, simulated by using the three-dimensional Gross-Pitaevskii equation, self-helicity of a system of two interacting vortex rings remains conserved. By resolving the fine structure of the vortex cores, we demonstrate that the total length of the vortex system reaches a maximum at the reconnection time, while both writhe helicity and twist helicity remain separately unchanged throughout the process. Self-helicity is computed by two independent methods, and topological information is based on the extraction and analysis of geometric quantities such as writhe, total torsion, and intrinsic twist of the reconnecting vortex rings.

Reactor design for uniform chemical vapor deposition-grown films without substrate rotation

DOEpatents

Wanlass, M.

1985-02-19

A quartz reactor vessel for growth of uniform semiconductor films includes a vertical, cylindrical reaction chamber in which a substrate-supporting pedestal provides a horizontal substrate-supporting surface spaced on its perimeter from the chamber wall. A cylindrical confinement chamber of smaller diameter is disposed coaxially above the reaction chamber and receives reaction gas injected at a tangent to the inside chamber wall, forming a helical gas stream that descends into the reaction chamber. In the reaction chamber, the edge of the substrate-supporting pedestal is a separation point for the helical flow, diverting part of the flow over the horizontal surface of the substrate in an inwardly spiraling vortex.

Reactor design for uniform chemical vapor deposition-grown films without substrate rotation

DOEpatents

Wanlass, Mark

1987-01-01

A quartz reactor vessel for growth of uniform semiconductor films includes a vertical, cylindrical reaction chamber in which a substrate-supporting pedestal provides a horizontal substrate-supporting surface spaced on its perimeter from the chamber wall. A cylindrical confinement chamber of smaller diameter is disposed coaxially above the reaction chamber and receives reaction gas injected at a tangent to the inside chamber wall, forming a helical gas stream that descends into the reaction chamber. In the reaction chamber, the edge of the substrate-supporting pedestal is a separation point for the helical flow, diverting part of the flow over the horizontal surface of the substrate in an inwardly spiraling vortex.

Predicting the helix packing of globular proteins by self-correcting distance geometry.

PubMed

Mumenthaler, C; Braun, W

1995-05-01

A new self-correcting distance geometry method for predicting the three-dimensional structure of small globular proteins was assessed with a test set of 8 helical proteins. With the knowledge of the amino acid sequence and the helical segments, our completely automated method calculated the correct backbone topology of six proteins. The accuracy of the predicted structures ranged from 2.3 A to 3.1 A for the helical segments compared to the experimentally determined structures. For two proteins, the predicted constraints were not restrictive enough to yield a conclusive prediction. The method can be applied to all small globular proteins, provided the secondary structure is known from NMR analysis or can be predicted with high reliability.

Structural models of the MscL gating mechanism

NASA Technical Reports Server (NTRS)

Sukharev, S.; Durell, S. R.; Guy, H. R.

2001-01-01

Three-dimensional structural models of the mechanosensitive channel of large conductance, MscL, from the bacteria Mycobacterium tuberculosis and Escherichia coli were developed for closed, intermediate, and open conformations. The modeling began with the crystal structure of M. tuberculosis MscL, a homopentamer with two transmembrane alpha-helices, M1 and M2, per subunit. The first 12 N-terminal residues, not resolved in the crystal structure, were modeled as an amphipathic alpha-helix, called S1. A bundle of five parallel S1 helices are postulated to form a cytoplasmic gate. As membrane tension induces expansion, the tilts of M1 and M2 are postulated to increase as they move away from the axis of the pore. Substantial expansion is postulated to occur before the increased stress in the S1 to M1 linkers pulls the S1 bundle apart. During the opening transition, the S1 helices and C-terminus amphipathic alpha-helices, S3, are postulated to dock parallel to the membrane surface on the perimeter of the complex. The proposed gating mechanism reveals critical spatial relationships between the expandable transmembrane barrel formed by M1 and M2, the gate formed by S1 helices, and "strings" that link S1s to M1s. These models are consistent with numerous experimental results and modeling criteria.

Computational Prediction of Atomic Structures of Helical Membrane Proteins Aided by EM Maps

PubMed Central

Kovacs, Julio A.; Yeager, Mark; Abagyan, Ruben

2007-01-01

Integral membrane proteins pose a major challenge for protein-structure prediction because only ≈100 high-resolution structures are available currently, thereby impeding the development of rules or empirical potentials to predict the packing of transmembrane α-helices. However, when an intermediate-resolution electron microscopy (EM) map is available, it can be used to provide restraints which, in combination with a suitable computational protocol, make structure prediction feasible. In this work we present such a protocol, which proceeds in three stages: 1), generation of an ensemble of α-helices by flexible fitting into each of the density rods in the low-resolution EM map, spanning a range of rotational angles around the main helical axes and translational shifts along the density rods; 2), fast optimization of side chains and scoring of the resulting conformations; and 3), refinement of the lowest-scoring conformations with internal coordinate mechanics, by optimizing the van der Waals, electrostatics, hydrogen bonding, torsional, and solvation energy contributions. In addition, our method implements a penalty term through a so-called tethering map, derived from the EM map, which restrains the positions of the α-helices. The protocol was validated on three test cases: GpA, KcsA, and MscL. PMID:17496035

How Rosalind Franklin Discovered the Helical Structure of DNA: Experiments in Diffraction

ERIC Educational Resources Information Center

Braun, Gregory; Tierney, Dennis; Schmitzer, Heidrun

2011-01-01

Rosalind Franklin, a chemical physicist (1920-1958), used x-ray diffraction to determine the structure of DNA. What exactly could she read out from her x-ray pattern, shown in Fig. 1? In lecture notes dated November 1951, R. Franklin wrote the following: "The results suggest a helical structure (which must be very closely packed) containing 2, 3…

The crystal structure of the calcium-bound con-G[Q6A] peptide reveals a novel metal-dependent helical trimer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cnudde, Sara E.; Prorok, Mary; Jia, Xaofei

2012-02-15

The ability to form and control both secondary structure and oligomerization in short peptides has proven to be challenging owing to the structural instability of such peptides. The conantokin peptides are a family of {gamma}-carboxyglutamic acid containing peptides produced in the venoms of predatory sea snails of the Conus family. They are examples of short peptides that form stable helical structures, especially in the presence of divalent cations. Both monomeric and dimeric conantokin peptides have been identified and represent a new mechanism of helix association, 'the metallozipper motif' that is devoid of a hydrophobic interface between monomers. In the presentmore » study, a parallel/antiparallel three-helix bundle was identified and its crystal structure determined at high resolution. The three helices are almost perfectly parallel and represent a novel helix-helix association. The trimer interface is dominated by metal chelation between the three helices, and contains no interfacial hydrophobic interactions. It is now possible to produce stable monomeric, dimeric, or trimeric metallozippers depending on the peptide sequence and metal ion. Such structures have important applications in protein design.« less

Heat Transfer Enhancement in a Helically Coiled Tube with Al2O3/WATER Nanofluid Under Laminar Flow Condition

NASA Astrophysics Data System (ADS)

Kumar, P. C. Mukesh; Kumar, J.; Suresh, S.; Babu, K. Praveen

2012-10-01

In this experimental investigation, the heat transfer coefficients of a shell and helically coiled tube heat exchanger using Al2O3/water nanofluid under laminar flow condition were studied. The Al2O3 nanoparticles were characterized by X-Ray diffraction (XRD). The Al2O3/water nanofluid at 0.1%, 0.4% and 0.8% particle volume concentration were prepared by using two step method. The prepared nanofluid was characterized by scanning electron microscope (SEM). It is observed that the overall heat transfer coefficient, inner heat transfer coefficient and experimental inner Nusselt number increase while increasing particle volume concentration and increasing inner Dean number. The enhancement of overall heat transfer coefficient was found to be 7%, 16.9% and 24.2% at 0.1%, 0.4% and 0.8% Al2O3/water nanofluid respectively when compared with water. The enhancement of tube side experimental Nusselt number was found to be 17%, 22.9% and 28% at 0.1%, 0.4% and 0.8% particle volume concentration of Al2O3/water nanofluid respectively when compared with water at fixed Dean number. The tests were conducted in the range of 1600 < De < 2700, and 5200 < Re < 8600 under laminar flow condition and counter flow configuration. These enhancements are due to higher thermal conductivity of nanofluid while increasing particle volume concentration and Brownian motion of nanoparticles. It is studied that there is no negative impact on formation of secondary flow and mixing of fluid when nanofluid passes through the helically coiled tube.

A NEW SIMPLE DYNAMO MODEL FOR STELLAR ACTIVITY CYCLE

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yokoi, N.; Hamba, F.; Schmitt, D.

2016-06-20

A new simple dynamo model for stellar activity cycle is proposed. By considering an inhomogeneous flow effect on turbulence, it is shown that turbulent cross helicity (velocity–magnetic-field correlation) enters the expression of turbulent electromotive force as the coupling coefficient for the mean absolute vorticity. This makes the present model different from the current α –Ω-type models in two main ways. First, in addition to the usual helicity ( α ) and turbulent magnetic diffusivity ( β ) effects, we consider the cross-helicity effect as a key ingredient of the dynamo process. Second, the spatiotemporal evolution of cross helicity is solvedmore » simultaneously with the mean magnetic fields. The basic scenario is as follows. In the presence of turbulent cross helicity, the toroidal field is induced by the toroidal rotation. Then, as in usual models, the α effect generates the poloidal field from the toroidal one. This induced poloidal field produces a turbulent cross helicity whose sign is opposite to the original one (negative production). With this cross helicity of the reversed sign, a reversal in field configuration starts. Eigenvalue analyses of the simplest possible model give a butterfly diagram, which confirms the above scenario and the equatorward migrations, the phase relationship between the cross helicity and magnetic fields. These results suggest that the oscillation of the turbulent cross helicity is a key for the activity cycle. The reversal of the cross helicity is not the result of the magnetic-field reversal, but the cause of the latter. This new model is expected to open up the possibility of the mean-field or turbulence closure dynamo approaches.« less

Data on diverse roles of helix perturbations in membrane proteins.

PubMed

Shelar, Ashish; Bansal, Manju

2016-12-01

The various structural variations observed in TM helices of membrane proteins have been deconstructed into 9 distinct types of helix perturbations. These perturbations are defined by the deviation of TM helices from the predominantly observed linear α-helical conformation, to form 3 10 - and π-helices, as well as adopting curved and kinked geometries. The data presented here supplements the article 'Helix perturbations in Membrane Proteins Assist in Inter-helical Interactions and Optimal Helix Positioning in the Bilayer' (A. Shelar, M. Bansal, 2016) [1]. This data provides strong evidence for the role of various helix perturbations in influencing backbone torsion angles of helices, mediating inter-helical interactions, oligomer formation and accommodation of hydrophobic residues within the bilayer. The methodology used for creation of various datasets of membrane protein families (Sodium/Calcium exchanger and Heme Copper Oxidase) has also been mentioned.

The Great Solar Active Region NOAA 12192: Helicity Transport, Filament Formation, and Impact on the Polar Field

DOE Office of Scientific and Technical Information (OSTI.GOV)

McMaken, Tyler C.; Petrie, Gordon J. D., E-mail: tmcmaken@gmail.com, E-mail: gpetrie@noao.edu

The solar active region (AR), NOAA 12192, appeared in 2014 October as the largest AR in 24 years. Here we examine the counterintuitive nature of two diffusion-driven processes in the region: the role of helicity buildup in the formation of a major filament, and the relationship between the effects of supergranular diffusion and meridional flow on the AR and on the polar field. Quantitatively, calculations of current helicity and magnetic twist from Helioseismic and Magnetic Imager (HMI) vector magnetograms indicate that, though AR 12192 emerged with negative helicity, positive helicity from subsequent flux emergence, consistent with the hemispheric sign-preference ofmore » helicity, increased over time within large-scale, weak-field regions such as those near the polarity inversion line (PIL). Morphologically, Atmospheric Imaging Assembly observations of filament barbs, sigmoidal patterns, and bases of Fe xii stalks initially exhibited signatures of negative helicity, and the long filament that subsequently formed had a strong positive helicity consistent with the helicity buildup along the PIL. We find from full-disk HMI magnetograms that AR 12192's leading positive flux was initially closer to the equator but, owing either to the region’s magnetic surroundings or to its asymmetric flux density distribution, was transported poleward more quickly on average than its trailing negative flux, contrary to the canonical pattern of bipole flux transport. This behavior caused the AR to have a smaller effect on the polar fields than expected and enabled the formation of the very long neutral line where the filament formed.« less

Wind Tunnel Investigation of the Near-wake Flow Dynamics of a Horizontal Axis Wind Turbine

NASA Astrophysics Data System (ADS)

Hashemi-Tari, P.; Siddiqui, K.; Refan, M.; Hangan, H.

2014-06-01

Experiments conducted in a large wind tunnel set-up investigate the 3D flow dynamics within the near-wake region of a horizontal axis wind turbine. Particle Image Velocimetry (PIV) measurements quantify the mean and turbulent components of the flow field. Measurements are performed in multiple adjacent horizontal planes in order to cover the area behind the rotor in a large radial interval, at several locations downstream of the rotor. The measurements were phase-locked in order to facilitate the re-construction of the threedimensional flow field. The mean velocity and turbulence characteristics clearly correlate with the near-wake vortex dynamics and in particular with the helical structure of the flow, formed immediately behind the turbine rotor. Due to the tip and root vortices, the mean and turbulent characteristics of the flow are highly dependent on the azimuth angle in regions close to the rotor and close to the blade tip and root. Further from the rotor, the characteristics of the flow become phase independent. This can be attributed to the breakdown of the vortical structure of the flow, resulting from the turbulent diffusion. In general, the highest levels of turbulence are observed in shear layer around the tip of the blades, which decrease rapidly downstream. The shear zone grows in the radial direction as the wake moves axially, resulting in velocity recovery toward the centre of the rotor due to momentum transport.

Recognition of DNA bulges by dinuclear iron(II) metallosupramolecular helicates.

PubMed

Malina, Jaroslav; Hannon, Michael J; Brabec, Viktor

2014-02-01

Bulged DNA structures are of general biological significance because of their important roles in a number of biochemical processes. Compounds capable of targeting bulged DNA sequences can be used as probes for studying their role in nucleic acid function, or could even have significant therapeutic potential. The interaction of [Fe(2)L(3)](4+) metallosupramolecular helicates (L = C(25)H(20)N(4)) with DNA duplexes containing bulges has been studied by measurement of the DNA melting temperature and gel electrophoresis. This study was aimed at exploring binding affinities of the helicates for DNA bulges of various sizes and nucleotide sequences. The studies reported herein reveal that both enantiomers of [Fe(2)L(3)](4+) bind to DNA bulges containing at least two unpaired nucleotides. In addition, these helicates show considerably enhanced affinity for duplexes containing unpaired pyrimidines in the bulge and/or pyrimidines flanking the bulge on both sides. We suggest that the bulge creates the structural motif, such as the triangular prismatic pocket formed by the unpaired bulge bases, to accommodate the [Fe(2)L(3)](4+) helicate molecule, and is probably responsible for the affinity for duplexes with a varying number of bulge bases. Our results reveal that DNA bulges represent another example of unusual DNA structures recognized by dinuclear iron(II) ([Fe(2)L(3)](4+)) supramolecular helicates. © 2013 FEBS.

Radial vorticity constraint in core flow modeling

NASA Astrophysics Data System (ADS)

Asari, S.; Lesur, V.

2011-11-01

We present a new method for estimating core surface flows by relaxing the tangentially geostrophic (TG) constraint. Ageostrophic flows are allowed if they are consistent with the radial component of the vorticity equation under assumptions of the magnetostrophic force balance and an insulating mantle. We thus derive a tangentially magnetostrophic (TM) constraint for flows in the spherical harmonic domain and implement it in a least squares inversion of GRIMM-2, a recently proposed core field model, for temporally continuous core flow models (2000.0-2010.0). Comparing the flows calculated using the TG and TM constraints, we show that the number of degrees of freedom for the poloidal flows is notably increased by admitting ageostrophic flows compatible with the TM constraint. We find a significantly improved fit to the GRIMM-2 secular variation (SV) by including zonal poloidal flow in TM flow models. Correlations between the predicted and observed length-of-day variations are equally good under the TG and TM constraints. In addition, we estimate flow models by imposing the TM constraint together with other dynamical constraints: either purely toroidal (PT) flow or helical flow constraint. For the PT case we cannot find any flow which explains the observed SV, while for the helical case the SV can be fitted. The poor compatibility between the TM and PT constraints seems to arise from the absence of zonal poloidal flows. The PT flow assumption is likely to be negated when the radial magnetostrophic vorticity balance is taken into account, even if otherwise consistent with magnetic observations.

Generation of large-scale vorticity in rotating stratified turbulence with inhomogeneous helicity: mean-field theory

NASA Astrophysics Data System (ADS)

Kleeorin, N.

2018-06-01

We discuss a mean-field theory of the generation of large-scale vorticity in a rotating density stratified developed turbulence with inhomogeneous kinetic helicity. We show that the large-scale non-uniform flow is produced due to either a combined action of a density stratified rotating turbulence and uniform kinetic helicity or a combined effect of a rotating incompressible turbulence and inhomogeneous kinetic helicity. These effects result in the formation of a large-scale shear, and in turn its interaction with the small-scale turbulence causes an excitation of the large-scale instability (known as a vorticity dynamo) due to a combined effect of the large-scale shear and Reynolds stress-induced generation of the mean vorticity. The latter is due to the effect of large-scale shear on the Reynolds stress. A fast rotation suppresses this large-scale instability.

Anomalous transport and generalized axial charge

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kirilin, Vladimir P.; Sadofyev, Andrey V.

For this article, we continue studying the modification of the axial charge in chiral media by macroscopic helicities. Recently it was shown that magnetic reconnections result in a persistent current of zero mode along flux tubes. Here we argue that in general a change in the helical part of the generalized axial charge results in the same phenomenon. Thus one may say that there is a novel realization of chiral effects requiring no initial chiral asymmetry. The transfer of flow helicity to zero modes is analyzed in a toy model based on a vortex reconnection in a chiral superfluid. Then,more » we discuss the balance between the two competing processes effect of reconnections and the chiral instability on the example of magnetic helicity. We argue that in the general case there is a possibility for the distribution of the axial charge between the magnetic and fermionic forms at the end of the instability.« less

Anomalous transport and generalized axial charge

DOE PAGES

Kirilin, Vladimir P.; Sadofyev, Andrey V.

2017-07-25

For this article, we continue studying the modification of the axial charge in chiral media by macroscopic helicities. Recently it was shown that magnetic reconnections result in a persistent current of zero mode along flux tubes. Here we argue that in general a change in the helical part of the generalized axial charge results in the same phenomenon. Thus one may say that there is a novel realization of chiral effects requiring no initial chiral asymmetry. The transfer of flow helicity to zero modes is analyzed in a toy model based on a vortex reconnection in a chiral superfluid. Then,more » we discuss the balance between the two competing processes effect of reconnections and the chiral instability on the example of magnetic helicity. We argue that in the general case there is a possibility for the distribution of the axial charge between the magnetic and fermionic forms at the end of the instability.« less

Instrumental Implementation of an Experiment to Demonstrate αω -dynamos in Accretion Disks

NASA Astrophysics Data System (ADS)

Si, Jiahe; Sonnenfeld, Richard; Colgate, Art; Li, Hui; Nornberg, Mark

2016-10-01

The New Mexico Liquid Metal αω -dynamo experiment is aimed to demonstrate a galactic dynamo. Our goal is to generate the ω-effect and α-effect by two semi-coherent flows in laboratory. Two coaxial cylinders are used to generate Taylor-Couette flows to simulate the differential rotation of accretion disks. Plumes induced by jets injected into the Couette flows are expected to produce helicities necessary for the α-effect. We have demonstrated an 8-fold poloidal-to-toroidal flux amplification from differential rotation (the ω-effect) by minimizing turbulence in our apparatus. To demonstrate the α-effect, the experimental apparatus is undergoing significant upgrade. We have constructed a helicity injection facility, and are also designing and testing a new data acquisition system capable of transmitting data in a high speed rotating frame. Additional magnetic field diagnostics will also be included. The upgrade is intended to answer the question of whether a self-sustaining αω -dynamo can be constructed with a realistic fluid flow field, as well as to obtain more details to understand dynamo action in highly turbulent Couette flow.

Topological properties of microwave magnetoelectric fields.

PubMed

Berezin, M; Kamenetskii, E O; Shavit, R

2014-02-01

Collective excitations of electron spins in a ferromagnetic sample dominated by the magnetic dipole-dipole interaction strongly influence the field structure of microwave radiation. A small quasi-two-dimensional ferrite disk with magnetic-dipolar-mode (MDM) oscillation spectra can behave as a source of specific fields in vacuum, termed magnetoelectric (ME) fields. A coupling between the time-varying electric and magnetic fields in the ME-field structures is different from such a coupling in regular electromagnetic fields. The ME fields are characterized by strong energy confinement at a subwavelength region of microwave radiation, topologically distinctive power-flow vortices, and helicity parameters [E. O. Kamenetskii, R. Joffe, and R. Shavit, Phys. Rev. E 87, 023201 (2013)]. We study topological properties of microwave ME fields by loading a MDM ferrite particle with different dielectric samples. We establish a close connection between the permittivity parameters of dielectric environment and the topology of ME fields. We show that the topology of ME fields is strongly correlated with the Fano-resonance spectra observed at terminals of a microwave structure. We reveal specific thresholds in the Fano-resonance spectra appearing at certain permittivity parameters of dielectric samples. We show that ME fields originated from MDM ferrite disks can be distinguished by topological portraits of the helicity parameters and can have a torsion degree of freedom. Importantly, the ME-field phenomena can be viewed as implementations of space-time coordinate transformations on waves.

Chitin: Formation of Helically Structured Chitin/CaCO3 Hybrids through an Approach Inspired by the Biomineralization Processes of Crustacean Cuticles (Small 38/2015).

PubMed

Matsumura, Shunichi; Kajiyama, Satoshi; Nishimura, Tatsuya; Kato, Takashi

2015-10-01

Biomineral-inspired hybrids forming helically ordered structures are developed by T. Kato and co-workers on page 5127. These helical hybrids consist of liquid-crystalline chitin and CaCO3 . They resemble the structures of crustacean cuticles such as the exoskeleton of a lobster or crayfish. These hybrids are formed through CaCO3 crystallization on the liquidcrystalline chitin templates. Polymer-stabilized amorphous CaCO3 is incorporated into the liquid-crystalline chitin templates. This approach is useful for the development of new hierarchical hybrid materials from abundant natural resources. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Cooperative alpha-helix formation of beta-lactoglobulin induced by sodium n-alkyl sulfates.

PubMed

Chamani, J; Moosavi-Movahedi, A A; Rajabi, O; Gharanfoli, M; Momen-Heravi, M; Hakimelahi, G H; Neamati-Baghsiah, A; Varasteh, A R

2006-01-01

It is generally assumed that folding intermediates contain partially formed native-like secondary structures. However, if we consider the fact that the conformational stability of the intermediate state is simpler than that of the native state, it would be expected that the secondary structures in a folding intermediate would not necessarily be similar to those of the native state. beta-Lactoglobulin is a predominantly beta-sheet protein, although it has a markedly high intrinsic preference for alpha-helical structure. The formation of non-native alpha-helical intermediate of beta-lactoglobulin was induced by n-alkyl sulfates including sodium octyl sulfate, SOS; sodium decyl sulfate, SDeS; sodium dodecyl sulfate, SDS; and sodium tetradecyl sulfate, STS at special condition. The effect of n-alkyl sulfates on the structure of native beta-lactoglobulin at pH 2 was utilized to investigate the contribution of hydrophobic interactions to the stability of non-native alpha-helical intermediate. The addition of various concentrations of n-alkyl sulfates to the native state of beta-lactoglobulin (pH 2) appears to support the stabilized form of non-native alpha-helical intermediate at pH 2. The m values of the intermediate state of beta-lactoglobulin by SOS, SDeS, SDS and STS showed substantial variation. The enhancement of m values as the stability criterion of non-native alpha-helical intermediate state corresponded with increasing chain length of the cited n-alkyl sulfates. The present results suggest that the folding reaction of beta-lactoglobulin follows a non-hierarchical mechanism and hydrophobic interactions play important roles in stabilizing the non-native alpha-helical intermediate state.

Accurate determination of interfacial protein secondary structure by combining interfacial-sensitive amide I and amide III spectral signals.

PubMed

Ye, Shuji; Li, Hongchun; Yang, Weilai; Luo, Yi

2014-01-29

Accurate determination of protein structures at the interface is essential to understand the nature of interfacial protein interactions, but it can only be done with a few, very limited experimental methods. Here, we demonstrate for the first time that sum frequency generation vibrational spectroscopy can unambiguously differentiate the interfacial protein secondary structures by combining surface-sensitive amide I and amide III spectral signals. This combination offers a powerful tool to directly distinguish random-coil (disordered) and α-helical structures in proteins. From a systematic study on the interactions between several antimicrobial peptides (including LKα14, mastoparan X, cecropin P1, melittin, and pardaxin) and lipid bilayers, it is found that the spectral profiles of the random-coil and α-helical structures are well separated in the amide III spectra, appearing below and above 1260 cm(-1), respectively. For the peptides with a straight backbone chain, the strength ratio for the peaks of the random-coil and α-helical structures shows a distinct linear relationship with the fraction of the disordered structure deduced from independent NMR experiments reported in the literature. It is revealed that increasing the fraction of negatively charged lipids can induce a conformational change of pardaxin from random-coil to α-helical structures. This experimental protocol can be employed for determining the interfacial protein secondary structures and dynamics in situ and in real time without extraneous labels.

RNAHelix: computational modeling of nucleic acid structures with Watson-Crick and non-canonical base pairs.

PubMed

Bhattacharyya, Dhananjay; Halder, Sukanya; Basu, Sankar; Mukherjee, Debasish; Kumar, Prasun; Bansal, Manju

2017-02-01

Comprehensive analyses of structural features of non-canonical base pairs within a nucleic acid double helix are limited by the availability of a small number of three dimensional structures. Therefore, a procedure for model building of double helices containing any given nucleotide sequence and base pairing information, either canonical or non-canonical, is seriously needed. Here we describe a program RNAHelix, which is an updated version of our widely used software, NUCGEN. The program can regenerate duplexes using the dinucleotide step and base pair orientation parameters for a given double helical DNA or RNA sequence with defined Watson-Crick or non-Watson-Crick base pairs. The original structure and the corresponding regenerated structure of double helices were found to be very close, as indicated by the small RMSD values between positions of the corresponding atoms. Structures of several usual and unusual double helices have been regenerated and compared with their original structures in terms of base pair RMSD, torsion angles and electrostatic potentials and very high agreements have been noted. RNAHelix can also be used to generate a structure with a sequence completely different from an experimentally determined one or to introduce single to multiple mutation, but with the same set of parameters and hence can also be an important tool in homology modeling and study of mutation induced structural changes.

Structure-Preserving Variational Multiscale Modeling of Turbulent Incompressible Flow with Subgrid Vortices

NASA Astrophysics Data System (ADS)

Evans, John; Coley, Christopher; Aronson, Ryan; Nelson, Corey

2017-11-01

In this talk, a large eddy simulation methodology for turbulent incompressible flow will be presented which combines the best features of divergence-conforming discretizations and the residual-based variational multiscale approach to large eddy simulation. In this method, the resolved motion is represented using a divergence-conforming discretization, that is, a discretization that preserves the incompressibility constraint in a pointwise manner, and the unresolved fluid motion is explicitly modeled by subgrid vortices that lie within individual grid cells. The evolution of the subgrid vortices is governed by dynamical model equations driven by the residual of the resolved motion. Consequently, the subgrid vortices appropriately vanish for laminar flow and fully resolved turbulent flow. As the resolved velocity field and subgrid vortices are both divergence-free, the methodology conserves mass in a pointwise sense and admits discrete balance laws for energy, enstrophy, and helicity. Numerical results demonstrate the methodology yields improved results versus state-of-the-art eddy viscosity models in the context of transitional, wall-bounded, and rotational flow when a divergence-conforming B-spline discretization is utilized to represent the resolved motion.

Impact of hydrodynamic stresses on bacterial flagella

NASA Astrophysics Data System (ADS)

Das, Debasish; Riley, Emily; Lauga, Eric

2017-11-01

The locomotion of bacteria powered by helical filaments, such as Escherichia coli, critically involves the generation of flows and hydrodynamic stresses which lead to forces and moments balanced by the moment applied by the bacterial rotary motor (which is embedded in the cell wall) and the deformation of the short flexible hook. In this talk we use numerical computations to accurately compute these hydrodynamic stresses, to show how they critically lead to fluid-structure instabilities at the whole-cell level, and enquire if they can be used to rationalise experimental measurements of bacterial motor torques. ERC Consolidator Grant.

Unfolding four-helix bundles

NASA Astrophysics Data System (ADS)

Gray, Harry B.; Winkler, Jay R.; Kozak, John J.

2011-03-01

A geometrical model has been developed to describe the early stages of unfolding of cytochromes c‧ and c-b562 . Calculations are based on a step-wise extension of the polypeptide chain subject to the constraint that the spatial relationship among the residues of each triplet is fixed by the native-state crystallographic data. The response of each protein to these structural perturbations allows the evolution of each of the four helices in these two proteins to be differentiated. It is found that the two external helices in c‧ unfold before its two internal helices, whereas exactly the opposite behaviour is demonstrated by c-b562 . Each of these cytochromes has an extended, internal, non-helical ('turning') region that initially lags behind the most labile helix but then, at a certain stage (identified for each cytochrome), unravels before any of the four helices present in the native structure. It is believed that these predictions will be useful in guiding future experimental studies on the unfolding of these two cytochromes.

The Origins of Magnetic Structure in the Corona and Wind

NASA Technical Reports Server (NTRS)

Antiochos, Spiro K.

2010-01-01

One of the most important and most puzzling features of the coronal magnetic field is that it appears to have smooth magnetic structure with little evidence for non-potentiality except at two special locations: photospheric polarity inversions lines. (non-potentiality observed as a filament channel) and coronal hole boundaries, (observed as the slow solar wind). This characteristic feature of the closed-field corona is highly unexpected given that its magnetic field is continuously tangled by photospheric motions. Although reconnection can eliminate some of the injected structure, it cannot destroy the helicity, which should build up to produce observable complexity. I propose that an inverse cascade process transports the injected helicity from the interior of closed flux regions to their boundaries inversion lines and coronal holes, creating both filament channels and the slow wind. We describe how the helicity is injected and transported and calculate the relevant rates. I argue that one process, helicity transport, can explain both the observed lack and presence of structure in the coronal magnetic field. This work has been supported by the NASA HTP, SR&T, and LWS programs.

NMR structure of the water soluble Aβ17-34 peptide.

PubMed

Fonar, Genadiy; Samson, Abraham O

2014-11-24

Alzheimer's disease is the most common neurodegenerative disorder in the world. Its most significant symptoms are memory loss and decrease in cognition. Alzheimer's disease is characterized by aggregation of two proteins in the brain namely Aβ (amyloid β) and tau. Recent evidence suggests that the interaction of soluble Aβ with nAChR (nicotinic acetylcholine receptors) contributes to disease progression. In this study, we determine the NMR structure of an Aβ17-34 peptide solubilized by the addition of two glutamic acids at each terminus. Our results indicate that the Aβ peptide adopts an α-helical structure for residues 19-26 and 28-33. The α-helical structure is broken around residues S26, N27 and K28, which form a kink in the helical conformation. This α-helix was not described earlier in an aqueous solution without organic solvents, and at physiological conditions (pH 7). These data are in agreement with Aβ adopting an α-helical conformation in the membrane before polymerizing into amyloid β-sheets and provide insight into the intermediate state of Aβ in Alzheimer's disease.

Helix-packing motifs in membrane proteins.

PubMed

Walters, R F S; DeGrado, W F

2006-09-12

The fold of a helical membrane protein is largely determined by interactions between membrane-imbedded helices. To elucidate recurring helix-helix interaction motifs, we dissected the crystallographic structures of membrane proteins into a library of interacting helical pairs. The pairs were clustered according to their three-dimensional similarity (rmsd

Measurement of intercolumnar forces between parallel guanosine four-stranded helices.

PubMed Central

Mariani, P; Saturni, L

1996-01-01

The deoxyguanosine-5'-monophosphate in aqueous solution self-associates into stable structures, which include hexagonal and cholesteric columnar phases. The structural unit is a four-stranded helix, composed of a stacked array of Hoogsteen-bonded guanosine quartets. We have measured by osmotic stress method the force per unit length versus interaxial distance between helices in the hexagonal phase under various ionic conditions. Two contributions have been recognized: the first one is purely electrostatic, is effective at large distances, and shows a strong dependence on the salt concentration of the solution. The second contribution is short range, dominates at interaxial separations smaller than about 30-32 A, and rises steeply as the columns approach each other, preventing the coalescence of the helices. This repulsion has an exponential nature and shows a magnitude and a decay length insensitive to the ionic strength of the medium. Because these features are distinctive of the hydration force detected between phospholipid bilayers or between several linear macromolecules (DNA, polysaccharides, collagen), we conclude that the dominant force experienced by deoxyguanosine helices approaching contact is hydration repulsion. The observed decay length of about 0.7 A has been rationalized to emerge from the coupling between the 3-A decay length of water solvent and the helically ordered structure of the hydrophilic groups on the opposing surfaces. The present results agree with recent measurements, also showing the dependence of the hydration force decay on the structure of interacting surfaces and confirm the correlations between force and structure. Images FIGURE 1 PMID:8744324

Measurements of the canonical helicity evolution of a gyrating kinked plasma column

NASA Astrophysics Data System (ADS)

von der Linden, Jens; Sears, Jason; Intrator, Thomas; You, Setthivoine

2017-10-01

Conversions between kinetic and magnetic energy occur over a wide range of plasma scales as exhibited in astrophysical and solar dynamos, and reconnection in the solar corona and laboratory experiments. Canonical flux tubes present the distinct advantage of reconciling all plasma regimes - e.g. kinetic, two-fluid, and MHD - with the topological concept of helicity: twists, writhes, and linkages. This poster presents the first visualization and analysis of the 3D dynamics of canonical flux tubes and their relative helicity evolution from experimental measurements. Ion and electron canonical flux tubes are visualized from Mach, triple, and Ḃ probe measurements at over 10,000 spatial locations of a gyrating kinked plasma column. The flux tubes co-gyrate with the peak density and electron temperature in and out of a measurement volume. The electron and ion canonical flux tubes twist with opposite handedness and the ion flux tube writhes around the electron flux tube. The relative cross helicity between the magnetic and ion flow vorticity flux tubes dominates the relative ion canonical helicity and is anticorrelated with the relative magnetic helicity. The 3D nature of the kink and a reverse eddy current affect the helicity evolution. This work is supported by DOE Grant DE-SC0010340 and the DOE Office of Science Graduate Student Research Program and prepared in part by LLNL under Contract DE-AC52-07NA27344. LLNL-ABS-734669.

Numerical analysis of wall shear stress in ascending aorta before tearing in type A aortic dissection.

PubMed

Chi, Qingzhuo; He, Ying; Luan, Yong; Qin, Kairong; Mu, Lizhong

2017-10-01

Although the incidence of many cardiovascular diseases has declined as medical treatments have improved, the prevalence of aortic dissection (AD) has increased. Compared to type B dissections, type A dissections are more severe, and most patients with type A dissections require surgical treatment. The objective of this study was to investigate the relationships between the wall shear stress (WSS) on the aortic endothelium and the frequent tearing positions using computational fluid dynamics. Five type A dissection cases and two normal aortas were included in the study. First, the structures of the aortas before the type A dissection were reconstructed on the basis of the original imaging data. Analyses of flow in the reconstructed premorbid structures reveals that the rupture positions in three of the five cases corresponded to the area of maximum elevated WSS. Moreover, the WSS at the junction of the aortic arch and descending aorta was found to be elevated, which is considered to be related to the locally disturbed helical flow. Meanwhile, the highest WSS in the patients with premorbid AD was found to be almost double that of the control group. Due to the noticeable morphological differences between the AD cases and the control group, the WSSs in the premorbid structures without vasodilation in the ascending part were estimated. The computational results revealed that the WSS was lower in the aorta without vasodilation, but the pressure drop in this situation was higher than that with vasodilation in the ascending aorta. Significant differences were seen between the AD cases and the control group in the angles of the side branches of the aortic arch and its bending degree. Dilation of the ascending aorta and alterations in the branching angles may be the key determinants of a high WSS that leads to type A dissection. Greater tortuosity of the aortic arch leads to stronger helical flow through the distal aortic arch, which may be related to tears in this region. Copyright © 2017 Elsevier Ltd. All rights reserved.

Numerical investigation of Dean vortices in a curved pipe

NASA Astrophysics Data System (ADS)

Bernad, S. I.; Totorean, A.; Bosioc, A.; Stanciu, R.; Bernad, E. S.

2013-10-01

This study is devoted to the three-dimensional numerical simulation of developing secondary flows of Newtonian fluid through a curved circular duct. The numerical simulations produced for different Dean numbers show clearly the presence of two steady Dean vortices. Therefore, results confirm that helical flow constitutes an important flow signature in vessels, and its strength as a fluid dynamic index.

Robust integer and fractional helical modes in the quantum Hall effect

NASA Astrophysics Data System (ADS)

Ronen, Yuval; Cohen, Yonatan; Banitt, Daniel; Heiblum, Moty; Umansky, Vladimir

2018-04-01

Electronic systems harboring one-dimensional helical modes, where spin and momentum are locked, have lately become an important field of their own. When coupled to a conventional superconductor, such systems are expected to manifest topological superconductivity; a unique phase hosting exotic Majorana zero modes. Even more interesting are fractional helical modes, yet to be observed, which open the route for realizing generalized parafermions. Possessing non-Abelian exchange statistics, these quasiparticles may serve as building blocks in topological quantum computing. Here, we present a new approach to form protected one-dimensional helical edge modes in the quantum Hall regime. The novel platform is based on a carefully designed double-quantum-well structure in a GaAs-based system hosting two electronic sub-bands; each tuned to the quantum Hall effect regime. By electrostatic gating of different areas of the structure, counter-propagating integer, as well as fractional, edge modes with opposite spins are formed. We demonstrate that, due to spin protection, these helical modes remain ballistic over large distances. In addition to the formation of helical modes, this platform can serve as a rich playground for artificial induction of compounded fractional edge modes, and for construction of edge-mode-based interferometers.

Measurement of the dynamo effect in a plasma

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ji, H.; Prager, S.C.; Almagri, A.F.

1995-11-01

A series of the detailed experiments has been conducted in three laboratory plasma devices to measure the dynamo electric field along the equilibrium field line (the {alpha} effect) arising from the correlation between the fluctuating flow velocity and magnetic field. The fluctuating flow velocity is obtained from probe measurement of the fluctuating E x B drift and electron diamagnetic drift. The three major findings are (1) the {alpha} effect accounts for the dynamo current generation, even in the time dependence through a ``sawtooth`` cycle; (2) at low collisionality the dynamo is explained primarily by the widely studied pressureless Magnetohydrodynamic (MHD)more » model, i.e., the fluctuating velocity is dominated by the E x B drift; (3) at high collisionality, a new ``electron diamagnetic dynamo`` is observed, in which the fluctuating velocity is dominated by the diamagnetic drift. In addition, direct measurements of the helicity flux indicate that the dynamo activity transports magnetic helicity from one part of the plasma to another, but the total helicity is roughly conserved, verifying J.B. Taylor`s conjecture.« less

Helicity in Supercritical O2/H2 and C7H16/N2 Mixing Layers

NASA Technical Reports Server (NTRS)

Okongo, Nora; Bellan, Josette

2004-01-01

This report describes a study of databases produced by direct numerical simulation of mixing layers developing between opposing flows of two fluids under supercritical conditions, the purpose of the study being to elucidate chemical-species-specific aspects of turbulence, with emphasis on helicity. The simulations were performed for two different fluid pairs -- O2/H2 and C7H16/N2 -- at similar values of reduced pressure.

Helical Antimicrobial Sulfono- {gamma} -AApeptides

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Yaqiong; Wu, Haifan; Teng, Peng

Host-defense peptides (HDPs) such as magainin 2 have emerged as potential therapeutic agents combating antibiotic resistance. Inspired by their structures and mechanism of action, herein we report the fi rst example of antimicrobial helical sulfono- γ - AApeptide foldamers. The lead molecule displays broad-spectrum and potent antimicrobial activity against multi-drug-resistant Gram- positive and Gram-negative bacterial pathogens. Time-kill studies and fl uorescence microscopy suggest that sulfono- γ -AApeptides eradicate bacteria by taking a mode of action analogous to that of HDPs. Clear structure - function relationships exist in the studied sequences. Longer sequences, presumably adopting more-de fi ned helical structures, aremore » more potent than shorter ones. Interestingly, the sequence with less helical propensity in solution could be more selective than the stronger helix-forming sequences. Moreover, this class of antimicrobial agents are resistant to proteolytic degradation. These results may lead to the development of a new class of antimicrobial foldamers combating emerging antibiotic-resistant pathogens.« less

Control of the Helicity Content of a Gun-Generated Spheromak by Incorporating a Conducting Shell into a Magnetized Coaxial Plasma Gun

NASA Astrophysics Data System (ADS)

Matsumoto, Tadafumi; Sekiguchi, Jun'ichi; Asai, Tomohiko

In the formation of magnetized plasmoid by a magnetized coaxial plasma gun (MCPG), the magnetic helicity content of the generated plasmoid is one of the critical parameters. Typically, the bias coil to generate a poloidal flux is mounted either on the outer electrode or inside the inner electrode. However, most of the flux generated in the conventional method spreads even radially outside of the formation region. Thus, only a fraction of the total magnetic flux is actually exploited for helicity generation in the plasmoid. In the proposed system, the plasma gun incorporates a copper shell mounted on the outer electrode. By changing the rise time of the discharge bias coil current and the geometrical structure of the shell, the magnetic field structure and its time evolution can be controlled. The effect of the copper shell has been numerically simulated for the actual gun structure, and experimentally confirmed. This may increase the magnetic helicity content results, through increased poloidal magnetic field.

Specific arrangement of alpha-helical coiled coils in the core domain of the bacterial flagellar hook for the universal joint function.

PubMed

Fujii, Takashi; Kato, Takayuki; Namba, Keiichi

2009-11-11

The bacterial flagellar hook is a short, highly curved tubular structure connecting the rotary motor to the filament acting as a helical propeller. The bending flexibility of the hook allows it to work as a universal joint. A partial atomic model of the hook revealed a sliding intersubunit domain interaction along the protofilament to produce bending flexibility. However, it remained unclear how the tightly packed inner core domains can still permit axial extension and compression. We report advances in cryoEM image analysis for high-resolution, high-throughput structural analysis and a density map of the hook that reveals most of the secondary structures, including the terminal alpha helices forming a coiled coil. The orientations and axial packing interactions of these two alpha helices are distinctly different from those of the filament, allowing them to have a room for axial compression and extension for bending flexibility without impairing the mechanical stability of the hook.

NMR determination of an incommensurate helical antiferromagnetic structure in EuCo 2 As 2

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ding, Q. -P.; Higa, N.; Sangeetha, N. S.

In this paper, we report 153Eu, 75As, and 59Co nuclear magnetic resonance (NMR) results on EuCo 2As 2 single crystal. Observations of 153Eu and 75As NMR spectra in zero magnetic field at 4.3 K below an antiferromagnetic (AFM) ordering temperature T N = 45 K and its external magnetic field dependence clearly evidence an incommensurate helical AFM structure in EuCo 2As 2. Furthermore, based on 59Co NMR data in both the paramagnetic and the incommensurate AFM states, we have determined the model-independent value of the AFM propagation vector k = (0,0,0.73 ± 0.07)2π/c, where c is the c lattice parameter.more » Finally, the incommensurate helical AFM state was characterized by only NMR data with model-independent analyses, showing NMR to be a unique tool for determination of the spin structure in incommensurate helical AFMs.« less

NMR determination of an incommensurate helical antiferromagnetic structure in EuCo 2 As 2

DOE PAGES

Ding, Q. -P.; Higa, N.; Sangeetha, N. S.; ...

2017-05-05

In this paper, we report 153Eu, 75As, and 59Co nuclear magnetic resonance (NMR) results on EuCo 2As 2 single crystal. Observations of 153Eu and 75As NMR spectra in zero magnetic field at 4.3 K below an antiferromagnetic (AFM) ordering temperature T N = 45 K and its external magnetic field dependence clearly evidence an incommensurate helical AFM structure in EuCo 2As 2. Furthermore, based on 59Co NMR data in both the paramagnetic and the incommensurate AFM states, we have determined the model-independent value of the AFM propagation vector k = (0,0,0.73 ± 0.07)2π/c, where c is the c lattice parameter.more » Finally, the incommensurate helical AFM state was characterized by only NMR data with model-independent analyses, showing NMR to be a unique tool for determination of the spin structure in incommensurate helical AFMs.« less

Magneto-orbital helices: a novel coupling mechanism between magnetism and ferroelectricity in multiferroic CaMn7O12

NASA Astrophysics Data System (ADS)

Radaelli, Paolo G.; Perks, Natasha; Johnson, Roger D.; Martin, Christine; Chapon, Laurent

2013-03-01

The trigonal quadruple perovskite CaMn7O12 displays one of the largest magnetically induced ferroelectric polarisations measured to date (2870 μC m-2). Ferroelectricity appears below 90 K, together with an incommensurate helical magnetic modulation, and cannot be explained within the framework developed for cycloidal magnets. We report an unprecedented magneto-orbital texture in multiferroic CaMn7O12, which is directly connected to ferroelectricity. X-ray and neutron diffraction characterisation of the structural and magnetic modulations in these ``magneto-orbital helices'', and analysis of magnetic exchange shows that orbital order is crucial in stabilising a chiral magnetic structure. Additionally, the presence of a global structural rotation enables the magnetic helicity to couple with the lattice, giving rise to electric polarisation. These novel principles open up the possibility of discovering new multiferroics with even larger polarization and higher transition temperatures. Work at Oxford was funded by EPSRC grant EP/J003557/1.

The spatial configuration of ordered polynucleotide chains. II. The poly(rA) helix.

PubMed Central

Olson, W K

1975-01-01

Approximate details of the spatial configuration of the ordered single-stranded poly(rA) molecule in dilute solution have been obtained in a combined theoretical analysis of base stacking and chain flexibility. Only those regularly repeating structures which fulfill the criterion of conformational flexibility (based upon all available experimental and theoretical evidence of preferred bond rotations) and which also exhibit the right-handed base stacking pattern observed in nmr investigations of poly(rA) are deemed suitable single-stranded helices. In addition, the helical geometry of the stacked structures is required to be consistent with the experimentally observed dimensions of both completely ordered and partially ordered poly(rA) chains. Only a single category of poly(rA) helices (very similar in all conformational details to the individual chains of the poly(rA) double-stranded X-ray structure) is thus obtained. Other conformationally feasible polynucleotide helices characterized simply by a parallel and overlapping base stacking arrangement are also discussed. PMID:1052529

Contribution of long-range interactions to the secondary structure of an unfolded globin.

PubMed

Fedyukina, Daria V; Rajagopalan, Senapathy; Sekhar, Ashok; Fulmer, Eric C; Eun, Ye-Jin; Cavagnero, Silvia

2010-09-08

This work explores the effect of long-range tertiary contacts on the distribution of residual secondary structure in the unfolded state of an alpha-helical protein. N-terminal fragments of increasing length, in conjunction with multidimensional nuclear magnetic resonance, were employed. A protein representative of the ubiquitous globin fold was chosen as the model system. We found that, while most of the detectable alpha-helical population in the unfolded ensemble does not depend on the presence of the C-terminal region (corresponding to the native G and H helices), specific N-to-C long-range contacts between the H and A-B-C regions enhance the helical secondary structure content of the N terminus (A-B-C regions). The simple approach introduced here, based on the evaluation of N-terminal polypeptide fragments of increasing length, is of general applicability to identify the influence of long-range interactions in unfolded proteins. Copyright 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.

THE FORMATION AND ERUPTION OF A SMALL CIRCULAR FILAMENT DRIVEN BY ROTATING MAGNETIC STRUCTURES IN THE QUIET SUN

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Bo; Jiang, Yunchun; Yang, Jiayan

We present the first observation of the formation and eruption of a small circular filament driven by a rotating network magnetic field (RNF) in the quiet Sun. In the negative footpoint region of an inverse J-shaped dextral filament, the RNF was formed by the convergence to supergranular junctions of several magnetic flux patches of the same polarity, and it then rotated counterclockwise (CCW) for approximately 11 hr and showed up as a CCW rotating EUV cyclone, during which time the filament gradually evolved into a circular filament that surrounded the cyclone. When the calculated convergence and vortex flows appeared aroundmore » the RNF during its formation and rotation phases, the injected magnetic helicity calculation also showed negative helicity accumulation during the RNF rotation that was consistent with the dextral chirality of the filament. Finally, the RNF rotation stopped and the cyclone disappeared, and, probably due to an emerging bipole and its forced cancellation with the RNF, the closure filament underwent an eruption along its axis in the (clockwise) direction opposite to the rotation directions of the RNF and cyclone. These observations suggest that the RNFs might play an important role in the formation of nearby small-scale circular filaments as they transport and inject magnetic energy and helicity, and the formation of the EUV cyclones may be a further manifestation of the helicity injected into the corona by the rotation of the RNFs in the photosphere. In addition, the new emerging bipole observed before the filament eruption might be responsible for destabilizing the system and triggering the magnetic reconnection which proves useful for the filament eruption.« less

Experimental investigation of the wake behind a rotating sphere

NASA Astrophysics Data System (ADS)

Skarysz, M.; Rokicki, J.; Goujon-Durand, S.; Wesfreid, J. E.

2018-01-01

The wake behind a sphere, rotating about an axis aligned with the streamwise direction, has been experimentally investigated in a low-velocity water tunnel using laser-induced fluorescence visualizations and particle image velocimetry measurements. The measurements focused on the evolution of the flow regimes that appear depending on two control parameters: the Reynolds number Re and the dimensionless rotation or swirl rate Ω , which is the ratio of the maximum azimuthal velocity of the body to the free-stream velocity. In the present investigation, we cover the range of Re smaller than 400 and Ω from 0 and 4. Different wakes regimes such as an axisymmetric flow, a low helical state, and a high helical mode are represented in the (Re, Ω ) parameter plane.

Stimuli-Driven Control of the Helical Axis of Self-Organized Soft Helical Superstructures.

PubMed

Bisoyi, Hari Krishna; Bunning, Timothy J; Li, Quan

2018-06-01

Supramolecular and macromolecular functional helical superstructures are ubiquitous in nature and display an impressive catalog of intriguing and elegant properties and performances. In materials science, self-organized soft helical superstructures, i.e., cholesteric liquid crystals (CLCs), serve as model systems toward the understanding of morphology- and orientation-dependent properties of supramolecular dynamic helical architectures and their potential for technological applications. Moreover, most of the fascinating device applications of CLCs are primarily determined by different orientations of the helical axis. Here, the control of the helical axis orientation of CLCs and its dynamic switching in two and three dimensions using different external stimuli are summarized. Electric-field-, magnetic-field-, and light-irradiation-driven orientation control and reorientation of the helical axis of CLCs are described and highlighted. Different techniques and strategies developed to achieve a uniform lying helix structure are explored. Helical axis control in recently developed heliconical cholesteric systems is examined. The control of the helical axis orientation in spherical geometries such as microdroplets and microshells fabricated from these enticing photonic fluids is also explored. Future challenges and opportunities in this exciting area involving anisotropic chiral liquids are then discussed. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Zn(II) coordination polymers with flexible V-shaped dicarboxylate ligand: Syntheses, helical structures and properties

NASA Astrophysics Data System (ADS)

Li, Lin; Liu, Chong-Bo; Yang, Gao-Shan; Xiong, Zhi-Qiang; Liu, Hong; Wen, Hui-Liang

2015-11-01

Hydrothermal reactions of 2,2‧-[hexafluoroisopropylidenebis(p-phenyleneoxy)]diacetic acid (H2L) and zinc ions in the presence of N-donor ancillary ligands afford four novel coordination polymers, namely, [Zn2(μ2-OH)(μ4-O)0.5(L)]·0.5H2O (1), [Zn(L)(2,2‧-bipy)(H2O)] (2), [Zn3(L)3(phen)2]·H2O (3) and [Zn2(L)2(4,4‧-bipy)] (4) (2,2‧-bipy=2,2‧-bipyridine; 4,4‧-bipy=4,4‧-bipyridine; phen=1,10-phenanthroline). Their structures have been determined by single-crystal X-ray diffraction analyses, elemental analyses, IR spectra, powder X-ray diffraction (PXRD), and thermogravimetric (TG) analyses. Complex 1 shows a 3-D clover framework consisting of [Zn4(μ4-O)(μ2-OH)2]4+ clusters, and exhibits a novel (3,8)-connected topological net with the Schläfli symbol of {3·4·5}2{34·44·52·66·710·82}, and contains double-stranded and two kinds of meso-helices. 2 displays a helical chain structure, which is further extended via hydrogen bonds into a 3-D supramolecular structure with meso-helix chains. 3 displays a 2-D {44·62} parallelogram structure, which is further extended via hydrogen bonds into a 3-D supramolecular structure with single-stranded helical chains. 4 shows a 2-D {44·62} square structure with left- and right-handed helical chains. Moreover, the luminescent properties of 1-4 have been investigated.

Ultrastructural organization of connective tissue microfibrils in the posterior chamber of the eye in vivo and in vitro.

PubMed

Inoue, S

1995-02-01

The ultrastructural organization of connective tissue microfibrils was studied in the mouse eye and also by means of in vitro experiments for reconstituting microfibrils. In the posterior chamber of the eye of the C57BL/6J mouse, 3 nm-wide ribbon-like double-tracked structures were present and were periodically associated on either side with 3.5 nm-wide particulate structures identified as pentosomes, the subunits of amyloid P component (AP). At certain sites, such composite structures were observed in various stages of helical winding, and in these helices, pentosomes were preferentially localized internally. In helices in the final stages of winding, the resulting rods appeared increasingly similar to those of microfibrils. In experiments in vitro, incubation of chondroitin sulfate proteoglycan (CSPG) in TRIS buffer, pH 7.4, at 35 degrees C for 1 h produced random aggregates of 3 nm-wide double-tracked structures similar to those observed in the eye. Co-incubation of CSPG and AP resulted in the formation of rod-like structures arranged parallel to one another in approximately 50 nm-thick sheet-like layers. These rods were ultrastructurally similar to microfibrils and were made up of helically wound, 3 nm-wide double-tracked structures containing pentosomes within their core. The results of in vivo as well as in vitro experiments suggest the possibility that the connective tissue microfibril is composed of helically wound, CSPG-containing, 3 nm-wide double-tracked structures periodically associated with pentosomes which, as the helix becomes progressively tighter, fit with one another at the core of the helix to form successive 8.5 nm-wide disks of AP segments.

Water-stable helical structure of tertiary amides of bicyclic β-amino acid bearing 7-azabicyclo[2.2.1]heptane. Full control of amide cis-trans equilibrium by bridgehead substitution.

PubMed

Hosoya, Masahiro; Otani, Yuko; Kawahata, Masatoshi; Yamaguchi, Kentaro; Ohwada, Tomohiko

2010-10-27

Helical structures of oligomers of non-natural β-amino acids are significantly stabilized by intramolecular hydrogen bonding between main-chain amide moieties in many cases, but the structures are generally susceptible to the environment; that is, helices may unfold in protic solvents such as water. For the generation of non-hydrogen-bonded ordered structures of amides (tertiary amides in most cases), control of cis-trans isomerization is crucial, even though there is only a small sterical difference with respect to cis and trans orientations. We have established methods for synthesis of conformationally constrained β-proline mimics, that is, bridgehead-substituted 7-azabicyclo[2.2.1]heptane-2-endo-carboxylic acids. Our crystallographic, 1D- and 2D-NMR, and CD spectroscopic studies in solution revealed that a bridgehead methoxymethyl substituent completely biased the cis-trans equilibrium to the cis-amide structure along the main chain, and helical structures based on the cis-amide linkage were generated independently of the number of residues, from the minimalist dimer through the tetramer, hexamer, and up to the octamer, and irrespective of the solvent (e.g., water, alcohol, halogenated solvents, and cyclohexane). Generality of the control of the amide equilibrium by bridgehead substitution was also examined.

Structural dynamics of free proteins in diffraction.

PubMed

Lin, Milo M; Shorokhov, Dmitry; Zewail, Ahmed H

2011-10-26

Among the macromolecular patterns of biological significance, right-handed α-helices are perhaps the most abundant structural motifs. Here, guided by experimental findings, we discuss both ultrafast initial steps and longer-time-scale structural dynamics of helix-coil transitions induced by a range of temperature jumps in large, isolated macromolecular ensembles of an α-helical protein segment thymosin β(9) (Tβ(9)), and elucidate the comprehensive picture of (un)folding. In continuation of an earlier theoretical work from this laboratory that utilized a simplistic structure-scrambling algorithm combined with a variety of self-avoidance thresholds to approximately model helix-coil transitions in Tβ(9), in the present contribution we focus on the actual dynamics of unfolding as obtained from massively distributed ensemble-convergent MD simulations which provide an unprecedented scope of information on the nature of transient macromolecular structures, and with atomic-scale spatiotemporal resolution. In addition to the use of radial distribution functions of ultrafast electron diffraction (UED) simulations in gaining an insight into the elementary steps of conformational interconversions, we also investigate the structural dynamics of the protein via the native (α-helical) hydrogen bonding contact metric which is an intuitive coarse graining approach. Importantly, the decay of α-helical motifs and the (globular) conformational annealing in Tβ(9) occur consecutively or competitively, depending on the magnitude of temperature jump.

ON THE INJECTION OF HELICITY BY THE SHEARING MOTION OF FLUXES IN RELATION TO FLARES AND CORONAL MASS EJECTIONS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vemareddy, P.; Ambastha, A.; Maurya, R. A.

An investigation of helicity injection by photospheric shear motions is carried out for two active regions (ARs), NOAA 11158 and 11166, using line-of-sight magnetic field observations obtained from the Helioseismic and Magnetic Imager on board the Solar Dynamics Observatory. We derived the horizontal velocities in the ARs from the differential affine velocity estimator (DAVE) technique. Persistent strong shear motions at maximum velocities in the range of 0.6-0.9 km s{sup -1} along the magnetic polarity inversion line and outward flows from the peripheral regions of the sunspots were observed in the two ARs. The helicities injected in NOAA 11158 and 11166more » during their six-day evolution period were estimated as 14.16 Multiplication-Sign 10{sup 42} Mx{sup 2} and 9.5 Multiplication-Sign 10{sup 42} Mx{sup 2}, respectively. The estimated injection rates decreased up to 13% by increasing the time interval between the magnetograms from 12 minutes to 36 minutes, and increased up to 9% by decreasing the DAVE window size from 21 Multiplication-Sign 18 to 9 Multiplication-Sign 6 pixel{sup 2}, resulting in 10% variation in the accumulated helicity. In both ARs, the flare-prone regions (R2) had inhomogeneous helicity flux distribution with mixed helicities of both signs and coronal mass ejection (CME) prone regions had almost homogeneous distribution of helicity flux dominated by a single sign. The temporal profiles of helicity injection showed impulsive variations during some flares/CMEs due to negative helicity injection into the dominant region of positive helicity flux. A quantitative analysis reveals a marginally significant association of helicity flux with CMEs but not flares in AR 11158, while for the AR 11166, we find a marginally significant association of helicity flux with flares but not CMEs, providing evidence of the role of helicity injection at localized sites of the events. These short-term variations of helicity flux are further discussed in view of possible flare-related effects. This study suggests that flux motions and spatial distribution of helicity injection are important to understanding the complex nature of the magnetic flux system of the AR, and how it can lead to conditions favorable for eruptive events.« less

SIMULATING THE IN SITU CONDENSATION PROCESS OF SOLAR PROMINENCES

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xia, C.; Keppens, R.; Antolin, P.

2014-09-10

Prominences in the solar corona are a hundredfold cooler and denser than their surroundings, with a total mass of 10{sup 13} up to 10{sup 15} g. Here, we report on the first comprehensive simulations of three-dimensional, thermally and gravitationally stratified magnetic flux ropes where in situ condensation to a prominence occurs due to radiative losses. After a gradual thermodynamic adjustment, we witness a phase where runaway cooling occurs while counter-streaming shearing flows drain off mass along helical field lines. After this drainage, a prominence-like condensation resides in concave upward field regions, and this prominence retains its overall characteristics for moremore » than two hours. While condensing, the prominence establishes a prominence-corona transition region where magnetic field-aligned thermal conduction is operative during the runaway cooling. The prominence structure represents a force-balanced state in a helical flux rope. The simulated condensation demonstrates a right-bearing barb, as a remnant of the drainage. Synthetic images at extreme ultraviolet wavelengths follow the onset of the condensation, and confirm the appearance of horns and a three-part structure for the stable prominence state, as often seen in erupting prominences. This naturally explains recent Solar Dynamics Observatory views with the Atmospheric Imaging Assembly on prominences in coronal cavities demonstrating horns.« less

Kinetic Aspects of Surfactant-Induced Structural Changes of Proteins - Unsolved Problems of Two-State Model for Protein Denaturation -.

PubMed

Takeda, Kunio; Moriyama, Yoshiko

2015-01-01

The kinetic mechanism of surfactant-induced protein denaturation is discussed on the basis of not only stopped-flow kinetic data but also the changes of protein helicities caused by the surfactants and the discontinuous mobility changes of surfactant-protein complexes. For example, the α-helical structures of bovine serum albumin (BSA) are partially disrupted due to the addition of sodium dodecyl sulfate (SDS). Formation of SDS-BSA complex can lead to only four complex types with specific mobilities depending on the surfactant concentration. On the other hand, the apparent rate constant of the structural change of BSA increases with an increase of SDS concentration, indicating that the rate of the structural change becomes fast as the degree of the change increases. When a certain amount of surfactant ions bind to proteins, their native structures transform directly to particular structures without passing through intermediate stages that might be induced due to the binding of fewer amounts of the surfactant ions. Furthermore, this review brings up a question about two-state and three-state models, N⇌D and N⇌D'⇌D (N: native state, D: denatured sate, D': intermediate between N and D), which have been often adopted without hesitation in discussion on general denaturations of proteins. First of all, doubtful is whether any equilibrium relationship exists in such denaturation reactions. It cannot be disregarded that the D states in these models differ depending on the changes of intensities of the denaturing factors. The authors emphasize that the denaturations or the structural changes of proteins should be discussed assuming one-way reaction models with no backward processes rather than assuming the reversible two-state reaction models or similar modified reaction models.

Scale Dependence of Magnetic Helicity in the Solar Wind

NASA Technical Reports Server (NTRS)

Brandenburg, Axel; Subramanian, Kandaswamy; Balogh, Andre; Goldstein, Melvyn L.

2011-01-01

We determine the magnetic helicity, along with the magnetic energy, at high latitudes using data from the Ulysses mission. The data set spans the time period from 1993 to 1996. The basic assumption of the analysis is that the solar wind is homogeneous. Because the solar wind speed is high, we follow the approach first pioneered by Matthaeus et al. by which, under the assumption of spatial homogeneity, one can use Fourier transforms of the magnetic field time series to construct one-dimensional spectra of the magnetic energy and magnetic helicity under the assumption that the Taylor frozen-in-flow hypothesis is valid. That is a well-satisfied assumption for the data used in this study. The magnetic helicity derives from the skew-symmetric terms of the three-dimensional magnetic correlation tensor, while the symmetric terms of the tensor are used to determine the magnetic energy spectrum. Our results show a sign change of magnetic helicity at wavenumber k approximately equal to 2AU(sup -1) (or frequency nu approximately equal to 2 microHz) at distances below 2.8AU and at k approximately equal to 30AU(sup -1) (or nu approximately equal to 25 microHz) at larger distances. At small scales the magnetic helicity is positive at northern heliographic latitudes and negative at southern latitudes. The positive magnetic helicity at small scales is argued to be the result of turbulent diffusion reversing the sign relative to what is seen at small scales at the solar surface. Furthermore, the magnetic helicity declines toward solar minimum in 1996. The magnetic helicity flux integrated separately over one hemisphere amounts to about 10(sup 45) Mx(sup 2) cycle(sup -1) at large scales and to a three times lower value at smaller scales.

Non-lignified helical cell wall thickenings in root cortical cells of Aspleniaceae (Polypodiales): histology and taxonomical significance

PubMed Central

Leroux, O.; Bagniewska-Zadworna, A.; Rambe, S. K.; Knox, J. P.; Marcus, S. E.; Bellefroid, E.; Stubbe, D.; Chabbert, B.; Habrant, A.; Claeys, M.; Viane, R. L. L.

2011-01-01

Background and Aims Extraxylary helical cell wall thickenings in vascular plants are not well documented, except for those in orchid velamen tissues which have been studied extensively. Reports on their occurrence in ferns exist, but detailed information is missing. The aim of this study is to focus on the broad patterns of structure and composition and to study the taxonomic occurrence of helical cell wall thickenings in the fern family Aspleniaceae. Methods Structural and compositional aspects of roots have been examined by means of light, electron, epifluorescence and laser scanning confocal microscopy. To assess the taxonomical distribution of helical cell wall thickenings a molecular phylogenetic analysis based on rbcL sequences of 64 taxa was performed. Key Results The helical cell wall thickenings of all examined species showed considerable uniformity of design. The pattern consists of helical, regularly bifurcating and anastomosing strands. Compositionally, the cell wall thickenings were found to be rich in homogalacturonan, cellulose, mannan and xyloglucan. Thioacidolysis confirmed our negative phloroglucinol staining tests, demonstrating the absence of lignins in the root cortex. All taxa with helical cell wall thickenings formed a monophyletic group supported by a 100 % bootstrap value and composed of mainly epiphytic species. Conclusions This is the first report of non-lignified pectin-rich secondary cell walls in ferns. Based on our molecular analysis, we reject the hypothesis of parallel evolution of helical cell wall thickenings in Aspleniaceae. Helical cell wall thickenings can mechanically stabilize the cortex tissue, allowing maximal uptake of water and nutrients during rainfall events. In addition, it can also act as a boundary layer increasing the diffusive pathway towards the atmosphere, preventing desiccation of the stele of epiphytic growing species. PMID:21118842

Three-dimensional observation of an helical hot structure during a sawtooth crash in the WT-3 tokamak.

PubMed

Yamaguchi, S; Igami, H; Tanaka, H; Maekawa, T

2004-07-23

Sawtooth crashes in an Ohmically heated plasma in the WT-3 tokamak have been observed by using soft x-ray computer tomography at three different poloidal cross sections around the torus. Initially, collapsing proceeds slowly with keeping the helical structure of an m = 1/n = 1 hot core around the torus. It accelerates as the helical hot structure is strongly deformed and fades away in the manner that the hot core at the high field side becomes obscure and disappears, while that at the low field side is deformed into a thin crescent aligned along the inversion circle, which survives even at the completion of the crash. Copyright 2004 The American Physical Society

How Rosalind Franklin Discovered the Helical Structure of DNA: Experiments in Diffraction

NASA Astrophysics Data System (ADS)

Braun, Gregory; Tierney, Dennis; Schmitzer, Heidrun

2011-03-01

Rosalind Franklin, a chemical physicist (1920-1958), used x-ray diffraction to determine the structure of DNA. What exactly could she read out from her x-ray pattern, shown in Fig. 1? In lecture notes dated November 1951, R. Franklin wrote the following: "The results suggest a helical structure (which must be very closely packed) containing 2, 3 or 4 co-axial nucleic acid chains per helical unit, and having the phosphate groups near the outside."2 This was 16 months before J. D. Watson and F. Crick published their description of DNA, which was based on R. Franklin's x-ray photos. How they gained access to her x-ray photos is a fascinating tale of clashing personalities and male chauvinism.2,3

Slow wave structures using twisted waveguides for charged particle applications

DOEpatents

Kang, Yoon W.; Fathy, Aly E.; Wilson, Joshua L.

2012-12-11

A rapidly twisted electromagnetic accelerating structure includes a waveguide body having a central axis, one or more helical channels defined by the body and disposed around a substantially linear central axial channel, with central portions of the helical channels merging with the linear central axial channel. The structure propagates electromagnetic waves in the helical channels which support particle beam acceleration in the central axial channel at a phase velocity equal to or slower than the speed of light in free space. Since there is no variation in the shape of the transversal cross-section along the axis of the structure, inexpensive mechanical fabrication processes can be used to form the structure, such as extrusion, casting or injection molding. Also, because the field and frequency of the resonant mode depend on the whole structure rather than on dimensional tolerances of individual cells, no tuning of individual cells is needed. Accordingly, the overall operating frequency may be varied with a tuning/phase shifting device located outside the resonant waveguide structure.

Experimental Study of the Structure of a Wingtip Vortex

NASA Technical Reports Server (NTRS)

Anderson, Elgin A.; Wright, Christopher T.

2000-01-01

A complete look at the near-field development and subsequent role-up of a wingtip vortex from a NACA 0015 wing section is investigated. Two separate but equally important surveys of the vortex structure in the region adjacent to the wingtip and approximately one chord length downstream of the trailing edge are performed. The two surveys provide qualitative flow-visualization an quantitative velocity measurement data. The near-field development and subsequent role-up of the vortex structures is strongly influenced by the angle-of-attack and the end-cap treatment of the wing section. The velocity field near the wingtip of the NACA 0015 wing section was measured with a triple-sensor hot wire probe and compared to flow visualization images produced with titanium tetrachloride smoke injection and laser illumination. The flat end-cap results indicate the formation of multiple, relatively strong vortex structures as opposed to the formation of a single vortex produced with the round end-cap. The multiple vortices generated by the flat end-cap are seen to rotate around a common ce te in a helical pattern until they eventually merge into a single vortex. Compared to a non-dimensional loading parameter, the results of the velocity and flow visualization data shows a "jetlike" axial velocity profile for loading parameter values on the order of 0.1 and a "wakelike" profile for much lower loading parameter values.

Current trends in α-helical membrane protein crystallization: An update

PubMed Central

Parker, Joanne L; Newstead, Simon

2012-01-01

α-Helical membrane proteins (MPs) are the targets for many pharmaceutical drugs and play important roles in human physiology. In recent years, significant progress has been made in determining their atomic structure using X-ray crystallography. However, a major bottleneck in MP crystallography still remains, namely, the identification of conditions that give crystals that are suitable for structural determination. In 2008, we undertook an analysis of the crystallization conditions for 121 α-helical MPs to design a rationalized sparse matrix crystallization screen, MemGold. We now report an updated analysis that includes a further 133 conditions. The results reveal the current trends in α-helical MP crystallization with notable differences since 2008. The updated information has been used to design new crystallization and additive screens that should prove useful for both initial crystallization scouting and subsequent crystal optimization. PMID:22811290

Transition from Direct to Inverse Cascade in Three-Dimensional Turbulence

NASA Astrophysics Data System (ADS)

Sahoo, G.; Biferale, L.; Alexakis, A.

2017-12-01

Direction of energy transfer among the scales in a turbulent flow has asignificant role in the macroscopic properties of the flow. It has been arguedthat the dimensionality and the ideal invariants of the flow determine thedirection of the cascade of energy. Because of two sign definite invariants,energy and enstrophy, of two-dimensional turbulence, energy is transferredbackwards from small scales to larger scales and enstrophy is transferred tosmaller scales. However in three-dimensions, while energy is sign-definite, theother invariant helicity does not have a definite sign and therefore there isno constraint on the direction of transfer. It is merely an empiricalobservation that the energy and helicity cascade to the smaller scales in athree-dimensional turbulent flow. Many systems, however, show bidirectionalsplit energy transfer, e.g., flows under strong rotation and stratification, inthin layers or under external magnetic field. The appearance of inverse energyflux in such systems are often considered as a result of enhancement ofquasi-2D Fourier interactions in a 3D background. We designed a model system[1] where the triadic interactions in Navier-Stokes equations are enhanced orsuppressed in a controlled manner without affecting the degrees of freedom,ideal invariants or breaking any of the symmetries of NSE. In our numericalsimulations that uses the tool of helical decomposition of velocity Fouriermodes, we introduced a parameter (0 ≤ λ ≤ 1) that controls therelative weight among homochiral triads and all the others in the nonlinearevolution. We show that by using this weighting protocol the turbulentevolution displays a sharp transition, for a critical value of the controlparameter, from forward to backward energy transfer but still keeping thedynamics fully three dimensional, isotropic, and parity invariant. [1] G Sahoo, A Alexakis and L Biferale, Phys. Rev. Lett. 118, 164501 (2017).

Optimization of nanoparticle focusing by coupling thermophoresis and engineered vortex in a microfluidic channel

NASA Astrophysics Data System (ADS)

Zhao, Chao; Cao, Zhibo; Fraser, John; Oztekin, Alparslan; Cheng, Xuanhong

2017-01-01

Enriching nanoparticles in an aqueous solution is commonly practiced for various applications. Despite recent advances in microfluidic technologies, a general method to concentrate nanoparticles in a microfluidic channel in a label free and continuous flow fashion is not yet available, due to strong Brownian motion on the nanoscale. Recent research of thermophoresis indicates that thermophoretic force can overcome the Brownian force to direct nanoparticle movement. Coupling thermophoresis with natural convection on the microscale has been shown to induce significant enrichment of biomolecules in a thermal diffusion column. However, the column operates in a batch process, and the concentrated samples are inconvenient to retrieve. We have recently designed a microfluidic device that combines a helical fluid motion and simple one-dimensional temperature gradient to achieve effective nanoparticle focusing in a continuous flow. The helical convection is introduced by microgrooves patterned on the channel floor, which directly controls the focusing speed and power. Here, COMSOL simulations are conducted to study how the device geometry and flow rate influence transport and subsequent nanoparticle focusing, with a constant temperature gradient. The results demonstrate a complex dependence of nanoparticle accumulation on the microgroove tilting angle, depth, and spacing, as well as channel width and flow rate. Further dimensional analyses reveal that the ratio between particle velocities induced by thermophoretic and fluid inertial forces governs the particle concentration factor, with a maximum concentration at a ratio of approximately one. This simple relationship provides fundamental insights about nanoparticle transport in coupled flow and thermal fields. The study also offers a useful guideline to the design and operation of nanoparticle concentrators based on combining engineered helical fluid motion subject to phoretic fields.

Numerical analysis on a passive chaotic micromixer with helical microchannel.

PubMed

Wang, Ruijin; Lin, Jianzhong

2006-01-01

In order to improve the mixing efficiency, the diffusion and mixing of species in the helical micro-mixer are simulated numerically. The results show that the mixing efficiency in the helical micromixer is much higher than that in the straight micro-channel and obviously higher than that in the serpentine micro-channel when Reynolds number is low. At high Reynolds number, even though the mixing efficiency in the helical micro-mixer is still much higher than that in the straight micro-channel, no obvious difference of mixing efficiency in the helical micro-mixer and serpentine micro-channel is found. The conclusions are helpful to optimize the structure of the micro-mixer.

Spirulina-Templated Metal Microcoils with Controlled Helical Structures for THz Electromagnetic Responses

PubMed Central

Kamata, Kaori; Piao, Zhenzi; Suzuki, Soichiro; Fujimori, Takahiro; Tajiri, Wataru; Nagai, Keiji; Iyoda, Tomokazu; Yamada, Atsushi; Hayakawa, Toshiaki; Ishiwara, Mitsuteru; Horaguchi, Satoshi; Belay, Amha; Tanaka, Takuo; Takano, Keisuke; Hangyo, Masanori

2014-01-01

Microstructures in nature are ultrafine and ordered in biological roles, which have attracted material scientists. Spirulina forms three-dimensional helical microstructure, one of remarkable features in nature beyond our current processing technology such as lithography in terms of mass-productivity and structural multiplicity. Spirulina varies its diameter, helical pitch, and/or length against growing environment. This unique helix is suggestive of a tiny electromagnetic coil, if composed of electro-conductive metal, which brought us main concept of this work. Here, we describe the biotemplating process onto Spirulina surface to fabricate metal microcoils. Structural parameters of the microcoil can be controlled by the cultivation conditions of Spirulina template and also purely one-handed microcoil can be fabricated. A microcoil dispersion sheet exhibited optically active response attributed to structural resonance in terahertz-wave region. PMID:24815190

Finite-temperature effects in helical quantum turbulence

NASA Astrophysics Data System (ADS)

Clark Di Leoni, Patricio; Mininni, Pablo D.; Brachet, Marc E.

2018-04-01

We perform a study of the evolution of helical quantum turbulence at different temperatures by solving numerically the Gross-Pitaevskii and the stochastic Ginzburg-Landau equations, using up to 40963 grid points with a pseudospectral method. We show that for temperatures close to the critical one, the fluid described by these equations can act as a classical viscous flow, with the decay of the incompressible kinetic energy and the helicity becoming exponential. The transition from this behavior to the one observed at zero temperature is smooth as a function of temperature. Moreover, the presence of strong thermal effects can inhibit the development of a proper turbulent cascade. We provide Ansätze for the effective viscosity and friction as a function of the temperature.

Hexagonally Ordered Arrays of α-Helical Bundles Formed from Peptide-Dendron Hybrids

DOE Office of Scientific and Technical Information (OSTI.GOV)

Barkley, Deborah A.; Rokhlenko, Yekaterina; Marine, Jeannette E.

Combining monodisperse building blocks that have distinct folding properties serves as a modular strategy for controlling structural complexity in hierarchically organized materials. We combine an α-helical bundle-forming peptide with self-assembling dendrons to better control the arrangement of functional groups within cylindrical nanostructures. Site-specific grafting of dendrons to amino acid residues on the exterior of the α-helical bundle yields monodisperse macromolecules with programmable folding and self-assembly properties. The resulting hybrid biomaterials form thermotropic columnar hexagonal mesophases in which the peptides adopt an α-helical conformation. Bundling of the α-helical peptides accompanies self-assembly of the peptide-dendron hybrids into cylindrical nanostructures. The bundle stoichiometrymore » in the mesophase agrees well with the size found in solution for α-helical bundles of peptides with a similar amino acid sequence.« less

Hierarchical Helical Order in the Twisted Growth of Plant Organs

NASA Astrophysics Data System (ADS)

Wada, Hirofumi

2012-09-01

The molecular and cellular basis of left-right asymmetry in plant morphogenesis is a fundamental issue in biology. A rapidly elongating root or hypocotyl of twisting mutants of Arabidopsis thaliana exhibits a helical growth with a handedness opposite to that of the underlying cortical microtubule arrays in epidermal cells. However, how such a hierarchical helical order emerges is currently unknown. We propose a model for investigating macroscopic chiral asymmetry in Arabidopsis mutants. Our elastic model suggests that the helical pattern observed is a direct consequence of the simultaneous presence of anisotropic growth and tilting of cortical microtubule arrays. We predict that the root helical pitch angle is a function of the microtubule helical angle and elastic moduli of the tissues. The proposed model is versatile and is potentially important for other biological systems ranging from protein fibrous structures to tree trunks.

Ratio of ellipticities between 192 and 208 nm (R1 ): An effective electronic circular dichroism parameter for characterization of the helical components of proteins and peptides.

PubMed

Banerjee, Raja; Sheet, Tridip

2017-11-01

Circular dichroism (CD) spectroscopy represents an important tool for characterization of the peptide and protein secondary structures that mainly arise from the conformational disposition of the peptide backbone in solution. In 1991 Manning and Woody proposed that, in addition to the signal intensity, the ratio between [θ]nπ* and [θ]ππ*ǁ ((R 2 ) ≅ [θ] 222 /[θ] 208 ), along with [θ]ππ*⊥ and [θ]ππ*ǁ ((R 1 ) ≅ [θ] 192 /[θ] 208 ), may be utilized towards identifying the peptide/protein conformation (especially 3 10 - and α-helices). However, till date the use of the ratiometric ellipticity component for helical structure analysis of peptides and proteins has not been reported. We studied a series of temperature dependent CD spectra of a thermally stable, model helical peptide and its related analogs in water as a function of added 2,2,2-trifluoroethanol (TFE) in order to explore their landscape of helicity. For the first time, we have experimentally shown here that the R 1 parameter can characterize better the individual helices, while the other parameter R 2 and the signal intensity do not always converge. We emphasize the use of the R 1 ratio of ellipticities for helical characterization because of the common origin of these two bands (exciton splitting of the amide π→ π* transition in a helical polypeptide). This approach may become worthwhile and timely with the increasing accessibility of CD synchrotron sources. © 2017 Wiley Periodicals, Inc.

Investigation of internal magnetic structures and comparison with two-fluid equilibrium configurations in the multi-pulsing CHI on HIST

NASA Astrophysics Data System (ADS)

Nakayama, T.; Hanao, T.; Hirono, H.; Hyobu, T.; Ito, K.; Matsumoto, K.; Kikuchi, Y.; Fukumoto, N.; Nagata, M.; Kanki, T.

2012-10-01

Spherical torus (ST) plasmas have been successfully maintained by Muti-pulsing Coaxial Helicity Injection (M-CHI) on HIST. This research object is to clarify relations between plasma characteristics and magnetic flux amplifications, and to compare magnetic field structures measured in the plasma interior to a flowing equilibrium calculation. Two-dimensional magnetic probe array has been newly introduced nearby the gun muzzle. The initial result shows that the diverter configuration with a single X-point can be formed after a bubble burst process of the plasma. The closed magnetic flux is surrounded by the open magnetic field lines intersecting with the gun electrodes. To evaluate the sustained configurations, we use the two-fluid equilibrium code containing generalized Bernoulli and Grad-Shafranov equations which was developed by L.C. Steinhauer. The radial profiles of plasma flow, density and magnetic fields measured on the midplane of the FC are consistent to the calculation. We also found that the poloidal shear flow generation is attributed to ExB drift and ion diamagnetic drift. In addition, we will study temporal behaviors of impurity lines such as OV and OVI during the flux amplification by VUV spectroscopic measurements.

A diffusion tensor imaging tractography algorithm based on Navier-Stokes fluid mechanics.

PubMed

Hageman, Nathan S; Toga, Arthur W; Narr, Katherine L; Shattuck, David W

2009-03-01

We introduce a fluid mechanics based tractography method for estimating the most likely connection paths between points in diffusion tensor imaging (DTI) volumes. We customize the Navier-Stokes equations to include information from the diffusion tensor and simulate an artificial fluid flow through the DTI image volume. We then estimate the most likely connection paths between points in the DTI volume using a metric derived from the fluid velocity vector field. We validate our algorithm using digital DTI phantoms based on a helical shape. Our method segmented the structure of the phantom with less distortion than was produced using implementations of heat-based partial differential equation (PDE) and streamline based methods. In addition, our method was able to successfully segment divergent and crossing fiber geometries, closely following the ideal path through a digital helical phantom in the presence of multiple crossing tracts. To assess the performance of our algorithm on anatomical data, we applied our method to DTI volumes from normal human subjects. Our method produced paths that were consistent with both known anatomy and directionally encoded color images of the DTI dataset.

A Diffusion Tensor Imaging Tractography Algorithm Based on Navier-Stokes Fluid Mechanics

PubMed Central

Hageman, Nathan S.; Toga, Arthur W.; Narr, Katherine; Shattuck, David W.

2009-01-01

We introduce a fluid mechanics based tractography method for estimating the most likely connection paths between points in diffusion tensor imaging (DTI) volumes. We customize the Navier-Stokes equations to include information from the diffusion tensor and simulate an artificial fluid flow through the DTI image volume. We then estimate the most likely connection paths between points in the DTI volume using a metric derived from the fluid velocity vector field. We validate our algorithm using digital DTI phantoms based on a helical shape. Our method segmented the structure of the phantom with less distortion than was produced using implementations of heat-based partial differential equation (PDE) and streamline based methods. In addition, our method was able to successfully segment divergent and crossing fiber geometries, closely following the ideal path through a digital helical phantom in the presence of multiple crossing tracts. To assess the performance of our algorithm on anatomical data, we applied our method to DTI volumes from normal human subjects. Our method produced paths that were consistent with both known anatomy and directionally encoded color (DEC) images of the DTI dataset. PMID:19244007

High salt solution structure of a left-handed RNA double helix

PubMed Central

Popenda, Mariusz; Milecki, Jan; Adamiak, Ryszard W.

2004-01-01

Right-handed RNA duplexes of (CG)n sequence undergo salt-induced helicity reversal, forming left-handed RNA double helices (Z-RNA). In contrast to the thoroughly studied Z-DNA, no Z-RNA structure of natural origin is known. Here we report the NMR structure of a half-turn, left-handed RNA helix (CGCGCG)2 determined in 6 M NaClO4. This is the first nucleic acid motif determined at such high salt. Sequential assignments of non-exchangeable proton resonances of the Z-form were based on the hitherto unreported NOE connectivity path [H6(n)-H5′/H5″(n)-H8(n+1)-H1′(n+1)-H6(n+2)] found for left-handed helices. Z-RNA structure shows several conformational features significantly different from Z-DNA. Intra-strand but no inter-strand base stacking was observed for both CpG and GpC steps. Helical twist angles for CpG steps have small positive values (4–7°), whereas GpC steps have large negative values (−61°). In the full-turn model of Z-RNA (12.4 bp per turn), base pairs are much closer to the helix axis than in Z-DNA, thus both the very deep, narrow minor groove with buried cytidine 2′-OH groups, and the major groove are well defined. The 2′-OH group of cytidines plays a crucial role in the Z-RNA structure and its formation; 2′-O-methylation of cytidine, but not of guanosine residues prohibits A to Z helicity reversal. PMID:15292450

A rare polyglycine type II-like helix motif in naturally occurring proteins.

PubMed

Warkentin, Eberhard; Weidenweber, Sina; Schühle, Karola; Demmer, Ulrike; Heider, Johann; Ermler, Ulrich

2017-11-01

Common structural elements in proteins such as α-helices or β-sheets are characterized by uniformly repeating, energetically favorable main chain conformations which additionally exhibit a completely saturated hydrogen-bonding network of the main chain NH and CO groups. Although polyproline or polyglycine type II helices (PP II or PG II ) are frequently found in proteins, they are not considered as equivalent secondary structure elements because they do not form a similar self-contained hydrogen-bonding network of the main chain atoms. In this context our finding of an unusual motif of glycine-rich PG II -like helices in the structure of the acetophenone carboxylase core complex is of relevance. These PG II -like helices form hexagonal bundles which appear to fulfill the criterion of a (largely) saturated hydrogen-bonding network of the main-chain groups and therefore may be regarded in this sense as a new secondary structure element. It consists of a central PG II -like helix surrounded by six nearly parallel PG II -like helices in a hexagonal array, plus an additional PG II -like helix extending the array outwards. Very related structural elements have previously been found in synthetic polyglycine fibers. In both cases, all main chain NH and CO groups of the central PG II -helix are saturated by either intra- or intermolecular hydrogen-bonds, resulting in a self-contained hydrogen-bonding network. Similar, but incomplete PG II -helix patterns were also previously identified in a GTP-binding protein and an antifreeze protein. © 2017 Wiley Periodicals, Inc.

Structural Plasticity of Helical Nanotubes Based on Coiled-Coil Assemblies

DOE PAGES

Egelman, Edward H.; Xu, C.; DiMaio, F.; ...

2015-01-22

Numerous instances can be seen in evolution in which protein quaternary structures have diverged while the sequences of the building blocks have remained fairly conserved. However, the path through which such divergence has taken place is usually not known. We have designed two synthetic 29-residue α-helical peptides, based on the coiled-coil structural motif, that spontaneously self-assemble into helical nanotubes in vitro. Using electron cryomicroscopy with a newly available direct electron detection capability, we can achieve near-atomic resolution of these thin structures. We show how conservative changes of only one or two amino acids result in dramatic changes in quaternary structure,more » in which the assemblies can be switched between two very different forms. This system provides a framework for understanding how small sequence changes in evolution can translate into very large changes in supramolecular structure, a phenomenon that may have significant implications for the de novo design of synthetic peptide assemblies.« less

Helical self-organization and hierarchical self-assembly of an oligoheterocyclic pyridine-pyridazine strand into extended supramolecular fibers.

PubMed

Cuccia, Louis A; Ruiz, Eliseo; Lehn, Jean-Marie; Homo, Jean-Claude; Schmutz, Marc

2002-08-02

The synthesis and characterization of an alternating pyridine-pyridazine strand comprising thirteen heterocycles are described. Spontaneous folding into a helical secondary structure is based on a general molecular self-organization process enforced by the conformational information encoded within the primary structure of the molecular strand itself. Conformational control based on heterocyclic "helicity codons" illustrates a strategy for designing folding properties into synthetic oligomers (foldamers). Strong intermolecular interactions of the highly ordered lock-washer subunits of compound 3 results in hierarchical supramolecular self-assembly into protofibrils and fibrils. Compound 3 also forms mechanically stable two-dimensional Langmuir-Blodgett and cast thin films.

Flow Patterns in the Jugular Veins of Pulsatile Tinnitus Patients

PubMed Central

Kao, Evan; Kefayati, Sarah; Amans, Matthew R.; Faraji, Farshid; Ballweber, Megan; Halbach, Van; Saloner, David

2017-01-01

Pulsatile Tinnitus (PT) is a pulse-synchronous sound heard in the absence of an external source. PT is often related to abnormal flow in vascular structures near the cochlea. One vascular territory implicated in PT is the internal jugular vein (IJV). Using computational fluid dynamics (CFD) based on patient-specific Magnetic Resonance Imaging (MRI), we investigated the flow within the IJV of seven subjects, four symptomatic and three asymptomatic of PT. We found that there were two extreme anatomic types classified by the shape and position of the jugular bulbs: elevated and rounded. PT patients had elevated jugular bulbs that led to a distinctive helical flow pattern within the proximal internal jugular vein. Asymptomatic subjects generally had rounded jugular bulbs that neatly redirected flow from the sigmoid sinus directly into the jugular vein. These two flow patterns were quantified by calculating the length-averaged streamline curvature of the flow within the proximal jugular vein: 130.3 ± 8.1 m-1 for geometries with rounded bulbs, 260.7 ± 29.4 m-1 for those with elevated bulbs (P < 0.005). Our results suggest that variations in the jugular bulb geometry lead to distinct flow patterns that are linked to PT, but further investigation is needed to determine if the vortex pattern is causal to sound generation. PMID:28057349

Structure of Voltage-gated Two-pore Channel TPC1 from Arabidopsis thaliana

PubMed Central

Guo, Jiangtao; Zeng, Weizhong; Chen, Qingfeng; Lee, Changkeun; Chen, Liping; Yang, Yi; Cang, Chunlei; Ren, Dejian; Jiang, Youxing

2015-01-01

Two-pore channels (TPCs) contain two copies of a Shaker-like six-transmembrane (6-TM) domain in each subunit and are ubiquitously expressed in both animals and plants as organellar cation channels. Here, we present the first crystal structure of a vacuolar two-pore channel from Arabidopsis thaliana, AtTPC1, which functions as a homodimer. AtTPC1 activation requires both voltage and cytosolic Ca2+. Ca2+ binding to the cytosolic EF-hand domain triggers conformational changes coupled to the pair of pore-lining inner helices (IS6 helices) from the first 6-TM domains, whereas membrane potential only activates the second voltage-sensing domain (VSD2) whose conformational changes are coupled to the pair of inner helices (IIS6 helices) from the second 6-TM domains. Luminal Ca2+ or Ba2+ can modulate voltage activation by stabilizing VSD2 in the resting state and shifts voltage activation towards more positive potentials. Our Ba2+ bound AtTPC1 structure reveals a voltage sensor in the resting state, providing hitherto unseen structural insight into the general voltage-gating mechanism among voltage-gated channels. PMID:26689363

Fifty years of coiled-coils and alpha-helical bundles: a close relationship between sequence and structure.

PubMed

Parry, David A D; Fraser, R D Bruce; Squire, John M

2008-09-01

alpha-Helical coiled coils are remarkable for the diversity of related conformations that they adopt in both fibrous and globular proteins, and for the range of functions that they exhibit. The coiled coils are based on a heptad (7-residue), hendecad (11-residue) or a related quasi-repeat of apolar residues in the sequences of the alpha-helical regions involved. Most of these, however, display one or more sequence discontinuities known as stutters or stammers. The resulting coiled coils vary in length, in the number of chains participating, in the relative polarity of the contributing alpha-helical regions (parallel or antiparallel), and in the pitch length and handedness of the supercoil (left- or right-handed). Functionally, the concept that a coiled coil can act only as a static rod is no longer valid, and the range of roles that these structures have now been shown to exhibit has expanded rapidly in recent years. An important development has been the recognition that the delightful simplicity that exists between sequence and structure, and between structure and function, allows coiled coils with specialized features to be designed de novo.

Transient α-helices in the disordered RPEL motifs of the serum response factor coactivator MKL1

NASA Astrophysics Data System (ADS)

Mizuguchi, Mineyuki; Fuju, Takahiro; Obita, Takayuki; Ishikawa, Mitsuru; Tsuda, Masaaki; Tabuchi, Akiko

2014-06-01

The megakaryoblastic leukemia 1 (MKL1) protein functions as a transcriptional coactivator of the serum response factor. MKL1 has three RPEL motifs (RPEL1, RPEL2, and RPEL3) in its N-terminal region. MKL1 binds to monomeric G-actin through RPEL motifs, and the dissociation of MKL1 from G-actin promotes the translocation of MKL1 to the nucleus. Although structural data are available for RPEL motifs of MKL1 in complex with G-actin, the structural characteristics of RPEL motifs in the free state have been poorly defined. Here we characterized the structures of free RPEL motifs using NMR and CD spectroscopy. NMR and CD measurements showed that free RPEL motifs are largely unstructured in solution. However, NMR analysis identified transient α-helices in the regions where helices α1 and α2 are induced upon binding to G-actin. Proline mutagenesis showed that the transient α-helices are locally formed without helix-helix interactions. The helix content is higher in the order of RPEL1, RPEL2, and RPEL3. The amount of preformed structure may correlate with the binding affinity between the intrinsically disordered protein and its target molecule.

Analysis of inter-residue contacts reveals folding stabilizers in P-loops of potassium, sodium, and TRPV channels.

PubMed

Korkosh, V S; Zhorov, B S; Tikhonov, D B

2016-05-01

The family of P-loop channels includes potassium, sodium, calcium, cyclic nucleotide-gated and TRPV channels, as well as ionotropic glutamate receptors. Despite vastly different physiological and pharmacological properties, the channels have structurally conserved folding of the pore domain. Furthermore, crystallographic data demonstrate surprisingly similar mutual disposition of transmembrane and membrane-diving helices. To understand determinants of this conservation, here we have compared available high-resolution structures of sodium, potassium, and TRPV1 channels. We found that some residues, which are in matching positions of the sequence alignment, occur in different positions in the 3D alignment. Surprisingly, we found 3D mismatches in well-packed P-helices. Analysis of energetics of individual residues in Monte Carlo minimized structures revealed cyclic patterns of energetically favorable inter- and intra-subunit contacts of P-helices with S6 helices. The inter-subunit contacts are rather conserved in all the channels, whereas the intra-subunit contacts are specific for particular types of the channels. Our results suggest that these residue-residue contacts contribute to the folding stabilization. Analysis of such contacts is important for structural and phylogenetic studies of homologous proteins.

NIMROD simulations and physics assessment of possible designs for a next generation Steady Inductive Helicity Injection HIT device

NASA Astrophysics Data System (ADS)

Penna, James; Morgan, Kyle; Grubb, Isaac; Jarboe, Thomas

2017-10-01

The Helicity Injected Torus - Steady Inductive 3 (HIT-SI3) experiment forms and maintains spheromaks via Steady Inductive Helicity Injection (SIHI) using discrete injectors that inject magnetic helicity via a non-axisymmetric perturbation and drive toroidally symmetric current. Newer designs for larger SIHI-driven spheromaks incorporate a set of injectors connected to a single external manifold to allow more freedom for the toroidal structure of the applied perturbation. Simulations have been carried out using the NIMROD code to assess the effectiveness of various imposed mode structures and injector schema in driving current via Imposed Dynamo Current Drive (IDCD). The results are presented here for varying flux conserver shapes on a device approximately 1.5 times larger than the current HIT-SI3 experiment. The imposed mode structures and spectra of simulated spheromaks are analyzed in order to examine magnetic structure and stability and determine an optimal regime for IDCD sustainment in a large device. The development of scaling laws for manifold operation is also presented, and simulation results are analyzed and assessed as part of the development path for the large scale device.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mei, Yang; Ramanathan, Arvind; Glover, Karen

BECN1 is essential for autophagy, a critical eukaryotic cellular homeostasis pathway. Here we delineate a highly conserved BECN1 domain located between previously characterized BH3 and coiled-coil domains and elucidate its structure and role in autophagy. The 2.0 angstrom sulfur-single-wavelength anomalous dispersion X-ray crystal structure of this domain demonstrates that its N-terminal half is unstructured while its C-terminal half is helical; hence, we name it the flexible helical domain (FHD). Circular dichroism spectroscopy, double electron electron resonance electron paramagnetic resonance, and small-angle X-ray scattering (SAXS) analyses confirm that the FHD is partially disordered, even in the context of adjacent BECN1 domains.more » Molecular dynamic simulations fitted to SAXS data indicate that the FHD transiently samples more helical conformations. FHD helicity increases in 2,2,2-trifluoroethanol, suggesting it may become more helical upon binding. Lastly, cellular studies show that conserved FHD residues are required for starvation-induced autophagy. Thus, the FHD likely undergoes a binding-associated disorder to-helix transition, and conserved residues critical for this interaction are essential for starvation-induced autophagy.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mei, Yang; Ramanathan, Arvind; Glover, Karen

BECN1 is essential for autophagy, a critical eukaryotic cellular homeostasis pathway. Here in this study, we delineate a highly conserved BECN1 domain located between previously characterized BH3 and coiled-coil domains and elucidate its structure and role in autophagy. The 2.0 Å sulfur-single-wavelength anomalous dispersion X-ray crystal structure of this domain demonstrates that its N-terminal half is unstructured while its C-terminal half is helical; hence, we name it the flexible helical domain (FHD). Circular dichroism spectroscopy, double electron–electron resonance–electron paramagnetic resonance, and small-angle X-ray scattering (SAXS) analyses confirm that the FHD is partially disordered, even in the context of adjacent BECN1more » domains. Molecular dynamic simulations fitted to SAXS data indicate that the FHD transiently samples more helical conformations. FHD helicity increases in 2,2,2-trifluoroethanol, suggesting it may become more helical upon binding. Finally, cellular studies show that conserved FHD residues are required for starvation-induced autophagy. Thus, the FHD likely undergoes a binding-associated disorder-to-helix transition, and conserved residues critical for this interaction are essential for starvation-induced autophagy.« less

Open and Lys–His Hexacoordinated Closed Structures of a Globin with Swapped Proximal and Distal Sites

PubMed Central

Teh, Aik-Hong; Saito, Jennifer A.; Najimudin, Nazalan; Alam, Maqsudul

2015-01-01

Globins are haem-binding proteins with a conserved fold made up of α-helices and can possess diverse properties. A putative globin-coupled sensor from Methylacidiphilum infernorum, HGbRL, contains an N-terminal globin domain whose open and closed structures reveal an untypical dimeric architecture. Helices E and F fuse into an elongated helix, resulting in a novel site-swapped globin fold made up of helices A–E, hence the distal site, from one subunit and helices F–H, the proximal site, from another. The open structure possesses a large cavity binding an imidazole molecule, while the closed structure forms a unique Lys–His hexacoordinated species, with the first turn of helix E unravelling to allow Lys52(E10) to bind to the haem. Ligand binding induces reorganization of loop CE, which is stabilized in the closed form, and helix E, triggering a large conformational movement in the open form. These provide a mechanical insight into how a signal may be relayed between the globin domain and the C-terminal domain of HGbRL, a Roadblock/LC7 domain. Comparison with HGbI, a closely related globin, further underlines the high degree of structural versatility that the globin fold is capable of, enabling it to perform a diversity of functions. PMID:26094577

Flow-driven rotor simulation of vertical axis tidal turbines: A comparison of helical and straight blades

NASA Astrophysics Data System (ADS)

Le, Tuyen Quang; Lee, Kwang-Soo; Park, Jin-Soon; Ko, Jin Hwan

2014-06-01

In this study, flow-driven rotor simulations with a given load are conducted to analyze the operational characteristics of a vertical-axis Darrieus turbine, specifically its self-starting capability and fluctuations in its torque as well as the RPM. These characteristics are typically observed in experiments, though they cannot be acquired in simulations with a given tip speed ratio (TSR). First, it is shown that a flow-driven rotor simulation with a two-dimensional (2D) turbine model obtains power coefficients with curves similar to those obtained in a simulation with a given TSR. 3D flowdriven rotor simulations with an optimal geometry then show that a helical-bladed turbine has the following prominent advantages over a straight-bladed turbine of the same size: an improvement of its self-starting capabilities and reduced fluctuations in its torque and RPM curves as well as an increase in its power coefficient from 33% to 42%. Therefore, it is clear that a flow-driven rotor simulation provides more information for the design of a Darrieus turbine than a simulation with a given TSR before experiments.

Helicity of short E-R/K peptides.

PubMed

Sommese, Ruth F; Sivaramakrishnan, Sivaraj; Baldwin, Robert L; Spudich, James A

2010-10-01

Understanding the secondary structure of peptides is important in protein folding, enzyme function, and peptide-based drug design. Previous studies of synthetic Ala-based peptides (>12 a.a.) have demonstrated the role for charged side chain interactions involving Glu/Lys or Glu/Arg spaced three (i, i + 3) or four (i, i + 4) residues apart. The secondary structure of short peptides (<9 a.a.), however, has not been investigated. In this study, the effect of repetitive Glu/Lys or Glu/Arg side chain interactions, giving rise to E-R/K helices, on the helicity of short peptides was examined using circular dichroism. Short E-R/K-based peptides show significant helix content. Peptides containing one or more E-R interactions display greater helicity than those with similar E-K interactions. Significant helicity is achieved in Arg-based E-R/K peptides eight, six, and five amino acids long. In these short peptides, each additional i + 3 and i + 4 salt bridge has substantial contribution to fractional helix content. The E-R/K peptides exhibit a strongly linear melt curve indicative of noncooperative folding. The significant helicity of these short peptides with predictable dependence on number, position, and type of side chain interactions makes them an important consideration in peptide design.

Differentiating Left- and Right-Handed Carbon Nanotubes by DNA.

PubMed

Ao, Geyou; Streit, Jason K; Fagan, Jeffrey A; Zheng, Ming

2016-12-28

New structural characteristics emerge when solid-state crystals are constructed in lower dimensions. This is exemplified by single-wall carbon nanotubes, which exhibit a degree of freedom in handedness and a multitude of helicities that give rise to three distinct types of electronic structures: metals, quasi-metals, and semiconductors. Here we report the use of intrinsically chiral single-stranded DNA to achieve simultaneous handedness and helicity control for all three types of nanotubes. We apply polymer aqueous two-phase systems to select special DNA-wrapped carbon nanotubes, each of which we argue must have an ordered DNA structure that binds to a nanotube of defined handedness and helicity and resembles a well-folded biomacromolecule with innate stereoselectivity. We have screened over 300 short single-stranded DNA sequences with palindrome symmetry, leading to the selection of more than 20 distinct carbon nanotube structures that have defined helicity and handedness and cover the entire chiral angle range and all three electronic types. The mechanism of handedness selection is illustrated by a DNA sequence that adopts two distinct folds on a pair of (6,5) nanotube enantiomers, rendering them large differences in fluorescence intensity and chemical reactivity. This result establishes a first example of functionally distinguishable left- and right-handed carbon nanotubes. Taken together, our work demonstrates highly efficient enantiomer differentiation by DNA and offers a first comprehensive solution to achieve simultaneous handedness and helicity control for all three electronic types of carbon nanotubes.

Differentiating Left- and Right-handed Carbon Nanotubes by DNA

NASA Astrophysics Data System (ADS)

Zheng, Ming

New structural characteristics emerge when solid-state crystals are constructed in lower dimensions. This is exemplified by single-wall carbon nanotubes, which exhibit a degree of freedom in handedness, and a multitude of helicity that gives rise to three distinct types of electronic structures - metals, quasi-metals, and semiconductors. Here, we report the use of intrinsically chiral single-stranded DNA to achieve simultaneous handedness and helicity control for all three types of nanotubes. We apply polymer aqueous two-phase systems to select special DNA-wrapped carbon nanotubes, each of which we argue must have an ordered DNA structure bound to a nanotube of defined handedness and helicity, resembling a well-folded biomacromolecule with innate stereo-selectivity. We have screened over 300 short single-stranded DNA sequences with palindrome symmetry, leading to the selection of more than 20 distinct carbon nanotube structures that have defined helicity and handedness and cover the entire chiral angle range and all three electronic types. The mechanism of handedness selection is illustrated by a DNA sequence that adopts two distinct folds on a pair of (6,5) nanotube enantiomers, respectively, rendering them large differences in fluorescence intensity and chemical reactivity. This result establishes a first example of functionally distinguishable left- and right-handed carbon nanotubes. Taken together, our work demonstrates highly efficient enantiomer differentiation by DNA, and offers a first comprehensive solution to achieve simultaneous handedness and helicity control for all three electronic types of carbon nanotubes. .

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Hongqi; Brandenburg, Axel; Sokoloff, D. D., E-mail: hzhang@bao.ac.cn

We adopt an isotropic representation of the Fourier-transformed two-point correlation tensor of the magnetic field to estimate the magnetic energy and helicity spectra as well as current helicity spectra of two individual active regions (NOAA 11158 and NOAA 11515) and the change of the spectral indices during their development as well as during the solar cycle. The departure of the spectral indices of magnetic energy and current helicity from 5/3 are analyzed, and it is found that it is lower than the spectral index of the magnetic energy spectrum. Furthermore, the fractional magnetic helicity tends to increase when the scale of themore » energy-carrying magnetic structures increases. The magnetic helicity of NOAA 11515 violates the expected hemispheric sign rule, which is interpreted as an effect of enhanced field strengths at scales larger than 30–60 Mm with opposite signs of helicity. This is consistent with the general cycle dependence, which shows that around the solar maximum the magnetic energy and helicity spectra are steeper, emphasizing the large-scale field.« less

Interaction of rotating helical magnetic field with the HIST spherical torus plasmas

NASA Astrophysics Data System (ADS)

Kikuchi, Yusuke; Sugahara, Masato; Yamada, Satoshi; Yoshikawa, Tatsuya; Fukumoto, Naoyuki; Nagata, Masayoshi

2006-10-01

The physical mechanism of current drive by co-axial helicity injection (CHI) has been experimentally investigated on both spheromak and spherical torus (ST) configurations on the HIST device [1]. It has been observed that the n = 1 kink mode rotates toroidally with a frequency of 10-20 kHz in the ExB direction. It seems that the induced toroidal current by CHI strongly relates with the observed rotating kink mode. On the other hand, it is well known that MHD instabilities can be controlled or even suppressed by an externally applied helical magnetic field in tokamak devices. Therefore, we have started to install two sets of external helical coils in order to produce a rotating helical magnetic field on HIST. Mode structures of the generated rotating helical magnetic field and preliminary experimental results of the interaction of the rotating helical magnetic field with the HIST plasmas will be shown in the conference. [1] M. Nagata, et al., Physics of Plasmas 10, 2932 (2003)

Suction performance and internal flow of a 2-bladed helical inducer with inlet asymmetric plate

NASA Astrophysics Data System (ADS)

Watanabe, S.; Uchinono, Y.; Ishizaka, K.; Furukawa, A.; Kim, J.-H.

2013-10-01

It has been found in our past studies that the installation of asymmetric plate at the inlet of inducer is effective for the suppression of cavitation surge phenomenon. In the present study, the suction performance of 2-bladed helical inducer with an inlet asymmetric plate is experimentally investigated. It is observed that the suction performance in large flow rate conditions is not significantly influenced by the asymmetric plate, whereas the head of inducer with the asymmetric plate increases just before the head breakdown in partial flow conditions. To understand the mechanism of this additional head, the flow measurements and the numerical simulations are carried out. It is found that the circumferential component of absolute velocity at the exit of inducer slightly increases with the development of cavitation in both cases with and without the inlet asymmetric plate, indicating the increase of the theoretical head. The theoretical head increase with the inlet asymmetric plate is also confirmed by the unsteady numerical simulations, suggesting that the additional head is achieved through the increase of the theoretical head with the change of the exiting flow from the inducer associated with some amount of cavitation.

Structural mechanics and helical geometry of thin elastic composites.

PubMed

Wada, Hirofumi

2016-09-21

Helices are ubiquitous in nature, and helical shape transition is often observed in residually stressed bodies, such as composites, wherein materials with different mechanical properties are glued firmly together to form a whole body. Inspired by a variety of biological examples, the basic physical mechanism responsible for the emergence of twisting and bending in such thin composite structures has been extensively studied. Here, we propose a simplified analytical model wherein a slender membrane tube undergoes a helical transition driven by the contraction of an elastic ribbon bound to the membrane surface. We analytically predict the curvature and twist of an emergent helix as functions of differential strains and elastic moduli, which are confirmed by our numerical simulations. Our results may help understand shapes observed in different biological systems, such as spiral bacteria, and could be applied to novel designs of soft machines and robots.

Synthesis, structure, and magnetic properties of two 1-D helical coordination polymeric Cu(II) complexes

NASA Astrophysics Data System (ADS)

Bian, He-Dong; Yang, Xiao-E.; Yu, Qing; Chen, Zi-Lu; Liang, Hong; Yan, Shi-Ping; Liao, Dai-Zheng

2008-01-01

Two helical coordination polymeric copper(II) complexes bearing amino acid Schiff bases HL or HL', which are condensed from 2-hydroxy-1-naphthaldehyde with 2-aminobenzoic acid or L-valine, respectively, have been prepared and characterised by X-ray crystallography. In [CuL] n ( 1) the copper(II) atoms are bridged by syn- anti carboxylate groups giving infinite 1-D right-handed helical chains which are further connected by weak C-H⋯Cu interactions to build a 2-D network. While in [CuL'] n ( 2) the carboxylate group acts as a rare monatomic bridge to connect the adjacent copper(II) atoms leading to the formation of a left-handed helical chain. Magnetic susceptibility measurements indicate that 1 exhibits weak ferromagnetic interactions whereas an antiferromagnetic coupling is established for 2. The magnetic behavior can be satisfactorily explained on the basis of the structural data.

Flow-induced oscillations of a floating moored cylinder

NASA Astrophysics Data System (ADS)

Carlson, Daniel; Modarres-Sadeghi, Yahya

2016-11-01

An experimental study of flow-induced oscillations of a floating model spar buoy was conducted. The model spar consisted of a floating uniform cylinder moored in a water tunnel test section, and free to oscillate about its mooring attachment point near the center of mass. For the bare cylinder, counter-clockwise (CCW) figure-eight trajectories approaching A* =1 in amplitude were observed at the lower part of the spar for a reduced velocity range of U* =4-11, while its upper part experienced clockwise (CW) orbits. It was hypothesized that the portion of the spar undergoing CCW figure eights is the portion within which the flow excites the structure. By adding helical strakes to the portion of the cylinder with CCW figure eights, the response amplitude was significantly reduced, while adding strakes to portions with clockwise orbital motion had a minimal influence on the amplitude of response. This work is partially supported by the NSF-sponsored IGERT: Offshore Wind Energy Engineering, Environmental Science, and Policy (Grant Number 1068864).

Bracket formulations and energy- and helicity-preserving numerical methods for incompressible two-phase flows

NASA Astrophysics Data System (ADS)

Suzuki, Yukihito

2018-03-01

A diffuse interface model for three-dimensional viscous incompressible two-phase flows is formulated within a bracket formalism using a skew-symmetric Poisson bracket together with a symmetric negative semi-definite dissipative bracket. The budgets of kinetic energy, helicity, and enstrophy derived from the bracket formulations are properly inherited by the finite difference equations obtained by invoking the discrete variational derivative method combined with the mimetic finite difference method. The Cahn-Hilliard and Allen-Cahn equations are employed as diffuse interface models, in which the equalities of densities and viscosities of two different phases are assumed. Numerical experiments on the motion of periodic arrays of tubes and those of droplets have been conducted to examine the properties and usefulness of the proposed method.

Planar optics with patterned chiral liquid crystals

NASA Astrophysics Data System (ADS)

Kobashi, Junji; Yoshida, Hiroyuki; Ozaki, Masanori

2016-06-01

Reflective metasurfaces based on metallic and dielectric nanoscatterers have attracted interest owing to their ability to control the phase of light. However, because such nanoscatterers require subwavelength features, the fabrication of elements that operate in the visible range is challenging. Here, we show that chiral liquid crystals with a self-organized helical structure enable metasurface-like, non-specular reflection in the visible region. The phase of light that is Bragg-reflected off the helical structure can be controlled over 0-2π depending on the spatial phase of the helical structure; thus planar elements with arbitrary reflected wavefronts can be created via orientation control. The circular polarization selectivity and external field tunability of Bragg reflection open a wide variety of potential applications for this family of functional devices, from optical isolators to wearable displays.

Polymorphic transformation of helical flagella of bacteria

NASA Astrophysics Data System (ADS)

Lim, Sookkyung; Howard Berg Collaboration; William Ko Collaboration; Yongsam Kim Collaboration; Wanho Lee Collaboration; Charles Peskin Collaboration

2016-11-01

Bacteria such as E. coli swim in an aqueous environment by utilizing the rotation of flagellar motors and alternate two modes of motility, runs and tumbles. Runs are steady forward swimming driven by bundles of flagellar filaments whose motors are turning CCW; tumbles involve a reorientation of the direction of swimming triggered by motor reversals. During tumbling, the helical flagellum undergoes polymorphic transformations, which is a local change in helical pitch, helical radius, and handedness. In this work, we investigate the underlying mechanism of structural conformation and how this polymorphic transition plays a role in bacterial swimming. National Science Foundation.

Improved particle confinement in transition from multiple-helicity to quasi-single-helicity regimes of a reversed-field pinch.

PubMed

Frassinetti, L; Predebon, I; Koguchi, H; Yagi, Y; Hirano, Y; Sakakita, H; Spizzo, G; White, R B

2006-10-27

The quasi-single-helicity (QSH) state of a reversed-field pinch (RFP) plasma is a regime in which the RFP configuration can be sustained by a dynamo produced mainly by a single tearing mode and in which a helical structure with well-defined magnetic flux surfaces arises. In this Letter, we show that spontaneous transitions to the QSH regime enhance the particle confinement. This improvement is originated by the simultaneous and cooperative action of the increase of the magnetic island and the reduction of the magnetic stochasticity.

ARE TORNADO-LIKE MAGNETIC STRUCTURES ABLE TO SUPPORT SOLAR PROMINENCE PLASMA?

DOE Office of Scientific and Technical Information (OSTI.GOV)

Luna, M.; Moreno-Insertis, F.; Priest, E.

Recent high-resolution and high-cadence observations have surprisingly suggested that prominence barbs exhibit apparent rotating motions suggestive of a tornado-like structure. Additional evidence has been provided by Doppler measurements. The observations reveal opposite velocities for both hot and cool plasma on the two sides of a prominence barb. This motion is persistent for several hours and has been interpreted in terms of rotational motion of prominence feet. Several authors suggest that such barb motions are rotating helical structures around a vertical axis similar to tornadoes on Earth. One of the difficulties of such a proposal is how to support cool prominencemore » plasma in almost-vertical structures against gravity. In this work we model analytically a tornado-like structure and try to determine possible mechanisms to support the prominence plasma. We have found that the Lorentz force can indeed support the barb plasma provided the magnetic structure is sufficiently twisted and/or significant poloidal flows are present.« less

Analytical and experimental study of flow phenomena in noncavitating rocket pump inducers

NASA Technical Reports Server (NTRS)

Lakshminarayana, B.

1981-01-01

The flow processes in rocket pump inducers are summarized. The experimental investigations were carried out with air as the test medium. The major characteristics features of the rocket pump inducers are low flow coefficient (0.05 to 0.2) large stagger angle (70 deg to 85 deg) and high solidity blades of little or no camber. The investigations are concerned with the effect of viscosity not the effects of cavitation. Flow visualization, conventional and hot wire probe measurement inside and at the exit of the blade passage, were the analytical methods used. The experiment was carried out using four three and two bladed inducers with cambered blades. Both the passage and the exit flow were measured. The basic research and boundary layer investigation was carried out using a helical flat plate (of some dimensions as the inducer blades tested), and flat plate helical inducer (four bladed). Detailed mean and turbulence flow field inside the passage as well as the exit of the rotor were derived from these measurement. The boundary layer, endwall, and other passage data reveal extremely complex nature of the flow, with major effects of viscosity present across the entire passage. Several analyses were carried out to predict the flow field in inducers. These included an approximate analysis, the shear pumping analysis, and a numerical solution of exact viscous equations with approximate modeling for the viscous terms.

Interaction of anesthetic molecules with α-helix and polyproline II extended helix of long-chain poly-L-lysine

NASA Astrophysics Data System (ADS)

Cieślik-Boczula, Katarzyna; Rospenk, Maria

2018-01-01

The effect of halothane, enflurane, sevoflurane, and isoflurane molecules, as volatile anesthetics, on the α-helices and polyproline II extended helices (PPII) of long-chain poly-L-lysine (PLL) were studied using Fourier-transform infrared and vibrational circular dichroism spectroscopy. Uncharged and charged α-helices, as well as charged extended PPII helices, were subjected to anesthetic actions in solvents with different pD values or methanol to water ratios. A crucial factor responsible for hindering the anesthetic-PLL interactions is shown to be the ionization of amino groups of the PLL side chains. The α-helix to β-sheet transition was triggered only for the uncharged α-helical structures of PLL by the nonpolar anesthetics under study.

Multilayer DNA origami packed on hexagonal and hybrid lattices.

PubMed

Ke, Yonggang; Voigt, Niels V; Gothelf, Kurt V; Shih, William M

2012-01-25

"Scaffolded DNA origami" has been proven to be a powerful and efficient approach to construct two-dimensional or three-dimensional objects with great complexity. Multilayer DNA origami has been demonstrated with helices packing along either honeycomb-lattice geometry or square-lattice geometry. Here we report successful folding of multilayer DNA origami with helices arranged on a close-packed hexagonal lattice. This arrangement yields a higher density of helical packing and therefore higher resolution of spatial addressing than has been shown previously. We also demonstrate hybrid multilayer DNA origami with honeycomb-lattice, square-lattice, and hexagonal-lattice packing of helices all in one design. The availability of hexagonal close-packing of helices extends our ability to build complex structures using DNA nanotechnology. © 2011 American Chemical Society

Orientational preferences of neighboring helices can drive ER insertion of a marginally hydrophobic transmembrane helix

PubMed Central

Öjemalm, Karin; Halling, Katrin K.; Nilsson, IngMarie; von Heijne, Gunnar

2013-01-01

Summary α-helical integral membrane proteins critically depend on the correct insertion of their transmembrane α-helices into the lipid bilayer for proper folding, yet a surprisingly large fraction of the transmembrane α-helices in multispanning integral membrane proteins are not sufficiently hydrophobic to insert into the target membrane by themselves. How can such marginally hydrophobic segments nevertheless form transmembrane helices in the folded structure? Here, we show that a transmembrane helix with a strong orientational preference (Ncyt-Clum or Nlum-Ccyt) can both increase and decrease the hydrophobicity threshold for membrane insertion of a neighboring, marginally hydrophobic helix. This effect helps explain the ‘missing hydrophobicity’ in polytopic membrane proteins. PMID:22281052

Hall effect on a Merging Formation Process of a Field-Reversed Configuration

NASA Astrophysics Data System (ADS)

Kaminou, Yasuhiro; Guo, Xuehan; Inomoto, Michiaki; Ono, Yasushi; Horiuchi, Ritoku

2015-11-01

Counter-helicity spheromak merging is one of the formation methods of a Field-Reversed Configuration (FRC). In counter-helicity spheromak merging, two spheromaks with opposing toroidal fields merge together, through magnetic reconnection events and relax into a FRC, which has no or little toroidal field. This process contains magnetic reconnection and a relaxation phenomena, and the Hall effect has some essential effects on these process because the X-point in the magnetic reconnection or the O-point of the FRC has no or little magnetic field. However, the Hall effect as both global and local effect on counter-helicity spheromak merging has not been elucidated. In this poster, we conducted 2D/3D Hall-MHD simulations and experiments of counter-helicity spheromak merging. We find that the Hall effect enhances the reconnection rate, and reduces the generation of toroidal sheared-flow. The suppression of the ``slingshot effect'' affects the relaxation process. We will discuss details in the poster.

Integrated reformer and shift reactor

DOEpatents

Bentley, Jeffrey M.; Clawson, Lawrence G.; Mitchell, William L.; Dorson, Matthew H.

2006-06-27

A hydrocarbon fuel reformer for producing diatomic hydrogen gas is disclosed. The reformer includes a first reaction vessel, a shift reactor vessel annularly disposed about the first reaction vessel, including a first shift reactor zone, and a first helical tube disposed within the first shift reactor zone having an inlet end communicating with a water supply source. The water supply source is preferably adapted to supply liquid-phase water to the first helical tube at flow conditions sufficient to ensure discharge of liquid-phase and steam-phase water from an outlet end of the first helical tube. The reformer may further include a first catalyst bed disposed in the first shift reactor zone, having a low-temperature shift catalyst in contact with the first helical tube. The catalyst bed includes a plurality of coil sections disposed in coaxial relation to other coil sections and to the central longitudinal axis of the reformer, each coil section extending between the first and second ends, and each coil section being in direct fluid communication with at least one other coil section.

Theoretical and experimental studies of hyperreflective polymer-network cholesteric liquid crystal structures with helicity inversion

NASA Astrophysics Data System (ADS)

Tasolamprou, A. C.; Mitov, M.; Zografopoulos, D. C.; Kriezis, E. E.

2009-03-01

Single-layer cholesteric liquid crystals exhibit a reflection coefficient which is at most 50% for unpolarized incident light. We give theoretical and experimental evidence of single-layer polymer-stabilized cholesteric liquid-crystalline structures that demonstrate hyper-reflective properties. Such original features are derived by the concurrent and randomly interlaced presence of both helicities. The fundamental properties of such structures are revealed by detailed numerical simulations based on a stochastic approach.

[DNA structure from A to Z--biological implications of structural diversity of DNA].

PubMed

Bukowiecka-Matusiak, Małgorzata; Woźniak, Lucyna A

2006-01-01

Deoxyribonucleic acid (DNA) is a biopolymer of nucleotides, usually adopting a double-stranded helical form in cells, with complementary base pairing holding the two strands together. The most stable is B-DNA conformation, although numerous other double helical structures can occur under specific conditions (A-DNA, Z-DNA, P-DNA). The existence of multiple-stranded (triplex, tetraplex) forms in vivo and their biological function in cells are subject of intensive studies.

Structure and molecular mechanism of a nucleobase-cation-symport-1 family transporter.

PubMed

Weyand, Simone; Shimamura, Tatsuro; Yajima, Shunsuke; Suzuki, Shun'ichi; Mirza, Osman; Krusong, Kuakarun; Carpenter, Elisabeth P; Rutherford, Nicholas G; Hadden, Jonathan M; O'Reilly, John; Ma, Pikyee; Saidijam, Massoud; Patching, Simon G; Hope, Ryan J; Norbertczak, Halina T; Roach, Peter C J; Iwata, So; Henderson, Peter J F; Cameron, Alexander D

2008-10-31

The nucleobase-cation-symport-1 (NCS1) transporters are essential components of salvage pathways for nucleobases and related metabolites. Here, we report the 2.85-angstrom resolution structure of the NCS1 benzyl-hydantoin transporter, Mhp1, from Microbacterium liquefaciens. Mhp1 contains 12 transmembrane helices, 10 of which are arranged in two inverted repeats of five helices. The structures of the outward-facing open and substrate-bound occluded conformations were solved, showing how the outward-facing cavity closes upon binding of substrate. Comparisons with the leucine transporter LeuT(Aa) and the galactose transporter vSGLT reveal that the outward- and inward-facing cavities are symmetrically arranged on opposite sides of the membrane. The reciprocal opening and closing of these cavities is synchronized by the inverted repeat helices 3 and 8, providing the structural basis of the alternating access model for membrane transport.

Four highly pseudosymmetric and/or twinned structures of d(CGCGCG) 2 extend the repertoire of crystal structures of Z-DNA

DOE Office of Scientific and Technical Information (OSTI.GOV)

Luo, Zhipu; Dauter, Zbigniew; Gilski, Miroslaw

DNA oligomer duplexes containing alternating cytosines and guanines in their sequences tend to form left-handed helices of the Z-DNA type, with the sugar and phosphate backbone in a zigzag conformation and a helical repeat of two successive nucleotides. Z-DNA duplexes usually crystallize as hexagonally arranged parallel helical tubes, with various relative orientations and translation of neighboring duplexes. Four novel high-resolution crystal structures of d(CGCGCG) 2duplexes are described here. They are characterized by a high degree of pseudosymmetry and/or twinning, with three or four independent duplexes differently oriented in a monoclinicP2 1lattice of hexagonal metric. The various twinning criteria give somewhatmore » conflicting indications in these complicated cases of crystal pathology. The details of molecular packing in these crystal structures are compared with other known crystal forms of Z-DNA.« less

Assembly, maturation and three-dimensional helical structure of the teratogenic rubella virus

PubMed Central

Mangala Prasad, Vidya

2017-01-01

Viral infections during pregnancy are a significant cause of infant morbidity and mortality. Of these, rubella virus infection is a well-substantiated example that leads to miscarriages or severe fetal defects. However, structural information about the rubella virus has been lacking due to the pleomorphic nature of the virions. Here we report a helical structure of rubella virions using cryo-electron tomography. Sub-tomogram averaging of the surface spikes established the relative positions of the viral glycoproteins, which differed from the earlier icosahedral models of the virus. Tomographic analyses of in vitro assembled nucleocapsids and virions provide a template for viral assembly. Comparisons of immature and mature virions show large rearrangements in the glycoproteins that may be essential for forming the infectious virions. These results present the first known example of a helical membrane-enveloped virus, while also providing a structural basis for its assembly and maturation pathway. PMID:28575072

Assembly, maturation and three-dimensional helical structure of the teratogenic rubella virus.

PubMed

Mangala Prasad, Vidya; Klose, Thomas; Rossmann, Michael G

2017-06-01

Viral infections during pregnancy are a significant cause of infant morbidity and mortality. Of these, rubella virus infection is a well-substantiated example that leads to miscarriages or severe fetal defects. However, structural information about the rubella virus has been lacking due to the pleomorphic nature of the virions. Here we report a helical structure of rubella virions using cryo-electron tomography. Sub-tomogram averaging of the surface spikes established the relative positions of the viral glycoproteins, which differed from the earlier icosahedral models of the virus. Tomographic analyses of in vitro assembled nucleocapsids and virions provide a template for viral assembly. Comparisons of immature and mature virions show large rearrangements in the glycoproteins that may be essential for forming the infectious virions. These results present the first known example of a helical membrane-enveloped virus, while also providing a structural basis for its assembly and maturation pathway.

Structure elucidation of dimeric transmembrane domains of bitopic proteins.

PubMed

Bocharov, Eduard V; Volynsky, Pavel E; Pavlov, Konstantin V; Efremov, Roman G; Arseniev, Alexander S

2010-01-01

The interaction between transmembrane helices is of great interest because it directly determines biological activity of a membrane protein. Either destroying or enhancing such interactions can result in many diseases related to dysfunction of different tissues in human body. One much studied form of membrane proteins known as bitopic protein is a dimer containing two membrane-spanning helices associating laterally. Establishing structure-function relationship as well as rational design of new types of drugs targeting membrane proteins requires precise structural information about this class of objects. At present time, to investigate spatial structure and internal dynamics of such transmembrane helical dimers, several strategies were developed based mainly on a combination of NMR spectroscopy, optical spectroscopy, protein engineering and molecular modeling. These approaches were successfully applied to homo- and heterodimeric transmembrane fragments of several bitopic proteins, which play important roles in normal and in pathological conditions of human organism.

Extending Three-Dimensional Weighted Cone Beam Filtered Backprojection (CB-FBP) Algorithm for Image Reconstruction in Volumetric CT at Low Helical Pitches

PubMed Central

Hsieh, Jiang; Nilsen, Roy A.; McOlash, Scott M.

2006-01-01

A three-dimensional (3D) weighted helical cone beam filtered backprojection (CB-FBP) algorithm (namely, original 3D weighted helical CB-FBP algorithm) has already been proposed to reconstruct images from the projection data acquired along a helical trajectory in angular ranges up to [0, 2 π]. However, an overscan is usually employed in the clinic to reconstruct tomographic images with superior noise characteristics at the most challenging anatomic structures, such as head and spine, extremity imaging, and CT angiography as well. To obtain the most achievable noise characteristics or dose efficiency in a helical overscan, we extended the 3D weighted helical CB-FBP algorithm to handle helical pitches that are smaller than 1: 1 (namely extended 3D weighted helical CB-FBP algorithm). By decomposing a helical over scan with an angular range of [0, 2π + Δβ] into a union of full scans corresponding to an angular range of [0, 2π], the extended 3D weighted function is a summation of all 3D weighting functions corresponding to each full scan. An experimental evaluation shows that the extended 3D weighted helical CB-FBP algorithm can improve noise characteristics or dose efficiency of the 3D weighted helical CB-FBP algorithm at a helical pitch smaller than 1: 1, while its reconstruction accuracy and computational efficiency are maintained. It is believed that, such an efficient CB reconstruction algorithm that can provide superior noise characteristics or dose efficiency at low helical pitches may find its extensive applications in CT medical imaging. PMID:23165031

Heterogeneity in iota-carrageenan molecular structure: insights for polymorph II→III transition in the presence of calcium ions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Janaswamy, Srinivas; Chandrasekaran, Rengaswami

2008-06-24

Iota-carrageenan is used in pharmaceutical and food applications due to its ability to complex with other hydrocolloids and proteins. Six distinct cation dependent allomorphs, consistent with its versatile functionality, have so far been observed in the solid state. In this contribution, X-ray structural details of calcium iota-carrageenan (form III) are reported. The polysaccharide retains the half-staggered, parallel, 3-fold, right-handed double helix stabilized by interchain hydrogen bonds from O-2H and O-6H in the Galp units. Results show that there are four helices, rather than one in I or three in II, organized in a larger pseudo-trigonal unit cell of dimensions a=27.44,more » c=13.01 A, and gamma=120 degrees . The four helices have similar core structures, but their sulfate group orientations are quite different. Fifteen calcium ions and 64 water molecules hold the helices together and promote helix-helix interactions. The results portray how the helices would shuffle around in an orchestrated manner to yield calcium iota-carrageenan III from II.« less

Is the Lecompte technique the last word on transposition of the great arteries repair for all patients? A magnetic resonance imaging study including a spiral technique two decades postoperatively.

PubMed

Rickers, Carsten; Kheradvar, Arash; Sievers, Hans-Hinrich; Falahatpisheh, Ahmad; Wegner, Philip; Gabbert, Dominik; Jerosch-Herold, Michael; Hart, Chris; Voges, Inga; Putman, Léon M; Kristo, Ines; Fischer, Gunther; Scheewe, Jens; Kramer, Hans-Heiner

2016-06-01

To compare the Lecompte technique and the spiral anastomosis (complete anatomic correction) two decades after arterial switch operation (ASO). Nine patients after primary ASO with Lecompte and 6 selected patients after spiral anastomosis were evaluated 20.8 ± 2.1 years after ASO versus matched controls. Blood flow dynamics and flow profiles (e.g. vorticity, helicity) in the great arteries were quantified from time-resolved 3D magnetic resonance imaging (MRI) phase contrast flow measurements (4D flow MR) in addition to a comprehensive anatomical and functional cardiovascular MRI analysis. Compared with spiral reconstruction, patients with Lecompte showed more vortex formation, supranatural helical blood flow (relative helicity in aorta: 0.036 vs 0.089; P < 0.01), a reduced indexed cross-sectional area of the left pulmonary artery (155 vs 85 mm²/m²; P < 0.001) and more semilunar valve dysfunctions (n = 5 vs 1). There was no difference in elastic aortic wall properties, ventricular function, myocardial perfusion and myocardial fibrosis between the two groups. Cross-sectional area of the aortic sinus was larger in patients than in controls (669 vs 411 mm²/m²; P < 0.01). In the spiral group, the pulmonary root was rotated after ASO more towards the normal left position (P < 0.01). In this study, selected patients with spiral anastomoses showed, two decades after ASO, better physiologically adapted blood flow dynamics, and attained a closer to normal anatomical position of their great arteries, as well as less valve dysfunction. Considering the limitations related to the small number of patients and the novel MRI imaging techniques, these data may provoke reconsidering the optimal surgical approaches to transposition of the great arteries repair. © The Author 2016. Published by Oxford University Press on behalf of the European Association for Cardio-Thoracic Surgery. All rights reserved.

Helical structures in a Rosette elephant trunk

NASA Astrophysics Data System (ADS)

Carlqvist, Per; Kristen, Helmuth; Gahm, Gosta F.

1998-04-01

We discuss small-scale, helical, interstellar filaments on the basis of optical observations of an elephant trunk in the Rosette nebula. The trunk studied is composed of a number of sinusoidal or serpentine-like dark filaments, preferentially in the outer part of the trunk, where their wavelength is 7-9 times the trunk radius. The diameters are down to the limit of resolution of 1.0 arcsec, corresponding to 1600 au, and ranging up to about 6400 au. At some positions filament crossings give rise to enhanced extinction. We suggest that the sinusoidal filaments are helices lined up by magnetic fields. We derive average extinctions of 0.5-1.0 mag in the filaments, implying molecular densities of n_H2 ~ 10(4) cm(-3) . From existing data on the Rosette HiI region, we conclude that the surrounding kinetic and dynamic pressure and the background radiation field suffice to balance even the denser filaments and to exert drag forces on the trunk as a whole, consistent with evidence of stretching of the trunk. The helical magnetic structures imply the presence of electric currents along the trunk axis. These currents should form a nearly force-free geometry and are consistent with a model consisting of 4-7 helical cables on the surface of a cylinder and which produce the observed wavelength of the helices. We suggest that the Rosette elephant trunks form an interconnected system of rope-like structures which are relics from filamentary skeletons of magnetic fields in the primordial cloud. Based on observations collected at the Nordic Optical Telescope, La Palma, Spain

Hierarchically arranged helical fibre actuators driven by solvents and vapours.

PubMed

Chen, Peining; Xu, Yifan; He, Sisi; Sun, Xuemei; Pan, Shaowu; Deng, Jue; Chen, Daoyong; Peng, Huisheng

2015-12-01

Mechanical responsiveness in many plants is produced by helical organizations of cellulose microfibrils. However, simple mimicry of these naturally occurring helical structures does not produce artificial materials with the desired tunable actuations. Here, we show that actuating fibres that respond to solvent and vapour stimuli can be created through the hierarchical and helical assembly of aligned carbon nanotubes. Primary fibres consisting of helical assemblies of multiwalled carbon nanotubes are twisted together to form the helical actuating fibres. The nanoscale gaps between the nanotubes and micrometre-scale gaps among the primary fibres contribute to the rapid response and large actuation stroke of the actuating fibres. The compact coils allow the actuating fibre to rotate reversibly. We show that these fibres, which are lightweight, flexible and strong, are suitable for a variety of applications such as energy-harvesting generators, deformable sensing springs and smart textiles.

Hierarchically arranged helical fibre actuators driven by solvents and vapours

NASA Astrophysics Data System (ADS)

Chen, Peining; Xu, Yifan; He, Sisi; Sun, Xuemei; Pan, Shaowu; Deng, Jue; Chen, Daoyong; Peng, Huisheng

2015-12-01

Mechanical responsiveness in many plants is produced by helical organizations of cellulose microfibrils. However, simple mimicry of these naturally occurring helical structures does not produce artificial materials with the desired tunable actuations. Here, we show that actuating fibres that respond to solvent and vapour stimuli can be created through the hierarchical and helical assembly of aligned carbon nanotubes. Primary fibres consisting of helical assemblies of multiwalled carbon nanotubes are twisted together to form the helical actuating fibres. The nanoscale gaps between the nanotubes and micrometre-scale gaps among the primary fibres contribute to the rapid response and large actuation stroke of the actuating fibres. The compact coils allow the actuating fibre to rotate reversibly. We show that these fibres, which are lightweight, flexible and strong, are suitable for a variety of applications such as energy-harvesting generators, deformable sensing springs and smart textiles.

Numerical investigation of fluid-particle interactions for embolic stroke

NASA Astrophysics Data System (ADS)

Mukherjee, Debanjan; Padilla, Jose; Shadden, Shawn C.

2016-04-01

Roughly one-third of all strokes are caused by an embolus traveling to a cerebral artery and blocking blood flow in the brain. The objective of this study is to gain a detailed understanding of the dynamics of embolic particles within arteries. Patient computed tomography image is used to construct a three-dimensional model of the carotid bifurcation. An idealized carotid bifurcation model of same vessel diameters was also constructed for comparison. Blood flow velocities and embolic particle trajectories are resolved using a coupled Euler-Lagrange approach. Blood is modeled as a Newtonian fluid, discretized using the finite volume method, with physiologically appropriate inflow and outflow boundary conditions. The embolus trajectory is modeled using Lagrangian particle equations accounting for embolus interaction with blood as well as vessel wall. Both one- and two-way fluid-particle coupling are considered, the latter being implemented using momentum sources augmented to the discretized flow equations. It was observed that for small-to-moderate particle sizes (relative to vessel diameters), the estimated particle distribution ratio—with and without the inclusion of two-way fluid-particle momentum exchange—were found to be similar. The maximum observed differences in distribution ratio with and without the coupling were found to be higher for the idealized bifurcation model. Additionally, the distribution was found to be reasonably matching the volumetric flow distribution for the idealized model, while a notable deviation from volumetric flow was observed in the anatomical model. It was also observed from an analysis of particle path lines that particle interaction with helical flow, characteristic of anatomical vasculature models, could play a prominent role in transport of embolic particle. The results indicate therefore that flow helicity could be an important hemodynamic indicator for analysis of embolus particle transport. Additionally, in the presence of helical flow, and vessel curvature, inclusion of two-way momentum exchange was found to have a secondary effect for transporting small to moderate embolus particles—and one-way coupling could be used as a reasonable approximation, thereby causing substantial savings in computational resources.

Comparative analysis of the folding dynamics and kinetics of an engineered knotted protein and its variants derived from HP0242 of Helicobacter pylori

NASA Astrophysics Data System (ADS)

Wang, Liang-Wei; Liu, Yu-Nan; Lyu, Ping-Chiang; Jackson, Sophie E.; Hsu, Shang-Te Danny

2015-09-01

Understanding the mechanism by which a polypeptide chain thread itself spontaneously to attain a knotted conformation has been a major challenge in the field of protein folding. HP0242 is a homodimeric protein from Helicobacter pylori with intertwined helices to form a unique pseudo-knotted folding topology. A tandem HP0242 repeat has been constructed to become the first engineered trefoil-knotted protein. Its small size renders it a model system for computational analyses to examine its folding and knotting pathways. Here we report a multi-parametric study on the folding stability and kinetics of a library of HP0242 variants, including the trefoil-knotted tandem HP0242 repeat, using far-UV circular dichroism and fluorescence spectroscopy. Equilibrium chemical denaturation of HP0242 variants shows the presence of highly populated dimeric and structurally heterogeneous folding intermediates. Such equilibrium folding intermediates retain significant amount of helical structures except those at the N- and C-terminal regions in the native structure. Stopped-flow fluorescence measurements of HP0242 variants show that spontaneous refolding into knotted structures can be achieved within seconds, which is several orders of magnitude faster than previously observed for other knotted proteins. Nevertheless, the complex chevron plots indicate that HP0242 variants are prone to misfold into kinetic traps, leading to severely rolled-over refolding arms. The experimental observations are in general agreement with the previously reported molecular dynamics simulations. Based on our results, kinetic folding pathways are proposed to qualitatively describe the complex folding processes of HP0242 variants.

Discontinuous Transition from Direct to Inverse Cascade in Three-Dimensional Turbulence

NASA Astrophysics Data System (ADS)

Sahoo, Ganapati; Alexakis, Alexandros; Biferale, Luca

2017-04-01

Inviscid invariants of flow equations are crucial in determining the direction of the turbulent energy cascade. In this work we investigate a variant of the three-dimensional Navier-Stokes equations that shares exactly the same ideal invariants (energy and helicity) and the same symmetries (under rotations, reflections, and scale transforms) as the original equations. It is demonstrated that the examined system displays a change in the direction of the energy cascade when varying the value of a free parameter which controls the relative weights of the triadic interactions between different helical Fourier modes. The transition from a forward to inverse cascade is shown to occur at a critical point in a discontinuous manner with diverging fluctuations close to criticality. Our work thus supports the observation that purely isotropic and three-dimensional flow configurations can support inverse energy transfer when interactions are altered and that inside all turbulent flows there is a competition among forward and backward transfer mechanisms which might lead to multiple energy-containing turbulent states.

High heat flux burnout in subcooled flow boiling

NASA Astrophysics Data System (ADS)

Celata, G. P.; Cumo, M.; Mariani, A.

1995-09-01

The paper reports the results of an experimental research carried out at the Heat Transfer Division of the Energy Department, C.R. Casaccia, on the thermal hydraulic characterization of subcooled flow boiling CHF under typical conditions of thermonuclear fusion reactors, i.e. high liquid velocity and subcooling. The experiment was carried out exploring the following parameters: channel diameter (from 2.5 to 8.0 mm), heated length (10 and 15 cm), liquid velocity (from 2 to 40 m/s), exit pressure (from atmospheric to 5.0 MPa), inlet temperature (from 30 to 80 °C), channel orientation (vertical and horizontal). A maximum CHF value of 60.6 MW/m2 has been obtained under the following conditions: T in=30°, p=2.5 MPa, u=40 m/s, D=2.5 mm (smooth channel) Turbulence promoters (helically coiled wires) have been employed to further enhance the CHF attainable with subcooled flow boiling. Helically coiled wires allow an increase of 50% of the maximum CHF obtained with smooth channels.

Helical vortices generated by flapping wings of bumblebees

NASA Astrophysics Data System (ADS)

Engels, Thomas; Kolomenskiy, Dmitry; Schneider, Kai; Farge, Marie; Lehmann, Fritz-Olaf; Sesterhenn, Jörn

2018-02-01

High resolution direct numerical simulations of rotating and flapping bumblebee wings are presented and their aerodynamics is studied focusing on the role of leading edge vortices and the associated helicity production. We first study the flow generated by only one rotating bumblebee wing in circular motion with 45◦ angle of attack. We then consider a model bumblebee flying in a numerical wind tunnel, which is tethered and has rigid wings flapping with a prescribed generic motion. The inflow condition of the wind varies from laminar to strongly turbulent regimes. Massively parallel simulations show that inflow turbulence does not significantly alter the wings’ leading edge vortex, which enhances lift production. Finally, we focus on studying the helicity of the generated vortices and analyze their contribution at different scales using orthogonal wavelets.

Unwinding motion of a twisted active region filament

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yan, X. L.; Xue, Z. K.; Kong, D. F.

To better understand the structures of active region filaments and the eruption process, we study an active region filament eruption in active region NOAA 11082 in detail on 2010 June 22. Before the filament eruption, the opposite unidirectional material flows appeared in succession along the spine of the filament. The rising of the filament triggered two B-class flares at the upper part of the filament. As the bright material was injected into the filament from the sites of the flares, the filament exhibited a rapid uplift accompanying the counterclockwise rotation of the filament body. From the expansion of the filament,more » we can see that the filament consisted of twisted magnetic field lines. The total twist of the filament is at least 5π obtained by using a time slice method. According to the morphology change during the filament eruption, it is found that the active region filament was a twisted flux rope and its unwinding motion was like a solar tornado. We also find that there was a continuous magnetic helicity injection before and during the filament eruption. It is confirmed that magnetic helicity can be transferred from the photosphere to the filament. Using the extrapolated potential fields, the average decay index of the background magnetic fields over the filament is 0.91. Consequently, these findings imply that the mechanism of solar filament eruption could be due to the kink instability and magnetic helicity accumulation.« less

Experimental and theoretical developments in the Mochi project

NASA Astrophysics Data System (ADS)

You, Setthivoine; von der Linden, Jens; Vereen, Keon; Lavine, Eric Sander; Carroll, Evan; Card, Alexander; Azuara-Rosales, Manuel; Quinley, Morgan; Yun, Gunsu

2015-11-01

The Mochi project investigates the interaction between magnetic fields and plasma flows in cylindrical and toroidal geometries. The configuration is designed to tailor the radial electric field profile with three annular electrodes and allow for shear helical flows in magnetized plasma jets or merging spheromaks. First plasma has been achieved and characterization is in progress with images, magnetic probes, an energy analyzer, an interferometer, a fast ion gauge, and optical and RF spectroscopy. Vector tomography of ion Doppler spectroscopy is progressing with the design of the custom fiber bundle and implementation of the numerical code. The first experiments are investigating the coupling of sausage and kink instabilities, comparing measurements to a new stability criterion and a numerical stability code. A new canonical field theory has been developed to help interpret the dynamics of plasma self-organization. The theory augments the Lagrangian of general dynamical systems to rigourously demonstrate that canonical helicity transport is valid across single particle, kinetic and fluid regimes, that dynamical equations can be re-formulated as a form of Maxwell's equations, and that helicity is conserved only when density gradients are shallow. This work is supported by US DOE Grant DE-SC0010340.

Ribbon structure stabilized by C10 and C12 turns in αγ hybrid peptide.

PubMed

Wani, Naiem Ahmad; Kant, Rajni; Gupta, Vivek Kumar; Aravinda, Subrayashastry; Rai, Rajkishor

2016-04-01

The present study describes the synthesis and crystallographic analysis of αγ hybrid peptides, Boc-Gpn-L-Pro-NHMe (1), Boc-Aib-Gpn-L-Pro-NHMe (2), and Boc-L-Pro-Aib-Gpn-L-Pro-NHMe (3). Peptides 1 and 2 adopt expanded 12-membered (C12 ) helical turn over γα segment. Peptide 3 promotes the ribbon structure stabilized by type II β-turn (C10 ) followed by the expanded C12 helical γα turn. Both right-handed and left-handed helical conformations for Aib residue are observed in peptides 2 and 3, respectively. Copyright © 2016 European Peptide Society and John Wiley & Sons, Ltd.

Thermodynamic confinement and alpha-helix persistence length in poly(gamma-benzyl-L-glutamate)-b-poly(dimethyl siloxane)-b-poly(gamma-benzyl-L-glutamate) triblock copolymers.

PubMed

Papadopoulos, P; Floudas, G; Schnell, I; Lieberwirth, I; Nguyen, T Q; Klok, H-A

2006-02-01

The structure and the associated dynamics of a series of poly(gamma-benzyl-L-glutamate)-b-poly(dimethyl siloxane)-b-poly(gamma-benzyl-L-glutamate) (PBLG-b-PDMS-b-PBLG) triblock copolymers were investigated using small- and wide-angle X-ray scattering, NMR, transmission electron microscopy, and dielectric spectroscopy, respectively. The structural analysis revealed phase separation in the case of the longer blocks with defected alpha-helical segments embedded within the block copolymer nanodomains. The alpha-helical persistence length was found to depend on the degree of segregation; thermodynamic confinement and chain stretching results in the partial annihilation of helical defects.

A Cobalt Supramolecular Triple-Stranded Helicate-based Discrete Molecular Cage

PubMed Central

Mai, Hien Duy; Kang, Philjae; Kim, Jin Kyung; Yoo, Hyojong

2017-01-01

We report a strategy to achieve a discrete cage molecule featuring a high level of structural hierarchy through a multiple-assembly process. A cobalt (Co) supramolecular triple-stranded helicate (Co-TSH)-based discrete molecular cage (1) is successfully synthesized and fully characterized. The solid-state structure of 1 shows that it is composed of six triple-stranded helicates interconnected by four linking cobalt species. This is an unusual example of a highly symmetric cage architecture resulting from the coordination-driven assembly of metallosupramolecular modules. The molecular cage 1 shows much higher CO2 uptake properties and selectivity compared with the separate supramolecular modules (Co-TSH, complex 2) and other molecular platforms. PMID:28262690

Catalytic reactor

DOEpatents

Aaron, Timothy Mark [East Amherst, NY; Shah, Minish Mahendra [East Amherst, NY; Jibb, Richard John [Amherst, NY

2009-03-10

A catalytic reactor is provided with one or more reaction zones each formed of set(s) of reaction tubes containing a catalyst to promote chemical reaction within a feed stream. The reaction tubes are of helical configuration and are arranged in a substantially coaxial relationship to form a coil-like structure. Heat exchangers and steam generators can be formed by similar tube arrangements. In such manner, the reaction zone(s) and hence, the reactor is compact and the pressure drop through components is minimized. The resultant compact form has improved heat transfer characteristics and is far easier to thermally insulate than prior art compact reactor designs. Various chemical reactions are contemplated within such coil-like structures such that as steam methane reforming followed by water-gas shift. The coil-like structures can be housed within annular chambers of a cylindrical housing that also provide flow paths for various heat exchange fluids to heat and cool components.

Spectroscopic Measurement of Ion Flow During Merging Start-up of Field-Reversed Configuration

NASA Astrophysics Data System (ADS)

Oka, Hirotaka; Inomoto, Michiaki; Tanabe, Hiroshi; Annoura, Masanobu; Ono, Yasushi; Nemoto, Koshichi

2012-10-01

The counter-helicity merging method [1] of field-reversed configuration (FRC) formation involves generation of bidirectional toroidal flow, known as a ``sling-shot.'' In two fluids regime, reconnection process is strongly affected by the Hall effect [2]. In this study, we have investigated the behavior of toroidal bidirectional flow generated by the counter-helicity merging in two-fluids regime. We use 2D Ion Doppler Spectroscopy to mesure toroidal ion flow during merging start-up of FRC from Ar gas. We defined two cases: one case with a radially pushed-in X line (case I) and the other case with a radially pushed-out X line(case O). The flow during the plasma merging shows radial asymmetry, as expected from the magnetic measurement, but finally relaxes to a unidirectional flow in plasma current direction in both cases. We observed larger toroidal flow in the plasma current direction in case I after FRC is formed, though the FRC in case O has larger magnetic flux. These results suggest that more ions are lost during merging start-up in case I. This selective ion loss might account for stability and confinement of FRCs probably maintained by high energy ions.[4pt] [1] Y. Ono, et al., Nucl. Fusion 39, pp. 2001-2008 (1999).[0pt] [2] M. Inomoto, et al., Phys. Rev. Lett., 97, 135002, (2006)

Mechanical and structural characteristics of the new BONE-LOK cortical-cancellous internal fixation device.

PubMed

Cachia, Victor V; Culbert, Brad; Warren, Chris; Oka, Richard; Mahar, Andrew

2003-01-01

The purpose of this study was to evaluate the structural and mechanical characteristics of a new and unique titanium cortical-cancellous helical compression anchor with BONE-LOK (Triage Medical, Inc., Irvine, CA) technology for compressive internal fixation of fractures and osteotomies. This device provides fixation through the use of a distal helical anchor and a proximal retentive collar that are united by an axially movable pin (U.S. and international patents issued and pending). The helical compression anchor (2.7-mm diameter) was compared with 3.0-mm diameter titanium cancellous screws (Synthes, Paoli, PA) for pullout strength and compression in 7# and 12# synthetic rigid polyurethane foam (simulated bone matrix), and for 3-point bending stiffness. The following results (mean +/- standard deviation) were obtained: foam block pullout strength in 12# foam: 2.7-mm helical compression anchor 70 +/- 2.0 N and 3.0-mm titanium cancellous screws 37 +/- 11 N; in 7# foam: 2.7-mm helical compression anchor 33 +/- 3 N and 3.0-mm titanium cancellous screws 31 +/- 12 N. Three-point bending stiffness, 2.7-mm helical compression anchor 988 +/- 68 N/mm and 3.0-mm titanium cancellous screws 845 +/- 88 N/mm. Compression strength testing in 12# foam: 2.7-mm helical compression anchor 70.8 +/- 4.8 N and 3.0-mm titanium cancellous screws 23.0 +/- 3.1 N, in 7# foam: 2.7-mm helical compression anchor 42.6 +/- 3.2 N and 3.0-mm titanium cancellous screws 10.4 +/- 0.9 N. Results showed greater pullout strength, 3-point bending stiffness, and compression strength for the 2.7-mm helical compression anchor as compared with the 3.0-mm titanium cancellous screws in these testing models. This difference represents a distinct advantage in the new device that warrants further in vivo testing.

Hub vortex helical instability as the origin of wake meandering in the lee of a model wind-turbine

NASA Astrophysics Data System (ADS)

Viola, Francesco; Iungo, Giacomo Valerio; Camarri, Simone; Porte-Agel, Fernando; Gallaire, Francois

2012-11-01

Wind tunnel measurements were performed for the wake produced by a three-bladed wind turbine immersed in uniform flow. These tests show the presence of a vorticity structure in the near wake region mainly oriented along the streamwise direction, which is denoted as hub vortex. The hub vortex is characterized by oscillations with frequencies lower than the one connected to the rotational velocity of the rotor, which are ascribed to wake meandering by previous works. This phenomenon consists in transversal oscillations of the wind turbine wake, which are excited by the shedding of vorticity structures from the rotor disc acting as a bluff body. In this work temporal and spatial linear stability analyses of a wind turbine wake are performed on a base flow obtained through time-averaged wind tunnel velocity measurements. This study shows that the low frequency spectral component detected experimentally is the result of a convective instability of the hub vortex, which is characterized by a counter-winding single-helix structure. Simultaneous hot-wire measurements confirm the presence of a helicoidal unstable mode of the hub vortex with a streamwise wavenumber roughly equal to the one predicted from the linear instability analysis.

Small differences in amylopectin fine structure may explain large functional differences of starch.

PubMed

Bertoft, Eric; Annor, George A; Shen, Xinyu; Rumpagaporn, Pinthip; Seetharaman, Koushik; Hamaker, Bruce R

2016-04-20

Four amylose-free waxy rice starches were found to give rise to gels with clearly different morphology after storage for seven days at 4°C. The thermal and rheological properties of these gels were also different. This was remarkable in light of the subtle differences in the molecular structure of the amylopectin in the samples. Addition of iodine to the amylopectin samples suggested that not only external chains, but also the internal chains of amylopectin, could form helical inclusion complexes. It is suggested that these internal helical segments participate in the retrogradation of amylopectin, thereby stabilising the gels through double helical structures with external chains of adjacent molecules. Albeit few in number, such interactions appear to have important influences on starch functional properties. Copyright © 2015 Elsevier Ltd. All rights reserved.

The influence of the Hall term on the development of magnetized laser-produced plasma jets

NASA Astrophysics Data System (ADS)

Hamlin, N. D.; Seyler, C. E.; Khiar, B.

2018-04-01

We present 2D axisymmetric simulation results describing the influence of the Hall term on laser-produced plasma jets and their interaction with an applied magnetic field parallel to the laser axis. Bending of the poloidal B-field lines produces an MHD shock structure surrounding a conical cavity, and a jet is produced from the convergence of the shock envelope. Both the jet and the conical cavity underneath it are bound by fast MHD shocks. We compare the MHD results generated using the extended-MHD code Physics as an Extended-MHD Relaxation System with an Efficient Upwind Scheme (PERSEUS) with MHD results generated using GORGON and find reasonable agreement. We then present extended-MHD results generated using PERSEUS, which show that the Hall term has several effects on the plasma jet evolution. A hot low-density current-carrying layer of plasma develops just outside the plume, which results in a helical rather than a purely poloidal B-field, and reduces magnetic stresses, resulting in delayed flow convergence and jet formation. The flow is partially frozen into the helical field, resulting in azimuthal rotation of the jet. The Hall term also produces field-aligned current in strongly magnetized regions. In particular, we find the influence of Hall physics on this problem to be scale-dependent. This points to the importance of mitigating the Hall effect in a laboratory setup, by increasing the jet density and system dimensions, in order to avoid inaccurate extrapolation to astrophysical scales.

Helicity within the vortex filament model.

PubMed

Hänninen, R; Hietala, N; Salman, H

2016-11-24

Kinetic helicity is one of the invariants of the Euler equations that is associated with the topology of vortex lines within the fluid. In superfluids, the vorticity is concentrated along vortex filaments. In this setting, helicity would be expected to acquire its simplest form. However, the lack of a core structure for vortex filaments appears to result in a helicity that does not retain its key attribute as a quadratic invariant. By defining a spanwise vector to the vortex through the use of a Seifert framing, we are able to introduce twist and henceforth recover the key properties of helicity. We present several examples for calculating internal twist to illustrate why the centreline helicity alone will lead to ambiguous results if a twist contribution is not introduced. Our choice of the spanwise vector can be expressed in terms of the tangential component of velocity along the filament. Since the tangential velocity does not alter the configuration of the vortex at later times, we are able to recover a similar equation for the internal twist angle to that of classical vortex tubes. Our results allow us to explain how a quasi-classical limit of helicity emerges from helicity considerations for individual superfluid vortex filaments.

Helicity within the vortex filament model

PubMed Central

Hänninen, R.; Hietala, N.; Salman, H.

2016-01-01

Kinetic helicity is one of the invariants of the Euler equations that is associated with the topology of vortex lines within the fluid. In superfluids, the vorticity is concentrated along vortex filaments. In this setting, helicity would be expected to acquire its simplest form. However, the lack of a core structure for vortex filaments appears to result in a helicity that does not retain its key attribute as a quadratic invariant. By defining a spanwise vector to the vortex through the use of a Seifert framing, we are able to introduce twist and henceforth recover the key properties of helicity. We present several examples for calculating internal twist to illustrate why the centreline helicity alone will lead to ambiguous results if a twist contribution is not introduced. Our choice of the spanwise vector can be expressed in terms of the tangential component of velocity along the filament. Since the tangential velocity does not alter the configuration of the vortex at later times, we are able to recover a similar equation for the internal twist angle to that of classical vortex tubes. Our results allow us to explain how a quasi-classical limit of helicity emerges from helicity considerations for individual superfluid vortex filaments. PMID:27883029

DOE Office of Scientific and Technical Information (OSTI.GOV)

Merzari, E.; Yuan, Haomin; Kraus, A.

The NEAMS program aims to develop an integrated multi-physics simulation capability “pellet-to-plant” for the design and analysis of future generations of nuclear power plants. In particular, the Reactor Product Line code suite's multi-resolution hierarchy is being designed to ultimately span the full range of length and time scales present in relevant reactor design and safety analyses, as well as scale from desktop to petaflop computing platforms. Flow-induced vibration (FIV) is widespread problem in energy systems because they rely on fluid movement for energy conversion. Vibrating structures may be damaged as fatigue or wear occurs. Given the importance of reliable componentsmore » in the nuclear industry, flow-induced vibration has long been a major concern in safety and operation of nuclear reactors. In particular, nuclear fuel rods and steam generators have been known to suffer from flow-induced vibration and related failures. Advanced reactors, such as integral Pressurized Water Reactors (PWRs) considered for Small Modular Reactors (SMR), often rely on innovative component designs to meet cost and safety targets. One component that is the subject of advanced designs is the steam generator, some designs of which forego the usual shell-and-tube architecture in order to fit within the primary vessel. In addition to being more cost- and space-efficient, such steam generators need to be more reliable, since failure of the primary vessel represents a potential loss of coolant and a safety concern. A significant amount of data exists on flow-induced vibration in shell-and-tube heat exchangers, and heuristic methods are available to predict their occurrence based on a set of given assumptions. In contrast, advanced designs have far less data available. Advanced modeling and simulation based on coupled structural and fluid simulations have the potential to predict flow-induced vibration in a variety of designs, reducing the need for expensive experimental programs, especially at the design stage. Over the past five years, the Reactor Product Line has developed the integrated multi-physics code suite SHARP. The goal of developing such a tool is to perform multi-physics neutronics, thermal/fluid, and structural mechanics modeling of the components inside the full reactor core or portions of it with a user-specified fidelity. In particular SHARP contains high-fidelity single-physics codes Diablo for structural mechanics and Nek5000 for fluid mechanics calculations. Both codes are state-of-the-art, highly scalable tools that have been extensively validated. These tools form a strong basis on which to build a flow-induced vibration modeling capability. In this report we discuss one-way coupled calculations performed with Nek5000 and Diablo aimed at simulating available FIV experiments in helical steam generators in the turbulent buffeting regime. In this regime one-way coupling is judged sufficient because 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 PWRs. The legacy data is obtained from two datasets developed at Argonne and B&W.« less

Intermolecular detergent-membrane protein noes for the characterization of the dynamics of membrane protein-detergent complexes.

PubMed

Eichmann, Cédric; Orts, Julien; Tzitzilonis, Christos; Vögeli, Beat; Smrt, Sean; Lorieau, Justin; Riek, Roland

2014-12-11

The interaction between membrane proteins and lipids or lipid mimetics such as detergents is key for the three-dimensional structure and dynamics of membrane proteins. In NMR-based structural studies of membrane proteins, qualitative analysis of intermolecular nuclear Overhauser enhancements (NOEs) or paramagnetic resonance enhancement are used in general to identify the transmembrane segments of a membrane protein. Here, we employed a quantitative characterization of intermolecular NOEs between (1)H of the detergent and (1)H(N) of (2)H-perdeuterated, (15)N-labeled α-helical membrane protein-detergent complexes following the exact NOE (eNOE) approach. Structural considerations suggest that these intermolecular NOEs should show a helical-wheel-type behavior along a transmembrane helix or a membrane-attached helix within a membrane protein as experimentally demonstrated for the complete influenza hemagglutinin fusion domain HAfp23. The partial absence of such a NOE pattern along the amino acid sequence as shown for a truncated variant of HAfp23 and for the Escherichia coli inner membrane protein YidH indicates the presence of large tertiary structure fluctuations such as an opening between helices or the presence of large rotational dynamics of the helices. Detergent-protein NOEs thus appear to be a straightforward probe for a qualitative characterization of structural and dynamical properties of membrane proteins embedded in detergent micelles.

Crystal and Molecular Structure of a Collagen-Like Peptide at 1.9 overset{circ}{A} Resolution

NASA Astrophysics Data System (ADS)

Bella, Jordi; Eaton, Mark; Brodsky, Barbara; Berman, Helen M.

1994-10-01

The structure of a protein triple helix has been determined at 1.9 angstrom resolution by x-ray crystallographic studies of a collagen-like peptide containing a single substitution of the consensus sequence. This peptide adopts a triple-helical structure that confirms the basic features determined from fiber diffraction studies on collagen: supercoiling of polyproline II helices and interchain hydrogen bonding that follows the model II of Rich and Crick. In addition, the structure provides new information concerning the nature of this protein fold. Each triple helix is surrounded by a cylinder of hydration, with an extensive hydrogen bonding network between water molecules and peptide acceptor groups. Hydroxyproline residues have a critical role in this water network. The interaxial spacing of triple helices in the crystal is similar to that in collagen fibrils, and the water networks linking adjacent triple helices in the crystal structure are likely to be present in connective tissues. The breaking of the repeating (X-Y-Gly)_n pattern by a Gly-->Ala substitution results in a subtle alteration of the conformation, with a local untwisting of the triple helix. At the substitution site, direct interchain hydrogen bonds are replaced with interstitial water bridges between the peptide groups. Similar conformational changes may occur in Gly-->X mutated collagens responsible for the diseases osteogenesis imperfecta, chondrodysplasias, and Ehlers-Danlos syndrome IV.

Cholesteric-nematic transitions induced by a shear flow and a magnetic field

NASA Astrophysics Data System (ADS)

Zakhlevnykh, A. N.; Makarov, D. V.; Novikov, A. A.

2017-10-01

The untwisting of the helical structure of a cholesteric liquid crystal under the action of a magnetic field and a shear flow has been studied theoretically. Both factors can induce the cholesteric-nematic transition independently; however, the difference in the orienting actions of the magnetic field and the shear flow leads to competition between magnetic and hydrodynamic mechanisms of influence on the cholesteric liquid crystal. We have analyzed different orientations of the magnetic field relative to the direction of the flow in the shear plane. In a number of limiting cases, the analytic dependences are obtained for the pitch of the cholesteric helix deformed by the shear flow. The phase diagrams of the cholesteric-nematic transitions and the pitch of the cholesteric helix are calculated for different values of the magnetic field strength and the angle of orientation, the flow velocity gradient, and the reactive parameter. It is shown that the magnetic field stabilizes the orientation of the director in the shear flow and expands the boundaries of orientability of cholesterics. It has been established that the shear flow shifts the critical magnetic field strength of the transition. It is shown that a sequence of reentrant orientational cholesteric-nematic-cholesteric transitions can be induced by rotating the magnetic field in certain intervals of its strength and shear flow velocity gradients.

Vacuum Plasma Spray (VPS) Forming of Solar Thermal Propulsion Components Using Refractory Metals

NASA Technical Reports Server (NTRS)

Zimmerman, Frank; Gerish, Harold; Davis, William; Hissam, D. Andy

1998-01-01

The Thermal Spray Laboratory at NASA's Marshall Space Flight Center has developed and demonstrated a fabrication technique using Vacuum Plasma Spray (VPS) to form structural components from a tungsten/rhenium alloy. The components were assembled into an absorption cavity for a fully-functioning, ground test unit of a solar thermal propulsion engine. The VPS process deposits refractory metal onto a graphite mandrel of the desired shape. The mandrel acts as a male mold, forming the required contour and dimensions of the inside surface of the deposit. Tungsten and tungsten/25% rhenium were used in the development and production of several absorber cavity components. These materials were selected for their high temperature (less than 2500 C) strength. Each absorber cavity comprises 3 coaxial shells with two, double-helical flow passages through which the propellant gas flows. This paper describes the processing techniques, design considerations, and process development associated with forming these engine components.

Secondary structure propensity and chirality of the amyloidophilic peptide p5 and its analogues impacts ligand binding - In vitro characterization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wall, Jonathan S.; Williams, Angela; Wooliver, Craig

Here, polybasic helical peptides, such as peptide p5, bind human amyloid extracts and synthetic amyloid fibrils. When radio labeled, peptide p5 has been shown to specifically bind amyloid in vivo thereby allowing imaging of the disease. Structural requirements for heparin and amyloid binding have been studied using analogues of p5 that modify helicity and chirality.

Secondary structure propensity and chirality of the amyloidophilic peptide p5 and its analogues impacts ligand binding - In vitro characterization

DOE PAGES

Wall, Jonathan S.; Williams, Angela; Wooliver, Craig; ...

2016-08-11

Here, polybasic helical peptides, such as peptide p5, bind human amyloid extracts and synthetic amyloid fibrils. When radio labeled, peptide p5 has been shown to specifically bind amyloid in vivo thereby allowing imaging of the disease. Structural requirements for heparin and amyloid binding have been studied using analogues of p5 that modify helicity and chirality.

Silica biomineralization via the self-assembly of helical biomolecules.

PubMed

Liu, Ben; Cao, Yuanyuan; Huang, Zhehao; Duan, Yingying; Che, Shunai

2015-01-21

The biomimetic synthesis of relevant silica materials using biological macromolecules as templates via silica biomineralization processes attract rapidly rising attention toward natural and artificial materials. Biomimetic synthesis studies are useful for improving the understanding of the formation mechanism of the hierarchical structures found in living organisms (such as diatoms and sponges) and for promoting significant developments in the biotechnology, nanotechnology and materials chemistry fields. Chirality is a ubiquitous phenomenon in nature and is an inherent feature of biomolecular components in organisms. Helical biomolecules, one of the most important types of chiral macromolecules, can self-assemble into multiple liquid-crystal structures and be used as biotemplates for silica biomineralization, which renders them particularly useful for fabricating complex silica materials under ambient conditions. Over the past two decades, many new silica materials with hierarchical structures and complex morphologies have been created using helical biomolecules. In this review, the developments in this field are described and the recent progress in silica biomineralization templating using several classes of helical biomolecules, including DNA, polypeptides, cellulose and rod-like viruses is summarized. Particular focus is placed on the formation mechanism of biomolecule-silica materials (BSMs) with hierarchical structures. Finally, current research challenges and future developments are discussed in the conclusion. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Conformational Flexibility Enables the Function of a BECN1 Region Essential for Starvation-Mediated Autophagy

DOE PAGES

Mei, Yang; Ramanathan, Arvind; Glover, Karen; ...

2016-03-03

BECN1 is essential for autophagy, a critical eukaryotic cellular homeostasis pathway. Here in this study, we delineate a highly conserved BECN1 domain located between previously characterized BH3 and coiled-coil domains and elucidate its structure and role in autophagy. The 2.0 Å sulfur-single-wavelength anomalous dispersion X-ray crystal structure of this domain demonstrates that its N-terminal half is unstructured while its C-terminal half is helical; hence, we name it the flexible helical domain (FHD). Circular dichroism spectroscopy, double electron–electron resonance–electron paramagnetic resonance, and small-angle X-ray scattering (SAXS) analyses confirm that the FHD is partially disordered, even in the context of adjacent BECN1more » domains. Molecular dynamic simulations fitted to SAXS data indicate that the FHD transiently samples more helical conformations. FHD helicity increases in 2,2,2-trifluoroethanol, suggesting it may become more helical upon binding. Finally, cellular studies show that conserved FHD residues are required for starvation-induced autophagy. Thus, the FHD likely undergoes a binding-associated disorder-to-helix transition, and conserved residues critical for this interaction are essential for starvation-induced autophagy.« less

On the Helicity in 3D-Periodic Navier-Stokes Equations II: The Statistical Case

NASA Astrophysics Data System (ADS)

Foias, Ciprian; Hoang, Luan; Nicolaenko, Basil

2009-09-01

We study the asymptotic behavior of the statistical solutions to the Navier-Stokes equations using the normalization map [9]. It is then applied to the study of mean energy, mean dissipation rate of energy, and mean helicity of the spatial periodic flows driven by potential body forces. The statistical distribution of the asymptotic Beltrami flows are also investigated. We connect our mathematical analysis with the empirical theory of decaying turbulence. With appropriate mathematically defined ensemble averages, the Kolmogorov universal features are shown to be transient in time. We provide an estimate for the time interval in which those features may still be present. Our collaborator and friend Basil Nicolaenko passed away in September of 2007, after this work was completed. Honoring his contribution and friendship, we dedicate this article to him.

Essential arginine in subunit a and aspartate in subunit c of FoF1 ATP synthase: effect of repositioning within helix 4 of subunit a and helix 2 of subunit c.

PubMed

Langemeyer, Lars; Engelbrecht, Siegfried

2007-07-01

FoF1 ATP synthase couples proton flow through the integral membrane portion Fo (ab2c10) to ATP-synthesis in the extrinsic F1-part ((alphabeta)3gammadeltaepsilon) (Escherichia coli nomenclature and stoichiometry). Coupling occurs by mechanical rotation of subunits c10gammaepsilon relative to (alphabeta)3deltaab2. Two residues were found to be essential for proton flow through ab2c10, namely Arg210 in subunit a (aR210) and Asp61 in subunits c (cD61). Their deletion abolishes proton flow, but "horizontal" repositioning, by anchoring them in adjacent transmembrane helices, restores function. Here, we investigated the effects of "vertical" repositioning aR210, cD61, or both by one helical turn towards the N- or C-termini of their original helices. Other than in the horizontal the vertical displacement changes the positions of the side chains within the depth of the membrane. Mutant aR210A/aN214R appeared to be short-circuited in that it supported proton conduction only through EF1-depleted EFo, but not in EFoEF1, nor ATP-driven proton pumping. Mutant cD61N/cM65D grew on succinate, retained the ability to synthesize ATP and supported passive proton conduction but apparently not ATP hydrolysis-driven proton pumping.

Research on the influence of helical strakes on dynamic response of floating wind turbine platform

NASA Astrophysics Data System (ADS)

Ding, Qin-wei; Li, Chun

2017-04-01

The stability of platform structure is the paramount guarantee of the safe operation of the offshore floating wind turbine. The NREL 5MW floating wind turbine is established based on the OC3-Hywind Spar Buoy platform with the supplement of helical strakes for the purpose to analyze the impact of helical strakes on the dynamic response of the floating wind turbine Spar platform. The dynamic response of floating wind turbine Spar platform under wind, wave and current loading from the impact of number, height and pitch ratio of the helical strakes is analysed by the radiation and diffraction theory, the finite element method and orthogonal design method. The result reveals that the helical strakes can effectively inhibit the dynamic response of the platform but enlarge the wave exciting force; the best parameter combination is two pieces of helical strakes with the height of 15% D ( D is the diameter of the platform) and the pitch ratio of 5; the height of the helical strake and its pitch ratio have significant influence on pitch response.

Helicity-dependent single-walled carbon nanotube alignment on graphite for helical angle and handedness recognition

PubMed Central

Chen, Yabin; Shen, Ziyong; Xu, Ziwei; Hu, Yue; Xu, Haitao; Wang, Sheng; Guo, Xiaolei; Zhang, Yanfeng; Peng, Lianmao; Ding, Feng; Liu, Zhongfan; Zhang, Jin

2013-01-01

Aligned single-walled carbon nanotube arrays provide a great potential for the carbon-based nanodevices and circuit integration. Aligning single-walled carbon nanotubes with selected helicities and identifying their helical structures remain a daunting issue. The widely used gas-directed and surface-directed growth modes generally suffer the drawbacks of mixed and unknown helicities of the aligned single-walled carbon nanotubes. Here we develop a rational approach to anchor the single-walled carbon nanotubes on graphite surfaces, on which the orientation of each single-walled carbon nanotube sensitively depends on its helical angle and handedness. This approach can be exploited to conveniently measure both the helical angle and handedness of the single-walled carbon nanotube simultaneously at a low cost. In addition, by combining with the resonant Raman spectroscopy, the (n,m) index of anchored single-walled carbon nanotube can be further determined from the (d,θ) plot, and the assigned (n,m) values by this approach are validated by both the electronic transition energy Eii measurement and nanodevice application. PMID:23892334

A tendril perversion in a helical oligomer: trapping and characterizing a mobile screw-sense reversal† †Electronic supplementary information (ESI) available. CCDC X-ray crystal data for 1a and 1b have been deposited with the CCDC, deposition numbers 1518806 and 1518807. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c6sc05474a Click here for additional data file. Click here for additional data file.

PubMed Central

Tomsett, Michael; Maffucci, Irene; Le Bailly, Bryden A. F.; Byrne, Liam; Bijvoets, Stefan M.; Lizio, M. Giovanna; Raftery, James; Butts, Craig P.; Webb, Simon J.; Contini, Alessandro

2017-01-01

Helical oligomers of achiral monomers adopt domains of uniform screw sense, which are occasionally interrupted by screw-sense reversals. These rare, elusive, and fast-moving features have eluded detailed characterization. We now describe the structure and habits of a screw-sense reversal trapped within a fragment of a helical oligoamide foldamer of the achiral quaternary amino acid 2-aminoisobutyric acid (Aib). The reversal was enforced by compelling the amide oligomer to adopt a right-handed screw sense at one end and a left-handed screw sense at the other. The trapped reversal was characterized by X-ray crystallography, and its dynamic properties were monitored by NMR and circular dichroism, and modelled computationally. Raman spectroscopy indicated that a predominantly helical architecture was maintained despite the reversal. NMR and computational results indicated a stepwise shift from one screw sense to another on moving along the helical chain, indicating that in solution the reversal is not localised at a specific location, but is free to migrate across a number of residues. Analogous unconstrained screw-sense reversals that are free to move within a helical structure are likely to provide the mechanism by which comparable helical polymers and foldamers undergo screw-sense inversion. PMID:28451368

Hematopoietic cytokines: similarities and differences in the structures, with implications for receptor binding.

PubMed Central

Wlodawer, A.; Pavlovsky, A.; Gustchina, A.

1993-01-01

Crystal and NMR structures of helical cytokines--interleukin-4 (IL-4), granulocyte-macrophage colony-stimulating factor (GM-CSF), and interleukin-2 (IL-2)--have been compared. Root mean square deviations in the C alpha coordinates for the conserved regions of the helices were 1-2 A between different cytokines, about twice the differences observed for independently determined crystal and solution structures of IL-4. Considerable similarity in amino acid sequence in the areas expected to interact with the receptors was detected, and the available mutagenesis data for these cytokines were correlated with structure conservation. Models of cytokine-receptor interactions were postulated for IL-4 based on its structure as well as on the published structure of human growth hormone interacting with its receptors (de Vos, A.M., Ultsch, M., & Kossiakoff, A.A., 1992, Science 255, 306-312). Patches of positively charged residues on the surfaces of helices C and D of IL-4 may be responsible for the interactions with the negatively charged residues found in the complementary parts of the IL-4 receptors. PMID:8401223

A four-way junction with triple-helical arms: design, characterization, and stability.

PubMed

Makube, N; Klump, H H

2000-05-01

The formation of the four-way junction containing four triple-helical arms has been demonstrated using chemical methods (polyacrylamide gel electrophoresis and chemical footprinting using OsO(4) as a probe) and physical methods (UV absorbance melting and DSC). The junction J(T1T3) was assembled from two 20-mer purine strands and two 44-mer pyrimidine strands. To determine the contribution of the different arms to the stability of the complete structure of J(T1T3), the junction was compared to two simplified substructures, J(T1) and J(T3), respectively. Common to these complexes is the underlying double-helical four-way junction Js. Addition of Na(+) had a profound effect on stabilizing and subsequently folding the junctions into the stacked X-structures. The following results support the structure present: (i) The native polyacrylamide electrophoresis exhibits only a single band(s) corresponding to one species present when all four single strands are mixed in equal amounts. (ii) OsO(4) modifications were investigated at pH 5.0 and in the presence of 10 mM Mg(2+) and 100 mM Na(+). There is no cleavage of thymine residues at the branch point and throughout the structure. (iii) The thermal unfolding of J(T1) and J(T3) illustrates that the triple-helical arms are more stable than the double-helical arms which are contained in these junctions and that J(T1T3) with four triple-helical arms is slightly more stable than J(T1) and J(T3). (iv) The calorimetric transition enthalpies determined for the arms of J(T1T3) are comparable to those associated with the unfolding of its corresponding arms in J(T1) and J(T3). The results also illustrate that the formation of the junctions is not restricted by the pH, [Na(+)], sequence composition of the arms, and/or the loop position. Copyright 2000 Academic Press.

Development of potent anti-infective agents from Silurana tropicalis: conformational analysis of the amphipathic, alpha-helical antimicrobial peptide XT-7 and its non-haemolytic analogue [G4K]XT-7.

PubMed

Subasinghage, Anusha P; Conlon, J Michael; Hewage, Chandralal M

2010-04-01

Peptide XT-7 (GLLGP(5)LLKIA(10)AKVGS(15)NLL.NH(2)) is a cationic, leucine-rich peptide, first isolated from skin secretions of the frog, Silurana tropicalis (Pipidae). The peptide shows potent, broad-spectrum antimicrobial activity but its therapeutic potential is limited by haemolytic activity (LC(50)=140 microM). The analogue [G4K]XT-7, however, retains potent antimicrobial activity but is non-haemolytic (LC(50)>500 microM). In order to elucidate the molecular basis for this difference in properties, the three dimensional structures of XT-7 and the analogue have been investigated by proton NMR spectroscopy and molecular modelling. In aqueous solution, both peptides lack secondary structure. In a 2,2,2-trifluoroethanol (TFE-d(3))-H(2)O mixed solvent system, XT-7 is characterised by a right handed alpha-helical conformation between residues Leu(3) and Leu(17) whereas [G4K]XT-7 adopts a more restricted alpha-helical conformation between residues Leu(6) and Leu(17). A similar conformation for XT-7 in 1,2-dihexanoyl-sn-glycero-3-phosphocholine (DHPC) micellular media was observed with a helical segment between Leu(3) and Leu(17). However, differences in side chain orientations restricting the hydrophilic residues to a smaller patch resulted in an increased hydrophobic surface relative to the conformation in TFE-H(2)O. Molecular modelling of the structures obtained in our study demonstrates the amphipathic character of the helical segments. It is proposed that the marked decrease in haemolytic activity produced by the substitution Gly(4)-->Lys in XT-7 arises from a decrease in both helicity and hydrophobicity. These studies may facilitate the development of potent but non-toxic anti-infective agents based upon the structure of XT-7. Copyright 2009 Elsevier B.V. All rights reserved.

The structure of the ends of α-helices in globular proteins: effect of additional hydrogen bonds and implications for helix formation.

PubMed

Leader, David P; Milner-White, E James

2011-03-01

We prepared a set of about 2000 α-helices from a relational database of high-resolution three-dimensional structures of globular proteins, and identified additional main chain i ← i+3 hydrogen bonds at the ends of the helices (i.e., where the hydrogen bonding potential is not fulfilled by canonical i ← i+4 hydrogen bonds). About one-third of α-helices have such additional hydrogen bonds at the N-terminus, and more than half do so at the C-terminus. Although many of these additional hydrogen bonds at the C-terminus are associated with Schellman loops, the majority are not. We compared the dihedral angles at the termini of α-helices having or lacking the additional hydrogen bonds. Significant differences were found, especially at the C-terminus, where the dihedral angles at positions C2 and C1 in the absence of additional hydrogen bonds deviate substantially from those occurring within the α-helix. Using a novel approach we show how the structure of the C-terminus of the α-helix can emerge from that of constituent overlapping α-turns and β-turns, which individually show a variation in dihedral angles at different positions. We have also considered the direction of propagation of the α-helix using this approach. If one assumes that helices start as a single α-turn and grow by successive addition of further α-turns, the paths for growth in the N → C and C → N directions differ in a way that suggests that extension in the C → N direction is favored. Copyright © 2010 Wiley-Liss, Inc.

Structural basis of molecular recognition of helical histone H3 tail by PHD finger domains.

PubMed

Bortoluzzi, Alessio; Amato, Anastasia; Lucas, Xavier; Blank, Manuel; Ciulli, Alessio

2017-05-04

The plant homeodomain (PHD) fingers are among the largest family of epigenetic domains, first characterized as readers of methylated H3K4. Readout of histone post-translational modifications by PHDs has been the subject of intense investigation; however, less is known about the recognition of secondary structure features within the histone tail itself. We solved the crystal structure of the PHD finger of the bromodomain adjacent to zinc finger 2A [BAZ2A, also known as TIP5 (TTF-I/interacting protein 5)] in complex with unmodified N-terminal histone H3 tail. The peptide is bound in a helical folded-back conformation after K4, induced by an acidic patch on the protein surface that prevents peptide binding in an extended conformation. Structural bioinformatics analyses identify a conserved Asp/Glu residue that we name 'acidic wall', found to be mutually exclusive with the conserved Trp for K4Me recognition. Neutralization or inversion of the charges at the acidic wall patch in BAZ2A, and homologous BAZ2B, weakened H3 binding. We identify simple mutations on H3 that strikingly enhance or reduce binding, as a result of their stabilization or destabilization of H3 helicity. Our work unravels the structural basis for binding of the helical H3 tail by PHD fingers and suggests that molecular recognition of secondary structure motifs within histone tails could represent an additional layer of regulation in epigenetic processes. © 2017 The Author(s).

Mode selection in swirling jet experiments: a linear stability analysis

NASA Astrophysics Data System (ADS)

Gallaire, François; Chomaz, Jean-Marc

2003-11-01

The primary goal of the study is to identify the selection mechanism responsible for the appearance of a double-helix structure in the pre-breakdown stage of so-called screened swirling jets for which the circulation vanishes away from the jet. The family of basic flows under consideration combines the azimuthal velocity profiles of Carton & McWilliams (1989) and the axial velocity profiles of Monkewitz (1988). This model satisfactorily represents the nozzle exit velocity distributions measured in the swirling jet experiment of Billant et al. (1998). Temporal and absolute/convective instability properties are directly retrieved from numerical simulations of the linear impulse response for different swirl parameter settings. A large range of negative helical modes, winding with the basic flow, are destabilized as swirl is increased, and their characteristics for large azimuthal wavenumbers are shown to agree with the asymptotic analysis of Leibovich & Stewartson (1983). However, the temporal study fails to yield a clear selection principle. The absolute/convective instability regions are mapped out in the plane of the external axial flow and swirl parameters. The absolutely unstable domain is enhanced by rotation and it remains open for arbitrarily large swirl. The swirling jet with zero external axial flow is found to first become absolutely unstable to a mode of azimuthal wavenumber m {=} {-}2, winding with the jet. It is suggested that this selection mechanism accounts for the experimental observation of a double-helix structure.

Structural elucidation of a heteroglycan from the fruiting bodies of Agaricus blazei Murill.

PubMed

Liu, Jicheng; Zhang, Chunjing; Wang, Yajun; Yu, Haitao; Liu, Han; Wang, Liping; Yang, Xiuzhen; Liu, Zhecheng; Wen, Xianchun; Sun, Yongxu; Yu, Chunlei; Liu, Lei

2011-11-01

One water-soluble polysaccharide (ABP-W1) was purified from the fruiting bodies of Agaricus blazei by DEAE Sepharose Fast Flow and Sepharose 6 Fast Flow column chromatography. Its molecular weight was about 3.9×10(2) kDa as determined by high-performance size-exclusion chromatography (HPSEC). The structural feature of ABP-W1 was investigated by a combination of chemical and instrumental analysis, including partial hydrolysis with acid, periodate oxidation-Smith degradation, acetylation, methylation analysis and nuclear magnetic resonance spectroscopy (NMR (1)H, (13)C). The results revealed that ABP-W1 had a backbone consisting of (1→6)-linked-α-D-galactopyranosyl and (1→2,6)-linked-α-D-glucopyranosyl, which was branched with one single terminal (1→)-α-D-glucopyranosyl at the O-2 position of (1→2,6)-linked-α-D-glucopyranosyl along the main chain in the ratio of 1:1:1. The observation of the complex-formation between ABP-W1 and Congo Red indicated that ABP-W1 probably existed in a triple-strand helical conformation in water. Based on the data obtained, ABP-W1 was composed of a repeating unit with a structure as below: [structure: see text]. Copyright © 2011 Elsevier B.V. All rights reserved.

Bifurcated helical core equilibrium states in tokamaks

NASA Astrophysics Data System (ADS)

Cooper, W. A.; Chapman, I. T.; Schmitz, O.; Turnbull, A. D.; Tobias, B. J.; Lazarus, E. A.; Turco, F.; Lanctot, M. J.; Evans, T. E.; Graves, J. P.; Brunetti, D.; Pfefferlé, D.; Reimerdes, H.; Sauter, O.; Halpern, F. D.; Tran, T. M.; Coda, S.; Duval, B. P.; Labit, B.; Pochelon, A.; Turnyanskiy, M. R.; Lao, L.; Luce, T. C.; Buttery, R.; Ferron, J. R.; Hollmann, E. M.; Petty, C. C.; van Zeeland, M.; Fenstermacher, M. E.; Hanson, J. M.; Lütjens, H.

2013-07-01

Tokamaks with weak to moderate reversed central shear in which the minimum inverse rotational transform (safety factor) qmin is in the neighbourhood of unity can trigger bifurcated magnetohydrodynamic equilibrium states, one of which is similar to a saturated ideal internal kink mode. Peaked prescribed pressure profiles reproduce the ‘snake’ structures observed in many tokamaks which has led to a novel explanation of the snake as a bifurcated equilibrium state. Snake equilibrium structures are computed in simulations of the tokamak à configuration variable (TCV), DIII-D and mega amp spherical torus (MAST) tokamaks. The internal helical deformations only weakly modulate the plasma-vacuum interface which is more sensitive to ripple and resonant magnetic perturbations. On the other hand, the external perturbations do not alter the helical core deformation in a significant manner. The confinement of fast particles in MAST simulations deteriorate with the amplitude of the helical core distortion. These three-dimensional bifurcated solutions constitute a paradigm shift that motivates the applications of tools developed for stellarator research in tokamak physics investigations.

Chiral monolithic absorbent constructed by optically active helical-substituted polyacetylene and graphene oxide: preparation and chiral absorption capacity.

PubMed

Li, Weifei; Wang, Bo; Yang, Wantai; Deng, Jianping

2015-02-01

Chiral monolithic absorbent is successfully constructed for the first time by using optically active helical-substituted polyacetylene and graphene oxide (GO). The preparative strategy is facile and straightforward, in which chiral-substituted acetylene monomer (Ma), cross-linker (Mb), and alkynylated GO (Mc) undergo copolymerization to form the desired monolithic absorbent in quantitative yield. The resulting monoliths are characterized by circular dichroism, UV-vis absorption, scanning electron microscopy (SEM), FT-IR, Raman, energy-dispersive spectrometer (EDS), X-ray diffraction (XRD), Brunauer-Emmett-Teller (BET), XPS, and thermogravimetric analysis (TGA) techniques. The polymer chains derived from Ma form chiral helical structures and thus provide optical activity to the monoliths, while GO sheets contribute to the formation of porous structures. The porous structure enables the monolithic absorbents to demonstrate a large swelling ratio in organic solvents, and more remarkably, the helical polymer chains provide optical activity and further enantio-differentiating absorption ability. The present study establishes an efficient and versatile methodology for preparing novel functional materials, in particular monolithic chiral materials based on substituted polyacetylene and GO. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

X-ray diffraction from nonuniformly stretched helical molecules

DOE Office of Scientific and Technical Information (OSTI.GOV)

Prodanovic, Momcilo; Irving, Thomas C.; Mijailovich, Srboljub M.

2016-04-18

The fibrous proteins in living cells are exposed to mechanical forces interacting with other subcellular structures. X-ray fiber diffraction is often used to assess deformation and movement of these proteins, but the analysis has been limited to the theory for fibrous molecular systems that exhibit helical symmetry. However, this approach cannot adequately interpret X-ray data from fibrous protein assemblies where the local strain varies along the fiber length owing to interactions of its molecular constituents with their binding partners. To resolve this problem a theoretical formulism has been developed for predicting the diffraction from individual helical molecular structures nonuniformly strainedmore » along their lengths. This represents a critical first step towards modeling complex dynamical systems consisting of multiple helical structures using spatially explicit, multi-scale Monte Carlo simulations where predictions are compared with experimental data in a `forward' process to iteratively generate ever more realistic models. Here the effects of nonuniform strains and the helix length on the resulting magnitude and phase of diffraction patterns are quantitatively assessed. Examples of the predicted diffraction patterns of nonuniformly deformed double-stranded DNA and actin filaments in contracting muscle are presented to demonstrate the feasibly of this theoretical approach.« less

Wind tunnel study of helical and straight-bladed vertical-axis wind turbine wakes

NASA Astrophysics Data System (ADS)

Bagheri, Maryam; Araya, Daniel

2017-11-01

It is hypothesized that blade curvature can serve as a passive means to control fluid entrainment and wake recovery in vertical-axis wind turbine (VAWT) arrays. We test this experimentally in a wind tunnel using two different VAWT configurations, one with straight blades and another with helical blades, keeping all other experimental parameters fixed. A small-scale, commercially available VAWT (15W max power) is used as the baseline wind tunnel model in each case. The commercial VAWT blades are replaced with either straight or helical blades that are 3D-printed extrusions of the same airfoil cross-section. Results from smoke flow visualization, three-component wake velocity measurements, and turbine power data are presented. These results give insight into the potential use of VAWTs with curved blades in utility-scale wind farms.

Helical 4D CT and Comparison with Cine 4D CT

NASA Astrophysics Data System (ADS)

Pan, Tinsu

4D CT was one of the most important developments in radiation oncology in the last decade. Its early development in single slice CT and commercialization in multi-slice CT has radically changed our practice in radiation treatment of lung cancer, and has enabled the stereotactic radiosurgery of early stage lung cancer. In this chapter, we will document the history of 4D CT development, detail the data sufficiency condition governing the 4D CT data collection; present the design of the commercial helical 4D CTs from Philips and Siemens; compare the differences between the helical 4D CT and the GE cine 4D CT in data acquisition, slice thickness, acquisition time and work flow; review the respiratory monitoring devices; and understand the causes of image artifacts in 4D CT.

Camps 2.0: exploring the sequence and structure space of prokaryotic, eukaryotic, and viral membrane proteins.

PubMed

Neumann, Sindy; Hartmann, Holger; Martin-Galiano, Antonio J; Fuchs, Angelika; Frishman, Dmitrij

2012-03-01

Structural bioinformatics of membrane proteins is still in its infancy, and the picture of their fold space is only beginning to emerge. Because only a handful of three-dimensional structures are available, sequence comparison and structure prediction remain the main tools for investigating sequence-structure relationships in membrane protein families. Here we present a comprehensive analysis of the structural families corresponding to α-helical membrane proteins with at least three transmembrane helices. The new version of our CAMPS database (CAMPS 2.0) covers nearly 1300 eukaryotic, prokaryotic, and viral genomes. Using an advanced classification procedure, which is based on high-order hidden Markov models and considers both sequence similarity as well as the number of transmembrane helices and loop lengths, we identified 1353 structurally homogeneous clusters roughly corresponding to membrane protein folds. Only 53 clusters are associated with experimentally determined three-dimensional structures, and for these clusters CAMPS is in reasonable agreement with structure-based classification approaches such as SCOP and CATH. We therefore estimate that ∼1300 structures would need to be determined to provide a sufficient structural coverage of polytopic membrane proteins. CAMPS 2.0 is available at http://webclu.bio.wzw.tum.de/CAMPS2.0/. Copyright © 2011 Wiley Periodicals, Inc.

Pseudo-enantiomeric chiral components and formation of the helical micro- and nanostructures in charge-transfer complexes

NASA Astrophysics Data System (ADS)

Langer, Jerzy J.; Hreczycho, Grzegorz

2018-03-01

Helical organic micro- and nanostructures are formed by a charge-transfer complex, cinchonidine-TCNQ. These unusual forms result from the chirality, the steric structure and specific interactions of cinchonidine molecules. These materials are semiconductors (10-4 S cm-1), with the typical absorption spectra in IR and UV-vis, but also have a characteristic of CD spectrum. Surprisingly, conductive micro and nano helices are not formed in pseudo-enantiomeric cinchonine, i.e. the complex of cinchonine and TCNQ.

Diastereoselective cyclization of an aminobenzoic acid derivative and chiroptical properties of triple-stranded helical bis(phenylethynyl)benzene.

PubMed

Yamakado, Ryohei; Matsuoka, Shin-ichi; Suzuki, Masato; Takeuchi, Daisuke; Masu, Hyuma; Azumaya, Isao; Takagi, Koji

2015-04-04

The diastereoselective cyclization of 2,5-dibromo-4-hexylaminobenzoic acid was achieved by the microwave-assisted condensation using SiCl4. Moreover, the triple-stranded helical structure of bis(phenylethynyl)benzene units embedded in the cyclic tri(benzamide) scaffold was obtained by a Sonogashira-Hagihara coupling reaction. Two optically active enantiomers that do not racemize even at the elevated temperature were separated by chiral HPLC. The chiral helical topology was revealed by the spectroscopic data and theoretical calculation.

Optimization of view weighting in tilted-plane-based reconstruction algorithms to minimize helical artifacts in multi-slice helical CT

NASA Astrophysics Data System (ADS)

Tang, Xiangyang

2003-05-01

In multi-slice helical CT, the single-tilted-plane-based reconstruction algorithm has been proposed to combat helical and cone beam artifacts by tilting a reconstruction plane to fit a helical source trajectory optimally. Furthermore, to improve the noise characteristics or dose efficiency of the single-tilted-plane-based reconstruction algorithm, the multi-tilted-plane-based reconstruction algorithm has been proposed, in which the reconstruction plane deviates from the pose globally optimized due to an extra rotation along the 3rd axis. As a result, the capability of suppressing helical and cone beam artifacts in the multi-tilted-plane-based reconstruction algorithm is compromised. An optomized tilted-plane-based reconstruction algorithm is proposed in this paper, in which a matched view weighting strategy is proposed to optimize the capability of suppressing helical and cone beam artifacts and noise characteristics. A helical body phantom is employed to quantitatively evaluate the imaging performance of the matched view weighting approach by tabulating artifact index and noise characteristics, showing that the matched view weighting improves both the helical artifact suppression and noise characteristics or dose efficiency significantly in comparison to the case in which non-matched view weighting is applied. Finally, it is believed that the matched view weighting approach is of practical importance in the development of multi-slive helical CT, because it maintains the computational structure of fan beam filtered backprojection and demands no extra computational services.

On the inverse transfer of (non-)helical magnetic energy in a decaying magnetohydrodynamic turbulence

NASA Astrophysics Data System (ADS)

Park, Kiwan

2017-12-01

In our conventional understanding, large-scale magnetic fields are thought to originate from an inverse cascade in the presence of magnetic helicity, differential rotation or a magneto-rotational instability. However, as recent simulations have given strong indications that an inverse cascade (transfer) may occur even in the absence of magnetic helicity, the physical origin of this inverse cascade is still not fully understood. We here present two simulations of freely decaying helical and non-helical magnetohydrodynamic (MHD) turbulence. We verified the inverse transfer of helical and non-helical magnetic fields in both cases, but we found the underlying physical principles to be fundamentally different. In the former case, the helical magnetic component leads to an inverse cascade of magnetic energy. We derived a semi-analytic formula for the evolution of large-scale magnetic field using α coefficient and compared it with the simulation data. But in the latter case, the α effect, including other conventional dynamo theories, is not suitable to describe the inverse transfer of non-helical magnetic energy. To obtain a better understanding of the physics at work here, we introduced a 'field structure model' based on the magnetic induction equation in the presence of inhomogeneities. This model illustrates how the curl of the electromotive force leads to the build up of a large-scale magnetic field without the requirement of magnetic helicity. And we applied a quasi-normal approximation to the inverse transfer of magnetic energy.

Starch Catabolism by a Prominent Human Gut Symbiont Is Directed by the Recognition of Amylose Helices

DOE Office of Scientific and Technical Information (OSTI.GOV)

Koropatkin, Nicole M.; Martens, Eric C.; Gordon, Jeffrey I.

2009-01-12

The human gut microbiota performs functions that are not encoded in our Homo sapiens genome, including the processing of otherwise undigestible dietary polysaccharides. Defining the structures of proteins involved in the import and degradation of specific glycans by saccharolytic bacteria complements genomic analysis of the nutrient-processing capabilities of gut communities. Here, we describe the atomic structure of one such protein, SusD, required for starch binding and utilization by Bacteroides thetaiotaomicron, a prominent adaptive forager of glycans in the distal human gut microbiota. The binding pocket of this unique {alpha}-helical protein contains an arc of aromatic residues that complements the naturalmore » helical structure of starch and imposes this conformation on bound maltoheptaose. Furthermore, SusD binds cyclic oligosaccharides with higher affinity than linear forms. The structures of several SusD/oligosaccharide complexes reveal an inherent ligand recognition plasticity dominated by the three-dimensional conformation of the oligosaccharides rather than specific interactions with the composite sugars.« less

On the influence of curvature and torsion on turbulence in helically coiled pipes

NASA Astrophysics Data System (ADS)

Ciofalo, M.; Di Liberto, M.; Marotta, G.

2014-04-01

Turbulent flow and heat transfer in helically coiled pipes at Reτ=400 was investigated by DNS using finite volume grids with up to 2.36×107 nodes. Two curvatures (0.1 and 0.3) and two torsions (0 and 0.3) were considered. The flow was fully developed hydrodynamically and thermally. The central discretization scheme was adopted for diffusion and advection terms, and the second order backward Euler scheme for time advancement. The grid spacing in wall units was ~3 radially, 7.5 circumferentially and 20 axially. The time step was equal to one viscous wall unit and simulations were typically protracted for 8000 time steps, the last 4000 of which were used to compute statistics. The results showed that curvature affects the flow significantly. As it increases from 0.1 to 0.3 the friction coefficient and the Nusselt number increase and the secondary flow becomes stronger; axial velocity fluctuations decrease, but the main Reynolds shear stress increases. Torsion, at least at the moderate level tested (0.3), has only a minor effect on mean and turbulence quantities, yielding only a slight reduction of peak turbulence levels while leaving pressure drop and heat transfer almost unaffected.

Unsteady numerical analysis of solid-liquid two-phase flow in stirred tank with double helical ribbon impeller

NASA Astrophysics Data System (ADS)

Bai, He; Chen, Xiangshan; Zhao, Guangyu; Xiao, Chenglei; Li, Chen; Zhong, Cheng; Chen, Yu

2017-08-01

In order to enhance the mixing process of soil contaminated by oil and water, one kind of double helical ribbon (DHR) impeller was developed. In this study, the unsteady simulation analysis of solid-liquid two-phase flow in stirring tank with DHR impeller was conducted by the the computational fluid dynamics and the multi-reference frame (MRF) method. It was found that at 0-3.0 s stage, the rate of liquid was greater than the rate of solid particles, while the power consumption was 5-6 times more than the smooth operation. The rates of the liquid and the solid particles were almost the same, and the required power was 32 KW at t > 3.0 s. The flow of the solid particles in the tank was a typical axial circle flow, and the dispersed sequence of the solid that was accumulated at the bottom of the tank was: the bottom loop region, the annular region near the wall of the groove and finally the area near axial center. The results show that the DHR impeller was suitable for the mixing of liquid-solid two-phase.

Acetone-Linked Peptides: A Convergent Approach for Peptide Macrocyclization and Labeling.

PubMed

Assem, Naila; Ferreira, David J; Wolan, Dennis W; Dawson, Philip E

2015-07-20

Macrocyclization is a broadly applied approach for overcoming the intrinsically disordered nature of linear peptides. Herein, it is shown that dichloroacetone (DCA) enhances helical secondary structures when introduced between peptide nucleophiles, such as thiols, to yield an acetone-linked bridge (ACE). Aside from stabilizing helical structures, the ketone moiety embedded in the linker can be modified with diverse molecular tags by oxime ligation. Insights into the structure of the tether were obtained through co-crystallization of a constrained S-peptide in complex with RNAse S. The scope of the acetone-linked peptides was further explored through the generation of N-terminus to side chain macrocycles and a new approach for generating fused macrocycles (bicycles). Together, these studies suggest that acetone linking is generally applicable to peptide macrocycles with a specific utility in the synthesis of stabilized helices that incorporate functional tags. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Structure of a short-chain dehydrogenase/reductase from Bacillus anthracis

PubMed Central

Hou, Jing; Wojciechowska, Kamila; Zheng, Heping; Chruszcz, Maksymilian; Cooper, David R.; Cymborowski, Marcin; Skarina, Tatiana; Gordon, Elena; Luo, Haibin; Savchenko, Alexei; Minor, Wladek

2012-01-01

The crystal structure of a short-chain dehydrogenase/reductase from Bacillus anthracis strain ‘Ames Ancestor’ complexed with NADP has been determined and refined to 1.87 Å resolution. The structure of the enzyme consists of a Rossmann fold composed of seven parallel β-strands sandwiched by three α-­helices on each side. An NADP molecule from an endogenous source is bound in the conserved binding pocket in the syn conformation. The loop region responsible for binding another substrate forms two perpendicular short helices connected by a sharp turn. PMID:22684058

Functional interactions between A' helices in the C-linker of open CNG channels.

PubMed

Hua, Li; Gordon, Sharona E

2005-03-01

Cyclic nucleotide-gated (CNG) channels are nonselective cation channels that are activated by the direct binding of the cyclic nucleotides cAMP and cGMP. The region linking the last membrane-spanning region (S6) to the cyclic nucleotide binding domain in the COOH terminus, termed the C-linker, has been shown to play an important role in coupling cyclic nucleotide binding to opening of the pore. In this study, we explored the intersubunit proximity between the A' helices of the C-linker regions of CNGA1 in functional channels using site-specific cysteine substitution. We found that intersubunit disulfide bonds can be formed between the A' helices in open channels, and that inducing disulfide bonds in most of the studied constructs resulted in potentiation of channel activation. This suggests that the A' helices of the C-linker regions are in close proximity when the channel is in the open state. Our finding is not compatible with a homology model of the CNGA1 C-linker made from the recently published X-ray crystallographic structure of the hyperpolarization-activated, cyclic nucleotide-modulated (HCN) channel COOH terminus, and leads us to suggest that the C-linker region depicted in the crystal structure may represent the structure of the closed state. The opening conformational change would then involve a movement of the A' helices from a position parallel to the axis of the membrane to one perpendicular to the axis of the membrane.

Visualization of bacterial flagella dynamics in a viscous shear flow

NASA Astrophysics Data System (ADS)

Ali, Jamel; Kim, Minjun

2016-11-01

We report on the dynamics of tethered bacterial flagella in an applied viscous shear flow and analyze their behavior using image processing. Flagellin proteins were repolymerized into flagellar filaments functionalized with biotin at their proximal end, and allowed to self-assemble within a micro channel coated with streptavidin. It was observed that all attached flagellar filaments aligned with the steady shear flow of various polymeric solutions. Furthermore it was observed that many of the filaments were stretched, and at elevated flow rates began to undergo polymorphic transformations, which were initiated at one end of the flagellum. When undergoing a change to a different helical form the flagellum was observed to transform to an oppositely handed helix, as to counteract the viscous torque imparted by the shear flow. It was also observed that some flagellar filaments did not undergo polymorphic transformations, but rotated about their helical axis. The rate of this rotation appears to be a function of the applied flow rate. These results expand on previous experimental work and aid in the development of a novel platform that harnesses the autonomic response of a 'forest' of bacterial flagella for engineering applications. This work was funded by NSF Grant CMMI-1000255, KEIT MOTIE Grant No. 10052980, and with Government support under and awarded by DoD, Air Force Office of Scientific Research, National Defense Science and Engineering Graduate (NDSEG) Fellowship, 32 CFR 168a.

RELATIONSHIPS BETWEEN FLUID VORTICITY, KINETIC HELICITY, AND MAGNETIC FIELD ON SMALL-SCALES (QUIET-NETWORK) ON THE SUN

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sangeetha, C. R.; Rajaguru, S. P., E-mail: crsangeetha@iiap.res.in

We derive horizontal fluid motions on the solar surface over large areas covering the quiet-Sun magnetic network from local correlation tracking of convective granules imaged in continuum intensity and Doppler velocity by the Helioseismic and Magnetic Imager (HMI) on board the Solar Dynamics Observatory . From these we calculate the horizontal divergence, the vertical component of vorticity, and the kinetic helicity of fluid motions. We study the correlations between fluid divergence and vorticity, and between vorticity (kinetic helicity) and the magnetic field. We find that the vorticity (kinetic helicity) around small-scale fields exhibits a hemispherical pattern (in sign) similar tomore » that followed by the magnetic helicity of large-scale active regions (containing sunspots). We identify this pattern to be a result of the Coriolis force acting on supergranular-scale flows (both the outflows and inflows), consistent with earlier studies using local helioseismology. Furthermore, we show that the magnetic fields cause transfer of vorticity from supergranular inflow regions to outflow regions, and that they tend to suppress the vortical motions around them when magnetic flux densities exceed about 300 G (from HMI). We also show that such an action of the magnetic fields leads to marked changes in the correlations between fluid divergence and vorticity. These results are speculated to be of importance to local dynamo action (if present) and to the dynamical evolution of magnetic helicity at the small-scale.« less

Influence of Na+ and Mg2+ ions on RNA structures studied with molecular dynamics simulations.

PubMed

Fischer, Nina M; Polêto, Marcelo D; Steuer, Jakob; van der Spoel, David

2018-06-01

The structure of ribonucleic acid (RNA) polymers is strongly dependent on the presence of, in particular Mg2+ cations to stabilize structural features. Only in high-resolution X-ray crystallography structures can ions be identified reliably. Here, we perform molecular dynamics simulations of 24 RNA structures with varying ion concentrations. Twelve of the structures were helical and the others complex folded. The aim of the study is to predict ion positions but also to evaluate the impact of different types of ions (Na+ or Mg2+) and the ionic strength on structural stability and variations of RNA. As a general conclusion Mg2+ is found to conserve the experimental structure better than Na+ and, where experimental ion positions are available, they can be reproduced with reasonable accuracy. If a large surplus of ions is present the added electrostatic screening makes prediction of binding-sites less reproducible. Distinct differences in ion-binding between helical and complex folded structures are found. The strength of binding (ΔG‡ for breaking RNA atom-ion interactions) is found to differ between roughly 10 and 26 kJ/mol for the different RNA atoms. Differences in stability between helical and complex folded structures and of the influence of metal ions on either are discussed.

Effects of hydrophobic and dipole-dipole interactions on the conformational transitions of a model polypeptide

NASA Astrophysics Data System (ADS)

Mu, Yan; Gao, Yi Qin

2007-09-01

We studied the effects of hydrophobicity and dipole-dipole interactions between the nearest-neighbor amide planes on the secondary structures of a model polypeptide by calculating the free energy differences between different peptide structures. The free energy calculations were performed with low computational costs using the accelerated Monte Carlo simulation (umbrella sampling) method, with a bias-potential method used earlier in our accelerated molecular dynamics simulations. It was found that the hydrophobic interaction enhances the stability of α helices at both low and high temperatures but stabilizes β structures only at high temperatures at which α helices are not stable. The nearest-neighbor dipole-dipole interaction stabilizes β structures under all conditions, especially in the low temperature region where α helices are the stable structures. Our results indicate clearly that the dipole-dipole interaction between the nearest neighboring amide planes plays an important role in determining the peptide structures. Current research provides a more unified and quantitative picture for understanding the effects of different forms of interactions on polypeptide structures. In addition, the present model can be extended to describe DNA/RNA, polymer, copolymer, and other chain systems.

Random single amino acid deletion sampling unveils structural tolerance and the benefits of helical registry shift on GFP folding and structure.

PubMed

Arpino, James A J; Reddington, Samuel C; Halliwell, Lisa M; Rizkallah, Pierre J; Jones, D Dafydd

2014-06-10

Altering a protein's backbone through amino acid deletion is a common evolutionary mutational mechanism, but is generally ignored during protein engineering primarily because its effect on the folding-structure-function relationship is difficult to predict. Using directed evolution, enhanced green fluorescent protein (EGFP) was observed to tolerate residue deletion across the breadth of the protein, particularly within short and long loops, helical elements, and at the termini of strands. A variant with G4 removed from a helix (EGFP(G4Δ)) conferred significantly higher cellular fluorescence. Folding analysis revealed that EGFP(G4Δ) retained more structure upon unfolding and refolded with almost 100% efficiency but at the expense of thermodynamic stability. The EGFP(G4Δ) structure revealed that G4 deletion caused a beneficial helical registry shift resulting in a new polar interaction network, which potentially stabilizes a cis proline peptide bond and links secondary structure elements. Thus, deletion mutations and registry shifts can enhance proteins through structural rearrangements not possible by substitution mutations alone. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

Helical circulations in the typhoon boundary layer

NASA Astrophysics Data System (ADS)

Ellis, Ryan; Businger, Steven

2010-03-01

Low-level wind data from the WSR-88D in Guam obtained in Typhoon Dale (1996) and Typhoon Keith (1997) are analyzed for coherent structures. Consistent with the results of previous studies of Atlantic hurricanes, velocity anomalies associated with coherent structures were found in the boundary layer of both storms. A total of 99 cases of coherent structures, also known as roll vortices, were documented during a 6 h evaluation period for each storm. Storm-relative roll location, roll vorticity, asymmetries in the upward and downward momentum fluxes, and signatures of circulations transverse to the mean flow associated with roll circulations were explored. The effects of terrain and convective precipitation systems, such as rainbands, on the occurrence of rolls were investigated. The results support and extend prior findings of roll observations, and can be used to help validate theoretical and numerical models of coherent structures within tropical cyclones. Moreover, the wind variations documented in this study may have application for wave runup and wind damage potential in tropical cyclones.

Design of the Helicity Injected Torus with Steady Inductive Helicity Injection (HIT-SI)

NASA Astrophysics Data System (ADS)

Sieck, P. E.; Gu, P.; Hamp, W. T.; Izzo, V. A.; McCollam, K. J.; Jarboe, T. R.; Nelson, B. A.; Redd, A. J.; Rogers, J. A.; Shumlak, U.

2000-10-01

Steady Inductive Helicity Injection (SIHI) is an inductive current drive method that injects helicity at a nearly constant rate, without open field lines, and without removing any helicity or magnetic energy from the plasma(T.R. Jarboe, Fusion Technology 36), p. 85, 1999. SIHI directly produces a rotating magnetic field structure, and the current profile is nearly time independent in the frame of the rotating field. The Helicity Injected Torus with SIHI (HIT-SI) is a ``bow tie'' spheromak designed to implement SIHI so that the current profile in the rotating frame is optimized. SIHI is accomplished using two inductive helicity injectors that operate 90^o out of phase with each other. Each helicity injector is a 180^o segment of a ZT-P size (a ≈ 8cm, R ≈ 32cm) RFP. The presence of a spheromak equilibrium will be readily apparent on several diagnostics, including the surface magnetic probes. The design of HIT-SI is presented, including the manufacturing techniques and metallurgical processes being used in the construction of the one-meter diameter close-fitting flux conserver. Several small prototype tests have been performed to prove the vacuum seal and electrical insulation capabilities of the design, and a finite element stress analysis of the flux conserver will be presented.

Triplex-forming oligonucleotides: a third strand for DNA nanotechnology

PubMed Central

2018-01-01

Abstract DNA self-assembly has proved to be a useful bottom-up strategy for the construction of user-defined nanoscale objects, lattices and devices. The design of these structures has largely relied on exploiting simple base pairing rules and the formation of double-helical domains as secondary structural elements. However, other helical forms involving specific non-canonical base-base interactions have introduced a novel paradigm into the process of engineering with DNA. The most notable of these is a three-stranded complex generated by the binding of a third strand within the duplex major groove, generating a triple-helical (‘triplex’) structure. The sequence, structural and assembly requirements that differentiate triplexes from their duplex counterparts has allowed the design of nanostructures for both dynamic and/or structural purposes, as well as a means to target non-nucleic acid components to precise locations within a nanostructure scaffold. Here, we review the properties of triplexes that have proved useful in the engineering of DNA nanostructures, with an emphasis on applications that hitherto have not been possible by duplex formation alone. PMID:29228337

Direct folding simulation of helical proteins using an effective polarizable bond force field.

PubMed

Duan, Lili; Zhu, Tong; Ji, Changge; Zhang, Qinggang; Zhang, John Z H

2017-06-14

We report a direct folding study of seven helical proteins (, Trpcage, , C34, N36, , ) ranging from 17 to 53 amino acids through standard molecular dynamics simulations using a recently developed polarizable force field-Effective Polarizable Bond (EPB) method. The backbone RMSDs, radius of gyrations, native contacts and native helix content are in good agreement with the experimental results. Cluster analysis has also verified that these folded structures with the highest population are in good agreement with their corresponding native structures for these proteins. In addition, the free energy landscape of seven proteins in the two dimensional space comprised of RMSD and radius of gyration proved that these folded structures are indeed of the lowest energy conformations. However, when the corresponding simulations were performed using the standard (nonpolarizable) AMBER force fields, no stable folded structures were observed for these proteins. Comparison of the simulation results based on a polarizable EPB force field and a nonpolarizable AMBER force field clearly demonstrates the importance of polarization in the folding of stable helical structures.

Characterization of the geometry and topology of DNA pictured as a discrete collection of atoms

PubMed Central

Olson, Wilma K.

2014-01-01

The structural and physical properties of DNA are closely related to its geometry and topology. The classical mathematical treatment of DNA geometry and topology in terms of ideal smooth space curves was not designed to characterize the spatial arrangements of atoms found in high-resolution and simulated double-helical structures. We present here new and rigorous numerical methods for the rapid and accurate assessment of the geometry and topology of double-helical DNA structures in terms of the constituent atoms. These methods are well designed for large DNA datasets obtained in detailed numerical simulations or determined experimentally at high-resolution. We illustrate the usefulness of our methodology by applying it to the analysis of three canonical double-helical DNA chains, a 65-bp minicircle obtained in recent molecular dynamics simulations, and a crystallographic array of protein-bound DNA duplexes. Although we focus on fully base-paired DNA structures, our methods can be extended to treat the geometry and topology of melted DNA structures as well as to characterize the folding of arbitrary molecules such as RNA and cyclic peptides. PMID:24791158