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.

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

Tomographic reconstruction of heat release rate perturbations induced by helical modes in turbulent swirl flames

NASA Astrophysics Data System (ADS)

Moeck, Jonas P.; Bourgouin, Jean-François; Durox, Daniel; Schuller, Thierry; Candel, Sébastien

2013-04-01

Swirl flows with vortex breakdown are widely used in industrial combustion systems for flame stabilization. This type of flow is known to sustain a hydrodynamic instability with a rotating helical structure, one common manifestation of it being the precessing vortex core. The role of this unsteady flow mode in combustion is not well understood, and its interaction with combustion instabilities and flame stabilization remains unclear. It is therefore important to assess the structure of the perturbation in the flame that is induced by this helical mode. Based on principles of tomographic reconstruction, a method is presented to determine the 3-D distribution of the heat release rate perturbation associated with the helical mode. Since this flow instability is rotating, a phase-resolved sequence of projection images of light emitted from the flame is identical to the Radon transform of the light intensity distribution in the combustor volume and thus can be used for tomographic reconstruction. This is achieved with one stationary camera only, a vast reduction in experimental and hardware requirements compared to a multi-camera setup or camera repositioning, which is typically required for tomographic reconstruction. Different approaches to extract the coherent part of the oscillation from the images are discussed. Two novel tomographic reconstruction algorithms specifically tailored to the structure of the heat release rate perturbations related to the helical mode are derived. The reconstruction techniques are first applied to an artificial field to illustrate the accuracy. High-speed imaging data acquired in a turbulent swirl-stabilized combustor setup with strong helical mode oscillations are then used to reconstruct the 3-D structure of the associated perturbation in the flame.

Dipole Alignment in Rotating MHD Turbulence

NASA Technical Reports Server (NTRS)

Shebalin, John V.; Fu, Terry; Morin, Lee

2012-01-01

We present numerical results from long-term CPU and GPU simulations of rotating, homogeneous, magnetohydrodynamic (MHD) turbulence, and discuss their connection to the spherically bounded case. We compare our numerical results with a statistical theory of geodynamo action that has evolved from the absolute equilibrium ensemble theory of ideal MHD turbulence, which is based on the ideal MHD invariants are energy, cross helicity and magnetic helicity. However, for rotating MHD turbulence, the cross helicity is no longer an exact invariant, although rms cross helicity becomes quasistationary during an ideal MHD simulation. This and the anisotropy imposed by rotation suggests an ansatz in which an effective, nonzero value of cross helicity is assigned to axisymmetric modes and zero cross helicity to non-axisymmetric modes. This hybrid statistics predicts a large-scale quasistationary magnetic field due to broken ergodicity , as well as dipole vector alignment with the rotation axis, both of which are observed numerically. We find that only a relatively small value of effective cross helicity leads to the prediction of a dipole moment vector that is closely aligned (less than 10 degrees) with the rotation axis. We also discuss the effect of initial conditions, dissipation and grid size on the numerical simulations and statistical theory.

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.

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.

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.

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

Propulsion of flexible polymer structures in a rotating magnetic field.

PubMed

Garstecki, Piotr; Tierno, Pietro; Weibel, Douglas B; Sagués, Francesc; Whitesides, George M

2009-05-20

We demonstrate a new concept for the propulsions of abiological structures at low Reynolds numbers. The approach is based on the design of flexible, planar polymer structures with a permanent magnetic moment. In the presence of an external, uniform, rotating magnetic field these structures deform into three-dimensional shapes that have helical symmetry and translate linearly through fluids at Re between 10(-1) and 10. The mechanism for the motility of these structures involves reversible deformation that breaks their planar symmetry and generates propulsion. These elastic propellers resemble microorganisms that use rotational mechanisms based on flagella and cilia for their motility in fluids at low Re.

Tempest in a glass tube: A helical vortex formation in a complex plasma

NASA Astrophysics Data System (ADS)

Saitou, Yoshifumi; Ishihara, Osamu; Ishihara

2014-12-01

A collective behavior of dust particles in a complex plasma with a magnetic field (up to 4 kG) is investigated. Dust particles form a dust disk which is rotating in a horizontal plane pushed by ions rotating with the E × B drift as a trigger force. The thickness of the disk is determined by controlling the experimental conditions. The disk rotates in a horizontal plane and forms a two-dimensional thin structure when the pressure pAr is relatively high. The dust particles are ejected from near the disk center and form a rotation in the vertical plane and, hence, forms a helical vortex when the disk is thick for relatively low pAr . The reason the dust disk has the different thickness is due to the neutral pressure. Under a higher (lower) neutral gas pressure, the disk becomes two (three) dimensional due to the influence of the neutral drag force.

Helical core reconstruction of a DIII-D hybrid scenario tokamak discharge

DOE PAGES

Cianciosa, Mark; Wingen, Andreas; Hirshman, Steven P.; ...

2017-05-18

Our paper presents the first fully 3-dimensional (3D) equilibrium reconstruction of a helical core in a tokamak device. Using a new parallel implementation of the Variational Moments Equilibrium Code (PARVMEC) coupled to V3FIT, 3D reconstructions can be performed at resolutions necessary to produce helical states in nominally axisymmetric tokamak equilibria. In a flux pumping experiment performed on DIII-D, an external n=1 field was applied while a 3/2 neoclassical tearing mode was suppressed using ECCD. The externally applied field was rotated past a set of fixed diagnostics at a 20 Hz frequency. Furthermore, the modulation, were found to be strongest in the core SXR and MSE channels, indicates a localized rotating 3D structure locked in phase with the applied field. Signals from multiple time slices are converted to a virtual rotation of modeled diagnostics adding 3D signal information. In starting from an axisymmetric equilibrium reconstruction solution, the reconstructed broader current profile flattens the q-profile, resulting in an m=1, n=1 perturbation of the magnetic axis that ismore » $$\\sim 50\\times $$ larger than the applied n=1 deformation of the edge. Error propagation confirms that the displacement of the axis is much larger than the uncertainty in the axis position validating the helical equilibrium.« less

Helical core reconstruction of a DIII-D hybrid scenario tokamak discharge

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

Cianciosa, Mark; Wingen, Andreas; Hirshman, Steven P.

Our paper presents the first fully 3-dimensional (3D) equilibrium reconstruction of a helical core in a tokamak device. Using a new parallel implementation of the Variational Moments Equilibrium Code (PARVMEC) coupled to V3FIT, 3D reconstructions can be performed at resolutions necessary to produce helical states in nominally axisymmetric tokamak equilibria. In a flux pumping experiment performed on DIII-D, an external n=1 field was applied while a 3/2 neoclassical tearing mode was suppressed using ECCD. The externally applied field was rotated past a set of fixed diagnostics at a 20 Hz frequency. Furthermore, the modulation, were found to be strongest in the core SXR and MSE channels, indicates a localized rotating 3D structure locked in phase with the applied field. Signals from multiple time slices are converted to a virtual rotation of modeled diagnostics adding 3D signal information. In starting from an axisymmetric equilibrium reconstruction solution, the reconstructed broader current profile flattens the q-profile, resulting in an m=1, n=1 perturbation of the magnetic axis that ismore » $$\\sim 50\\times $$ larger than the applied n=1 deformation of the edge. Error propagation confirms that the displacement of the axis is much larger than the uncertainty in the axis position validating the helical equilibrium.« less

Polarized excitons and optical activity in single-wall carbon nanotubes

NASA Astrophysics Data System (ADS)

Chang, Yao-Wen; Jin, Bih-Yaw

2018-05-01

The polarized excitons and optical activity of single-wall carbon nanotubes (SWNTs) are studied theoretically by π -electron Hamiltonian and helical-rotational symmetry. By taking advantage of the symmetrization, the single-particle energy and properties of a SWNT are characterized with the corresponding helical band structure. The dipole-moment matrix elements, magnetic-moment matrix elements, and the selection rules can also be derived. Based on different selection rules, the optical transitions can be assigned as the parallel-polarized, left-handed circularly-polarized, and right-handed circularly-polarized transitions, where the combination of the last two gives the cross-polarized transition. The absorption and circular dichroism (CD) spectra are simulated by exciton calculation. The calculated results are well comparable with the reported measurements. Built on the foundation, magnetic-field effects on the polarized excitons and optical activity of SWNTs are studied. Dark-bright exciton splitting and interband Faraday effect in the CD spectrum of SWNTs under an axial magnetic field are predicted. The Faraday rotation dispersion can be analyzed according to the selection rules of circular polarizations and the helical band structure.

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

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.

Rotational reorganization of doped cholesteric liquid crystalline films.

PubMed

Eelkema, Rienk; Pollard, Michael M; Katsonis, Nathalie; Vicario, Javier; Broer, Dirk J; Feringa, Ben L

2006-11-08

In this paper an unprecedented rotational reorganization of cholesteric liquid crystalline films is described. This rotational reorganization results from the conversion of a chiral molecular motor dopant to an isomer with a different helical twisting power, leading to a change in the cholesteric pitch. The direction of this reorganization is correlated to the sign of the change in helical twisting power of the dopant. The rotational reorganization of the liquid crystalline film was used to rotate microscopic objects 4 orders of magnitude larger than the bistable dopants in the film, which shows that molecular motors and switches can perform work. The surface of the doped cholesteric liquid crystalline films was found to possess a regular surface relief, whose periodicity coincides with typical cholesteric polygonal line textures. These surface features originate from the cholesteric superstructure in the liquid crystalline film, which in turn is the result of the presence of the chiral dopant. As such, the presence of the dopant is expressed in these distinct surface structures. A possible mechanism at the origin of the rotational reorganization of liquid crystalline films and the cholesteric surface relief is discussed.

Helicity dynamics in stratified turbulence in the absence of forcing.

PubMed

Rorai, C; Rosenberg, D; Pouquet, A; Mininni, P D

2013-06-01

A numerical study of decaying stably stratified flows is performed. Relatively high stratification (Froude number ≈10(-2)-10(-1)) and moderate Reynolds (Re) numbers (Re≈ 3-6×10(3)) are considered and a particular emphasis is placed on the role of helicity (velocity-vorticity correlations), which is not an invariant of the nondissipative equations. The problem is tackled by integrating the Boussinesq equations in a periodic cubical domain using different initial conditions: a nonhelical Taylor-Green (TG) flow, a fully helical Beltrami [Arnold-Beltrami-Childress (ABC)] flow, and random flows with a tunable helicity. We show that for stratified ABC flows helicity undergoes a substantially slower decay than for unstratified ABC flows. This fact is likely associated to the combined effect of stratification and large-scale coherent structures. Indeed, when the latter are missing, as in random flows, helicity is rapidly destroyed by the onset of gravitational waves. A type of large-scale dissipative "cyclostrophic" balance can be invoked to explain this behavior. No production of helicity is observed, contrary to the case of rotating and stratified flows. When helicity survives in the system, it strongly affects the temporal energy decay and the energy distribution among Fourier modes. We discover in fact that the decay rate of energy for stratified helical flows is much slower than for stratified nonhelical flows and can be considered with a phenomenological model in a way similar to what is done for unstratified rotating flows. We also show that helicity, when strong, has a measurable effect on the Fourier spectra, in particular at scales larger than the buoyancy scale, for which it displays a rather flat scaling associated with vertical shear, as observed in the planetary boundary layer.

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

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.

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.

Small-scale anisotropy induced by spectral forcing and by rotation in non-helical and helical turbulence

NASA Astrophysics Data System (ADS)

Vallefuoco, Donato; Naso, Aurore; Godeferd, Fabien S.

2018-02-01

We study the effect of large-scale spectral forcing on the scale-dependent anisotropy of the velocity field in direct numerical simulations of homogeneous turbulence. ABC-type forcing and helical or non-helical Euler-type forcing are considered. We propose a scale-dependent characterisation of anisotropy based on a modal decomposition of the two-point velocity tensor spectrum. This produces direction-dependent spectra of energy, helicity and polarisation. We examine the conditions that allow anisotropy to develop in the small scales due to forcing and we show that the theoretically expected isotropy is not exactly obtained, even in the smallest scales, for ABC and helical Euler forcings. When adding rotation, the anisotropy level in ABC-forced simulations is similar to that of lower Rossby number Euler-forced runs. Moreover, even at low rotation rate, the natural anisotropy induced by the Coriolis force is visible at all scales, and two distinct wavenumber ranges appear from our fine-grained characterisation, not separated by the Zeman scale but by a scale where rotation and dissipation are balanced.

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.

Symmetry, Statistics and Structure in MHD Turbulence

NASA Technical Reports Server (NTRS)

Shebalin, John V.

2007-01-01

Here, we examine homogeneous MHD turbulence in terms of truncated Fourier series. The ideal MHD equations and the associated statistical theory of absolute equilibrium ensembles are symmetric under P, C and T. However, the presence of invariant helicities, which are pseudoscalars under P and C, dynamically breaks this symmetry. This occurs because the surface of constant energy in phase space has disjoint parts, called components: while ensemble averages are taken over all components, a dynamical phase trajectory is confined to only one component. As the Birkhoff-Khinchin theorem tells us, ideal MHD turbulence is thus non-ergodic. This non-ergodicity manifests itself in low-wave number Fourier modes that have large mean values (while absolute ensemble theory predicts mean values of zero). Therefore, we have coherent structure in ideal MHD turbulence. The level of non-ergodicity and amount of energy contained in the associated coherent structure depends on the values of the helicities, as well as on the presence, or not, of a mean magnetic field and/or overall rotation. In addition to the well known cross and magnetic helicities, we also present a new invariant, which we call the parallel helicity, since it occurs when mean field and rotation axis are aligned. The question of applicability of these results to real (i.e., dissipative) MHD turbulence is also examined. Several long-time numerical simulations on a 64(exp 3) grid are given as examples. It is seen that coherent structure begins to form before decay dominates over nonlinearity. The connection of these results with inverse spectral cascades, selective decay, and magnetic dynamos is also discussed.

EVOLUTION OF SPINNING AND BRAIDING HELICITY FLUXES IN SOLAR ACTIVE REGION NOAA 10930

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

Ravindra, B.; Yoshimura, Keiji; Dasso, Sergio, E-mail: ravindra@iiap.res.in, E-mail: yosimura@solar.physics.montana.edu, E-mail: dasso@df.uba.ar

2011-12-10

The line-of-sight magnetograms from Solar Optical Telescope Narrowband Filter Imager observations of NOAA Active Region 10930 have been used to study the evolution of spinning and braiding helicities over a period of five days starting from 2006 December 9. The north (N) polarity sunspot was the follower and the south (S) polarity sunspot was the leader. The N-polarity sunspot in the active region was rotating in the counterclockwise direction. The rate of rotation was small during the first two days of observations and it increased up to 8 Degree-Sign hr{sup -1} on the third day of the observations. On themore » fourth and fifth days it remained at 4 Degree-Sign hr{sup -1} with small undulations in its magnitude. The sunspot rotated about 260 Degree-Sign in the last three days. The S-polarity sunspot did not complete more than 20 Degree-Sign in five days. However, it changed its direction of rotation five times over a period of five days and injected both the positive and negative type of spin helicity fluxes into the corona. Through the five days, both the positive and negative sunspot regions injected equal amounts of spin helicity. The total injected helicity is predominantly negative in sign. However, the sign of the spin and braiding helicity fluxes computed over all the regions were reversed from negative to positive five times during the five-day period of observations. The reversal in spinning helicity flux was found before the onset of the X3.4-class flare, too. Though, the rotating sunspot has been observed in this active region, the braiding helicity has contributed more to the total accumulated helicity than the spinning helicity. The accumulated helicity is in excess of -7 Multiplication-Sign 10{sup 43} Mx{sup 2} over a period of five days. Before the X3.4-class flare that occurred on 2006 December 13, the rotation speed and spin helicity flux increased in the S-polarity sunspot. Before the flare, the total injected helicity was larger than -6 Multiplication-Sign 10{sup 43} Mx{sup 2}. The observed reversal in the sign of spinning and braiding helicity fluxes could be the signature of the emergence of a twisted flux tube, which acquires the writhe of an opposite sign. The magnetic cloud associated with the ejected mass has carried about -7 Multiplication-Sign 10{sup 41} Mx{sup 2} of helicity. A time integration of helicity flux of about 1.2 hr integrated backward in time of the observation of the coronal mass ejection is sufficient for this event.« less

Dynamic Structure of Bombolitin II Bound to Lipid Bilayers as Revealed by Solid-state NMR and Molecular-Dynamics Simulation

PubMed Central

Toraya, Shuichi; Javkhlantugs, Namsrai; Mishima, Daisuke; Nishimura, Katsuyuki; Ueda, Kazuyoshi; Naito, Akira

2010-01-01

Bombolitin II (BLT2) is one of the hemolytic heptadecapeptides originally isolated from the venom of a bumblebee. Structure and orientation of BLT2 bound to 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) membranes were determined by solid-state 31P and 13C NMR spectroscopy. 31P NMR spectra showed that BLT2-DPPC membranes were disrupted into small particles below the gel-to-liquid crystalline phase transition temperature (Tc) and fused to form a magnetically oriented vesicle system where the membrane surface is parallel to the magnetic fields above the Tc. 13C NMR spectra of site-specifically 13C-labeled BLT2 at the carbonyl carbons were observed and the chemical shift anisotropies were analyzed to determine the dynamic structure of BLT2 bound to the magnetically oriented vesicle system. It was revealed that the membrane-bound BLT2 adopted an α-helical structure, rotating around the membrane normal with the tilt angle of the helical axis at 33°. Interatomic distances obtained from rotational-echo double-resonance experiments further showed that BLT2 adopted a straight α-helical structure. Molecular dynamics simulation performed in the BLT2-DPPC membrane system showed that the BLT2 formed a straight α-helix and that the C-terminus was inserted into the membrane. The α-helical axis is tilted 30° to the membrane normal, which is almost the same as the value obtained from solid-state NMR. These results suggest that the membrane disruption induced by BLT2 is attributed to insertion of BLT2 into the lipid bilayers. PMID:21081076

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

Helical axis stellarator with noninterlocking planar coils

DOEpatents

Reiman, A.; Boozer, A.H.

1984-03-06

The present invention generates stellarator fields having favorable properties (magnetic well and large rotational transform) by a simple coil system consisting only of unlinked planar non-circular coils. At large rotational transform toroidal effects on magnetic well and rotational transform are small and can be ignored. We do so herein, specializing in straight helical systems.

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.

Flexible helical-axis stellarator

DOEpatents

Harris, Jeffrey H.; Hender, Timothy C.; Carreras, Benjamin A.; Cantrell, Jack L.; Morris, Robert N.

1988-01-01

An 1=1 helical winding which spirals about a conventional planar, circular central conductor of a helical-axis stellarator adds a significant degree of flexibility by making it possible to control the rotational transform profile and shear of the magnetic fields confining the plasma in a helical-axis stellarator. The toroidal central conductor links a plurality of toroidal field coils which are separately disposed to follow a helical path around the central conductor in phase with the helical path of the 1=1 winding. This coil configuration produces bean-shaped magnetic flux surfaces which rotate around the central circular conductor in the same manner as the toroidal field generating coils. The additional 1=1 winding provides flexible control of the magnetic field generated by the central conductor to prevent the formation of low-order resonances in the rotational transform profile which can produce break-up of the equilibrium magnetic surfaces. Further, this additional winding can deepen the magnetic well which together with the flexible control provides increased stability.

TH-C-18A-11: Investigating the Minimum Scan Parameters Required to Generate Free-Breathing Fast-Helical CT Scans Without Motion-Artifacts

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

Thomas, D; Neylon, J; Dou, T

Purpose: A recently proposed 4D-CT protocol uses deformable registration of free-breathing fast-helical CT scans to generate a breathing motion model. In order to allow accurate registration, free-breathing images are required to be free of doubling-artifacts, which arise when tissue motion is greater than scan speed. This work identifies the minimum scanner parameters required to successfully generate free-breathing fast-helical scans without doubling-artifacts. Methods: 10 patients were imaged under free breathing conditions 25 times in alternating directions with a 64-slice CT scanner using a low dose fast helical protocol. A high temporal resolution (0.1s) 4D-CT was generated using a patient specific motionmore » model and patient breathing waveforms, and used as the input for a scanner simulation. Forward projections were calculated using helical cone-beam geometry (800 projections per rotation) and a GPU accelerated reconstruction algorithm was implemented. Various CT scanner detector widths and rotation times were simulated, and verified using a motion phantom. Doubling-artifacts were quantified in patient images using structural similarity maps to determine the similarity between axial slices. Results: Increasing amounts of doubling-artifacts were observed with increasing rotation times > 0.2s for 16×1mm slice scan geometry. No significant increase in doubling artifacts was observed for 64×1mm slice scan geometry up to 1.0s rotation time although blurring artifacts were observed >0.6s. Using a 16×1mm slice scan geometry, a rotation time of less than 0.3s (53mm/s scan speed) would be required to produce images of similar quality to a 64×1mm slice scan geometry. Conclusion: The current generation of 16 slice CT scanners, which are present in most Radiation Oncology departments, are not capable of generating free-breathing sorting-artifact-free images in the majority of patients. The next generation of CT scanners should be capable of at least 53mm/s scan speed in order to use a fast-helical 4D-CT protocol to generate a motion-artifact free 4D-CT. NIH R01CA096679.« less

Helical vortices: viscous dynamics and instability

NASA Astrophysics Data System (ADS)

Rossi, Maurice; Selcuk, Can; Delbende, Ivan; Ijlra-Upmc Team; Limsi-Cnrs Team

2014-11-01

Understanding the dynamical properties of helical vortices is of great importance for numerous applications such as wind turbines, helicopter rotors, ship propellers. Locally these flows often display a helical symmetry: fields are invariant through combined axial translation of distance Δz and rotation of angle θ = Δz / L around the same z-axis, where 2 πL denotes the helix pitch. A DNS code with built-in helical symmetry has been developed in order to compute viscous quasi-steady basic states with one or multiple vortices. These states will be characterized (core structure, ellipticity, ...) as a function of the pitch, without or with an axial flow component. The instability modes growing in the above base flows and their growth rates are investigated by a linearized version of the DNS code coupled to an Arnoldi procedure. This analysis is complemented by a helical thin-cored vortex filaments model. ANR HELIX.

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.

Dynamo action in dissipative, forced, rotating MHD turbulence

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

Shebalin, John V.

2016-06-15

Magnetohydrodynamic (MHD) turbulence is an inherent feature of large-scale, energetic astrophysical and geophysical magnetofluids. In general, these are rotating and are energized through buoyancy and shear, while viscosity and resistivity provide a means of dissipation of kinetic and magnetic energy. Studies of unforced, rotating, ideal (i.e., non-dissipative) MHD turbulence have produced interesting results, but it is important to determine how these results are affected by dissipation and forcing. Here, we extend our previous work and examine dissipative, forced, and rotating MHD turbulence. Incompressibility is assumed, and finite Fourier series represent turbulent velocity and magnetic field on a 64{sup 3} grid.more » Forcing occurs at an intermediate wave number by a method that keeps total energy relatively constant and allows for injection of kinetic and magnetic helicity. We find that 3-D energy spectra are asymmetric when forcing is present. We also find that dynamo action occurs when forcing has either kinetic or magnetic helicity, with magnetic helicity injection being more important. In forced, dissipative MHD turbulence, the dynamo manifests itself as a large-scale coherent structure that is similar to that seen in the ideal case. These results imply that MHD turbulence, per se, may play a fundamental role in the creation and maintenance of large-scale (i.e., dipolar) stellar and planetary magnetic fields.« less

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.

Granular Material Scoop and Near-Vertical Lifting Feeder/Conveyor

NASA Technical Reports Server (NTRS)

Walton, Otis (Inventor); Vollmer, Hubert J. (Inventor)

2017-01-01

An integrated granular-material scoop and near-vertical lifting feeder/conveyor includes special connections and skirts between a bullnose rotating scoop and an open-helical screw that provides the rotations and material lift and evacuation. A conical working-face of the bullnose rotating scoop has symmetrically distributed graters and vents to break loose and force-in granular material from natural deposits and cargo holds. The bullnose rotating scoop and the open-helical screw its attached to move the material into a continuous layer on the inside surface of an outer stationary sheathing. A motor drive attached to the open-helical screw above at the delivery end provides the lifting force necessary.

Cervical helical axis characteristics and its center of rotation during active head and upper arm movements-comparisons of whiplash-associated disorders, non-specific neck pain and asymptomatic individuals.

PubMed

Grip, Helena; Sundelin, Gunnevi; Gerdle, Björn; Stefan Karlsson, J

2008-09-18

The helical axis model can be used to describe translation and rotation of spine segments. The aim of this study was to investigate the cervical helical axis and its center of rotation during fast head movements (side rotation and flexion/extension) and ball catching in patients with non-specific neck pain or pain due to whiplash injury as compared with matched controls. The aim was also to investigate correlations with neck pain intensity. A finite helical axis model with a time-varying window was used. The intersection point of the axis during different movement conditions was calculated. A repeated-measures ANOVA model was used to investigate the cervical helical axis and its rotation center for consecutive levels of 15 degrees during head movement. Irregularities in axis movement were derived using a zero-crossing approach. In addition, head, arm and upper body range of motion and velocity were observed. A general increase of axis irregularity that correlated to pain intensity was observed in the whiplash group. The rotation center was superiorly displaced in the non-specific neck pain group during side rotation, with the same tendency for the whiplash group. During ball catching, an anterior displacement (and a tendency to an inferior displacement) of the center of rotation and slower and more restricted upper body movements implied a changed movement strategy in neck pain patients, possibly as an attempt to stabilize the cervical spine during head movement.

HELICAL MOTIONS OF FINE-STRUCTURE PROMINENCE THREADS OBSERVED BY HINODE AND IRIS

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

Okamoto, Takenori J.; Liu, Wei; Tsuneta, Saku, E-mail: joten.okamoto@nao.ac.jp

Fine-structure dynamics in solar prominences holds critical clues to understanding their physical nature of significant space-weather implications. We report evidence of rotational motions of horizontal helical threads in two active-region prominences observed by the Hinode and/or Interface Region Imaging Spectrograph satellites at high resolution. In the first event, we found transverse motions of brightening threads at speeds up to 55 km s{sup -1} seen in the plane of the sky. Such motions appeared as sinusoidal space–time trajectories with a typical period of ∼390 s, which is consistent with plane-of-sky projections of rotational motions. Phase delays at different locations suggest themore » propagation of twists along the threads at phase speeds of 90–270 km s{sup -1}. At least 15 episodes of such motions occurred in two days, none associated with an eruption. For these episodes, the plane-of-sky speed is linearly correlated with the vertical travel distance, suggestive of a constant angular speed. In the second event, we found Doppler velocities of 30–40 km s{sup -1} in opposite directions in the top and bottom portions of the prominence, comparable to the plane-of-sky speed. The moving threads have about twice broader line widths than stationary threads. These observations, when taken together, provide strong evidence for rotations of helical prominence threads, which were likely driven by unwinding twists triggered by magnetic reconnection between twisted prominence magnetic fields and ambient coronal fields.« less

Flux rope breaking and formation of a rotating blowout jet

NASA Astrophysics Data System (ADS)

Joshi, Navin Chandra; Nishizuka, Naoto; Filippov, Boris; Magara, Tetsuya; Tlatov, Andrey G.

2018-05-01

We analysed a small flux rope eruption converted into a helical blowout jet in a fan-spine configuration using multiwavelength observations taken by Solar Dynamics Observatory, which occurred near the limb on 2016 January 9. In our study, first, we estimated the fan-spine magnetic configuration with the potential-field calculation and found a sinistral small filament inside it. The filament along with the flux rope erupted upwards and interacted with the surrounding fan-spine magnetic configuration, where the flux rope breaks in the middle section. We observed compact brightening, flare ribbons, and post-flare loops underneath the erupting filament. The northern section of the flux rope reconnected with the surrounding positive polarity, while the southern section straightened. Next, we observed the untwisting motion of the southern leg, which was transformed into a rotating helical blowout jet. The sign of the helicity of the mini-filament matches the one of the rotating jets. This is consistent with recent jet models presented by Adams et al. and Sterling et al. We focused on the fine thread structure of the rotating jet and traced three blobs with the speed of 60-120 km s- 1, while the radial speed of the jet is ˜400 km s- 1. The untwisting motion of the jet accelerated plasma upwards along the collimated outer spine field lines, and it finally evolved into a narrow coronal mass ejection at the height of ˜9Rsun. On the basis of detailed analysis, we discussed clear evidence of the scenario of the breaking of the flux rope and the formation of the helical blowout jet in the fan-spine magnetic configuration.

Generation of a Large-scale Magnetic Field in a Convective Full-sphere Cross-helicity Dynamo

NASA Astrophysics Data System (ADS)

Pipin, V. V.; Yokoi, N.

2018-05-01

We study the effects of the cross-helicity in the full-sphere large-scale mean-field dynamo models of a 0.3 M ⊙ star rotating with a period of 10 days. In exploring several dynamo scenarios that stem from magnetic field generation by the cross-helicity effect, we found that the cross-helicity provides the natural generation mechanisms for the large-scale scale axisymmetric and nonaxisymmetric magnetic field. Therefore, the rotating stars with convective envelopes can produce a large-scale magnetic field generated solely due to the turbulent cross-helicity effect (we call it γ 2-dynamo). Using mean-field models we compare the properties of the large-scale magnetic field organization that stems from dynamo mechanisms based on the kinetic helicity (associated with the α 2 dynamos) and cross-helicity. For the fully convective stars, both generation mechanisms can maintain large-scale dynamos even for the solid body rotation law inside the star. The nonaxisymmetric magnetic configurations become preferable when the cross-helicity and the α-effect operate independently of each other. This corresponds to situations with purely γ 2 or α 2 dynamos. The combination of these scenarios, i.e., the γ 2 α 2 dynamo, can generate preferably axisymmetric, dipole-like magnetic fields at strengths of several kGs. Thus, we found a new dynamo scenario that is able to generate an axisymmetric magnetic field even in the case of a solid body rotation of the star. We discuss the possible applications of our findings to stellar observations.

Statistical Theory of the Ideal MHD Geodynamo

NASA Technical Reports Server (NTRS)

Shebalin, J. V.

2012-01-01

A statistical theory of geodynamo action is developed, using a mathematical model of the geodynamo as a rotating outer core containing an ideal (i.e., no dissipation), incompressible, turbulent, convecting magnetofluid. On the concentric inner and outer spherical bounding surfaces the normal components of the velocity, magnetic field, vorticity and electric current are zero, as is the temperature fluctuation. This allows the use of a set of Galerkin expansion functions that are common to both velocity and magnetic field, as well as vorticity, current and the temperature fluctuation. The resulting dynamical system, based on the Boussinesq form of the magnetohydrodynamic (MHD) equations, represents MHD turbulence in a spherical domain. These basic equations (minus the temperature equation) and boundary conditions have been used previously in numerical simulations of forced, decaying MHD turbulence inside a sphere [1,2]. Here, the ideal case is studied through statistical analysis and leads to a prediction that an ideal coherent structure will be found in the form of a large-scale quasistationary magnetic field that results from broken ergodicity, an effect that has been previously studied both analytically and numerically for homogeneous MHD turbulence [3,4]. The axial dipole component becomes prominent when there is a relatively large magnetic helicity (proportional to the global correlation of magnetic vector potential and magnetic field) and a stationary, nonzero cross helicity (proportional to the global correlation of velocity and magnetic field). The expected angle of the dipole moment vector with respect to the rotation axis is found to decrease to a minimum as the average cross helicity increases for a fixed value of magnetic helicity and then to increase again when average cross helicity approaches its maximum possible value. Only a relatively small value of cross helicity is needed to produce a dipole moment vector that is aligned at approx.10deg with the rotation axis.

Magnetohydrodynamic Models of Molecular Tornadoes

NASA Astrophysics Data System (ADS)

Au, Kelvin; Fiege, Jason D.

2017-07-01

Recent observations near the Galactic Center (GC) have found several molecular filaments displaying striking helically wound morphology that are collectively known as molecular tornadoes. We investigate the equilibrium structure of these molecular tornadoes by formulating a magnetohydrodynamic model of a rotating, helically magnetized filament. A special analytical solution is derived where centrifugal forces balance exactly with toroidal magnetic stress. From the physics of torsional Alfvén waves we derive a constraint that links the toroidal flux-to-mass ratio and the pitch angle of the helical field to the rotation laws, which we find to be an important component in describing the molecular tornado structure. The models are compared to the Ostriker solution for isothermal, nonmagnetic, nonrotating filaments. We find that neither the analytic model nor the Alfvén wave model suffer from the unphysical density inversions noted by other authors. A Monte Carlo exploration of our parameter space is constrained by observational measurements of the Pigtail Molecular Cloud, the Double Helix Nebula, and the GC Molecular Tornado. Observable properties such as the velocity dispersion, filament radius, linear mass, and surface pressure can be used to derive three dimensionless constraints for our dimensionless models of these three objects. A virial analysis of these constrained models is studied for these three molecular tornadoes. We find that self-gravity is relatively unimportant, whereas magnetic fields and external pressure play a dominant role in the confinement and equilibrium radial structure of these objects.

Global-Scale Consequences of Magnetic-Helicity Injection and Condensation on the Sun

NASA Technical Reports Server (NTRS)

Mackay, Duncan H.; DeVore, C. Richard; Antiochos, Spiro K.

2013-01-01

In the recent paper of Antiochos, a new concept for the injection of magnetic helicity into the solar corona by small-scale convective motions and its condensation onto polarity inversion lines (PILs) has been developed. We investigate this concept through global simulations of the Sun's photospheric and coronal magnetic fields and compare the results with the hemispheric pattern of solar filaments. Assuming that the vorticity of the cells is predominately counter-clockwise/clockwise in the northern/southern hemisphere, the convective motions inject negative/positive helicity into each hemisphere. The simulations show that: (i) On a north-south orientated PIL, both differential rotation and convective motions inject the same sign of helicity which matches that required to reproduce the hemispheric pattern of filaments. (ii) On a high latitude east-west orientated polar crown or sub-polar crown PIL, the vorticity of the cells has to be approximately 2-3 times greater than the local differential rotation gradient in order to overcome the incorrect sign of helicity injection from differential rotation. (iii) In the declining phase of the cycle, as a bipole interacts with the polar field, in some cases helicity condensation can reverse the effect of differential rotation along the East-West lead arm, but not in all cases. The results show that this newly developed concept of magnetic helicity injection and condensation is a viable method to explain the hemispheric pattern of filaments in conjunction with the mechanisms used in Yeates et al. (2008). Future observational studies should focus on determining the vorticity component within convective motions to determine, both its magnitude and latitudinal variation relative to the differential rotation gradient on the Sun.

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.

Helical and rod-shaped bacteria swim in helical trajectories with little additional propulsion from helical shape

PubMed Central

Constantino, Maira A.; Jabbarzadeh, Mehdi; Fu, Henry C.; Bansil, Rama

2016-01-01

It has frequently been hypothesized that the helical body shapes of flagellated bacteria may yield some advantage in swimming ability. In particular, the helical-shaped pathogen Helicobacter pylori is often claimed to swim like a corkscrew through its harsh gastric habitat, but there has been no direct confirmation or quantification of such claims. Using fast time-resolution and high-magnification two-dimensional (2D) phase-contrast microscopy to simultaneously image and track individual bacteria in bacterial broth as well as mucin solutions, we show that both helical and rod-shaped H. pylori rotated as they swam, producing a helical trajectory. Cell shape analysis enabled us to determine shape as well as the rotational and translational speed for both forward and reverse motions, thereby inferring flagellar kinematics. Using the method of regularized Stokeslets, we directly compare observed speeds and trajectories to numerical calculations for both helical and rod-shaped bacteria in mucin and broth to validate the numerical model. Although experimental observations are limited to select cases, the model allows quantification of the effects of body helicity, length, and diameter. We find that due to relatively slow body rotation rates, the helical shape makes at most a 15% contribution to propulsive thrust. The effect of body shape on swimming speeds is instead dominated by variations in translational drag required to move the cell body. Because helical cells are one of the strongest candidates for propulsion arising from the cell body, our results imply that quite generally, swimming speeds of flagellated bacteria can only be increased a little by body propulsion. PMID:28138539

On the Mysterious Propulsion of Synechococcus

PubMed Central

Ehlers, Kurt; Oster, George

2012-01-01

We propose a model for the self-propulsion of the marine bacterium Synechococcus utilizing a continuous looped helical track analogous to that found in Myxobacteria [1]. In our model cargo-carrying protein motors, driven by proton-motive force, move along a continuous looped helical track. The movement of the cargo creates surface distortions in the form of small amplitude traveling ridges along the S-layer above the helical track. The resulting fluid motion adjacent to the helical ribbon provides the propulsive thrust. A variation on the helical rotor model of [1] allows the motors to be anchored to the peptidoglycan layer, where they drive rotation of the track creating traveling helical waves along the S-layer. We derive expressions relating the swimming speed to the amplitude, wavelength, and velocity of the surface waves induced by the helical rotor, and show that they fall in reasonable ranges to explain the velocity and rotation rate of swimming Synechococcus. PMID:22567124

On the Magnetism and Dynamics of Prominence Legs Hosting Tornadoes

NASA Astrophysics Data System (ADS)

Martínez González, M. J.; Asensio Ramos, A.; Arregui, I.; Collados, M.; Beck, C.; de la Cruz Rodríguez, J.

2016-07-01

Solar tornadoes are dark vertical filamentary structures observed in the extreme ultraviolet associated with prominence legs and filament barbs. Their true nature and relationship to prominences requires an understanding of their magnetic structure and dynamic properties. Recently, a controversy has arisen: is the magnetic field organized forming vertical, helical structures or is it dominantly horizontal? And concerning their dynamics, are tornadoes really rotating or is it just a visual illusion? Here we analyze four consecutive spectro-polarimetric scans of a prominence hosting tornadoes on its legs, which helps us shed some light on their magnetic and dynamical properties. We show that the magnetic field is very smooth in all the prominence, which is probably an intrinsic property of the coronal field. The prominence legs have vertical helical fields that show slow temporal variation that is probably related to the motion of the fibrils. Concerning the dynamics, we argue that (1) if rotation exists, it is intermittent, lasting no more than one hour, and (2) the observed velocity pattern is also consistent with an oscillatory velocity pattern (waves).

ON THE MAGNETISM AND DYNAMICS OF PROMINENCE LEGS HOSTING TORNADOES

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

Martínez González, M. J.; Ramos, A. Asensio; Arregui, I.

2016-07-10

Solar tornadoes are dark vertical filamentary structures observed in the extreme ultraviolet associated with prominence legs and filament barbs. Their true nature and relationship to prominences requires an understanding of their magnetic structure and dynamic properties. Recently, a controversy has arisen: is the magnetic field organized forming vertical, helical structures or is it dominantly horizontal? And concerning their dynamics, are tornadoes really rotating or is it just a visual illusion? Here we analyze four consecutive spectro-polarimetric scans of a prominence hosting tornadoes on its legs, which helps us shed some light on their magnetic and dynamical properties. We show thatmore » the magnetic field is very smooth in all the prominence, which is probably an intrinsic property of the coronal field. The prominence legs have vertical helical fields that show slow temporal variation that is probably related to the motion of the fibrils. Concerning the dynamics, we argue that (1) if rotation exists, it is intermittent, lasting no more than one hour, and (2) the observed velocity pattern is also consistent with an oscillatory velocity pattern (waves).« less

Methods of fabricating a conductor assembly having a curvilinear arcuate shape

DOEpatents

Meinke, Rainer [Melbourne, FL

2011-08-23

A method for manufacture of a conductor assembly along a curvilinear axis. The assembly may be of the type which, when conducting current, generates a magnetic field or in which, in the presence of a changing magnetic field, a voltage is induced. In one example, the assembly includes a structure having a curved shape extending along the axis. A surface of the structure is positioned for formation of a channel along the curved shape. The structure is rotated about a second axis. While rotating the structure, a channel is formed in the surface that results in a helical shape in the structure. The channel extends both around and along the first axis.

The swimming of a perfect deforming helix

NASA Astrophysics Data System (ADS)

Koens, Lyndon; Zhang, Hang; Mourran, Ahmed; Lauga, Eric

2017-11-01

Many bacteria rotate helical flagellar filaments in order to swim. When at rest or rotated counter-clockwise these flagella are left handed helices but they undergo polymorphic transformations to right-handed helices when the motor is reversed. These helical deformations themselves can generate motion, with for example Rhodobacter sphaeroides using the polymorphic transformation of the flagellum to generate rotation, or Spiroplasma propagating a change of helix handedness across its body's length to generate forward motion. Recent experiments reported on an artificial helical microswimmer generating motion without a propagating change in handedness. Made of a temperature sensitive gel, these swimmers moved by changing the dimensions of the helix in a non-reciprocal way. Inspired by these results and helix's ubiquitous presence in the bacterial world, we investigate how a deforming helix moves within a viscous fluid. Maintaining a single handedness along its entire length, we discuss how a perfect deforming helix can create a non-reciprocal swimming stroke, identify its principle directions of motion, and calculate the swimming kinematics asymptotically.

Large-scale models reveal the two-component mechanics of striated muscle.

PubMed

Jarosch, Robert

2008-12-01

This paper provides a comprehensive explanation of striated muscle mechanics and contraction on the basis of filament rotations. Helical proteins, particularly the coiled-coils of tropomyosin, myosin and alpha-actinin, shorten their H-bonds cooperatively and produce torque and filament rotations when the Coulombic net-charge repulsion of their highly charged side-chains is diminished by interaction with ions. The classical "two-component model" of active muscle differentiated a "contractile component" which stretches the "series elastic component" during force production. The contractile components are the helically shaped thin filaments of muscle that shorten the sarcomeres by clockwise drilling into the myosin cross-bridges with torque decrease (= force-deficit). Muscle stretch means drawing out the thin filament helices off the cross-bridges under passive counterclockwise rotation with torque increase (= stretch activation). Since each thin filament is anchored by four elastic alpha-actinin Z-filaments (provided with force-regulating sites for Ca(2+) binding), the thin filament rotations change the torsional twist of the four Z-filaments as the "series elastic components". Large scale models simulate the changes of structure and force in the Z-band by the different Z-filament twisting stages A, B, C, D, E, F and G. Stage D corresponds to the isometric state. The basic phenomena of muscle physiology, i. e. latency relaxation, Fenn-effect, the force-velocity relation, the length-tension relation, unexplained energy, shortening heat, the Huxley-Simmons phases, etc. are explained and interpreted with the help of the model experiments.

Large-scale Models Reveal the Two-component Mechanics of Striated Muscle

PubMed Central

Jarosch, Robert

2008-01-01

This paper provides a comprehensive explanation of striated muscle mechanics and contraction on the basis of filament rotations. Helical proteins, particularly the coiled-coils of tropomyosin, myosin and α-actinin, shorten their H-bonds cooperatively and produce torque and filament rotations when the Coulombic net-charge repulsion of their highly charged side-chains is diminished by interaction with ions. The classical “two-component model” of active muscle differentiated a “contractile component” which stretches the “series elastic component” during force production. The contractile components are the helically shaped thin filaments of muscle that shorten the sarcomeres by clockwise drilling into the myosin cross-bridges with torque decrease (= force-deficit). Muscle stretch means drawing out the thin filament helices off the cross-bridges under passive counterclockwise rotation with torque increase (= stretch activation). Since each thin filament is anchored by four elastic α-actinin Z-filaments (provided with force-regulating sites for Ca2+ binding), the thin filament rotations change the torsional twist of the four Z-filaments as the “series elastic components”. Large scale models simulate the changes of structure and force in the Z-band by the different Z-filament twisting stages A, B, C, D, E, F and G. Stage D corresponds to the isometric state. The basic phenomena of muscle physiology, i. e. latency relaxation, Fenn-effect, the force-velocity relation, the length-tension relation, unexplained energy, shortening heat, the Huxley-Simmons phases, etc. are explained and interpreted with the help of the model experiments. PMID:19330099

A Parametric Study of Erupting Flux Rope Rotation: Modeling the 'Cartwheel CME' on 9 April 2008

NASA Technical Reports Server (NTRS)

Kliem, B.; Toeroek, T.; Thompson, W. T.

2012-01-01

The rotation of erupting filaments in the solar corona is addressed through a parametric simulation study of unstable, rotating flux ropes in bipolar force-free initial equilibrium. The Lorentz force due to the external shear-field component and the relaxation of tension in the twisted field are the major contributors to the rotation in this model, while reconnection with the ambient field is of minor importance, due to the field's simple structure. In the low-beta corona, the rotation is not guided by the changing orientation of the vertical field component's polarity inversion line with height. The model yields strong initial rotations which saturate in the corona and differ qualitatively from the profile of rotation vs. height obtained in a recent simulation of an eruption without preexisting flux rope. Both major mechanisms writhe the flux rope axis, converting part of the initial twist helicity, and produce rotation profiles which, to a large part, are very similar within a range of shear-twist combinations. A difference lies in the tendency of twist-driven rotation to saturate at lower heights than shear-driven rotation. For parameters characteristic of the source regions of erupting filaments and coronal mass ejections, the shear field is found to be the dominant origin of rotations in the corona and to be required if the rotation reaches angles of order 90 degrees and higher; it dominates even if the twist exceeds the threshold of the helical kink instability. The contributions by shear and twist to the total rotation can be disentangled in the analysis of observations if the rotation and rise profiles are simultaneously compared with model calculations. The resulting twist estimate allows one to judge whether the helical kink instability occurred. This is demonstrated for the erupting prominence in the "Cartwheel CME" on 9 April 2008, which has shown a rotation of approximately 115 deg. up to a height of 1.5 Solar R above the photosphere. Out of a range of initial equilibria which include strongly kink-unstable (Phi = 5 pi), weakly kink-unstable (Phi = 3.5 pi), and kink-stable (Phi = 2.5 pi) configurations, only the evolution of the weakly kink-unstable flux rope matches the observations in their entirety.

Pressure dependence of the magnetic ground states in MnP

DOE PAGES

Matsuda, Masaaki; Ye, Feng; Dissanayake, Sachith E.; ...

2016-03-17

MnP, a superconductor under pressure, exhibits a ferromagnetic order below TC~290 K followed by a helical order with the spins lying in the ab plane and the helical rotation propagating along the c axis below Ts~50 K at ambient pressure. We performed single-crystal neutron diffraction experiments to determine the magnetic ground states under pressure. Both TC and Ts are gradually suppressed with increasing pressure and the helical order disappears at ~1.2 GPa. At intermediate pressures of 1.8 and 2.0 GPa, the ferromagnetic order first develops and changes to a conical or two-phase (ferromagnetic and helical) structure with the propagation alongmore » the b axis below a characteristic temperature. At 3.8 GPa, a helical magnetic order appears below 208 K, which hosts the spins in the ac plane and the propagation along the b axis. The period of this b axis modulation is shorter than that at 1.8 GPa. Here, our results indicate that the magnetic phase in the vicinity of the superconducting phase may have a helical magnetic correlation along the b axis.« less

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.

Conservation law of angular momentum in helicity-dependent Raman and Rayleigh scattering

NASA Astrophysics Data System (ADS)

Tatsumi, Yuki; Kaneko, Tomoaki; Saito, Riichiro

2018-05-01

In first-order Raman scattering, helicity of circularly polarized incident light is either conserved or changed depending on the Raman modes. When the helicity of incident light changes in the scattered light, the angular momentum of a photon is transferred to the material. Here, we present the conservation law of pseudoangular momentum in the helicity-dependent Raman scattering for a N -fold (N =1 -4 ,6 ) rotational symmetry of a crystal. Furthermore, the conservation law of electron-phonon interaction is discussed by considering the vibration direction of a phonon that has the same or lower symmetry than the symmetry of the crystal, which is essential to allow the helicity change in Raman scattering in a highly symmetric material, such as graphene. We also discuss the conservation law of pseudoangular momentum in Rayleigh scattering and show that the helicity change is allowed only in the crystal with one- or twofold rotational symmetry.

Magnetohydrodynamic Models of Molecular Tornadoes

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

Au, Kelvin; Fiege, Jason D., E-mail: fiege@physics.umanitoba.ca

Recent observations near the Galactic Center (GC) have found several molecular filaments displaying striking helically wound morphology that are collectively known as molecular tornadoes. We investigate the equilibrium structure of these molecular tornadoes by formulating a magnetohydrodynamic model of a rotating, helically magnetized filament. A special analytical solution is derived where centrifugal forces balance exactly with toroidal magnetic stress. From the physics of torsional Alfvén waves we derive a constraint that links the toroidal flux-to-mass ratio and the pitch angle of the helical field to the rotation laws, which we find to be an important component in describing the molecularmore » tornado structure. The models are compared to the Ostriker solution for isothermal, nonmagnetic, nonrotating filaments. We find that neither the analytic model nor the Alfvén wave model suffer from the unphysical density inversions noted by other authors. A Monte Carlo exploration of our parameter space is constrained by observational measurements of the Pigtail Molecular Cloud, the Double Helix Nebula, and the GC Molecular Tornado. Observable properties such as the velocity dispersion, filament radius, linear mass, and surface pressure can be used to derive three dimensionless constraints for our dimensionless models of these three objects. A virial analysis of these constrained models is studied for these three molecular tornadoes. We find that self-gravity is relatively unimportant, whereas magnetic fields and external pressure play a dominant role in the confinement and equilibrium radial structure of these objects.« less

A macroscopic scale model of bacterial flagellar bundling

NASA Astrophysics Data System (ADS)

Kim, Munju; Bird, James C.; van Parys, Annemarie J.; Breuer, Kenneth S.; Powers, Thomas R.

2003-12-01

Escherichia coli and other bacteria use rotating helical filaments to swim. Each cell typically has about four filaments, which bundle or disperse depending on the sense of motor rotation. To study the bundling process, we built a macroscopic scale model consisting of stepper motor-driven polymer helices in a tank filled with a high-viscosity silicone oil. The Reynolds number, the ratio of viscous to elastic stresses, and the helix geometry of our experimental model approximately match the corresponding quantities of the full-scale E. coli cells. We analyze digital video images of the rotating helices to show that the initial rate of bundling is proportional to the motor frequency and is independent of the characteristic relaxation time of the filament. We also determine which combinations of helix handedness and sense of motor rotation lead to bundling.

Point of optimal kinematic error: improvement of the instantaneous helical pivot method for locating centers of rotation.

PubMed

De Rosario, Helios; Page, Alvaro; Mata, Vicente

2014-05-07

This paper proposes a variation of the instantaneous helical pivot technique for locating centers of rotation. The point of optimal kinematic error (POKE), which minimizes the velocity at the center of rotation, may be obtained by just adding a weighting factor equal to the square of angular velocity in Woltring׳s equation of the pivot of instantaneous helical axes (PIHA). Calculations are simplified with respect to the original method, since it is not necessary to make explicit calculations of the helical axis, and the effect of accidental errors is reduced. The improved performance of this method was validated by simulations based on a functional calibration task for the gleno-humeral joint center. Noisy data caused a systematic dislocation of the calculated center of rotation towards the center of the arm marker cluster. This error in PIHA could even exceed the effect of soft tissue artifacts associated to small and medium deformations, but it was successfully reduced by the POKE estimation. Copyright © 2014 Elsevier Ltd. All rights reserved.

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.

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.

π Spin Berry Phase in a Quantum-Spin-Hall-Insulator-Based Interferometer: Evidence for the Helical Spin Texture of the Edge States

NASA Astrophysics Data System (ADS)

Chen, Wei; Deng, Wei-Yin; Hou, Jing-Min; Shi, D. N.; Sheng, L.; Xing, D. Y.

2016-08-01

The quantum spin Hall insulator is characterized by helical edge states, with the spin polarization of the electron being locked to its direction of motion. Although the edge-state conduction has been observed, unambiguous evidence of the helical spin texture is still lacking. Here, we investigate the coherent edge-state transport in an interference loop pinched by two point contacts. Because of the helical character, the forward interedge scattering enforces a π spin rotation. Two successive processes can only produce a nontrivial 2 π or trivial 0 spin rotation, which can be controlled by the Rashba spin-orbit coupling. The nontrivial spin rotation results in a geometric π Berry phase, which can be detected by a π phase shift of the conductance oscillation relative to the trivial case. Our results provide smoking gun evidence for the helical spin texture of the edge states. Moreover, it also provides the opportunity to all electrically explore the trajectory-dependent spin Berry phase in condensed matter.

Second Harmonic Generation Optical Rotation Solely Attributable to Chirality in Plasmonic Metasurfaces.

PubMed

Collins, Joel T; Hooper, David C; Mark, Andrew G; Kuppe, Christian; Valev, Ventsislav Kolev

2018-05-31

Chiral plasmonic nanostructures, those lacking mirror symmetry, can be designed to manipulate the polarization of incident light resulting in chiroptical (chiral optical) effects such as circular dichroism (CD) and optical rotation (OR). Due to high symmetry sensitivity, corresponding effects in second harmonic generation (SHG-CD and SHG-OR) are typically much stronger in comparison. These nonlinear effects have long been used for chiral molecular analysis and characterization, however both linear and nonlinear optical rotation can occur even in achiral structures, if the structure is birefringent due to anisotropy. Crucially, chiroptical effects resulting from anisotropy typically exhibit a strong dependence on structural orientation. Here we report large second-harmonic generation optical rotation of ±45°, due to intrinsic chirality in a highly anisotropic helical metamaterial. The SHG intensity is found to strongly relate to the structural anisotropy, however the angle of SHG-OR is invariant under sample rotation. We show that by tuning the geometry of anisotropic nanostructures, the interaction between anisotropy, chirality, and experiment geometry can allow even greater control over the chiroptical properties of plasmonic metamaterials.

Three-dimensional printing of freeform helical microstructures: a review.

PubMed

Farahani, R D; Chizari, K; Therriault, D

2014-09-21

Three-dimensional (3D) printing is a fabrication method that enables creation of structures from digital models. Among the different structures fabricated by 3D printing methods, helical microstructures attracted the attention of the researchers due to their potential in different fields such as MEMS, lab-on-a-chip systems, microelectronics and telecommunications. Here we review different types of 3D printing methods capable of fabricating 3D freeform helical microstructures. The techniques including two more common microfabrication methods (i.e., focused ion beam chemical vapour deposition and microstereolithography) and also five methods based on computer-controlled robotic direct deposition of ink filament (i.e., fused deposition modeling, meniscus-confined electrodeposition, conformal printing on a rotating mandrel, UV-assisted and solvent-cast 3D printings) and their advantages and disadvantages regarding their utilization for the fabrication of helical microstructures are discussed. Focused ion beam chemical vapour deposition and microstereolithography techniques enable the fabrication of very precise shapes with a resolution down to ∼100 nm. However, these techniques may have material constraints (e.g., low viscosity) and/or may need special process conditions (e.g., vacuum chamber) and expensive equipment. The five other techniques based on robotic extrusion of materials through a nozzle are relatively cost-effective, however show lower resolution and less precise features. The popular fused deposition modeling method offers a wide variety of printable materials but the helical microstructures manufactured featured a less precise geometry compared to the other printing methods discussed in this review. The UV-assisted and the solvent-cast 3D printing methods both demonstrated high performance for the printing of 3D freeform structures such as the helix shape. However, the compatible materials used in these methods were limited to UV-curable polymers and polylactic acid (PLA), respectively. Meniscus-confined electrodeposition is a flexible, low cost technique that is capable of fabricating 3D structures both in nano- and microscales including freeform helical microstructures (down to few microns) under room conditions using metals. However, the metals suitable for this technique are limited to those that can be electrochemically deposited with the use of an electrolyte solution. The highest precision on the helix geometry was achieved using the conformal printing on a rotating mandrel. This method offers the lowest shape deformation after printing but requires more tools (e.g., mandrel, motor) and the printed structure must be separated from the mandrel. Helical microstructures made of multifunctional materials (e.g., carbon nanotube nanocomposites, metallic coated polymer template) were used in different technological applications such as strain/load sensors, cell separators and micro-antennas. These innovative 3D microsystems exploiting the unique helix shape demonstrated their potential for better performance and more compact microsystems.

Dual-body magnetic helical robot for drilling and cargo delivery in human blood vessels

NASA Astrophysics Data System (ADS)

Lee, Wonseo; Jeon, Seungmun; Nam, Jaekwang; Jang, Gunhee

2015-05-01

We propose a novel dual-body magnetic helical robot (DMHR) manipulated by a magnetic navigation system. The proposed DMHR can generate helical motions to navigate in human blood vessels and to drill blood clots by an external rotating magnetic field. It can also generate release motions which are relative rotational motions between dual-bodies to release the carrying cargos to a target region by controlling the magnitude of an external magnetic field. Constraint equations were derived to selectively manipulate helical and release motions by controlling external magnetic fields. The DMHR was prototyped and various experiments were conducted to demonstrate its motions and verify its manipulation methods.

General rotating quantum vortex filaments in the low-temperature Svistunov model of the local induction approximation

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

Van Gorder, Robert A., E-mail: rav@knights.ucf.edu

2014-06-15

In his study of superfluid turbulence in the low-temperature limit, Svistunov [“Superfluid turbulence in the low-temperature limit,” Phys. Rev. B 52, 3647 (1995)] derived a Hamiltonian equation for the self-induced motion of a vortex filament. Under the local induction approximation (LIA), the Svistunov formulation is equivalent to a nonlinear dispersive partial differential equation. In this paper, we consider a family of rotating vortex filament solutions for the LIA reduction of the Svistunov formulation, which we refer to as the 2D LIA (since it permits a potential formulation in terms of two of the three Cartesian coordinates). This class of solutionsmore » holds the well-known Hasimoto-type planar vortex filament [H. Hasimoto, “Motion of a vortex filament and its relation to elastica,” J. Phys. Soc. Jpn. 31, 293 (1971)] as one reduction and helical solutions as another. More generally, we obtain solutions which are periodic in the space variable. A systematic analytical study of the behavior of such solutions is carried out. In the case where vortex filaments have small deviations from the axis of rotation, closed analytical forms of the filament solutions are given. A variety of numerical simulations are provided to demonstrate the wide range of rotating filament behaviors possible. Doing so, we are able to determine a number of vortex filament structures not previously studied. We find that the solution structure progresses from planar to helical, and then to more intricate and complex filament structures, possibly indicating the onset of superfluid turbulence.« less

Magnetic stripes and skyrmions with helicity reversals.

PubMed

Yu, Xiuzhen; Mostovoy, Maxim; Tokunaga, Yusuke; Zhang, Weizhu; Kimoto, Koji; Matsui, Yoshio; Kaneko, Yoshio; Nagaosa, Naoto; Tokura, Yoshinori

2012-06-05

It was recently realized that topological spin textures do not merely have mathematical beauty but can also give rise to unique functionalities of magnetic materials. An example is the skyrmion--a nano-sized bundle of noncoplanar spins--that by virtue of its nontrivial topology acts as a flux of magnetic field on spin-polarized electrons. Lorentz transmission electron microscopy recently emerged as a powerful tool for direct visualization of skyrmions in noncentrosymmetric helimagnets. Topologically, skyrmions are equivalent to magnetic bubbles (cylindrical domains) in ferromagnetic thin films, which were extensively explored in the 1970s for data storage applications. In this study we use Lorentz microscopy to image magnetic domain patterns in the prototypical magnetic oxide-M-type hexaferrite with a hint of scandium. Surprisingly, we find that the magnetic bubbles and stripes in the hexaferrite have a much more complex structure than the skyrmions and spirals in helimagnets, which we associate with the new degree of freedom--helicity (or vector spin chirality) describing the direction of spin rotation across the domain walls. We observe numerous random reversals of helicity in the stripe domain state. Random helicity of cylindrical domain walls coexists with the positional order of magnetic bubbles in a triangular lattice. Most unexpectedly, we observe regular helicity reversals inside skyrmions with an unusual multiple-ring structure.

The Structural Basis for Matrix Metalloproteinase 1 Catalyzed Collagenolysis

PubMed Central

Bertini, Ivano; Fragai, Marco; Luchinat, Claudio; Melikian, Maxime; Toccafondi, Mirco; Lauer, Janelle L.; Fields, Gregg B.

2012-01-01

The proteolysis of collagen triple-helical structure (collagenolysis) is a poorly understood yet critical physiological process. Presently, matrix metalloproteinase 1 (MMP-1) and collagen triple-helical peptide models have been utilized to characterize the events and calculate the energetics of collagenolysis via NMR spectroscopic analysis of 12 enzyme-substrate complexes. The triple-helix is bound initially by the MMP-1 hemopexin-like (HPX) domain via a four amino acid stretch (analogous to type I collagen residues 782–785). The triple-helix is then presented to the MMP-1 catalytic (CAT) domain in a distinct orientation. The HPX and CAT domains are rotated with respect to one another compared with the X-ray “closed” conformation of MMP-1. Back-rotation of the CAT and HPX domains to the X-ray closed conformation releases one chain out of the triple-helix, and this chain is properly positioned in the CAT domain active site for subsequent hydrolysis. The aforementioned steps provide a detailed, experimentally-derived, and energetically favorable collagenolytic mechanism, as well as significant insight into the roles of distinct domains in extracellular protease function. PMID:22239621

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.

Axial rotation of sliding actin filaments revealed by single-fluorophore imaging

PubMed Central

Sase, Ichiro; Miyata, Hidetake; Ishiwata, Shin’ichi; Kinosita, Kazuhiko

1997-01-01

In the actomyosin motor, myosin slides along an actin filament that has a helical structure with a pitch of ≈72 nm. Whether myosin precisely follows this helical track is an unanswered question bearing directly on the motor mechanism. Here, axial rotation of actin filaments sliding over myosin molecules fixed on a glass surface was visualized through fluorescence polarization imaging of individual tetramethylrhodamine fluorophores sparsely bound to the filaments. The filaments underwent one revolution per sliding distance of ≈1 μm, which is much greater than the 72 nm pitch. Thus, myosin does not “walk” on the helical array of actin protomers; rather it “runs,” skipping many protomers. Possible mechanisms involving sequential interaction of myosin with successive actin protomers are ruled out at least for the preparation described here in which the actin filaments ran rather slowly compared with other in vitro systems. The result also indicates that each “kick” of myosin is primarily along the axis of the actin filament. The successful, real-time observation of the changes in the orientation of a single fluorophore opens the possibility of detecting a conformational change(s) of a single protein molecule at the moment it functions. PMID:9159126

Axial rotation of sliding actin filaments revealed by single-fluorophore imaging.

PubMed

Sase, I; Miyata, H; Ishiwata, S; Kinosita, K

1997-05-27

In the actomyosin motor, myosin slides along an actin filament that has a helical structure with a pitch of approximately 72 nm. Whether myosin precisely follows this helical track is an unanswered question bearing directly on the motor mechanism. Here, axial rotation of actin filaments sliding over myosin molecules fixed on a glass surface was visualized through fluorescence polarization imaging of individual tetramethylrhodamine fluorophores sparsely bound to the filaments. The filaments underwent one revolution per sliding distance of approximately 1 microm, which is much greater than the 72 nm pitch. Thus, myosin does not "walk" on the helical array of actin protomers; rather it "runs," skipping many protomers. Possible mechanisms involving sequential interaction of myosin with successive actin protomers are ruled out at least for the preparation described here in which the actin filaments ran rather slowly compared with other in vitro systems. The result also indicates that each "kick" of myosin is primarily along the axis of the actin filament. The successful, real-time observation of the changes in the orientation of a single fluorophore opens the possibility of detecting a conformational change(s) of a single protein molecule at the moment it functions.

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

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.

Evolution of space open electric arc burning in the external axial magnetic field

NASA Astrophysics Data System (ADS)

Urusova, I. R.; Urusova, T. E.

2018-06-01

The calculation was made for open DC electric arc burning in an external uniform axial magnetic field. It was performed within the framework of a nonstationary three-dimensional mathematical model in approximation of partial local thermodynamic equilibrium of plasma. A "schematic" analog of electron temperature fluctuations was proposed for numerical realization of the open electric arc column of a helical shape. According to calculations, it was established that the column of the open electric arc takes a helical space shape. Plasma rotates around a longitudinal axis of the arc, at that the directions of plasma rotation near the cathode and the anode are opposite. In the arc cross-sections, the velocity of plasma rotation is unequal and the deviation value of the same part of the arc from the central axis varies in time. A helical shape of the open arc is not stable and varies in time. Apparently, the open arc cannot remain stable and invariable in the time helical shape in the external axial magnetic field.

Helical plasma thruster

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

Beklemishev, A. D., E-mail: bekl@bk.ru

2015-10-15

A new scheme of plasma thruster is proposed. It is based on axial acceleration of rotating magnetized plasmas in magnetic field with helical corrugation. The idea is that the propellant ionization zone can be placed into the local magnetic well, so that initially the ions are trapped. The E × B rotation is provided by an applied radial electric field that makes the setup similar to a magnetron discharge. Then, from the rotating plasma viewpoint, the magnetic wells of the helically corrugated field look like axially moving mirror traps. Specific shaping of the corrugation can allow continuous acceleration of trapped plasma ionsmore » along the magnetic field by diamagnetic forces. The accelerated propellant is expelled through the expanding field of magnetic nozzle. By features of the acceleration principle, the helical plasma thruster may operate at high energy densities but requires a rather high axial magnetic field, which places it in the same class as the VASIMR{sup ®} rocket engine.« less

Magnetic Helicities and Dynamo Action in Magneto-rotational Turbulence

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

Bodo, G.; Rossi, P.; Cattaneo, F.

We examine the relationship between magnetic flux generation, taken as an indicator of large-scale dynamo action, and magnetic helicity, computed as an integral over the dynamo volume, in a simple dynamo. We consider dynamo action driven by magneto-rotational turbulence (MRT) within the shearing-box approximation. We consider magnetically open boundary conditions that allow a flux of helicity in or out of the computational domain. We circumvent the problem of the lack of gauge invariance in open domains by choosing a particular gauge—the winding gauge—that provides a natural interpretation in terms of the average winding number of pairwise field lines. We usemore » this gauge precisely to define and measure the helicity and the helicity flux for several realizations of dynamo action. We find in these cases that the system as a whole does not break reflectional symmetry and that the total helicity remains small even in cases when substantial magnetic flux is generated. We find no particular connection between the generation of magnetic flux and the helicity or the helicity flux through the boundaries. We suggest that this result may be due to the essentially nonlinear nature of the dynamo processes in MRT.« less

Helical and rod-shaped bacteria swim in helical trajectories with little additional propulsion from helical shape

NASA Astrophysics Data System (ADS)

Fu, Henry; Constantino, Maira; Jabbarzadeh, Mehdi; Bansil, Rama

2017-11-01

It has frequently been hypothesized that the helical body shapes of flagellated bacteria may yield some advantage in swimming ability. The helical-shaped pathogen Helicobacter pylori allows us to test these claims. Using fast time-resolution and high-magnification phase-contrast microscopy to simultaneously image and track individual bacteria we determine cell body shape as well as rotational and translational speeds. Using the method of regularized Stokeslets, we directly compare observed speeds and trajectories to numerical calculations to validate the numerical model. Although experimental observations are limited to select cases, the model allows quantification of the effects of body helicity, length, and diameter. We find that due to relatively slow body rotation rates, the helical shape makes at most a 15% contribution to propulsive thrust. The effect of body shape on swimming speeds is instead dominated by variations in translational drag required to move the cell body. Because helical cells are one of the strongest candidates for propulsion arising from the cell body, our results imply that quite generally, swimming speeds of flagellated bacteria can only be increased a little by by body propulsion.

Effect of Relative Marker Movement on the Calculation of the Foot Torsion Axis Using a Combined Cardan Angle and Helical Axis Approach

PubMed Central

Graf, Eveline S.; Wright, Ian C.; Stefanyshyn, Darren J.

2012-01-01

The two main movements occurring between the forefoot and rearfoot segment of a human foot are flexion at the metatarsophalangeal joints and torsion in the midfoot. The location of the torsion axis within the foot is currently unknown. The purpose of this study was to develop a method based on Cardan angles and the finite helical axis approach to calculate the torsion axis without the effect of flexion. As the finite helical axis method is susceptible to error due to noise with small helical rotations, a minimal amount of rotation was defined in order to accurately determine the torsion axis location. Using simulation, the location of the axis based on data containing noise was compared to the axis location of data without noise with a one-sample t-test and Fisher's combined probability score. When using only data with helical rotation of seven degrees or more, the location of the torsion axis based on the data with noise was within 0.2 mm of the reference location. Therefore, the proposed method allowed an accurate calculation of the foot torsion axis location. PMID:22666303

Instabilities of a rotating helical rod

NASA Astrophysics Data System (ADS)

Park, Yunyoung; Ko, William; Kim, Yongsam; Lim, Sookkyung

2016-11-01

Bacteria such as Escherichia coli and Vibrio alginolyticus have helical flagellar filament. By rotating a motor, which is located at the bottom end of the flagellar filament embedded in the cell body, CCW or CW, they swim forward or backward. We model a left-handed helix by the Kirchhoff rod theory and use regularized Stokes formulation to study an interaction between the surrounding fluid and the flagellar filament. We perform numerical studies focusing on relations between physical parameters and critical angular frequency of the motor, which separates overwhiring from twirling. We are also interested in the buckling instability of the hook, which is very flexible elastic rod. By measuring buckling angle, which is an angle between rotational axis and helical axis, we observe the effects of physical parameters on buckling of the hook.

Stabilizing interactions between aromatic and basic side chains in alpha-helical peptides and proteins. Tyrosine effects on helix circular dichroism.

PubMed

Andrew, Charles D; Bhattacharjee, Samita; Kokkoni, Nicoleta; Hirst, Jonathan D; Jones, Gareth R; Doig, Andrew J

2002-10-30

Here we investigate the structures and energetics of interactions between aromatic (Phe or Tyr) and basic (Lys or Arg) amino acids in alpha-helices. Side chain interaction energies are measured using helical peptides, by quantifying their helicities with circular dichroism at 222 nm and interpreting the results with Lifson-Roig-based helix/coil theory. A difficulty in working with Tyr is that the aromatic ring perturbs the CD spectrum, giving an incorrect helicity. We calculated the effect of Tyr on the CD at 222 nm by deriving the intensities of the bands directly from the electronic and magnetic transition dipole moments through the rotational strengths corresponding to each excited state of the polypeptide. This gives an improved value of the helix preference of Tyr (from 0.48 to 0.35) and a correction to the helicity for the peptides containing Tyr. We find that Phe-Lys, Lys-Phe, Phe-Arg, Arg-Phe, and Tyr-Lys are all stabilizing by -0.10 to -0.18 kcal.mol-1 when placed i, i + 4 on the surface of a helix in aqueous solution, despite the great difference in polarity between these residues. Interactions between these side chains have previously been attributed to cation-pi bonds. A survey of protein structures shows that they are in fact predominantly hydrophobic interactions between the CH2 groups of Lys or Arg and the aromatic rings.

Helical axis stellarator with noninterlocking planar coils

DOEpatents

Reiman, Allan; Boozer, Allen H.

1987-01-01

A helical axis stellarator using only noninterlocking planar, non-circular coils, generates magnetic fields having a magnetic well and large rotational transform with resultant large equilibrium beta.

Counter-Rotatable Fan Gas Turbine Engine with Axial Flow Positive Displacement Worm Gas Generator

NASA Technical Reports Server (NTRS)

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

2014-01-01

A counter-rotatable fan turbine engine includes a counter-rotatable fan section, a worm gas generator, and a low pressure turbine to power the counter-rotatable fan section. The low pressure turbine maybe counter-rotatable or have a single direction of rotation in which case it powers the counter-rotatable fan section through a gearbox. The gas generator has inner and outer bodies having offset inner and outer axes extending through first, second, and third sections of a core assembly. 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 and extending radially outwardly and inwardly respectively. The helical blades have first, second, and third twist slopes in the first, second, and third sections respectively. A combustor section extends through at least a portion of the second section.

Real-Time Imaging of Fluorescent Flagellar Filaments of Rhizobium lupini H13-3: Flagellar Rotation and pH-Induced Polymorphic Transitions

PubMed Central

Scharf, Birgit

2002-01-01

The soil bacterium Rhizobium lupini H13-3 has complex right-handed flagellar filaments with unusual ridged, grooved surfaces. Clockwise (CW) rotation propels the cells forward, and course changes (tumbling) result from changes in filament speed instead of the more common change in direction of rotation. In view of these novelties, fluorescence labeling was used to analyze the behavior of single flagellar filaments during swimming and tumbling, leading to a model for directional changes in R. lupini. Also, flagellar filaments were investigated for helical conformational changes, which have not been previously shown for complex filaments. During full-speed CW rotation, the flagellar filaments form a propulsive bundle that pushes the cell on a straight path. Tumbling is caused by asynchronous deceleration and stops of individual filaments, resulting in dissociation of the propulsive bundle. R. lupini tumbles were not accompanied by helical conformational changes as are tumbles in other organisms including enteric bacteria. However, when pH was experimentally changed, four different polymorphic forms were observed. At a physiological pH of 7, normal flagellar helices were characterized by a pitch angle of 30°, a pitch of 1.36 μm, and a helical diameter of 0.50 μm. As pH increased from 9 to 11, the helices transformed from normal to semicoiled to straight. As pH decreased from 5 to 3, the helices transformed from normal to curly to straight. Transient conformational changes were also noted at high viscosity, suggesting that the R. lupini flagellar filament may adapt to high loads in viscous environments (soil) by assuming hydrodynamically favorable conformations. PMID:12374832

Temporal resolution measurement of 128-slice dual source and 320-row area detector computed tomography scanners in helical acquisition mode using the impulse method.

PubMed

Hara, Takanori; Urikura, Atsushi; Ichikawa, Katsuhiro; Hoshino, Takashi; Nishimaru, Eiji; Niwa, Shinji

2016-04-01

To analyse the temporal resolution (TR) of modern computed tomography (CT) scanners using the impulse method, and assess the actual maximum TR at respective helical acquisition modes. To assess the actual TR of helical acquisition modes of a 128-slice dual source CT (DSCT) scanner and a 320-row area detector CT (ADCT) scanner, we assessed the TRs of various acquisition combinations of a pitch factor (P) and gantry rotation time (R). The TR of the helical acquisition modes for the 128-slice DSCT scanner continuously improved with a shorter gantry rotation time and greater pitch factor. However, for the 320-row ADCT scanner, the TR with a pitch factor of <1.0 was almost equal to the gantry rotation time, whereas with pitch factor of >1.0, it was approximately one half of the gantry rotation time. The maximum TR values of single- and dual-source helical acquisition modes for the 128-slice DSCT scanner were 0.138 (R/P=0.285/1.5) and 0.074s (R/P=0.285/3.2), and the maximum TR values of the 64×0.5- and 160×0.5-mm detector configurations of the helical acquisition modes for the 320-row ADCT scanner were 0.120 (R/P=0.275/1.375) and 0.195s (R/P=0.3/0.6), respectively. Because the TR of a CT scanner is not accurately depicted in the specifications of the individual scanner, appropriate acquisition conditions should be determined based on the actual TR measurement. Copyright © 2016 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

"Corkscrew" vs. "tank-treading" propulsion of spirochetes.

NASA Astrophysics Data System (ADS)

Leshansky, Alexander; Kenneth, Oded

2010-11-01

We consider the potential mechanism of spirochete propulsion driven by twirling of the outer cell surface coupled to counter-rotation of the helical body. We construct a proper slender body theory and use particle-based numerical approach allowing for modeling of locomotion in heterogeneous viscous environment. Depending on the helical pitch angle, two distinct propulsion gaits are identified: corkscrew-like locomotion, similar to propulsion powered by rotating helical flagellum, and surface tank-treading mode relying on hydrodynamic self-interaction of curved helical coils. The latter mechanism is closely related to the considered earlier propulsion of Purcell's toroidal swimmer (Kenneth and Leshansky, Phys. Fluids 20, 063104, 2008). Significant augmentation of corkscrew propulsion gait in heterogeneous viscous medium anticipated from the numerical model is in accord with experimental observations of enhanced spirochete propulsion in polymer gels.

Faraday signature of magnetic helicity from reduced depolarization

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

Brandenburg, Axel; Stepanov, Rodion

2014-05-10

Using one-dimensional models, we show that a helical magnetic field with an appropriate sign of helicity can compensate the Faraday depolarization resulting from the superposition of Faraday-rotated polarization planes from a spatially extended source. For radio emission from a helical magnetic field, the polarization as a function of the square of the wavelength becomes asymmetric with respect to zero. Mathematically speaking, the resulting emission occurs then either at observable or at unobservable (imaginary) wavelengths. We demonstrate that rotation measure (RM) synthesis allows for the reconstruction of the underlying Faraday dispersion function in the former case, but not in the latter.more » The presence of positive magnetic helicity can thus be detected by observing positive RM in highly polarized regions in the sky and negative RM in weakly polarized regions. Conversely, negative magnetic helicity can be detected by observing negative RM in highly polarized regions and positive RM in weakly polarized regions. The simultaneous presence of two magnetic constituents with opposite signs of helicity is shown to possess signatures that can be quantified through polarization peaks at specific wavelengths and the gradient of the phase of the Faraday dispersion function. Similar polarization peaks can tentatively also be identified for the bi-helical magnetic fields that are generated self-consistently by a dynamo from helically forced turbulence, even though the magnetic energy spectrum is then continuous. Finally, we discuss the possibility of detecting magnetic fields with helical and non-helical properties in external galaxies using the Square Kilometre Array.« less

Heat Transfer Measurements of Internally Finned Rotating Heat Pipes.

DTIC Science & Technology

1983-12-01

42 C. RESULTS OF STRAIGHT 22 FIN CONDENSER o . o . 51 D. RESULTS OF HELICAL 14 AND 16 FIN CONDENSER o 51 E. RESULTS OF HELICAL 36 FIN...88 C.6 RESULTS OF STRAIGHT 22 FIN CONDENSER AT 2800 RPM . . . . . . . . . . . . . . . . . . . . 89 C.7 RESULTS OF HELICAL 16 FIN CONDENSER ...AT 700 RPM . 90 C.8 RESULTS OF HELICAL 16 PIN CONDENSER AT 1600 RPM . 91 C.9 RESULTS OF HELICAL 16 PIN CONDENSER AT 2800 RPM . 92 C. 10 RESULTS OF

Single Molecule Stepping and Structural Dynamics of Myosin X

PubMed Central

Sun, Yujie; Sato, Osamu; Ruhnow, Felix; Arsenault, Mark E.; Ikebe, Mitsuo; Goldman, Yale E.

2010-01-01

Myosin X is an unconventional myosin with puzzling motility properties. We studied the motility of dimerized myosin X using single molecule fluorescence techniques – polTIRF, FIONA, and Parallax to measure rotation angles and 3-dimensional position of the molecule during its walk. It was found that Myosin X steps processively in a hand-over-hand manner following a left-handed helical path along both single actin filaments and bundles. Its step size and velocity are smaller on actin bundles than individual filaments, suggesting myosin X often steps onto neighboring filaments in a bundle. The data suggest that a previously postulated single α-helical domain mechanically extends the 3-IQ motif lever arm and either the neck-tail hinge or the tail is flexible. These structural features, in conjunction with the membrane and microtubule binding domains, enable myosin X to perform multiple functions on varied actin structures in cells. PMID:20364131

Programmable Bidirectional Folding of Metallic Thin Films for 3D Chiral Optical Antennas.

PubMed

Mao, Yifei; Zheng, Yun; Li, Can; Guo, Lin; Pan, Yini; Zhu, Rui; Xu, Jun; Zhang, Weihua; Wu, Wengang

2017-05-01

3D structures with characteristic lengths ranging from nanometer to micrometer scale often exhibit extraordinary optical properties, and have been becoming an extensively explored field for building new generation nanophotonic devices. Albeit a few methods have been developed for fabricating 3D optical structures, constructing 3D structures with nanometer accuracy, diversified materials, and perfect morphology is an extremely challenging task. This study presents a general 3D nanofabrication technique, the focused ion beam stress induced deformation process, which allows a programmable and accurate bidirectional folding (-70°-+90°) of various metal and dielectric thin films. Using this method, 3D helical optical antennas with different handedness, improved surface smoothness, and tunable geometries are fabricated, and the strong optical rotation effects of single helical antennas are demonstrated. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Nonlinear calculation of the m=1 internal kink instability in current carrying stellarators

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

Wakatani, M.

1978-02-01

Nonlinear properties of the m=1 internal kink mode are shown in a low beta current carrying stellarator. The effects of the external helical magnetic fields are considered through a rotational transform and the magnetic surface is assumed to be circular. Magnetic surfaces inside the iota sub eta + iota sub sigma = 1 surface shift and deform non-circularly, while magnetic surfaces outside the iota sub eta + iota sub sigma = 1 are not disturbed, where iota sub eta is a rotational transform due to helical magnetic fields and iota sub sigma is due to a plasma current. Many highermore » harmonics are excited after the fundamental mode saturates. When the external helical magnetic fields are lowered, the m=1 tearing mode similar to that in a low beta Tokamak grows and magnetic islands appear near the iota sub eta + iota sub sigma = 1 surface. For adequate helical magnetic fields, the current carrying stellarator becomes stable against both the m=1 internal kink mode and the m=1 internal kink mode and the m=1 tearing mode, without lowering the rotational transform.« less

Geometrical principles of homomeric β-barrels and β-helices: Application to modeling amyloid protofilaments.

PubMed

Hayward, Steven; Milner-White, E James

2017-10-01

Examples of homomeric β-helices and β-barrels have recently emerged. Here we generalize the theory for the shear number in β-barrels to encompass β-helices and homomeric structures. We introduce the concept of the "β-strip," the set of parallel or antiparallel neighboring strands, from which the whole helix can be generated giving it n-fold rotational symmetry. In this context, the shear number is interpreted as the sum around the helix of the fixed register shift between neighboring identical β-strips. Using this approach, we have derived relationships between helical width, pitch, angle between strand direction and helical axis, mass per length, register shift, and number of strands. The validity and unifying power of the method is demonstrated with known structures including α-hemolysin, T4 phage spike, cylindrin, and the HET-s(218-289) prion. From reported dimensions measured by X-ray fiber diffraction on amyloid fibrils, the relationships can be used to predict the register shift and the number of strands within amyloid protofilaments. This was used to construct models of transthyretin and Alzheimer β(40) amyloid protofilaments that comprise a single strip of in-register β-strands folded into a "β-strip helix." Results suggest both stabilization of an individual β-strip helix and growth by addition of further β-strip helices can involve the same pair of sequence segments associating with β-sheet hydrogen bonding at the same register shift. This process would be aided by a repeat sequence. Hence, understanding how the register shift (as the distance between repeat sequences) relates to helical dimensions will be useful for nanotube design. © 2017 Wiley Periodicals, Inc.

Dispersion relation for electromagnetic propagation in stochastic dielectric and magnetic helical photonic crystals

NASA Astrophysics Data System (ADS)

Avendaño, Carlos G.; Reyes, Arturo

2017-03-01

We theoretically study the dispersion relation for axially propagating electromagnetic waves throughout a one-dimensional helical structure whose pitch and dielectric and magnetic properties are spatial random functions with specific statistical characteristics. In the system of coordinates rotating with the helix, by using a matrix formalism, we write the set of differential equations that governs the expected value of the electromagnetic field amplitudes and we obtain the corresponding dispersion relation. We show that the dispersion relation depends strongly on the noise intensity introduced in the system and the autocorrelation length. When the autocorrelation length increases at fixed fluctuation and when the fluctuation augments at fixed autocorrelation length, the band gap widens and the attenuation coefficient of electromagnetic waves propagating in the random medium gets larger. By virtue of the degeneracy in the imaginary part of the eigenvalues associated with the propagating modes, the random medium acts as a filter for circularly polarized electromagnetic waves, in which only the propagating backward circularly polarized wave can propagate with no attenuation. Our results are valid for any kind of dielectric and magnetic structures which possess a helical-like symmetry such as cholesteric and chiral smectic-C liquid crystals, structurally chiral materials, and stressed cholesteric elastomers.

PI-line-based image reconstruction in helical cone-beam computed tomography with a variable pitch.

PubMed

Zou, Yu; Pan, Xiaochuan; Xia, Dan; Wang, Ge

2005-08-01

Current applications of helical cone-beam computed tomography (CT) involve primarily a constant pitch where the translating speed of the table and the rotation speed of the source-detector remain constant. However, situations do exist where it may be more desirable to use a helical scan with a variable translating speed of the table, leading a variable pitch. One of such applications could arise in helical cone-beam CT fluoroscopy for the determination of vascular structures through real-time imaging of contrast bolus arrival. Most of the existing reconstruction algorithms have been developed only for helical cone-beam CT with constant pitch, including the backprojection-filtration (BPF) and filtered-backprojection (FBP) algorithms that we proposed previously. It is possible to generalize some of these algorithms to reconstruct images exactly for helical cone-beam CT with a variable pitch. In this work, we generalize our BPF and FBP algorithms to reconstruct images directly from data acquired in helical cone-beam CT with a variable pitch. We have also performed a preliminary numerical study to demonstrate and verify the generalization of the two algorithms. The results of the study confirm that our generalized BPF and FBP algorithms can yield exact reconstruction in helical cone-beam CT with a variable pitch. It should be pointed out that our generalized BPF algorithm is the only algorithm that is capable of reconstructing exactly region-of-interest image from data containing transverse truncations.

Actively suspended counter-rotating machine

NASA Technical Reports Server (NTRS)

Studer, Philip A. (Inventor)

1983-01-01

A counter-rotating machine, such as a positive displacement pump having a pair of meshed, non-contacting helical screws (10,12), subjects its rotating members to axial and radial thrust forces when used for such purposes as compression of liquid or gaseous phase fluids while transporting them through a pump cavity (11,13). Each helical screw (10,12) has a shaft (17,17') which is actively suspended at opposite ends (11a,11b) of the pump cavity by a servo-controlled magnetic bearing assembly (19) and a servo-controlled rotary drive motor (20). Both bearing assemblies and drive motors are mounted on the outside of the pump cavity (11,13). Opto-electric angular position sensors (250) provide synchronization between radial orientation of the drive motors. The bearing assemblies and drive motors conjugately provide axial stabilization and radial centering of the helical screws during volumetric compression of aspirated liquid or gaseous phase fluids.

Helical Growth of Aluminum Nitride: New Insights into Its Growth Habit from Nanostructures to Single Crystals

PubMed Central

Zhang, Xing-Hong; Shao, Rui-Wen; Jin, Lei; Wang, Jian-Yu; Zheng, Kun; Zhao, Chao-Liang; Han, Jie-Cai; Chen, Bin; Sekiguchi, Takashi; Zhang, Zhi; Zou, Jin; Song, Bo

2015-01-01

By understanding the growth mechanism of nanomaterials, the morphological features of nanostructures can be rationally controlled, thereby achieving the desired physical properties for specific applications. Herein, the growth habits of aluminum nitride (AlN) nanostructures and single crystals synthesized by an ultrahigh-temperature, catalyst-free, physical vapor transport process were investigated by transmission electron microscopy. The detailed structural characterizations strongly suggested that the growth of AlN nanostructures including AlN nanowires and nanohelixes follow a sequential and periodic rotation in the growth direction, which is independent of the size and shape of the material. Based on these experimental observations, an helical growth mechanism that may originate from the coeffect of the polar-surface and dislocation-driven growth is proposed, which offers a new insight into the related growth kinetics of low-dimensional AlN structures and will enable the rational design and synthesis of novel AlN nanostructures. Further, with the increase of temperature, the growth process of AlN grains followed the helical growth model. PMID:25976071

In-flight measurement of propeller noise on the fuselage of an airplane

NASA Technical Reports Server (NTRS)

Pla, Frederic G.; Ranaudo, Richard; Woodward, Richard P.

1989-01-01

In-flight measurements of propeller noise on the fuselage of an OV-10A aircraft were obtained using a horizontal and a vertical microphone array. A wide range of flight conditions were tested including changes in angle of attack, sideslip angle, power coefficient, helical tip Mach number and advance ratio, and propeller direction of rotation. Results show a dependence of the level and directivity of the tones on the angle of attack and on the sideslip angle with the propeller direction of rotation, which is similar to results obtained in wind tunnel tests with advanced propeller designs. The level of the tones at each microphone increases with increasing angle of attack for inboard-down propeller rotation and decreases for inboard-up rotation. The level also increases with increasing slideslip angle for both propeller directions of rotation. Increasing the power coefficient results in a slight increase in the level of the tones. A strong shock wave is generated by the propeller blades even at relatively low helical tip Mach numbers resulting in high harmonic levels. As the helical tip Mach number and the advance ratio are increased, the level of the higher harmonics increases much faster than the level of the blade passage frequency.

Concept for a 3D-printed soft rotary actuator driven by a shape-memory alloy

NASA Astrophysics Data System (ADS)

Yuan, Han; Chapelle, Frédéric; Fauroux, Jean-Christophe; Balandraud, Xavier

2018-05-01

In line with the recent development of soft actuators involving shape-memory alloys (SMAs) embedded in compliant structures, this paper proposes a concept for a rotary actuator driven by a SMA wire placed inside a 3D-printed helical structure. The concept consists of using the one-way memory effect of the SMA (activated by Joule heating) to create the rotation of a material point of the structure, while the inverse rotation is obtained during the return to ambient temperature thanks to the structure’s elasticity. The study was performed in three steps. First, a prototype was designed from a chain of design rules, and tested to validate the feasibility of the concept. Thermal and geometrical measurements were performed using infrared and visible-range stereo cameras. A clockwise rotation (250°) followed by an anti-clockwise rotation (‑200°) were obtained, enabling us to validate the concept despite the partial reversibility of the movement. Second, finite element simulations were performed to improve rotation reversibility. The high compliance of the mechanical system required a framework of large displacements for the calculations (in the strength of materials sense), due to the high structural flexibility. Finally, a second prototype was constructed and tested. Attention was paid to the rotation (fully reversible rotation of 150° reached) as well as to parasitic movements due to overall structural deformation. This study opens new prospects for the design and analysis of 3D-printed soft actuators activated by smart materials.

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.

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.

Helical screw viscometer

DOEpatents

Aubert, J.H.; Chapman, R.N.; Kraynik, A.M.

1983-06-30

A helical screw viscometer for the measurement of the viscosity of Newtonian and non-Newtonian fluids comprising an elongated cylindrical container closed by end caps defining a circular cylindrical cavity within the container, a cylindrical rotor member having a helical screw or ribbon flight carried by the outer periphery thereof rotatably carried within the cavity whereby the fluid to be measured is confined in the cavity filling the space between the rotor and the container wall. The rotor member is supported by axle members journaled in the end caps, one axle extending through one end cap and connectable to a drive source. A pair of longitudinally spaced ports are provided through the wall of the container in communication with the cavity and a differential pressure meter is connected between the ports for measuring the pressure drop caused by the rotation of the helical screw rotor acting on the confined fluid for computing viscosity.

NMR and rotational angles in solution conformation of polypeptides

NASA Astrophysics Data System (ADS)

Bystrov, V. F.

1985-01-01

Professor San-Ichiro Mizushima and Professor Yonezo Morino's classical contributions provided unique means and firm basis for understanding of conformational states and internal rotation in polypeptide molecules. Now the NMR spectroscopy is the best choice to study molecular conformation, mechanism of action and structure-functional relationships of peptide and proteins in solution under conditions approaching those of their physiological environments. Crucial details of spatial structure and interactions of these molecules in solution are revealed by using proton-proton and carbon-proton vicinal coupling constants, proton nuclear Overhauser effect and spectral perturbation techniques. The results of NMR conformational analysis are presented for valinomycin "bracelet", gramicidin A double helices, honey-bee neurotoxin apamin, scorpion insectotoxins and snake neurotoxins of long and short types.

Numerical simulation of a low-swirl impinging jet with a rotating convergent nozzle

NASA Astrophysics Data System (ADS)

Borynyak, K.; Hrebtov, M.; Bobrov, M.; Kozyulin, N.

2018-03-01

The paper presents the results of Large Eddy Simulation of a swirling impinging jet with moderate Reynolds number (104), where the swirl is organized via the rotation of a convergent nozzle. The results show that the effect of the swirl in this configuration leads to an increase of axial velocity, compared to the non-swirling case. It is shown that turbulent stress plays an important role in this effect. The vortex structure of the jet consists of multiple pairs of nearly parallel helical vortices with opposite signs of rotation. The interaction of vortices in the near region of the jet leads to radial contraction of the jet’s core which in turn, causes an the increase in the axial velocity.

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.

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

DNS of helicity-induced stratified turbulent flow

NASA Astrophysics Data System (ADS)

Chandy, Abhilash J.; Rahimi, Abbas

2013-11-01

Helical flows undergoing density stratification have wide applications in meteorological phenomena such as dust devils, tornadoes, and hurricanes due to the complexity and disasters caused by them. Direct numerical simulations (DNS) of transition to turbulence in a stably stratified Boussinesq fluid are presented for different rotation and stratification intensities. In order to understand the effect of velocity on the energy cascade, comparisons are made between helicity initiated and non-helical flows. Results show that stratification decelerates the helicity decay and causes velocity and vorticity to align with each other. With respect to the helical and non-helical flow comparisons, the total energy in the presence of stratification decays faster with helicity. In addition, the behavior of length scales were examined by comparing temporal variations of the vertical shearing of velocities. Results showed a growing asymmetry with time in the case of helical flow, while non-helical flow stayed close to begin symmetric.

Studies of Solar Helicity Using Vector Magnetograms

NASA Technical Reports Server (NTRS)

Hagyard, Mona J.; Pevstov, Alexei A.

1999-01-01

observations of photospheric magnetic fields made with vector magnetographs have been used recently to study solar helicity. In this paper we indicate what can and cannot be derived from vector magnetograms, and point out some potential problems in these data that could affect the calculations of 'helicity'. Among these problems are magnetic saturation, Faraday rotation, low spectral resolution, and the method of resolving the ambiguity in the azimuth.

Mutational Analyses of HAMP Helices Suggest a Dynamic Bundle Model of Input-Output Signaling in Chemoreceptors

PubMed Central

Zhou, Qin; Ames, Peter; Parkinson, John S.

2009-01-01

SUMMARY To test the gearbox model of HAMP signaling in the E. coli serine receptor, Tsr, we generated a series of amino acid replacements at each residue of the AS1 and AS2 helices. The residues most critical for Tsr function defined hydrophobic packing faces consistent with a 4-helix bundle. Suppression patterns of helix lesions conformed to the the predicted packing layers in the bundle. Although the properties and patterns of most AS1 and AS2 lesions were consistent with both proposed gearbox structures, some mutational features specifically indicate the functional importance of an x-da bundle over an alternative a-d bundle. These genetic data suggest that HAMP signaling could simply involve changes in the stability of its x-da bundle. We propose that Tsr HAMP controls output signals by modulating destabilizing phase clashes between the AS2 helices and the adjoining kinase control helices. Our model further proposes that chemoeffectors regulate HAMP bundle stability through a control cable connection between the transmembrane segments and AS1 helices. Attractant stimuli, which cause inward piston displacements in chemoreceptors, should reduce cable tension, thereby stabilizing the HAMP bundle. This study shows how transmembrane signaling and HAMP input-output control could occur without the helix rotations central to the gearbox model. PMID:19656294

Signatures of Relativistic Helical Motion in the Rotation Measures of Active Galactic Nucleus Jets

NASA Astrophysics Data System (ADS)

Broderick, Avery E.; Loeb, Abraham

2009-10-01

Polarization has proven to be an invaluable tool for probing magnetic fields in relativistic jets. Maps of the intrinsic polarization vectors have provided the best evidence to date for uniform, toroidally dominated magnetic fields within jets. More recently, maps of the rotation measure (RM) in jets have for the first time probed the field geometry of the cool, moderately relativistic surrounding material. In most cases, clear signatures of the toroidal magnetic field are detected, corresponding to gradients in RM profiles transverse to the jet. However, in many objects, these profiles also display marked asymmetries that are difficult to explain in simple helical jet models. Furthermore, in some cases, the RM profiles are strongly frequency and/or time dependent. Here we show that these features may be naturally accounted for by including relativistic helical motion in the jet model. In particular, we are able to reproduce bent RM profiles observed in a variety of jets, frequency-dependent RM profile morphologies, and even the time dependence of the RM profiles of knots in 3C 273. Finally, we predict that some sources may show reversals in their RM profiles at sufficiently high frequencies, depending upon the ratio of the components of jet sheath velocity transverse and parallel to the jet. Thus, multi-frequency RM maps promise a novel way in which to probe the velocity structure of relativistic outflows.

A widespread family of serine/threonine protein phosphatases shares a common regulatory switch with proteasomal proteases

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

Bradshaw, Niels; Levdikov, Vladimir M.; Zimanyi, Christina M.

PP2C phosphatases control biological processes including stress responses, development, and cell division in all kingdoms of life. Diverse regulatory domains adapt PP2C phosphatases to specific functions, but how these domains control phosphatase activity was unknown. We present structures representing active and inactive states of the PP2C phosphatase SpoIIE from Bacillus subtilis. Based on structural analyses and genetic and biochemical experiments, we identify an α-helical switch that shifts a carbonyl oxygen into the active site to coordinate a metal cofactor. Our analysis indicates that this switch is widely conserved among PP2C family members, serving as a platform to control phosphatase activitymore » in response to diverse inputs. Remarkably, the switch is shared with proteasomal proteases, which we identify as evolutionary and structural relatives of PP2C phosphatases. Although these proteases use an unrelated catalytic mechanism, rotation of equivalent helices controls protease activity by movement of the equivalent carbonyl oxygen into the active site.« less

Some consequences of shear on galactic dynamos with helicity fluxes

NASA Astrophysics Data System (ADS)

Zhou, Hongzhe; Blackman, Eric G.

2017-08-01

Galactic dynamo models sustained by supernova (SN) driven turbulence and differential rotation have revealed that the sustenance of large-scale fields requires a flux of small-scale magnetic helicity to be viable. Here we generalize a minimalist analytic version of such galactic dynamos to explore some heretofore unincluded contributions from shear on the total turbulent energy and turbulent correlation time, with the helicity fluxes maintained by either winds, diffusion or magnetic buoyancy. We construct an analytic framework for modelling the turbulent energy and correlation time as a function of SN rate and shear. We compare our prescription with previous approaches that include only rotation. The solutions depend separately on the rotation period and the eddy turnover time and not just on their ratio (the Rossby number). We consider models in which these two time-scales are allowed to be independent and also a case in which they are mutually dependent on radius when a radial-dependent SN rate model is invoked. For the case of a fixed rotation period (or a fixed radius), we show that the influence of shear is dramatic for low Rossby numbers, reducing the correlation time of the turbulence, which, in turn, strongly reduces the saturation value of the dynamo compared to the case when the shear is ignored. We also show that even in the absence of winds or diffusive fluxes, magnetic buoyancy may be able to sustain sufficient helicity fluxes to avoid quenching.

Effects of number and configuration of flagella on motility of Helicobacter species.

NASA Astrophysics Data System (ADS)

Constantino, Maira A.; Sharba, Sinan; Shen, Zeli; Fox, James G.; Haesebrouck, Freddy; Linden, Sara; Bansil, Rama

Helicobacters are ulcer-causing bacteria that colonize the viscoelastic gastric mucus layer of mammals. Previous studies have shown that motility and colonization are affected by helical body shape, number and configuration of flagella. In a recent study, using fast time-resolution and high-magnification 2-D phase-contrast microscopy to image individual helical and rod-shaped H. pylori we measured the rotation rate of the cell body and flagella and found that helical shape produces less than 15% changes in swimming speeds as compared to the rod-shaped cell. Motility of H. pylori was strongly influenced by its multiple unipolar flagella. Here we compare rotational and translational speeds of H. cetorum and H. suis which have bipolar flagella, with H. cetorum having single bipolar flagella and H. suis having multiple flagella. Preliminary results show that H. suis bacteria swim slower but rotate at the same rate as H. pylori and present two swimming modes. It can swim as a pusher, with one active rotating bundle and one inactive bundle, wrapped around the body or with both bundles active. Similar work on H. cetorum is ongoing and will also be presented. NSF PHY 1410798.

Modeling vibration response and damping of cables and cabled structures

NASA Astrophysics Data System (ADS)

Spak, Kaitlin S.; Agnes, Gregory S.; Inman, Daniel J.

2015-02-01

In an effort to model the vibration response of cabled structures, the distributed transfer function method is developed to model cables and a simple cabled structure. The model includes shear effects, tension, and hysteretic damping for modeling of helical stranded cables, and includes a method for modeling cable attachment points using both linear and rotational damping and stiffness. The damped cable model shows agreement with experimental data for four types of stranded cables, and the damped cabled beam model shows agreement with experimental data for the cables attached to a beam structure, as well as improvement over the distributed mass method for cabled structure modeling.

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.

Twist planet drive

NASA Technical Reports Server (NTRS)

Vranish, John M. (Inventor)

1996-01-01

A planetary gear system includes a sun gear coupled to an annular ring gear through a plurality of twist-planet gears, a speeder gear, and a ground structure having an internal ring gear. Each planet gear includes a solid gear having a first half portion in the form of a spur gear which includes vertical gear teeth and a second half portion in the form of a spur gear which includes helical gear teeth that are offset from the vertical gear teeth and which contact helical gear teeth on the speeder gear and helical gear teeth on the outer ring gear. One half of the twist planet gears are preloaded downward, while the other half are preloaded upwards, each one alternating with the other so that each one twists in a motion opposite to its neighbor when rotated until each planet gear seats against the sun gear, the outer ring gear, the speeder gear, and the inner ring gear. The resulting configuration is an improved stiff anti-backlash gear system.

The alpha dynamo parameter and measurability of helicities in magnetohydrodynamic turbulence

NASA Technical Reports Server (NTRS)

Matthaeus, W. H.; Goldstein, M. L.; Lantz, S. R.

1986-01-01

Alpha, an important parameter in dynamo theory, is shown to be proportional to either the kinetic, current, magnetic, or velocity helicities of the fluctuating magnetic field and fluctuating velocity field. The particular helicity to which alpha is proportional depends on the assumptions used in deriving the first-order smoothed equations that describe the alpha effect. In two cases, viz., when alpha is proportional to either the magnetic helicity or velocity helicity, alpha can be determined experimentally from two-point measurements of the fluctuating fields in incompressible, homogeneous turbulence with arbitrary rotational symmetry. For the other two possibilities, alpha can be determined if the turbulence is isotropic.

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.

Influence of a change in helical twisting power of photoresponsive chiral dopants on rotational manipulation of micro-objects on the surface of chiral nematic liquid crystalline films.

PubMed

Thomas, Reji; Yoshida, Yohei; Akasaka, Takehito; Tamaoki, Nobuyuki

2012-09-24

Herein we report a group of five planar chiral molecules as photon-mode chiral switches for the reversible control of the self-assembled superstructures of doped chiral nematic liquid crystals. The chiral switches are composed of an asymmetrically substituted aromatic moiety and a photoisomerizing azobenzene unit connected in a cyclic manner through methylene spacers of varying lengths. All the molecules show conformational restriction in the rotation of the asymmetrically substituted aromatic moiety in both the E and Z states of the azobenzene units resulting in planar chirality with separable enantiomers. Our newly synthesized compounds in pure enantiomeric form show high helical twisting power (HTP) in addition to an improved change in HTP between the E and Z states. The molecule with a diphenylnaphthalene unit shows the highest ever known initial helical twisting power among chiral dopants with planar chirality. In addition to the reversible tuning of reflection colors, we employed the enantiomers of these five compounds in combination with four nematic liquid crystalline hosts to study their properties as molecular machines; the change in HTP of the chiral dopant upon photoisomerization induces rotation of the texture of the liquid crystal surfaces. Importantly, this study has revealed a linear dependence of the ratio of the difference between HTPs before and after irradiation against the absolute value of the initial HTP, not the absolute value of the change in helical twisting power between two states, on the angle of rotation of micro-objects on chiral nematic liquid crystalline films. This study has also revealed that a change in irradiation intensity does not affect the maximum angle of rotation, but it does affect the speed of rotational reorganization of the cholesteric helix. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Helical waves in easy-plane antiferromagnets

NASA Astrophysics Data System (ADS)

Semenov, Yuriy G.; Li, Xi-Lai; Xu, Xinyi; Kim, Ki Wook

2017-12-01

Effective spin torques can generate the Néel vector oscillations in antiferromagnets (AFMs). Here, it is theoretically shown that these torques applied at one end of a normal AFM strip can excite a helical type of spin wave in the strip whose properties are drastically different from characteristic spin waves. An analysis based on both a Néel vector dynamical equation and the micromagnetic simulation identifies the direction of magnetic anisotropy and the damping factor as the two key parameters determining the dynamics. Helical wave propagation requires the hard axis of the easy-plane AFM to be aligned with the traveling direction, while the damping limits its spatial extent. If the damping is neglected, the calculation leads to a uniform periodic domain wall structure. On the other hand, finite damping decelerates the helical wave rotation around the hard axis, ultimately causing stoppage of its propagation along the strip. With the group velocity staying close to spin-wave velocity at the wave front, the wavelength becomes correspondingly longer away from the excitation point. In a sufficiently short strip, a steady-state oscillation can be established whose frequency is controlled by the waveguide length as well as the excitation energy or torque.

Realistic simulations of the coupling between the protomotive force and the mechanical rotation of the F0-ATPase

PubMed Central

Mukherjee, Shayantani; Warshel, Arieh

2012-01-01

The molecular origin of the action of the F0 proton gradient-driven rotor presents a major puzzle despite significant structural advances. Although important conceptual models have provided guidelines of how such systems should work, it has been challenging to generate a structure-based molecular model using physical principles that will consistently lead to the unidirectional proton-driven rotational motion during ATP synthesis. This work uses a coarse-grained (CG) model to simulate the energetics of the F0-ATPase system in the combined space defined by the rotational coordinate and the proton transport (PTR) from the periplasmic side (P) to the cytoplasmic side (N). The model establishes the molecular origin of the rotation, showing that this effect is due to asymmetry in the energetics of the proton path rather than only the asymmetry of the interaction of the Asp on the c-ring helices and Arg on the subunit-a. The simulation provides a clear conceptual background for further exploration of the electrostatic basis of proton-driven mechanochemical systems. PMID:22927379

Energetic-ion-driven global instabilities in stellarator/helical plasmas and comparison with tokamak plasmas

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

Toi, K.; Ogawa, K.; Isobe, M.

2011-01-01

Comprehensive understanding of energetic-ion-driven global instabilities such as Alfven eigenmodes (AEs) and their impact on energetic ions and bulk plasma is crucially important for tokamak and stellarator/helical plasmas and in the future for deuterium-tritium (DT) burning plasma experiments. Various types of global modes and their associated enhanced energetic ion transport are commonly observed in toroidal plasmas. Toroidicity-induced AEs and ellipticity-induced AEs, whose gaps are generated through poloidal mode coupling, are observed in both tokamak and stellarator/helical plasmas. Global AEs and reversed shear AEs, where toroidal couplings are not as dominant were also observed in those plasmas. Helicity induced AEs thatmore » exist only in 3D plasmas are observed in the large helical device (LHD) and Wendelstein 7 Advanced Stellarator plasmas. In addition, the geodesic acoustic mode that comes from plasma compressibility is destabilized by energetic ions in both tokamak and LHD plasmas. Nonlinear interaction of these modes and their influence on the confinement of the bulk plasma as well as energetic ions are observed in both plasmas. In this paper, the similarities and differences in these instabilities and their consequences for tokamak and stellarator/helical plasmas are summarized through comparison with the data sets obtained in LHD. In particular, this paper focuses on the differences caused by the rotational transform profile and the 2D or 3D geometrical structure of the plasma equilibrium. Important issues left for future study are listed.« less

Chemically related 4,5-linked aminoglycoside antibiotics drive subunit rotation in opposite directions

PubMed Central

Wasserman, Michael R.; Pulk, Arto; Zhou, Zhou; Altman, Roger B.; Zinder, John C.; Green, Keith D.; Garneau-Tsodikova, Sylvie; Doudna Cate, Jamie H.; Blanchard, Scott C.

2015-01-01

Dynamic remodelling of intersubunit bridge B2, a conserved RNA domain of the bacterial ribosome connecting helices 44 (h44) and 69 (H69) of the small and large subunit, respectively, impacts translation by controlling intersubunit rotation. Here we show that aminoglycosides chemically related to neomycin—paromomycin, ribostamycin and neamine—each bind to sites within h44 and H69 to perturb bridge B2 and affect subunit rotation. Neomycin and paromomycin, which only differ by their ring-I 6′-polar group, drive subunit rotation in opposite directions. This suggests that their distinct actions hinge on the 6′-substituent and the drug's net positive charge. By solving the crystal structure of the paromomycin–ribosome complex, we observe specific contacts between the apical tip of H69 and the 6′-hydroxyl on paromomycin from within the drug's canonical h44-binding site. These results indicate that aminoglycoside actions must be framed in the context of bridge B2 and their regulation of subunit rotation. PMID:26224058

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.

Dynamics of arbitrary shaped propellers driven by a rotating magnetic field

NASA Astrophysics Data System (ADS)

Morozov, Konstantin I.; Mirzae, Yoni; Kenneth, Oded; Leshansky, Alexander M.

2017-04-01

Motion in fluids at the micro(nano)metric scale is dominated by viscosity. One efficient propulsion method relies on a weak uniform rotating magnetic field that drives a chiral object. From bacterial flagella to artificial magnetic micro- or nanohelices, rotation of a corkscrew is considered as a universally efficient propulsion gait in viscous environments. However, recent experimental studies have demonstrated that geometrically achiral microscale objects or random-shaped magnetic aggregates can propel similarly to helical micromotors. Although approximate theories concerning dynamics of helical magnetic propellers are available, propulsion of achiral particles or objects with complex shapes is not understood. Here we present a general theory of rotation and propulsion of magnetized object of arbitrary shape driven by a rotating magnetic field. Intrinsic symmetries of the viscous mobility tensors yield compact classification of stable rotational states depending on the orientation of the magnetic moment with respect to principal rotation axes of the object. Propulsion velocity can be written in terms of geometry-dependent chirality matrix Ch , where both the diagonal elements (owing to orientation-dependent handedness) and off-diagonal entries (that do not necessitate handedness) contribute in a similar way. In general, the theory anticipates multiplicity of stable rotational states corresponding to two (complimentary to π ) angles the magnetization forms with the field rotation axis. Thus, two identical magnetic objects may propel with different speeds or even in opposite directions. However, for a class of simple achiral objects, there is a particular magnetization whereas the pair of symmetric rotational states gives rise to a unique chiral-like propulsion gait, closely resembling that of an ideal helical propeller. In other words, a geometrically achiral object can acquire apparent chirality due to its interaction with the external magnetic field. The developed theory is further applied to study the dynamics of achiral, chiral, and random-shaped magnetic propellers, rationalizing previously unexplained experimental observations. The genetic search algorithm based on the proposed theory reveals that an arc-shaped segment is the optimal (fastest) achiral propeller, while the optimal skew-symmetric shape deviates considerably from a helix. Remarkably, an optimized arc-shaped propeller warrants propulsion speeds comparable to those of the optimally magnetized helix. Although random shaped magnetic aggregates appear to be poor swimmers at low actuation frequency, at higher frequency, whereas the helical propeller ceases to rotate in-sync with the field, the propulsion speed of the aggregates could be comparable, or even higher, than that of a helix.

Can a pure vector gravitational wave mimic a pure tensor one?

NASA Astrophysics Data System (ADS)

Allen, Bruce

2018-06-01

In the general theory of relativity, gravitational waves have two possible polarizations, which are transverse and traceless with helicity ±2 . Some alternative theories contain additional helicity 0 and helicity ±1 polarization modes. Here, we consider a hypothetical "pure vector" theory in which gravitational waves have only two possible polarizations, with helicity ±1 . We show that if these polarizations are allowed to rotate as the wave propagates, then for certain source locations on the sky, the strain outputs of three ideal interferometric gravitational wave detectors can exactly reproduce the strain outputs predicted by general relativity.

Geometry motivated alternative view on local protein backbone structures.

PubMed

Zacharias, Jan; Knapp, Ernst Walter

2013-11-01

We present an alternative to the classical Ramachandran plot (R-plot) to display local protein backbone structure. Instead of the (φ, ψ)-backbone angles relating to the chemical architecture of polypeptides generic helical parameters are used. These are the rotation or twist angle ϑ and the helical rise parameter d. Plots with these parameters provide a different view on the nature of local protein backbone structures. It allows to display the local structures in polar (d, ϑ)-coordinates, which is not possible for an R-plot, where structural regimes connected by periodicity appear disconnected. But there are other advantages, like a clear discrimination of the handedness of a local structure, a larger spread of the different local structure domains--the latter can yield a better separation of different local secondary structure motives--and many more. Compared to the R-plot we are not aware of any major disadvantage to classify local polypeptide structures with the (d, ϑ)-plot, except that it requires some elementary computations. To facilitate usage of the new (d, ϑ)-plot for protein structures we provide a web application (http://agknapp.chemie.fu-berlin.de/secsass), which shows the (d, ϑ)-plot side-by-side with the R-plot. © 2013 The Protein Society.

Vibratory high pressure coal feeder having a helical ramp

DOEpatents

Farber, Gerald

1978-01-01

Apparatus and method for feeding powdered coal from a helical ramp into a high pressure, heated, reactor tube containing hydrogen for hydrogenating the coal and/or for producing useful products from coal. To this end, the helical ramp is vibrated to feed the coal cleanly at an accurately controlled rate in a simple reliable and trouble-free manner that eliminates complicated and expensive screw feeders, and/or complicated and expensive seals, bearings and fully rotating parts.

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.

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.

Molecular dynamics simulations of theoretical cellulose nanotube models.

PubMed

Uto, Takuya; Kodama, Yuta; Miyata, Tatsuhiko; Yui, Toshifumi

2018-06-15

Nanotubes are remarkable nanoscale architectures for a wide range of potential applications. In the present paper, we report a molecular dynamics (MD) study of the theoretical cellulose nanotube (CelNT) models to evaluate their dynamic behavior in solution (either chloroform or benzene). Based on the one-quarter chain staggering relationship, we constructed six CelNT models by combining the two chain polarities (parallel (P) and antiparallel (AP)) and three symmetry operations (helical right (H R ), helical left (H L ), and rotation (R)) to generate a circular arrangement of molecular chains. Among the four models that retained the tubular form (P-H R , P-H L , P-R, and AP-R), the P-R and AP-R models have the lowest steric energies in benzene and chloroform, respectively. The structural features of the CelNT models were characterized in terms of the hydroxymethyl group conformation and intermolecular hydrogen bonds. Solvent structuring more clearly occurred with benzene than chloroform, suggesting that the CelNT models may disperse in benzene. Copyright © 2018 Elsevier Ltd. All rights reserved.

The structure of the protein phosphatase 2A PR65/A subunit reveals the conformation of its 15 tandemly repeated HEAT motifs.

PubMed

Groves, M R; Hanlon, N; Turowski, P; Hemmings, B A; Barford, D

1999-01-08

The PR65/A subunit of protein phosphatase 2A serves as a scaffolding molecule to coordinate the assembly of the catalytic subunit and a variable regulatory B subunit, generating functionally diverse heterotrimers. Mutations of the beta isoform of PR65 are associated with lung and colon tumors. The crystal structure of the PR65/Aalpha subunit, at 2.3 A resolution, reveals the conformation of its 15 tandemly repeated HEAT sequences, degenerate motifs of approximately 39 amino acids present in a variety of proteins, including huntingtin and importin beta. Individual motifs are composed of a pair of antiparallel alpha helices that assemble in a mainly linear, repetitive fashion to form an elongated molecule characterized by a double layer of alpha helices. Left-handed rotations at three interrepeat interfaces generate a novel left-hand superhelical conformation. The protein interaction interface is formed from the intrarepeat turns that are aligned to form a continuous ridge.

A HELICAL MAGNET DESIGN FOR RHIC.

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

WILLEN,E.; GUPTA,R.; JAIN,A.

1997-05-12

Helical dipole magnets are required in a project for the Relativistic Heavy Ion Collider (RHIC) to control and preserve the beam polarization in order to allow the collision of polarized proton beams. Specifications are for low current superconducting magnets with a 100 mm coil aperture and a 4 Tesla field in which the field rotates 360 degrees over a distance of 2.4 meters. A magnet meeting the requirements has been developed that uses a small diameter cable wound into helical grooves machined into a thick-walled aluminum cylinder.

A widespread family of serine/threonine protein phosphatases shares a common regulatory switch with proteasomal proteases

PubMed Central

Bradshaw, Niels; Levdikov, Vladimir M; Zimanyi, Christina M; Gaudet, Rachelle; Wilkinson, Anthony J; Losick, Richard

2017-01-01

PP2C phosphatases control biological processes including stress responses, development, and cell division in all kingdoms of life. Diverse regulatory domains adapt PP2C phosphatases to specific functions, but how these domains control phosphatase activity was unknown. We present structures representing active and inactive states of the PP2C phosphatase SpoIIE from Bacillus subtilis. Based on structural analyses and genetic and biochemical experiments, we identify an α-helical switch that shifts a carbonyl oxygen into the active site to coordinate a metal cofactor. Our analysis indicates that this switch is widely conserved among PP2C family members, serving as a platform to control phosphatase activity in response to diverse inputs. Remarkably, the switch is shared with proteasomal proteases, which we identify as evolutionary and structural relatives of PP2C phosphatases. Although these proteases use an unrelated catalytic mechanism, rotation of equivalent helices controls protease activity by movement of the equivalent carbonyl oxygen into the active site. DOI: http://dx.doi.org/10.7554/eLife.26111.001 PMID:28527238

The Effect of Terminal Substitution on the Helical Carbon Structure of Fluoro-Alkane Chains: a Pure Rotational Study of CH2OH-Cn-1F2n-1 (n = 4, 5,& 6)

NASA Astrophysics Data System (ADS)

Schwartz, Aaron Z. A.; Maturo, Mark P.; Obenchain, Daniel A.; Cooke, S. A.

2016-06-01

Continuing a series of studies to investigate the change in structure of hydrocarbons as the amount of fluorination is increased to varying degrees of substitution, we present a survey on the change in the helical nature of the fluorinated carbon backbone when a -CH2OH group is substituted for a terminal - CF3 group. Spectra for 1H,1H-heptafluorobutan-1-ol, 1H,1H-nonafluoropentan-1-ol, and 1H,1H-undecafluorohexan-1-ol were collected separately using a chirped-pulse FTMW spectrometer in the range of 7-13 GHz. Only one conformation was observed for each molecule. Additional measurements of the 1H,1H-heptafluorobutan-1-ol were completed using a Balle-Flygare cavity instrument. Assignments of the singly-substituted 13C isotopologues of the 1H,1H-heptafluorobutan-1-ol were also measured. A comparison of both ab initio and experimental structures will be presented.

DEPENDENCE OF STELLAR MAGNETIC ACTIVITY CYCLES ON ROTATIONAL PERIOD IN A NONLINEAR SOLAR-TYPE DYNAMO

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

Pipin, V. V.; Kosovichev, A. G.

2016-06-01

We study the turbulent generation of large-scale magnetic fields using nonlinear dynamo models for solar-type stars in the range of rotational periods from 14 to 30 days. Our models take into account nonlinear effects of dynamical quenching of magnetic helicity, and escape of magnetic field from the dynamo region due to magnetic buoyancy. The results show that the observed correlation between the period of rotation and the duration of activity cycles can be explained in the framework of a distributed dynamo model with a dynamical magnetic feedback acting on the turbulent generation from either magnetic buoyancy or magnetic helicity. Wemore » discuss implications of our findings for the understanding of dynamo processes operating in solar-like stars.« less

The fine structure of spermatozoa of Hydrolagus colliei (Chondrichthyes, Holocephali).

PubMed

Stanley, H P

1983-05-01

The ultrastructure of spermatozoa in Hydrolagus colliei is described. Basic similarities of structure to the sperm of the related elasmobranch fish are noted. The most significant features of sperm structure in Hydrolagus that differ from those of elasmobranch fish occur in the tail. The axoneme is eccentrically located and forms a double helix with a single longitudinal column. A second longitudinal column is reduced to a short remnant at the base of the tail. Microtubules within the axoneme are also helically disposed, a feature that is consistent with the rotating motion of the sperm. Abundant glycogen reserves are stored along the length of the tail.

Molecular dynamics simulations on discoidal HDL particles suggest a mechanism for rotation in the apo A-I belt model.

PubMed

Klon, Anthony E; Segrest, Jere P; Harvey, Stephen C

2002-12-06

Apolipoprotein A-I (apo A-I) is the major protein component of high-density lipoprotein (HDL) particles. Elevated levels of HDL in the bloodstream have been shown to correlate strongly with a reduced risk factor for atherosclerosis. Molecular dynamics simulations have been carried out on three separate model discoidal high-density lipoprotein particles (HDL) containing two monomers of apo A-I and 160 molecules of palmitoyloleoylphosphatidylcholine (POPC), to a time-scale of 1ns. The starting structures were on the basis of previously published molecular belt models of HDL consisting of the lipid-binding C-terminal domain (residues 44-243) wrapped around the circumference of a discoidal HDL particle. Subtle changes between two of the starting structures resulted in significantly different behavior during the course of the simulation. The results provide support for the hypothesis of Segrest et al. that helical registration in the molecular belt model of apo A-I is modulated by intermolecular salt bridges. In addition, we propose an explanation for the presence of proline punctuation in the molecular belt model, and for the presence of two 11-mer helical repeats interrupting the otherwise regular pattern of 22-mer helical repeats in the lipid-binding domain of apo A-I.

Spiroplasma swim by a processive change in body helicity.

NASA Astrophysics Data System (ADS)

Shaevitz, Joshua

2006-03-01

Microscopic organisms must rely on very different strategies than their macroscopic counterparts to swim through liquid. To date, the best understood method for prokaryotic swimming employs the rotation of flagella. I will present data that Spiroplasma, tiny helical bacteria that infect plants and insects, use a very different approach. By measuring cell kinematics during free swimming, we find that propulsion is generated by the propagation of kink pairs down the length of the cell body. A processive change in the helicity of the body creates these waves and enables directional movement. Unlike the motion of other helical swimmers such as Spirochetes, Spiroplasma swimming velocity increases with increasing viscosity. In addition, cell morphological parameters such as helical pitch and cell length influence swimming velocity.

Matter-induced magnetic moment and neutrino helicity rotation in external fields

NASA Astrophysics Data System (ADS)

Ternov, Alexei I.

2016-11-01

The induced magnetic moment that arises due to the propagation of neutrinos in a dispersive medium can affect the dynamics of the neutrino spin in an external electromagnetic field. In particular, it can cause a helicity flip of a massive neutrino in a magnetic field. In some astrophysical media, this helicity transition mechanism could be more effective than a similar process caused by the anomalous magnetic moment of the neutrino. If the neutrino energy is sufficiently high, the two helicity transition mechanisms mentioned above can compensate each other. Then a helicity flip in an external field will not occur. Calculations are carried out using both the methods of relativistic quantum mechanics and the quasiclassical Bargmann-Michel-Telegdi equation.

Helicity in dynamic atmospheric processes

NASA Astrophysics Data System (ADS)

Kurgansky, M. V.

2017-03-01

An overview on the helicity of the velocity field and the role played by this concept in modern research in the field of geophysical fluid dynamics and dynamic meteorology is given. Different (both previously known in the literature and first presented) formulations of the equation of helicity balance in atmospheric motions (including those with allowance for effects of air compressibility and Earth's rotation) are brought together. Equations and relationships are given which are valid in different approximations accepted in dynamic meteorology: Boussinesq approximation, quasi-static approximation, and quasi-geostrophic approximation. Emphasis is placed on the analysis of helicity budget in large-scale quasi-geostrophic systems of motion; a formula for the helicity flux across the upper boundary of the nonlinear Ekman boundary layer is given, and this flux is shown to be exactly compensated for by the helicity destruction inside the Ekman boundary layer.

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.

Molecular mechanics of 30S subunit head rotation.

PubMed

Mohan, Srividya; Donohue, John Paul; Noller, Harry F

2014-09-16

During ribosomal translocation, a process central to the elongation phase of protein synthesis, movement of mRNA and tRNAs requires large-scale rotation of the head domain of the small (30S) subunit of the ribosome. It has generally been accepted that the head rotates by pivoting around the neck helix (h28) of 16S rRNA, its sole covalent connection to the body domain. Surprisingly, we observe that the calculated axis of rotation does not coincide with the neck. Instead, comparative structure analysis across 55 ribosome structures shows that 30S head movement results from flexing at two hinge points lying within conserved elements of 16S rRNA. Hinge 1, although located within the neck, moves by straightening of the kinked helix h28 at the point of contact with the mRNA. Hinge 2 lies within a three-way helix junction that extends to the body through a second, noncovalent connection; its movement results from flexing between helices h34 and h35 in a plane orthogonal to the movement of hinge 1. Concerted movement at these two hinges accounts for the observed magnitudes of head rotation. Our findings also explain the mode of action of spectinomycin, an antibiotic that blocks translocation by binding to hinge 2.

Molecular mechanics of 30S subunit head rotation

PubMed Central

Mohan, Srividya; Donohue, John Paul; Noller, Harry F.

2014-01-01

During ribosomal translocation, a process central to the elongation phase of protein synthesis, movement of mRNA and tRNAs requires large-scale rotation of the head domain of the small (30S) subunit of the ribosome. It has generally been accepted that the head rotates by pivoting around the neck helix (h28) of 16S rRNA, its sole covalent connection to the body domain. Surprisingly, we observe that the calculated axis of rotation does not coincide with the neck. Instead, comparative structure analysis across 55 ribosome structures shows that 30S head movement results from flexing at two hinge points lying within conserved elements of 16S rRNA. Hinge 1, although located within the neck, moves by straightening of the kinked helix h28 at the point of contact with the mRNA. Hinge 2 lies within a three-way helix junction that extends to the body through a second, noncovalent connection; its movement results from flexing between helices h34 and h35 in a plane orthogonal to the movement of hinge 1. Concerted movement at these two hinges accounts for the observed magnitudes of head rotation. Our findings also explain the mode of action of spectinomycin, an antibiotic that blocks translocation by binding to hinge 2. PMID:25187561

Hybrid helical magnetic microrobots obtained by 3D template-assisted electrodeposition.

PubMed

Zeeshan, Muhammad A; Grisch, Roman; Pellicer, Eva; Sivaraman, Kartik M; Peyer, Kathrin E; Sort, Jordi; Özkale, Berna; Sakar, Mahmut S; Nelson, Bradley J; Pané, Salvador

2014-04-09

Hybrid helical magnetic microrobots are achieved by sequential electrodeposition of a CoNi alloy and PPy inside a photoresist template patterned by 3D laser lithography. A controlled actuation of the microrobots by a rotating magnetic field is demonstrated in a fluidic environment. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Tornado-like Evolution of a Kink-unstable Solar Prominence

NASA Astrophysics Data System (ADS)

Wang, Wensi; Liu, Rui; Wang, Yuming

2017-01-01

We report on the tornado-like evolution of a quiescent prominence on 2014 November 1. The eastern section of the prominence first rose slowly, transforming into an arch-shaped structure as high as ˜150 Mm above the limb; the arch then writhed moderately in a left-handed sense, while the original dark prominence material emitted in the Fe ix 171 Å passband, and a braided structure appeared at the eastern edge of the warped arch. The unraveling of the braided structure was associated with a transient brightening in the EUV and apparently contributed to the formation of a curtain-like structure (CLS). The CLS consisted of myriad thread-like loops rotating counterclockwise about the vertical if viewed from above. Heated prominence material was observed to slide along these loops and land outside the filament channel. The tornado eventually disintegrated and the remaining material flew along a left-handed helical path constituting approximately a full turn, as corroborated through stereoscopic reconstruction, into the cavity of the stable, western section of the prominence. We suggest that the tornado-like evolution of the prominence was governed by the helical kink instability, and that the CLS formed through magnetic reconnections between the prominence field and the overlying coronal field.

Dynamics of a flexible helical filament rotating in a viscous fluid near a rigid boundary

NASA Astrophysics Data System (ADS)

Jawed, M. K.; Reis, P. M.

2017-03-01

We study the effect of a no-slip rigid boundary on the dynamics of a flexible helical filament rotating in a viscous fluid, at low Reynolds number conditions (Stokes limit). This system is taken as a reduced model for the propulsion of uniflagellar bacteria, whose locomotion is known to be modified near solid boundaries. Specifically, we focus on how the propulsive force generated by the filament, as well as its buckling onset, are modified by the presence of a wall. We tackle this problem through numerical simulations that couple the elasticity of the filament, the hydrodynamic loading, and the wall effect. Each of these three ingredients is respectively modeled by the discrete elastic rods method (for a geometrically nonlinear description of the filament), Lighthill's slender body theory (for a nonlocal fluid force model), and the method of images (to emulate the boundary). The simulations are systematically validated by precision experiments on a rescaled macroscopic apparatus. We find that the propulsive force increases near the wall, while the critical rotation frequency for the onset of buckling usually decreases. A systematic parametric study is performed to quantify the dependence of the wall effects on the geometric parameters of the helical filament.

Helical magnetic fields in molecular clouds?. A new method to determine the line-of-sight magnetic field structure in molecular clouds

NASA Astrophysics Data System (ADS)

Tahani, M.; Plume, R.; Brown, J. C.; Kainulainen, J.

2018-06-01

Context. Magnetic fields pervade in the interstellar medium (ISM) and are believed to be important in the process of star formation, yet probing magnetic fields in star formation regions is challenging. Aims: We propose a new method to use Faraday rotation measurements in small-scale star forming regions to find the direction and magnitude of the component of magnetic field along the line of sight. We test the proposed method in four relatively nearby regions of Orion A, Orion B, Perseus, and California. Methods: We use rotation measure data from the literature. We adopt a simple approach based on relative measurements to estimate the rotation measure due to the molecular clouds over the Galactic contribution. We then use a chemical evolution code along with extinction maps of each cloud to find the electron column density of the molecular cloud at the position of each rotation measure data point. Combining the rotation measures produced by the molecular clouds and the electron column density, we calculate the line-of-sight magnetic field strength and direction. Results: In California and Orion A, we find clear evidence that the magnetic fields at one side of these filamentary structures are pointing towards us and are pointing away from us at the other side. Even though the magnetic fields in Perseus might seem to suggest the same behavior, not enough data points are available to draw such conclusions. In Orion B, as well, there are not enough data points available to detect such behavior. This magnetic field reversal is consistent with a helical magnetic field morphology. In the vicinity of available Zeeman measurements in OMC-1, OMC-B, and the dark cloud Barnard 1, we find magnetic field values of - 23 ± 38 μG, - 129 ± 28 μG, and 32 ± 101 μG, respectively, which are in agreement with the Zeeman measurements. Tables 1 to 7 are only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (ftp://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/614/A100

Conformational Changes in the Epidermal Growth Factor Receptor: Role of the Transmembrane Domain Investigated by Coarse-Grained MetaDynamics Free Energy Calculations

PubMed Central

2016-01-01

The epidermal growth factor receptor (EGFR) is a dimeric membrane protein that regulates key aspects of cellular function. Activation of the EGFR is linked to changes in the conformation of the transmembrane (TM) domain, brought about by changes in interactions of the TM helices of the membrane lipid bilayer. Using an advanced computational approach that combines Coarse-Grained molecular dynamics and well-tempered MetaDynamics (CG-MetaD), we characterize the large-scale motions of the TM helices, simulating multiple association and dissociation events between the helices in membrane, thus leading to a free energy landscape of the dimerization process. The lowest energy state of the TM domain is a right-handed dimer structure in which the TM helices interact through the N-terminal small-X3-small sequence motif. In addition to this state, which is thought to correspond to the active form of the receptor, we have identified further low-energy states that allow us to integrate with a high level of detail a range of previous experimental observations. These conformations may lead to the active state via two possible activation pathways, which involve pivoting and rotational motions of the helices, respectively. Molecular dynamics also reveals correlation between the conformational changes of the TM domains and of the intracellular juxtamembrane domains, paving the way for a comprehensive understanding of EGFR signaling at the cell membrane. PMID:27459426

Conformational Changes in the Epidermal Growth Factor Receptor: Role of the Transmembrane Domain Investigated by Coarse-Grained MetaDynamics Free Energy Calculations.

PubMed

Lelimousin, Mickaël; Limongelli, Vittorio; Sansom, Mark S P

2016-08-24

The epidermal growth factor receptor (EGFR) is a dimeric membrane protein that regulates key aspects of cellular function. Activation of the EGFR is linked to changes in the conformation of the transmembrane (TM) domain, brought about by changes in interactions of the TM helices of the membrane lipid bilayer. Using an advanced computational approach that combines Coarse-Grained molecular dynamics and well-tempered MetaDynamics (CG-MetaD), we characterize the large-scale motions of the TM helices, simulating multiple association and dissociation events between the helices in membrane, thus leading to a free energy landscape of the dimerization process. The lowest energy state of the TM domain is a right-handed dimer structure in which the TM helices interact through the N-terminal small-X3-small sequence motif. In addition to this state, which is thought to correspond to the active form of the receptor, we have identified further low-energy states that allow us to integrate with a high level of detail a range of previous experimental observations. These conformations may lead to the active state via two possible activation pathways, which involve pivoting and rotational motions of the helices, respectively. Molecular dynamics also reveals correlation between the conformational changes of the TM domains and of the intracellular juxtamembrane domains, paving the way for a comprehensive understanding of EGFR signaling at the cell membrane.

Rotational 3D printing of damage-tolerant composites with programmable mechanics

PubMed Central

Raney, Jordan R.; Compton, Brett G.; Ober, Thomas J.; Shea, Kristina; Lewis, Jennifer A.

2018-01-01

Natural composites exhibit exceptional mechanical performance that often arises from complex fiber arrangements within continuous matrices. Inspired by these natural systems, we developed a rotational 3D printing method that enables spatially controlled orientation of short fibers in polymer matrices solely by varying the nozzle rotation speed relative to the printing speed. Using this method, we fabricated carbon fiber–epoxy composites composed of volume elements (voxels) with programmably defined fiber arrangements, including adjacent regions with orthogonally and helically oriented fibers that lead to nonuniform strain and failure as well as those with purely helical fiber orientations akin to natural composites that exhibit enhanced damage tolerance. Our approach broadens the design, microstructural complexity, and performance space for fiber-reinforced composites through site-specific optimization of their fiber orientation, strain, failure, and damage tolerance. PMID:29348206

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

NASA Technical Reports Server (NTRS)

Nishikawa, K.-I.; Sakai, J.-I.; Zhao, Jie; Neubert, T.; Buneman, Oscar

1994-01-01

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

A novel method to correct for pitch and yaw patient setup errors in helical tomotherapy.

PubMed

Boswell, Sarah A; Jeraj, Robert; Ruchala, Kenneth J; Olivera, Gustavo H; Jaradat, Hazim A; James, Joshua A; Gutierrez, Alonso; Pearson, Dave; Frank, Gary; Mackie, T Rock

2005-06-01

An accurate means of determining and correcting for daily patient setup errors is important to the cancer outcome in radiotherapy. While many tools have been developed to detect setup errors, difficulty may arise in accurately adjusting the patient to account for the rotational error components. A novel, automated method to correct for rotational patient setup errors in helical tomotherapy is proposed for a treatment couch that is restricted to motion along translational axes. In tomotherapy, only a narrow superior/inferior section of the target receives a dose at any instant, thus rotations in the sagittal and coronal planes may be approximately corrected for by very slow continuous couch motion in a direction perpendicular to the scanning direction. Results from proof-of-principle tests indicate that the method improves the accuracy of treatment delivery, especially for long and narrow targets. Rotational corrections about an axis perpendicular to the transverse plane continue to be implemented easily in tomotherapy by adjustment of the initial gantry angle.

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.

Modeling polymorphic transformation of rotating bacterial flagella in a viscous fluid

NASA Astrophysics Data System (ADS)

Ko, William; Lim, Sookkyung; Lee, Wanho; Kim, Yongsam; Berg, Howard C.; Peskin, Charles S.

2017-06-01

The helical flagella that are attached to the cell body of bacteria such as Escherichia coli and Salmonella typhimurium allow the cell to swim in a fluid environment. These flagella are capable of polymorphic transformation in that they take on various helical shapes that differ in helical pitch, radius, and chirality. We present a mathematical model of a single flagellum described by Kirchhoff rod theory that is immersed in a fluid governed by Stokes equations. We perform numerical simulations to demonstrate two mechanisms by which polymorphic transformation can occur, as observed in experiments. First, we consider a flagellar filament attached to a rotary motor in which transformations are triggered by a reversal of the direction of motor rotation [L. Turner et al., J. Bacteriol. 182, 2793 (2000), 10.1128/JB.182.10.2793-2801.2000]. We then consider a filament that is fixed on one end and immersed in an external fluid flow [H. Hotani, J. Mol. Biol. 156, 791 (1982), 10.1016/0022-2836(82)90142-5]. The detailed dynamics of the helical flagellum interacting with a viscous fluid is discussed and comparisons with experimental and theoretical results are provided.

Overview of HIT-SI3 experiment: Simulations, Diagnostics, and Summary of Current Results

NASA Astrophysics Data System (ADS)

Penna, James; Jarboe, Thomas; Nelson, Brian; Hossack, Aaron; Sutherland, Derek; Morgan, Kyle; Hansen, Chris; Benedett, Thomas; Everson, Chris; Victor, Brian

2016-10-01

The Helicity Injected Torus - Steady Inductive 3(HIT-SI3)experiment forms and maintains spheromaks via Steady Inductive Helicity Injection (SIHI). Three injector units allow for continuous injection of helicity into a copper flux conserver in order to sustain a spheromak. Firing of the injectors with a phase difference allows finite rotation of the plasma to provide a stabilizing effect. Simulations in the MHD code NIMROD and the fluid-model code PSI-TET provide validation and a basis for interpretation of the observed experimental data. Thompson Scattering (TS) and Far Infrared (FIR) Interferometer systems allow temperature and line-averaged density measurements to be taken. An Ion Doppler Spectroscopy (IDS) system allows measurement of the plasma rotation and velocity. HIT-SI3 data has been used for validation of IDCD predictions, in particular the projected impedance of helicity injectors according to the theory. The experimental impedances have been calculated here for the first time for different HIT-SI3 regimes. Such experimental evidence will contribute to the design of future experiments employing IDCD as a current-drive mechanism. Work supported by the D.O.E., Office of Science, Office of Fusion Science.

Revisiting the NMR structure of the ultrafast downhill folding protein gpW from bacteriophage λ.

PubMed

Sborgi, Lorenzo; Verma, Abhinav; Muñoz, Victor; de Alba, Eva

2011-01-01

GpW is a 68-residue protein from bacteriophage λ that participates in virus head morphogenesis. Previous NMR studies revealed a novel α+β fold for this protein. Recent experiments have shown that gpW folds in microseconds by crossing a marginal free energy barrier (i.e., downhill folding). These features make gpW a highly desirable target for further experimental and computational folding studies. As a step in that direction, we have re-determined the high-resolution structure of gpW by multidimensional NMR on a construct that eliminates the purification tags and unstructured C-terminal tail present in the prior study. In contrast to the previous work, we have obtained a full manual assignment and calculated the structure using only unambiguous distance restraints. This new structure confirms the α+β topology, but reveals important differences in tertiary packing. Namely, the two α-helices are rotated along their main axis to form a leucine zipper. The β-hairpin is orthogonal to the helical interface rather than parallel, displaying most tertiary contacts through strand 1. There also are differences in secondary structure: longer and less curved helices and a hairpin that now shows the typical right-hand twist. Molecular dynamics simulations starting from both gpW structures, and calculations with CS-Rosetta, all converge to our gpW structure. This confirms that the original structure has strange tertiary packing and strained secondary structure. A comparison of NMR datasets suggests that the problems were mainly caused by incomplete chemical shift assignments, mistakes in NOE assignment and the inclusion of ambiguous distance restraints during the automated procedure used in the original study. The new gpW corrects these problems, providing the appropriate structural reference for future work. Furthermore, our results are a cautionary tale against the inclusion of ambiguous experimental information in the determination of protein structures.

Flow Patterns During Friction Stir Welding

NASA Technical Reports Server (NTRS)

Guerra, M.; Schmidt, C.; McClure, J. C.; Murr, L. E.; Nunes, A. C.; Munafo, Paul M. (Technical Monitor)

2002-01-01

Friction Stir Welding is a relatively new technique for welding that uses a cylindrical pin or nib inserted along the weld seam. The nib (usually threaded) and the shoulder in which it is mounted are rapidly rotated and advanced along the seam. Extreme deformation takes place leaving a fine equiaxed structure in the weld region., The flow of metal during Friction Stir Welding is investigated using a faying surface tracer and a nib frozen in place during welding. It is shown that material is transported by two processes. The first is a wiping of material from the advancing front side of the nib onto a zone of material that rotates and advances with the nib. The material undergoes a helical motion within the rotational zone that both rotates and advances and descends in the wash of the threads on the nib and rises on the outer part of the rotational zone. After one or more rotations, this material is sloughed off in its wake of the nib, primarily on the advancing side. The second process is an entrainment of material from the front retreating side of the nib that fills in between the sloughed off pieces from the advancing side.

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

Feasibility of Whole-Body Functional Mouse Imaging Using Helical Pinhole SPECT

PubMed Central

Metzler, Scott D.; Vemulapalli, Sreekanth; Jaszczak, Ronald J.; Akabani, Gamal; Chin, Bennett B.

2010-01-01

Purpose Detailed in vivo whole-body biodistributions of radiolabeled tracers may characterize the longitudinal progression of disease, and changes with therapeutic interventions. Small-animal imaging in mice is particularly attractive due to the wide array of well characterized genetically and surgically created models of disease. Single Photon Emission Computed Tomography (SPECT) imaging using pinhole collimation provides high resolution and sensitivity, but conventional methods using circular acquisitions result in severe image truncation and incomplete sampling of data which prevent the accurate determination of whole-body radiotracer biodistributions. This study describes the feasibility of helical acquisition paths to mitigate these effects. Procedures Helical paths of pinhole apertures were implemented using an external robotic stage aligned with the axis of rotation (AOR) of the scanner. Phantom and mouse scans were performed using helical paths and either circular or bi-circular orbits at the same radius of rotation (ROR). The bi-circular orbits consisted of two 360-degree scans separated by an axial shift to increase the axial field of view (FOV) and to improve the complete-sampling properties. Results Reconstructions of phantoms and mice acquired with helical paths show good image quality and are visually free of both truncation and axial-blurring artifacts. Circular orbits yielded reconstructions with both artifacts and a limited effective FOV. The bi-circular scans enlarged the axial FOV, but still suffered from truncation and sampling artifacts. Conclusions Helical paths can provide complete sampling data and large effective FOV, yielding 3D full-body in vivo biodistributions while still maintaining a small distance from the aperture to the object for good sensitivity and resolution. PMID:19521736

Predicting stability of alpha-helical, orthogonal-bundle proteins on surfaces

NASA Astrophysics Data System (ADS)

Wei, Shuai; Knotts, Thomas A.

2010-09-01

The interaction of proteins with surfaces is a key phenomenon in many applications, but current understanding of the biophysics involved is lacking. At present, rational design of such emerging technologies is difficult as no methods or theories exist that correctly predict how surfaces influence protein behavior. Using molecular simulation and a coarse-grain model, this study illustrates for the first time that stability of proteins on surfaces can be correlated with tertiary structural elements for alpha-helical, orthogonal-bundle proteins. Results show that several factors contribute to stability on surfaces including the nature of the loop region where the tether is placed and the ability of the protein to freely rotate on the surface. A thermodynamic analysis demonstrates that surfaces stabilize proteins entropically and that any destabilization is an enthalpic effect. Moreover, the entropic effects are concentrated on the unfolded state of the protein while the ethalpic effects are focused on the folded state.

Response to “Comment on ‘General rotating quantum vortex filaments in the low-temperature Svistunov model of the local induction approximation’” [Phys. Fluids 26, 119101 (2014)

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

Van Gorder, Robert A., E-mail: rav@knights.ucf.edu

2014-11-15

In R. A. Van Gorder, “General rotating quantum vortex filaments in the low-temperature Svistunov model of the local induction approximation,” Phys. Fluids 26, 065105 (2014) I discussed properties of generalized vortex filaments exhibiting purely rotational motion under the low-temperature Svistunov model of the local induction approximation. Such solutions are stationary in terms of translational motion. In the Comment [N. Hietala, “Comment on ‘General rotating quantum vortex filaments in the low-temperature Svistunov model of the local induction approximation’ [Phys. Fluids 26, 065105 (2014)],” Phys. Fluids 26, 119101 (2014)], the author criticizes my paper for not including translational motion (although it wasmore » clearly stated that the filament motion was assumed rotational). As it turns out, if one is interested in studying the geometric structure of solutions (which was the point of my paper), one obtains the needed qualitative results on the structure of such solutions by studying the purely rotational case. Nevertheless, in this Response I shall discuss the vortex filaments that have both rotational and translational motions. I then briefly discuss why one might want to study such generalized rotating filament solutions, in contrast to simple the standard helical or planar examples (which are really special cases). I also discuss how one can study the time evolution of filaments which exhibit more complicated dynamics than pure translation and rotation. Doing this, one can study non-stationary solutions which initially appear purely rotational and gradually display other dynamics as the filaments evolve.« less

Simulation of Non-resonant Internal Kink Mode with Toroidal Rotation in NSTX

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

Fu, Guoyong

2013-07-16

Plasmas in spherical and conventional tokamaks, with weakly reversed shear q pro le and minimum q above but close to unity, are susceptible to an non-resonant (m, n ) = (1, 1) internal kink mode. This mode can saturate and persist and can induce a (2; 1) seed island for Neoclassical Tearing Mode (NTMs)1 . The mode can also lead to large energetic particle transport and signi cant broadening of beam-driven current. Motivated by these important e ects, we have carried out extensive nonlinear simulations of the mode with nite toroidal rotation using parameters and pro les of an NTSXmore » plasma with a weakly reversed shear pro le. The numerical results show that, at the experimental level, plasma rotation has little e ect on either equilibrium or linear stability. However, rotation can signi cantly inuence the nonlinear dynamics of the (1, 1) mode and the the induced (2, 1) magnetic island. The simulation results show that a rotating helical equilibrium is formed and maintained in the nonlinear phase at nite plasma rotation. In contrast, for non-rotating cases, the nonlinear evolution exhibits dynamic oscillations between a quasi-2D state and a helical state. Furthermore, the e ects of rotation are found to greatly suppress the (2, 1) magnetic island even at a low level.« less

Structure and ion channel activity of the human respiratory syncytial virus (hRSV) small hydrophobic protein transmembrane domain

PubMed Central

Gan, Siok Wan; Ng, Lifang; Lin, Xin; Gong, Xiandi; Torres, Jaume

2008-01-01

The small hydrophobic (SH) protein from the human respiratory syncytial virus (hRSV) is a glycoprotein of ∼64 amino acids with one putative α-helical transmembrane domain. Although SH protein is important for viral infectivity, its exact role during viral infection is not clear. Herein, we have studied the secondary structure, orientation, and oligomerization of the transmembrane domain of SH (SH-TM) in the presence of lipid bilayers. Only one oligomer, a pentamer, was observed in PFO-PAGE. Using polarized attenuated total reflection-Fourier transform infrared (PATR-FTIR) spectroscopy, we show that the SH-TM is α-helical. The rotational orientation of SH-TM was determined by site-specific infrared dichroism (SSID) at two consecutive isotopically labeled residues. This orientation is consistent with that of an evolutionary conserved pentameric model obtained from a global search protocol using 13 homologous sequences of RSV. Conductance studies of SH-TM indicate ion channel activity, which is cation selective, and inactive below the predicted pKa of histidine. Thus, our results provide experimental evidence that the transmembrane domain of SH protein forms pentameric α-helical bundles that form cation-selective ion channels in planar lipid bilayers. We provide a model for this pore, which should be useful in mutagenesis studies to elucidate its role during the virus cycle. PMID:18369195

Bio-inspired robot design for viscous fluids

NASA Astrophysics Data System (ADS)

Ma, Grace; Lipman, Tyler; Jung, Sunghwan

Many modern micro-robots are designed for biomedical applications to transport drugs to targets or to operate tests in the body for diagnosis. However, most micro-robots simply mimic the morphology and the propulsive mechanism of micro-organisms without understanding the underlying physics of low-Re swimming. Two types of swimming motions have been observed in micro-organisms; stresslet and source-dipole swimming. The stresslet swimmer (e.g. E. coli) uses a rotating helical appendage, whereas the source-dipole swimmer (e.g. Paramecium) creates surface velocity for propulsion. Using this principle, we designed a robot to swim in very viscous fluids either by rotating a helix or creating surface velocity, simply by changing the orientation of the appendage. Further, we will discuss the performance of this robot (swimming speed and rotation speed) with respect to the number, winding angle, and radius of helices in a very viscous fluid.

Rotational 3D printing of damage-tolerant composites with programmable mechanics.

PubMed

Raney, Jordan R; Compton, Brett G; Mueller, Jochen; Ober, Thomas J; Shea, Kristina; Lewis, Jennifer A

2018-02-06

Natural composites exhibit exceptional mechanical performance that often arises from complex fiber arrangements within continuous matrices. Inspired by these natural systems, we developed a rotational 3D printing method that enables spatially controlled orientation of short fibers in polymer matrices solely by varying the nozzle rotation speed relative to the printing speed. Using this method, we fabricated carbon fiber-epoxy composites composed of volume elements (voxels) with programmably defined fiber arrangements, including adjacent regions with orthogonally and helically oriented fibers that lead to nonuniform strain and failure as well as those with purely helical fiber orientations akin to natural composites that exhibit enhanced damage tolerance. Our approach broadens the design, microstructural complexity, and performance space for fiber-reinforced composites through site-specific optimization of their fiber orientation, strain, failure, and damage tolerance. Copyright © 2018 the Author(s). Published by PNAS.

Surface-Chemistry-Mediated Control of Individual Magnetic Helical Microswimmers in a Swarm.

PubMed

Wang, Xiaopu; Hu, Chengzhi; Schurz, Lukas; De Marco, Carmela; Chen, Xiangzhong; Pané, Salvador; Nelson, Bradley J

2018-05-31

Magnetic helical microswimmers, also known as artificial bacterial flagella (ABFs), perform 3D navigation in various liquids under low-strength rotating magnetic fields by converting rotational motion to translational motion. ABFs have been widely studied as carriers for targeted delivery and release of drugs and cells. For in vivo/ in vitro therapeutic applications, control over individual groups of swimmers within a swarm is necessary for several biomedical applications such as drug delivery or small-scale surgery. In this work, we present the selective control of individual swimmers in a swarm of geometrically and magnetically identical ABFs by modifying their surface chemistry. We confirm experimentally and analytically that the forward/rotational velocity ratio of ABFs is independent of their surface coatings when the swimmers are operated below their step-out frequency (the frequency requiring the entire available magnetic torque to maintain synchronous rotation). We also show that ABFs with hydrophobic surfaces exhibit larger step-out frequencies and higher maximum forward velocities compared to their hydrophilic counterparts. Thus, selective control of a group of swimmers within a swarm of ABFs can be achieved by operating the selected ABFs at a frequency that is below their step-out frequencies but higher than the step-out frequencies of unselected ABFs. The feasibility of this method is investigated in water and in biologically relevant solutions. Selective control is also demonstrated inside a Y-shaped microfluidic channel. Our results present a systematic approach for realizing selective control within a swarm of magnetic helical microswimmers.

Tornado-Like Evolution of A Kink-Unstable Solar Prominence

NASA Astrophysics Data System (ADS)

Wang, W.; Liu, R.; Wang, Y.

2016-12-01

We report on the tornado-like evolution of a quiescent prominence on 2014 November 1. The evolution started with a slow rise of the eastern section of the prominence into an arch-shaped structure as high as 150 Mm above the limb, and then the arch experienced a moderate, left-handed writhing. Following the writhing, the originally dark prominence material became in emission in the Fe IX 171 °A passband, and a braiding structure appeared at the eastern edge of the writhing prominence body, whose unraveling process was associated with a transient brightening in EUV and apparently contributed to the formation of a curtain-like structure (CLS), which consisted of myriads of thread-like loops rotating counterclockwise about the vertical if viewed from above. Material sliding along these loops landed outside of the prominence channel. The tornado was eventually disintegrated and the remaining material flew along a lefthanded helical path of approximately a full turn, as confirmed through stereoscopic reconstruction, into the cavity of the stable, western section of the prominence. We suggest that the tornado-like evolution of the prominence was regulated by the helical kink instability, and that the CLS forms through magnetic reconnections between the flux-rope flux and the overlying flux.

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.

Superposition and detection of two helical beams for optical orbital angular momentum communication

NASA Astrophysics Data System (ADS)

Liu, Yi-Dong; Gao, Chunqing; Gao, Mingwei; Qi, Xiaoqing; Weber, Horst

2008-07-01

A loop-like system with a Dove prism is used to generate a collinear superposition of two helical beams with different azimuthal quantum numbers in this manuscript. After the generation of the helical beams distributed on the circle centered at the optical axis by using a binary amplitude grating, the diffractive field is separated into two polarized ones with the same distribution. Rotated by the Dove prism in the loop-like system in counter directions and combined together, the two fields will generate the collinear superposition of two helical beams in certain direction. The experiment shows consistency with the theoretical analysis. This method has potential applications in optical communication by using orbital angular momentum of laser beams (optical vortices).

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.

A broadband helical saline water liquid antenna for wearable systems

NASA Astrophysics Data System (ADS)

Li, Gaosheng; Huang, Yi; Gao, Gui; Yang, Cheng; Lu, Zhonghao; Liu, Wei

2018-04-01

A broadband helical liquid antenna made of saline water is proposed. A transparent hollow support is employed to fabricate the antenna. The rotation structure is fabricated with a thin flexible tube. The saline water with a concentration of 3.5% can be injected into or be extracted out from the tube to change the quantity of the solution. Thus, the tunability of the radiation pattern could be realised by applying the fluidity of the liquid. The radiation feature of the liquid antenna is compared with that of a metal one, and fairly good agreement has been achieved. Furthermore, three statements of the radiation performance corresponding to the ratio of the diameter to the wavelength of the helical saline water antenna have been proposed. It has been found that the resonance frequency increases when the length of the feeding probe or the radius of the vertical part of the liquid decreases. The fractional bandwidth can reach over 20% with a total height of 185 mm at 1.80 GHz. The measured results indicate reasonable approximation to the simulated. The characteristics of the liquid antenna make it a good candidate for various wireless applications, especially the wearable systems.

HELICAL MAGNETIC FIELDS IN THE NGC 1333 IRAS 4A PROTOSTELLAR OUTFLOWS

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

Ching, Tao-Chung; Lai, Shih-Ping; Zhang, Qizhou

We present Submillimeter Array polarization observations of the CO J = 3–2 line toward NGC 1333 IRAS 4A. The CO Stokes I maps at an angular resolution of ∼1″ reveal two bipolar outflows from the binary sources of NGC 1333 IRAS 4A. The kinematic features of the CO emission can be modeled by wind-driven outflows at ∼20° inclined from the plane of the sky. Close to the protostars the CO polarization, at an angular resolution of ∼2.″3, has a position angle approximately parallel to the magnetic field direction inferred from the dust polarizations. The CO polarization direction appears to vary smoothly frommore » an hourglass field around the core to an arc-like morphology wrapping around the outflow, suggesting a helical structure of magnetic fields that inherits the poloidal fields at the launching point and consists of toroidal fields at a farther distance of outflow. The helical magnetic field is consistent with the theoretical expectations for launching and collimating outflows from a magnetized rotating disk. Considering that the CO polarized emission is mainly contributed from the low-velocity and low-resolution data, the helical magnetic field is likely a product of the wind–envelope interaction in the wind-driven outflows. The CO data reveal a PA of ∼30° deflection in the outflows. The variation in the CO polarization angle seems to correlate with the deflections. We speculate that the helical magnetic field contributes to ∼10° deflection of the outflows by means of Lorentz force.« less

TORNADO-LIKE EVOLUTION OF A KINK-UNSTABLE SOLAR PROMINENCE

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

Wang, Wensi; Liu, Rui; Wang, Yuming, E-mail: rliu@ustc.edu.cn

We report on the tornado-like evolution of a quiescent prominence on 2014 November 1. The eastern section of the prominence first rose slowly, transforming into an arch-shaped structure as high as ∼150 Mm above the limb; the arch then writhed moderately in a left-handed sense, while the original dark prominence material emitted in the Fe ix 171 Å passband, and a braided structure appeared at the eastern edge of the warped arch. The unraveling of the braided structure was associated with a transient brightening in the EUV and apparently contributed to the formation of a curtain-like structure (CLS). The CLSmore » consisted of myriad thread-like loops rotating counterclockwise about the vertical if viewed from above. Heated prominence material was observed to slide along these loops and land outside the filament channel. The tornado eventually disintegrated and the remaining material flew along a left-handed helical path constituting approximately a full turn, as corroborated through stereoscopic reconstruction, into the cavity of the stable, western section of the prominence. We suggest that the tornado-like evolution of the prominence was governed by the helical kink instability, and that the CLS formed through magnetic reconnections between the prominence field and the overlying coronal field.« less

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.

Sensitivity of finite helical axis parameters to temporally varying realistic motion utilizing an idealized knee model.

PubMed

Johnson, T S; Andriacchi, T P; Erdman, A G

2004-01-01

Various uses of the screw or helical axis have previously been reported in the literature in an attempt to quantify the complex displacements and coupled rotations of in vivo human knee kinematics. Multiple methods have been used by previous authors to calculate the axis parameters, and it has been theorized that the mathematical stability and accuracy of the finite helical axis (FHA) is highly dependent on experimental variability and rotation increment spacing between axis calculations. Previous research has not addressed the sensitivity of the FHA for true in vivo data collection, as required for gait laboratory analysis. This research presents a controlled series of experiments simulating continuous data collection as utilized in gait analysis to investigate the sensitivity of the three-dimensional finite screw axis parameters of rotation, displacement, orientation and location with regard to time step increment spacing, utilizing two different methods for spatial location. Six-degree-of-freedom motion parameters are measured for an idealized rigid body knee model that is constrained to a planar motion profile for the purposes of error analysis. The kinematic data are collected using a multicamera optoelectronic system combined with an error minimization algorithm known as the point cluster method. Rotation about the screw axis is seen to be repeatable, accurate and time step increment insensitive. Displacement along the axis is highly dependent on time step increment sizing, with smaller rotation angles between calculations producing more accuracy. Orientation of the axis in space is accurate with only a slight filtering effect noticed during motion reversal. Locating the screw axis by a projected point onto the screw axis from the mid-point of the finite displacement is found to be less sensitive to motion reversal than finding the intersection of the axis with a reference plane. A filtering effect of the spatial location parameters was noted for larger time step increments during periods of little or no rotation.

Direct Measurement of Helical Cell Motion of the Spirochete Leptospira

PubMed Central

Nakamura, Shuichi; Leshansky, Alexander; Magariyama, Yukio; Namba, Keiichi; Kudo, Seishi

2014-01-01

Leptospira are spirochete bacteria distinguished by a short-pitch coiled body and intracellular flagella. Leptospira cells swim in liquid with an asymmetric morphology of the cell body; the anterior end has a long-pitch spiral shape (S-end) and the posterior end is hook-shaped (H-end). Although the S-end and the coiled cell body called the protoplasmic cylinder are thought to be responsible for propulsion together, most observations on the motion mechanism have remained qualitative. In this study, we analyzed the swimming speed and rotation rate of the S-end, protoplasmic cylinder, and H-end of individual Leptospira cells by one-sided dark-field microscopy. At various viscosities of media containing different concentrations of Ficoll, the rotation rate of the S-end and protoplasmic cylinder showed a clear correlation with the swimming speed, suggesting that these two helical parts play a central role in the motion of Leptospira. In contrast, the H-end rotation rate was unstable and showed much less correlation with the swimming speed. Forces produced by the rotation of the S-end and protoplasmic cylinder showed that these two helical parts contribute to propulsion at nearly equal magnitude. Torque generated by each part, also obtained from experimental motion parameters, indicated that the flagellar motor can generate torque >4000 pN nm, twice as large as that of Escherichia coli. Furthermore, the S-end torque was found to show a markedly larger fluctuation than the protoplasmic cylinder torque, suggesting that the unstable H-end rotation might be mechanically related to changes in the S-end rotation rate for torque balance of the entire cell. Variations in torque at the anterior and posterior ends of the Leptospira cell body could be transmitted from one end to the other through the cell body to coordinate the morphological transformations of the two ends for a rapid change in the swimming direction. PMID:24411236

Direct measurement of helical cell motion of the spirochete leptospira.

PubMed

Nakamura, Shuichi; Leshansky, Alexander; Magariyama, Yukio; Namba, Keiichi; Kudo, Seishi

2014-01-07

Leptospira are spirochete bacteria distinguished by a short-pitch coiled body and intracellular flagella. Leptospira cells swim in liquid with an asymmetric morphology of the cell body; the anterior end has a long-pitch spiral shape (S-end) and the posterior end is hook-shaped (H-end). Although the S-end and the coiled cell body called the protoplasmic cylinder are thought to be responsible for propulsion together, most observations on the motion mechanism have remained qualitative. In this study, we analyzed the swimming speed and rotation rate of the S-end, protoplasmic cylinder, and H-end of individual Leptospira cells by one-sided dark-field microscopy. At various viscosities of media containing different concentrations of Ficoll, the rotation rate of the S-end and protoplasmic cylinder showed a clear correlation with the swimming speed, suggesting that these two helical parts play a central role in the motion of Leptospira. In contrast, the H-end rotation rate was unstable and showed much less correlation with the swimming speed. Forces produced by the rotation of the S-end and protoplasmic cylinder showed that these two helical parts contribute to propulsion at nearly equal magnitude. Torque generated by each part, also obtained from experimental motion parameters, indicated that the flagellar motor can generate torque >4000 pN nm, twice as large as that of Escherichia coli. Furthermore, the S-end torque was found to show a markedly larger fluctuation than the protoplasmic cylinder torque, suggesting that the unstable H-end rotation might be mechanically related to changes in the S-end rotation rate for torque balance of the entire cell. Variations in torque at the anterior and posterior ends of the Leptospira cell body could be transmitted from one end to the other through the cell body to coordinate the morphological transformations of the two ends for a rapid change in the swimming direction. Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.

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.

Determining the Evolution and Propagation of CME Flux Ropes from the Sun to Earth

NASA Astrophysics Data System (ADS)

Palmerio, E.; Kilpua, E.; Mierla, M.; Rodriguez, L.; Isavnin, A.; Zhukov, A.

2017-12-01

Coronal mass ejections (CMEs) are the main drivers of space weather phenomena at the Earth. They form in the solar atmosphere as helical magnetic field structures known as flux ropes. The key parameter that defines the ability of a CME to drive geomagnetic storms is the North-South magnetic field component. One of the most significant problems in current long-term space weather forecasts is that there is no practical method to measure the magnetic structure of CMEs routinely in the corona. The magnetic structure of erupting flux ropes can however be inferred based on the properties of the CME's source region characteristics, e.g.filament details, coronal EUV arcades, X-ray/EUV sigmoids, taking into account nearby coronal and photospheric features. These proxies are useful for reconstructing the "instrinsic flux rope type" at the time of the eruption. However, the knowledge of the flux rope's magnetic structure at the Sun does not always imply a successful prediction of the magnetic structure at the Earth. This is because CMEs can change their orientation due to deflections, rotations, and deformations. We present here examples of CMEs for which we have determined their magnetic structure when launched from the Sun by using a synthesis of indirect proxies based on multiwavelength remote-sensing observations. When compared to their in situ counterparts, these CMEs present a different magnetic configuration, implying a high amount of rotation of their central axis during their propagation. We study the early evolution of these CMEs both on the solar disk and in coronagraph images though different techniques, e.g. forward modelling and tie-pointing technique. When possible, we study the CME structure in situ at other planets. We aim at determining where the rotation occurs and the rate of rotation during the CME evolution from the Sun to Earth, and possibly estimating the causes of such a high amount of rotation.

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

Structure, signaling mechanism and regulation of the natriuretic peptide receptor guanylate cyclase.

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

Misono, K. S.; Philo, J. S.; Arakawa, T.

2011-06-01

Atrial natriuretic peptide (ANP) and the homologous B-type natriuretic peptide are cardiac hormones that dilate blood vessels and stimulate natriuresis and diuresis, thereby lowering blood pressure and blood volume. ANP and B-type natriuretic peptide counterbalance the actions of the renin-angiotensin-aldosterone and neurohormonal systems, and play a central role in cardiovascular regulation. These activities are mediated by natriuretic peptide receptor-A (NPRA), a single transmembrane segment, guanylyl cyclase (GC)-linked receptor that occurs as a homodimer. Here, we present an overview of the structure, possible chloride-mediated regulation and signaling mechanism of NPRA and other receptor GCs. Earlier, we determined the crystal structures ofmore » the NPRA extracellular domain with and without bound ANP. Their structural comparison has revealed a novel ANP-induced rotation mechanism occurring in the juxtamembrane region that apparently triggers transmembrane signal transduction. More recently, the crystal structures of the dimerized catalytic domain of green algae GC Cyg12 and that of cyanobacterium GC Cya2 have been reported. These structures closely resemble that of the adenylyl cyclase catalytic domain, consisting of a C1 and C2 subdomain heterodimer. Adenylyl cyclase is activated by binding of G{sub s}{alpha} to C2 and the ensuing 7{sup o} rotation of C1 around an axis parallel to the central cleft, thereby inducing the heterodimer to adopt a catalytically active conformation. We speculate that, in NPRA, the ANP-induced rotation of the juxtamembrane domains, transmitted across the transmembrane helices, may induce a similar rotation in each of the dimerized GC catalytic domains, leading to the stimulation of the GC catalytic activity.« 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

The nature of the globular- to fibrous-actin transition.

PubMed

Oda, Toshiro; Iwasa, Mitsusada; Aihara, Tomoki; Maéda, Yuichiro; Narita, Akihiro

2009-01-22

Actin plays crucial parts in cell motility through a dynamic process driven by polymerization and depolymerization, that is, the globular (G) to fibrous (F) actin transition. Although our knowledge about the actin-based cellular functions and the molecules that regulate the G- to F-actin transition is growing, the structural aspects of the transition remain enigmatic. We created a model of F-actin using X-ray fibre diffraction intensities obtained from well oriented sols of rabbit skeletal muscle F-actin to 3.3 A in the radial direction and 5.6 A along the equator. Here we show that the G- to F-actin conformational transition is a simple relative rotation of the two major domains by about 20 degrees. As a result of the domain rotation, the actin molecule in the filament is flat. The flat form is essential for the formation of stable, helical F-actin. Our F-actin structure model provides the basis for understanding actin polymerization as well as its molecular interactions with actin-binding proteins.

Langevin Equation for DNA Dynamics

NASA Astrophysics Data System (ADS)

Grych, David; Copperman, Jeremy; Guenza, Marina

Under physiological conditions, DNA oligomers can contain well-ordered helical regions and also flexible single-stranded regions. We describe the site-specific motion of DNA with a modified Rouse-Zimm Langevin equation formalism that describes DNA as a coarse-grained polymeric chain with global structure and local flexibility. The approach has successfully described the protein dynamics in solution and has been extended to nucleic acids. Our approach provides diffusive mode analytical solutions for the dynamics of global rotational diffusion and internal motion. The internal DNA dynamics present a rich energy landscape that accounts for an interior where hydrogen bonds and base-stacking determine structure and experience limited solvent exposure. We have implemented several models incorporating different coarse-grained sites with anisotropic rotation, energy barrier crossing, and local friction coefficients that include a unique internal viscosity and our models reproduce dynamics predicted by atomistic simulations. The models reproduce bond autocorrelation along the sequence as compared to that directly calculated from atomistic molecular dynamics simulations. The Langevin equation approach captures the essence of DNA dynamics without a cumbersome atomistic representation.

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

Variable loading roller

DOEpatents

Williams, Daniel M.

1989-01-01

An automatic loading roller for transmitting torque in traction drive devices in manipulator arm joints includes a two-part camming device having a first cam portion rotatable in place on a shaft by an input torque and a second cam portion coaxially rotatable and translatable having a rotating drive surface thereon for engaging the driven surface of an output roller with a resultant force proportional to the torque transmitted. Complementary helical grooves on the respective cam portions interconnected through ball bearings interacting with those grooves effect the rotation and translation of the second cam portion in response to rotation of the first.

Variable loading roller

DOEpatents

Williams, D.M.

1988-01-21

An automatic loading roller for transmitting torque in traction drive devices in manipulator arm joints includes a two-part camming device having a first cam portion rotatable in place on a shaft by an input torque and a second cam portion coaxially rotatable and translatable having a rotating drive surface thereon for engaging the driven surface of an output roller with a resultant force proportional to the torque transmitted. Complementary helical grooves in the respective cam portions interconnected through ball bearings interacting with those grooves effect the rotation and translation of the second cam portion in response to rotation of the first. 14 figs.

On a chiral analog of the Einstein-de Haas effect

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

Zakharov, V. I., E-mail: vzakharov@itep.ru

The Einstein-de Haas effect reveals a transfer of angular momentum from microscopic constituents (electrons) to a macroscopic body, but in the case of massless fermions, one could expect the transfer of the chirality of constituents to macroscopic helical motion. For such a picture to be consistent, the macroscopic helicity is to be conserved classically, to echo the conservation of the angular momentum of a rotating body. The helicity conservation would in turn impose constraints on hydrodynamics of chiral liquids (whose constituents are massless fermions). Essentially, the chiral liquids are dissipation-free, on the classical level. Reservations and alternatives to this scenariomore » are discussed.« less

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.

Eukaryotic RNA polymerase subunit RPB8 is a new relative of the OB family.

PubMed

Krapp, S; Kelly, G; Reischl, J; Weinzierl, R O; Matthews, S

1998-02-01

RNA polymerase II subunit RPB8 is an essential subunit that is highly conserved throughout eukaryotic evolution and is present in all three types of nuclear RNA polymerases. We report the first high resolution structural insight into eukaryotic RNA polymerase architecture with the solution structure of RPB8 from Saccharomyces cerevisiae. It consists of an eight stranded, antiparallel beta-barrel, four short helical regions and a large, unstructured omega-loop. The strands are connected in classic Greek-key fashion. The overall topology is unusual and contains a striking C2 rotational symmetry. Furthermore, it is most likely a novel associate of the oligonucleotide/oligosaccharide (OB) binding protein class.

Investigation on the Characteristics of Pellet Ablation in a Toroidal Plasma

NASA Astrophysics Data System (ADS)

Sato, K. N.; Sakakita, H.; Fujita, H.

2003-06-01

Characteristics of a cloud ablated from an ice pellet has been investigated in detail in the JIPP T-IIU tokamak plasma by utilizing a new scheme of pellet injection system, "the injection-angle controllable system". A long "helical tail" of ablation light has been observed using CCD cameras and a high speed framing photograph in the case of on-axis and off-axis injection with the injection angle smaller than a certain value. The direction of the helical tail is found to be independent to that of the total magnetic field lines of the torus. From the experiments with the combination of two toroildal filed directions and two plasma current directions, it is considered that the tail seems to rotate, in most cases, to the electron diamagnetic direction poloidally, and to the opposite to the plasma current direction toroidally. Consideration on various cross sections including charge exchange, ionization and elastic collisions leads us to the conclusion that the tail-shaped phenomena may come from the situation of charge exchange equilibrium of hydrogen ions and neutrals at extremely high density regime in the cloud. The relation of ablation behavior with plasma potential and rotation has also been studied. Potential measurements of pellet-injected plasmas using heavy ion beam probe (HIBP) method were carried out for the first time. In the case of an injection angle to be anti-parallel to the electron diamagnetic direction in the poloidal plane, the result shows that the direction of potential change is negative, and consequently the potential after the injection should be negative because it has been measured to be negative in usual ohmic plasmas without pellet injection. Thus, the direction of the "tail" structure seems to be consistent to that of the plasma potential measured, if it is considered that tail structure may be caused by the effect of the plasma potential and the rotation.

Current Noise from a Magnetic Moment in a Helical Edge

NASA Astrophysics Data System (ADS)

Väyrynen, Jukka I.; Glazman, Leonid I.

2017-03-01

We calculate the two-terminal current noise generated by a magnetic moment coupled to a helical edge of a two-dimensional topological insulator. When the system is symmetric with respect to in-plane spin rotation, the noise is dominated by the Nyquist component even in the presence of a voltage bias V . The corresponding noise spectrum S (V ,ω ) is determined by a modified fluctuation-dissipation theorem with the differential conductance G (V ,ω ) in place of the linear one. The differential noise ∂S /∂V , commonly measured in experiments, is strongly dependent on frequency on a small scale τK-1≪T set by the Korringa relaxation rate of the local moment. This is in stark contrast to the case of conventional mesoscopic conductors where ∂S /∂V is frequency independent and defined by the shot noise. In a helical edge, a violation of the spin-rotation symmetry leads to the shot noise, which becomes important only at a high bias. Uncharacteristically for a fermion system, this noise in the backscattered current is super-Poissonian.

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.

Biomechanical characterisation of osteosyntheses for proximal femur fractures: helical blade versus screw.

PubMed

Al-Munajjed, Amir A; Hammer, Joachim; Mayr, Edgar; Nerlich, Michael; Lenich, Andreas

2008-01-01

Proximal femur fractures are of main concern for elderly and especially osteoporotic patients. Despite advanced implant modifications and surgical techniques, serious mechanical complication rates between 4-18% are found in conventional osteosyntheses of proximal femur fractures. Clinical complications such as the rotation of the femoral head and the cut-out phenomenon of the fracture fixation bolt are often diagnosed during post-operative treatments. Therefore, efforts in new intramedulary techniques focus on the load bearing characteristics of the implant by developing new geometries to improve the implant-tissue interface. The objective of this investigation was to analyse the osteosynthesis/femur head interaction of two commonly used osteosyntheses, one with a helical blade and the other one with a screw design under different loading conditions. For the comparative investigation the helical blade of the Proximal Femur Nail Antirotation was investigated versus the screw system of the Dynamic Hip Screw. After implantation in a femoral head the loads for rotational overwinding of the implants were analysed. Pull-out forces with suppressed rotation were investigated with analysis of the influence of the previous overwinding. All investigations were performed on human femoral heads taken of patients with average age of 70.3+/-11.8. The bone mineral densities of the human specimens were detected by QCT-scans (average BMD: 338.9+/- 61.3$\\frac[\\mathit[mg

Heavy impurity confinement in hybrid operation scenario plasmas with a rotating 1/1 continuous mode

NASA Astrophysics Data System (ADS)

Raghunathan, M.; Graves, J. P.; Nicolas, T.; Cooper, W. A.; Garbet, X.; Pfefferlé, D.

2017-12-01

In future tokamaks like ITER with tungsten walls, it is imperative to control tungsten accumulation in the core of operational plasmas, especially since tungsten accumulation can lead to radiative collapse and disruption. We investigate the behavior of tungsten trace impurities in a JET-like hybrid scenario with both axisymmetric and saturated 1/1 ideal helical core in the presence of strong plasma rotation. For this purpose, we obtain the equilibria from VMEC and use VENUS-LEVIS, a guiding-center orbit-following code, to follow heavy impurity particles. In this work, VENUS-LEVIS has been modified to account for strong plasma flows with associated neoclassical effects arising from such flows. We find that the combination of helical core and plasma rotation augments the standard neoclassical inward pinch compared to axisymmetry, and leads to a strong inward pinch of impurities towards the magnetic axis despite the strong outward diffusion provided by the centrifugal force, as frequently observed in experiments.

Strong-field approximation in a rotating frame: High-order harmonic emission from p states in bicircular fields

NASA Astrophysics Data System (ADS)

Pisanty, Emilio; Jiménez-Galán, Álvaro

2017-12-01

High-order harmonic generation with bicircular fields—the combination of counter-rotating circularly polarized pulses at different frequencies—results in a series of short-wavelength XUV harmonics with alternating circular polarizations, and experiments show that there is an asymmetry in the emission between the two helicities: a slight one in helium and a larger one in neon and argon, where the emission is carried out by p -shell electrons. Here we analyze this asymmetry by switching to a rotating frame in which the field is linearly polarized; this induces an effective magnetic field which lowers the ionization potential of the p + orbital that corotates with the lower-frequency driver, enhancing its harmonic emission and the overall helicity of the generated harmonics, while also introducing nontrivial effects from the transformation to a noninertial frame in complex time. In addition, this analysis directly relates the small asymmetry produced by s -shell emission to the imaginary part of the recollision velocity in the standard strong-field-approximation formalism.

A GLOBAL GALACTIC DYNAMO WITH A CORONA CONSTRAINED BY RELATIVE HELICITY

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

Prasad, A.; Mangalam, A., E-mail: avijeet@iiap.res.in, E-mail: mangalam@iiap.res.in

We present a model for a global axisymmetric turbulent dynamo operating in a galaxy with a corona that treats the parameters of turbulence driven by supernovae and by magneto-rotational instability under a common formalism. The nonlinear quenching of the dynamo is alleviated by the inclusion of small-scale advective and diffusive magnetic helicity fluxes, which allow the gauge-invariant magnetic helicity to be transferred outside the disk and consequently to build up a corona during the course of dynamo action. The time-dependent dynamo equations are expressed in a separable form and solved through an eigenvector expansion constructed using the steady-state solutions ofmore » the dynamo equation. The parametric evolution of the dynamo solution allows us to estimate the final structure of the global magnetic field and the saturated value of the turbulence parameter α{sub m}, even before solving the dynamical equations for evolution of magnetic fields in the disk and the corona, along with α-quenching. We then solve these equations simultaneously to study the saturation of the large-scale magnetic field, its dependence on the small-scale magnetic helicity fluxes, and the corresponding evolution of the force-free field in the corona. The quadrupolar large-scale magnetic field in the disk is found to reach equipartition strength within a timescale of 1 Gyr. The large-scale magnetic field in the corona obtained is much weaker than the field inside the disk and has only a weak impact on the dynamo operation.« less

Dynamic helical computed tomography of the pituitary gland in healthy dogs.

PubMed

Van der Vlugt-Meijer, Roselinda H; Meij, Björn P; Voorhout, George

2007-01-01

Dynamic helical computed tomography (CT) of the pituitary gland can be used to image the three-dimensional shape and dimensions of abnormalities within the pituitary gland. The aim of this study was to develop a protocol for dynamic helical CT of the pituitary gland in healthy dogs as a future reference study for patients with pituitary disease. Dynamic helical series of nine scans of the pituitary gland during and following contrast medium injection were performed in six healthy dogs using the following protocols: a series with 1 mm collimation and a table feed per X-ray tube rotation of 2 mm (pitch of 2) in six dogs, a series with 2 mm collimation and pitch of 2 in three dogs, and a series with 1 mm collimation and pitch of 1 in three other dogs. Multiplanar reconstructions of the images were made using a reconstruction index of 0.5. Images of all series were assessed visually for enhancement of the arteries, the neurohypophysis, and the adenohypophysis. The enhancement pattern of the neurohypophysis was distinguished adequately from that of the adenohypophysis in five dogs that were scanned with 1 mm collimation and pitch of 2, but the difference was less discernable when the other protocols were used. The carotid artery, its trifurcation, and the arterial cerebral circle were best visualized in dorsal reconstructions. Dynamic helical CT of the pituitary gland in healthy dogs can be performed with 1 mm collimation and pitch of 2, and a scan length that includes the entire pituitary region. Using this protocol, with the specific scanner used, the neurohypophysis, the adenohypophysis, and the surrounding vascular structures are adequately visualized.

Parsec-scale Faraday rotation and polarization of 20 active galactic nuclei jets

NASA Astrophysics Data System (ADS)

Kravchenko, E. V.; Kovalev, Y. Y.; Sokolovsky, K. V.

2017-05-01

We perform polarimetry analysis of 20 active galactic nuclei jets using the very long baseline array at 1.4, 1.6, 2.2, 2.4, 4.6, 5.0, 8.1, 8.4 and 15.4 GHz. The study allowed us to investigate linearly polarized properties of the jets at parsec scales: distribution of the Faraday rotation measure (RM) and fractional polarization along the jets, Faraday effects and structure of Faraday-corrected polarization images. Wavelength dependence of the fractional polarization and polarization angle is consistent with external Faraday rotation, while some sources show internal rotation. The RM changes along the jets, systematically increasing its value towards synchrotron self-absorbed cores at shorter wavelengths. The highest core RM reaches 16 900 rad m-2 in the source rest frame for the quasar 0952+179, suggesting the presence of highly magnetized, dense media in these regions. The typical RM of transparent jet regions has values of an order of a hundred rad m-2. Significant transverse RM gradients are observed in seven sources. The magnetic field in the Faraday screen has no preferred orientation, and is observed to be random or regular from source to source. Half of the sources show evidence for the helical magnetic fields in their rotating magneto-ionic media. At the same time jets themselves contain large-scale, ordered magnetic fields and tend to align its direction with the jet flow. The observed variety of polarized signatures can be explained by a model of spine-sheath jet structure.

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.

A dynamic model to determine vibrations in involute helical gears

NASA Astrophysics Data System (ADS)

Andersson, A.; Vedmar, L.

2003-02-01

A method to determine the dynamic load between two rotating elastic helical gears is presented. The stiffness of the gear teeth is calculated using the finite element method and includes the contribution from the elliptic distributed tooth load. To make sure that the new incoming contacts which are the main excitation source are properly simulated, the necessary deformation of the gears is determined by using the true geometry and positions of the gears for every time step of the dynamic calculation. This allows the contact to be positioned outside the plane of action. A numerical example is presented with figures that show the behaviour of the dynamic transmission error as well as the variation of the contact pressure due to the dynamic load for different rotational speeds.

Flexible helical yarn swimmers.

PubMed

Zakharov, A P; Leshansky, A M; Pismen, L M

2016-09-01

We investigate the motion of a flexible Stokesian flagellar swimmer realised as a yarn made of two intertwined elastomer fibres, one active, that can reversibly change its length in response to a local excitation causing transition to the nematic state or swelling, and the other one, a passive isotropic elastomer with identical mechanical properties. A propagating chemical wave may provide an excitation mechanism ensuring a constant length of the excited region. Generally, the swimmer moves along a helical trajectory, and the propagation and rotation velocity are very sensitive to the ratio of the excited region to the pitch of the yarn, as well as to the size of a carried load. External excitation by a moving actuating beam is less effective, unless the direction of the beam is adjusted to rotation of the swimmer.

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.

Method and apparatus for maintaining equilibrium in a helical axis stellarator

DOEpatents

Reiman, Allan; Boozer, Allen

1987-01-01

Apparatus for maintaining three-dimensional MHD equilibrium in a plasma contained in a helical axis stellerator includes a resonant coil system, having a configuration such that current therethrough generates a magnetic field cancelling the resonant magnetic field produced by currents driven by the plasma pressure on any given flux surface resonating with the rotational transform of another flux surface in the plasma. Current through the resonant coil system is adjusted as a function of plasma beta.

Method and apparatus for maintaining equilibrium in a helical axis stellarator

DOEpatents

Reiman, A.; Boozer, A.

1984-10-31

Apparatus for maintaining three-dimensional MHD equilibrium in a plasma contained in a helical axis stellarator includes a resonant coil system, having a configuration such that current therethrough generates a magnetic field cancelling the resonant magnetic field produced by currents driven by the plasma pressure on any given flux surface resonating with the rotational transform of another flux surface in the plasma. Current through the resonant coil system is adjusted as a function of plasma beta.

Application of an Externally Applied Rotating Magnetic Field for Control of MHD Relaxation Phenomena in the HIST Spherical Torus Device

NASA Astrophysics Data System (ADS)

Kikuchi, Yusuke; Yoshikawa, Tatsuya; Nishioka, Tsutomu; Hashimoto, Shotaro; Fukumoto, Naoyuki; Nagata, Masayoshi

Application of an externally applied rotating magnetic field (RMF) for control of MHD relaxation phenomena driven by a coaxial helicity injection has been proposed in the HIST spherical torus device. In this letter, the plasma responses to the RMF evaluated by magnetic fields inside the plasma in HIST are shown.

Torque Induced on Lipid Microtubules with Optical Tweezers

NASA Astrophysics Data System (ADS)

wichean, T. Na; Charrunchon, S.; Pattanaporkratana, A.; Limtrakul, J.; Chattham, N.

2017-09-01

Chiral Phospholipids are found self-assembled into cylindrical tubules of 500 nm in diameter by helical winding of bilayer stripes under cooling in ethanol and water solution. Theoretical prediction and experimental evidence reported so far confirmed the modulated tilt direction in a helical striped pattern of the tubules. This molecular orientation morphology results in optically birefringent tubules. We investigate an individual lipid microtubule under a single optical trap of 532 nm linearly polarized laser. Spontaneous rotation of a lipid tubule induced by radiation torque was observed with only one sense of rotation caused by chirality of a lipid tubule. Rotation discontinued once the high refractive index axis of a lipid tubule aligned with a polarization axis of the laser. We further explored a lipid tubule under circularly polarized optical trap. It was found that a lipid tubule was continuously rotated confirming the tubule birefringent property. We modified the shape of optical trap by cylindrical lens obtaining an elliptical profile optical trap. A lipid tubule can be aligned along the elongated length of optical trap. We reported an investigation of competition between polarized light torque on a birefringent lipid tubule versus torque from intensity gradient of an elongated optical trap.

Regular Mechanical Transformation of Rotations Into Translations: Part 1. Kinematic Analysis and Definition of the Basic Characteristics

NASA Astrophysics Data System (ADS)

Abadjieva, Emilia; Abadjiev, Valentin

2017-06-01

The science that study the processes of motions transformation upon a preliminary defined law between non-coplanar axes (in general case) axes of rotations or axis of rotation and direction of rectilinear translation by three-link mechanisms, equipped with high kinematic joints, can be treated as an independent branch of Applied Mechanics. It deals with mechanical behaviour of these multibody systems in relation to the kinematic and geometric characteristics of the elements of the high kinematic joints, which form them. The object of study here is the process of regular transformation of rotation into translation. The developed mathematical model is subjected to the defined task for studying the sliding velocity vector function at the contact point from the surfaces elements of arbitrary high kinematic joints. The main kinematic characteristics of the studied type motions transformation (kinematic cylinders on level, kinematic relative helices (helical conoids) and kinematic pitch configurations) are defined on the bases of the realized analysis. These features expand the theoretical knowledge, which is the objective of the gearing theory. They also complement the system of kinematic and geometric primitives, that form the mathematical model for synthesis of spatial rack mechanisms.

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

Influence of gravitation on the propagation of electromagnetic radiation

NASA Technical Reports Server (NTRS)

Mashhoon, B.

1975-01-01

The existence of a general helicity-rotation coupling is demonstrated for electromagnetic waves propagating in the field of a slowly rotating body and in the Goedel universe. This coupling leads to differential focusing of circularly polarized radiation by a gravitational field which is detectable for a rapidly rotating collapsed body. The electromagnetic perturbations and their frequency spectrum are given for the Goedel universe. The spectrum of frequencies is bounded from below by the characteristic rotation frequency of the Goedel universe. If the universe were rotating, the differential focusing effect would be extremely small due to the present upper limit on the anisotropy of the microwave background radiation.

'Boomerang'-like insertion of a fusogenic peptide in a lipid membrane revealed by solid-state 19F NMR.

PubMed

Afonin, Sergii; Dürr, Ulrich H N; Glaser, Ralf W; Ulrich, Anne S

2004-02-01

Solid state (19)F NMR revealed the conformation and alignment of the fusogenic peptide sequence B18 from the sea urchin fertilization protein bindin embedded in flat phospholipid bilayers. Single (19)F labels were introduced into nine distinct positions along the wild-type sequence by substituting each hydrophobic amino acid, one by one, with L-4-fluorophenylglycine. Their anisotropic chemical shifts were measured in uniaxially oriented membrane samples and used as orientational constraints to model the peptide structure in the membrane-bound state. Previous (1)H NMR studies of B18 in 30% TFE and in detergent micelles had shown that the peptide structure consists of two alpha-helical segments that are connected by a flexible hinge. This helix-break-helix motif was confirmed here by the solid-state (19)F NMR data, while no other secondary structure (beta-sheet, 3(10)-helix) was compatible with the set of orientational constraints. For both alpha-helical segments we found that the helical conformation extends all the way to the respective N- and C-termini of the peptide. Analysis of the corresponding tilt and azimuthal rotation angles showed that the N-terminal helix of B18 is immersed obliquely into the bilayer (at a tilt angle tau approximately 54 degrees), whereas the C-terminus is peripherally aligned (tau approximately 91 degrees). The azimuthal orientation of the two segments is consistent with the amphiphilic distribution of side-chains. The observed 'boomerang'-like mode of insertion into the membrane may thus explain how peptide binding leads to lipid dehydration and acyl chain perturbation as a prerequisite for bilayer fusion to occur. Copyright 2004 John Wiley & Sons, Ltd.

Structural basis of gating of CNG channels.

PubMed

Giorgetti, Alejandro; Nair, Anil V; Codega, Paolo; Torre, Vincent; Carloni, Paolo

2005-03-28

Cyclic nucleotide-gated (CNG) ion channels, underlying sensory transduction in vertebrate photoreceptors and olfactory sensory neurons, require cyclic nucleotides to open. Here, we present structural models of the tetrameric CNG channel pore from bovine rod in both open and closed states, as obtained by combining homology modeling-based techniques, experimentally derived spatial constraints and structural patterns present in the PDB database. Gating is initiated by an anticlockwise rotation of the N-terminal region of the C-linker, which is then, transmitted through the S6 transmembrane helices to the P-helix, and in turn from this to the pore lumen, which opens up from 2 to 5A thus allowing for ion permeation. The approach, here presented, is expected to provide a general methodology for model ion channels and their gating when structural templates are available and an extensive electrophysiological analysis has been performed.

Microwave Spectrum of Hydrogen Bonded HEXAFLUOROISOPROPANOL•••WATER Complex

NASA Astrophysics Data System (ADS)

Shahi, Abhishek; Arunan, Elangannan

2014-06-01

Stabilizing α-helical structure of protein and dissolving a hard to dissolve polymer, polythene terphthalete, are some of the unique properties of the organic solvent Hexafluoroisopropanol (HFIP). After determining the complete microwave spectrum of HFIP monomer, we have recorded the spectrum of HFIP***H_2O complex. Ab initio calculations were used to optimize three different possible structures. The global minimum, structure 1, had HFIP as proton donor. Another promising structure, Structure 2, has been obtained from a molecular dynamic study. A total of 46 observed lines have been fitted well for obtaining the rotational and distortion constants within experimental uncertainty. The observed rotational constants are A = 1134.53898(77) MHz, B = 989.67594(44) MHz and C = 705.26602(20) MHz. Interestingly, the rotational constants of structure 1, structure 2 and experiments were very close. Experimentally observed distortion constants were close to structure 1. b-type transitions were stronger than c-type which is also consistent with the calculated dipole moment components of structure 1. Calculations predict a non-zero a-dipole moment but experimentally a-type transitions were absent. Microwave spectra of two of the deuterium isotopologues of this complex i.e. HFIP***D_2O (30 transitions) and HFIP***HOD (33 transitions) have been also observed. Search for other isotopologues are in progress. To characterize the nature of hydrogen bonding, Atoms in Molecules and Natural Bond Orbital theoretical analysis have been done. Experimental structure and these theoretical analyses indicate that the hydrogen bonding in HFIP***H_2O complex is stronger than that in water dimer. A. Shahi and E. Arunan, Talk number RK16, 68th International Symposium on Molecular Spectroscopy 2013, Ohio, USA. Yamaguchi, T.; Imura, S.; Kai, T.; Yoshida, K. Zeitschrift für Naturforsch. A 2013, 68a, 145.

External reflection FTIR of peptide monolayer films in situ at the air/water interface: experimental design, spectra-structure correlations, and effects of hydrogen-deuterium exchange.

PubMed Central

Flach, C R; Brauner, J W; Taylor, J W; Baldwin, R C; Mendelsohn, R

1994-01-01

A Fourier transform infrared spectrometer has been interfaced with a surface balance and a new external reflection infrared sampling accessory, which permits the acquisition of spectra from protein monolayers in situ at the air/water interface. The accessory, a sample shuttle that permits the collection of spectra in alternating fashion from sample and background troughs, reduces interference from water vapor rotation-vibration bands in the amide I and amide II regions of protein spectra (1520-1690 cm-1) by nearly an order of magnitude. Residual interference from water vapor absorbance ranges from 50 to 200 microabsorbance units. The performance of the device is demonstrated through spectra of synthetic peptides designed to adopt alpha-helical, antiparallel beta-sheet, mixed beta-sheet/beta-turn, and unordered conformations at the air/water interface. The extent of exchange on the surface can be monitored from the relative intensities of the amide II and amide I modes. Hydrogen-deuterium exchange may lower the amide I frequency by as much as 11-12 cm-1 for helical secondary structures. This shifts the vibrational mode into a region normally associated with unordered structures and leads to uncertainties in the application of algorithms commonly used for determination of secondary structure from amide I contours of proteins in D2O solution. PMID:7919013

SU-E-I-49: Influence of Scanner Output Measurement Technique on KERMA Ratios in CT.

PubMed

Ogden, K; Roskopf, M; Scalzetti, E

2012-06-01

KERMA ratios (RK) are defined as the ratio of KERMA measured at a specific phantom location (K) to in-air isocenter CT scanner output (KCT). In this work we investigate the impact of measurement methodology on KCT values. OSL dosimeter chips were used to measure KCT for a GE VCT scanner (GE Medical Systems, Waukesha WI), using the 40 mm nominal beam width. Methods included a single point measurement at the center of the beam (1 tube rotation), and extended z-axis measurements using multiple adjacent OSL's (7.5 cm extent), with single tube rotation, multiple contiguous axial scans, and helical scans (pitch of 1.375). Measurements were made in air and on the scan table at 80 and 120 kV. Averaged single point measurements were consistent, with a mean coefficient of variation of 2.5%. For extended measurements with a single tube rotation, the mean value was equivalent to the single point measurements. For multiple contiguous axial scans, the in-air KCT values were higher than the single rotation mean value and single point measurements by 13% and 10.3% at 120 and 80 kV, respectively, and for the on-table measurements the values were 14.9% and 8.1% higher at 120 and 80 kV, respectively. The increase is due to beam overlap caused by z- axis over-beaming. Extended measurements using helical scanning were equivalent to the multiple rotation axial measurements when corrected for the helical pitch. For all methodologies, the in-air values exceeded the on- table measurements by an average of 23% and 19.4% at 80 and 120 kV, respectively. Scanner KCT values must be measured to allow organ dose estimation using published RK values. It is imperative that the KCT measurement methodology is the same as for the published values, or large errors may be introduced into the resulting organ dose estimates. © 2012 American Association of Physicists in Medicine.

Helicon modes in uniform plasmas. I. Low m modes

NASA Astrophysics Data System (ADS)

Urrutia, J. M.; Stenzel, R. L.

2015-09-01

Helicons are whistler modes with azimuthal wave numbers. They arise in bounded gaseous and solid state plasmas, but the present work shows that very similar modes also exist in unbounded uniform plasmas. The antenna properties determine the mode structure. A simple antenna is a magnetic loop with dipole moment aligned either along or across the ambient background magnetic field B0. For such configurations, the wave magnetic field has been measured in space and time in a large and uniform laboratory plasma. The observed wave topology for a dipole along B0 is similar to that of an m = 0 helicon mode. It consists of a sequence of alternating whistler vortices. For a dipole across B0, an m = 1 mode is excited which can be considered as a transverse vortex which rotates around B0. In m = 0 modes, the field lines are confined to each half-wavelength vortex while for m = 1 modes they pass through the entire wave train. A subset of m = 1 field lines forms two nested helices which rotate in space and time like corkscrews. Depending on the type of the antenna, both m = + 1 and m = -1 modes can be excited. Helicons in unbounded plasmas also propagate transverse to B0. The transverse and parallel wave numbers are about equal and form oblique phase fronts as in whistler Gendrin modes. By superimposing small amplitude fields of several loop antennas, various antenna combinations have been created. These include rotating field antennas, helical antennas, and directional antennas. The radiation efficiency is quantified by the radiation resistance. Since helicons exist in unbounded laboratory plasmas, they can also arise in space plasmas.

Structure determination of a peptide model of the repeated helical domain in Samia cynthia ricini silk fibroin before spinning by a combination of advanced solid-state NMR methods.

PubMed

Nakazawa, Yasumoto; Asakura, Tetsuo

2003-06-18

Fibrous proteins unlike globular proteins, contain repetitive amino acid sequences, giving rise to very regular secondary protein structures. Silk fibroin from a wild silkworm, Samia cynthia ricini, consists of about 100 repeats of alternating polyalanine (poly-Ala) regions of 12-13 residues in length and Gly-rich regions. In this paper, the precise structure of the model peptide, GGAGGGYGGDGG(A)(12)GGAGDGYGAG, which is a typical repeated sequence of the silk fibroin, was determined using a combination of three kinds of solid-state NMR studies; a quantitative use of (13)C CP/MAS NMR chemical shift with conformation-dependent (13)C chemical shift contour plots, 2D spin diffusion (13)C solid-state NMR under off magic angle spinning and rotational echo double resonance. The structure of the model peptide corresponding to the silk fibroin structure before spinning was determined. The torsion angles of the central Ala residue, Ala(19), in the poly-Ala region were determined to be (phi, psi) = (-59 degrees, -48 degrees ) which are values typically associated with alpha-helical structures. However, the torsion angles of the Gly(25) residue adjacent to the C-terminal side of the poly-Ala chain were determined to be (phi, psi) = (-66 degrees, -22 degrees ) and those of Gly(12) and Ala(13) residues at the N-terminal of the poly-Ala chain to be (phi, psi) = (-70 degrees, -30 degrees ). In addition, REDOR experiments indicate that the torsion angles of the two C-terminal Ala residues, Ala(23) and Ala(24), are (phi, psi) = (-66 degrees, -22 degrees ) and those of N-terminal two Ala residues, Ala(13) and Ala(14) are (phi, psi) = (-70 degrees, -30 degrees ). Thus, the local structure of N-terminal and C-terminal residues, and also the neighboring residues of alpha-helical poly-Ala chain in the model peptide is a more strongly wound structure than found in typical alpha-helix structures.

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

Ligand reprogramming in dinuclear helicate complexes: a consequence of allosteric or electrostatic effects?

PubMed

Jeffery, John C; Rice, Craig R; Harding, Lindsay P; Baylies, Christian J; Riis-Johannessen, Thomas

2007-01-01

The ditopic ligand 6,6'-bis(4-methylthiazol-2-yl)-3,3'-([18]crown-6)-2,2'-bipyridine (L(1)) contains both a potentially tetradentate pyridyl-thiazole (py-tz) N-donor chain and an additional "external" crown ether binding site which spans the central 2,2'-bipyridine unit. In polar solvents (MeCN, MeNO(2)) this ligand forms complexes with Zn(II), Cd(II), Hg(II) and Cu(I) ions via coordination of the N donors to the metal ion. Reaction with both Hg(II) and Cu(I) ions results in the self-assembly of dinuclear double-stranded helicate complexes. The ligands are partitioned by rotation about the central py--py bond, such that each can coordinate to both metals as a bis-bidentate donor ligand. With Zn(II) ions a single-stranded mononuclear species is formed in which one ligand coordinates the metal ion in a planar tetradentate fashion. Reaction with Cd(II) ions gives rise to an equilibrium between both the dinuclear double-stranded helicate and the mononuclear species. These complexes can further coordinate s-block metal cations via the remote crown ether O-donor domains; a consequence of which are some remarkable changes in the binding modes of the N-donor domains. Reaction of the Hg(II)- or Cd(II)-containing helicate with either Ba(2+) or Sr(2+) ions effectively reprogrammes the ligand to form only the single-stranded heterobinuclear complexes [MM'(L(1))](4+) (M=Hg(II), Cd(II); M'=Ba(2+), Sr(2+)), where the transition and s-block cations reside in the N- and O-donor sites, respectively. In contrast, the same ions have only a minor structural impact on the Zn(II) species, which already exists as a single-stranded mononuclear complex. Similar reactions with the Cd(II) system result in a shift in equilibrium towards the single-stranded species, the extent of which depends on the size and charge of the s-block cation in question. Reaction of the dicopper(I) double-stranded helicate with Ba(2+) shows that the dinuclear structure still remains intact but the pitch length is significantly increased.

Ultrastable pRNA hexameric ring gearing hexameric phi29 DNA-packaging motor by revolving without rotating and coiling

PubMed Central

Schwartz, Chad; Guo, Peixuan

2013-01-01

Biomotors have previously been classified into two categories: linear and rotational motors. It has long been popularly believed that viral DNA packaging motors are rotation motors. We have recently found that the DNA-packaging motor of bacteriophage phi29 uses a third mechanism: revolution without rotation. phi29 motor consists of three-coaxial rings of hexameric RNA, a hexameric ATPase, and a dodecameric channel. The motor uses six ATP to revolve one helical turn of dsDNA around the hexameric ring of ATPase gp16. Each dodecameric segment tilts at a 30°-angle and runs anti-parallel to the dsDNA helix to facilitate translation in one direction. The negatively charged phosphate backbone interacts with four positively charged lysine rings, resulting in four steps of transition. This review will discuss how the novel pRNA meets motor requirements for translocation concerning structure, stoichiometry, and thermostability; how pRNA studies have led to the generation of the concept of RNA nanotechnology; and how pRNA is fabricated into nanoparticles to deliver siRNA, miRNA, and ribozymes to cancer and virus-infected cells. PMID:23683853

Modeling non-stationary, non-axisymmetric heat patterns in DIII-D tokamak

DOE PAGES

Ciro, D.; Evans, T. E.; Caldas, I. L.

2016-10-27

Non-axisymmetric stationary magnetic perturbations lead to the formation of homoclinic tangles near the divertor magnetic saddle in tokamak discharges. These tangles intersect the divertor plates in static helical structures that delimit the regions reached by open magnetic field lines reaching the plasma column and leading the charged particles to the strike surfaces by parallel transport. In this article we introduce a non-axisymmetric rotating magnetic perturbation to model the time evolution of the three-dimensional magnetic field of a singlenull DIII-D tokamak discharge developing a rotating tearing mode. The non-axiymmetric field is modeled using the magnetic signals to adjust the phases andmore » currents of a set of internal filamentary currents that approximate the magnetic field in the plasma edge region. The stable and unstable manifolds of the asymmetric magnetic saddle are obtained through an adaptive calculation providing the cuts at a given poloidal plane and the strike surfaces. Lastly, for the modeled shot, the experimental heat pattern and its time development are well described by the rotating unstable manifold, indicating the emergence of homoclinic lobes in a rotating frame due to the plasma instabilities.« less

Modeling non-stationary, non-axisymmetric heat patterns in DIII-D tokamak

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

Ciro, D.; Evans, T. E.; Caldas, I. L.

Non-axisymmetric stationary magnetic perturbations lead to the formation of homoclinic tangles near the divertor magnetic saddle in tokamak discharges. These tangles intersect the divertor plates in static helical structures that delimit the regions reached by open magnetic field lines reaching the plasma column and leading the charged particles to the strike surfaces by parallel transport. In this article we introduce a non-axisymmetric rotating magnetic perturbation to model the time evolution of the three-dimensional magnetic field of a singlenull DIII-D tokamak discharge developing a rotating tearing mode. The non-axiymmetric field is modeled using the magnetic signals to adjust the phases andmore » currents of a set of internal filamentary currents that approximate the magnetic field in the plasma edge region. The stable and unstable manifolds of the asymmetric magnetic saddle are obtained through an adaptive calculation providing the cuts at a given poloidal plane and the strike surfaces. Lastly, for the modeled shot, the experimental heat pattern and its time development are well described by the rotating unstable manifold, indicating the emergence of homoclinic lobes in a rotating frame due to the plasma instabilities.« less

Assessment of temporal resolution of multi-detector row computed tomography in helical acquisition mode using the impulse method.

PubMed

Ichikawa, Katsuhiro; Hara, Takanori; Urikura, Atsushi; Takata, Tadanori; Ohashi, Kazuya

2015-06-01

The purpose of this study was to propose a method for assessing the temporal resolution (TR) of multi-detector row computed tomography (CT) (MDCT) in the helical acquisition mode using temporal impulse signals generated by a metal ball passing through the acquisition plane. An 11-mm diameter metal ball was shot along the central axis at approximately 5 m/s during a helical acquisition, and the temporal sensitivity profile (TSP) was measured from the streak image intensities in the reconstructed helical CT images. To assess the validity, we compared the measured and theoretical TSPs for the 4-channel modes of two MDCT systems. A 64-channel MDCT system was used to compare TSPs and image quality of a motion phantom for the pitch factors P of 0.6, 0.8, 1.0 and 1.2 with a rotation time R of 0.5 s, and for two R/P combinations of 0.5/1.2 and 0.33/0.8. Moreover, the temporal transfer functions (TFs) were calculated from the obtained TSPs. The measured and theoretical TSPs showed perfect agreement. The TSP narrowed with an increase in the pitch factor. The image sharpness of the 0.33/0.8 combination was inferior to that of the 0.5/1.2 combination, despite their almost identical full width at tenth maximum values. The temporal TFs quantitatively confirmed these differences. The TSP results demonstrated that the TR in the helical acquisition mode significantly depended on the pitch factor as well as the rotation time, and the pitch factor and reconstruction algorithm affected the TSP shape. Copyright © 2015 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

TALE proteins search DNA using a rotationally decoupled mechanism.

PubMed

Cuculis, Luke; Abil, Zhanar; Zhao, Huimin; Schroeder, Charles M

2016-10-01

Transcription activator-like effector (TALE) proteins are a class of programmable DNA-binding proteins used extensively for gene editing. Despite recent progress, however, little is known about their sequence search mechanism. Here, we use single-molecule experiments to study TALE search along DNA. Our results show that TALEs utilize a rotationally decoupled mechanism for nonspecific search, despite remaining associated with DNA templates during the search process. Our results suggest that the protein helical structure enables TALEs to adopt a loosely wrapped conformation around DNA templates during nonspecific search, facilitating rapid one-dimensional (1D) diffusion under a range of solution conditions. Furthermore, this model is consistent with a previously reported two-state mechanism for TALE search that allows these proteins to overcome the search speed-stability paradox. Taken together, our results suggest that TALE search is unique among the broad class of sequence-specific DNA-binding proteins and supports efficient 1D search along DNA.

Influence of rotational speed on the cyclic fatigue of rotary nickel-titanium endodontic instruments.

PubMed

Lopes, Hélio P; Ferreira, Alessandra A P; Elias, Carlos N; Moreira, Edson J L; de Oliveira, Júlio C Machado; Siqueira, José F

2009-07-01

During the preparation of curved canals, rotary nickel-titanium (NiTi) instruments are subjected to cyclic fatigue, which can lead to instrument fracture. Although several factors may influence the cyclic fatigue resistance of instruments, the role of the rotational speed remains uncertain. This study was intended to evaluate the effects of rotational speed on the number of cycles to fracture of rotary NiTi instruments. ProTaper Universal instruments F3 and F4 (Maillefer SA, Ballaigues, Switzerland) were used in an artificial curved canal under rotational speeds of 300 rpm or 600 rpm. The artificial canal was made of stainless steel, with an inner diameter of 1.5 mm, total length of 20 mm, and arc at the end with a curvature radius of 6 mm. The arc length was 9.4 mm and 10.6 mm on the straight part. The number of cycles required to fracture was recorded. Fractured surfaces and the helical shafts of the fractured instruments were analyzed by scanning electron microscopy. The results showed approximately a 30% reduction in the observed number of cycles to fracture as rotational speed was increased from 300 to 600 RPM (p < 0.05). The morphology of the fractured surface was always of ductile type, and no plastic deformation was observed on the helical shaft of fractured instruments. The present findings for both F3 and F4 ProTaper instruments revealed that the increase in rotational speed significantly reduced the number of cycles to fracture.

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

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.

Comparison of helical scan and standard rotation methods in single-crystal X-ray data collection strategies.

PubMed

Polsinelli, Ivan; Savko, Martin; Rouanet-Mehouas, Cecile; Ciccone, Lidia; Nencetti, Susanna; Orlandini, Elisabetta; Stura, Enrico A; Shepard, William

2017-01-01

X-ray radiation in macromolecular crystallography can chemically alter the biological material and deteriorate the integrity of the crystal lattice with concomitant loss of resolution. Typical alterations include decarboxylation of glutamic and aspartic residues, breaking of disulfide bonds and the reduction of metal centres. Helical scans add a small translation to the crystal in the rotation method, so that for every image the crystal is shifted to expose a fresh part. On beamline PROXIMA 2A at Synchrotron SOLEIL, this procedure has been tested with various parameters in an attempt to understand how to mitigate the effects of radiation damage. Here, the strategies used and the crystallographic metrics for various scenarios are reported. Among these, the loss of bromine from bromophenyl moieties appears to be a useful monitor of radiation damage as the carbon-bromine bond is very sensitive to X-ray irradiation. Two cases are focused on where helical scans are shown to be superior in obtaining meaningful data compared with conventional methods. In one case the initial resolution of the crystal is extended over time, and in the second case the anomalous signal is preserved to provide greater effective multiplicity and easier phasing.

A trap potential model investigation of the optical activity induced in dye-DNA intercalation complexes

NASA Astrophysics Data System (ADS)

Kamiya, Mamoru

1988-02-01

The fundamental features of the optical activity induced in dye-DNA intercalation complexes are studied by application of the trap potential model which is useful to evaluate the induced rotational strength without reference to detailed geometrical information about the intercalation complexes. The specific effect of the potential depth upon the induced optical activity is explained in terms of the relative magnitudes of the wave-phase and helix-phase variations in the path of an electron moving on a restricted helical segment just like an exciton trapped around the dye intercalation site. The parallel and perpendicular components of the induced rotational strength well reflect basic properties of the helicity effects about the longitudinal and tangential axes of the DNA helical cylinder. The trap potential model is applied to optimize the potential parameters so as to reproduce the ionic strength effect upon the optical activity induced to proflavine-DNA intercalation complexes. From relationships between the optimized potential parameters and ionic strengths, it is inferred that increase in the ionic strength contributes to the optical activity induced by the nearest-neighbour interaction between intercalated proflavine and DNA base pairs.

MHD Simulation of the HIT-SI Experiment

NASA Astrophysics Data System (ADS)

Marklin, George

2003-10-01

The Helicity Injected Torus (HIT) experiment at the University of Washington has been reconfigured into a high beta spheromak with steady state AC current drive [1]. Helicity is injected by two half torus Reversed Field Pinches (RFP's) connected to the ends of the cylindrically symmetric flux conserver, rotated by 90 degrees from each other. The RFP's are driven with sinusoidally varying voltage and flux. Each side has its voltage and flux in phase, but is 90 degrees out of phase from the other side. The helicity injection rate, which is proportional to the voltage times the flux, goes like sin(wt)^2 on one side and cos(wt)^2 on the other, making the total injection rate constant in time. The complex multiply connected 3-dimensional geometry of this device make it difficult to simulate with existing codes that typically use a structured mesh. This poster will describe a new 3D MHD simulation code and a new 3D Taylor state code which both use an unstructured finite element mesh. The mesh is generated from a CAD-like description of an arbitrary arrangement of 3D geometrical objects. Taylor states in the HIT-SI geometry will be shown for different combinations of fluxes in the two injectors. MHD simulation results will be shown starting from a Taylor state with uniform density and temperature and continuing through several cycles of time dependent helicity injection. Field line tracing plots will show the quality of the flux surfaces at various stages in the injection cycle. [1] T. R. Jarboe, Fusion Technology, vol. 36, p. 85, 1999

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.

Measurements of the Rotation of the Flagellar Motor by Bead Assay.

PubMed

Kasai, Taishi; Sowa, Yoshiyuki

2017-01-01

The bacterial flagellar motor is a reversible rotary nano-machine powered by the ion flux across the cytoplasmic membrane. Each motor rotates a long helical filament that extends from the cell body at several hundreds revolutions per second. The output of the motor is characterized by its generated torque and rotational speed. The torque can be calculated as the rotational frictional drag coefficient multiplied by the angular velocity. Varieties of methods, including a bead assay, have been developed to measure the flagellar rotation rate under various load conditions on the motor. In this chapter, we describe a method to monitor the motor rotation through a position of a 1 μm bead attached to a truncated flagellar filament.

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.

Amplification of large scale magnetic fields in a decaying MHD system

NASA Astrophysics Data System (ADS)

Park, Kiwan

2017-10-01

Dynamo theory explains the amplification of magnetic fields in the conducting fluids (plasmas) driven by the continuous external energy. It is known that the nonhelical continuous kinetic or magnetic energy amplifies the small scale magnetic field; and the helical energy, the instability, or the shear with rotation effect amplifies the large scale magnetic field. However, recently it was reported that the decaying magnetic energy independent of helicity or instability could generate the large scale magnetic field. This phenomenon may look somewhat contradictory to the conventional dynamo theory. But it gives us some clues to the fundamental mechanism of energy transfer in the magnetized conducting fluids. It also implies that an ephemeral astrophysical event emitting the magnetic and kinetic energy can be a direct cause of the large scale magnetic field observed in space. As of now the exact physical mechanism is not yet understood in spite of several numerical results. The plasma motion coupled with a nearly conserved vector potential in the magnetohydrodynamic (MHD) system may transfer magnetic energy to the large scale. Also the intrinsic property of the scaling invariant MHD equation may decide the direction of energy transfer. In this paper we present the simulation results of inversely transferred helical and nonhelical energy in a decaying MHD system. We introduce a field structure model based on the MHD equation to show that the transfer of magnetic energy is essentially bidirectional depending on the plasma motion and initial energy distribution. And then we derive α coefficient algebraically in line with the field structure model to explain how the large scale magnetic field is induced by the helical energy in the system regardless of an external forcing source. And for the algebraic analysis of nonhelical magnetic energy, we use the eddy damped quasinormalized Markovian approximation to show the inverse transfer of magnetic energy.

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

Influence of gantry rotation time and scan mode on image quality in ultra-high-resolution CT system.

PubMed

Honda, Osamu; Yanagawa, Masahiro; Hata, Akinori; Kikuchi, Noriko; Miyata, Tomo; Tsukagoshi, Shinsuke; Uranishi, Ayumi; Tomiyama, Noriyuki

2018-06-01

To investigate the image quality of helical scan (HS) mode and non-helical scan (non-HS) mode on ultra-high-resolution CT in different gantry rotation time. non-HS with 0.35 s/rot (non-HS200 mA/0.35 s). Three observers compared each non-HS image with HS image, and scored non-HS images by using 3-point scale, paying attention to normal findings, abnormal findings, noise, streak artifact, and overall image quality. Statistical analysis was performed with Steel-Dwass test. Overall image quality (score: 2.45) and noise (score: 2.42) of non-HS 200 mA/1.5s was statistically best (p < 0.0005). Overall Image quality and noise of non-HS200 mA/0.75 s (score: 2.0) was comparable to that of HS200 mA/1.5 s. CTDIvol of HS200 mA/1.5 s is 23.2 mGy. CTDIvol of non-HS200 mA/1.5 s, non-HS200 mA/0.75 s, non-HS200 mA/0.35 s is 19.2 mGy, 9.8 mGy, 4.7 mGy. Overall image quality and noise of non-helical scan is better than that of helical scan in the same rotation time. Overall Image quality of non-HS200 mA/0.75 s is comparable to that of HS200 mA/1.5 s, though the radiation dose of non-HS200 mA/0.75 s is lower than that of HS200 mA/1.5 s. Copyright © 2018 Elsevier B.V. All rights reserved.

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.

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).

Dynamo generation of a magnetic field by decaying Lehnert waves in a highly conducting plasma

NASA Astrophysics Data System (ADS)

Mizerski, Krzysztof A.; Moffatt, H. K.

2018-03-01

Random waves in a uniformly rotating plasma in the presence of a locally uniform seed magnetic field and subject to weak kinematic viscosity ? and resistivity ? are considered. These "Lehnert" waves may have either positive or negative helicity, and it is supposed that waves of a single sign of helicity are preferentially excited by a symmetry-breaking mechanism. A mean electromotive force proportional to ? is derived, demonstrating the conflicting effects of the two diffusive processes. Attention is then focussed on the situation ?, relevant to conditions in the universe before and during galaxy formation. An ?-effect, axisymmetric about the rotation vector, is derived, decaying on a time-scale proportional to ?; this amplifies a large-scale seed magnetic field to a level independent of ?, this field being subsequently steady and having the character of a "fossil field". Subsequent evolution of this fossil field is briefly discussed.

Coiled to diffuse: Brownian motion of a helical bacterium.

PubMed

Butenko, Alexander V; Mogilko, Emma; Amitai, Lee; Pokroy, Boaz; Sloutskin, Eli

2012-09-11

We employ real-time three-dimensional confocal microscopy to follow the Brownian motion of a fixed helically shaped Leptospira interrogans (LI) bacterium. We extract from our measurements the translational and the rotational diffusion coefficients of this bacterium. A simple theoretical model is suggested, perfectly reproducing the experimental diffusion coefficients, with no tunable parameters. An older theoretical model, where edge effects are neglected, dramatically underestimates the observed rates of translation. Interestingly, the coiling of LI increases its rotational diffusion coefficient by a factor of 5, compared to a (hypothetical) rectified bacterium of the same contour length. Moreover, the translational diffusion coefficients would have decreased by a factor of ~1.5, if LI were rectified. This suggests that the spiral shape of the spirochaete bacteria, in addition to being employed for their active twisting motion, may also increase the ability of these bacteria to explore the surrounding fluid by passive Brownian diffusion.

Biopolymer dynamics driven by helical flagella

NASA Astrophysics Data System (ADS)

Balin, Andrew K.; Zöttl, Andreas; Yeomans, Julia M.; Shendruk, Tyler N.

2017-11-01

Microbial flagellates typically inhabit complex suspensions of polymeric material which can impact the swimming speed of motile microbes, filter feeding of sessile cells, and the generation of biofilms. There is currently a need to better understand how the fundamental dynamics of polymers near active cells or flagella impacts these various phenomena, in particular, the hydrodynamic and steric influence of a rotating helical filament on suspended polymers. Our Stokesian dynamics simulations show that as a stationary rotating helix pumps fluid along its long axis, polymers migrate radially inward while being elongated. We observe that the actuation of the helix tends to increase the probability of finding polymeric material within its pervaded volume. This accumulation of polymers within the vicinity of the helix is stronger for longer polymers. We further analyze the stochastic work performed by the helix on the polymers and show that this quantity is positive on average and increases with polymer contour length.

Computational assessment of folding energy landscapes in heterodimeric coiled coils.

PubMed

André, Ingemar; Bjelic, Sinisa

2018-07-01

The coiled coil structural motif consists of alpha helices supercoiling around each other to form staggered knobs-into-holes packing. Such structures are deceptively simple, especially as they often can be described with parametric equations, but are known to exist in various conformations. Even the simplest systems, consisting of 2 monomers, can assemble into a wide range of states. They can form canonical as well as noncanonical coiled coils, be parallel or antiparallel, where helices associate with different degrees of shift, tilt, and rotation. Here, we investigate the energy landscape of heterodimeric coiled coils by carrying out de novo folding simulations starting from amino acid sequence. We folded a diverse set of 22 heterodimers and demonstrate that the approach is capable of identifying the atomic details in the experimental structure in the majority of cases. Our methodology also enables exploration of alternative states that can be accessible in solution beyond the experimentally determined structure. For many systems, we observe folding energy landscapes with multiple energy minima and several isoenergetic states. By comparing coiled coils from single domains and those extracted from larger proteins, we find that standalone coiled coils have deeper energy wells at the experimentally determined conformation. By folding the competing homodimeric states in addition to the heterodimers, we observe that the structural specificity towards the heteromeric state is often small. Taken together, our results demonstrate that de novo folding simulations can be a powerful tool to characterize structural specificity of coiled coils when coupled to assessment of energy landscapes. © 2018 Wiley Periodicals, Inc.

Site-directed spin labeling reveals a conformational switch in the phosphorylation domain of smooth muscle myosin.

PubMed

Nelson, Wendy D; Blakely, Sarah E; Nesmelov, Yuri E; Thomas, David D

2005-03-15

We have used site-directed spin labeling and EPR spectroscopy to detect structural changes within the regulatory light chain (RLC) of smooth muscle myosin upon phosphorylation. Smooth muscle contraction is activated by phosphorylation of S19 on RLC, but the structural basis of this process is unknown. There is no crystal structure containing a phosphorylated RLC, and there is no crystal structure for the N-terminal region of any RLC. Therefore, we have prepared single-Cys mutations throughout RLC, exchanged each mutant onto smooth muscle heavy meromyosin, verified normal regulatory function, and used EPR to determine dynamics and solvent accessibility at each site. A survey of spin-label sites throughout the RLC revealed that only the N-terminal region (first 24 aa) shows a significant change in dynamics upon phosphorylation, with most of the first 17 residues showing an increase in rotational amplitude. Therefore, we focused on this N-terminal region. Additional structural information was obtained from the pattern of oxygen accessibility along the sequence. In the absence of phosphorylation, little or no periodicity was observed, suggesting a lack of secondary structural order in this region. However, phosphorylation induced a strong helical pattern (3.6-residue periodicity) in the first 17 residues, while increasing accessibility throughout the first 24 residues. We have identified a domain within RLC, the N-terminal phosphorylation domain, in which phosphorylation increases helical order, internal dynamics, and accessibility. These results support a model in which this disorder-to-order transition within the phosphorylation domain results in decreased head-head interactions, activating myosin in smooth muscle.

Tailored optical vector fields for ultrashort-pulse laser induced complex surface plasmon structuring.

PubMed

Ouyang, J; Perrie, W; Allegre, O J; Heil, T; Jin, Y; Fearon, E; Eckford, D; Edwardson, S P; Dearden, G

2015-05-18

Precise tailoring of optical vector beams is demonstrated, shaping their focal electric fields and used to create complex laser micro-patterning on a metal surface. A Spatial Light Modulator (SLM) and a micro-structured S-waveplate were integrated with a picosecond laser system and employed to structure the vector fields into radial and azimuthal polarizations with and without a vortex phase wavefront as well as superposition states. Imprinting Laser Induced Periodic Surface Structures (LIPSS) elucidates the detailed vector fields around the focal region. In addition to clear azimuthal and radial plasmon surface structures, unique, variable logarithmic spiral micro-structures with a pitch Λ ∼1μm, not observed previously, were imprinted on the surface, confirming unambiguously the complex 2D focal electric fields. We show clearly also how the Orbital Angular Momentum(OAM) associated with a helical wavefront induces rotation of vector fields along the optic axis of a focusing lens and confirmed by the observed surface micro-structures.

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

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

Multipinhole SPECT helical scan parameters and imaging volume

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

Yao, Rutao, E-mail: rutaoyao@buffalo.edu; Deng, Xiao; Wei, Qingyang

Purpose: The authors developed SPECT imaging capability on an animal PET scanner using a multiple-pinhole collimator and step-and-shoot helical data acquisition protocols. The objective of this work was to determine the preferred helical scan parameters, i.e., the angular and axial step sizes, and the imaging volume, that provide optimal imaging performance. Methods: The authors studied nine helical scan protocols formed by permuting three rotational and three axial step sizes. These step sizes were chosen around the reference values analytically calculated from the estimated spatial resolution of the SPECT system and the Nyquist sampling theorem. The nine helical protocols were evaluatedmore » by two figures-of-merit: the sampling completeness percentage (SCP) and the root-mean-square (RMS) resolution. SCP was an analytically calculated numerical index based on projection sampling. RMS resolution was derived from the reconstructed images of a sphere-grid phantom. Results: The RMS resolution results show that (1) the start and end pinhole planes of the helical scheme determine the axial extent of the effective field of view (EFOV), and (2) the diameter of the transverse EFOV is adequately calculated from the geometry of the pinhole opening, since the peripheral region beyond EFOV would introduce projection multiplexing and consequent effects. The RMS resolution results of the nine helical scan schemes show optimal resolution is achieved when the axial step size is the half, and the angular step size is about twice the corresponding values derived from the Nyquist theorem. The SCP results agree in general with that of RMS resolution but are less critical in assessing the effects of helical parameters and EFOV. Conclusions: The authors quantitatively validated the effective FOV of multiple pinhole helical scan protocols and proposed a simple method to calculate optimal helical scan parameters.« less

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

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.

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.

β-D-(1→4), β-D-(1→3) 'mixed linkage' xylans from red seaweeds of the order Nemaliales and Palmariales.

PubMed

Viana, Adriano G; Noseda, Miguel D; Gonçalves, Alan G; Duarte, Maria Eugênia R; Yokoya, Nair; Matulewicz, Maria C; Cerezo, Alberto S

2011-06-01

Xylans from five seaweeds belonging to the order Nemaliales (Galaxaura marginata, Galaxaura obtusata, Tricleocarpacylindrica, Tricleocarpa fragilis, and Scinaia halliae) and one of the order Palmariales (Palmaria palmata) collected on the Brazilian coasts were extracted with hot water and purified from acid xylomannans and/or xylogalactans through Cetavlon precipitation of the acid polysaccharides. The β-D-(1→4), β-D-(1→3) 'mixed linkage' structures were determined using methylation analysis and 1D and 2D NMR spectroscopy. The presence of large sequences of β-(1→4)-linked units suggests transient aggregates of ribbon- or helical-ordered structures that would explain the low optical rotations. Copyright © 2011 Elsevier Ltd. All rights reserved.

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.

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.

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.

Iridescent cellulose nanocrystal films: the link between structural colour and Bragg’s law

NASA Astrophysics Data System (ADS)

Nguyen, Thanh-Dinh; Sierra, Egoitz; Eguiraun, Harkaitz; Lizundia, Erlantz

2018-07-01

Structural colour is a phenomenon found in nature, which provides plants and animals with vibrant optical properties. The production of this colour is based on the interaction of incident light with the hierarchical organisation of submicron- and micron-sized layered structures. Cellulose nanocrystals (CNCs) are anisotropic building units formed by acid hydrolysis of native cellulose microfibers, which can disperse in aqueous media to form a photonic liquid crystal. One fascinating example of the appearance of biomimetic colour is the supramolecular assembly of CNCs into iridescent layered structures that rotate along a helical screw to yield a long-range chiral nematic order. A quick, simple and engaging experiment that allows the establishment of a direct relation between the structural colour and underlying mechanism of the light interaction with these hierarchically structured materials is reported. The obtained colour changes are explained within the theoretical framework provided by Bragg’s law and may provide an easy way to observe the macroscopic manifestation of this often abstract concept.

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.

Sunspot rotation. II. Effects of varying the field strength and twist of an emerging flux tube

NASA Astrophysics Data System (ADS)

Sturrock, Z.; Hood, A. W.

2016-09-01

Context. Observations of flux emergence indicate that rotational velocities may develop within sunspots. However, the dependence of this rotation on sub-photospheric field strength and twist remains largely unknown. Aims: We investigate the effects of varying the initial field strength and twist of an emerging sub-photospheric magnetic flux tube on the rotation of the sunspots at the photosphere. Methods: We consider a simple model of a stratified domain with a sub-photospheric interior layer and three overlying atmospheric layers. A twisted arched flux tube is inserted in the interior and is allowed to rise into the atmosphere. To achieve this, the magnetohydrodynamic equations are solved using the Lagrangian-remap code, Lare3d. We perform a parameter study by independently varying the sub-photospheric magnetic field strength and twist. Results: Altering the initial magnetic field strength and twist of the flux tube significantly affects the tube's evolution and the rotational motions that develop at the photosphere. The rotation angle, vorticity, and current show a direct dependence on the initial field strength. We find that an increase in field strength increases the angle through which the fieldlines rotate, the length of the fieldlines extending into the atmosphere, and the magnetic energy transported to the atmosphere. This also affects the amount of residual twist in the interior. The length of the fieldlines is crucial as we predict the twist per unit length equilibrates to a lower value on longer fieldlines. No such direct dependence is found when we modify the twist of the magnetic field owing to the complex effect this has on the tension force acting on the tube. However, there is still a clear ordering in quantities such as the rotation angle, helicity, and free energy with higher initial twist cases being related to sunspots that rotate more rapidly, transporting more helicity and magnetic energy to the atmosphere.

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.

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.

A model for straight and helical solar jets: II. Parametric study of the plasma beta.

PubMed

Pariat, E; Dalmasse, K; DeVore, C R; Antiochos, S K; Karpen, J T

2016-12-01

Jets are dynamic, impulsive, well-collimated plasma events that develop at many different scales and in different layers of the solar atmosphere. Jets are believed to be induced by magnetic reconnection, a process central to many astrophysical phenomena. Within the solar atmosphere, jet-like events develop in many different environments, e.g., in the vicinity of active regions as well as in coronal holes, and at various scales, from small photospheric spicules to large coronal jets. In all these events, signatures of helical structure and/or twisting/rotating motions are regularly observed. The present study aims to establish that a single model can generally reproduce the observed properties of these jet-like events. In this study, using our state-of-the-art numerical solver ARMS, we present a parametric study of a numerical tridimensional magnetohydrodynamic (MHD) model of solar jet-like events. Within the MHD paradigm, we study the impact of varying the atmospheric plasma β on the generation and properties of solar-like jets. The parametric study validates our model of jets for plasma β ranging from 10 -3 to 1, typical of the different layers and magnetic environments of the solar atmosphere. Our model of jets can robustly explain the generation of helical solar jet-like events at various β ≤ 1. This study introduces the new original result that the plasma β modifies the morphology of the helical jet, explaining the different observed shapes of jets at different scales and in different layers of the solar atmosphere. Our results allow us to understand the energisation, triggering, and driving processes of jet-like events. Our model allows us to make predictions of the impulsiveness and energetics of jets as determined by the surrounding environment, as well as the morphological properties of the resulting jets.

Bundling of elastic filaments induced by hydrodynamic interactions

NASA Astrophysics Data System (ADS)

Man, Yi; Page, William; Poole, Robert J.; Lauga, Eric

2017-12-01

Peritrichous bacteria swim in viscous fluids by rotating multiple helical flagellar filaments. As the bacterium swims forward, all its flagella rotate in synchrony behind the cell in a tight helical bundle. When the bacterium changes its direction, the flagellar filaments unbundle and randomly reorient the cell for a short period of time before returning to their bundled state and resuming swimming. This rapid bundling and unbundling is, at its heart, a mechanical process whereby hydrodynamic interactions balance with elasticity to determine the time-varying deformation of the filaments. Inspired by this biophysical problem, we present in this paper what is perhaps the simplest model of bundling whereby two or more straight elastic filaments immersed in a viscous fluid rotate about their centerline, inducing rotational flows which tend to bend the filaments around each other. We derive an integrodifferential equation governing the shape of the filaments resulting from mechanical balance in a viscous fluid at low Reynolds number. We show that such equation may be evaluated asymptotically analytically in the long-wavelength limit, leading to a local partial differential equation governed by a single dimensionless bundling number. A numerical study of the dynamics predicted by the model reveals the presence of two configuration instabilities with increasing bundling numbers: first to a crossing state where filaments touch at one point and then to a bundled state where filaments wrap along each other in a helical fashion. We also consider the case of multiple filaments and the unbundling dynamics. We next provide an intuitive physical model for the crossing instability and show that it may be used to predict analytically its threshold and adapted to address the transition to a bundling state. We then use a macroscale experimental implementation of the two-filament configuration in order to validate our theoretical predictions and obtain excellent agreement. This long-wavelength model of bundling will be applicable to other problems in biological physics and provides the groundwork for further, more realistic, models of flagellar bundling.

Self-assembly of dendronized perylene bisimides into complex helical columns.

PubMed

Percec, Virgil; Peterca, Mihai; Tadjiev, Timur; Zeng, Xiangbing; Ungar, Goran; Leowanawat, Pawaret; Aqad, Emad; Imam, Mohammad R; Rosen, Brad M; Akbey, Umit; Graf, Robert; Sekharan, Sivakumar; Sebastiani, Daniel; Spiess, Hans W; Heiney, Paul A; Hudson, Steven D

2011-08-10

The synthesis of perylene 3,4:9,10-tetracarboxylic acid bisimides (PBIs) dendronized with first-generation dendrons containing 0 to 4 methylenic units (m) between the imide group and the dendron, (3,4,5)12G1-m-PBI, is reported. Structural analysis of their self-organized arrays by DSC, X-ray diffraction, molecular modeling, and solid-state (1)H NMR was carried out on oriented samples with heating and cooling rates of 20 to 0.2 °C/min. At high temperature, (3,4,5)12G1-m-PBI self-assemble into 2D-hexagonal columnar phases with intracolumnar order. At low temperature, they form orthorhombic (m = 0, 2, 3, 4) and monoclinic (m = 1) columnar arrays with 3D periodicity. The orthorhombic phase has symmetry close to hexagonal. For m = 0, 2, 3, 4 ,they consist of tetramers as basic units. The tetramers contain a pair of two molecules arranged side by side and another pair in the next stratum of the column, turned upside-down and rotated around the column axis at different angles for different m. In contrast, for m = 1, there is only one molecule in each stratum, with a four-strata 2(1) helical repeat. All molecules face up in one column, and down in the second column, of the monoclinic cell. This allows close and extended π-stacking, unlike in the disruptive up-down alteration from the case of m = 0, 2, 3, 4. Most of the 3D structures were observed only by cooling at rates of 1 °C/min or less. This complex helical self-assembly is representative for other classes of dendronized PBIs investigated for organic electronics and solar cells. © 2011 American Chemical Society

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.

Cooperative macromolecular device revealed by meta-analysis of static and time-resolved structures

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

Ren, Zhong; Šrajer, Vukica; Knapp, James E.

2013-04-08

Here we present a meta-analysis of a large collection of static structures of a protein in the Protein Data Bank in order to extract the progression of structural events during protein function. We apply this strategy to the homodimeric hemoglobin HbI from Scapharca inaequivalvis. We derive a simple dynamic model describing how binding of the first ligand in one of the two chemically identical subunits facilitates a second binding event in the other partner subunit. The results of our ultrafast time-resolved crystallographic studies support this model. We demonstrate that HbI functions like a homodimeric mechanical device, such as pliers ormore » scissors. Ligand-induced motion originating in one subunit is transmitted to the other via conserved pivot points, where the E and F' helices from two partner subunits are 'bolted' together to form a stable dimer interface permitting slight relative rotation but preventing sliding.« less

A comparison between soft x-ray and magnetic phase data on the Madison symmetric torus

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

VanMeter, P. D., E-mail: pvanmeter@wisc.edu; Reusch, L. M.; Sarff, J. S.

The Soft X-Ray (SXR) tomography system on the Madison Symmetric Torus uses four cameras to determine the emissivity structure of the plasma. This structure should directly correspond to the structure of the magnetic field; however, there is an apparent phase difference between the emissivity reconstructions and magnetic field reconstructions when using a cylindrical approximation. The difference between the phase of the dominant rotating helical mode of the magnetic field and the motion of the brightest line of sight for each SXR camera is dependent on both the camera viewing angle and the plasma conditions. Holding these parameters fixed, this phasemore » difference is shown to be consistent over multiple measurements when only toroidal or poloidal magnetic field components are considered. These differences emerge from physical effects of the toroidal geometry which are not captured in the cylindrical approximation.« less

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

Fluid-Dynamic Optimal Design of Helical Vascular Graft for Stenotic Disturbed Flow

PubMed Central

Ha, Hojin; Hwang, Dongha; Choi, Woo-Rak; Baek, Jehyun; Lee, Sang Joon

2014-01-01

Although a helical configuration of a prosthetic vascular graft appears to be clinically beneficial in suppressing thrombosis and intimal hyperplasia, an optimization of a helical design has yet to be achieved because of the lack of a detailed understanding on hemodynamic features in helical grafts and their fluid dynamic influences. In the present study, the swirling flow in a helical graft was hypothesized to have beneficial influences on a disturbed flow structure such as stenotic flow. The characteristics of swirling flows generated by helical tubes with various helical pitches and curvatures were investigated to prove the hypothesis. The fluid dynamic influences of these helical tubes on stenotic flow were quantitatively analysed by using a particle image velocimetry technique. Results showed that the swirling intensity and helicity of the swirling flow have a linear relation with a modified Germano number (Gn*) of the helical pipe. In addition, the swirling flow generated a beneficial flow structure at the stenosis by reducing the size of the recirculation flow under steady and pulsatile flow conditions. Therefore, the beneficial effects of a helical graft on the flow field can be estimated by using the magnitude of Gn*. Finally, an optimized helical design with a maximum Gn* was suggested for the future design of a vascular graft. PMID:25360705

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.

Probing magnetic helicity with synchrotron radiation and Faraday rotation

NASA Astrophysics Data System (ADS)

Oppermann, N.; Junklewitz, H.; Robbers, G.; Enßlin, T. A.

2011-06-01

We present a first application of the recently proposed LITMUS test for magnetic helicity, as well as a thorough study of its applicability under different circumstances. In order to apply this test to the galactic magnetic field, the newly developed critical filter formalism is used to produce an all-sky map of the Faraday depth. The test does not detect helicity in the galactic magnetic field. To understand the significance of this finding, we made an applicability study, showing that a definite conclusion about the absence of magnetic helicity in the galactic field has not yet been reached. This study is conducted by applying the test to simulated observational data. We consider simulations in a flat sky approximation and all-sky simulations, both with assumptions of constant electron densities and realistic distributions of thermal and cosmic ray electrons. Our results suggest that the LITMUS test does indeed perform very well in cases where constant electron densities can be assumed, both in the flat-sky limit and in the galactic setting. Non-trivial distributions of thermal and cosmic ray electrons, however, may complicate the scenario to the point where helicity in the magnetic field can escape detection.

Low edge safety factor operation and passive disruption avoidance in current carrying plasmas by the addition of stellarator rotational transform

NASA Astrophysics Data System (ADS)

Pandya, M. D.; ArchMiller, M. C.; Cianciosa, M. R.; Ennis, D. A.; Hanson, J. D.; Hartwell, G. J.; Hebert, J. D.; Herfindal, J. L.; Knowlton, S. F.; Ma, X.; Massidda, S.; Maurer, D. A.; Roberds, N. A.; Traverso, P. J.

2015-11-01

Low edge safety factor operation at a value less than two ( q (a )=1 /ι̷tot(a )<2 ) is routine on the Compact Toroidal Hybrid device with the addition of sufficient external rotational transform. Presently, the operational space of this current carrying stellarator extends down to q (a )=1.2 without significant n = 1 kink mode activity after the initial plasma current rise phase of the discharge. The disruption dynamics of these low edge safety factor plasmas depend upon the fraction of helical field rotational transform from external stellarator coils to that generated by the plasma current. We observe that with approximately 10% of the total rotational transform supplied by the stellarator coils, low edge q disruptions are passively suppressed and avoided even though q(a) < 2. When the plasma does disrupt, the instability precursors measured and implicated as the cause are internal tearing modes with poloidal, m, and toroidal, n, helical mode numbers of m /n =3 /2 and 4/3 observed on external magnetic sensors and m /n =1 /1 activity observed on core soft x-ray emissivity measurements. Even though the edge safety factor passes through and becomes much less than q(a) < 2, external n = 1 kink mode activity does not appear to play a significant role in the disruption phenomenology observed.

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

The monomeric, tetrameric, and fibrillar organization of Fib: the dynamic building block of the bacterial linear motor of Spiroplasma melliferum BC3.

PubMed

Cohen-Krausz, Sara; Cabahug, Pamela C; Trachtenberg, Shlomo

2011-07-08

Spiroplasmas belong to the class Mollicutes, representing the minimal, free-living, and self-replicating forms of life. Spiroplasmas are helical wall-less bacteria and the only ones known to swim by means of a linear motor (rather than the near-universal rotary bacterial motor). The linear motor follows the shortest path along the cell's helical membranal tube. The motor is composed of a flat monolayered ribbon of seven parallel fibrils and is believed to function in controlling cell helicity and motility through dynamic, coordinated, differential length changes in the fibrils. The latter cause local perturbations of helical symmetry, which are essential for net directional displacement in environments with a low Reynolds number. The underlying fibrils' core building block is a circular tetramer of the 59-kDa protein Fib. The fibrils' differential length changes are believed to be driven by molecular switching of Fib, leading consequently to axial ratio and length changes in tetrameric rings. Using cryo electron microscopy, diffractometry, single-particle analysis of isolated ribbons, and sequence analyses of Fib, we determined the overall molecular organization of the Fib monomer, tetramer, fibril, and linear motor of Spiroplasma melliferum BC3 that underlies cell geometry and motility. Fib appears to be a bidomained molecule, of which the N-terminal half is apparently a globular phosphorylase. By a combination of reversible rotation and diagonal shift of Fib monomers, the tetramer adopts either a cross-like nonhanded conformation or a ring-like handed conformation. The sense of Fib rotation may determine the handedness of the linear motor and, eventually, of the cell. A further change in the axial ratio of the ring-like tetramers controls fibril lengths and the consequent helical geometry. Analysis of tetramer quadrants from adjacent fibrils clearly demonstrates local differential fibril lengths. Copyright © 2011 Elsevier Ltd. All rights reserved.

The six degrees of freedom motion of the human head, spine, and pelvis in a frontal impact.

PubMed

Lopez-Valdes, F J; Riley, P O; Lessley, D J; Arbogast, K B; Seacrist, T; Balasubramanian, S; Maltese, M; Kent, R

2014-01-01

The goal of this study is to characterize the in situ 6-degree-of-freedom kinematics of the head, 3 vertebrae (T1, T8, and L2), and the pelvis in a 40 km/h frontal impact. Three postmortem human surrogates (PMHS) were exposed to a deceleration of 15 g over 125 ms and the motion of selected anatomical structures (head, T1, T8, L2, and pelvis) was tracked at 1000 Hz using an optoelectric stereophotogrammetric system. Displacements of the analyzed structures are reported in the sagittal and the transverse planes. Rotations of the structures are described using the finite helical axis of the motion. Anterior displacements were 530.5 ± 39.4 mm (head), 434.7 ± 20.0 mm (T1), 353.3 ± 29.6 mm (T8), 219.9 ± 19.3 mm (L2), and 78.9 ± 22.1 mm (pelvis). The ratio between peak anterior and lateral displacement was up to 19 percent (T1) and 26 percent (head). Magnitudes of the rotation of the head (69.9 ± 1.5°), lumbar (66.5 ± 9.1°), and pelvis (63.8 ± 11.8°) were greater than that of the thoracic vertebrae (T1: 49.1 ± 7.8°; T8: 47.7 ± 6.3°). Thoracic vertebrae exhibited a complex rotation behavior caused by the asymmetric loading of the shoulder belt. Rotation of the lumbar vertebra and pelvis occurred primarily within the sagittal plane (flexion). Despite the predominance of the sagittal motion of the occupant in a pure (12 o'clock) frontal impact, the asymmetry of belt loading induced other relevant displacements and rotations of the head and thoracic spine. Attempts to model occupant kinematics in a frontal impact should consider these results to biofidelically describe the interaction of the torso with the belt.

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.

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.

Transitions in rapidly rotating convection dynamos

NASA Astrophysics Data System (ADS)

Tilgner, A.

2013-12-01

It is commonly assumed that buoyancy in the fluid core powers the geodynamo. We study here the minimal model of a convection driven dynamo, which is a horizontal plane layer in a gravity field, filled with electrically conducting fluid, heated from below and cooled from above, and rotating about a vertical axis. Such a plane layer may be viewed as a local approximation to the geophysically more relevant spherical geometry. The numerical simulations have been run on graphics processing units with at least 960 cores. If the convection is driven stronger and stronger at fixed rotation rate, the flow behaves at some point as if it was not rotating. This transition shows in the scaling of the heat transport which can be used to distinguish slow from rapid rotation. One expects dynamos to behave differently in these two flow regimes. But even within the convection flows which are rapidly rotating according to this criterion, it will be shown that different types of dynamos exist. In one state, the magnetic field strength obeys a scaling indicative of a magnetostrophic balance, in which the Lorentz force is in equilibrium with the Coriolis force. The flow in this case is helical. A different state exists at higher magnetic Reynolds numbers, in which the magnetic energy obeys a different scaling law and the helicity of the flow is much reduced. As one increases the Rayleigh number, all other parameters kept constant, one may find both types of dynamos separated by an interval of Rayleigh numbers in which there are no dynamos at all. The effect of these transitions on energy dissipation and mean field generation have also been studied.

Ab initio modeling of CW-ESR spectra of the double spin labeled peptide Fmoc-(Aib-Aib-TOAC)2-Aib-OMe in acetonitrile.

PubMed

Zerbetto, Mirco; Carlotto, Silvia; Polimeno, Antonino; Corvaja, Carlo; Franco, Lorenzo; Toniolo, Claudio; Formaggio, Fernando; Barone, Vincenzo; Cimino, Paola

2007-03-15

In this work we address the interpretation, via an ab initio integrated computational approach, of the CW-ESR spectra of the double spin labeled, 310-helical, peptide Fmoc-(Aib-Aib-TOAC)2-Aib-OMe dissolved in acetonitrile. Our approach is based on the determination of geometric and local magnetic parameters of the heptapeptide by quantum mechanical density functional calculations taking into account solvent and, when needed, vibrational averaging contributions. The system is then described by a stochastic Liouville equation for the two electron spins interacting with each other and with two 14N nuclear spins, in the presence of diffusive rotational dynamics. Parametrization of the diffusion rotational tensor is provided by a hydrodynamic model. CW-ESR spectra are simulated with minimal resorting to fitting procedures, proving that the combination of sensitive ESR spectroscopy and sophisticated modeling can be highly helpful in providing 3D structural and dynamic information on molecular systems.

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.

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.

Rotational multispectral fluorescence lifetime imaging and intravascular ultrasound: bimodal system for intravascular applications

PubMed Central

Ma, Dinglong; Bec, Julien; Yankelevich, Diego R.; Gorpas, Dimitris; Fatakdawala, Hussain; Marcu, Laura

2014-01-01

Abstract. We report the development and validation of a hybrid intravascular diagnostic system combining multispectral fluorescence lifetime imaging (FLIm) and intravascular ultrasound (IVUS) for cardiovascular imaging applications. A prototype FLIm system based on fluorescence pulse sampling technique providing information on artery biochemical composition was integrated with a commercial IVUS system providing information on artery morphology. A customized 3-Fr bimodal catheter combining a rotational side-view fiberoptic and a 40-MHz IVUS transducer was constructed for sequential helical scanning (rotation and pullback) of tubular structures. Validation of this bimodal approach was conducted in pig heart coronary arteries. Spatial resolution, fluorescence detection efficiency, pulse broadening effect, and lifetime measurement variability of the FLIm system were systematically evaluated. Current results show that this system is capable of temporarily resolving the fluorescence emission simultaneously in multiple spectral channels in a single pullback sequence. Accurate measurements of fluorescence decay characteristics from arterial segments can be obtained rapidly (e.g., 20 mm in 5 s), and accurate co-registration of fluorescence and ultrasound features can be achieved. The current finding demonstrates the compatibility of FLIm instrumentation with in vivo clinical investigations and its potential to complement conventional IVUS during catheterization procedures. PMID:24898604

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.

Shear load transfer in high and low stress tendons.

PubMed

Kondratko-Mittnacht, Jaclyn; Duenwald-Kuehl, Sarah; Lakes, Roderic; Vanderby, Ray

2015-05-01

Tendon is an integral part of joint movement and stability, as it functions to transmit load from muscle to bone. It has an anisotropic, fibrous hierarchical structure that is generally loaded in the direction of its fibers/fascicles. Internal load distributions are altered when joint motion rotates an insertion site or when local damage disrupts fibers/fascicles, potentially causing inter-fiber (or inter-fascicular) shear. Tendons with different microstructures (helical versus linear) may redistribute loads differently. This study explored how shear redistributes axial loads in rat tail tendon (low stress tendons with linear microstructure) and porcine flexor tendon (high stress with helical microstructure) by creating lacerations on opposite sides of the tendon, ranging from about 20% to 60% of the tendon width, to create various magnitudes of shear. Differences in fascicular orientation were quantified using polarized light microscopy. Unexpectedly, both tendon types maintained about 20% of pre-laceration stress values after overlapping cuts of 60% of tendon width (no intact fibers end to end) suggesting that shear stress transfer can contribute more to overall tendon strength and stiffness than previously reported. All structural parameters for both tendon types decreased linearly with increasing laceration depth. The tail tendon had a more rapid decline in post-laceration elastic stress and modulus parameters as well as a more linear and less tightly packed fascicular structure, suggesting that positional tendons may be less well suited to redistribute loads via a shear mechanism. Copyright © 2015 Elsevier Ltd. All rights reserved.

Shear Load Transfer in High and Low Stress Tendons

PubMed Central

Kondratko-Mittnacht, Jaclyn; Duenwald-Kuehl, Sarah; Lakes, Roderic; Vanderby, Ray

2016-01-01

Background Tendon is an integral part of joint movement and stability, as it functions to transmit load from muscle to bone. It has an anisotropic, fibrous hierarchical structure that is generally loaded in the direction of its fibers/fascicles. Internal load distributions are altered when joint motion rotates an insertion site or when local damage disrupts fibers/fascicles, potentially causing inter-fiber (or inter-fascicular) shear. Tendons with different microstructure (helical versus linear) may redistribute loads differently. Method of Approach This study explored how shear redistributes axial loads in rat tail tendon (low stress tendons with linear microstructure) and porcine flexor tendon (high stress with helical microstructure) by creating lacerations on opposite sides of the tendon, ranging from about 20-60% of the tendon width, to create various magnitudes of shear. Differences in fascicular orientation were quantified using polarized light microscopy. Results and Conclusions Unexpectedly, both tendon types maintained about 20% of pre-laceration stress values after overlapping cuts of 60% of tendon width (no intact fibers end to end) suggesting that shear stress transfer can contribute more to overall tendon strength and stiffness than previously reported. All structural parameters for both tendon types decreased linearly with increasing laceration depth. The tail tendon had a more rapid decline in post-laceration elastic stress and modulus parameters as well as a more linear and less tightly packed fascicular structure, suggesting that positional tendons may be less well suited to redistribute loads via a shear mechanism. PMID:25700261

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.

Double acting stirling engine phase control

DOEpatents

Berchowitz, David M.

1983-01-01

A mechanical device for effecting a phase change between the expansion and compression volumes of a double-acting Stirling engine uses helical elements which produce opposite rotation of a pair of crankpins when a control rod is moved, so the phase between two pairs of pistons is changed by +.psi. and the phase between the other two pairs of pistons is changed by -.psi.. The phase can change beyond .psi.=90.degree. at which regenerative braking and then reversal of engine rotation occurs.

Eigenvalue problems for Beltrami fields arising in a three-dimensional toroidal magnetohydrodynamic equilibrium problem

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

Hudson, S. R.; Hole, M. J.; Dewar, R. L.

2007-05-15

A generalized energy principle for finite-pressure, toroidal magnetohydrodynamic (MHD) equilibria in general three-dimensional configurations is proposed. The full set of ideal-MHD constraints is applied only on a discrete set of toroidal magnetic surfaces (invariant tori), which act as barriers against leakage of magnetic flux, helicity, and pressure through chaotic field-line transport. It is argued that a necessary condition for such invariant tori to exist is that they have fixed, irrational rotational transforms. In the toroidal domains bounded by these surfaces, full Taylor relaxation is assumed, thus leading to Beltrami fields {nabla}xB={lambda}B, where {lambda} is constant within each domain. Two distinctmore » eigenvalue problems for {lambda} arise in this formulation, depending on whether fluxes and helicity are fixed, or boundary rotational transforms. These are studied in cylindrical geometry and in a three-dimensional toroidal region of annular cross section. In the latter case, an application of a residue criterion is used to determine the threshold for connected chaos.« less

Cam-Operated Pitch-Change Apparatus

NASA Technical Reports Server (NTRS)

Barnes, P. E. (Inventor)

1978-01-01

A pitch-change apparatus for a ducted thrust fan having a plurality of variable pitch blades employs a camming ring mounted coaxially at the hub at an axially fixed station along the hub axis for rotation about the hub axis both with the blades and relative to the blades. The ring has a generally spherical outer periphery and a plurality of helical camming grooves extending in a generally spherical plane on the periphery. Each of the variable pitch blades is connected to a pitch-change horn having a cam follower mounted on its outer end, and the camming ring and the horns are so arranged about the hub axis that the plurality of followers on the horns engage respectively the plurality of helical camming grooves. Rotary drive means rotates the camming ring relative to the blades to cause blade pitch to be changed through the cooperative operation of the camming grooves on the ring and the cam followers on the pitch-change horns.

Hydrodynamics of bacteriophages

NASA Astrophysics Data System (ADS)

Katsamba, Panayiota; Lauga, Eric

2017-11-01

Bacteriophage viruses, one of the most abundant entities in our planet, lack the ability to move independently. Instead, they crowd fluid environments in anticipation of a random encounter with bacteria. Once they 'land' on their victim's surface, they eject their genetic material inside the host cell. A big fraction of phage species, however, first attach to the flagella of bacteria. Being immotile, these so-called flagellotropic phages still manage to reach the cell body for infection, and the process by which they move up the flagellum has intrigued the scientific community for over four decades. In 1973 Berg and Anderson proposed the nut-and-bolt mechanism in which, just like a nut being rotated moves along a bolt, the phage wraps itself around a flagellum possessing helical grooves (due to the helical rows of flagellin molecules) and exploits the rotation of the flagellum in order to passively travel along it. We provide here a first-principle theoretical model for this nut-and-bolt mechanism and show that it is able to predict experiment observations.

Multi-region relaxed magnetohydrodynamics in plasmas with slowly changing boundaries -- Resonant response of a plasma slab

DOE PAGES

Dewar, R. L.; Hudson, S. R.; Bhattacharjee, A.; ...

2017-04-03

The adiabatic limit of a recently proposed dynamical extension of Taylor relaxation, multi-region relaxed magnetohydrodynamics (MRxMHD), is summarized, with special attention to the appropriate definition of a relative magnetic helicity. The formalism is illustrated using a simple two-region, sheared-magnetic-field model similar to the Hahm-Kulsrud-Taylor (HKT) rippled-boundary slab model. In MRxMHD, a linear Grad-Shafranov equation applies, even at finite ripple amplitude. The adiabatic switching on of boundary ripple excites a shielding current sheet opposing reconnection at a resonant surface. The perturbed magnetic field as a function of ripple amplitude is calculated by invoking the conservation of magnetic helicity in the twomore » regions separated by the current sheet. Here, at low ripple amplitude, "half islands" appear on each side of the current sheet, locking the rotational transform at the resonant value. Beyond a critical amplitude, these islands disappear and the rotational transform develops a discontinuity across the current sheet. Published by AIP Publishing.« less

Multi-region relaxed magnetohydrodynamics in plasmas with slowly changing boundaries -- Resonant response of a plasma slab

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

Dewar, R. L.; Hudson, S. R.; Bhattacharjee, A.

The adiabatic limit of a recently proposed dynamical extension of Taylor relaxation, multi-region relaxed magnetohydrodynamics (MRxMHD), is summarized, with special attention to the appropriate definition of a relative magnetic helicity. The formalism is illustrated using a simple two-region, sheared-magnetic-field model similar to the Hahm-Kulsrud-Taylor (HKT) rippled-boundary slab model. In MRxMHD, a linear Grad-Shafranov equation applies, even at finite ripple amplitude. The adiabatic switching on of boundary ripple excites a shielding current sheet opposing reconnection at a resonant surface. The perturbed magnetic field as a function of ripple amplitude is calculated by invoking the conservation of magnetic helicity in the twomore » regions separated by the current sheet. Here, at low ripple amplitude, "half islands" appear on each side of the current sheet, locking the rotational transform at the resonant value. Beyond a critical amplitude, these islands disappear and the rotational transform develops a discontinuity across the current sheet. Published by AIP Publishing.« less

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

Pivotal role of extended linker 2 in the activation of Gα by G protein-coupled receptor.

PubMed

Huang, Jianyun; Sun, Yutong; Zhang, J Jillian; Huang, Xin-Yun

2015-01-02

G protein-coupled receptors (GPCRs) relay extracellular signals mainly to heterotrimeric G-proteins (Gαβγ) and they are the most successful drug targets. The mechanisms of G-protein activation by GPCRs are not well understood. Previous studies have revealed a signal relay route from a GPCR via the C-terminal α5-helix of Gα to the guanine nucleotide-binding pocket. Recent structural and biophysical studies uncover a role for the opening or rotating of the α-helical domain of Gα during the activation of Gα by a GPCR. Here we show that β-adrenergic receptors activate eight Gαs mutant proteins (from a screen of 66 Gαs mutants) that are unable to bind Gβγ subunits in cells. Five of these eight mutants are in the αF/Linker 2/β2 hinge region (extended Linker 2) that connects the Ras-like GTPase domain and the α-helical domain of Gαs. This extended Linker 2 is the target site of a natural product inhibitor of Gq. Our data show that the extended Linker 2 is critical for Gα activation by GPCRs. We propose that a GPCR via its intracellular loop 2 directly interacts with the β2/β3 loop of Gα to communicate to Linker 2, resulting in the opening and closing of the α-helical domain and the release of GDP during G-protein activation. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Ultrasonic rotary-hammer drill

NASA Technical Reports Server (NTRS)

Bar-Cohen, Yoseph (Inventor); Badescu, Mircea (Inventor); Sherrit, Stewart (Inventor); Kassab, Steve (Inventor); Bao, Xiaoqi (Inventor)

2010-01-01

A mechanism for drilling or coring by a combination of sonic hammering and rotation. The drill includes a hammering section with a set of preload weights mounted atop a hammering actuator and an axial passage through the hammering section. In addition, a rotary section includes a motor coupled to a drive shaft that traverses the axial passage through the hammering section. A drill bit is coupled to the drive shaft for drilling by a combination of sonic hammering and rotation. The drill bit includes a fluted shaft leading to a distal crown cutter with teeth. The bit penetrates sampled media by repeated hammering action. In addition, the bit is rotated. As it rotates the fluted bit carries powdered cuttings helically upward along the side of the bit to the surface.

Advanced methods for controlling untethered magnetic devices using rotating magnetic fields

NASA Astrophysics Data System (ADS)

Mahoney, Arthur W., Jr.

This dissertation presents results documenting advancements on the control of untethered magnetic devices, such as magnetic "microrobots" and magnetically actuated capsule endoscopes, motivated by problems in minimally invasive medicine. This dissertation focuses on applying rotating magnetic fields for magnetic manipulation. The contributions include advancements in the way that helical microswimmers (devices that mimic the propulsion of bacterial flagella) are controlled in the presence of gravitational forces, advancements in ways that groups of untethered magnetic devices can be differentiated and semi-independently controlled, advancements in the way that untethered magnetic device can be controlled with a single rotating permanent magnet, and an improved understanding in the nature of the magnetic force applied to an untethered device by a rotating magnet.

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.

Metering Wheel-Wire Track Wire Boom Deployment Mechanism

NASA Technical Reports Server (NTRS)

Granoff, Mark S.

2014-01-01

The NASA MMS Spin Plane Double Probe (SDP) Deployer utilizes a helical path, rotating Metering Wheel and a spring loaded Wire "Holding" Track to pay out a "fixed end" 57 meter x 1.5 mm diameter Wire Boom stored between concentric storage cylinders. Unlike rotating spool type storage devices, the storage cylinders remain stationary, and the boom wire is uncoiled along the length of the cylinder via the rotation of the Metering Wheel. This uncoiling action avoids the need for slip-ring contacts since the ends of the wire can remain stationary. Conventional fixed electrical connectors (Micro-D type) are used to terminate to operational electronics.

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.

Apparatus and methods for cooling and sealing rotary helical screw compressors

DOEpatents

Fresco, A.N.

1997-08-05

In a compression system which incorporates a rotary helical screw compressor, and for any type of gas or refrigerant, the working liquid oil is atomized through nozzles suspended in, and parallel to, the suction gas flow, or alternatively the nozzles are mounted on the suction piping. In either case, the aim is to create positively a homogeneous mixture of oil droplets to maximize the effectiveness of the working liquid oil in improving the isothermal and volumetric efficiencies. The oil stream to be atomized may first be degassed at compressor discharge pressure by heating within a pressure vessel and recovering the energy added by using the outgoing oil stream to heat the incoming oil stream. The stripped gas is typically returned to the compressor discharge flow. In the preferred case, the compressor rotors both contain a hollow cavity through which working liquid oil is injected into channels along the edges of the rotors, thereby forming a continuous and positive seal between the rotor edges and the compressor casing. In the alternative method, working liquid oil is injected either in the same direction as the rotor rotation or counter to rotor rotation through channels in the compressor casing which are tangential to the rotor edges and parallel to the rotor center lines or alternatively the channel paths coincide with the helical path of the rotor edges. 14 figs.

Apparatus and methods for cooling and sealing rotary helical screw compressors

DOEpatents

Fresco, Anthony N.

1997-01-01

In a compression system which incorporates a rotary helical screw compressor, and for any type of gas or refrigerant, the working liquid oil is atomized through nozzles suspended in, and parallel to, the suction gas flow, or alternatively the nozzles are mounted on the suction piping. In either case, the aim is to create positively a homogeneous mixture of oil droplets to maximize the effectiveness of the working liquid oil in improving the isothermal and volumetric efficiencies. The oil stream to be atomized may first be degassed at compressor discharge pressure by heating within a pressure vessel and recovering the energy added by using the outgoing oil stream to heat the incoming oil stream. The stripped gas is typically returned to the compressor discharge flow. In the preferred case, the compressor rotors both contain a hollow cavity through which working liquid oil is injected into channels along the edges of the rotors, thereby forming a continuous and positive seal between the rotor edges and the compressor casing. In the alternative method, working liquid oil is injected either in the same direction as the rotor rotation or counter to rotor rotation through channels in the compressor casing which are tangential to the rotor edges and parallel to the rotor centerlines or alternatively the channel paths coincide with the helical path of the rotor edges.

Giant Faraday effect due to Pauli exclusion principle in 3D topological insulators.

PubMed

Paudel, Hari P; Leuenberger, Michael N

2014-02-26

Experiments using ARPES, which is based on the photoelectric effect, show that the surface states in 3D topological insulators (TI) are helical. Here we consider Weyl interface fermions due to band inversion in narrow-bandgap semiconductors, such as Pb1-xSnxTe. The positive and negative energy solutions can be identified by means of opposite helicity in terms of the spin helicity operator in 3D TI as ĥ(TI) = (1/ |p|_ |) β (σ|_ x p|_ ) · z^, where β is a Dirac matrix and z^ points perpendicular to the interface. Using the 3D Dirac equation and bandstructure calculations we show that the transitions between positive and negative energy solutions, giving rise to electron-hole pairs, obey strict optical selection rules. In order to demonstrate the consequences of these selection rules, we consider the Faraday effect due to the Pauli exclusion principle in a pump-probe setup using a 3D TI double interface of a PbTe/Pb₀.₃₁Sn₀.₆₉Te/PbTe heterostructure. For that we calculate the optical conductivity tensor of this heterostructure, which we use to solve Maxwell's equations. The Faraday rotation angle exhibits oscillations as a function of probe wavelength and thickness of the heterostructure. The maxima in the Faraday rotation angle are of the order of mrds.

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.

Dual lead-crowning for helical gears with anti-twist tooth flanks on the internal gear honing machine

NASA Astrophysics Data System (ADS)

Tran, Van-Quyet; Wu, Yu-Ren

2017-12-01

For some specific purposes, a helical gear with wide face-width is applied for meshing with two other gears simultaneously, such as the idle pinions in the vehicle differential. However, due to the fact of gear deformation, the tooth edge contact and stress concentration might occur. Single lead-crowning is no more suitable for such a case to get the appropriate position of contact pattern and improve the load distribution on tooth surfaces. Therefore, a novel *Email: method is proposed in this paper to achieve the wide-face-width helical gears with the dual lead-crowned and the anti-twisted tooth surfaces by controlling the swivel angle and the rotation angle of the honing wheel respectively on an internal gear honing machine. Numerical examples are practiced to illustrate and verified the merits of the proposed method.

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.

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.

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.

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).

Assembly of mesoscale helices with near-unity enantiomeric excess and light-matter interactions for chiral semiconductors.

PubMed

Feng, Wenchun; Kim, Ji-Young; Wang, Xinzhi; Calcaterra, Heather A; Qu, Zhibei; Meshi, Louisa; Kotov, Nicholas A

2017-03-01

Semiconductors with chiral geometries at the nanoscale and mesoscale provide a rich materials platform for polarization optics, photocatalysis, and biomimetics. Unlike metallic and organic optical materials, the relationship between the geometry of chiral semiconductors and their chiroptical properties remains, however, vague. Homochiral ensembles of semiconductor helices with defined geometries open the road to understanding complex relationships between geometrical parameters and chiroptical properties of semiconductor materials. We show that semiconductor helices can be prepared with an absolute yield of ca 0.1% and an enantiomeric excess (e.e.) of 98% or above from cysteine-stabilized cadmium telluride nanoparticles (CdTe NPs) dispersed in methanol. This high e.e. for a spontaneously occurring chemical process is attributed to chiral self-sorting based on the thermodynamic preference of NPs to assemble with those of the same handedness. The dispersions of homochiral self-assembled helices display broadband visible and near-infrared (Vis-NIR) polarization rotation with anisotropy ( g ) factors approaching 0.01. Calculated circular dichroism (CD) spectra accurately reproduced experimental CD spectra and gave experimentally validated spectral predictions for different geometrical parameters enabling de novo design of chiroptical semiconductor materials. Unlike metallic, ceramic, and polymeric helices that serve predominantly as scatterers, chiroptical properties of semiconductor helices have nearly equal contribution of light absorption and scattering, which is essential for device-oriented, field-driven light modulation. Deconstruction of a helix into a series of nanorods provides a simple model for the light-matter interaction and chiroptical activity of helices. This study creates a framework for further development of polarization-based optics toward biomedical applications, telecommunications, and hyperspectral imaging.

A refined technique to calculate finite helical axes from rigid body trackers.

PubMed

McLachlin, Stewart D; Ferreira, Louis M; Dunning, Cynthia E

2014-12-01

Finite helical axes (FHAs) are a potentially effective tool for joint kinematic analysis. Unfortunately, no straightforward guidelines exist for calculating accurate FHAs using prepackaged six degree-of-freedom (6 DOF) rigid body trackers. Thus, this study aimed to: (1) describe a protocol for calculating FHA parameters from 6 DOF rigid body trackers using the screw matrix and (2) to maximize the number of accurate FHAs generated from a given data set using a moving window analysis. Four Optotrak® Smart Markers were used as the rigid body trackers, two moving and two fixed, at different distances from the hinge joint of a custom-machined jig. 6D OF pose information was generated from 51 static positions of the jig rotated and fixed in 0.5 deg increments up to 25 deg. Output metrics included the FHA direction cosines, the rotation about the FHA, the translation along the axis, and the intercept of the FHA with the plane normal to the jig's hinge joint. FHA metrics were calculated using the relative tracker rotation from the starting position, and using a moving window analysis to define a minimum acceptable rotational displacement between the moving tracker data points. Data analysis found all FHA rotations calculated from the starting position were within 0.15 deg of the prescribed jig rotation. FHA intercepts were most stable when determined using trackers closest to the hinge axis. Increasing the moving window size improved the FHA direction cosines and center of rotation accuracy. Window sizes larger than 2 deg had an intercept deviation of less than 1 mm. Furthermore, compared to the 0 deg window size, the 2 deg window had a 90% improvement in FHA intercept precision while generating almost an equivalent number of FHA axes. This work identified a solution to improve FHA calculations for biomechanical researchers looking to describe changes in 3D joint motion.

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.

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.

Helical paths, gravitaxis, and separation phenomena for mass-anisotropic self-propelling colloids: Experiment versus theory

NASA Astrophysics Data System (ADS)

Campbell, Andrew I.; Wittkowski, Raphael; ten Hagen, Borge; Löwen, Hartmut; Ebbens, Stephen J.

2017-08-01

The self-propulsion mechanism of active colloidal particles often generates not only translational but also rotational motion. For particles with an anisotropic mass density under gravity, the motion is usually influenced by a downwards oriented force and an aligning torque. Here we study the trajectories of self-propelled bottom-heavy Janus particles in three spatial dimensions both in experiments and by theory. For a sufficiently large mass anisotropy, the particles typically move along helical trajectories whose axis is oriented either parallel or antiparallel to the direction of gravity (i.e., they show gravitaxis). In contrast, if the mass anisotropy is small and rotational diffusion is dominant, gravitational alignment of the trajectories is not possible. Furthermore, the trajectories depend on the angular self-propulsion velocity of the particles. If this component of the active motion is strong and rotates the direction of translational self-propulsion of the particles, their trajectories have many loops, whereas elongated swimming paths occur if the angular self-propulsion is weak. We show that the observed gravitational alignment mechanism and the dependence of the trajectory shape on the angular self-propulsion can be used to separate active colloidal particles with respect to their mass anisotropy and angular self-propulsion, respectively.

The principal motions involved in the coupling mechanism of the recovery stroke of the myosin motor

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

Mesentean, Sidonia; Koppole, Sampath; Smith, Jeremy C

2006-12-01

Muscle contraction is driven by a cycle of conformational changes in the myosin II head. After myosin binds ATP and releases from the actin fibril, myosin prepares for the next power stroke by rotating back the converter domain that carries the lever arm by {approx}60 degrees. This recovery stroke is coupled to the activation of myosin's ATPase by a mechanism that is essential for an efficient motor cycle. The mechanics of this coupling have been proposed to occur via two distinct and successive motions of the two helices that hold the converter domain: in a first phase a see-saw motionmore » of the relay helix, followed by a piston/seesaw motion of the SH1 helix in a second phase. To test this model, we have determined the principal motions of these structural elements during equilibrium molecular dynamics simulations of the crystallographic end states of the recovery stroke by using Principal Component Analysis. This reveals that the only principal motions of these two helices that make a large amplitude contribution towards the conformational change of the recovery stroke are indeed the predicted seesaw and piston motions.« less

Characterization of local motions in proteins detected by nuclear magnetic resonance relaxation studies

NASA Astrophysics Data System (ADS)

Fischer, Mark William Frederick

1998-08-01

The study of protein structure and function is incomplete without an understanding of protein dynamics. We use nuclear magnetic resonance (NMR) relaxation studies to probe pico and nano second dynamics in E. coli flavodoxin, measuring both 15N and 13C/sp/prime relaxation. Observing poor correlation between the generalized order parameters, S2, for the N-NH and C'-Cα vectors in this nearly spherical molecule, we conclude that local or semi-local anisotropic motions are present. A new experiment is introduced from which the cross correlation, Rcc, between the carbonyl chemical shift anisotropy relaxation and the C'- Cα dipole-dipole relaxation is obtained. Theoretical modeling of the behavior of S2 N- NH,/ S2C/sp/prime-C/sb[α], and Rcc under specific anisotropic motions allows the construction of motional restriction maps. Analyzing our experimental data in terms of these motional maps allows for the identification of local motions which might otherwise have gone undetected and, more importantly, allows for the nature of the motions to be characterized. This is demonstrated for several helices of flavodoxin which appear to be executing concerted limited rotations about their helical axes.

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.

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.

Volumetric CT with sparse detector arrays (and application to Si-strip photon counters).

PubMed

Sisniega, A; Zbijewski, W; Stayman, J W; Xu, J; Taguchi, K; Fredenberg, E; Lundqvist, Mats; Siewerdsen, J H

2016-01-07

Novel x-ray medical imaging sensors, such as photon counting detectors (PCDs) and large area CCD and CMOS cameras can involve irregular and/or sparse sampling of the detector plane. Application of such detectors to CT involves undersampling that is markedly different from the commonly considered case of sparse angular sampling. This work investigates volumetric sampling in CT systems incorporating sparsely sampled detectors with axial and helical scan orbits and evaluates performance of model-based image reconstruction (MBIR) with spatially varying regularization in mitigating artifacts due to sparse detector sampling. Volumetric metrics of sampling density and uniformity were introduced. Penalized-likelihood MBIR with a spatially varying penalty that homogenized resolution by accounting for variations in local sampling density (i.e. detector gaps) was evaluated. The proposed methodology was tested in simulations and on an imaging bench based on a Si-strip PCD (total area 5 cm  ×  25 cm) consisting of an arrangement of line sensors separated by gaps of up to 2.5 mm. The bench was equipped with translation/rotation stages allowing a variety of scanning trajectories, ranging from a simple axial acquisition to helical scans with variable pitch. Statistical (spherical clutter) and anthropomorphic (hand) phantoms were considered. Image quality was compared to that obtained with a conventional uniform penalty in terms of structural similarity index (SSIM), image uniformity, spatial resolution, contrast, and noise. Scan trajectories with intermediate helical width (~10 mm longitudinal distance per 360° rotation) demonstrated optimal tradeoff between the average sampling density and the homogeneity of sampling throughout the volume. For a scan trajectory with 10.8 mm helical width, the spatially varying penalty resulted in significant visual reduction of sampling artifacts, confirmed by a 10% reduction in minimum SSIM (from 0.88 to 0.8) and a 40% reduction in the dispersion of SSIM in the volume compared to the constant penalty (both penalties applied at optimal regularization strength). Images of the spherical clutter and wrist phantoms confirmed the advantages of the spatially varying penalty, showing a 25% improvement in image uniformity and 1.8  ×  higher CNR (at matched spatial resolution) compared to the constant penalty. The studies elucidate the relationship between sampling in the detector plane, acquisition orbit, sampling of the reconstructed volume, and the resulting image quality. They also demonstrate the benefit of spatially varying regularization in MBIR for scenarios with irregular sampling patterns. Such findings are important and integral to the incorporation of a sparsely sampled Si-strip PCD in CT imaging.

Volumetric CT with sparse detector arrays (and application to Si-strip photon counters)

NASA Astrophysics Data System (ADS)

Sisniega, A.; Zbijewski, W.; Stayman, J. W.; Xu, J.; Taguchi, K.; Fredenberg, E.; Lundqvist, Mats; Siewerdsen, J. H.

2016-01-01

Novel x-ray medical imaging sensors, such as photon counting detectors (PCDs) and large area CCD and CMOS cameras can involve irregular and/or sparse sampling of the detector plane. Application of such detectors to CT involves undersampling that is markedly different from the commonly considered case of sparse angular sampling. This work investigates volumetric sampling in CT systems incorporating sparsely sampled detectors with axial and helical scan orbits and evaluates performance of model-based image reconstruction (MBIR) with spatially varying regularization in mitigating artifacts due to sparse detector sampling. Volumetric metrics of sampling density and uniformity were introduced. Penalized-likelihood MBIR with a spatially varying penalty that homogenized resolution by accounting for variations in local sampling density (i.e. detector gaps) was evaluated. The proposed methodology was tested in simulations and on an imaging bench based on a Si-strip PCD (total area 5 cm  ×  25 cm) consisting of an arrangement of line sensors separated by gaps of up to 2.5 mm. The bench was equipped with translation/rotation stages allowing a variety of scanning trajectories, ranging from a simple axial acquisition to helical scans with variable pitch. Statistical (spherical clutter) and anthropomorphic (hand) phantoms were considered. Image quality was compared to that obtained with a conventional uniform penalty in terms of structural similarity index (SSIM), image uniformity, spatial resolution, contrast, and noise. Scan trajectories with intermediate helical width (~10 mm longitudinal distance per 360° rotation) demonstrated optimal tradeoff between the average sampling density and the homogeneity of sampling throughout the volume. For a scan trajectory with 10.8 mm helical width, the spatially varying penalty resulted in significant visual reduction of sampling artifacts, confirmed by a 10% reduction in minimum SSIM (from 0.88 to 0.8) and a 40% reduction in the dispersion of SSIM in the volume compared to the constant penalty (both penalties applied at optimal regularization strength). Images of the spherical clutter and wrist phantoms confirmed the advantages of the spatially varying penalty, showing a 25% improvement in image uniformity and 1.8  ×  higher CNR (at matched spatial resolution) compared to the constant penalty. The studies elucidate the relationship between sampling in the detector plane, acquisition orbit, sampling of the reconstructed volume, and the resulting image quality. They also demonstrate the benefit of spatially varying regularization in MBIR for scenarios with irregular sampling patterns. Such findings are important and integral to the incorporation of a sparsely sampled Si-strip PCD in CT imaging.

Volumetric CT with sparse detector arrays (and application to Si-strip photon counters)

PubMed Central

Sisniega, A; Zbijewski, W; Stayman, J W; Xu, J; Taguchi, K; Fredenberg, E; Lundqvist, Mats; Siewerdsen, J H

2016-01-01

Novel x-ray medical imaging sensors, such as photon counting detectors (PCDs) and large area CCD and CMOS cameras can involve irregular and/or sparse sampling of the detector plane. Application of such detectors to CT involves undersampling that is markedly different from the commonly considered case of sparse angular sampling. This work investigates volumetric sampling in CT systems incorporating sparsely sampled detectors with axial and helical scan orbits and evaluates performance of model-based image reconstruction (MBIR) with spatially varying regularization in mitigating artifacts due to sparse detector sampling. Volumetric metrics of sampling density and uniformity were introduced. Penalized-likelihood MBIR with a spatially varying penalty that homogenized resolution by accounting for variations in local sampling density (i.e. detector gaps) was evaluated. The proposed methodology was tested in simulations and on an imaging bench based on a Si-strip PCD (total area 5 cm × 25 cm) consisting of an arrangement of line sensors separated by gaps of up to 2.5 mm. The bench was equipped with translation/rotation stages allowing a variety of scanning trajectories, ranging from a simple axial acquisition to helical scans with variable pitch. Statistical (spherical clutter) and anthropomorphic (hand) phantoms were considered. Image quality was compared to that obtained with a conventional uniform penalty in terms of structural similarity index (SSIM), image uniformity, spatial resolution, contrast, and noise. Scan trajectories with intermediate helical width (~10 mm longitudinal distance per 360° rotation) demonstrated optimal tradeoff between the average sampling density and the homogeneity of sampling throughout the volume. For a scan trajectory with 10.8 mm helical width, the spatially varying penalty resulted in significant visual reduction of sampling artifacts, confirmed by a 10% reduction in minimum SSIM (from 0.88 to 0.8) and a 40% reduction in the dispersion of SSIM in the volume compared to the constant penalty (both penalties applied at optimal regularization strength). Images of the spherical clutter and wrist phantoms confirmed the advantages of the spatially varying penalty, showing a 25% improvement in image uniformity and 1.8 × higher CNR (at matched spatial resolution) compared to the constant penalty. The studies elucidate the relationship between sampling in the detector plane, acquisition orbit, sampling of the reconstructed volume, and the resulting image quality. They also demonstrate the benefit of spatially varying regularization in MBIR for scenarios with irregular sampling patterns. Such findings are important and integral to the incorporation of a sparsely sampled Si-strip PCD in CT imaging. PMID:26611740

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.

Homochiral Evolution in Self-Assembled Chiral Polymers and Block Copolymers.

PubMed

Wen, Tao; Wang, Hsiao-Fang; Li, Ming-Chia; Ho, Rong-Ming

2017-04-18

The significance of chirality transfer is not only involved in biological systems, such as the origin of homochiral structures in life but also in man-made chemicals and materials. How the chiral bias transfers from molecular level (molecular chirality) to helical chain (conformational chirality) and then to helical superstructure or phase (hierarchical chirality) from self-assembly is vital for the chemical and biological processes in nature, such as communication, replication, and enzyme catalysis. In this Account, we summarize the methodologies for the examination of homochiral evolution at different length scales based on our recent studies with respect to the self-assembly of chiral polymers and chiral block copolymers (BCPs*). A helical (H*) phase to distinguish its P622 symmetry from that of normal hexagonally packed cylinder phase was discovered in the self-assembly of BCPs* due to the chirality effect on BCP self-assembly. Enantiomeric polylactide-containing BCPs*, polystyrene-b-poly(l-lactide) (PS-PLLA) and polystyrene-b-poly(d-lactide) (PS-PDLA), were synthesized for the examination of homochiral evolution. The optical activity (molecular chirality) of constituted chiral repeating unit in the chiral polylactide is detected by electronic circular dichroism (ECD) whereas the conformational chirality of helical polylactide chain can be explicitly determined by vibrational circular dichroism (VCD). The H* phases of the self-assembled polylactide-containing BCPs* can be directly visualized by 3D transmission electron microscopy (3D TEM) technique at which the handedness (hierarchical chirality) of the helical nanostructure is thus determined. The results from the ECD, VCD, and 3D TEM for the investigated chirality at different length scales suggest the homochiral evolution in the self-assembly of the BCPs*. For chiral polylactides, twisted lamellae in crystalline banded spherulite can be formed by dense packing scheme and effective interactions upon helical chains from self-assembly. The handedness of the twisted lamella can be determined by using rotation experiment of polarized light microscopy (PLM). Similar to the self-assembly of BCPs*, the examined results suggest the homochiral evolution in the crystallized chiral polylactides. The results presented in this Account demonstrate the notable progress in the spectral and morphological determination for the examination of molecular, conformational, and hierarchical chirality in self-assembled twisted superstructures of chiral polymers and helical phases of block copolymers and suggest the attainability of homochiral evolution in the self-assembly of chiral homopolymers and BCPs*. The suggested methodologies for the understanding of the mechanisms of the chirality transfer at different length scales provide the approaches to give Supporting Information for disclosing the mysteries of the homochiral evolution from molecular level.

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.

Imprints of magnetic power and helicity spectra on radio polarimetry statistics

NASA Astrophysics Data System (ADS)

Junklewitz, H.; Enßlin, T. A.

2011-06-01

The statistical properties of turbulent magnetic fields in radio-synchrotron sources should be imprinted on the statistics of polarimetric observables. In search of these imprints, i.e. characteristic modifications of the polarimetry statistics caused by magnetic field properties, we calculate correlation and cross-correlation functions from a set of observables that contain total intensity I, polarized intensity P, and Faraday depth φ. The correlation functions are evaluated for all combinations of observables up to fourth order in magnetic field B. We derive these analytically as far as possible and from first principles using only some basic assumptions, such as Gaussian statistics for the underlying magnetic field in the observed region and statistical homogeneity. We further assume some simplifications to reduce the complexity of the calculations, because for a start we were interested in a proof of concept. Using this statistical approach, we show that it is possible to gain information about the helical part of the magnetic power spectrum via the correlation functions < P(kperp) φ(k'_{perp)φ(k''perp)>B} and < I(kperp) φ(k'_{perp)φ(k''perp)>B}. Using this insight, we construct an easy-to-use test for helicity called LITMUS (Local Inference Test for Magnetic fields which Uncovers heliceS), which gives a spectrally integrated measure of helicity. For now, all calculations are given in a Faraday-free case, but set up so that Faraday rotational effects can be included later.

Simulation of the development and interaction of instabilities in a relativistic electron beam under variation of the beam wall thickness

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

Badarin, A. A.; Kurkin, S. A.; Koronovskii, A. A.

The development and interaction of Bursian and diocotron instabilities in an annular relativistic electron beam propagating in a cylindrical drift chamber are investigated analytically and numerically as functions of the beam wall thickness and the magnitude of the external uniform magnetic field. It is found that the interaction of instabilities results in the formation of a virtual cathode with a complicated rotating helical structure and several reflection regions (electron bunches) in the azimuthal direction. It is shown that the number of electron bunches in the azimuthal direction increases with decreasing beam wall thickness and depends in a complicated manner onmore » the magnitude of the external magnetic field.« less

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.

Extreme Ultraviolet Fractional Orbital Angular Momentum Beams from High Harmonic Generation

PubMed Central

Turpin, Alex; Rego, Laura; Picón, Antonio; San Román, Julio; Hernández-García, Carlos

2017-01-01

We investigate theoretically the generation of extreme-ultraviolet (EUV) beams carrying fractional orbital angular momentum. To this end, we drive high-order harmonic generation with infrared conical refraction (CR) beams. We show that the high-order harmonic beams emitted in the EUV/soft x-ray regime preserve the characteristic signatures of the driving beam, namely ringlike transverse intensity profile and CR-like polarization distribution. As a result, through orbital and spin angular momentum conservation, harmonic beams are emitted with fractional orbital angular momentum, and they can be synthesized into structured attosecond helical beams –or “structured attosecond light springs”– with rotating linear polarization along the azimuth. Our proposal overcomes the state of the art limitations for the generation of light beams far from the visible domain carrying non-integer orbital angular momentum and could be applied in fields such as diffraction imaging, EUV lithography, particle trapping, and super-resolution imaging. PMID:28281655

Structural mechanism of voltage-dependent gating in an isolated voltage-sensing domain.

PubMed

Li, Qufei; Wanderling, Sherry; Paduch, Marcin; Medovoy, David; Singharoy, Abhishek; McGreevy, Ryan; Villalba-Galea, Carlos A; Hulse, Raymond E; Roux, Benoît; Schulten, Klaus; Kossiakoff, Anthony; Perozo, Eduardo

2014-03-01

The transduction of transmembrane electric fields into protein motion has an essential role in the generation and propagation of cellular signals. Voltage-sensing domains (VSDs) carry out these functions through reorientations of positive charges in the S4 helix. Here, we determined crystal structures of the Ciona intestinalis VSD (Ci-VSD) in putatively active and resting conformations. S4 undergoes an ~5-Å displacement along its main axis, accompanied by an ~60° rotation. This movement is stabilized by an exchange in countercharge partners in helices S1 and S3 that generates an estimated net charge transfer of ~1 eo. Gating charges move relative to a ''hydrophobic gasket' that electrically divides intra- and extracellular compartments. EPR spectroscopy confirms the limited nature of S4 movement in a membrane environment. These results provide an explicit mechanism for voltage sensing and set the basis for electromechanical coupling in voltage-dependent enzymes and ion channels.

Generation of dynamo magnetic fields in thin Keplerian disks

NASA Technical Reports Server (NTRS)

Stepinski, T. F.; Levy, E. H.

1990-01-01

The combined action of nonuniform rotation and helical convection in protoplanetary disks, in the Galaxy, or in accretion disks surrounding black holes and other compact objects, enables an alpha-omega dynamo to generate a large-scale magnetic field. In this paper, the properties of such magnetic fields are investigated using a two-dimensional, partially numerical method. The structures of the lowest-order steady state and oscillatory modes are calculated for two kinds of external boundary conditions. A quadruple, steady state, highly localized mode is the most easily excited for low values of the dynamo number. The results indicate that, except under special conditions, disk dynamo modes tend to consist of relatively localized rings structures. For large values of the dynamo number, the magnetic field consists of a number of quasi-independent, spatially localized modes generated in various concentric rings filling the disk inward of a dynamo generation 'front'.

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

Bellows sealed plug valve

DOEpatents

Dukas, Jr., Stephen J.

1990-01-01

A bellows sealed plug valve includes a valve body having an inlet passage and an outlet passage, a valve chamber between the inlet and outlet passages. A valve plug has substantially the same shape as the valve chamber and is rotatably disposed therein. A shaft is movable linearly in response to a signal from a valve actuator. A bellows is sealingly disposed between the valve chamber and the valve actuator and means are located between the bellows and the valve plug for converting linear movement of the shaft connected to the valve actuator to rotational movement of the plug. Various means are disclosed including helical thread mechanism, clevis mechanism and rack and pinion mechanism, all for converting linear motion to rotational motion.

The behavior of bouncing disks and pizza tossing

NASA Astrophysics Data System (ADS)

Liu, K.-C.; Friend, J.; Yeo, L.

2009-03-01

We investigate the dynamics of a disk bouncing on a vibrating platform - a variation of the classic bouncing ball problem - that captures the physics of pizza tossing and the operation of certain standing-wave ultrasonic motors (SWUMs). The system's dynamics explains why certain tossing motions are used by dough-toss performers for different tricks: a helical trajectory is used in single tosses because it maximizes energy efficiency and the dough's airborne rotational speed, a semi-elliptical motion is used in multiple tosses because it is easier for maintaining dough rotation at the maximum rotational speed. The system's bifurcation diagram and basins of attraction also informs SWUM designers about the optimal design for high speed and minimal sensitivity to perturbation.

Propulsion of rotationally actuated soft magnetic microswimmers

NASA Astrophysics Data System (ADS)

Samsami, Kiarash; Mirbagheri, Seyed Amir; Meshkati, Farshad; Fu, Henry

2017-11-01

Microrobotic swimmers have been the subject of many studies recently because of their possible biomedical applications such as drug delivery and micro manipulation. We examine rigid magnetic microrobots that are propelled by rotation induced by a rotating magnetic field, thought to be the most promising class of microrobots. Previous studies have considered ferromagnetic swimmers with permanent magnetizations and paramagnetic swimmers, but many experimental realizations are in fact soft magnets. Here we investigate how soft magnetic swimmers differ from ferromagnetic and paramagnetic swimmers. We specifically investigate the behavior of step-out frequencies, velocity-frequency response, and the stability and multiplicity of stable swimming modes for microrobots with nonmagnetic helical tails and ellipsoidal soft magnetic heads.

A swirling jet in the quasar 1308+326

NASA Astrophysics Data System (ADS)

Britzen, S.; Qian, S.-J.; Steffen, W.; Kun, E.; Karouzos, M.; Gergely, L.; Schmidt, J.; Aller, M.; Aller, H.; Krause, M.; Fendt, C.; Böttcher, M.; Witzel, A.; Eckart, A.; Moser, L.

2017-06-01

Context. Despite numerous and detailed studies of the jets of active galactic nuclei (AGN) on pc-scales, many questions are still debated. The physical nature of the jet components is one of the most prominent unsolved problems, as is the launching mechanism of jets in AGN. The quasar 1308+326 (z = 0.997) allows us to study the overall properties of its jet in detail and to derive a more physical understanding of the nature and origin of jets in general. The long-term data provided by the Monitoring Of Jets in Active galactic nuclei with Very Long Baseline Array (VLBA) experiments (MOJAVE) survey permit us to trace out the structural changes in 1308+326 that we present here. The long-lived jet features in this source can be followed for about two decades. Aims: We investigate the very long baseline interferomety (VLBI) morphology and kinematics of the jet of 1308+326 to understand the physical nature of this jet and jets in general, the role of magnetic fields, and the causal connection between jet features and the launching process. Methods: Fifty VLBA observations performed at 15 GHz from the MOJAVE survey were re-modeled with Gaussian components and re-analyzed (the time covered: 20 Jan. 1995-25 Jan. 2014). The analysis was supplemented by multi-wavelength radio-data (UMRAO, at 4.8, 8.0, and 14.5 GHz) in polarization and total intensity. We fit the apparent motion of the jet features with the help of a model of a precessing nozzle. Results: The jet features seem to be emitted with varying viewing angles and launched into an ejection cone. Tracing the component paths yields evidence for rotational motion. Radio flux-density variability can be explained as a consequence of enhanced Doppler boosting corresponding to the motion of the jet relative to the line of sight. Based on the presented kinematics and other indicators, such as electric-vector polarization position-angle (EVPA) rotation, we conclude that the jet of 1308+326 has a helical structure, meaning that the components are moving along helical trajectories and the trajectories themselves are also experiencing a precessing motion. A model of a precessing nozzle was applied to the data and a subset of the observed jet feature paths can be modeled successfully within this model. The data till 2012 are consistent with a swing period of 16.9 yr. We discuss several scenarios to explain the observed motion phenomena, including a binary black hole model. It seems unlikely that the accretion disk around the primary black hole, which is disturbed by the tidal forces of the secondary black hole, is able to launch a persistent axisymmetric jet. Conclusions: We conclude that we are observing a rotating helix. In particular, the observed EVPA swings can be explained by a shock moving through a straight jet that is pervaded by a helical magnetic field. We compare our results for 1308+326 with other astrophysical scenarios where similar, wound-up filamentary structures are found. They are all related to accretion-driven processes. A helically moving or wound up object is often explained by filamentary features moving along magnetic field lines of magnetic flux tubes. It seems that a "component" comprises plasma tracing the magnetic field, which guides the motion of the radiating radio-band plasma. Further investigations and modeling are in preparation. The reduced Figs. A.1-A.13 (FITS files) are only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (http://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/602/A29 http://www.physics.purdue.edu/astro/MOJAVE/ http://www.physics.purdue.edu/astro/MOJAVE/ http://www.physics.purdue.edu/astro/MOJAVE/animated/1308+326.I.mpg http://www.physics.purdue.edu/MOJAVE/sourcepages/1308+326.shtml

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.

Geometry and surface controlled formation of nanoparticle helical ribbons

NASA Astrophysics Data System (ADS)

Pham, Jonathan; Lawrence, Jimmy; Lee, Dong; Grason, Gregory; Emrick, Todd; Crosby, Alfred

2013-03-01

Helical structures are interesting because of their space efficiency, mechanical tunability and everyday uses in both the synthetic and natural world. In general, the mechanisms governing helix formation are limited to bilayer material systems and chiral molecular structures. However, in a special range of dimensions where surface energy dominates (i.e. high surface to volume ratio), geometry rather than specific materials can drive helical formation of thin asymmetric ribbons. In an evaporative assembly technique called flow coating, based from the commonly observed coffee ring effect, we create nanoparticle ribbons possessing non-rectangular nanoscale cross-sections. When released into a liquid medium of water, interfacial tension between the asymmetric ribbon and water balances with the elastic cost of bending to form helices with a preferred radius of curvature and a minimum pitch. We demonstrate that this is a universal mechanism that can be used with a wide range of materials, such as quantum dots, metallic nanoparticles, or polymers. Nanoparticle helical ribbons display excellent structural integrity with spring-like characteristics and can be extended high strains.

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.

HBT-EP Program: MHD Dynamics and Active Control through 3D Fields and Currents

NASA Astrophysics Data System (ADS)

Navratil, G. A.; Bialek, J.; Brooks, J. W.; Byrne, P. J.; Desanto, S.; Levesque, J. P.; Mauel, M. E.; Stewart, I. G.; Hansen, C. J.

2017-10-01

The HBT-EP active mode control research program aims to: (i) advance understanding of the effects of 3D shaping on advanced tokamak fusion performance, (ii) resolve important MHD issues associated with disruptions, and (iii) measure and mitigate the effects of 3D scrape-off layer (SOL) currents through active and passive control of the plasma edge and conducting boundary structures. Comparison of kink mode structure and RMP response in circular versus diverted plasmas shows good agreement with DCON modeling. SOL current measurements have been used to study SOL current dynamics and current-sharing with the vacuum vessel wall during kink-mode growth and disruptions. A multi-chord extreme UV/soft X-ray array is being installed to provide detailed internal mode structure information. Internal local electrodes were used to apply local bias voltage at two radial locations to study the effect of rotation profile on MHD mode rotation and stability and radial current flow through the SOL. A GPU-based low latency control system using 96 inputs and 64 outputs to apply magnetic perturbations for active control of kink modes is extended to directly control the SOL currents for kink-mode control. An extensive array of SOL current monitors and edge drive electrodes are being installed for pioneering studies of helical edge current control. Supported by U.S. DOE Grant DE-FG02-86ER53222.

Fast, label-free super-resolution live-cell imaging using rotating coherent scattering (ROCS) microscopy

NASA Astrophysics Data System (ADS)

Jünger, Felix; Olshausen, Philipp V.; Rohrbach, Alexander

2016-07-01

Living cells are highly dynamic systems with cellular structures being often below the optical resolution limit. Super-resolution microscopes, usually based on fluorescence cell labelling, are usually too slow to resolve small, dynamic structures. We present a label-free microscopy technique, which can generate thousands of super-resolved, high contrast images at a frame rate of 100 Hertz and without any post-processing. The technique is based on oblique sample illumination with coherent light, an approach believed to be not applicable in life sciences because of too many interference artefacts. However, by circulating an incident laser beam by 360° during one image acquisition, relevant image information is amplified. By combining total internal reflection illumination with dark-field detection, structures as small as 150 nm become separable through local destructive interferences. The technique images local changes in refractive index through scattered laser light and is applied to living mouse macrophages and helical bacteria revealing unexpected dynamic processes.

Fast, label-free super-resolution live-cell imaging using rotating coherent scattering (ROCS) microscopy

PubMed Central

Jünger, Felix; Olshausen, Philipp v.; Rohrbach, Alexander

2016-01-01

Living cells are highly dynamic systems with cellular structures being often below the optical resolution limit. Super-resolution microscopes, usually based on fluorescence cell labelling, are usually too slow to resolve small, dynamic structures. We present a label-free microscopy technique, which can generate thousands of super-resolved, high contrast images at a frame rate of 100 Hertz and without any post-processing. The technique is based on oblique sample illumination with coherent light, an approach believed to be not applicable in life sciences because of too many interference artefacts. However, by circulating an incident laser beam by 360° during one image acquisition, relevant image information is amplified. By combining total internal reflection illumination with dark-field detection, structures as small as 150 nm become separable through local destructive interferences. The technique images local changes in refractive index through scattered laser light and is applied to living mouse macrophages and helical bacteria revealing unexpected dynamic processes. PMID:27465033

Structural basis for profilin-mediated actin nucleotide exchange

PubMed Central

Porta, Jason C.; Borgstahl, Gloria E.O.

2015-01-01

Actin is a ubiquitous eukaryotic protein that is responsible for cellular scaffolding, motility and division. The ability of actin to form a helical filament is the driving force behind these cellular activities. Formation of a filament is dependent the successful exchange of actin’s ADP for ATP. Mammalian profilin is a small actin binding protein that catalyzes the exchange of nucleotide and facilitates the addition of an actin monomer to a growing filament. Here, crystal structures of profilin:actin have been determined showing an actively exchanging ATP. The structural analysis shows how the binding of profilin to the barbed end of actin causes a rotation of the small domain relative to the large domain. This conformational change is propagated to the ATP site and causes a shift in the nucleotide loops which in turn causes a repositioning of Ca2+ to its canonical position as the cleft closes around ATP. Reversing the solvent exposure of Trp-356 is also involved in cleft closure. In addition, secondary calcium binding sites were identified. PMID:22366544

Torque measurements reveal sequence-specific cooperative transitions in supercoiled DNA

PubMed Central

Oberstrass, Florian C.; Fernandes, Louis E.; Bryant, Zev

2012-01-01

B-DNA becomes unstable under superhelical stress and is able to adopt a wide range of alternative conformations including strand-separated DNA and Z-DNA. Localized sequence-dependent structural transitions are important for the regulation of biological processes such as DNA replication and transcription. To directly probe the effect of sequence on structural transitions driven by torque, we have measured the torsional response of a panel of DNA sequences using single molecule assays that employ nanosphere rotational probes to achieve high torque resolution. The responses of Z-forming d(pGpC)n sequences match our predictions based on a theoretical treatment of cooperative transitions in helical polymers. “Bubble” templates containing 50–100 bp mismatch regions show cooperative structural transitions similar to B-DNA, although less torque is required to disrupt strand–strand interactions. Our mechanical measurements, including direct characterization of the torsional rigidity of strand-separated DNA, establish a framework for quantitative predictions of the complex torsional response of arbitrary sequences in their biological context. PMID:22474350

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

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.

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

Assembly of mesoscale helices with near-unity enantiomeric excess and light-matter interactions for chiral semiconductors

PubMed Central

Feng, Wenchun; Kim, Ji-Young; Wang, Xinzhi; Calcaterra, Heather A.; Qu, Zhibei; Meshi, Louisa; Kotov, Nicholas A.

2017-01-01

Semiconductors with chiral geometries at the nanoscale and mesoscale provide a rich materials platform for polarization optics, photocatalysis, and biomimetics. Unlike metallic and organic optical materials, the relationship between the geometry of chiral semiconductors and their chiroptical properties remains, however, vague. Homochiral ensembles of semiconductor helices with defined geometries open the road to understanding complex relationships between geometrical parameters and chiroptical properties of semiconductor materials. We show that semiconductor helices can be prepared with an absolute yield of ca 0.1% and an enantiomeric excess (e.e.) of 98% or above from cysteine-stabilized cadmium telluride nanoparticles (CdTe NPs) dispersed in methanol. This high e.e. for a spontaneously occurring chemical process is attributed to chiral self-sorting based on the thermodynamic preference of NPs to assemble with those of the same handedness. The dispersions of homochiral self-assembled helices display broadband visible and near-infrared (Vis-NIR) polarization rotation with anisotropy (g) factors approaching 0.01. Calculated circular dichroism (CD) spectra accurately reproduced experimental CD spectra and gave experimentally validated spectral predictions for different geometrical parameters enabling de novo design of chiroptical semiconductor materials. Unlike metallic, ceramic, and polymeric helices that serve predominantly as scatterers, chiroptical properties of semiconductor helices have nearly equal contribution of light absorption and scattering, which is essential for device-oriented, field-driven light modulation. Deconstruction of a helix into a series of nanorods provides a simple model for the light-matter interaction and chiroptical activity of helices. This study creates a framework for further development of polarization-based optics toward biomedical applications, telecommunications, and hyperspectral imaging. PMID:28275728

A general method for the derivation of the functional forms of the effective energy terms in coarse-grained energy functions of polymers. I. Backbone potentials of coarse-grained polypeptide chains

NASA Astrophysics Data System (ADS)

Sieradzan, Adam K.; Makowski, Mariusz; Augustynowicz, Antoni; Liwo, Adam

2017-03-01

A general and systematic method for the derivation of the functional expressions for the effective energy terms in coarse-grained force fields of polymer chains is proposed. The method is based on the expansion of the potential of mean force of the system studied in the cluster-cumulant series and expanding the all-atom energy in the Taylor series in the squares of interatomic distances about the squares of the distances between coarse-grained centers, to obtain approximate analytical expressions for the cluster cumulants. The primary degrees of freedom to average about are the angles for collective rotation of the atoms contained in the coarse-grained interaction sites about the respective virtual-bond axes. The approach has been applied to the revision of the virtual-bond-angle, virtual-bond-torsional, and backbone-local-and-electrostatic correlation potentials for the UNited RESidue (UNRES) model of polypeptide chains, demonstrating the strong dependence of the torsional and correlation potentials on virtual-bond angles, not considered in the current UNRES. The theoretical considerations are illustrated with the potentials calculated from the ab initio potential-energy surface of terminally blocked alanine by numerical integration and with the statistical potentials derived from known protein structures. The revised torsional potentials correctly indicate that virtual-bond angles close to 90° result in the preference for the turn and helical structures, while large virtual-bond angles result in the preference for polyproline II and extended backbone geometry. The revised correlation potentials correctly reproduce the preference for the formation of β-sheet structures for large values of virtual-bond angles and for the formation of α-helical structures for virtual-bond angles close to 90°.

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

On Three-dimensional Structures in Relativistic Hydrodynamic Jets

NASA Astrophysics Data System (ADS)

Hardee, Philip E.

2000-04-01

The appearance of wavelike helical structures on steady relativistic jets is studied using a normal mode analysis of the linearized fluid equations. Helical structures produced by the normal modes scale relative to the resonant (most unstable) wavelength and not with the absolute wavelength. The resonant wavelength of the normal modes can be less than the jet radius even on highly relativistic jets. High-pressure regions helically twisted around the jet beam may be confined close to the jet surface, penetrate deeply into the jet interior, or be confined to the jet interior. The high-pressure regions range from thin and ribbon-like to thick and tubelike depending on the mode and wavelength. The wave speeds can be significantly different at different wavelengths but are less than the flow speed. The highest wave speed for the jets studied has a Lorentz factor somewhat more than half that of the underlying flow speed. A maximum pressure fluctuation criterion found through comparison between theory and a set of relativistic axisymmetric jet simulations is applied to estimate the maximum amplitudes of the helical, elliptical, and triangular normal modes. Transverse velocity fluctuations for these asymmetric modes are up to twice the amplitude of those associated with the axisymmetric pinch mode. The maximum amplitude of jet distortions and the accompanying velocity fluctuations at, for example, the resonant wavelength decreases as the Lorentz factor increases. Long-wavelength helical surface mode and shorter wavelength helical first body mode generated structures should be the most significant. Emission from high-pressure regions as they twist around the jet beam can vary significantly as a result of angular variation in the flow direction associated with normal mode structures if they are viewed at about the beaming angle θ=1/γ. Variation in the Doppler boost factor can lead to brightness asymmetries by factors up to 6 as long-wavelength helical structure produced by the helical surface mode winds around the jet. Higher order surface modes and first body modes produce less variation. Angular variation in the flow direction associated with the helical mode appears consistent with precessing jet models that have been proposed to explain the variability in 3C 273 and BL Lac object AO 0235+164. In particular, cyclic angular variation in the flow direction produced by the normal modes could produce the activity seen in BL Lac object OJ 287. Jet precession provides a mechanism for triggering the helical modes on multiple length scales, e.g., the galactic superluminal GRO J1655-40.

A Model for Straight and Helical Solar Jets: II. Parametric Study of the Plasma Beta

NASA Technical Reports Server (NTRS)

Pariat, E.; Dalmasse, K.; DeVore, C. R.; Antiochos, S. K.; Karpen, J. T.

2016-01-01

Context. Jets are dynamic, impulsive, well-collimated plasma events that develop at many different scales and in different layers of the solar atmosphere. Aims. Jets are believed to be induced by magnetic reconnection, a process central to many astrophysical phenomena. Within the solar atmosphere, jet-like events develop in many different environments, e.g. in the vicinity of active regions as well as in coronal holes, and at various scales, from small photospheric spicules to large coronal jets. In all these events, signatures of helical structure and/or twisting/rotating motions are regularly observed. The present study aims to establish that a single model can generally reproduce the observed properties of these jet-like events. Methods. In this study, using our state-of-the-art numerical solver ARMS, we present a parametric study of a numerical tridimensional magnetohydrodynamic (MHD) model of solar jet-like events. Within the MHD paradigm, we study the impact of varying the atmospheric plasma beta on the generation and properties of solar-like jets. Results. The parametric study validates our model of jets for plasma beta ranging from 10(sup 3) to 1, typical of the different layers and magnetic environments of the solar atmosphere. Our model of jets can robustly explain the generation of helical solar jet-like events at various beta less than or equal to 1. We show that the plasma beta modifies the morphology of the helical jet, explaining the different observed shapes of jets at different scales and in different layers of the solar atmosphere. Conclusions. Our results allow us to understand the energisation, triggering, and driving processes of jet-like events. Our model allows us to make predictions of the impulsiveness and energetics of jets as determined by the surrounding environment, as well as the morphological properties of the resulting jets.

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

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.

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.

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.

Fascicles from energy-storing tendons show an age-specific response to cyclic fatigue loading

PubMed Central

Thorpe, Chavaunne T.; Riley, Graham P.; Birch, Helen L.; Clegg, Peter D.; Screen, Hazel R. C.

2014-01-01

Some tendons, such as the human Achilles and equine superficial digital flexor tendon (SDFT), act as energy stores, stretching and recoiling to increase efficiency during locomotion. Our previous observations of rotation in response to applied strain in SDFT fascicles suggest a helical structure, which may provide energy-storing tendons with a greater ability to extend and recoil efficiently. Despite this specialization, energy-storing tendons are prone to age-related tendinopathy. The aim of this study was to assess the effect of cyclic fatigue loading (FL) on the microstructural strain response of SDFT fascicles from young and old horses. The data demonstrate two independent age-related mechanisms of fatigue failure; in young horses, FL caused low levels of matrix damage and decreased rotation. This suggests that loading causes alterations to the helix substructure, which may reduce their ability to recoil and recover. By contrast, fascicles from old horses, in which the helix is already compromised, showed greater evidence of matrix damage and suffer increased fibre sliding after FL, which may partially explain the age-related increase in tendinopathy. Elucidation of helix structure and the precise alterations occurring owing to both ageing and FL will help to develop appropriate preventative and repair strategies for tendinopathy. PMID:24402919

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.

Biotemplated flagellar nanoswimmers

NASA Astrophysics Data System (ADS)

Ali, Jamel; Cheang, U. Kei; Darvish, Armin; Kim, Hoyeon; Kim, Min Jun

2017-11-01

In this article, a porous hollow biotemplated nanoscale helix that can serve as a low Reynolds number robotic swimmer is reported. The nanorobot utilizes repolymerized bacterial flagella from Salmonella typhimurium as a nanotemplate for biomineralization. We demonstrate the ability to generate templated nanotubes with distinct helical geometries by using specific alkaline pH values to fix the polymorphic form of flagellar templates. Using uniform rotating magnetic fields to mimic the motion of the flagellar motor, we explore the swimming characteristics of these silica templated flagella and demonstrate the ability to wirelessly control their trajectories. The results suggest that the biotemplated nanoswimmer can be a cost-effective alternative to the current top-down methods used to produce helical nanorobots.

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.

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.

Forward and backward motion of artificial helical swimmers in cylindrical channels

NASA Astrophysics Data System (ADS)

Acemoglu, Alperen; Temel, Fatma Zeynep; Yesilyurt, Serhat

2013-11-01

Motion of micro swimmers in confined geometries such as channels is important due to its relevance in in vivo medical applications such as minimally invasive surgery and drug delivery. Here, swimmers with diameters 0.8 mm and lengths 2 to 3 mm are produced with a 3D printer and cylindrical Nd2Fe14B magnets are placed inside the bodies. Rotating external magnetic field is used for the actuation of artificial swimmers. Different body and tail geometries are produced and experiments are conducted with a glycerol filled circular channel. Result demonstrate that decreasing channel diameter directly affects the forward motion of the swimmer due to the increasing drag. It is observed that step-out frequency, which defines maximum frequency at which the swimmer can establish a synchronous rotation with the external magnetic field, depends on the geometry of the swimmer and the channel diameter. There are significant differences between low and high frequency motion and forward and backward swimming. Longer tails enable higher forward velocities in high frequencies than backward ones, whereas forward and backward velocities are approximately the same at low frequencies. Furthermore backward motion is more stable than the forward one; at high frequencies, swimmers travel almost at the center of the channel for backward motion, and follow a helical trajectory near the wall during the forward motion. According to simulation results there is a flow which is induced by the rotation of the swimmer rotation that affects the swimmer's trajectory. We acknowledge the support from TUBITAK (Techonological & Research Council of Turkey) under the grant no: 111M376.

Structure of the paramyxovirus parainfluenza virus 5 nucleoprotein–RNA complex

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

Alayyoubi, Maher; Leser, George P.; Kors, Christopher A.

Parainfluenza virus 5 (PIV5) is a member of the Paramyxoviridae family of membrane-enveloped viruses with a negative-sense RNA genome that is packaged and protected by long filamentous nucleocapsid-helix structures (RNPs). These RNPs, consisting of ~2,600 protomers of nucleocapsid (N) protein, form the template for viral transcription and replication. In this paper, we have determined the 3D X-ray crystal structure of the nucleoprotein (N)-RNA complex from PIV5 to 3.11-Å resolution. The structure reveals a 13-mer nucleocapsid ring whose diameter, cavity, and pitch/height dimensions agree with EM data from early studies on the Paramyxovirinae subfamily of native RNPs, indicating that it closelymore » represents one-turn in the building block of the RNP helices. The PIV5-N nucleocapsid ring encapsidates a nuclease resistant 78-nt RNA strand in its positively charged groove formed between the N-terminal (NTD) and C-terminal (CTD) domains of its successive N protomers. Six nucleotides precisely are associated with each N protomer, with alternating three-base-in three-base-out conformation. The binding of six nucleotides per protomer is consistent with the “rule of six” that governs the genome packaging of the Paramyxovirinae subfamily of viruses. PIV5-N protomer subdomains are very similar in structure to the previously solved Nipah-N structure, but with a difference in the angle between NTD/CTD at the RNA hinge region. Based on the Nipah-N structure we modeled a PIV5-N open conformation in which the CTD rotates away from the RNA strand into the inner spacious nucleocapsid-ring cavity. Finally, this rotation would expose the RNA for the viral polymerase activity without major disruption of the nucleocapsid structure.« less

Structure of the paramyxovirus parainfluenza virus 5 nucleoprotein–RNA complex

DOE PAGES

Alayyoubi, Maher; Leser, George P.; Kors, Christopher A.; ...

2015-03-23

Parainfluenza virus 5 (PIV5) is a member of the Paramyxoviridae family of membrane-enveloped viruses with a negative-sense RNA genome that is packaged and protected by long filamentous nucleocapsid-helix structures (RNPs). These RNPs, consisting of ~2,600 protomers of nucleocapsid (N) protein, form the template for viral transcription and replication. In this paper, we have determined the 3D X-ray crystal structure of the nucleoprotein (N)-RNA complex from PIV5 to 3.11-Å resolution. The structure reveals a 13-mer nucleocapsid ring whose diameter, cavity, and pitch/height dimensions agree with EM data from early studies on the Paramyxovirinae subfamily of native RNPs, indicating that it closelymore » represents one-turn in the building block of the RNP helices. The PIV5-N nucleocapsid ring encapsidates a nuclease resistant 78-nt RNA strand in its positively charged groove formed between the N-terminal (NTD) and C-terminal (CTD) domains of its successive N protomers. Six nucleotides precisely are associated with each N protomer, with alternating three-base-in three-base-out conformation. The binding of six nucleotides per protomer is consistent with the “rule of six” that governs the genome packaging of the Paramyxovirinae subfamily of viruses. PIV5-N protomer subdomains are very similar in structure to the previously solved Nipah-N structure, but with a difference in the angle between NTD/CTD at the RNA hinge region. Based on the Nipah-N structure we modeled a PIV5-N open conformation in which the CTD rotates away from the RNA strand into the inner spacious nucleocapsid-ring cavity. Finally, this rotation would expose the RNA for the viral polymerase activity without major disruption of the nucleocapsid structure.« less

Structure of the paramyxovirus parainfluenza virus 5 nucleoprotein-RNA complex.

PubMed

Alayyoubi, Maher; Leser, George P; Kors, Christopher A; Lamb, Robert A

2015-04-07

Parainfluenza virus 5 (PIV5) is a member of the Paramyxoviridae family of membrane-enveloped viruses with a negative-sense RNA genome that is packaged and protected by long filamentous nucleocapsid-helix structures (RNPs). These RNPs, consisting of ∼2,600 protomers of nucleocapsid (N) protein, form the template for viral transcription and replication. We have determined the 3D X-ray crystal structure of the nucleoprotein (N)-RNA complex from PIV5 to 3.11-Å resolution. The structure reveals a 13-mer nucleocapsid ring whose diameter, cavity, and pitch/height dimensions agree with EM data from early studies on the Paramyxovirinae subfamily of native RNPs, indicating that it closely represents one-turn in the building block of the RNP helices. The PIV5-N nucleocapsid ring encapsidates a nuclease resistant 78-nt RNA strand in its positively charged groove formed between the N-terminal (NTD) and C-terminal (CTD) domains of its successive N protomers. Six nucleotides precisely are associated with each N protomer, with alternating three-base-in three-base-out conformation. The binding of six nucleotides per protomer is consistent with the "rule of six" that governs the genome packaging of the Paramyxovirinae subfamily of viruses. PIV5-N protomer subdomains are very similar in structure to the previously solved Nipah-N structure, but with a difference in the angle between NTD/CTD at the RNA hinge region. Based on the Nipah-N structure we modeled a PIV5-N open conformation in which the CTD rotates away from the RNA strand into the inner spacious nucleocapsid-ring cavity. This rotation would expose the RNA for the viral polymerase activity without major disruption of the nucleocapsid structure.

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.

Na+-driven bacterial flagellar motors.

PubMed

Imae, Y; Atsumi, T

1989-12-01

Bacterial flagellar motors are the reversible rotary engine which propels the cell by rotating a helical flagellar filament as a screw propeller. The motors are embedded in the cytoplasmic membrane, and the energy for rotation is supplied by the electrochemical potential of specific ions across the membrane. Thus, the analysis of motor rotation at the molecular level is linked to an understanding of how the living system converts chemical energy into mechanical work. Based on the coupling ions, the motors are divided into two types; one is the H+-driven type found in neutrophiles such as Bacillus subtilis and Escherichia coli and the other is the Na+-driven type found in alkalophilic Bacillus and marine Vibrio. In this review, we summarize the current status of research on the rotation mechanism of the Na+-driven flagellar motors, which introduces several new aspects in the analysis.

Reduction of granular drag inspired by self-burrowing rotary seeds

NASA Astrophysics Data System (ADS)

Jung, Wonjong; Choi, Sung Mok; Kim, Wonjung; Kim, Ho-Young

2017-04-01

We present quantitative measurements and mat hematical analysis of the granular drag reduction by rotation, as motivated by the digging of Erodium and Pelargonium seeds. The seeds create a motion to dig into soil before germination using their moisture-responsive awns, which are originally helical shaped but reversibly deform to a linear configuration in a humid environment. We show that the rotation greatly lowers the resistance of soil against penetration because grain rearrangements near the intruder change the force chain network. We find a general correlation for the drag reduction by relative slip, leading to a mathematical model for the granular drag of a rotating intruder. In addition to shedding light on the mechanics of a rotating body in granular media, this work can guide us to design robots working in granular media with enhanced maneuverability.

Disordering Chain Motions in Fluoropolymers

NASA Astrophysics Data System (ADS)

Holt, David B.; Farmer, Barry L.

1998-03-01

Rotational and conformational disorder play important roles in the solid state phases of fluoropolymers such as polytetrafluoro- ethylene (PTFE). Modeling disordering processes and transitions which occur in fluoropolymers has been hampered due to a lack of force field parameters that adequately describe both the intra- and intermolecular characteristics (conformations and distances) of these polymers in the solid state. A force field has been developed which overcomes these inadequacies and has been utilized in molecular dynamics simulations on a system of PTFE oligomers to investigate two of the primary disordering processes that occur in the solid phases: rotations of chains about their helical axes and the formation and subsequent behavior of helix reversals. The simulation results confirm helix reversal activity at low temperatures and demonstrate correlations between chain segment rotations or librations and helix reversal motion. A mechanism for large scale chain segment rotations is proposed.

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.

Determination of consistent patterns of range of motion in the ankle joint with a computed tomography stress-test.

PubMed

Tuijthof, Gabriëlle Josephine Maria; Zengerink, Maartje; Beimers, Lijkele; Jonges, Remmet; Maas, Mario; van Dijk, Cornelis Niek; Blankevoort, Leendert

2009-07-01

Measuring the range of motion of the ankle joint can assist in accurate diagnosis of ankle laxity. A computed tomography-based stress-test (3D CT stress-test) was used that determines the three-dimensional position and orientation of tibial, calcaneal and talar bones. The goal was to establish a quantitative database of the normal ranges of motion of the talocrural and subtalar joints. A clinical case on suspected subtalar instability demonstrated the relevance the proposed method. The range of motion was measured for the ankle joints in vivo for 20 subjects using the 3D CT stress-test. Motion of the tibia and calcaneus relative to the talus for eight extreme foot positions were described by helical parameters. High consistency for finite helical axis orientation (n) and rotation (theta) was shown for: talocrural extreme dorsiflexion to extreme plantarflexion (root mean square direction deviation (eta) 5.3 degrees and theta: SD 11.0 degrees), talorucral and subtalar extreme combined eversion-dorsiflexion to combined inversion-plantarflexion (eta: 6.7 degrees , theta: SD 9.0 degrees and eta:6.3 degrees , theta: SD 5.1 degrees), and subtalar extreme inversion to extreme eversion (eta: 6.4 degrees, theta: SD 5.9 degrees). Nearly all dorsi--and plantarflexion occurs in the talocrural joint (theta: mean 63.3 degrees (SD 11 degrees)). The inversion and internal rotation components for extreme eversion to inversion were approximately three times larger for the subtalar joint (theta: mean 22.9 degrees and 29.1 degrees) than for the talocrural joint (theta: mean 8.8 degrees and 10.7 degrees). Comparison of the ranges of motion of the pathologic ankle joint with the healthy subjects showed an increased inversion and axial rotation in the talocrural joint instead of in the suspected subtalar joint. The proposed diagnostic technique and the acquired database of helical parameters of ankle joint ranges of motion are suitable to apply in clinical cases.

Impact of plasma response on plasma displacements in DIII-D during application of external 3D perturbations

DOE PAGES

Wingen, Andreas; Ferraro, Nathaniel M.; Shafer, Morgan W.; ...

2014-05-23

The effects of applied non-axisymmetric resonant magnetic perturbations (RMPs) are predicted without and with self-consistent plasma response by modeling of the magnetic field structure and two-fluid MHD simulations, respectively. A synthetic diagnostic is used to simulate soft X-ray (SXR) emission within the steep gradient region of the pedestal, 0.98 > ψ > 0.94. The entire pedestal and edge region is characterized by large changes in plasma rotation and current density. Those parameters are expected to strongly affect the plasma response to RMPs. The M3D-C1 code takes into account this response self-consistently. The plasma response is investigated in detail and usedmore » in the forward modeling of the simulated local SXR emission, within the framework of the synthetic diagnostic. The resulting synthetic emission is compared to measured SXR data. The latter clearly shows helical m = 11 ± 1 displacements around the 11/3 rational surface of sizes up to 5 cm, which change with the poloidal angle. The synthetic emission with plasma response is used to explain the nature of the measured displacements. Different approaches are tested. One approach is based on the magnetic field structure to simulate local emission, which shows additional structures at the separatrix, that are caused by the lobes. Especially without plasma response, almost only separatrix structures are generated while no significant displacements are found further inside. Another approach to model local emission uses the fluid quantities electron density and temperature, as calculated by M3D-C1. Compared to the previous approach, based on the magnetic field structure, the emission simulated by the fluid approach with plasma response shows better agreement with the measured SXR data. To be specific, it has comparable displacements in the steep gradient region and no lobe structures at all. The helical displacements around the 11/3 surface are identified to be directly related to the kink response, caused by non-resonant amplification of various poloidal RMP modes due to plasma response. Regarding the latter, the role of different plasma parameters is investigated, but it appears that the electron rotation plays a key role in the formation of screening and resonant amplification, while the kinking appears to be sensitive to the edge current density. As a result, it is also hypothesised that the strength of the kink response is also correlated to edge-localized-mode (ELM) stability.« less

Visualization of vortex structures and analysis of frequency of PVC

NASA Astrophysics Data System (ADS)

Gesheva, E. S.; Shtork, S. I.; Alekseenko, S. V.

2018-03-01

The paper presents the results of the study of large-scale vortex structures in a model chamber. Methods of forming quasi-stationary vortices of various shapes by changing the geometric parameters of the chamber have been proposed. In the model chamber with a tangential swirl of the flow, a rectilinear vortex, single helical and double helical vortices were obtained. The double helical structure of the vortex is unique due to its immovability around the axis of the chamber. The resulting structures slowly oscillate around their own axes, which is called the vortex core precession; while the oscillation frequency depends linearly on the liquid flow rate. The use of stationary vortex structures in power plants will increase the efficiency of combustion chambers and reduce slagging.

Turbulent Compressible Convection with Rotation. 2; Mean Flows and Differential Rotation

NASA Technical Reports Server (NTRS)

Brummell, Nicholas H.; Hurlburt, Neal E.; Toomre, Juri

1998-01-01

The effects of rotation on turbulent, compressible convection within stellar envelopes are studied through three-dimensional numerical simulations conducted within a local f-plane model. This work seeks to understand the types of differential rotation that can be established in convective envelopes of stars like the Sun, for which recent helioseismic observations suggest an angular velocity profile with depth and latitude at variance with many theoretical predictions. This paper analyzes the mechanisms that are responsible for the mean (horizontally averaged) zonal and meridional flows that are produced by convection influenced by Coriolis forces. The compressible convection is considered for a range of Rayleigh, Taylor, and Prandtl (and thus Rossby) numbers encompassing both laminar and turbulent flow conditions under weak and strong rotational constraints. When the nonlinearities are moderate, the effects of rotation on the resulting laminar cellular convection leads to distinctive tilts of the cell boundaries away from the vertical. These yield correlations between vertical and horizontal motions that generate Reynolds stresses that can drive mean flows, interpretable as differential rotation and meridional circulations. Under more vigorous forcing, the resulting turbulent convection involves complicated and contorted fluid particle trajectories, with few clear correlations between vertical and horizontal motions, punctuated by an evolving and intricate downflow network that can extend over much of the depth of the layer. Within such networks are some coherent structures of vortical downflow that tend to align with the rotation axis. These yield a novel turbulent alignment mechanism, distinct from the laminar tilting of cellular boundaries, that can provide the principal correlated motions and thus Reynolds stresses and subsequently mean flows. The emergence of such coherent structures that can persist amidst more random motions is a characteristic of turbulence with symmetries broken by rotation and stratification. Such structure is here found to play a crucial role in defining the mean zonal and meridional flows that coexist with the convection. Though they are subject to strong inertial oscillations, the strength and type of the mean flows are determined by a combination of the laminar tilting and the turbulent alignment mechanisms. Varying the parameters produces a wide range of mean motions. Among these, some turbulent solutions exhibit a mean zonal velocity profile that is nearly constant with depth, much as deduced by helioseismology at midlatitudes within the Sun. The solutions exhibit a definite handedness, with the direction of the persistent mean flows often prescribing a spiral with depth near the boundaries, also in accord with helioseismic deductions. The mean helicity has a profile that is positive in the upper portion of the domain and negative in the lower portion, a property bearing on magnetic dynamo processes that may be realized within such rotating layers of turbulent convection.

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.

Dynamic Receptor Team Formation Can Explain the High Signal Transduction Gain in Escherichia coli

PubMed Central

Albert, Réka; Chiu, Yu-wen; Othmer, Hans G.

2004-01-01

Evolution has provided many organisms with sophisticated sensory systems that enable them to respond to signals in their environment. The response frequently involves alteration in the pattern of movement, either by directed movement, a process called taxis, or by altering the speed or frequency of turning, which is called kinesis. Chemokinesis has been most thoroughly studied in the peritrichous bacterium Escherichia coli, which has four helical flagella distributed over the cell surface, and swims by rotating them. When rotated counterclockwise the flagella coalesce into a propulsive bundle, producing a relatively straight “run,” and when rotated clockwise they fly apart, resulting in a “tumble” which reorients the cell with little translocation. A stochastic process generates the runs and tumbles, and in a chemoeffector gradient, runs that carry the cell in a favorable direction are extended. The cell senses spatial gradients as temporal changes in receptor occupancy and changes the probability of counterclockwise rotation (the bias) on a fast timescale, but adaptation returns the bias to baseline on a slow timescale, enabling the cell to detect and respond to further concentration changes. The overall structure of the signal transduction pathways is well characterized in E. coli, but important details are still not understood. Only recently has a source of gain in the signal transduction network been identified experimentally, and here we present a mathematical model based on dynamic assembly of receptor teams that can explain this observation. PMID:15111386

Dynamic receptor team formation can explain the high signal transduction gain in Escherichia coli.

PubMed

Albert, Réka; Chiu, Yu-Wen; Othmer, Hans G

2004-05-01

Evolution has provided many organisms with sophisticated sensory systems that enable them to respond to signals in their environment. The response frequently involves alteration in the pattern of movement, either by directed movement, a process called taxis, or by altering the speed or frequency of turning, which is called kinesis. Chemokinesis has been most thoroughly studied in the peritrichous bacterium Escherichia coli, which has four helical flagella distributed over the cell surface, and swims by rotating them. When rotated counterclockwise the flagella coalesce into a propulsive bundle, producing a relatively straight "run," and when rotated clockwise they fly apart, resulting in a "tumble" which reorients the cell with little translocation. A stochastic process generates the runs and tumbles, and in a chemoeffector gradient, runs that carry the cell in a favorable direction are extended. The cell senses spatial gradients as temporal changes in receptor occupancy and changes the probability of counterclockwise rotation (the bias) on a fast timescale, but adaptation returns the bias to baseline on a slow timescale, enabling the cell to detect and respond to further concentration changes. The overall structure of the signal transduction pathways is well characterized in E. coli, but important details are still not understood. Only recently has a source of gain in the signal transduction network been identified experimentally, and here we present a mathematical model based on dynamic assembly of receptor teams that can explain this observation.

Helicity-Selective Enhancement and Polarization Control of Attosecond High Harmonic Waveforms Driven by Bichromatic Circularly Polarized Laser Fields.

PubMed

Dorney, Kevin M; Ellis, Jennifer L; Hernández-García, Carlos; Hickstein, Daniel D; Mancuso, Christopher A; Brooks, Nathan; Fan, Tingting; Fan, Guangyu; Zusin, Dmitriy; Gentry, Christian; Grychtol, Patrik; Kapteyn, Henry C; Murnane, Margaret M

2017-08-11

High harmonics driven by two-color counterrotating circularly polarized laser fields are a unique source of bright, circularly polarized, extreme ultraviolet, and soft x-ray beams, where the individual harmonics themselves are completely circularly polarized. Here, we demonstrate the ability to preferentially select either the right or left circularly polarized harmonics simply by adjusting the relative intensity ratio of the bichromatic circularly polarized driving laser field. In the frequency domain, this significantly enhances the harmonic orders that rotate in the same direction as the higher-intensity driving laser. In the time domain, this helicity-dependent enhancement corresponds to control over the polarization of the resulting attosecond waveforms. This helicity control enables the generation of circularly polarized high harmonics with a user-defined polarization of the underlying attosecond bursts. In the future, this technique should allow for the production of bright highly elliptical harmonic supercontinua as well as the generation of isolated elliptically polarized attosecond pulses.

Molecular mechanism of polyacrylate helix sense switching across its free energy landscape.

PubMed

Pietropaolo, Adriana; Nakano, Tamaki

2013-04-17

Helical polymers with switchable screw sense are versatile frameworks for chiral functional materials. In this work, we reconstructed the free energy landscape of helical poly(2,7-bis(4-tert-butylphenyl)fluoren-9-yl acrylate) [poly(BBPFA)], as its racemization is selectively driven by light without any rearrangement of chemical bonds. The chirality inversion was enforced by atomistic free energy simulations using chirality indices as reaction coordinates. The free energy landscape reproduced the experimental electronic circular dichroism spectra. We propose that the chirality inversion of poly(BBPFA) proceeds from a left-handed 31 helix via multistate free energy pathways to reach the right-handed 31 helix. The inversion is triggered by the rotation of biphenyl units with an activation barrier of 38 kcal/mol. To the best of our knowledge, this is the first report on the chiral inversion mechanism of a helical polymer determined in a quantitative way in the framework of atomistic free energy simulations.

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.

All-electric spin modulator based on a two-dimensional topological insulator

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

Xiao, Xianbo; Ai, Guoping; Liu, Ying

2016-01-18

We propose and investigate a spin modulator device consisting of two ferromagnetic leads connected by a two-dimensional topological insulator as the channel material. It exploits the unique features of the topological spin-helical edge states, such that the injected carriers with a non-collinear spin-polarization direction would travel through both edges and show interference effect. The conductance of the device can be controlled in a simple and all-electric manner by a side-gate voltage, which effectively rotates the spin-polarization of the carrier. At low voltages, the rotation angle is linear in the gate voltage, and the device can function as a good spin-polarizationmore » rotator by replacing the drain electrode with a non-magnetic material.« less

Microscopic artificial swimmers

NASA Astrophysics Data System (ADS)

Dreyfus, Rémi; Baudry, Jean; Roper, Marcus L.; Fermigier, Marc; Stone, Howard A.; Bibette, Jérôme

2005-10-01

Microorganisms such as bacteria and many eukaryotic cells propel themselves with hair-like structures known as flagella, which can exhibit a variety of structures and movement patterns. For example, bacterial flagella are helically shaped and driven at their bases by a reversible rotary engine, which rotates the attached flagellum to give a motion similar to that of a corkscrew. In contrast, eukaryotic cells use flagella that resemble elastic rods and exhibit a beating motion: internally generated stresses give rise to a series of bends that propagate towards the tip. In contrast to this variety of swimming strategies encountered in nature, a controlled swimming motion of artificial micrometre-sized structures has not yet been realized. Here we show that a linear chain of colloidal magnetic particles linked by DNA and attached to a red blood cell can act as a flexible artificial flagellum. The filament aligns with an external uniform magnetic field and is readily actuated by oscillating a transverse field. We find that the actuation induces a beating pattern that propels the structure, and that the external fields can be adjusted to control the velocity and the direction of motion.

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

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.

Conformational statistics of stiff macromolecules as solutions to partial differential equations on the rotation and motion groups

PubMed

Chirikjian; Wang

2000-07-01

Partial differential equations (PDE's) for the probability density function (PDF) of the position and orientation of the distal end of a stiff macromolecule relative to its proximal end are derived and solved. The Kratky-Porod wormlike chain, the Yamakawa helical wormlike chain, and the original and revised Marko-Siggia models are examples of stiffness models to which the present formulation is applied. The solution technique uses harmonic analysis on the rotation and motion groups to convert PDE's governing the PDF's of interest into linear algebraic equations which have mathematically elegant solutions.

Berezinskii-Kosterlitz-Thouless phase transition for the dilute planar rotator model on a triangular lattice

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

Sun Yunzhou; Yi Lin; Wysin, G. M.

2008-10-15

The Berezinskii-Kosterlitz-Thouless (BKT) phase transition for the dilute planar rotator model on a triangular lattice is studied by using a hybrid Monte Carlo method. The phase-transition temperatures for different nonmagnetic impurity densities are obtained by three approaches: finite-size scaling of plane magnetic susceptibility, helicity modulus, and Binder's fourth cumulant. It is found that the phase-transition temperature decreases with increasing impurity density {rho} and the BKT phase transition vanishes when the magnetic occupancy falls to the site percolation threshold: 1-{rho}{sub c}=p{sub c}=0.5.

Helicity and singular structures in fluid dynamics

PubMed Central

Moffatt, H. Keith

2014-01-01

Helicity is, like energy, a quadratic invariant of the Euler equations of ideal fluid flow, although, unlike energy, it is not sign definite. In physical terms, it represents the degree of linkage of the vortex lines of a flow, conserved when conditions are such that these vortex lines are frozen in the fluid. Some basic properties of helicity are reviewed, with particular reference to (i) its crucial role in the dynamo excitation of magnetic fields in cosmic systems; (ii) its bearing on the existence of Euler flows of arbitrarily complex streamline topology; (iii) the constraining role of the analogous magnetic helicity in the determination of stable knotted minimum-energy magnetostatic structures; and (iv) its role in depleting nonlinearity in the Navier-Stokes equations, with implications for the coherent structures and energy cascade of turbulence. In a final section, some singular phenomena in low Reynolds number flows are briefly described. PMID:24520175

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

Fluorescence Determination of Tryptophan Side-Chain Accessibility and Dynamics in Triple-Helical Collagen-Like Peptides

PubMed Central

Simon-Lukasik, Kristine V.; Persikov, Anton V.; Brodsky, Barbara; Ramshaw, John A. M.; Laws, William R.; Alexander Ross, J. B.; Ludescher, Richard D.

2003-01-01

We report tryptophan fluorescence measurements of emission intensity, iodide quenching, and anisotropy that describe the environment and dynamics at X and Y sites in stable collagen-like peptides of sequence (Gly-X-Y)n. About 90% of tryptophans at both sites have similar solvent exposed fluorescence properties and a lifetime of 8.5–9 ns. Analysis of anisotropy decays using an associative model indicates that these long lifetime populations undergo rapid depolarizing motion with a 0.5 ns correlation time; however, the extent of fast motion at the Y site is considerably less than the essentially unrestricted motion at the X site. About 10% of tryptophans at both sites have a shorter (∼3 ns) lifetime indicating proximity to a protein quenching group; these minor populations are immobile on the peptide surface, depolarizing only by overall trimer rotation. Iodide quenching indicates that tryptophans at the X site are more accessible to solvent. Side chains at X sites are more solvent accessible and considerably more mobile than residues at Y sites and can more readily fluctuate among alternate intermolecular interactions in collagen fibrils. This fluorescence analysis of collagen-like peptides lays a foundation for studies on the structure, dynamics, and function of collagen and of triple-helical junctions in gelatin gels. PMID:12524302

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.

Finding of widespread viral and bacterial revolution dsDNA translocation motors distinct from rotation motors by channel chirality and size

PubMed Central

2014-01-01

Background Double-stranded DNA translocation is ubiquitous in living systems. Cell mitosis, bacterial binary fission, DNA replication or repair, homologous recombination, Holliday junction resolution, viral genome packaging and cell entry all involve biomotor-driven dsDNA translocation. Previously, biomotors have been primarily classified into linear and rotational motors. We recently discovered a third class of dsDNA translocation motors in Phi29 utilizing revolution mechanism without rotation. Analogically, the Earth rotates around its own axis every 24 hours, but revolves around the Sun every 365 days. Results Single-channel DNA translocation conductance assay combined with structure inspections of motor channels on bacteriophages P22, SPP1, HK97, T7, T4, Phi29, and other dsDNA translocation motors such as bacterial FtsK and eukaryotic mimiviruses or vaccinia viruses showed that revolution motor is widespread. The force generation mechanism for revolution motors is elucidated. Revolution motors can be differentiated from rotation motors by their channel size and chirality. Crystal structure inspection revealed that revolution motors commonly exhibit channel diameters larger than 3 nm, while rotation motors that rotate around one of the two separated DNA strands feature a diameter smaller than 2 nm. Phi29 revolution motor translocated double- and tetra-stranded DNA that occupied 32% and 64% of the narrowest channel cross-section, respectively, evidencing that revolution motors exhibit channel diameters significantly wider than the dsDNA. Left-handed oriented channels found in revolution motors drive the right-handed dsDNA via anti-chiral interaction, while right-handed channels observed in rotation motors drive the right-handed dsDNA via parallel threads. Tethering both the motor and the dsDNA distal-end of the revolution motor does not block DNA packaging, indicating that no rotation is required for motors of dsDNA phages, while a small-angle left-handed twist of dsDNA that is aligned with the channel could occur due to the conformational change of the phage motor channels from a left-handed configuration for DNA entry to a right-handed configuration for DNA ejection for host cell infection. Conclusions The revolution motor is widespread among biological systems, and can be distinguished from rotation motors by channel size and chirality. The revolution mechanism renders dsDNA void of coiling and torque during translocation of the lengthy helical chromosome, thus resulting in more efficient motor energy conversion. PMID:24940480

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.

Measurement of ion velocities in the locked Single Helical Axis state in MST RFP plasmas

NASA Astrophysics Data System (ADS)

Boguski, J.; Nornberg, M. D.; Chapman, B. E.; Cianciosa, M.; den Hartog, D. J.; Craig, D.; McCollam, K. J.; Nishizawa, T.; Xing, Z. A.

2017-10-01

Charge Exchange Recombination Spectroscopy (CHERS) provides the first core-localized measurements of the 3D ion flow structure in Single Helical Axis (SHAx) plasmas. In high-current and low-density (large Lundquist number) RFP plasmas, the island associated with the innermost resonant tearing mode can grow to large amplitude and envelop the magnetic axis creating a 3D equilibrium. Measurements of the flow profile with various orientations (phases) of the helical structure relative to the CHERS diagnostic were achieved by locking the plasma with resonant magnetic perturbations. The flows persist despite mode locking, and are correlated with the amplitude and phase of the innermost resonant tearing mode. At mid-radius, a dominantly m =2 poloidal flow structure appears relative to the phase of the helical core. Near the core, non-axisymmetric flows become less pronounced, and cannot be distinguished at the innermost radii. These results place more significant constraints on the nature of the flow structure than previous line-integrated spectroscopy measurements and challenge predictions of visco-resistive MHD models of these helical RFP plasmas. This material is based upon work supported by the U.S. Department of Energy, Office of Science, Office of Fusion Energy Sciences program under Award No. DE-FC02-05ER54814.

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.

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

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.

The principal motions involved in the coupling mechanism of the recovery stroke of the myosin motor.

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

Mesentean, Sidonia; Koppole, Sampath; Smith, Jeremy C

2007-03-01

Muscle contraction is driven by a cycle of conformational changes in the myosin II head. After myosin binds ATP and releases from the actin fibril, myosin prepares for the next power stroke by rotating back the converter domain that carries the lever arm by 60{sup o}. This recovery stroke is coupled to the activation of myosin ATPase by a mechanism that is essential for an efficient motor cycle. The mechanics of this coupling have been proposed to occur via two distinct and successive motions of the two helices that hold the converter domain: in a first phase a seesaw motionmore » of the relay helix, followed by a piston-like motion of the SH1 helix in a second phase. To test this model, we have determined the principal motions of these structural elements during equilibrium molecular dynamics simulations of the crystallographic end states of the recovery-stroke by using principal component analysis. This reveals that the only principal motions of these two helices that make a large-amplitude contribution towards the conformational change of the recovery stroke are indeed the predicted seesaw and piston motions. Moreover, the results demonstrate that the seesaw motion of the relay helix dominates in the dynamics of the pre-recovery stroke structure, but not in the dynamics of the post-recovery stroke structure, and vice versa for the piston motion of the SH1 helix. This is consistent with the order of the proposed two-phase model for the coupling mechanism of the recovery stroke. Molecular movies of these principal motions are available at http://www.iwr.uni-heidelberg.de/groups/biocomp/fischer.« less

Characterization of metal oxide field-effect transistors for first helical tomotherapy Hi-Art II unit in India.

PubMed

Kinhikar, Rajesh A; Pai, Rajeshree; Master, Zubin; Deshpande, Deepak D

2009-01-01

To characterize metal oxide semiconductor field-effect transistors (MOSFETs) for a 6-MV photon beam with a first helical tomotherapy Hi-Art II unit in India. Standard sensitivity MOSFETs were first calibrated and then characterized for reproducibility, field size dependence, angular dependence, fade effects, and temperature dependence. The detector sensitivity was estimated for static as well as rotational modes for three jaw settings (1.0 cm x 40 cm, 2.5 cm x 40 cm, and 5 cm x 40 cm) at 1.5-cm depth with a source-to-axis distance (SAD) of 85 cm in virtual water slabs. The A1SL ion chamber and thermoluminescence dosimeters (TLDs) were used to compare the results. No significant difference was found in the detector sensitivity for static and rotational procedures. The average detector sensitivity for static procedures was 1.10 mV/cGy (SD 0.02) while it was 1.12 mV/cGy (SD 0.02) for rotational procedures. The average detector sensitivity found was the same within the experimental uncertainty for static and rotational dose deliveries. The MOSFET reading was consistent and its reproducibility was excellent (+0.5%) while there was no significant dependence of field size. The angular dependence of less than 1.0% was observed. There was negligible fading effect of the MOSFET. The MOSFET response was found independent of temperature in the range 18 degrees-30 degrees. The ion chamber readings were assumed to be a reference for the estimation of the MOSFET calibration factor. The ion chamber and the TLD were in good agreement (+2%) with each other. This study deals only with the measurements and calibration performed on the surface of the phantom. MOSFET was calibrated and validated for phantom surface measurements for a 6-MV photon beam generated by a tomotherapy machine. The sensitivity of the detector was the same for both modes of treatment delivery with tomotherapy. The performance of the MOSFET was validated for and satisfactory for the helical tomotherapy Hi-Art II unit. However, MOSFET may be used for in vivo surface dosimetry only after it is calibrated under the conditions replicating as much as possible the manner in which the dosimeter will be used clinically.

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.

Local study of helical magnetorotational instability in viscous Keplerian disks

NASA Astrophysics Data System (ADS)

MahdaviGharavi, M.; Hajisharifi, K.; Mehidan, H.

2018-03-01

In this paper, regarding the recent detection of significant azimuthal magnetic field in some accretion disks such as protostellar (Donati et al. in Nature 438:466, 2005), the multi-fluid model has been employed to analysis the stability of Keplerian rotational viscous dusty plasma system in a current-free helical magnetic field structure. Using the fluid-Maxwell equations, the general dispersion relation of the excited modes in the system has been obtained by applying the local approximation method in the linear perturbation theory. The typical numerical analysis of the obtained dispersion relation in the high-frequency regime shows that the presence of azimuthal magnetic field component in Keplerian flow has a considerable role in the stability conditions of the system. It also shows that the magnetic field helicity has a stabilization role against the magnetorotational instability (MRI) in the system due to contraction of the unstable wavelength region and decreasing the maximum growth rate of the instability. In this sense, the stabilization role of the viscosity term is more considerable for HMRI (instability in the presence of azimuthal magnetic field component) than the corresponding MRI (instability in the absence of azimuthal magnetic field component). Moreover, considering the discovered azimuthal magnetic field in these systems, the MRI can be arisen in the over-all range of dust grains construction values in contract with traditional MRI. This investigation can greatly contribute to better understanding the physics of some astrophysical phenomena, such as the main source of turbulence and angular momentum transport in protostellar and the other sufficiently ionized astrophysical disks, where the azimuthal magnetic field component in these systems can play a significant role.

Characteristics of Helical Flow through Neck Cutoffs

NASA Astrophysics Data System (ADS)

Richards, D.; Konsoer, K. M.; Turnipseed, C.; Willson, C. S.

2017-12-01

Meander cutoffs and oxbows lakes are a ubiquitous feature of riverine landscapes yet there is a paucity of detailed investigations concentrated on the three-dimensional flow structure through evolving neck cutoffs. The purpose of this research is to investigate and characterize helical flow through neck cutoffs with two different planform configurations: elongate meander loops and serpentine loops. Three-dimensional velocity measurements was collected with an acoustic Doppler current profiler for five cutoffs on the White River, Arkansas. Pronounced helical flow was found through all elongate loop cutoff sites, formed from the balance between centrifugal force resulting from the curving of flow through the cutoff channel and pressure gradient force resulting from water surface super-elevation between primary flow and flow at the entrance and exit of the abandoned loop. The sense of motion of the helical flow caused near-surface fluid to travel outward toward the abandoned loop while near-bed fluid was redirected toward the downstream channel. Another characteristic of the helical flow structure for elongate loop cutoffs was the reversal of helical flow over a relatively short distance, causing patterns of secondary circulation that differed from typical patterns observed through curved channels with point bars. Lastly, helical flow was revealed within zones of strong flow recirculation, enhanced by an exchange of streamwise momentum between shear layers.

Linear Transformation of the Polarization Modes in Coiled Optical Spun-Fibers with Strong Unperturbed Linear Birefringence. I. Nonresonant Transformation

NASA Astrophysics Data System (ADS)

Malykin, G. B.; Pozdnyakova, V. I.

2018-03-01

A linear transformation of orthogonal polarization modes in coiled optical spun-fibers with strong unperturbed linear birefringence, which causes the emergence of the dependences of the integrated elliptical birefringence and the ellipticity and azimuth of the major axis of the ellipse, as well as the polarization state of radiation (PSR), on the length of optical fiber has been considered. Optical spun-fibers are subjected to a strong mechanical twisting, which is frozen into the structure of the optical fiber upon cooling, in the process of being drawn out from the workpiece. Since the values of the local polarization parameters of coiled spunwaveguides vary according to a rather complex law, the calculations were carried out by numerical modeling of the parameters of the Jones matrices. Since the rotation speed of the axes of the birefringence is constant on a relatively short segment of a coiled optical spun-fiber in the accompanying torsion (helical) coordinate system, the so-called "Ginzburg helical polarization modes" (GHPMs)—two mutually orthogonal ellipses with the opposite directions of traversal, the axis of which rotate relative to the fixed coordinate system uniformly and unidirectionally—are approximately the local normal polarization modes of such optical fiber. It has been shown that, despite the fact that the unperturbed linear birefringence of the spun-fibers significantly exceeds the linear birefringence, which is caused by the winding on a coil, the integral birefringence of an extended segment of such a fiber coincides in order of magnitude with the linear birefringence, which is caused by the winding on the coil, and the integral polarization modes tend asymptotically to circular ones. It has been also shown that the values of the circular birefringence of twisted single-mode fibers, which were calculated in a nonrotating and torsion helical coordinate systems, differ significantly. It has been shown that the polarization phenomena occur in the process of linear transformation of local polarization modes, which lead to small quasi-harmonic oscillations of the birefringence integral parameters of the optical spun-fibers, which depend on their length, and the period of these oscillations is approximately equal to half of the effective period of polarization beating.

Use of chiral cell shape to ensure highly directional swimming in trypanosomes

PubMed Central

2017-01-01

Swimming cells typically move along a helical path or undergo longitudinal rotation as they swim, arising from chiral asymmetry in hydrodynamic drag or propulsion bending the swimming path into a helix. Helical paths are beneficial for some forms of chemotaxis, but why asymmetric shape is so prevalent when a symmetric shape would also allow highly directional swimming is unclear. Here, I analyse the swimming of the insect life cycle stages of two human parasites; Trypanosoma brucei and Leishmania mexicana. This showed quantitatively how chirality in T. brucei cell shape confers highly directional swimming. High speed videomicrographs showed that T. brucei, L. mexicana and a T. brucei RNAi morphology mutant have a range of shape asymmetries, from wild-type T. brucei (highly chiral) to L. mexicana (near-axial symmetry). The chiral cells underwent longitudinal rotation while swimming, with more rapid longitudinal rotation correlating with swimming path directionality. Simulation indicated hydrodynamic drag on the chiral cell shape caused rotation, and the predicted geometry of the resulting swimming path matched the directionality of the observed swimming paths. This simulation of swimming path geometry showed that highly chiral cell shape is a robust mechanism through which microscale swimmers can achieve highly directional swimming at low Reynolds number. It is insensitive to random variation in shape or propulsion (biological noise). Highly symmetric cell shape can give highly directional swimming but is at risk of giving futile circular swimming paths in the presence of biological noise. This suggests the chiral T. brucei cell shape (associated with the lateral attachment of the flagellum) may be an adaptation associated with the bloodstream-inhabiting lifestyle of this parasite for robust highly directional swimming. It also provides a plausible general explanation for why swimming cells tend to have strong asymmetries in cell shape or propulsion. PMID:28141804

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.

Evidence for Helical Magnetic fields in Kiloparsec-Scale AGN Jets and the Action of a Cosmic Battery

NASA Technical Reports Server (NTRS)

Gabuzda, D. C.; Christodoulou, D. M.; Contopulos, I.; Kazanas, D.

2012-01-01

A search for transverse kiloparsec-scale gradients in Faraday rotation-measure (RM) maps of extragalactic radio sources in the literature has yielded 6 AGNs displaying continuous, monotonic RM gradients across their jets, oriented roughly orthogonal to the local jet direction. The most natural interpretation of such transverse RM gradients is that they are caused by the systematic change in the line-of-sight components of helical magnetic fields associated with these jets. All the identified transverse RM gradients increase in the counterclockwise (CCW) direction on the sky relative to the centers of these AGNs. Taken together with the results of Contopoulos et al. who found evidence for a predominance of clockwise (CW) transverse RM gradients across parsec-scale (VLBI) jets, this provides new evidence for preferred orientations of RM gradients due to helical jet magnetic fields, with a reversal from CW in the inner jets to CCW farther from the centers of activity. This can be explained by the "Poynting-Robertson cosmic-battery" mechanism, which can generate helical magnetic fields with a. characteristic "twist," which are expelled with the jet outflows. If the Poynting-Robertson battery mechanism is not operating, an alternative mechanism must be identified, which is able to explain the 'predominance of CW /CCW RM gradients on parsec/kiloparsec scales.

Modeling the locomotion of the African trypanosome using multi-particle collision dynamics

NASA Astrophysics Data System (ADS)

Babu, Sujin B.; Stark, Holger

2012-08-01

The African trypanosome is a single flagellated micro-organism that causes the deadly sleeping sickness in humans and animals. We study the locomotion of a model trypanosome by modeling the spindle-shaped cell body using an elastic network of vertices with additional bending rigidity. The flagellum firmly attached to the model cell body is either straight or helical. A bending wave propagates along the flagellum and pushes the trypanosome forward in its viscous environment, which we simulate with the method of multi-particle collision dynamics. The relaxation dynamics of the model cell body due to a static bending wave reveals the sperm number from elastohydrodynamics as the relevant parameter. Characteristic cell body conformations for the helically attached flagellum resemble experimental observations. We show that the swimming velocity scales as the root of the angular frequency of the bending wave reminiscent of predictions for an actuated slender rod attached to a large viscous load. The swimming velocity for one geometry collapses on a single master curve when plotted versus the sperm number. The helically attached flagellum leads to a helical swimming path and a rotation of the model trypanosome about its long axis as observed in experiments. The simulated swimming velocity agrees with the experimental value.

Rotation profile flattening and toroidal flow shear reversal due to the coupling of magnetic islands in tokamaks

DOE PAGES

Tobias, B.; Chen, M.; Classen, I. G. J.; ...

2016-04-15

The electromagnetic coupling of helical modes, including those having different toroidal mode numbers, modifies the distribution of toroidal angular momentum in tokamak discharges. This can have deleterious effects on other transport channels as well as on magnetohydrodynamic (MHD) stability and disruptivity. At low levels of externally injected momentum, the coupling of core-localized modes initiates a chain of events, whereby flattening of the core rotation profile inside successive rational surfaces leads to the onset of a large m/n = 2/1 tearing mode and locked-mode disruption. Furthermore, with increased torque from neutral beam injection, neoclassical tearing modes in the core may phase-lockmore » to each other without locking to external fields or structures that are stationary in the laboratory frame. The dynamic processes observed in these cases are in general agreement with theory, and detailed diagnosis allows for momentum transport analysis to be performed, revealing a significant torque density that peaks near the 2/1 rational surface. However, as the coupled rational surfaces are brought closer together by reducing q95, additional momentum transport in excess of that required to attain a phase-locked state is sometimes observed. Rather than maintaining zero differential rotation (as is predicted to be dynamically stable by single-fluid, resistive MHD theory), these discharges develop hollow toroidal plasma fluid rotation profiles with reversed plasma flow shear in the region between the m/n = 3/2 and 2/1 islands. Additional forces expressed in this state are not readily accounted for, and therefore, analysis of these data highlights the impact of mode coupling on torque balance and the challenges associated with predicting the rotation dynamics of a fusion reactor-a key issue for ITER. Published by AIP Publishing.« less

Rotation profile flattening and toroidal flow shear reversal due to the coupling of magnetic islands in tokamaks

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

Tobias, B.; Grierson, B. A.; Okabayashi, M.

2016-05-15

The electromagnetic coupling of helical modes, even those having different toroidal mode numbers, modifies the distribution of toroidal angular momentum in tokamak discharges. This can have deleterious effects on other transport channels as well as on magnetohydrodynamic (MHD) stability and disruptivity. At low levels of externally injected momentum, the coupling of core-localized modes initiates a chain of events, whereby flattening of the core rotation profile inside successive rational surfaces leads to the onset of a large m/n = 2/1 tearing mode and locked-mode disruption. With increased torque from neutral beam injection, neoclassical tearing modes in the core may phase-lock to each othermore » without locking to external fields or structures that are stationary in the laboratory frame. The dynamic processes observed in these cases are in general agreement with theory, and detailed diagnosis allows for momentum transport analysis to be performed, revealing a significant torque density that peaks near the 2/1 rational surface. However, as the coupled rational surfaces are brought closer together by reducing q{sub 95}, additional momentum transport in excess of that required to attain a phase-locked state is sometimes observed. Rather than maintaining zero differential rotation (as is predicted to be dynamically stable by single-fluid, resistive MHD theory), these discharges develop hollow toroidal plasma fluid rotation profiles with reversed plasma flow shear in the region between the m/n = 3/2 and 2/1 islands. The additional forces expressed in this state are not readily accounted for, and therefore, analysis of these data highlights the impact of mode coupling on torque balance and the challenges associated with predicting the rotation dynamics of a fusion reactor—a key issue for ITER.« less

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.

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.

Fine Structure of the Core of the Blazar OJ 287-I

NASA Astrophysics Data System (ADS)

Matveyenko, L. I.; Sivakon', S. S.

2017-12-01

The fine structure of the active region, the bulge, of the blazar OJ 287 has been investigated with a resolution of 20 μas (0.1 pc) at a wavelength of 7 mm, the epochs of 2007-2017. The structure and kinematics correspond to a vortex nature. The surrounding matter, the plasma, is transferred to the center along two arms from opposite directions. The emerging excess angular momentum is carried away along the rotation axis by bipolar outflows, rotating coaxial tubes, in a direction X ≈ -120° in the plane of the sky as it is accumulated. The central high-velocity bipolar outflow has a helical shape. The diameters of the low-velocity flows are ø1 ≈ 0.3 and ø2 ≈ 0.65 mas, or 1.4 and 3 pc, respectively. Ring currents whose tangential directions are observed as parallel chains of components are excited in the flow walls. The peak brightness temperature of the nozzle reaches Tb ≈ 1012-1013 K. A "disk" with a diameter ø ≈ 0.5 mas (≈2.2 pc) is observed by the absorption of synchrotron radiation. The disk is inclined to the plane of the sky at an angle of 60° in the jet direction. The fragments are seen from a distance of ˜0.2 mas outside the absorption zone. The jet sizes exceed considerably the counterjet ones. An enhanced supply of plasma from the northern arm gives rise to an independent vortex 0.2 mas away from the central one in the NW direction. As in the first case, the helical central bipolar outflow is surrounded by a low-velocity component ø ≈ 0.28 mas in diameter with built-in ring currents. The jet is ejected in the direction X = -50° in the plane of the sky. The jet orientation changes, X = -130° at a distance of 1 mas. A high activity of the central and two side nozzles spaced 0.22 mas apart in the direction X = -40° is occasionally observed simultaneously. The active region of the blazar is observed through an ionized medium, a screen, whose influence is significant even at a wavelength of 7 mm. The absorption and refraction of the transmitted emission in the screen affect the apparent brightness relative to the positions of the fragments.

Bacteria exploit a polymorphic instability of the flagellar filament to escape from traps.

PubMed

Kühn, Marco J; Schmidt, Felix K; Eckhardt, Bruno; Thormann, Kai M

2017-06-13

Many bacterial species swim by rotating single polar helical flagella. Depending on the direction of rotation, they can swim forward or backward and change directions to move along chemical gradients but also to navigate their obstructed natural environment in soils, sediments, or mucus. When they get stuck, they naturally try to back out, but they can also resort to a radically different flagellar mode, which we discovered here. Using high-speed microscopy, we monitored the swimming behavior of the monopolarly flagellated species Shewanella putrefaciens with fluorescently labeled flagellar filaments at an agarose-glass interface. We show that, when a cell gets stuck, the polar flagellar filament executes a polymorphic change into a spiral-like form that wraps around the cell body in a spiral-like fashion and enables the cell to escape by a screw-like backward motion. Microscopy and modeling suggest that this propagation mode is triggered by an instability of the flagellum under reversal of the rotation and the applied torque. The switch is reversible and bacteria that have escaped the trap can return to their normal swimming mode by another reversal of motor direction. The screw-type flagellar arrangement enables a unique mode of propagation and, given the large number of polarly flagellated bacteria, we expect it to be a common and widespread escape or motility mode in complex and structured environments.

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.

Polymer dynamics driven by a helical filament

NASA Astrophysics Data System (ADS)

Balin, Andrew; Shendruk, Tyler; Zoettl, Andreas; Yeomans, Julia

Microbial flagellates typically inhabit complex suspensions of extracellular polymeric material which can impact the swimming speed of motile microbes, filter-feeding of sessile cells, and the generation of biofilms. There is currently a need to better understand how the fundamental dynamics of polymers near active cells or flagella impacts these various phenomena. We study the hydrodynamic and steric influence of a rotating helical filament on suspended polymers using Stokesian Dynamics simulations. Our results show that as a stationary rotating helix pumps fluid along its long axis, nearby polymers migrate radially inwards and are elongated in the process. We observe that the actuation of the helix tends to increase the probability of finding polymeric material within its pervaded volume. At larger Weissenberg numbers, this accumulation of polymers within the vicinity of the helix is greater. Further, we have analysed the stochastic work performed by the helix on the polymers and we show that this quantity is positive on average and increases with polymer contour length. Our results provide a basis for understanding the microscopic interactions that govern cell dynamics in complex media. This work was supported through funding from the ERC Advanced Grant 291234 MiCE and we acknowledge EMBO funding to TNS (ALTF181-2013).

Circularly polarized harmonic generation by intense bicircular laser pulses: electron recollision dynamics and frequency dependent helicity

NASA Astrophysics Data System (ADS)

Bandrauk, André D.; Mauger, François; Yuan, Kai-Jun

2016-12-01

Numerical solutions of time-dependent Schrödinger equations for one and two electron cyclic molecules {{{H}}}nq+ exposed to intense bichromatic circularly polarized laser pulses of frequencies {ω }1 and {ω }2, such that {ω }1/{ω }2={n}1/{n}2 (integer) produce circularly polarized high order harmonics with a cut-off recollision maximum energy at and greater than the linear polarization law (in atomic units) {N}m{ω }1={I}p+3.17{U}p, where I p is the ionization potential and {U}p={(2{E}0)}2/4{ω }2 is the ponderomotive energy defined by the field E 0 (intensity I={{cE}}02/8π ) from each pulse and mean frequency ω =({ω }1+{ω }2)/2 . An electron recollision model in a rotating frame at rotating frequency {{Δ }}ω =({ω }1-{ω }2)/2 predicts this simple result as a result of recollision dynamics in a combination of bichromatic circularly polarized pulses. The harmonic helicities and their intensities are shown to depend on compatible symmetries of the net pulse electric fields with that of the molecules.

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.

The structural coupling between ATPase activation and recovery stroke in the myosin II motor

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

Koppole, Sampath; Smith, Jeremy C; Fischer, S.

2007-07-01

Before the myosin motor head can perform the next power stroke, it undergoes a large conformational transition in which the converter domain, bearing the lever arm, rotates {approx} 65{sup o}. Simultaneous with this 'recovery stroke', myosin activates its ATPase function by closing the Switch-2 loop over the bound ATP. This coupling between the motions of the converter domain and of the 40 {angstrom}-distant Switch-2 loop is essential to avoid unproductive ATP hydrolysis. The coupling mechanism is determined here by finding a series of optimized intermediates between crystallographic end structures of the recovery stroke (Dictyostelium discoideum), yielding movies of the transitionmore » at atomic detail. The successive formation of two hydrogen bonds by the Switch-2 loop is correlated with the successive see-saw motions of the relay and SH1 helices that hold the converter domain. SH1 helix and Switch-2 loop communicate via a highly conserved loop that wedges against the SH1-helix upon Switch-2 closing.« less

The cuttlefish Sepia officinalis (Sepiidae, Cephalopoda) constructs cuttlebone from a liquid-crystal precursor

PubMed Central

Checa, Antonio G.; Cartwright, Julyan H. E.; Sánchez-Almazo, Isabel; Andrade, José P.; Ruiz-Raya, Francisco

2015-01-01

Cuttlebone, the sophisticated buoyancy device of cuttlefish, is made of extensive superposed chambers that have a complex internal arrangement of calcified pillars and organic membranes. It has not been clear how this structure is assembled. We find that the membranes result from a myriad of minor membranes initially filling the whole chamber, made of nanofibres evenly oriented within each membrane and slightly rotated with respect to those of adjacent membranes, producing a helical arrangement. We propose that the organism secretes a chitin–protein complex, which self-organizes layer-by-layer as a cholesteric liquid crystal, whereas the pillars are made by viscous fingering. The liquid crystallization mechanism permits us to homologize the elements of the cuttlebone with those of other coleoids and with the nacreous septa and the shells of nautiloids. These results challenge our view of this ultra-light natural material possessing desirable mechanical, structural and biological properties, suggesting that two self-organizing physical principles suffice to understand its formation. PMID:26086668

The structural coupling between ATPase activation and recovery stroke in the myosin II motor.

PubMed

Koppole, Sampath; Smith, Jeremy C; Fischer, Stefan

2007-07-01

Before the myosin motor head can perform the next power stroke, it undergoes a large conformational transition in which the converter domain, bearing the lever arm, rotates approximately 65 degrees . Simultaneous with this "recovery stroke," myosin activates its ATPase function by closing the Switch-2 loop over the bound ATP. This coupling between the motions of the converter domain and of the 40 A-distant Switch-2 loop is essential to avoid unproductive ATP hydrolysis. The coupling mechanism is determined here by finding a series of optimized intermediates between crystallographic end structures of the recovery stroke (Dictyostelium discoideum), yielding movies of the transition at atomic detail. The successive formation of two hydrogen bonds by the Switch-2 loop is correlated with the successive see-saw motions of the relay and SH1 helices that hold the converter domain. SH1 helix and Switch-2 loop communicate via a highly conserved loop that wedges against the SH1-helix upon Switch-2 closing.

Structural Mechanism of Voltage-Dependent Gating in an Isolated Voltage-Sensing Domain

PubMed Central

Li, Qufei; Wanderling, Sherry; Paduch, Marcin; Medovoy, David; Singharoy, Abhishek; McGreevy, Ryan; Villalba-Galea, Carlos; Hulse, Raymond E.; Roux, Benoit; Schulten, Klaus; Kossiakoff, Anthony; Perozo, Eduardo

2014-01-01

SUMMARY The transduction of transmembrane electric fields into protein motion plays an essential role in the generation and propagation of cellular signals. Voltage-sensing domains (VSD) carry out these functions through reorientations of S4 helix with discrete gating charges. Here, crystal structures of the VSD from Ci-VSP were determined in both, active (Up) and resting (Down) conformations. The S4 undergoes a ~5 Å displacement along its main axis accompanied by a ~60o rotation, consistent with the helix-screw gating mechanism. This movement is stabilized by a change in countercharge partners in helices S1 and S3, generating an estimated net charge transfer of ~1 eo. Gating charges move relative to a “hydrophobic gasket” that electrically divides intra and extracellular compartments. EPR spectroscopy confirms the limited nature of S4 movement in a membrane environment. These results provide an explicit mechanism for voltage sensing and set the basis for electromechanical coupling in voltage-dependent cellular activities. PMID:24487958

Structural and biomechanical characterizations of porcine myocardial extracellular matrix

PubMed Central

Wang, Bo; Tedder, Mary E.; Perez, Clara E.; Wang, Guangjun; de Jongh Curry, Amy L.; To, Filip; Elder, Steven H.; Williams, Lakiesha N.; Simionescu, Dan T.; Liao, Jun

2012-01-01

Extracellular matrix (ECM) of myocardium plays an important role to maintain a multilayered helical architecture of cardiomyocytes. In this study, we have characterized the structural and biomechanical properties of porcine myocardial ECM. Fresh myocardium were decellularized in a rotating bioreactor using 0.1 % sodium dodecyl sulfate solution. Masson’s trichrome staining and SEM demonstrated the removal of cells and preservation of the interconnected 3D cardiomyocyte lacunae. Movat’s pentachrome staining showed the preservation of cardiac elastin ultrastructure and vascular elastin distribution/alignment. DNA assay result confirmed a 98.59 % reduction in DNA content; the acellular myocardial scaffolds were found completely lack of staining for the porcine α-Gal antigen; and the accelerating enzymatic degradation assessment showed a constant degradation rate. Tensile and shear properties of the acellular myocardial scaffolds were also evaluated. Our observations showed that the acellular myocardial ECM possessed important traits of biodegradable scaffolds, indicating the potentials in cardiac regeneration and whole heart tissue engineering. PMID:22584822

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

Study on the Application of the Combination of TMD Simulation and Umbrella Sampling in PMF Calculation for Molecular Conformational Transitions

PubMed Central

Wang, Qing; Xue, Tuo; Song, Chunnian; Wang, Yan; Chen, Guangju

2016-01-01

Free energy calculations of the potential of mean force (PMF) based on the combination of targeted molecular dynamics (TMD) simulations and umbrella samplings as a function of physical coordinates have been applied to explore the detailed pathways and the corresponding free energy profiles for the conformational transition processes of the butane molecule and the 35-residue villin headpiece subdomain (HP35). The accurate PMF profiles for describing the dihedral rotation of butane under both coordinates of dihedral rotation and root mean square deviation (RMSD) variation were obtained based on the different umbrella samplings from the same TMD simulations. The initial structures for the umbrella samplings can be conveniently selected from the TMD trajectories. For the application of this computational method in the unfolding process of the HP35 protein, the PMF calculation along with the coordinate of the radius of gyration (Rg) presents the gradual increase of free energies by about 1 kcal/mol with the energy fluctuations. The feature of conformational transition for the unfolding process of the HP35 protein shows that the spherical structure extends and the middle α-helix unfolds firstly, followed by the unfolding of other α-helices. The computational method for the PMF calculations based on the combination of TMD simulations and umbrella samplings provided a valuable strategy in investigating detailed conformational transition pathways for other allosteric processes. PMID:27171075

Biopolymer Chain Elasticity: a novel concept and a least deformation energy principle predicts backbone and overall folding of DNA TTT hairpins in agreement with NMR distances

PubMed Central

Pakleza, Christophe; Cognet, Jean A. H.

2003-01-01

A new molecular modelling methodology is presented and shown to apply to all published solution structures of DNA hairpins with TTT in the loop. It is based on the theory of elasticity of thin rods and on the assumption that single-stranded B-DNA behaves as a continuous, unshearable, unstretchable and flexible thin rod. It requires four construction steps: (i) computation of the tri-dimensional trajectory of the elastic line, (ii) global deformation of single-stranded helical DNA onto the elastic line, (iii) optimisation of the nucleoside rotations about the elastic line, (iv) energy minimisation to restore backbone bond lengths and bond angles. This theoretical approach called ‘Biopolymer Chain Elasticity’ (BCE) is capable of reproducing the tri-dimensional course of the sugar–phosphate chain and, using NMR-derived distances, of reproducing models close to published solution structures. This is shown by computing three different types of distance criteria. The natural description provided by the elastic line and by the new parameter, Ω, which corresponds to the rotation angles of nucleosides about the elastic line, offers a considerable simplification of molecular modelling of hairpin loops. They can be varied independently from each other, since the global shape of the hairpin loop is preserved in all cases. PMID:12560506

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.

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