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Sample records for 1d helical chains

  1. The Eigenstate Thermalization Hypothesis in 1D Anyon Chains

    NASA Astrophysics Data System (ADS)

    Burnell, Fiona; Chandran, Anushya; Schulz, Marc

    For ergodic systems with Hilbert spaces satisfying a local product structure, the eigenstate thermalization hypothesis (ETH) is relatively well-established. Using exact diagonalization studies, we investigate whether quantum spin chains based on SU(2)_k anyon theories, which do not admit a Hilbert space with an exactly local product structure, also satisfy ETH, and which observables exhibit this behaviour.

  2. Stable double helical iodine chains inside single-walled carbon nanotubes

    NASA Astrophysics Data System (ADS)

    Yao, Zhen; Liu, Chun-Jian; Lv, Hang; Liu, Bing-Bing

    2016-08-01

    The helicity of stable double helical iodine chains inside single-walled carbon nanotubes (SWCNTs) is studied by calculating the systematic interaction energy. Our results present clear images of stable double helical structures inside SWCNTs. The optimum helical radius and helical angle increase and decrease with increasing diameter, respectively. The tube's diameter plays a leading role in the helicity of encapsulated structures, while the tube's chirality may induce different metastable structures. This study indicates that the observed double helical iodine chains in experiments are not necessarily the optimum structures, but may also be metastable structures.

  3. Stable single helical C- and I-chains inside single-walled carbon nanotubes

    NASA Astrophysics Data System (ADS)

    Yao, Z.; Liu, C. J.; Li, Y.; Jing, X. D.; Meng, F. S.; Zheng, S. P.; Zhao, X.; Li, J. H.; Qiu, Z. Y.; Yuan, Q.; Wang, W. X.; Bi, L.; Liu, H.; Zhang, Y. P.; Liu, B. B.

    2016-09-01

    The helicity of stable single helical carbon chains and iodine chains inside single-walled carbon nanotubes (SWCNTs) is studied by calculating the systematic van der Waals interaction energy. The results show that the optimal helical radius increases linearly with increasing tube radius, which produces a constant separation between the chain structure and the tube wall. The helical angle exhibits a ladder-like decrease with increasing tube radius, indicating that a large tube can produce a small helicity in the helical structures. Project supported by the National Basic Research Program of China (Grant No. 2011CB808200), the National Natural Science Foundation of China (Grant Nos. 11504150 and 51320105007), and the Cheung Kong Scholars Program of China.

  4. Cooperative microexcitations in 2+1D chain-bundle dusty plasma liquids

    SciTech Connect

    Io, C.-W.; Chan, C.-L.; Lin I

    2010-05-15

    Through direct visualization at the discrete level, the microexcitations in cold 2+1D dusty plasma liquids formed by negatively charged dusts suspended in low pressure gaseous discharges were experimentally investigated, in which the downward ion flow wake field induces strong vertical coupling and chain bundle structure. It is found that the horizontal structure and motion are similar to those of the two-dimensional liquid. Different types of basic cooperative chain excitations: straight vertical chains with small amplitude jittering, chain tilting-restraightening, bundle twisting-restraightening, and chain breaking-reconnection, are observed. The region with good (poor) horizontal structural order prefers the straight (tilted or broken) chains with little (large) titling and tilting rate.

  5. Cooperative microexcitations in 2+1D chain-bundle dusty plasma liquids

    NASA Astrophysics Data System (ADS)

    Io, Chong-Wai; Chan, Chia-Ling; I, Lin

    2010-05-01

    Through direct visualization at the discrete level, the microexcitations in cold 2+1D dusty plasma liquids formed by negatively charged dusts suspended in low pressure gaseous discharges were experimentally investigated, in which the downward ion flow wake field induces strong vertical coupling and chain bundle structure. It is found that the horizontal structure and motion are similar to those of the two-dimensional liquid. Different types of basic cooperative chain excitations: straight vertical chains with small amplitude jittering, chain tilting-restraightening, bundle twisting-restraightening, and chain breaking-reconnection, are observed. The region with good (poor) horizontal structural order prefers the straight (tilted or broken) chains with little (large) titling and tilting rate.

  6. A metallic carbon consisting of helical carbon triangle chains.

    PubMed

    Hu, Meng; Dong, Xiao; Pan, Yilong; Xu, Bo; Yu, Dongli; He, Julong

    2014-06-11

    Carbon is the basis of life on Earth and many technological applications. We computationally report an sp3-hybridization-assembled carbon allotrope constructed by helical triangle chains through the evolutionary structure prediction method. Different from the previous metallic carbon K4, this carbon, called Tri-carbon, is mechanically and dynamically stable at ambient pressure. High ring strain in the carbon triangle blocks forces the C–C bond in Tri-carbon to be a 'bent bond', rather than the common single bond in diamond or the π bond in graphite. Unlike the unstrained sp3-hybridization in semiconductive diamond, valence electrons in the 'bent bond' are recombined to form extremely anisotropic sp3-hybridized bonds, thus conferring metallicity to Tri-carbon. Under nonhydrostatic conditions, Tri-carbon shows significantly anisotropic ideal tensile and compressive strength. Tri-carbon is expected to be achieved through chemical methods, such as the synthesis of cyclopropane derivatives (e.g. triangulane and tetrahedrane). These methods eliminate the restriction of ultra-high pressure to obtain metallic carbons.

  7. A metallic carbon consisting of helical carbon triangle chains.

    PubMed

    Hu, Meng; Dong, Xiao; Pan, Yilong; Xu, Bo; Yu, Dongli; He, Julong

    2014-06-11

    Carbon is the basis of life on Earth and many technological applications. We computationally report an sp3-hybridization-assembled carbon allotrope constructed by helical triangle chains through the evolutionary structure prediction method. Different from the previous metallic carbon K4, this carbon, called Tri-carbon, is mechanically and dynamically stable at ambient pressure. High ring strain in the carbon triangle blocks forces the C–C bond in Tri-carbon to be a 'bent bond', rather than the common single bond in diamond or the π bond in graphite. Unlike the unstrained sp3-hybridization in semiconductive diamond, valence electrons in the 'bent bond' are recombined to form extremely anisotropic sp3-hybridized bonds, thus conferring metallicity to Tri-carbon. Under nonhydrostatic conditions, Tri-carbon shows significantly anisotropic ideal tensile and compressive strength. Tri-carbon is expected to be achieved through chemical methods, such as the synthesis of cyclopropane derivatives (e.g. triangulane and tetrahedrane). These methods eliminate the restriction of ultra-high pressure to obtain metallic carbons. PMID:25932471

  8. Propagation of excitation in long 1D chains: Transition from regular quantum dynamics to stochastic dynamics

    SciTech Connect

    Benderskii, V. A.; Kats, E. I.

    2013-01-15

    The quantum dynamics problem for a 1D chain consisting of 2N + 1 sites (N Much-Greater-Than 1) with the interaction of nearest neighbors and an impurity site at the middle differing in energy and in coupling constant from the sites of the remaining chain is solved analytically. The initial excitation of the impurity is accompanied by the propagation of excitation over the chain sites and with the emergence of Loschmidt echo (partial restoration of the impurity site population) in the recurrence cycles with a period proportional to N. The echo consists of the main (most intense) component modulated by damped oscillations. The intensity of oscillations increases with increasing cycle number and matrix element C of the interaction of the impurity site n = 0 with sites n = {+-}1 (0 < C {<=} 1; for the remaining neighboring sites, the matrix element is equal to unity). Mixing of the components of echo from neighboring cycles induces a transition from the regular to stochastic evolution. In the regular evolution region, the wave packet propagates over the chain at a nearly constant group velocity, embracing a number of sites varying periodically with time. In the stochastic regime, the excitation is distributed over a number of sites close to 2N, with the populations varying irregularly with time. The model explains qualitatively the experimental data on ballistic propagation of the vibrational energy in linear chains of CH{sub 2} fragments and predicts the possibility of a nondissipative energy transfer between reaction centers associated with such chains.

  9. Formation of Water Chains on CaO(001): What Drives the 1D Growth?

    PubMed

    Zhao, Xunhua; Shao, Xiang; Fujimori, Yuichi; Bhattacharya, Saswata; Ghiringhelli, Luca M; Freund, Hans-Joachim; Sterrer, Martin; Nilius, Niklas; Levchenko, Sergey V

    2015-04-01

    Formation of partly dissociated water chains is observed on CaO(001) films upon water exposure at 300 K. While morphology and orientation of the 1D assemblies are revealed from scanning tunneling microscopy, their atomic structure is identified with infrared absorption spectroscopy combined with density functional theory calculations. The latter exploit an ab initio genetic algorithm linked to atomistic thermodynamics to determine low-energy H2O configurations on the oxide surface. The development of 1D structures on the C4v symmetric CaO(001) is triggered by symmetry-broken water tetramers and a favorable balance between adsorbate-adsorbate versus adsorbate-surface interactions at the constraint of the CaO lattice parameter.

  10. Vibron properties in quasi 1D molecular structures: the case of two parallel unshifted macromolecuar chains

    NASA Astrophysics Data System (ADS)

    Čevizović, D.; Petković, S.; Galović, S.; Reshetnyak, A.; Chizhov, A.

    2016-01-01

    We study the hopping mechanism of the vibron excitation transport in the system of two parallel unshifted 1D macromolecuar chains in the framework of non-adiabatic polaron theory. We suppose that the vibron interaction with thermal oscillations of the macromolecular structural elements will result in vibron self-trapping and the formation of the partial dressed vibron state. We also suppose that quasiparticle motion takes place via a sequence of random sitejumps, in each of which the quasiparticle can migrate either to the first neighbor site of the macromolecular chain. With use of the modified Holstein polaron model, we calculate the vibron effective mass in dependence of the basic system parameters and temperature. Special attention is paid to the influence of interchain coupling on vibron dressing. We find that for certain values of the system parameters the quasiparticle mass abruptly changes.

  11. TCTEX1D4 Interactome in Human Testis: Unraveling the Function of Dynein Light Chain in Spermatozoa

    PubMed Central

    Freitas, Maria João; Korrodi-Gregório, Luís; Morais-Santos, Filipa; da Cruz e Silva, Edgar

    2014-01-01

    Abstract Studies were designed to identify the TCTEX1D4 interactome in human testis, with the purpose of unraveling putative protein complexes essential to male reproduction and thus novel TCTEX1D4 functions. TCTEX1D4 is a dynein light chain that belongs to the DYNT1/TCTEX1 family. In spermatozoa, it appears to be important to sperm motility, intraflagellar transport, and acrosome reaction. To contribute to the knowledge on TCTEX1D4 function in testis and spermatozoa, a yeast two-hybrid assay was performed in testis, which allowed the identification of 40 novel TCTEX1D4 interactors. Curiously, another dynein light chain, TCTEX1D2, was identified and its existence demonstrated for the first time in human spermatozoa. Immunofluorescence studies proved that TCTEX1D2 is an intra-acrosomal protein also present in the midpiece, suggesting a role in cargo movement in human spermatozoa. Further, an in silico profile of TCTEX1D4 revealed that most TCTEX1D4 interacting proteins were not previously characterized and the ones described present a very broad nature. This reinforces TCTEX1D4 as a dynein light chain that is capable of interacting with a variety of functionally different proteins. These observations collectively contribute to a deeper molecular understanding of the human spermatozoa function. PMID:24606217

  12. TCTEX1D4 interactome in human testis: unraveling the function of dynein light chain in spermatozoa.

    PubMed

    Freitas, Maria João; Korrodi-Gregório, Luís; Morais-Santos, Filipa; Cruz e Silva, Edgar da; Fardilha, Margarida

    2014-04-01

    Studies were designed to identify the TCTEX1D4 interactome in human testis, with the purpose of unraveling putative protein complexes essential to male reproduction and thus novel TCTEX1D4 functions. TCTEX1D4 is a dynein light chain that belongs to the DYNT1/TCTEX1 family. In spermatozoa, it appears to be important to sperm motility, intraflagellar transport, and acrosome reaction. To contribute to the knowledge on TCTEX1D4 function in testis and spermatozoa, a yeast two-hybrid assay was performed in testis, which allowed the identification of 40 novel TCTEX1D4 interactors. Curiously, another dynein light chain, TCTEX1D2, was identified and its existence demonstrated for the first time in human spermatozoa. Immunofluorescence studies proved that TCTEX1D2 is an intra-acrosomal protein also present in the midpiece, suggesting a role in cargo movement in human spermatozoa. Further, an in silico profile of TCTEX1D4 revealed that most TCTEX1D4 interacting proteins were not previously characterized and the ones described present a very broad nature. This reinforces TCTEX1D4 as a dynein light chain that is capable of interacting with a variety of functionally different proteins. These observations collectively contribute to a deeper molecular understanding of the human spermatozoa function.

  13. Markov Chain Monte Carlo Sampling Methods for 1D Seismic and EM Data Inversion

    2008-09-22

    This software provides several Markov chain Monte Carlo sampling methods for the Bayesian model developed for inverting 1D marine seismic and controlled source electromagnetic (CSEM) data. The current software can be used for individual inversion of seismic AVO and CSEM data and for joint inversion of both seismic and EM data sets. The structure of the software is very general and flexible, and it allows users to incorporate their own forward simulation codes and rockmore » physics model codes easily into this software. Although the softwae was developed using C and C++ computer languages, the user-supplied codes can be written in C, C++, or various versions of Fortran languages. The software provides clear interfaces for users to plug in their own codes. The output of this software is in the format that the R free software CODA can directly read to build MCMC objects.« less

  14. Unique microporous NbO-type CoII/ZnII MOFs from double helical chains: Sorption and luminescent properties

    NASA Astrophysics Data System (ADS)

    Dong, Wen-Wen; Xia, Liang; Peng, Zhen; Zhao, Jun; Wu, Ya-Pan; Zhang, Jian; Li, Dong-Sheng

    2016-06-01

    Under solvothermal conditions, the reactions of CoII/ZnII ions with bent ligand 3-(pyridin-4-yl)-5-(pyrazin-2-yl)-1H-1,2,4-triazole (4-Hpzpt) afford two compounds {[M(4-pzpt)2] guest}n (guest=H2O, M=CoII (1), ZnII (2)). Both compounds are the thermally and hydrolytically robust 4-connected 3D NbO framework, which formed by double helical chains to give rise to 1D hollow nanochannel with uncoordinated nitrogens completely exposed on the pore surface. Compound 1 exhibits improved N2, CO2 and H2 uptake capacities, while compound 2 displays the strong luminescent emission with obvious red shift.

  15. Measurement-induced disturbance and thermal negativity in 1D optical lattice chain

    SciTech Connect

    Guo, Jin-Liang; Lin-Wang; Long, Gui-Lu

    2013-03-15

    We study the measurement-induced disturbance (MID) in a 1D optical lattice chain with nonlinear coupling. Special attention is paid to the difference between the thermal entanglement and MID when considering the influences of the linear coupling constant, nonlinear coupling constant and external magnetic field. It is shown that MID is more robust than thermal entanglement against temperature T and external magnetic field B, and MID may reveal more properties about quantum correlations of the system, which can be seen from the point of view that MID can be nonzero when there is no thermal entanglement and MID can detect the critical point of quantum phase transition at finite temperature. - Highlights: Black-Right-Pointing-Pointer The nonlinear coupling constant can strengthen the quantum correlation. Black-Right-Pointing-Pointer MID is more robust than entanglement against temperature and magnetic field. Black-Right-Pointing-Pointer MID exhibits more information about quantum correlation than entanglement. Black-Right-Pointing-Pointer MID can detect the critical point of quantum phase transition at finite temperature.

  16. Quantum Creep and Quantum-Creep Transitions in 1D Sine-Gordon Chains.

    PubMed

    Krajewski, Florian R; Müser, Martin H

    2004-01-23

    Discrete sine-Gordon (SG) chains are studied with path-integral molecular dynamics. Chains commensurate with the substrate show the transition from pinning to quantum creep at bead masses slightly larger than in the continuous SG model. Within the creep regime, a field-driven transition from creep to complete depinning is identified. The effects of disorder on the chain's dynamics depend on the potential's roughness exponent H. For example, quantum fluctuations are generally too small to depin the chain if H=1/2, while an H=0 chain can be pinned or unpinned depending on the bead masses. Thermal fluctuations always depin the chain. PMID:14753858

  17. A Porous Metal-Organic Framework with Helical Chain Building Units Exhibiting Facile Transition from Micro- to Meso-porosity

    SciTech Connect

    Park, Jinhee; Li, Jian-Rong; Carolina Sañudo, E.; Yuan, Daqiang; Zhou, Hong-Cai

    2012-01-01

    A metal–organic framework (MOF) with helical channels has been constructed by bridging helical chain secondary building units with 2,6-di-p-carboxyphenyl-4,4'-bipyridine ligands. The activated MOF shows permanent porosity and gas adsorption selectivity. Remarkably, the MOF exhibits a facile transition from micro- to meso-porosity.

  18. The Relationship Between the Sloshing and Breathing Frequencies in a 1D Vertically Aligned Dust Particle Chain

    NASA Astrophysics Data System (ADS)

    Kong, Jie; Qiao, Ke; Sabo, Hannah; Matthews, Lorin; Hyde, Truell

    2013-10-01

    When confined in a glass box placed on the lower powered electrode of a GEC rf reference cell, dust particles immersed in plasma can form vertically aligned 1D chains. Both the formation and subsequent structural changes within this vertically aligned dust chain are controlled by the rf power, since the rf power effects the ionization rate in the cell, the screening parameter and the charge on the dust particles. In this study, oscillations of a 1D vertically aligned dust particle chain are employed to investigate the dust charge and screening length through measurement of the resonance frequency. It will be shown that the relationship between the sloshing and breathing frequencies indicates that the ion streaming effect plays an important role in vertical oscillations and must be included in any structural analysis of the system.

  19. Inter-helical interactions in membrane proteins: analysis based on the local backbone geometry and the side chain interactions.

    PubMed

    Jha, Anupam Nath; Vishveshwara, Saraswathi

    2009-06-01

    The availability of a significant number of the structures of helical membrane proteins has prompted us to investigate the mode of helix-helix packing. In the present study, we have considered a dataset of alpha-helical membrane proteins representing structures solved from all the known superfamilies. We have described the geometry of all the helical residues in terms of local coordinate axis at the backbone level. Significant inter-helical interactions have been considered as contacts by weighing the number of atom-atom contacts, including all the side-chain atoms. Such a definition of local axis and the contact criterion has allowed us to investigate the inter-helical interaction in a systematic and quantitative manner. We show that a single parameter (designated as alpha), which is derived from the parameters representing the mutual orientation of local axes, is able to accurately capture the details of helix-helix interaction. The analysis has been carried out by dividing the dataset into parallel, anti-parallel, and perpendicular orientation of helices. The study indicates that a specific range of alpha value is preferred for interactions among the anti-parallel helices. Such a preference is also seen among interacting residues of parallel helices, however to a lesser extent. No such preference is seen in the case of perpendicular helices, the contacts that arise mainly due to the interaction of surface helices with the end of the trans-membrane helices. The study supports the prevailing view that the anti-parallel helices are well packed. However, the interactions between helices of parallel orientation are non-trivial. The packing in alpha-helical membrane proteins, which is systematically and rigorously investigated in this study, may prove to be useful in modeling of helical membrane proteins.

  20. From 1D chain to 3D network: A theoretical study on TiO{sub 2} low dimensional structures

    SciTech Connect

    Guo, Ling-ju; He, Tao; Zeng, Zhi

    2015-06-14

    We have performed a systematic study on a series of low dimensional TiO{sub 2} nanostructures under density functional theory methods. The geometries, stabilities, growth mechanism, and electronic structures of 1D chain, 2D ring, 2D ring array, and 3D network of TiO{sub 2} nanostructures are analyzed. Based on the Ti{sub 2}O{sub 4} building unit, a series of 1D TiO{sub 2} nano chains and rings can be built. Furthermore, 2D ring array and 3D network nanostructures can be constructed from 1D chains and rings. Among non-periodic TiO{sub 2} chain and ring structures, one series of ring structures is found to be more stable. The geometry model of the 2D ring arrays and 3D network structures in this work has provided a theoretical understanding on the structure information in experiments. Based on these semiconductive low dimensional structures, moreover, it can help to understand and design new hierarchical TiO{sub 2} nanostructure in the future.

  1. Topological defect formation in 1D and 2D spin chains realized by network of optical parametric oscillators

    NASA Astrophysics Data System (ADS)

    Hamerly, Ryan; Inaba, Kensuke; Inagaki, Takahiro; Takesue, Hiroki; Yamamoto, Yoshihisa; Mabuchi, Hideo

    2016-09-01

    A network of optical parametric oscillators (OPOs) is used to simulate classical Ising and XY spin chains. The collective nonlinear dynamics of this network, driven by quantum noise rather than thermal fluctuations, seeks out the Ising/XY ground state as the system transitions from below to above the lasing threshold. We study the behavior of this “Ising machine” for three canonical problems: a 1D ferromagnetic spin chain, a 2D square lattice and problems where next-nearest-neighbor couplings give rise to frustration. If the pump turn-on time is finite, topological defects form (domain walls for the Ising model, winding number and vortices for XY) and their density can be predicted from a numerical model involving a linear “growth stage” and a nonlinear “saturation stage”. These predictions are compared against recent data for a 10,000-spin 1D Ising machine.

  2. Single molecule magnet behavior observed in a 1-D dysprosium chain with quasi-D5h symmetry.

    PubMed

    Huang, Xing-Cai; Zhang, Ming; Wu, Dayu; Shao, Dong; Zhao, Xin-Hua; Huang, Wei; Wang, Xin-Yi

    2015-12-28

    Two one-dimensional (1-D) chain complexes with pentagonal bipyramidal Dy(III) centers have been synthesized and magnetically characterized. Field-induced single molecule magnet behavior has been revealed in both compounds, which is still rarely reported in a lanthanide compound with a pentagonal bipyramidal coordination geometry. Their crystal field parameters and orientations of the magnetic easy axes were obtained from the simulation of the magnetic data and the electrostatic model calculation. PMID:26593051

  3. Crystal structures and thermodynamics/kinetics of Zn(II) coordination polymers with helical chains

    NASA Astrophysics Data System (ADS)

    He, Tian; Yue, Ke-Fen; Zhao, Yi-xing; Chen, San-Ping; Zhou, Chun-sheng; Yan, Ni

    2016-07-01

    Solvothermal reactions of Zn(II) acetates and four V-shaped carboxylates ligands in the presence of 1,4-Bis(2-methyl-imidazol-1-yl)butane afforded four interesting Zn(II) coordination polymers with helical chains, namely, {[Zn(bib)(atibdc)]·2H2O}n (1), {[Zn(bib)(atbip)]·H2O}n (2), [Zn(bib)(2,2‧-tda)]}n (3) and {[Zn(bib)(5-tbipa)]·EtOH}n (4), (H2atibdc=5-amino-2,4,6-triiodoisophthalic acid, H2atbip=5-amino-2,4,6-tribromoisophthalic acid, 2,2‧-H2tad=2,2‧-thiodiacetic acid, 5-H2tbipa=5-tert-butyl-isophthalic acid). 1 reveals a 3D chiral framework with three kinds of helical chains along a, b and c axis. 2 shows a 2D step-type chiral framework with right-handed helical chains. 3 displays a wavelike 2D layer network possessing alternate left- and right-handed helical chains. 4 presents a four-connected 3D framework with zigzag and meso-helical chains. The different spacers and substituent group of carboxylic acid ligands may lead to the diverse network structures of 1-4. The fluorescent properties of complexes 1-4 were studied. In addition, the thermal decompositions properties of 1-4 were investigated by simultaneous TG/DTG-DSC technique. The apparent activation energy E and the pre-exponential factor (A) of skeleton collapse for the complexes 1-4 are calculated by the integral Kissinger's method and Ozawa-Doyle's method. The activation energy E (E1=209.658 kJ·mol-1, E2=250.037 kJ mol-1, E3=225.300 kJ mol-1, E4=186.529 kJ·mol-1) demonstrates that the reaction rate of the melting decomposition is slow. The thermodynamic parameters (ΔH‡, ΔG‡ and ΔS‡) at the peak temperatures of the DTG curves were also calculated. ΔG‡>0 indicates that the skeleton collapse is not spontaneous. ΔHd>0 suggests that the skeleton collapse is endothermic, corresponding to the intense endothermic peak of the DSC curve. The structural stability could be illustrated from the point of thermodynamics and kinetics. Their thermal decompositions properties of 1-4 were

  4. Multiple mobility edges in a 1D Aubry chain with Hubbard interaction in presence of electric field: Controlled electron transport

    NASA Astrophysics Data System (ADS)

    Saha, Srilekha; Maiti, Santanu K.; Karmakar, S. N.

    2016-09-01

    Electronic behavior of a 1D Aubry chain with Hubbard interaction is critically analyzed in presence of electric field. Multiple energy bands are generated as a result of Hubbard correlation and Aubry potential, and, within these bands localized states are developed under the application of electric field. Within a tight-binding framework we compute electronic transmission probability and average density of states using Green's function approach where the interaction parameter is treated under Hartree-Fock mean field scheme. From our analysis we find that selective transmission can be obtained by tuning injecting electron energy, and thus, the present model can be utilized as a controlled switching device.

  5. Weakly nonlinear localization for a 1-D FPU chain with clustering zones

    NASA Astrophysics Data System (ADS)

    Martínez-Farías, F.; Panayotaros, P.; Olvera, A.

    2014-12-01

    We study weakly nonlinear spatially localized solutions of a Fermi-Pasta-Ulam model describing a unidimensional chain of particles interacting with a number of neighbors that can vary from site to site. The interaction potential contains quadratic and quartic terms, and is derived from a nonlinear elastic network model proposed by Juanico et al. [1]. The FPU model can be also derived for arbitrary dimensions, under a small angular displacement assumption. The variable interaction range is a consequence of the spatial inhomogeneity in the equilibrium particle distribution. We here study some simple one-dimensional examples with only a few, well defined agglomeration regions. These agglomerations are seen to lead to spatially localized linear modes and gaps in the linear spectrum, which in turn imply a normal form that has spatially localized periodic orbits.

  6. Characterizing gapped phases of a 1D spin chain with on-site and spatial symmetries

    NASA Astrophysics Data System (ADS)

    West, Colin; Prakash, Abhishodh; Wei, Tzu-Chieh

    We investigate the phase diagram of a spin-1 chain whose Hamiltonian is invariant under translation, lattice inversion and a global A4 symmetry in the spin degrees of freedom. The classification scheme by Chen, Gu, and Wen allows us to enumerate all possible phases under the given symmetry. Then, we determine which of these phases actually occur in the two-parameter Hamiltonian. Using numerical methods proposed by Pollmann and Turner (2012) we determine the characteristic projective parameters for the Symmetry Protected Topological (SPT) phases. In addition, we present a method for determining the projective commutation parameter in these phases. The resulting phase diagram is rich and contains at least nine different SPT phases. This work was supported in part by the National Science Foundation.

  7. The role of solitons in charge and energy transfer in 1D molecular chains

    NASA Astrophysics Data System (ADS)

    Ivić , Zoran

    1998-03-01

    The idea that polarons and solitons could play the crucial role in the transport processes in biological structures, has been critically reexamined on the basis of the general theory of self-trapping phenomena. The criteria which enable one to determine conditions for the existence and stability of polarons and solitons and to determine their character, in dependence of the values of the basic physical parameters of the system, were formulated. Validity of the so-called Davydov's soliton model was discussed on the basis of these criteria. It was found that the original Davydov's proposal, based upon the idea of the soliton creation due to the single excitation (particle, vibron, etc.) self-trapping, cannot explain the intramolecular energy transfer in α-helix and acetanilide. However, Davydov theory is flexible enough to describe the single electron transfer in some systems (α-helix and acetanilide for example). In the many-particle systems, dressing effect, due to the quantum nature of phonons, may cause the creation of the bound states of the several excitons in the molecular chain. The possibility of creation of the soliton states of this type is discussed for the simple Fröhlich's one-dimensional model. The regions of the system parameter space where different mechanisms dominate the behaviour of such entities are characterized.

  8. Synthesis, structure, and electrochemistry and magnetic properties of a novel 1D homochiral MnIII(5-Brsalen) coordination polymer with left-handed helical character

    NASA Astrophysics Data System (ADS)

    Dong, Dapeng; Yu, Naisen; Zhao, Haiyan; Liu, Dedi; Liu, Jia; Li, Zhenghua; Liu, Dongping

    2016-01-01

    A novel homochiral manganese (III) Mn(5-Brsalen) coordination polymer with left-handed helical character by spontaneous resolution on crystallization by using Mn(5-Brsalen) and 4,4-bipyridine, [MnIII(5-Brsalen)(4,4-bipy)]·ClO4·CH3OH (1) (4,4-bipy = 4,4-bipyridine) has been synthesized and structurally characterized by X-ray single-crystal diffraction, elemental analysis and infrared spectroscopy. In compound 1, each manganese(III) anion is six-coordinate octahedral being bonded to four atoms of 5-Brsalen ligand in an equatorial plane and two nitrogen atoms from a 4,4-bipyridine ligand in axial positions. The structure of compound 1 can be described a supramolecular 2D-like structure which was formed by the intermolecular π-stacking interactions between the neighboring chains of the aromatic rings of 4,4-bipyridine and 5-Brsalen molecules. UV-vis absorption spectrum, electrochemistry and magnetic properties of the compound 1 have also been studied.

  9. Crystalline structures of polymeric hydrocarbon with 3,4-fold helical chains

    PubMed Central

    Lian, Chao-Sheng; Li, Han-Dong; Wang, Jian-Tao

    2015-01-01

    Molecular hydrocarbons are well-known to polymerize under pressure to form covalently bonded frameworks. Here we predict by ab initio calculations two distinct three-dimensional hydrocarbon crystalline structures composed of 3-fold and 4-fold helical CH chains in rhombohedral () and tetragonal (I41/a) symmetry, respectively. Both structures with 1:1 stoichiometry are found to be energetically more favorable than solid acetylene and cubane, and even more stable than benzene II solid at high pressure. The calculations on vibrational, electronic, and optical properties reveal that the new chiral hydrocarbons are dynamically stable with large bulk moduli around 200 GPa, and exhibit a transparent insulating behavior with indirect band gaps of 5.9 ~ 6.7 eV and anisotropic adsorption spectra. Such forms of hydrocarbon, once synthesized, would have wide applications in mechanical, optoelectronic, and biological materials. PMID:25579707

  10. Structural variation from heterometallic cluster-based 1D chain to heterometallic tetranuclear cluster: Syntheses, structures and magnetic properties

    NASA Astrophysics Data System (ADS)

    Zhang, Shu-Hua; Zhao, Ru-Xia; Li, He-Ping; Ge, Cheng-Min; Li, Gui; Huang, Qiu-Ping; Zou, Hua-Hong

    2014-08-01

    Using the solvothermal method, we present the comparative preparation of {[Co3Na(dmaep)3(ehbd)(N3)3]·DMF}n (1) and [Co2Na2(hmbd)4(N3)2(DMF)2] (2), where Hehbd is 3-ethoxy-2-hydroxy-benzaldehyde, Hhmbd is 3-methoxy-2-hydroxy-benzaldehyde, and Hdmaep is 2-dimethylaminomethyl-6-ethoxy-phenol, which was synthesized by an in-situ reaction. Complexes 1 and 2 were characterized by elemental analysis, IR spectroscopy, and X-ray single-crystal diffraction. Complex 1 is a novel heterometallic cluster-based 1-D chain and 2 is a heterometallic tetranuclear cluster. The {Co3IINa} and {Co2IINa2} cores display dominant ferromagnetic interaction from the nature of the binding modes through μ1,1,1-N3- (end-on, EO).

  11. Structural variation from heterometallic cluster-based 1D chain to heterometallic tetranuclear cluster: Syntheses, structures and magnetic properties

    SciTech Connect

    Zhang, Shu-Hua; Zhao, Ru-Xia; Li, He-Ping; Ge, Cheng-Min; Li, Gui; Huang, Qiu-Ping; Zou, Hua-Hong

    2014-08-15

    Using the solvothermal method, we present the comparative preparation of ([Co{sub 3}Na(dmaep){sub 3}(ehbd)(N{sub 3}){sub 3}]·DMF){sub n} (1) and [Co{sub 2}Na{sub 2}(hmbd){sub 4}(N{sub 3}){sub 2}(DMF){sub 2}] (2), where Hehbd is 3-ethoxy-2-hydroxy-benzaldehyde, Hhmbd is 3-methoxy-2-hydroxy-benzaldehyde, and Hdmaep is 2-dimethylaminomethyl-6-ethoxy-phenol, which was synthesized by an in-situ reaction. Complexes 1 and 2 were characterized by elemental analysis, IR spectroscopy, and X-ray single-crystal diffraction. Complex 1 is a novel heterometallic cluster-based 1-D chain and 2 is a heterometallic tetranuclear cluster. The (Co{sub 3}{sup II}Na) and (Co{sub 2}{sup II}Na{sub 2}) cores display dominant ferromagnetic interaction from the nature of the binding modes through μ{sub 1,1,1}-N{sub 3}{sup –} (end-on, EO). - Graphical abstract: Two novel cobalt complexes have been prepared. Compound 1 consists of tetranuclear (Co{sub 3}{sup II}Na) units, which further formed a 1-D chain. Compound 2 is heterometallic tetranuclear cluster. Two complexes display dominant ferromagnetic interaction. - Highlights: • Two new heterometallic complexes have been synthesized by solvothermal method. • The stereospecific blockade of the ligands in the synthesis system seems to be the most important synthetic parameter. • The magnetism studies show that 1 and 2 exhibit ferromagnetic interactions. • Complex 1 shows slowing down of magnetization and not blocking of magnetization.

  12. Single-Crystal-to-Single-Crystal Transformations in One Dimensional Ag-Eu Helical System

    SciTech Connect

    Cai, Yue-Peng; Zhout, Xiu-Xia; Zhout, Zheng-Yuan; Zhu, Shi-Zheng; Thallapally, Praveen K.; Liu, Jun

    2009-07-06

    Single-crystal-to-single-crystal transformation of 1-D 4d-4f coordination polymers have been investigated for the first time. It displays high selectivity for Mg2+ and can be used as magnesium ion-selective luminescent probe. More importantly, we observed the transformation of meso-helical chain to rac-helical chain as a function of temperature.

  13. Salivary histatin 5: dependence of sequence, chain length, and helical conformation for candidacidal activity.

    PubMed

    Raj, P A; Edgerton, M; Levine, M J

    1990-03-01

    Histatin 5 (Asp1-Ser-His-Ala4-Lys-Arg-His-His8-Gly-Tyr-Lys-Arg12-Lys-Ph e-His-Glu16-Lys-His - His-Ser20-His-Arg-Gly-Tyr24), one of the basic histidine-rich peptides present in human parotid saliva and several of its fragments, 1-16 (N16), 9-24 (C16), 11-24 (C14), 13-24 (C12), 15-24 (C10), and 7-16 (M10), were synthesized by solid-phase procedures. Native histatin 5 from human parotid saliva was also purified. Their antifungal activities on two strains of Candida albicans have been studied and their conformational preferences both in aqueous and non-aqueous solutions examined by circular dichroism. The synthetic histatin 5, C16, and C14 peptides were highly active and inhibited the growth of C. albicans. The candidacidal activity data of synthetic histatin 5 were comparable to the values of the native histatin 5 isolated from parotid saliva and those reported previously, although the assay system used and the strains examined were different. The C16 fragment was as active as the whole peptide itself, whereas the N16 fragment was far less active than C14, suggesting that the sequence at the C-terminal is important for its fungicidal activity. An increase in the chain length of the C-terminal sequence from 12 to 16 residues increased the candidacidal activity, thereby indicating that a peptide chain length of at least 12 residues is necessary to elicit optimum biological activity. The CD spectra of these linear peptides showed that they are structurally more flexible, and they adopt different conformations depending on the solvent environment. CD studies provided evidence that histatin 5 and the longer fragments, C16, N16, and C14 preferred alpha-helical conformations in non-aqueous solvents such as trifluoroethanol and methanol, while in water and pH 7.4 phosphate buffers, they favored random coil structures. The shorter sequences seemed to adopt either turn structures or unordered structures both in aqueous and non-aqueous solutions. It appears that the sequence at

  14. New Mononuclear Cu(II) Complexes and 1D Chains with 4-Amino-4H-1,2,4-triazole

    PubMed Central

    Dîrtu, Marinela M.; Boland, Yves; Gillard, Damien; Tinant, Bernard; Robeyns, Koen; Safin, Damir A.; Devlin, Eamonn; Sanakis, Yiannis; Garcia, Yann

    2013-01-01

    The crystal structures of two mononuclear Cu(II) NH2trz complexes [Cu(NH2trz)4(H2O)](AsF6)2 (I) and [Cu(NH2trz)4(H2O)](PF6)2 (II) as well as two coordination polymers [Cu(μ2-NH2trz)2Cl]Cl·H2O (III) and [Cu(μ2-NH2trz)2Cl] (SiF6)0.5·1.5H2O (IV) are presented. Cationic 1D chains with bridging bis-monodentate μ2-coordinated NH2trz and bridging μ2-coordinated chloride ligands are present in III and IV. In these coordination polymers, the Cu(II) ions are strongly antiferromagnetically coupled with J = −128.4 cm−1 for III and J = −143 cm−1 for IV (H = −J∑SiSi+1), due to the nature of the bridges between spin centers. Inter-chain interactions present in the crystal structures were taken into consideration, as well as g factors, which were determined experimentally, for the quantitative modeling of their magnetic properties. PMID:24300095

  15. New Carbon Allotropes with Helical Chains of Complementary Chirality Connected by Ethene-type π-Conjugation

    PubMed Central

    Wang, Jian-Tao; Chen, Changfeng; Kawazoe, Yoshiyuki

    2013-01-01

    We here identify by ab initio calculations two distinct three-dimensional three-connected (3D3C) chiral framework structures of carbon in and I41/amd symmetry, respectively, which comprise 3-fold and 4-fold helical chains with complementary chirality. The helical carbon chains are connected by an ethene-type planar π-conjugation, and the resulting structures contain a network of sp2 carbon bonds with one-third being double bonds between the chains and two-thirds single bonds along the chains. Phonon and electronic band structure calculations show that these chiral carbene structures are dynamically stable and exhibit a large band gap (2.4 ~ 2.9 eV). This semiconducting nature reflects a key distinction from previously proposed metallic isomers of helical or zigzag carbon chains with twisted π states that are dynamically unstable. The present results solve the long-sought 3D3C all-sp2 carbon structures and may help design other covalent bonding networks. PMID:24165546

  16. Spontaneous resolution of a racemic nickel(II) complex and helicity induction via hydrogen bonding: the effect of chiral building blocks on the helicity of one-dimensional chains.

    PubMed

    Ou, Guang-Chuan; Jiang, Long; Feng, Xiao-Long; Lu, Tong-Bu

    2008-04-01

    The reactions of a racemic four-coordinated nickel(II) complex [Ni(alpha-rac-L)](ClO4)2 (containing equal amount of SS and RR enantiomers) with l- and d-phenylalanine in acetonitrile/water gave two less-soluble six-coordinated enantiomers of {[Ni( f-SS-L)(l-Phe)](ClO4)}n (Delta-1) and {[Ni(f- RR-L)(d-Phe)](ClO4)}n (Lambda-1), respectively. Evaporation the remaining solutions gave two six-coordinated diastereomers of {[Ni 3(f- RR-L)3(l-Phe)2(H 2O)](ClO4)4}n (a-2) and {[Ni3(f- SS-L)3(d-Phe)2(H2O)](ClO4)4}n (b-2), respectively (L = 5,5,7,12,12,14-hexamethyl-1,4,8,11-tetraazacyclotetradecane, Phe(-) = phenylalanine anion). The reaction of [Ni(alpha-rac-L)](ClO4)2 with dl-Phe(-) gave a conglomerate of c-1; in which, the SS and RR enantiomers preferentially coordinate to l- and d-Phe(-) respectively to give a racemic mixture of Delta-1 and Lambda-1, and the spontaneous resolution occurs during the reaction, in which each crystal crystallizes to become enantiopure. Removing Phe(-) from Delta-1 and Lambda-1 using perchloric acid gave two enantiomers of [Ni(alpha-SS-L)](ClO4)2 (S-3) and [Ni(alpha-RR-L)](ClO4)2 (R-3). Dissolving S-3 and R-3 in acetonitrile gave two six-coordinated enantiomers of [Ni( f-SS-L)(CH3CN)2](ClO4)2 (S-4) and [Ni( f- RR-L)(CH3CN)2](ClO4)2 (R-4), while dissolving [Ni(alpha-rac-L)](ClO4)2 in acetonitrile gave a racemic twining complex [Ni(f-rac-L)(CH3CN)2](ClO4)2 (rac-4). Delta-1 and Lambda-1 belong to supramolecular stereoisomers, which are constructed via hydrogen bond linking of [Ni( f-SS-L)(l-Phe)](+) and [Ni(f-RR-L)(d-Phe)](+) monomers to form 1D homochiral right-handed and left-handed helical chains, respectively. The reaction of S-3 with d-Phe(-) gave {[Ni(f-SS-L)(d-Phe)](ClO4)}n (5), which shows a motif of a 1D hydrogen bonded zigzag chain instead of a 1D helical chain. Compound a-2/ b-2 contains dimers of [{Ni(f-RR-L)}2(l-Phe)(H2O)](3+)/[{Ni( f- SS-L)}2(d-Phe)(H2O)](3+) and 1D zigzag chains of {[Ni(f-RR-L)(l-Phe)](+)}n /{[Ni

  17. Statistical mechanics of helical wormlike chains. XVI. Excluded-volume effect on the mean-square electric dipole moment

    NASA Astrophysics Data System (ADS)

    Yoshizaki, Takenao; Yamakawa, Hiromi

    1993-03-01

    The expansion factor αμ for the mean-square electric dipole moment is studied on the basis of the helical wormlike chain with the excluded-volume effect incorporated in the Yamakawa-Stockmayer-Shimada scheme. A general expression is formulated for the first-order perturbation coefficient Kμ(L) for the chain of total contour length L. The asymptotic solution for Kμ(L) in the limit of L→∞ is evaluated analytically in the Daniels approximation by an application of the operational method. In contradiction to the common notion, it is found that, in the case of κ0τ0≠0 with κ0 and τ0 being the constant curvature and torsion, respectively, of the characteristic helix, Kμ(∞) does not vanish even for the chain having a local electric dipole moment vector perpendicular to the chain contour, indicating that αμ diverges with increasing molecular weight.

  18. Structural Origins of Nitroxide Side Chain Dynamics on Membrane Protein [alpha]-Helical Sites

    SciTech Connect

    Kroncke, Brett M.; Horanyi, Peter S.; Columbus, Linda

    2010-12-07

    Understanding the structure and dynamics of membrane proteins in their native, hydrophobic environment is important to understanding how these proteins function. EPR spectroscopy in combination with site-directed spin labeling (SDSL) can measure dynamics and structure of membrane proteins in their native lipid environment; however, until now the dynamics measured have been qualitative due to limited knowledge of the nitroxide spin label's intramolecular motion in the hydrophobic environment. Although several studies have elucidated the structural origins of EPR line shapes of water-soluble proteins, EPR spectra of nitroxide spin-labeled proteins in detergents or lipids have characteristic differences from their water-soluble counterparts, suggesting significant differences in the underlying molecular motion of the spin label between the two environments. To elucidate these differences, membrane-exposed {alpha}-helical sites of the leucine transporter, LeuT, from Aquifex aeolicus, were investigated using X-ray crystallography, mutational analysis, nitroxide side chain derivatives, and spectral simulations in order to obtain a motional model of the nitroxide. For each crystal structure, the nitroxide ring of a disulfide-linked spin label side chain (R1) is resolved and makes contacts with hydrophobic residues on the protein surface. The spin label at site I204 on LeuT makes a nontraditional hydrogen bond with the ortho-hydrogen on its nearest neighbor F208, whereas the spin label at site F177 makes multiple van der Waals contacts with a hydrophobic pocket formed with an adjacent helix. These results coupled with the spectral effect of mutating the i {+-} 3, 4 residues suggest that the spin label has a greater affinity for its local protein environment in the low dielectric than on a water-soluble protein surface. The simulations of the EPR spectra presented here suggest the spin label oscillates about the terminal bond nearest the ring while maintaining weak contact

  19. The synthesis and structure of a chiral 1D aluminophosphate chain compound: d-Co(en) 3[AlP 2O 8]·6.5H 2O

    NASA Astrophysics Data System (ADS)

    Chen, Peng; Li, Jiyang; Yu, Jihong; Wang, Yu; Pan, Qinhe; Xu, Ruren

    2005-06-01

    A new chiral one-dimensional (1D) aluminophosphate chain compound [ d-Co(en) 3][AlP 2O 8]·6.5H 2O (designated AlPO-CJ22) has been hydrothermally synthesized by using the optically pure d-Co(en) 3I 3 complex as the template. Single-crystal structural analysis reveals that its structure is built up from alternating connection of AlO 4 and PO 2(=O 2) tetrahedra to form corner-shared Al 2P 2 four-membered ring (4-MR) chains. The d-Co(en) 33+ complex cations extended along the 2 1 screw axis interact with the inorganic chains through hydrogen-bonds of N⋯O atoms in a helical fashion. Optical rotation measurement shows that AlPO-CJ22 is chiral as with d-Co(en) 33+ complex cations. Crystal data: orthorhombic, I2 12 12 1, a=8.5573(8) Å, b=22.613(2) Å, c=22.605(2) Å, Z=8, R1=0.067, wR2=0.1291, and Flack parameter: -0.02(3). CCDC number: 254179.

  20. 1D zigzag chain and 0D monomer Cd(II)/Zn(II) compounds based on flexible phenylenediacetic ligand: Synthesis, crystal structures and fluorescent properties

    NASA Astrophysics Data System (ADS)

    Yang, Fang; Ren, Yixia; Li, Dongsheng; Fu, Feng; Qi, Guangcai; Wang, Yaoyu

    2008-12-01

    Three novel Cd(II)/Zn(II) compounds, [Cd 2(poda) 2(phen) 3(H 2O)] n· nEtOH·3 nH 2O (1), [Zn(poda) 2(bpy)(H 2O)] n(2) and [Zn(Hpoda) 2(bpy)] (3) (H 2poda = 1,2-phenylenediacetic acid, phen = 1,10-phenanthroline, bpy = 2,2'-bipyridyl), have been synthesized and characterized by IR, TG, fluorescent spectrum and single-crystal X-ray diffraction techniques. In 1, poda 2- anions link the adjacent Cd(II) centers to generate a 1D zigzag chain. Furthermore, an unprecedented four-footed "8-shaped" mixed water-ethanol (H 2O) 6(C 2H 5OH) 2 cluster connects four double chains based on 1D zigzag chain into 3D supramolecular architecture. By bis(chelate-monodentate) fashion of poda 2- ligand, compound 2 exhibits 1D zigzag chains, which forming a dense zipper-like 2D structure via strong π-π stacking interactions. Differed from 1 and 2, compound 3 has a mononuclear motif, and displays a 3D 6-connected α-Po net hydrogen-bonded topology. The structure-related solid-state fluorescence spectra of compounds 1 and 2 have been determined.

  1. Two novel CPs with double helical chains based rigid tripodal ligands: Syntheses, crystal structures, magnetic susceptibility and fluorescence properties

    NASA Astrophysics Data System (ADS)

    Wang, Xiao; Hou, Xiang-Yang; Zhai, Quan-Guo; Hu, Man-Cheng

    2016-11-01

    Two three-dimensional coordination polymers (CPs), namely [Cd(bpydb)- (H2bpydb)]n·0.5nH2O (1), and [Cu2(bpydb)2]n (2) (2,6-di-p-carboxyphenyl-4,4'- bipyridine1 = H2bpydb), containing a novel double-helical chains, which have been solvothermal synthesized, characterized, and structure determination. CPs 1-2 reveal the new (3,5)-net and (3,6)-net alb topology, respectively. The fluorescence properties of CPs 1-2 were investigated, and magnetic susceptibility measurements indicate that compound 1 has dominating antiferromagnetic couplings between metal ions.

  2. A new carbon allotrope with six-fold helical chains in all-sp2 bonding networks.

    PubMed

    Wang, Jian-Tao; Chen, Changfeng; Wang, Enge; Kawazoe, Yoshiyuki

    2014-01-01

    Using a recently developed approach to constructing covalent network structures from linear carbyne, we identify by ab initio calculations a new carbon allotrope in R3m (D(3d)(5) symmetry that comprises six-fold helical chains with alternating sp(2)-type single and double bonds along the chains that are connected via zigzag benzene rings. This 6-fold carbene is characterized as a three-dimensional three-connected chiral crystalline modification of graphite. Phonon and electronic band calculations indicate that this new structure is dynamically stable and is a semiconductor with a band gap of 0.47 eV, in contrast to the semimetallic nature of graphite. Simulated x-ray diffraction patterns of the 6-fold carbene provide an excellent match to the previously unexplained distinct diffraction peak of a new carbon allotrope found in recent detonation experiments. These results establish a new carbon phase and offer insights into its outstanding structural and electronic properties.

  3. Poly(quinoxaline-2,3-diyl)s bearing (S)-3-octyloxymethyl side chains as an efficient amplifier of alkane solvent effect leading to switch of main-chain helical chirality.

    PubMed

    Nagata, Yuuya; Nishikawa, Tsuyoshi; Suginome, Michinori

    2014-11-12

    Poly(quinoxaline-2,3-diyl) containing (S)-3-octyloxymethyl side chains was synthesized to investigate the induction of a single-handed helical sense to the main chain in various alkane solvents. The polymer showed an efficient solvent dependent helix inversion between n-octane (M-helix) and cyclooctane (P-helix). After a screening of alkane solvents, it was found that linear alkanes having large molecular aspect ratios induced M-helical structure, and branched or cyclic alkanes having small molecular aspect ratios induced P-helical structure. A polymer ligand containing (S)-3-octyloxymethyl side chains and diphenylphosphino pendants also exhibited solvent-dependent helical inversion between n-octane and cyclooctane, leading to the highly enantioselective production of the both enantiomeric product in a palladium-catalyzed asymmetric hydrosilylation reaction of styrene (R-product 94% ee in n-octane and S-product 90% ee in cyclooctane). PMID:25343492

  4. Quantification of transition dipole strengths using 1D and 2D spectroscopy for the identification of molecular structures via exciton delocalization: Application to α-helices

    NASA Astrophysics Data System (ADS)

    Grechko, Maksim; Zanni, Martin T.

    2012-11-01

    Vibrational and electronic transition dipole strengths are often good probes of molecular structures, especially in excitonically coupled systems of chromophores. One cannot determine transition dipole strengths using linear spectroscopy unless the concentration is known, which in many cases it is not. In this paper, we report a simple method for measuring transition dipole moments from linear absorption and 2D IR spectra that does not require knowledge of concentrations. Our method is tested on several model compounds and applied to the amide I' band of a polypeptide in its random coil and α-helical conformation as modulated by the solution temperature. It is often difficult to confidently assign polypeptide and protein secondary structures to random coil or α-helix by linear spectroscopy alone, because they absorb in the same frequency range. We find that the transition dipole strength of the random coil state is 0.12 ± 0.013 D2, which is similar to a single peptide unit, indicating that the vibrational mode of random coil is localized on a single peptide unit. In an α-helix, the lower bound of transition dipole strength is 0.26 ± 0.03 D2. When taking into account the angle of the amide I' transition dipole vector with respect to the helix axis, our measurements indicate that the amide I' vibrational mode is delocalized across a minimum of 3.5 residues in an α-helix. Thus, one can confidently assign secondary structure based on exciton delocalization through its effect on the transition dipole strength. Our method will be especially useful for kinetically evolving systems, systems with overlapping molecular conformations, and other situations in which concentrations are difficult to determine.

  5. Co-assembly of Zn(SPh){sub 2} and organic linkers into helical and zig-zag polymer chains

    SciTech Connect

    Liu Yi; Yu Lingmin; Loo, Say Chye Joachim; Blair, Richard G.; Zhang Qichun

    2012-07-15

    Two novel one-dimensional coordination polymers, single helicate [Zn(SPh){sub 2}(TPyTA)(EG)]{sub n} (EG=ethylene glycol) (1) and zig-zag structure [Zn(SPh){sub 2}(BPyVB)]{sub n} (2), were synthesized under solvothermal conditions at 150 Degree-Sign C or room temperature by the co-assembly of Zn(SPh){sub 2} and organic linkers such as 2,4,6-tri(4-pyridyl)-1,3,5-triazine (TPyTA) and 1,3-bis(trans-4-pyridylvinyl)benzene (BPyVB). X-ray crystallography study reveals that both polymers 1 and 2 crystallize in space group P2{sub 1}/c of the monoclinic system. The solid-state UV-vis absorption spectra show that 1 and 2 have maxium absorption onsets at 400 nm and 420 nm, respectively. TGA analysis indicates that 1 and 2 are stable up to 110 Degree-Sign C and 210 Degree-Sign C. - Graphical abstract: Two novel one-dimensional coordination polymers, single helicate [Zn(SPh){sub 2}(TPyTA)(EG)]{sub n} (1) and zig-zag structure [Zn(SPh){sub 2}(BPyVB)]{sub n} (2), were synthesized. Solid-state UV-vis absorptions show that 1 and 2 have maxium absorption onsets at 400 nm and 420 nm, respectively. TGA analysis indicates that 1 and 2 are stable up to 110 Degree-Sign C and 210 Degree-Sign C. Highlights: Black-Right-Pointing-Pointer Two novel one-dimensional coordination polymers have been synthesized. Black-Right-Pointing-Pointer TPyTA results in helical structures in 1 while BPyVB leads to zig-zag chains in 2. Black-Right-Pointing-Pointer Solid-state UV-vis absorption spectra and TGA analysis of the title polymers were studied.

  6. Helical unwinding and side-chain unlocking unravel the outward open conformation of the melibiose transporter

    PubMed Central

    Wang, Li-Ying; Ravi, Vidhya M.; Leblanc, Gérard; Padrós, Esteve; Cladera, Josep; Perálvarez-Marín, Alex

    2016-01-01

    Molecular dynamics simulations have been used to study the alternate access mechanism of the melibiose transporter from Escherichia coli. Starting from the outward-facing partially occluded form, 2 out of 12 simulations produced an outward full open form and one partially open, whereas the rest yielded fully or partially occluded forms. The shape of the outward-open form resembles other outward-open conformations of secondary transporters. During the transporter opening, conformational changes in some loops are followed by changes in the periplasm region of transmembrane helix 7. Helical curvature relaxation and unlocking of hydrophobic and ionic locks promote the outward opening of the transporter making accessible the substrate binding site. In particular, FRET studies on mutants of conserved aromatic residues of extracellular loop 4 showed lack of substrate binding, emphasizing the importance of this loop for making crucial interactions that control the opening of the periplasmic side. This study indicates that the alternate access mechanism for the melibiose transporter fits better into a flexible gating mechanism rather than the archetypical helical rigid-body rocker-switch mechanism. PMID:27658476

  7. Supramolecular open-framework based on 1-D iron phosphate-diphosphate chains assembled through hydrogen bonding

    SciTech Connect

    Salvado, Miguel A.; Pertierra, Pilar; Trobajo, Camino; Garcia, Jose R.

    2008-05-15

    Fe(H{sub 2}PO{sub 4})(H{sub 2}P{sub 2}O{sub 7}).C{sub 5}H{sub 5}N, a new iron(III) phosphate with an open-framework has been synthesized hydrothermally using pyridine as organic template. The crystal structure was solved ab initio using conventional powder X-ray diffraction data. The unit cell is orthorhombic, a=9.5075(2), b=10.1079(1), c=13.3195(2) A, space group P2{sub 1}2{sub 1}2{sub 1}, Z=4. The structure consists of FeO{sub 6} octahedra joined by H{sub 2}PO{sub 4} and H{sub 2}P{sub 2}O{sub 7} groups forming linear chains interconnected by hydrogen bonding to give rise to a supramolecular framework enclosing tunnels in which the pyridine molecules reside. - Graphical abstract: The low temperature hydrothermal synthesis offers many possibilities in the preparation of new materials with mixed octahedral-tetrahedral open-frameworks. Fe(H{sub 2}PO{sub 4})(H{sub 2}P{sub 2}O{sub 7}).C{sub 5}H{sub 5}N is constituted by linear chains of FeO{sub 6} octahedra joined through of both dihydrogenphosphate and dihydrogendiphosphate bridges, interconnected by hydrogen bonds, originating channels where the pyridine molecules are located.

  8. Chiral single-chain magnet: helically stacked [Mn(III)2Cu(II)] triangles.

    PubMed

    Shiga, Takuya; Maruyama, Kazuya; Newton, Graham N; Inglis, Ross; Brechin, Euan K; Oshio, Hiroki

    2014-05-01

    The one-dimensional complex [Mn(III)2Cu(II)(μ3-O)(Cl-sao)3(EtOH)2]·EtOH (Mn2Cu) was obtained by the metal replacement reaction of the trinuclear manganese complex (Et3NH)[Mn(III)3(μ3-O)Cl2(Cl-sao)3(MeOH)2(H2O)2] with [Cu(acac)2]. The Mn2Cu chain exhibits single-chain-magnet behavior with finite-size effects due to its large magnetic anisotropy.

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

    PubMed

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

    2015-03-01

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

  10. Synthesis and characterization of a 1D chain-like Cu{sub 6} substituted sandwich-type phosphotungstate with pendant dinuclear Cu–azido complexes

    SciTech Connect

    Li, Yan-Ying; Zhao, Jun-Wei; Wei, Qi; Yang, Bai-Feng; Yang, Guo-Yu

    2014-02-15

    A novel Cu–azido complex modified hexa-Cu{sup II} substituted sandwich-type phosphotungstate [Cu(en){sub 2}]([Cu{sub 2}(en){sub 2}(μ-1,1-N{sub 3}){sub 2}(H{sub 2}O)]{sub 2}[Cu{sub 6}(en){sub 2}(H{sub 2}O){sub 2}(B-α-PW{sub 9}O{sub 34}){sub 2}])·6H{sub 2}O (1) (en=ethylene-diamine) has been prepared under hydrothermal conditions and structurally characterized by elemental analyses, IR spectra, powder X-ray diffraction (PXRD) and single-crystal X-ray diffraction. 1 displays a beautiful 1-D chain architecture constructed from sandwich-type [Cu{sub 2}(en){sub 2}(μ-1,1-N{sub 3}){sub 2}(H{sub 2}O)]{sub 2}[Cu{sub 6}(en){sub 2}(H{sub 2}O){sub 2}(B-α-PW{sub 9}O{sub 34}){sub 2}]{sup 2−} units and [Cu(en){sub 2}]{sup 2+} linkers. To our knowledge, 1 represents the first hexa-Cu{sup II} sandwiched phosphotungstate with supporting Cu–azido complexes. - Graphical abstract: The first hexa-Cu{sup II} sandwiched phosphotungstate with supporting Cu–azido complexes has been prepared and characterized. Display Omitted - Highlights: • Hexa-copper-substituted phosphotungstate. • Cu–azido complexes modified hexa-Cu{sup II} substituted sandwich-type polyoxometalate. • 1-D chain architecture built by hexa-copper-substituted polyoxotungstate units.

  11. Multi-dimensional transition-metal coordination polymers of 4,4'-bipyridine-N,N'-dioxide: 1D chains and 2D sheets.

    PubMed

    Jia, Junhua; Blake, Alexander J; Champness, Neil R; Hubberstey, Peter; Wilson, Claire; Schröder, Martin

    2008-10-01

    Reaction of 4,4'-bipyridine -N, N' -dioxide (L) with a variety of transition-metal salts in MeOH affords a range of coordination polymer products. For the complexes [FeCl 3(mu-L)] infinity, 1, and ([Cu(L) 2(OHMe) 2(mu-L)].2PF 6. n(solv)) infinity, 2, 1D chain structures are observed, whereas ([Mn(mu-L) 3].2ClO 4) infinity, 3, and ([Cu(mu-L) 3].2BF 4) infinity, 4, both show 2D sheet architectures incorporating an unusual 3 (6)- hxl topology. The more common 4 (4)- sql topology is observed in [Cd(ONO 2) 2(mu-L) 2] infinity, 5, ([Cu(OHMe) 2(mu-L) 2].2ZrF 5) infinity, 6, ([Cu(L) 2(mu-L) 2].2EF 6) infinity ( 7 E = P; 8 E = Sb), and ([Et 4N][Cu(OHMe) 0.5(mu-L) 2(mu-FSiF 4F) 0.5].2SbF 6. n(solv)) infinity, 9. In 6, the [ZrF 5] (-) anion, formed in situ from [ZrF 6] (2-), forms 1D anionic chains ([ZrF 5] (-)) infinity of vertex-linked octahedra, and these chains thread through a pair of inclined polycatenated ([Cu(OHMe) 2(mu-L) 2] (2+)) infinity 4 (4)- sql grids to give a rare example of a triply intertwined coordination polymer. 9 also shows a 3D matrix structure with 4 (4)- sql sheets of stoichiometry ([Cu(L) 2] (2+)) infinity coordinatively linked by bridging [SiF 6] (2-) anions to give a structure of 5-c 4 (4).6 (6)- sqp topology. The mononuclear [Cu(L) 6].2BF 4 ( 10) and [Cd(L) 6].2NO 3 ( 11) and binuclear complexes [(Cu(L)(OH 2)) 2(mu-L) 2)].2SiF 6. n(solv), 12, are also reported. The majority of the coordination polymers are free of solvent and are nonporous. Thermal treatment of materials that do contain solvent results in structural disintegration of the complex structures giving no permanent porosity.

  12. Engineering the structure of an N-terminal β-turn to maximize screw-sense preference in achiral helical peptide chains.

    PubMed

    De Poli, Matteo; Byrne, Liam; Brown, Robert A; Solà, Jordi; Castellanos, Alejandro; Boddaert, Thomas; Wechsel, Romina; Beadle, Jonathan D; Clayden, Jonathan

    2014-05-16

    Oligomers of α-aminoisobutyric acid (Aib) are achiral peptides that typically adopt 310 helical conformations in which enantiomeric left- and right-handed conformers are, necessarily, equally populated. Incorporating a single protected chiral residue at the N-terminus of the peptide leads to induction of a screw-sense preference in the helical chain, which may be quantified (in the form of "helical excess") by NMR spectroscopy. Variation of this residue and its N-terminal protecting group leads to the conclusion that maximal levels of screw-sense preference are induced by bulky chiral tertiary amino acids carrying amide protecting groups or by chiral quaternary amino acids carrying carbamate protecting groups. Tertiary L-amino acids at the N-terminus of the oligomer induce a left-handed screw sense, while quaternary L-amino acids induce a right-handed screw sense. A screw-sense preference may also be induced from the second position of the chain, weakly by tertiary amino acids, and much more powerfully by quaternary amino acids. In this position, the L enantiomers of both families induce a right-handed screw sense. Maximal, and essentially quantitative, control is induced by an L-α-methylvaline residue at both positions 1 and 2 of the chain, carrying an N-terminal carbamate protecting group.

  13. Synthesis, structure and characterization of 4,4‧-bipyridine directed isolated cluster and 1D chain of iron sulfates

    NASA Astrophysics Data System (ADS)

    Xu, Zhiwei; Fu, Yunlong; Zhang, Yu

    2008-03-01

    Two 4,4'-bipyridine directed iron sulfates have been synthesized and characterized by single-crystal X-ray diffraction, infrared spectrum, powder X-ray diffraction, CHN elemental analysis, thermal gravimetric analysis and magnetic analysis. [C 10N 2H 10] 2[Fe 4O 2(SO 4) 6(H 2O) 4]·6H 2O, I, and [C 10N 2H 10][Fe(SO 4) 2(OH)]·H 2O, II, both crystallize in triclinic space group P (No. 2). Crystal data: for I, a = 9.2064(8) Å, b = 11.5548(11) Å, c = 11.8130(11) Å, α = 117.3070(10)°, β = 94.650(2)°, γ = 96.493(2)°, V = 1096.79(17) Å 3, Z = 1; for II, a = 7.0382(9) Å, b = 9.0625(12) Å, c = 11.8903(16) Å, α = 100.145(3)°, β = 98.701(2)°, γ = 91.047(3)°, V = 737.17(17) Å 3, Z = 2. Compound I exhibits a rare discrete sulfated tetra-nuclear iron oxo cluster with a butterfly-type arrangement, and II possesses 1D tancoite-type chains. Magnetic properties analysis of I reveals a transformation from ferromagnetism to antiferromagnetism at about 14 K.

  14. o-, m-, and p-Pyridyl isomer effects on construction of 1D loop-and-chains: Silver(I) coordination polymers with Y-type tridentate ligands

    NASA Astrophysics Data System (ADS)

    Kim, Jeong Gyun; Cho, Yoonjung; Lee, Haeri; Lee, Young-A.; Jung, Ok-Sang

    2016-10-01

    Self-assembly of silver(I) hexafluorophosphate with unique Y-type tridentate ligands (2,6-bis[(2-picolinoyloxy-5-methylphenyl)methyl]-p-tolylpicolinate (o-L), 2-nicotinoyloxy- (m-L), and 2-isonicotinoyloxy- (p-L)) produces single crystals consisting of 1D loop-and-chain coordination polymers of [Ag(o-L)](PF6)·Me2CO·CHCl3, [Ag(m-L)](PF6)·Me2CO, and [Ag3(p-L)2](PF6)3·2H2O·2C2H5OH·4CH2Cl2 with quite different trigonal prismatic, trigonal, and linear silver(I) coordination geometry, respectively. Coordinating ability of the three ligands for AgPF6 is in the order of p-L > o-L > m-L. The solvate molecules of [Ag(o-L)](PF6)·Me2CO·CHCl3 can be removed, and be replaced reversibly in the order of acetone ≫ chloroform ≈ dichloromethane ≫ benzene, without destruction of its skeleton.

  15. Complete primary structure of the triple-helical region and the carboxyl-terminal domain of a new type IV collagen chain, alpha 5(IV).

    PubMed

    Pihlajaniemi, T; Pohjolainen, E R; Myers, J C

    1990-08-15

    We have isolated and characterized overlapping cDNA clones which code for a previously unidentified human collagen chain. Although the cDNA-derived primary structure of this new polypeptide is very similar to the basement membrane collagen alpha 1(IV) and alpha 2(IV) chains, the carboxyl-terminal collagenous/non-collagenous junction sequence does not correspond to the junction sequence in either of the newly described alpha 3(IV) or alpha 4(IV) chains (Butkowski, R.J., Langeveld, J.P.M., Wieslander, J., Hamilton, J., and Hudson, B. G. (1987) J. Biol. Chem. 262, 7874-7877). Thus the protein presented here has been designated the alpha 5 chain of type IV collagen. Four clones encode an open reading frame of 1602 amino acids that cover about 95% of the entire chain including half of the amino-terminal 7S domain and all of the central triple-helical region and carboxyl-terminal NC1 domain. The collagenous region of the alpha 5(IV) chain contains 22 interruptions which are in most cases identical in distribution to those in both the alpha 1(IV) and alpha 2(IV) chains. Despite the relatively low degree of conservation among the amino acids in the triple-helical region of the three type IV collagen chains, analysis of the sequences clearly showed that alpha 5(IV) is more related to alpha 1(IV) than to alpha 2(IV). This similarity between the alpha 5(IV) and alpha 1(IV) chains is particularly evident in the NC1 domains where the two polypeptides are 83% identical in contrast to the alpha 5(IV) and alpha 2(IV) identity of 63%. In addition to greatly increasing the complexity of basement membranes, the alpha 5 chain of type IV collagen may be responsible for specialized functions of some of these extracellular matrices. In this regard, it is important to note that we have recently assigned the alpha 5(IV) gene to the region of the X chromosome containing the locus for a familial type of hereditary nephritis known as Alport syndrome (Myers, J.C., Jones, T.A., Pohjalainen, E

  16. Nanoscale stabilization of zintl compounds: 1D ionic Li-P double helix confined inside a carbon nanotube

    NASA Astrophysics Data System (ADS)

    Ivanov, Alexander S.; Kar, Tapas; Boldyrev, Alexander I.

    2016-02-01

    One-dimensional (1D) ionic nanowires are extremely rare materials due to the difficulty in stabilizing 1D chains of ions under ambient conditions. We demonstrate here a theoretical prediction of a novel hybrid material, a nanotube encapsulated 1D ionic lithium monophosphide (LiP) chain, featuring a unique double-helix structure, which is very unusual in inorganic chemistry. This nanocomposite has been investigated with density functional theory, including molecular dynamics simulations and electronic structure calculations. We find that the formation of the LiP double-helical nanowire is facilitated by strong interactions between LiP and CNTs resulting in a charge transfer. This work suggests that nanostructured confinement may be used to stabilize other polyphosphide 1D chains, thus opening new ways to study the chemistry of zintl compounds at the nanoscale.One-dimensional (1D) ionic nanowires are extremely rare materials due to the difficulty in stabilizing 1D chains of ions under ambient conditions. We demonstrate here a theoretical prediction of a novel hybrid material, a nanotube encapsulated 1D ionic lithium monophosphide (LiP) chain, featuring a unique double-helix structure, which is very unusual in inorganic chemistry. This nanocomposite has been investigated with density functional theory, including molecular dynamics simulations and electronic structure calculations. We find that the formation of the LiP double-helical nanowire is facilitated by strong interactions between LiP and CNTs resulting in a charge transfer. This work suggests that nanostructured confinement may be used to stabilize other polyphosphide 1D chains, thus opening new ways to study the chemistry of zintl compounds at the nanoscale. Electronic supplementary information (ESI) available: Additional DOS, band structures, and Bader charges for LiP@SWCNTs. See DOI: 10.1039/c5nr07713c

  17. Transfer of noncovalent chiral information along an optically inactive helical peptide chain: allosteric control of asymmetry of the C-terminal site by external molecule that binds to the N-terminal site.

    PubMed

    Ousaka, Naoki; Inai, Yoshihito

    2009-02-20

    This study aims at demonstrating end-to-end transfer of noncovalent chiral information along a peptide chain. The domino-type induction of helical sense is proven by using achiral peptides 1-m of bis-chromophoric sequence with different chain lengths: H-(Aib-Delta(Z)Phe)(m)-(Aib-Delta(Z)Bip)(2)-Aib-OCH(3) [m = 2, 4, and 6; Aib = alpha-aminoisobutyric acid; Delta(Z)Phe = (Z)-alpha,beta-didehydrophenylalanine; Delta(Z)Bip = (Z)-beta-(4,4'-biphenyl)-alpha,beta-didehydroalanine]. They all showed the tendency to adopt a 3(10)-helix. Whereas peptide 1-m originally shows no circular dichroism (CD) signals, marked CD signals were induced at around 270-320 nm based on both the beta-aryl didehydroresidues by chiral Boc-proline (Boc = tert-butoxycarbonyl). The observed CD spectra were interpreted on the basis of the exciton chirality method and theoretical CD simulation of several helical conformations that were energy-minimized. The experimental and theoretical CD analysis reveals that Boc-l-proline induces the preference for a right-handed helicity in the whole chain of 1-m. Such noncovalent chiral induction was not observed in the corresponding N-terminally protected 1-m. Obviously, helicity induction in 1-m originates from the binding of Boc-proline to the N-terminal site. In the 17-mer (1-6), the information of helix sense reaches the 16th residue from the N-terminus. We have monitored precise transfer of noncovalent chiral stimulus along a helical peptide chain. The present study also proposes a primitive allosteric model of a single protein-mimicking backbone. Here chiral molecule binding the N-terminal site of 1-6 controls the chiroptical signals and helical sense of the C-terminal site about 30 A away.

  18. Field and dilution effects on the magnetic relaxation behaviours of a 1D dysprosium(iii)-carboxylate chain built from chiral ligands.

    PubMed

    Han, Tian; Leng, Ji-Dong; Ding, You-Song; Wang, Yanyan; Zheng, Zhiping; Zheng, Yan-Zhen

    2015-08-14

    A one-dimensional dysprosium(iii)-carboxylate chain in which the Dy(III) ions sit in a pseudo D(2d)-symmetry environment is synthesized and shows different slow magnetic relaxation behaviours depending on the field and dilution effects. Besides, the chiral ligand introduces the additional functions of the Cotton effect and polarization for this compound. PMID:26159885

  19. Spin crossover and solvate effects in 1D Fe{sup II} chain compounds containig Bis(dipyridylamine)-linked triazine ligands.

    SciTech Connect

    Ross, , T. M.; Moubaraki, B.; Turner, D. R.; Halder, G. J.; Chastanet, G.; Neville, S. M.; Cashion, J. D.; Letard, J. F.; Batten, S. R.; Murray, K. S.

    2011-03-01

    A series of 1D polymeric FeII spin crossover (SCO) compounds of type trans-[FeII(NCX)2(L)] Solvent has been synthesised {l_brace}L = DPPyT = 1-[4,6-bis(dipyridin-2-ylamino)-1,3,5-triazin-2-yl]pyridin-4(1H)-one for 1-4{r_brace}; NCX = NCS- for 1 and 2, NCSe- for 3 and 4; Solvent = 2.5CH2Cl2 for 1, 2CHCl3 {center_dot} 0.5CH3OH for 2 and 4, CH2Cl2 for 3; L = DPT (6-phenoxy-N2,N2,N4,N4-tetra-2-pyridinyl-1,3,5-triazine-2,4-diamine) for 5; NCX = NCS- for 5; Solvent = 2CH3OH {center_dot} H2O for 5; L = DQT {l_brace}4-[4,6-bis(dipyridin-2-ylamino)-1,3,5-triazin-2-yloxy]phenol{r_brace} for 6-8; NCX- = NCS- for 6; Solvent = 2CH2Cl2 for 6; NCX- = NCSe- for 7; Solvent = CH2Cl2 {center_dot} CH2ClCH2Cl for 7; NCX- = NCSe- for 8; Solvent = 1.5CH2Cl2 {center_dot} 0.5CH3OH for 8. Two mononuclear complexes, trans-[FeII(NCS)2(DPT)2] {center_dot} 2CH3OH (9) and trans-[FeII(NCSe)2(DPT)2] {center_dot} 2CH3OH (10), contained the L ligand in a terminal bidentate coordination mode. As well as variations made in the NCX- ligands, variations were also made in substituent groups on the s-triazine 'core' of L to investigate their intermolecular/supramolecular role in crystal packing and, thus, their influence on SCO properties. All the complexes crystallised as solvates, and the influence of the latter on the magnetism and spin transitions was explored. A wide range of physical methods was employed, as a function of temperature, viz. crystallography, PXRD (synchrotron), susceptibilities, LIESST and Moessbauer effect, in order to probe magnetostructural correlations in these 1D families. New examples of half-crossovers, with ordered -LS-HS-LS-HS- intrachain states existing below T1/2, have been observed and comparisons made to related one- or two-step systems. All the observed transitions are gradual and non-hysteretic, and brief comments are made in relation to recent theoretical models for cooperativity, developed elsewhere.

  20. Three new 2-D metal-organic frameworks containing 1-D metal chains bridged by N-benzesulfonyl-glutamic acid: Syntheses, crystal structures and properties

    SciTech Connect

    Ma Lufang; Huo Xiankuan; Wang Liya Wang Jiange; Fan Yaoting

    2007-05-15

    To explore the possibility of obtaining the metal-organic frameworks (MOFs) bearing the bsgluH{sub 2} ligand, two new Cd(II) and one Cu(II) coordination polymers, [Cd(bsglu)(bipy)] {sub n} (1), [Cd(bsglu).(H{sub 2}O)] {sub n} (2) and {l_brace}[Cu{sub 2}(bsglu){sub 2}(bipy){sub 2}].4H{sub 2}O{r_brace} {sub n} (3) (bsglu=N-benzesulfonyl-glutamic acid bianion, bipy=2,2'-bipyridine) were synthesized and characterized by IR, elemental analysis and X-ray diffraction analysis. Compounds 1 and 3 exhibit one-dimensional coordination chains, which are further connected to form two-dimensional supramolecular networks through {pi}-{pi} aromatic stacking interactions in a novel zipper-like way. Compound 2 presents a two-dimensional layer structure. To the best of our knowledge, 2 is the first two-dimensional complex formed from transition metal and bsgluH{sub 2} ligand. Interestingly, the bsglu anion exhibits remarkable versatile coordination modes in these complexes. Fluorescent analyses show that 1 exhibits photoluminescence in the solid state. Magnetic measurements for 3 revealed that the Cu(II) chain exhibit a weak antiferromagnetic behavior with a J value of -0.606 cm{sup -1}. - Graphical abstract: Three new complexes, [Cd(bsglu)(bipy)] {sub n} (1), [Cd(bsglu).(H{sub 2}O)] {sub n} (2) and {l_brace}[Cu{sub 2}(bsglu){sub 2}(bipy){sub 2}].4H{sub 2}O{r_brace} {sub n} (3), constructed from Cd(II) or Cu(II) salt with N-benzesulfonyl-glutamic acid were synthesized and characterized. Compounds 1 and 3 exhibit one-dimensional chains which are further connected to form two-dimensional supramolecular networks through {pi}-{pi} aromatic stacking interactions in a novel zipper-like way. Compound 2 presents a two-dimensional layer structure. Luminescence of 1 and magnetic properties of 3 are also investigated.

  1. Helices Of Helices

    NASA Astrophysics Data System (ADS)

    Siavashpouri, Mahsa; Zakhary, Mark; Wachauf, Christian; Dietz, Hendrik; Dogic, Zvonimir

    Twisted ribbons are characteristic structural motifs that are prevalent in nature. However correlation between the macroscopic properties of the final self-assemblages and the microscopic features of the constituent molecules remain unknown. We describe a new class of supramolecular 1D assemblages with tunable mechanical properties. Using DNA origami technique, we design and structure rod-like colloidal particles that have excluded volume interactions and self-assemble into twisted ribbons in presence of attractive interactions mediated by non-absorbing polymers. By comparing behavior of DNA origami filaments and rodlike viruses we demonstrate that self-assembly into 1D twisted ribbons is universal and independent of the system materials. Tuning the molecular properties of the DNA origami particles, determines the physical properties of the entire self-assembled structures. Furthermore, to understand the connection between the chirality at the molecular scale and the macroscopic chiral structures, we measured twist periodicity (pitch) of cholesteric phase associated to various DNA origami designs which can develop a new framework in understanding microscopic origin of chirality in liquid crystals.

  2. The formation of organogels and helical nanofibers from simple organic salts.

    PubMed

    Yoshii, Yuya; Hoshino, Norihisa; Takeda, Takashi; Moritomo, Hiroki; Kawamata, Jun; Nakamura, Takayoshi; Akutagawa, Tomoyuki

    2014-12-01

    Simple organic salts based on aniline-derived cations and D-tartrate anions formed organogels and helical nanofibers. The organic salt (p-fluoroanilinium)(D-tartrate) was found to generate an organogel despite the absence of a hydrophobic alkyl chain, whereas (p-iodoanilinium)(D-tartrate) formed helical nanofibers in braided ropelike structures through a rolling-up process. The helicity of these nanofibers could be reversed by changing the growth solvent. The driving forces responsible for the formation of the nanofibers were determined to be 1D OH⋅⋅⋅O(-) hydrogen-bonding interactions between D-tartrate anions and π stacking of anilinium cations, as well as steric hindrance between the hydrogen-bonded chains.

  3. Dynamics and supramolecular organization of the 1D spin transition polymeric chain compound [Fe(NH2trz)3](NO3)2. Muon spin relaxation.

    PubMed

    Garcia, Yann; Campbell, Stewart J; Lord, James S; Boland, Yves; Ksenofontov, Vadim; Gütlich, Philipp

    2007-09-27

    The thermal spin transition that occurs in the polymeric chain compound [Fe(NH(2)trz)3](NO3)2 above room temperature has been investigated by zero-field muon spin relaxation (microSR) over the temperature range approximately 8-402 K. The depolarization curves are best described by a Lorentzian and a Gaussian line that represent fast and slow components, respectively. The spin transition is associated with a hysteresis loop of width DeltaT = 34 K (T1/2 upward arrow = 346 K and T1/2 downward arrow = 312 K) that has been delineated by the temperature variation of the initial asymmetry parameter, in good agreement with previously published magnetic measurements. Zero-field and applied field (20-2000 Oe) microSR measurements show the presence of diamagnetic muon species and paramagnetic muonium radical species (A = 753 +/- 77 MHz) over the entire temperature range. Fast dynamics have been revealed in the high-spin state of [Fe(NH(2)trz)3](NO3)2 with the presence of a Gaussian relaxation mode that is mostly due to the dipolar interaction with static nuclear moments. This situation, where the muonium radicals are totally decoupled and not able to sense paramagnetic fluctuations, implies that the high-spin dynamics fall outside the muon time scale. Insights to the origin of the cooperative effects associated with the spin transition of [Fe(NH(2)trz)3](NO3)2 through muon implantation are presented.

  4. Solvothermal synthesis and structure of a novel 3D zincophosphite |Co(en) 3|[Zn 4(HPO 3) 5(H 2PO 3)] containing helical chains

    NASA Astrophysics Data System (ADS)

    Qiao, Jian; Zhang, Lirong; Liu, Li; Yu, Yang; Bi, Minghui; Huo, Qisheng; Liu, Yunling

    2008-11-01

    A new three-dimensional (3D) zincophosphite |Co(en) 3| [Zn 4(HPO 3) 5(H 2PO 3)] ( 1) has been solvothermally synthesized by using a racemic mixture of a chiral cobaltammine complex Co(en) 3Cl 3 as the structure-directing agent. Single-crystal X-ray diffraction analysis reveals that compound 1 crystallizes in the monoclinic space group P2 1/ c (no. 14) with a=18.6180 (4) Å, b=8.7601(18) Å, c=17.4840(4) Å, β=93.42(3)°, V=2846.4(10) Å 3, Z=4 with R1=0.0530. Its structure is built up from strict alternation of ZnO 4 tetrahedra and HPO 3 pseudo-tetrahedra, giving rise to a 3D inorganic framework with 4-, 6-, 8-, 10- and 12 MRs, and the metal complex molecules, both the Δ and Λ enantiomers, sit in 10-MRs channels. In addition, it is worth noting that left- and right-handed helical chains exist in the framework, which is induced by chiral metal complex Co(en) 3Cl 3 template molecules. Further characterization of compound 1 has been performed, including X-ray powder diffraction, ICP, CHN, IR and TG analyses.

  5. New coordination polymers from 1D chain, 2D layer to 3D framework constructed from 1,2-phenylenediacetic acid and 1,3-bis(4-pyridyl)propane flexible ligands

    SciTech Connect

    Xin Lingyun; Liu Guangzhen; Wang Liya

    2011-06-15

    The hydrothermal reactions of Cd, Zn, or Cu(II) acetate salts with H{sub 2}PHDA and BPP flexible ligands afford three new coordination polymers, including [Cd(PHDA)(BPP)(H{sub 2}O)]{sub n}(1), [Zn(PHDA)(BPP)]{sub n}(2), and [Cu{sub 2}(PHDA){sub 2}(BPP)]{sub n}(3) (H{sub 2}PHDA=1,2-phenylenediacetic acid, BPP=1,3-bis(4-pyridyl)propane). The single-crystal X-ray diffractions reveal that all three complexes feature various metal carboxylate subunits extended further by the BPP ligands to form a diverse range of structures, displaying a remarked structural sensitivity to metal(II) cation. Complex 1 containing PHDA-bridged binuclear cadmium generates 1D double-stranded chain, complex 2 results in 2D{yields}2D interpenetrated (4,4) grids, and complex 3 displays a 3D self-penetrated framework with 4{sup 8}6{sup 6}8 rob topology. In addition, fluorescent analyses show that both 1 and 2 exhibit intense blue-violet photoluminescence in the solid state. - Graphical Abstract: We show diverse supramolecular frameworks based on the same ligands (PHDA and BPP) and different metal acetate salts including 1D double-stranded chain, 2D {yields} 2D twofold interpenetrated layer, and 3D self-penetration networks. Highlights: > Three metal(II = 2 /* ROMAN ) coordination polymers were synthesized using H{sub 2}PHDA and BPP. > The diversity of structures show a remarked sensitivity to metal(II) center. > Complexes show the enhancement of fluorescence compared to that of free ligand.

  6. A unified convention for biological assemblies with helical symmetry

    SciTech Connect

    Tsai, Chung-Jung; Nussinov, Ruth

    2011-08-01

    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, 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.

  7. Dissecting π-helices: sequence, structure and function.

    PubMed

    Kumar, Prasun; Bansal, Manju

    2015-11-01

    A new procedure for the identification of regular secondary structures using a C(α) trace has identified 659 π-helices in 3582 protein chains, solved at high resolution. Taking advantage of this significantly expanded database of π-helices, we have analysed the functional and structural roles of π-helices and determined the position-wise amino acid propensity within and around them. These helices range from 5 to 18 residues in length with the average twist and rise being 85.2 ± 7.2° and 1.28 ± 0.31 Å, respectively. A total of 546 (~ 83%) out of 659 π-helices occur in conjunction with α-helices, with 101 π-helices being interspersed between two α-helices. The majority of interspersed π-helices were found to be conserved across a large number of structures within a protein family and produce a significant bend in the overall helical segment as well as local distortions in the neighbouring α-helices. The presence of a π-helical fragment leads to appropriate orientation of the constituent residues, so as to facilitate favourable interactions and also help in proper folding of the protein chain. In addition to intra helical 6→1 N-H···O hydrogen bonds, π-helices are also stabilized by several other non-bonded interactions. π-Helices show distinct positional residue preferences, which are different from those of α-helices.

  8. Left-handed helical preference in an achiral peptide chain is induced by an L-amino acid in an N-terminal type II β-turn.

    PubMed

    De Poli, Matteo; De Zotti, Marta; Raftery, James; Aguilar, Juan A; Morris, Gareth A; Clayden, Jonathan

    2013-03-15

    Oligomers of the achiral amino acid Aib adopt helical conformations in which the screw-sense may be controlled by a single N-terminal residue. Using crystallographic and NMR techniques, we show that the left- or right-handed sense of helical induction arises from the nature of the β-turn at the N terminus: the tertiary amino acid L-Val induces a left-handed type II β-turn in both the solid state and in solution, while the corresponding quaternary amino acid L-α-methylvaline induces a right-handed type III β-turn.

  9. Vaporization-condensation-recrystallization process-mediated synthesis of helical m-aminobenzoic acid nanobelts.

    PubMed

    Yoon, Seok Min; Hwang, In-Chul; Shin, Namsoo; Ahn, Docheon; Lee, Sang Joo; Lee, Jin Yong; Choi, Hee Cheul

    2007-11-01

    One-dimensional (1D) helical organic nanostructures were synthesized by a modified vapor-solid (VS) process, called the vaporization-condensation-recrystallization (VCR) process. The conventional solution-phase synthetic methods generally mediate self-assemblies of repeating unit molecules. To provide enough intermolecular interaction forces among the unit molecules, such strategy requires specific designs and syntheses of complex unit molecules as they possess numerous functional groups including phenyl rings, hydroxyl groups, long aliphatic chains, etc. On the contrary, we found that small and simple organic molecules, for example, m-ABA, could be self-assembled by the VCR process, resulting in 1D helical organic nanostructures. When m-aminobenzoic acid (m-ABA) powders were vaporized and transported to be condensed on a cooler region, the condensates were recrystallized into 1D helical nanobelts. Each step of the VCR process was confirmed from control experiments performed by varying reaction times, substrate types, and reaction temperatures. Powder XRD data, SAED analysis, and theoretical calculations revealed that dimers of m-ABA molecules have repeating units, and the growth axis of m-ABA nanohelices is [100].

  10. omega-Helices in proteins.

    PubMed

    Enkhbayar, Purevjav; Boldgiv, Bazartseren; Matsushima, Norio

    2010-05-01

    A modification of the alpha-helix, termed the omega-helix, has four residues in one turn of a helix. We searched the omega-helix in proteins by the HELFIT program which determines the helical parameters-pitch, residues per turn, radius, and handedness-and p = rmsd/(N - 1)(1/2) estimating helical regularity, where "rmsd" is the root mean square deviation from the best fit helix and "N" is helix length. A total of 1,496 regular alpha-helices 6-9 residues long with p < or = 0.10 A were identified from 866 protein chains. The statistical analysis provides a strong evidence that the frequency distribution of helices versus n indicates the bimodality of typical alpha-helix and omega-helix. Sixty-two right handed omega-helices identified (7.2% of proteins) show non-planarity of the peptide groups. There is amino acid preference of Asp and Cys. These observations and analyses insist that the omega-helices occur really in proteins.

  11. omega-Helices in proteins.

    PubMed

    Enkhbayar, Purevjav; Boldgiv, Bazartseren; Matsushima, Norio

    2010-05-01

    A modification of the alpha-helix, termed the omega-helix, has four residues in one turn of a helix. We searched the omega-helix in proteins by the HELFIT program which determines the helical parameters-pitch, residues per turn, radius, and handedness-and p = rmsd/(N - 1)(1/2) estimating helical regularity, where "rmsd" is the root mean square deviation from the best fit helix and "N" is helix length. A total of 1,496 regular alpha-helices 6-9 residues long with p < or = 0.10 A were identified from 866 protein chains. The statistical analysis provides a strong evidence that the frequency distribution of helices versus n indicates the bimodality of typical alpha-helix and omega-helix. Sixty-two right handed omega-helices identified (7.2% of proteins) show non-planarity of the peptide groups. There is amino acid preference of Asp and Cys. These observations and analyses insist that the omega-helices occur really in proteins. PMID:20496104

  12. A two-fold interpenetrating 3D metal-organic framework material constructed from helical chains linked via 4,4'-H{sub 2}bpz fragments

    SciTech Connect

    Xie Yiming; Zhao Zhenguo; Wu Xiaoyuan; Zhang Qisheng; Chen Lijuan; Wang Fei; Chen Shanci; Lu Canzhong

    2008-12-15

    A 3-connected dia-f-type metal-organic framework compound {l_brace}[Ag(L){sub 3/2}H{sub 2}PO{sub 4}]{r_brace}{sub n} (1) has been synthesized by self-assembly of 4,4'-H{sub 2}bpz (L=4,4'-H{sub 2}bpz=3,3',5,5'-tetramethyl-4,4'-bipyrazole) and Ag{sub 4}P{sub 2}O{sub 7} under hydrothermal conditions. It crystallizes in the tetragonal space group I4{sub 1}/acd with a=21.406(4) A, b=21.406(4) A, c=36.298(8) A, Z=32. X-ray single-crystal diffraction reveals that 1 has a three-dimensional framework with an unprecedented alternate left- and right-handed helices structure, featuring a non-uniform two-fold interpenetrated (4.14{sup 2}) net. Photoluminescent investigation reveals that the title compound displays interesting emissions in a wide region, which shows that the title compound may be a good potential candidate as a photoelectric material. - Graphical abstract: A 3-connected dia-f-type metal-organic framework compound [Ag(4,4'-bpz){sub 3/2}H{sub 2}PO{sub 4}] shows unprecedented alternating left- and right-handed helices structure, featuring a non-uniform two-fold interpenetrated (4.14{sup 2}) net.

  13. Extraordinary Separation of Acetylene-Containing Mixtures with Microporous Metal-Organic Frameworks with Open O Donor Sites and Tunable Robustness through Control of the Helical Chain Secondary Building Units.

    PubMed

    Yao, Zizhu; Zhang, Zhangjing; Liu, Lizhen; Li, Ziyin; Zhou, Wei; Zhao, Yunfeng; Han, Yu; Chen, Banglin; Krishna, Rajamani; Xiang, Shengchang

    2016-04-11

    Acetylene separation is a very important but challenging industrial separation task. Here, through the solvothermal reaction of CuI and 5-triazole isophthalic acid in different solvents, two metal-organic frameworks (MOFs, FJU-21 and FJU-22) with open O donor sites and controllable robustness have been obtained for acetylene separation. They contain the same paddle-wheel {Cu2(COO2)4} nodes and metal-ligand connection modes, but with different helical chains as secondary building units (SBUs), leading to different structural robustness for the MOFs. FJU-21 and FJU-22 are the first examples in which the MOFs' robustness is controlled by adjusting the helical chain SBUs. Good robustness gives the activated FJU-22 a, which has higher surface area and gas uptakes than the flexible FJU-21 a. Importantly, FJU-22 a shows extraordinary separation of acetylene mixtures under ambient conditions. The separation capacity of FJU-22 a for 50:50 C2H2/CO2 mixtures is about twice that of the high-capacity HOF-3, and its actual separation selectivity for C2H2/C2H4 mixtures containing 1% acetylene is the highest among reported porous materials. Based on first-principles calculations, the extraordinary separation performance of C2H2 for FJU-22 a was attributed to hydrogen-bonding interactions between the C2H2 molecules with the open O donors on the wall, which provide better recognition ability for C2H2 than other functional sites, including open metal sites and amino groups.

  14. Two new helical compounds based on Keggin clusters and N-donor multidentate ligand: Syntheses, structures and properties

    SciTech Connect

    Zhou, Shi; Liu, Bo; Li, Xiao-Min; Shi, Tian; Chen, Ya-Guang

    2014-11-15

    Two isostructural polyoxometalate-based inorganic–organic hybrids with 1D helical chain, [CuH{sub 3}L{sub 2}(GeMo{sub 12}O{sub 40})]·2H{sub 2}O (1) and [CuH{sub 3}L{sub 2}(SiMo{sub 12}O{sub 40})]·2H{sub 2}O (2), where L=2,4,5-tri(4-pyridyl)-imidazole have been synthesized under hydrothermal conditions. It is the first time to use the L ligand to synthesis the Keggin-type polyoxometalate-based inorganic–organic hybrids. The two compounds possess the left- and right-handed helical chains and the POMs as pendants attach in the helical chains through Cu–O bonds. The two compounds have been characterized by elemental analyses, infrared (IR) spectroscopy, powder X-ray diffraction (PXRD), X-ray photoelectron spectra (XPS), thermogravimetric analysis (TGA) and photoluminescent spectroscopy. Moreover, nitrogen adsorption−desorption measurement, electrochemical and photocatalysis properties for degradation of methylene blue (MB) upon a UV irradiation of compound 1 have been examined. - Graphical abstract: Two new compounds, [CuH{sub 3}L{sub 2}(GeMo{sub 12}O{sub 40})]·2H{sub 2}O (1) and [CuH{sub 3}L{sub 2}(SiMo{sub 12}O{sub 40})]·2H{sub 2}O (2) have been synthesized under hydrothermal conditions. The two compounds possess the left- and right-handed helical chains. - Highlights: • The tridentate L ligand is first used to synthesis Keggin-type polyoxometalates. • The two compounds possess the left- and right-handed Cu–L helical chains. • Relationship between surface properties and photocatalytic activity was studied. • Two compounds exhibit photoluminescence of ligand-to-metal charge transfer.

  15. Two-dimensional surface chirality control by solvent-induced helicity inversion of a helical polyacetylene on graphite.

    PubMed

    Sakurai, Shin-ichiro; Okoshi, Kento; Kumaki, Jiro; Yashima, Eiji

    2006-05-01

    We report the direct evidence for the macromolecular helicity inversion of a helical poly(phenylacetylene) bearing l- or d-alanine pendants with a long alkyl chain in different solvents by atomic force microscopy observations of the diastereomeric helical structures. The diastereomeric helical poly(phenylacetylene)s induced in polar and nonpolar solvents self-assembled into ordered, two-dimensional helix bundles with controlled molecular packing, helical pitch, and handedness on graphite upon exposure of each solvent. The macromolecular helicity deposited on graphite from a polar solvent further inverted to the opposite handedness by exposure to a specific nonpolar solvent, and these changes in the surface chirality based on the inversion of helicity could be visualized by atomic force microscopy with molecular resolution, and the results were quantified by X-ray diffraction of the oriented liquid crystalline, diastereomeric helical polymer films.

  16. A substitution at a non-glycine position in the triple-helical domain of pro alpha 2(I) collagen chains present in an individual with a variant of the Marfan syndrome.

    PubMed Central

    Phillips, C L; Shrago-Howe, A W; Pinnell, S R; Wenstrup, R J

    1990-01-01

    A substitution for a highly conserved non-glycine residue in the triple-helical domain of the pro alpha 2(I) collagen molecule was found in an individual with a variant of the Marfan syndrome. A single base change resulted in substitution of arginine618 by glutamine at the Y position of a Gly-X-Y repeat, and is responsible for the decreased migration in SDS-polyacrylamide gels of some pro alpha 2(I) chains of type I collagen synthesized by dermal fibroblasts from this individual. Family studies suggest that this substitution was inherited from the individual's father who also produces abnormally migrating pro alpha 2(I) collagen chains and shares some of the abnormal skeletal features. This single base change creates a new Bsu36 I (Sau I, Mst II) restriction site detectable in genomic DNA by Southern blot analysis when probed with a COL1A2 fragment. The analysis of 52 control individuals (103 chromosomes) was negative for the new Bsu36 I site, suggesting that the substitution is not a common polymorphism. Images PMID:1978725

  17. 1D coordination polymers with polychalcogenides as linkers between metal atoms

    SciTech Connect

    Kysliak, Oleksandr; Beck, Johannes

    2013-07-15

    The reactions of zinc metal with elemental selenium and selenium/sulfur mixtures in liquid ammonia or methylamine under solvothermal conditions in closed glass ampoules at 50 °C lead within some days specifically to [Zn(NH{sub 3}){sub 2}Se{sub 4}]{sub n} (1), [Zn(MeNH{sub 2}){sub 2}Se{sub 4}]{sub n} (2), [Zn(NH{sub 3}){sub 2}Se{sub 2.23}S{sub 1.77}]{sub n} (3). From MnCl{sub 2}, Rb{sub 2}Se and excess Se in n-butylamine [Mn({sup n}BuNH{sub 2}){sub 4}Se{sub 6}]{sub n} (4) is obtained after prolonged reaction time at ambient temperature. The compounds are sensitive towards air and loss of NH{sub 3} or the amine ligands. The crystal structures were determined by single crystal diffraction at low temperatures. As a common structural feature, all compounds represent 1D coordination polymers with polychalcogenide chains as linkers between the metal atoms and consist of infinite [M–Ch{sub m}–]{sub n} chains (M=Zn, Mn; Ch{sub m}=Se{sub 4}, (S/Se){sub 4}, Se{sub 6}). The Zn central atoms in 1–3 have tetrahedral coordination with two amine ligands, the Mn atoms in 4 have octahedral coordination with four amine ligands and cis position of the two Se atoms. Raman spectra of 1–3 show the stretching mode vibrations of the Ch{sub 4} groups. The observation of S–S, S–Se, and Se–Se vibration bands in the spectrum of 3 indicates the presence of mixed S/Se polyanions. An optical band gap of 1.86(5) eV was determined for 2 by diffuse reflectance spectroscopy. - Graphical abstract: The reaction of Zn and Se in liquid methylamine yields dark red [Zn(NH{sub 2}CH{sub 3})Se{sub 4}], a 1D coordination polymer consisting of helical Zn–Se{sub 4}–Zn– chains. - Highlights: • A series of 1D coordination polymers consisting of metal amine complexes concatenated by polychalcogenide ions is presented. • Syntheses were performed as solvothermal reactions in liquid ammonia, liquid methylamine and n-butylamine. • Crystal structures are dominated by helices [M–Ch{sub m

  18. Helicity content and tokamak applications of helicity

    SciTech Connect

    Boozer, A.H.

    1986-05-01

    Magnetic helicity is approximately conserved by the turbulence associated with resistive instabilities of plasmas. To generalize the application of the concept of helicity, the helicity content of an arbitrary bounded region of space will be defined. The definition has the virtues that both the helicity content and its time derivative have simple expressions in terms of the poloidal and toroidal magnetic fluxes, the average toroidal loop voltage and the electric potential on the bounding surface, and the volume integral of E-B. The application of the helicity concept to tokamak plasmas is illustrated by a discussion of so-called MHD current drive, an example of a stable tokamak q profile with q less than one in the center, and a discussion of the possibility of a natural steady-state tokamak due to the bootstrap current coupling to tearing instabilities.

  19. Heterobimetallic lanthanide-gold coordination polymers: structure and emissive properties of isomorphous [(n)Bu4N]2[Ln(NO3)4Au(CN)2] 1-D chains.

    PubMed

    Roberts, Ryan J; Li, Xiaobo; Lacey, Tye F; Pan, Zhong; Patterson, Howard H; Leznoff, Daniel B

    2012-06-21

    A new series of lanthanide-containing dicyanoaurate coordination polymers, [(n)Bu(4)N](2)[Ln(NO(3))(4)Au(CN)(2)] (Ln = Nd, Eu, Gd or Tb), were synthesized and structurally characterized. They form an isomorphous series, crystallizing in the space group I2(1)2(1)2(1). The structure is composed of a one dimensional zigzag of Ln-N-C-Au-C-N-Ln chains with no intra- or inter-chain aurophilic interactions. The series is related to and can be described as a reduced dimensionality analogue of the previously studied Ln[Au(CN)(2)](3)·3H(2)O. Unlike the Ln[Au(CN)(2)](3)·3H(2)O series, there is no efficient energy transfer between dicyanoaurate and the lanthanide metal centers in the complexes and they essentially act as two separate emissive chromophores.

  20. Synthesis, crystal structure and properties of two 1D nano-chain coordination polymers constructed by lanthanide with pyridine-3,4-dicarboxylic acid and 1,10-phenanthroline

    SciTech Connect

    Song Huihua Li Yajuan; Song You; Han Zhangang; Yang Fang

    2008-05-15

    The hydrothermal reactions of LnCl{sub 3}.6H{sub 2}O (Ln=Eu, Tb), pyridine-3,4-dicarboxylic acid (3,4-pydaH{sub 2}), 1,10-phenthroline (phen) and NaOH in aqueous medium yield two metal-organic hybrid materials, [Eu{sub 2}(3,4-pyda){sub 3}(phen)(H{sub 2}O).H{sub 2}O]{sub n} (1) and [Tb{sub 2}(3,4-pyda){sub 3}(phen)(H{sub 2}O).H{sub 2}O]{sub n} (2), respectively. Both compounds have similar topology structure containing one-dimensional nano-chain, which is further assembled into a three-dimensional supramolecular network via {pi}-{pi} stacking interactions and hydrogen bonds. To the best of our knowledge, they represent the first example of nano-chain coordination polymers constructed by 3,4-pydaH{sub 2} and chelate heterocylic ligand. Interestingly, the 3,4-pyda anion exhibits three kinds of coordination modes in these complexes. The coordination modes of 3,4-pyda in complexes 1 and 2 have not been observed in other coordination polymers containing 3,4-pyda ligands. Compounds 1 and 2 exhibit strong fluorescent emission bands in the solid state at room temperature. Their magnetic analyses show that they exhibit different magnetic interactions. - Graphical abstract: Two novel lanthanide coordination polymers [M{sub 2}(pydc){sub 3}(phen)(H{sub 2}O).H{sub 2}O]{sub n} (M=Eu(1) and Tb(2), pydc=pyridine-3,4-dicarboxylate, phen=1,10-phenthroline) have been synthesized and characterized. Both compounds reveal a one-dimensional nano-chain, which is further assembled into a three-dimensional supramolecular network via {pi}-{pi} stacking interactions and hydrogen bonds. Their luminescent and magnetic properties have been investigated.

  1. On the Importance of Noncovalent Carbon-Bonding Interactions in the Stabilization of a 1D Co(II) Polymeric Chain as a Precursor of a Novel 2D Coordination Polymer.

    PubMed

    Pal, Pampi; Konar, Saugata; Lama, Prem; Das, Kinsuk; Bauzá, Antonio; Frontera, Antonio; Mukhopadhyay, Subrata

    2016-07-14

    A new cobalt(II) coordination polymer 2 with μ1,5 dicyanamide (dca) and a bidentate ligand 3,5-dimethyl-1-(2'-pyridyl)pyrazole (pypz) is prepared in a stepwise manner using the newly synthesized one-dimensional linear Co(II) coordination polymer 1 as a precursor. The structural and thermal characterizations elucidate that the more stable complex 2 shows a two-dimensional layer structural feature. Here, Co(II) atoms with μ1,5 dicyanamido bridges are linked by the ligand pypz forming a macrocyclic chain that runs along the crystallographic 'c' axis having 'sql' (Shubnikov notation) net topology with a 4-connected uninodal node having point symbol {4(4).6(2)}. The remarkable noncovalent carbon-bonding contacts detected in the X-ray structure of compound 1 are analyzed and characterized by density functional theory calculations and the analysis of electron charge density (atoms in molecules). PMID:27295490

  2. A pure inorganic 1D chain based on {Mo8O28} clusters and Mn(II) ions: [Mn(H2O)2Mo8O28 ] n 6 n -

    NASA Astrophysics Data System (ADS)

    Zhang, Xiaofen; Yan, Yonghong; Wu, Lizhou; Yu, Chengxin; Dong, Xinbo; Hu, Huaiming; Xue, Ganglin

    2016-01-01

    A new pure inorganic polymer, (NH4)6n[Mn(H2O)2Mo8O28)]n(H2O)2n(1), has been synthesized and characterized by elemental analyses, IR spectrum, UV-vis absorption spectra, TG-DSC and electrochemical studies. In 1, [Mo8O28]8- anions act as tetradentate ligands and are alternately linked by Mn(H2O)2 2 + ions into a one-dimensional chain structure. It is interesting that 1 represents the first example of pure inorganic-inorganic hybrid based on octamolybdate and transition metal ions. Moreover, it was indicated that 1 had definite catalytic activities on the probe reaction of benzyl alcohol oxidation to benzaldehyde with H2O2.

  3. On the Importance of Noncovalent Carbon-Bonding Interactions in the Stabilization of a 1D Co(II) Polymeric Chain as a Precursor of a Novel 2D Coordination Polymer.

    PubMed

    Pal, Pampi; Konar, Saugata; Lama, Prem; Das, Kinsuk; Bauzá, Antonio; Frontera, Antonio; Mukhopadhyay, Subrata

    2016-07-14

    A new cobalt(II) coordination polymer 2 with μ1,5 dicyanamide (dca) and a bidentate ligand 3,5-dimethyl-1-(2'-pyridyl)pyrazole (pypz) is prepared in a stepwise manner using the newly synthesized one-dimensional linear Co(II) coordination polymer 1 as a precursor. The structural and thermal characterizations elucidate that the more stable complex 2 shows a two-dimensional layer structural feature. Here, Co(II) atoms with μ1,5 dicyanamido bridges are linked by the ligand pypz forming a macrocyclic chain that runs along the crystallographic 'c' axis having 'sql' (Shubnikov notation) net topology with a 4-connected uninodal node having point symbol {4(4).6(2)}. The remarkable noncovalent carbon-bonding contacts detected in the X-ray structure of compound 1 are analyzed and characterized by density functional theory calculations and the analysis of electron charge density (atoms in molecules).

  4. Helicity in superfluids

    NASA Astrophysics Data System (ADS)

    Kedia, Hridesh; Kleckner, Dustin; Proment, Davide; Irvine, William T. M.

    Ideal fluid flow conserves a special quantity known as helicity, in addition to energy, momentum and angular momentum. Helicity can be understood as a measure of the knottedness of vortex lines of the flow, providing an important geometric tool to study diverse physical systems such as turbulent fluids and plasmas. Since superfluids flow without resistance just like ideal (Euler) fluids, a natural question arises: Is there an extra conserved quantity akin to helicity in superfluids? We address the question of a ''superfluid helicity'' theoretically and examine its consequences in numerical simulations.

  5. Hydrogen-bonded helical hydrazide oligomers and polymer that mimic the ion transport of gramicidin A.

    PubMed

    Xin, Pengyang; Zhu, Pingping; Su, Pei; Hou, Jun-Li; Li, Zhan-Ting

    2014-09-24

    A new series of hydrogen-bonded helical aromatic hydrazide oligomers and polymer that bear phenylalanine tripeptide chains have been designed and synthesized. It was revealed that the helical structures could insert into lipid bilayers to form unimolecular channels. The longest oligomeric and polymeric helical channels exhibited an NH4(+)/K(+) selectivity that was higher than that of natural gramicidin A, whereas the transport of a short helical channel for Tl(+) could achieve an efficiency as high as that of gramicidin A.

  6. Double Helical Fluid Containment

    NASA Astrophysics Data System (ADS)

    Lowry, Brian

    2003-11-01

    In the absence of gravity or at micro-scales, helical wires can support cylindrical volumes of fluid of infinite length, making them convenient as conduits. However, fixed contact line double helical fluid volumes have the additional property that they can be drained to zero volume without loss of stability to constant pressure disturbances. Thus the two-wire support is a convenient microgravity or micro-scale container as well as conduit. For evenly spaced wires, continuous draining of a cylindrical volume to zero is possible for double helices ranging from moderate pitch to the parallel wire case. Double helices of steeper pitch are stable as cylinders and at zero volume, but are unstable for some range of intermediate volumes. This unstable zone is very strongly dependent on the offset between the helical wires, varying rapidly for offsets other than 180 degrees. Preliminary experimental results validate the theoretical predictions.

  7. Four 1-D metal-organic polymers self-assembled from semi-flexible benzimidazole-based ligand: Syntheses, structures and fluorescent properties

    NASA Astrophysics Data System (ADS)

    Zhou, Chun-lin; Wang, Shi-min; Liu, Sai-nan; Yu, Tian-tian; Li, Rui-ying; Xu, Hong; Liu, Zhong-yi; Sun, Huan; Cheng, Jia-jia; Li, Jin-peng; Hou, Hong-wei; Chang, Jun-biao

    2016-08-01

    Four one-dimensional (1-D) metal-organic polymers based on methylene-bis(1,1‧-benzimidazole)(mbbz), namely, {[Hg(mbbz)(SCN)2]·1/3H2O}n (1), [Co(mbbz)(Cl)2]n (2), {[Co(mbbz)(SO4)]·CH3OH}n (3) and {[Zn(mbbz)(SO4)]·CH3OH}n (4) have been successfully synthesized and structurally characterized. Single-crystal X-ray diffraction reveals that polymers 1 and 2 exhibit interesting 1-D double helical chain structures, while polymers 3 and 4 are 1-D double chain structures due to the bridging effect of mbbz ligands and sulfate anions. These polymers containing the mbbz-based ligand have a high degree of dependence on the corresponding counter anions. Furthermore, the fluorescence properties of the four polymers were also investigated in the solid state, showing the fluorescence signal changes in comparing with that of free ligand mbbz.

  8. Hydrothermal synthesis and characterization of the first 1-D indiumphosphate chain In{sub 2}(HPO{sub 4}){sub 2}(H{sub 2}PO{sub 4}){sub 2}F{sub 2}.C{sub 4}N{sub 2}H{sub 12}, a precursor for high dimensional structures

    SciTech Connect

    Chen Chao; Yi Zhuo; Bi Minghui; Liu Yunling; Wang Chunyu; Liu Li; Zhao Zan; Pang Wenqin . E-mail: wqpang@mail.jlu.edu.cn

    2006-05-15

    The first one-dimensional (1-D) indiumphosphate chain, In{sub 2}(HPO{sub 4}){sub 2}(H{sub 2}PO{sub 4}){sub 2}F{sub 2}.C{sub 4}N{sub 2}H{sub 12} (1), has been hydrothermally prepared using piperazine (PIP) as a template. The structure consists of infinite chains of trans,trans-corners-sharing InO{sub 4}F{sub 2} octahedra with the adjacent octahedra being bridged by tetrahedral PO{sub 3}(OH) and PO{sub 2}(OH){sub 2} units, which are H-bonded with amine groups of the organic cations. Interestingly, this macroanionic chain InP{sub 2}O{sub 8}H{sub 3}F{sup -} is similar to that found in the mineral tancoite-like chains and has potential to further set up higher-dimensional networks. On heating 1 in the presence of additional phosphoric acid at 180 deg. C under hydrothermal condition, compound 2, In{sub 2}(OH)(H{sub 2}O)(PO{sub 4}){sub 2}.H{sub 3}O.H{sub 2}O, possessed a 3-D structure building from the repetition of a secondary building unit is obtained. When 1 is heated with additional PIP, an unknown phase, compound 3 is formed. Finally, on treatment with another amine, such as diethylenetriamine or 1,4-diaminobutane, at 180 deg. C, 1, as a precursor, can convert into a previously known 3-D framework structure with 16-membered ring compound 4. Compounds 1 and 2 are determined by single-crystal X-ray diffraction. Furthermore, 1 is characterized by X-ray powder diffraction, IR spectroscopy, inductively coupled plasma analysis, thermogravimetric analysis and differential thermal analysis.

  9. Severe Hypertriglyceridemia in Glut1D on Ketogenic Diet.

    PubMed

    Klepper, Joerg; Leiendecker, Baerbel; Heussinger, Nicole; Lausch, Ekkehart; Bosch, Friedrich

    2016-04-01

    High-fat ketogenic diets are the only treatment available for Glut1 deficiency (Glut1D). Here, we describe an 8-year-old girl with classical Glut1D responsive to a 3:1 ketogenic diet and ethosuximide. After 3 years on the diet a gradual increase of blood lipids was followed by rapid, severe asymptomatic hypertriglyceridemia (1,910 mg/dL). Serum lipid apheresis was required to determine liver, renal, and pancreatic function. A combination of medium chain triglyceride-oil and a reduction of the ketogenic diet to 1:1 ratio normalized triglyceride levels within days but triggered severe myoclonic seizures requiring comedication with sultiam. Severe hypertriglyceridemia in children with Glut1D on ketogenic diets may be underdiagnosed and harmful. In contrast to congenital hypertriglyceridemias, children with Glut1D may be treated effectively by dietary adjustments alone. PMID:26902182

  10. Helical superconducting black holes.

    PubMed

    Donos, Aristomenis; Gauntlett, Jerome P

    2012-05-25

    We construct novel static, asymptotically five-dimensional anti-de Sitter black hole solutions with Bianchi type-VII(0) symmetry that are holographically dual to superconducting phases in four spacetime dimensions with a helical p-wave order. We calculate the precise temperature dependence of the pitch of the helical order. At zero temperature the black holes have a vanishing entropy and approach domain wall solutions that reveal homogenous, nonisotropic dual ground states with an emergent scaling symmetry.

  11. Magnetic Helicity of Alfven Simple Waves

    NASA Technical Reports Server (NTRS)

    Webb, Gary M.; Hu, Q.; Dasgupta, B.; Zank, G. P.; Roberts, D.

    2010-01-01

    The magnetic helicity of fully nonlinear, multi-dimensional Alfven simple waves are investigated, by using relative helicity formulae and also by using an approach involving poloidal and toroidal decomposition of the magnetic field and magnetic vector potential. Different methods to calculate the magnetic vector potential are used, including the homotopy and Biot-Savart formulas. Two basic Alfven modes are identified: (a) the plane 1D Alfven simple wave given in standard texts, in which the Alfven wave propagates along the z-axis, with wave phase varphi=k_0(z-lambda t), where k_0 is the wave number and lambda is the group velocity of the wave, and (b)\\ the generalized Barnes (1976) simple Alfven wave in which the wave normal {bf n} moves in a circle in the xy-plane perpendicular to the mean field, which is directed along the z-axis. The plane Alfven wave (a) is analogous to the slab Alfven mode and the generalized Barnes solution (b) is analogous to the 2D mode in Alfvenic, incompressible turbulence. The helicity characteristics of these two basic Alfven modes are distinct. The helicity characteristics of more general multi-dimensional simple Alfven waves are also investigated. Applications to nonlinear Aifvenic fluctuations and structures observed in the solar wind are discussed.

  12. Magnetic Helicity of Alfven Simple Waves

    NASA Astrophysics Data System (ADS)

    Webb, G. M.; Hu, Q.; Dasgupta, B.; Zank, G. P.; Roberts, D.

    2010-12-01

    The magnetic helicity of fully nonlinear, multi-dimensional Alfven simple waves are investigated, by using relative helicity formulae and also by using an approach involving poloidal and toroidal decomposition of the magnetic field and magnetic vector potential. Different methods to calculate the magnetic vector potential are used, including the homotopy and Biot-Savart formulas. Two basic Alfven modes are identified: (a) the plane 1D Alfven simple wave given in standard texts, in which the Alfven wave propagates along the z-axis, with wave phase \\varphi=k0(z-λ t), where k0 is the wave number and λ is the group velocity of the wave, and (b) the generalized Barnes (1976) simple Alfvén wave in which the wave normal n moves in a circle in the xy-plane perpendicular to the mean field, which is directed along the z-axis. The plane Alfven wave (a) is analogous to the slab Alfven mode and the generalized Barnes solution (b) is analogous to the 2D mode in Alfvenic, incompressible turbulence. The helicity characteristics of these two basic Alfven modes are distinct. The helicity characteristics of more general multi-dimensional simple Alfven waves are also investigated. Applications to nonlinear Alfvenic fluctuations and structures observed in the solar wind are discussed.

  13. Helicity, Reconnection, and Dynamo Effects

    SciTech Connect

    Ji, Hantao

    1998-11-01

    The inter-relationships between magnetic helicity, magnetic reconnection, and dynamo effects are discussed. In laboratory experiments, where two plasmas are driven to merge, the helicity content of each plasma strongly affects the reconnection rate, as well as the shape of the diffusion region. Conversely, magnetic reconnection events also strongly affect the global helicity, resulting in efficient helicity cancellation (but not dissipation) during counter-helicity reconnection and a finite helicity increase or decrease (but less efficiently than dissipation of magnetic energy) during co-helicity reconnection. Close relationships also exist between magnetic helicity and dynamo effects. The turbulent electromotive force along the mean magnetic field (alpha-effect), due to either electrostatic turbulence or the electron diamagnetic effect, transports mean-field helicity across space without dissipation. This has been supported by direct measurements of helicity flux in a laboratory plasma. When the dynamo effect is driven by electromagnetic turbulence, helicity in the turbulent field is converted to mean-field helicity. In all cases, however, dynamo processes conserve total helicity except for a small battery effect, consistent with the observation that the helicity is approximately conserved during magnetic relaxation.

  14. Calreticulin Controls the Rate of Assembly of CD1d Molecules in the Endoplasmic Reticulum*

    PubMed Central

    Zhu, Yajuan; Zhang, Wei; Veerapen, Natacha; Besra, Gurdyal; Cresswell, Peter

    2010-01-01

    CD1d is an MHC class I-like molecule comprised of a transmembrane glycoprotein (heavy chain) associated with β2-microglobulin (β2m) that presents lipid antigens to NKT cells. Initial folding of the heavy chain involves its glycan-dependent association with calreticulin (CRT), calnexin (CNX), and the thiol oxidoreductase ERp57, and is followed by assembly with β2m to form the heterodimer. Here we show that in CRT-deficient cells CD1d heavy chains convert to β2m-associated dimers at an accelerated rate, indicating faster folding of the heavy chain, while the rate of intracellular transport after assembly is unaffected. Unlike the situation with MHC class I molecules, antigen presentation by CD1d is not impaired in the absence of CRT. Instead, there are elevated levels of stable and functional CD1d on the surface of CRT-deficient cells. Association of the heavy chains with the ER chaperones Grp94 and Bip is observed in the absence of CRT, and these may replace CRT in mediating CD1d folding and assembly. ER retention of free CD1d heavy chains is impaired in CRT-deficient cells, allowing their escape and subsequent expression on the plasma membrane. However, these free heavy chains are rapidly internalized and degraded in lysosomes, indicating that β2m association is required for the exceptional resistance of CD1d to lysosomal degradation that is normally observed. PMID:20861015

  15. Helical plasma thruster

    SciTech Connect

    Beklemishev, A. D.

    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 ions 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.

  16. Helical plasma thruster

    NASA Astrophysics Data System (ADS)

    Beklemishev, A. D.

    2015-10-01

    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 ions 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® rocket engine.

  17. 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.

  18. End-to-End Thiocyanato-Bridged Helical Chain Polymer and Dichlorido-Bridged Copper(II) Complexes with a Hydrazone Ligand: Synthesis, Characterisation by Electron Paramagnetic Resonance and Variable-Temperature Magnetic Studies, and Inhibitory Effects on Human Colorectal Carcinoma Cells.

    PubMed

    Das, Kuheli; Datta, Amitabha; Sinha, Chittaranjan; Huang, Jui-Hsien; Garribba, Eugenio; Hsiao, Ching-Sheng; Hsu, Chin-Lin

    2012-04-01

    The reactions of the tridentate hydrazone ligand, N'-[1-(pyridin-2-yl)ethylidene]acetohydrazide (HL), obtained by condensation of 2-acetylpyridine with acetic hyadrazide, with copper nitrate trihydrate in the presence of thiocyanate, or with CuCl2 produce two distinct coordination compounds, namely a one-dimensional helical coordination chain of [CuL(NCS)] n (1) units, and a doubly chlorido-bridged dinuclear complex [Cu2L2Cl2] (2) (where L=CH3C(O)=N-N=CCH3C5H4N). Single-crystal X-ray structural determination studies reveal that in complex 1, a deprotonated hydrazone ligand L(-) coordinates a copper(II) ion that is bridged to two neighbouring metal centres by SCN(-) anions, generating a one-dimensional helical coordination chain. In complex 2, two symmetry-related, adjacent copper(II) coordination entities are doubly chlorido-bridged, producing a dicopper entity with a Cu⋅⋅⋅Cu distance of 3.402 (1) Å. The two coordination compounds have been fully characterised by elemental analysis, spectroscopic techniques including IR, UV-vis and electron paramagnetic resonance, and variable-temperature magnetic studies. The biological effects of 1 and 2 on the viability of human colorectal carcinoma cells (COLO-205 and HT-29) were evaluated using an MTT assay, and the results indicate that these complexes induce a decrease in cell-population growth of human colorectal carcinoma cells with apoptosis.

  19. Helical-D pinch

    SciTech Connect

    Schaffer, M.J.

    1997-08-01

    A stabilized pinch configuration is described, consisting of a D-shaped plasma cross section wrapped tightly around a guiding axis. The {open_quotes}helical-D{close_quotes} geometry produces a very large axial (toroidal) transform of magnetic line direction that reverses the pitch of the magnetic lines without the need of azimuthal (poloidal) plasma current. Thus, there is no need of a {open_quotes}dynamo{close_quotes} process and its associated fluctuations. The resulting configuration has the high magnetic shear and pitch reversal of the reversed field pinch (RFP). (Pitch = P = qR, where R = major radius). A helical-D pinch might demonstrate good confinement at q << 1.

  20. Helicity and celestial magnetism

    NASA Astrophysics Data System (ADS)

    Moffatt, H. K.

    2016-06-01

    This informal article discusses the central role of magnetic and kinetic helicity in relation to the evolution of magnetic fields in geophysical and astrophysical contexts. It is argued that the very existence of magnetic fields of the intensity and scale observed is attributable in large part to the chirality of the background turbulence or random-wave field of flow, the simplest measure of this chirality being non-vanishing helicity. Such flows are responsible for the generation of large-scale magnetic fields which themselves exhibit magnetic helicity. In the geophysical context, the turbulence has a `magnetostrophic' character in which the force balance is primarily that between buoyancy forces, Coriolis forces and Lorentz forces associated with the dynamo-generated magnetic field; the dominant nonlinearity here arises from the convective transport of buoyant elements erupting from the `mushy zone' at the inner core boundary. At the opposite extreme, in a highly conducting low-density plasma, the near-invariance of magnetic field topology (and of associated helicity) presents the challenging problem of `magnetic relaxation under topological constraints', of central importance both in astrophysical contexts and in controlled-fusion plasma dynamics. These problems are reviewed and open issues, particularly concerning saturation mechanisms, are reconsidered.

  1. Electronic structure calculations on helical conducting polymers.

    PubMed

    Ripoll, Juan D; Serna, Andrei; Guerra, Doris; Restrepo, Albeiro

    2010-10-21

    We present a study of the electronic structure and derived properties of polyfurane (PFu), polypyrrol (PPy), and polythiophene (PTh). Two spatial arrangements are considered: trans chain (tc-PFu, tc-PPy, tc-PTh) and cis α-helical (α-PFu, α-PPy, α-PTh). Even at the small sizes considered here, helical conformations appear to be stable. Band gaps of pure, undoped oligomers fall into the semiconductor range. Density of states (DOS) analysis suggest dense valence and conduction bands. Bond length alternation analysis predicts almost complete delocalization of the π clouds in all spatial arrangements. Doping with electron donors or electron-withdrawing impurities reduces all band gaps close to the metallic regime in addition to increasing the DOS for the valence and conduction bands.

  2. Neodymium 1D systems: targeting new sources for field-induced slow magnetization relaxation.

    PubMed

    Jassal, Amanpreet Kaur; Aliaga-Alcalde, Núria; Corbella, Montserrat; Aravena, Daniel; Ruiz, Eliseo; Hundal, Geeta

    2015-09-28

    Two non-isostructural homometallic 1D neodymium species displaying field-induced slow magnetization relaxations are presented together with theoretical studies. It is established that both systems are better described as organized 1D single molecule magnets (SMMs). Studies show great potential of Nd(III) ions to provide homometallic chains with slow magnetic relaxation.

  3. A survey of left-handed polyproline II helices.

    PubMed Central

    Stapley, B. J.; Creamer, T. P.

    1999-01-01

    Left-handed polyproline II helices (PPII) are contiguous elements of protein secondary structure in which the phi and psi angles of constituent residues are restricted to around -75 degrees and 145 degrees, respectively. They are important in structural proteins, in unfolded states and as ligands for signaling proteins. Here, we present a survey of 274 nonhomologous polypeptide chains from proteins of known structure for regions that form these structures. Such regions are rare, but the majority of proteins contain at least one PPII helix. Most PPII helices are shorter than five residues, although the longest found contained 12 amino acids. Proline predominates in PPII, but Gln and positively charged residues are also favored. The basis of Gln's prevalence is its ability to form an i, i + 1 side-chain to main-chain hydrogen bond with the backbone carbonyl oxygen of the proceeding residue; this helps to fix the psi angle of the Gln and the phi and psi of the proceeding residue in PPII conformations and explains why Gln is favored at the first position in a PPII helix. PPII helices are highly solvent exposed, which explains why apolar amino acids are disfavored despite preferring this region of phi/psi space when in isolation. PPII helices have perfect threefold rotational symmetry and within these structures we find significant correlation between the hydrophobicity of residues at i and i + 3; thus, PPII helices in globular proteins can be considered to be amphipathic. PMID:10091661

  4. Helical sense selective domains and enantiomeric superhelices generated by Langmuir-Schaefer deposition of an axially racemic chiral helical polymer

    NASA Astrophysics Data System (ADS)

    Rodríguez, R.; Ignés-Mullol, J.; Sagués, F.; Quiñoá, E.; Riguera, R.; Freire, F.

    2016-02-01

    The chiral polymer poly-(R)-1 behaves in solution, despite its chiral pendants, as a dynamic axially racemic (i.e., 1 : 1) mixture of left- and right-handed helices, but its deposition on graphite by a Langmuir-Schaefer (LS) technique leads to a helical sense-selective packing that forms separate enantiomeric domains of left- and right-handed helical chains observed by high resolution atomic force microscopy (AFM). The polymer structure within these domains is very uniform, seldom altered by the presence of reversals, grouped always in contiguous pairs maintaining a single helical sense along the polymer chain. The LS deposition technique has been shown to be crucial to obtain good quality monolayers from poly-(R)-1 and other poly(phenylacetylene)s (PPAs: poly-2, poly-3 and poly-4) with short pendants, where spin coating, drop casting and Langmuir-Blodgett (LB) failed, and suggests that this technique could be the method of choice for the preparation of 2D monolayers for high resolution AFM studies of PPAs with short pendants. Key helical parameters (i.e., sense, pitch, packing angle) are easily measured in this way.The chiral polymer poly-(R)-1 behaves in solution, despite its chiral pendants, as a dynamic axially racemic (i.e., 1 : 1) mixture of left- and right-handed helices, but its deposition on graphite by a Langmuir-Schaefer (LS) technique leads to a helical sense-selective packing that forms separate enantiomeric domains of left- and right-handed helical chains observed by high resolution atomic force microscopy (AFM). The polymer structure within these domains is very uniform, seldom altered by the presence of reversals, grouped always in contiguous pairs maintaining a single helical sense along the polymer chain. The LS deposition technique has been shown to be crucial to obtain good quality monolayers from poly-(R)-1 and other poly(phenylacetylene)s (PPAs: poly-2, poly-3 and poly-4) with short pendants, where spin coating, drop casting and Langmuir

  5. Helically linked mirror arrangement

    SciTech Connect

    Ranjan, P.

    1986-08-01

    A scheme is described for helical linking of mirror sections, which endeavors to combine the better features of toroidal and mirror devices by eliminating the longitudinal loss of mirror machines, having moderately high average ..beta.. and steady state operation. This scheme is aimed at a device, with closed magnetic surfaces having rotational transform for equilibrium, one or more axisymmetric straight sections for reduced radial loss, a simple geometrical axis for the links and an overall positive magnetic well depth for stability. We start by describing several other attempts at linking of mirror sections, made both in the past and the present. Then a description of our helically linked mirror scheme is given. This example has three identical straight sections connected by three sections having helical geometric axes. A theoretical analysis of the magnetic field and single-particle orbits in them leads to the conclusion that most of the passing particles would be confined in the device and they would have orbits independent of pitch angle under certain conditions. Numerical results are presented, which agree well with the theoretical results as far as passing particle orbits are concerned.

  6. Helicity transport through the photosphere

    NASA Astrophysics Data System (ADS)

    Schuck, P. W.; Antiochos, S. K.; Linton, M.

    2013-12-01

    Solar eruptions are driven by energy and helicity transported through the photosphere and into the Corona. However, the mechanism by which helicity is transferred from the solar dynamo to coronal structures is pooly understood. We recast the Berger and Field (1984) helicity transport equation in manifestly gauge invariant form and examine the individual terms leading to the transport of helicity through the emergence of closed field, and twisting and tangling of potential fields. These theoretical results are applied to erupting active regions observed by SDO/HMI. The plasma velocity fields in the photosphere, necessary for computing energy and helicity fluxes are determined using an upgraded version of DAVE4VM that incorporates the spherical geometry of the solar images. We find that the bulk of the helicity into the corona is injected by twisting motions, and we discuss the implications of our results for understanding coronal activity. This work was supported, in part, by NASA.

  7. Helicity transport through the photosphere

    NASA Astrophysics Data System (ADS)

    Schuck, P. W.; Antiochos, S. K.; Linton, M.

    2013-05-01

    Solar eruptions are driven by energy and helicity transported through the photosphere and into the Corona. However, the mechanism by which helicity is transferred from the solar dynamo to coronal structures is pooly understood. We recast the Berger and Field (1984) helicity transport equation in manifestly gauge invariant form and examine the individual terms leading to the transport of helicity through the emergence of closed field, and twisting and tangling of potential fields. These theoretical results are applied to erupting active regions observed by SDO/HMI. The plasma velocity fields in the photosphere, necessary for computing energy and helicity fluxes are determined using an upgraded version of DAVE4VM that incorporates the spherical geometry of the solar images. We find that the bulk of the helicity into the corona is injected by twisting motions, and we discuss the implications of our results for understanding coronal activity.

  8. 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.

  9. Conservation of helicity in superfluids

    NASA Astrophysics Data System (ADS)

    Kedia, Hridesh; Kleckner, Dustin; Proment, Davide; Irvine, William T. M.

    2015-03-01

    Helicity arises as a special conserved quantity in ideal fluids, in addition to energy, momentum and angular momentum. As a measure of the knottedness of vortex lines, Helicity provides an important tool for studying a wide variety of physical systems such as plasmas and turbulent fluids. Superfluids flow without resistance just like ideal (Euler) fluids, making it natural to ask whether their knottedness is similarly preserved. We address the conservation of helicity in superfluids theoretically and examine its consequences in numerical simulations.

  10. Buckling transition in long α-helices

    SciTech Connect

    Palenčár, Peter; Bleha, Tomáš

    2014-11-07

    The treatment of bending and buckling of stiff biopolymer filaments by the popular worm-like chain model does not provide adequate understanding of these processes at the microscopic level. Thus, we have used the atomistic molecular-dynamic simulations and the Amber03 force field to examine the compression buckling of α-helix (AH) filaments at room temperature. It was found that the buckling instability occurs in AHs at the critical force f{sub c} in the range of tens of pN depending on the AH length. The decrease of the force f{sub c} with the contour length follows the prediction of the classic thin rod theory. At the force f{sub c} the helical filament undergoes the swift and irreversible transition from the smoothly bent structure to the buckled one. A sharp kink in the AH contour arises at the transition, accompanied by the disruption of the hydrogen bonds in its vicinity. The kink defect brings in an effective softening of the AH molecule at buckling. Nonbonded interactions between helical branches drive the rearrangement of a kinked AH into the ultimate buckled structure of a compact helical hairpin described earlier in the literature.

  11. Relativistic helicity and link in Minkowski space-time

    SciTech Connect

    Yoshida, Z.; Kawazura, Y.; Yokoyama, T.

    2014-04-15

    A relativistic helicity has been formulated in the four-dimensional Minkowski space-time. Whereas the relativistic distortion of space-time violates the conservation of the conventional helicity, the newly defined relativistic helicity conserves in a barotropic fluid or plasma, dictating a fundamental topological constraint. The relation between the helicity and the vortex-line topology has been delineated by analyzing the linking number of vortex filaments which are singular differential forms representing the pure states of Banach algebra. While the dimension of space-time is four, vortex filaments link, because vorticities are primarily 2-forms and the corresponding 2-chains link in four dimension; the relativistic helicity measures the linking number of vortex filaments that are proper-time cross-sections of the vorticity 2-chains. A thermodynamic force yields an additional term in the vorticity, by which the vortex filaments on a reference-time plane are no longer pure states. However, the vortex filaments on a proper-time plane remain to be pure states, if the thermodynamic force is exact (barotropic), thus, the linking number of vortex filaments conserves.

  12. Helicity-Density And Normalized-Helicity Maps Of Flows

    NASA Technical Reports Server (NTRS)

    Degani, David; Levy, Yuval; Seginer, Arnan

    1991-01-01

    Maps of helicity density and normalized helicity useful as graphical representations of important features of three-dimensional flow fields containg vortexes. Emphasize complicated and important parts of flow field, identify vortexes, differentiate between primary and secondary vortexes, indicate sense of swirling motion, locate free singular points, and trace vortex-core streamlines emanating from these points.

  13. Synthesis, characterization and crystal structure determination of Mn (II) ion based 1D polymer constructed from 2, 2‧ bipyridyl and azide group, its thermal stability, magnetic properties and Hirshfeld surface analysis

    NASA Astrophysics Data System (ADS)

    Mudsainiyan, R. K.; Jassal, Amanpreet Kaur; Chawla, S. K.

    2015-05-01

    The 1-D polymeric complex (I) is having formula [Mn(2,2‧-BP).(N3)2]n, which has been crystallized in distilled water and characterized by elemental analyses, FT-IR spectrum, powder X-ray diffraction analyses and single-crystal diffraction analysis. This polymer possesses 1D helical chains or coils where Mn-azide-Mn forms the base of the coil which is alternatively garlanded by rigid bi-pyridine rings, where coordinates are in anti-fashion. The Mn (II) ions in the repeating units are linked by two end-on azide groups which extend through the two end-to-end azide ligands to the next unit forming a 1-D polymeric chain. The present study suggests that the use of this rigid and neutral building block leads to give better arrangement of the polymeric motif with [010] chains in 2-c uninodal net. During investigation of strong or weak intermolecular interactions, X-ray diffraction analysis and Hirshfeld surface analysis give rise to comparable results but in Hirshfeld surface analysis, two-third times more results of close contacts are obtained. The fingerprint plots demonstrate that these weak non-bonding interactions are important for stabilizing the crystal packing. Magnetic properties of the complex (I) were analyzed on the basis of an alternating ferro- and antiferromagnetic Heisenberg chain of Mn (II) ions. The J-exchange parameters found are J1=64.3 K (45.3 cm-1), and J2=-75.7 K (-53.3 cm-1). Magnetic properties are discussed in comparison with those of other similar molecular magnets of [Mn(L-L)(N3)2]n type.

  14. Helical sense selective domains and enantiomeric superhelices generated by Langmuir-Schaefer deposition of an axially racemic chiral helical polymer.

    PubMed

    Rodríguez, R; Ignés-Mullol, J; Sagués, F; Quiñoá, E; Riguera, R; Freire, F

    2016-02-14

    The chiral polymer poly-(R)-1 behaves in solution, despite its chiral pendants, as a dynamic axially racemic (i.e., 1 : 1) mixture of left- and right-handed helices, but its deposition on graphite by a Langmuir-Schaefer (LS) technique leads to a helical sense-selective packing that forms separate enantiomeric domains of left- and right-handed helical chains observed by high resolution atomic force microscopy (AFM). The polymer structure within these domains is very uniform, seldom altered by the presence of reversals, grouped always in contiguous pairs maintaining a single helical sense along the polymer chain. The LS deposition technique has been shown to be crucial to obtain good quality monolayers from poly-(R)-1 and other poly(phenylacetylene)s (PPAs: poly-2, poly-3 and poly-4) with short pendants, where spin coating, drop casting and Langmuir-Blodgett (LB) failed, and suggests that this technique could be the method of choice for the preparation of 2D monolayers for high resolution AFM studies of PPAs with short pendants. Key helical parameters (i.e., sense, pitch, packing angle) are easily measured in this way. PMID:26791332

  15. Helical sense selective domains and enantiomeric superhelices generated by Langmuir-Schaefer deposition of an axially racemic chiral helical polymer.

    PubMed

    Rodríguez, R; Ignés-Mullol, J; Sagués, F; Quiñoá, E; Riguera, R; Freire, F

    2016-02-14

    The chiral polymer poly-(R)-1 behaves in solution, despite its chiral pendants, as a dynamic axially racemic (i.e., 1 : 1) mixture of left- and right-handed helices, but its deposition on graphite by a Langmuir-Schaefer (LS) technique leads to a helical sense-selective packing that forms separate enantiomeric domains of left- and right-handed helical chains observed by high resolution atomic force microscopy (AFM). The polymer structure within these domains is very uniform, seldom altered by the presence of reversals, grouped always in contiguous pairs maintaining a single helical sense along the polymer chain. The LS deposition technique has been shown to be crucial to obtain good quality monolayers from poly-(R)-1 and other poly(phenylacetylene)s (PPAs: poly-2, poly-3 and poly-4) with short pendants, where spin coating, drop casting and Langmuir-Blodgett (LB) failed, and suggests that this technique could be the method of choice for the preparation of 2D monolayers for high resolution AFM studies of PPAs with short pendants. Key helical parameters (i.e., sense, pitch, packing angle) are easily measured in this way.

  16. DNA three-way junction with a dinuclear iron(II) supramolecular helicate at the center: a NMR structural study.

    PubMed

    Cerasino, Leonardo; Hannon, Michael J; Sletten, Einar

    2007-08-01

    A tetracationic supramolecular helicate, [Fe2L3]4+ (L = C25H20N4), with a triple-helical architecture is found to induce the formation of a three-way junction (3WJ) of deoxyribonucleotides with the helicate located in the center of the junction. NMR spectroscopic studies of the interaction between the M enantiomer of the helicate and two different oligonucleotides, [5'-d(TATGGTACCATA)]2 and [5'-d(CGTACG)]2, show that, in each case, the 2-fold symmetry of the helicate is lifted, while the 3-fold symmetry around the helicate axis is retained. The 1:3 helicate/DNA stoichiometry estimated from 1D NMR spectra supports a molecular model of a three-way junction composed of three strands. Three separate double-helical arms of the three-way junction are chemically identical giving rise to one set of proton resonances. The NOE contacts between the helicate and DNA unambiguously show that the helicate is fitted into the center of the three-way junction experiencing a hydrophobic 3-fold symmetric environment. Close stacking interactions between the ligand phenyl groups and the nucleotide bases are demonstrated through unusually large downfield shifts (1-2 ppm) of the phenyl protons. The unprecedented 3WJ arrangement observed in solution has also been found to exist in the crystal structure of the helicate adduct of [d(CGTACG)2] (Angew. Chem., Int. Ed. 2006, 45, 1227).

  17. Nonlocal Order Parameters for the 1D Hubbard Model

    NASA Astrophysics Data System (ADS)

    Montorsi, Arianna; Roncaglia, Marco

    2012-12-01

    We characterize the Mott-insulator and Luther-Emery phases of the 1D Hubbard model through correlators that measure the parity of spin and charge strings along the chain. These nonlocal quantities order in the corresponding gapped phases and vanish at the critical point Uc=0, thus configuring as hidden order parameters. The Mott insulator consists of bound doublon-holon pairs, which in the Luther-Emery phase turn into electron pairs with opposite spins, both unbinding at Uc. The behavior of the parity correlators is captured by an effective free spinless fermion model.

  18. Magnetic design constraints of helical solenoids

    SciTech Connect

    Lopes, M. L.; Krave, S. T.; Tompkins, J. C.; Yonehara, K.; Flanagan, G.; Kahn, S. A.; Melconian, K.

    2015-01-30

    Helical solenoids have been proposed as an option for a Helical Cooling Channel for muons in a proposed Muon Collider. Helical solenoids can provide the required three main field components: solenoidal, helical dipole, and a helical gradient. In general terms, the last two are a function of many geometric parameters: coil aperture, coil radial and longitudinal dimensions, helix period and orbit radius. In this paper, we present design studies of a Helical Solenoid, addressing the geometric tunability limits and auxiliary correction system.

  19. Helicity patterns on the Sun

    NASA Astrophysics Data System (ADS)

    Pevtsov, A.

    Solar magnetic fields exhibit hemispheric preference for negative (pos- itive) helicity in northern (southern) hemisphere. The hemispheric he- licity rule, however, is not very strong, - the patterns of opposite sign helicity were observed on different spatial scales in each hemisphere. For instance, many individual sunspots exhibit patches of opposite he- licity inside the single polarity field. There are also helicity patterns on scales larger than the size of typical active region. Such patterns were observed in distribution of active regions with abnormal (for a give hemisphere) helicity, in large-scale photospheric magnetic fields and coronal flux systems. We will review the observations of large-scale pat- terns of helicity in solar atmosphere and their possible relationship with (sub-)photospheric processes. The emphasis will be on large-scale pho- tospheric magnetic field and solar corona.

  20. Winding light beams along elliptical helical trajectories

    NASA Astrophysics Data System (ADS)

    Wen, Yuanhui; Chen, Yujie; Zhang, Yanfeng; Chen, Hui; Yu, Siyuan

    2016-07-01

    Conventional caustic methods in real or Fourier space produced accelerating optical beams only with convex trajectories. We developed a superposition caustic method capable of winding light beams along nonconvex trajectories. We ascertain this method by constructing a one-dimensional (1D) accelerating beam moving along a sinusoidal trajectory, and subsequently extending to two-dimensional (2D) accelerating beams along arbitrarily elliptical helical trajectories. We experimentally implemented the method with a compact and robust integrated optics approach by fabricating micro-optical structures on quartz glass plates to perform the spatial phase and amplitude modulation to the incident light, generating beam trajectories highly consistent with prediction. The theoretical and implementation methods can in principle be extended to the construction of accelerating beams with a wide variety of nonconvex trajectories, thereby opening up a route of manipulating light beams for fundamental research and practical applications.

  1. The Advanced Helical Generator

    SciTech Connect

    Reisman, D B; Javedani, J B; Ellsworth, G F; Kuklo, R M; Goerz, D A; White, A D; Tallerico, L J; Gidding, D A; Murphy, M J; Chase, J B

    2009-10-26

    A high explosive pulsed power (HEPP) generator called the Advanced Helical Generator (AHG) has been designed, built, and successfully tested. The AHG incorporates design principles of voltage and current management to obtain a high current and energy gain. Its design was facilitated by the use of modern modeling tools as well as high precision manufacture. The result was a first-shot success. The AHG delivered 16 Mega-Amperes of current and 11 Mega-Joules of energy to a quasi-static 80 nH inductive load. A current gain of 154 times was obtained with a peak exponential rise time of 20 {micro}s. We will describe in detail the design and testing of the AHG.

  2. Molecular-dynamics simulation of crystallization in helical polymers.

    PubMed

    Yamamoto, Takashi; Sawada, Kaoru

    2005-12-15

    The molecular mechanism of crystallization in helical polymers is a fascinating but very difficult subject of research. We here report our recent efforts toward better understanding of the crystallization in helical polymers by use of molecular-dynamics simulation. With straightforward approaches to the problem being quite difficult, we adopt a different strategy of categorizing the helical polymers into two distinct types: one type is a simple bare helix which is essentially made of backbone atomic groups only and has smoother molecular contours, and the other is a more general helix having large side groups that would considerably hamper molecular motion and crystallization. Both types of helical polymers are here constructed by use of the united atom model, but they show quite distinct crystallization behavior; the crystallization of the former-type polymer is rather fast, while that of the latter-type polymer is extremely slow. We find that the bare helix, when rapidly cooled in free three-dimensional space, freezes into partially ordered state with limited intramolecular and intermolecular orders, and that remarkable improvement of order and growth of an ordered chain-folded crystallite occurs by very long-time annealing of the partially ordered state around the apparent freezing temperature. We also study crystallization of the bare helix upon a growth surface; the crystallization in this case proceeds much faster through highly cooperative process of the intermolecular and the intramolecular degrees of freedom. On the other hand, crystallization of the realistic model of isotactic polypropylene (iPP) having pendant methylene groups is found to be extremely sluggish. By restricting the spatial dimension of the system thereby fully disentangling the chain, we observe that the molecule of iPP crystallizes very quickly onto the crystal substrate made of the same iPP chain. Quite remarkable is that the molecule of iPP strictly recognizes the helical sense of the

  3. Self-assembly of double helical nanostructures inside carbon nanotubes

    NASA Astrophysics Data System (ADS)

    Lv, Cheng; Xue, Qingzhong; Shan, Meixia; Jing, Nuannuan; Ling, Cuicui; Zhou, Xiaoyan; Jiao, Zhiyong; Xing, Wei; Yan, Zifeng

    2013-05-01

    We use molecular dynamics (MD) simulations to show that a DNA-like double helix of two poly(acetylene) (PA) chains can form inside single-walled carbon nanotubes (SWNTs). The computational results indicate that SWNTs can activate and guide the self-assembly of polymer chains, allowing them to adopt a helical configuration in a SWNT through the combined action of the van der Waals potential well and the π-π stacking interaction between the polymer and the inner surface of SWNTs. Meanwhile both the SWNT size and polymer chain stiffness determine the outcome of the nanostructure. Furthermore, we also found that water clusters encourage the self-assembly of PA helical structures in the tube. This molecular model may lead to a better understanding of the formation of a double helix biological molecule inside SWNTs. Alternatively, it could form the basis of a novel nanoscale material by utilizing the `empty' spaces of SWNTs.We use molecular dynamics (MD) simulations to show that a DNA-like double helix of two poly(acetylene) (PA) chains can form inside single-walled carbon nanotubes (SWNTs). The computational results indicate that SWNTs can activate and guide the self-assembly of polymer chains, allowing them to adopt a helical configuration in a SWNT through the combined action of the van der Waals potential well and the π-π stacking interaction between the polymer and the inner surface of SWNTs. Meanwhile both the SWNT size and polymer chain stiffness determine the outcome of the nanostructure. Furthermore, we also found that water clusters encourage the self-assembly of PA helical structures in the tube. This molecular model may lead to a better understanding of the formation of a double helix biological molecule inside SWNTs. Alternatively, it could form the basis of a novel nanoscale material by utilizing the `empty' spaces of SWNTs. Electronic supplementary information (ESI) available. See DOI: 10.1039/c2nr33157h

  4. Self-assembly of magnetite nanocubes into helical superstructures.

    PubMed

    Singh, Gurvinder; Chan, Henry; Baskin, Artem; Gelman, Elijah; Repnin, Nikita; Král, Petr; Klajn, Rafal

    2014-09-01

    Organizing inorganic nanocrystals into complex architectures is challenging and typically relies on preexisting templates, such as properly folded DNA or polypeptide chains. We found that under carefully controlled conditions, cubic nanocrystals of magnetite self-assemble into arrays of helical superstructures in a template-free manner with >99% yield. Computer simulations revealed that the formation of helices is determined by the interplay of van der Waals and magnetic dipole-dipole interactions, Zeeman coupling, and entropic forces and can be attributed to spontaneous formation of chiral nanocube clusters. Neighboring helices within their densely packed ensembles tended to adopt the same handedness in order to maximize packing, thus revealing a novel mechanism of symmetry breaking and chirality amplification. PMID:25061133

  5. Potent neutralizing anti-CD1d antibody reduces lung cytokine release in primate asthma model.

    PubMed

    Nambiar, Jonathan; Clarke, Adam W; Shim, Doris; Mabon, David; Tian, Chen; Windloch, Karolina; Buhmann, Chris; Corazon, Beau; Lindgren, Matilda; Pollard, Matthew; Domagala, Teresa; Poulton, Lynn; Doyle, Anthony G

    2015-01-01

    CD1d is a receptor on antigen-presenting cells involved in triggering cell populations, particularly natural killer T (NKT) cells, to release high levels of cytokines. NKT cells are implicated in asthma pathology and blockade of the CD1d/NKT cell pathway may have therapeutic potential. We developed a potent anti-human CD1d antibody (NIB.2) that possesses high affinity for human and cynomolgus macaque CD1d (KD ∼100 pM) and strong neutralizing activity in human primary cell-based assays (IC50 typically <100 pM). By epitope mapping experiments, we showed that NIB.2 binds to CD1d in close proximity to the interface of CD1d and the Type 1 NKT cell receptor β-chain. Together with data showing that NIB.2 inhibited stimulation via CD1d loaded with different glycolipids, this supports a mechanism whereby NIB.2 inhibits NKT cell activation by inhibiting Type 1 NKT cell receptor β-chain interactions with CD1d, independent of the lipid antigen in the CD1d antigen-binding cleft. The strong in vitro potency of NIB.2 was reflected in vivo in an Ascaris suum cynomolgus macaque asthma model. Compared with vehicle control, NIB.2 treatment significantly reduced bronchoalveolar lavage (BAL) levels of Ascaris-induced cytokines IL-5, IL-8 and IL-1 receptor antagonist, and significantly reduced baseline levels of GM-CSF, IL-6, IL-15, IL-12/23p40, MIP-1α, MIP-1β, and VEGF. At a cellular population level NIB.2 also reduced numbers of BAL lymphocytes and macrophages, and blood eosinophils and basophils. We demonstrate that anti-CD1d antibody blockade of the CD1d/NKT pathway modulates inflammatory parameters in vivo in a primate inflammation model, with therapeutic potential for diseases where the local cytokine milieu is critical.

  6. Potent neutralizing anti-CD1d antibody reduces lung cytokine release in primate asthma model

    PubMed Central

    Nambiar, Jonathan; Clarke, Adam W; Shim, Doris; Mabon, David; Tian, Chen; Windloch, Karolina; Buhmann, Chris; Corazon, Beau; Lindgren, Matilda; Pollard, Matthew; Domagala, Teresa; Poulton, Lynn; Doyle, Anthony G

    2015-01-01

    CD1d is a receptor on antigen-presenting cells involved in triggering cell populations, particularly natural killer T (NKT) cells, to release high levels of cytokines. NKT cells are implicated in asthma pathology and blockade of the CD1d/NKT cell pathway may have therapeutic potential. We developed a potent anti-human CD1d antibody (NIB.2) that possesses high affinity for human and cynomolgus macaque CD1d (KD ∼100 pM) and strong neutralizing activity in human primary cell-based assays (IC50 typically <100 pM). By epitope mapping experiments, we showed that NIB.2 binds to CD1d in close proximity to the interface of CD1d and the Type 1 NKT cell receptor β-chain. Together with data showing that NIB.2 inhibited stimulation via CD1d loaded with different glycolipids, this supports a mechanism whereby NIB.2 inhibits NKT cell activation by inhibiting Type 1 NKT cell receptor β-chain interactions with CD1d, independent of the lipid antigen in the CD1d antigen-binding cleft. The strong in vitro potency of NIB.2 was reflected in vivo in an Ascaris suum cynomolgus macaque asthma model. Compared with vehicle control, NIB.2 treatment significantly reduced bronchoalveolar lavage (BAL) levels of Ascaris-induced cytokines IL-5, IL-8 and IL-1 receptor antagonist, and significantly reduced baseline levels of GM-CSF, IL-6, IL-15, IL-12/23p40, MIP-1α, MIP-1β, and VEGF. At a cellular population level NIB.2 also reduced numbers of BAL lymphocytes and macrophages, and blood eosinophils and basophils. We demonstrate that anti-CD1d antibody blockade of the CD1d/NKT pathway modulates inflammatory parameters in vivo in a primate inflammation model, with therapeutic potential for diseases where the local cytokine milieu is critical. PMID:25751125

  7. Turbulent Dynamos and Magnetic Helicity

    SciTech Connect

    Ji, Hantao

    1999-04-01

    It is shown that the turbulent dynamo alpha-effect converts magnetic helicity from the turbulent field to the mean field when the turbulence is electromagnetic while the magnetic helicity of the mean-field is transported across space when the turbulence is elcetrostatic or due to the elcetron diamagnetic effect. In all cases, however, the dynamo effect strictly conserves the total helicity expect for a battery effect which vanishes in the limit of magnetohydrodynamics. Implications for astrophysical situations, especially for the solar dynamo, are discussed.

  8. Upstream Design and 1D-CAE

    NASA Astrophysics Data System (ADS)

    Sawada, Hiroyuki

    Recently, engineering design environment of Japan is changing variously. Manufacturing companies are being challenged to design and bring out products that meet the diverse demands of customers and are competitive against those produced by rising countries(1). In order to keep and strengthen the competitiveness of Japanese companies, it is necessary to create new added values as well as conventional ones. It is well known that design at the early stages has a great influence on the final design solution. Therefore, design support tools for the upstream design is necessary for creating new added values. We have established a research society for 1D-CAE (1 Dimensional Computer Aided Engineering)(2), which is a general term for idea, methodology and tools applicable for the upstream design support, and discuss the concept and definition of 1D-CAE. This paper reports our discussion about 1D-CAE.

  9. Self-assembling phenylpropyl ether dendronized helical polyphenylacetylenes.

    PubMed

    Percec, Virgil; Peterca, Mihai; Rudick, Jonathan G; Aqad, Emad; Imam, Mohammad R; Heiney, Paul A

    2007-01-01

    The first example of a self-assembling phenylpropyl ether based dendronized polymer has been reported and its preferred helical handedness has been determined. Dendronized polymer poly(10) and its nondendritic analogue poly(8) are high-cis-content polyphenylacetylenes (PPAs) prepared by using [Rh(nbd)Cl]2/NEt3 (nbd: 2,5-norbornadiene). Both polymers possess a stereocenter in their side chain, which selects a preferred helical handedness. Based on negative exciton chirality observed in the CD spectra of poly(10), we have designated this molecule as a right-handed helical polymer, which persists over a wide temperature range. Poly(10) self-organizes into both Phiioh and Phih lattices in bulk. The Phiioh-to-Phih transition is associated with thermoreversible cis-cisoidal to cis-transoidal isomerization of the helical PPA, accompanied by a dramatic decrease in the column diameter and a decrease in the pi-stacking correlation length along the column. A model for the right-handed helical dendronized PPA has been proposed wherein dendrons from adjacent column strata interdigitate to effectively fill space.

  10. Helicity multiplexed broadband metasurface holograms

    PubMed Central

    Wen, Dandan; Yue, Fuyong; Li, Guixin; Zheng, Guoxing; Chan, Kinlong; Chen, Shumei; Chen, Ming; Li, King Fai; Wong, Polis Wing Han; Cheah, Kok Wai; Yue Bun Pun, Edwin; Zhang, Shuang; Chen, Xianzhong

    2015-01-01

    Metasurfaces are engineered interfaces that contain a thin layer of plasmonic or dielectric nanostructures capable of manipulating light in a desirable manner. Advances in metasurfaces have led to various practical applications ranging from lensing to holography. Metasurface holograms that can be switched by the polarization state of incident light have been demonstrated for achieving polarization multiplexed functionalities. However, practical application of these devices has been limited by their capability for achieving high efficiency and high image quality. Here we experimentally demonstrate a helicity multiplexed metasurface hologram with high efficiency and good image fidelity over a broad range of frequencies. The metasurface hologram features the combination of two sets of hologram patterns operating with opposite incident helicities. Two symmetrically distributed off-axis images are interchangeable by controlling the helicity of the input light. The demonstrated helicity multiplexed metasurface hologram with its high performance opens avenues for future applications with functionality switchable optical devices. PMID:26354497

  11. Magnetic Helicity and Planetary Dynamos

    NASA Technical Reports Server (NTRS)

    Shebalin, John V.

    2012-01-01

    A model planetary dynamo based on the Boussinesq approximation along with homogeneous boundary conditions is considered. A statistical theory describing a large-scale MHD dynamo is found, in which magnetic helicity is the critical parameter

  12. Tunable Helical Origami

    NASA Astrophysics Data System (ADS)

    Chen, Zi; Dai, Eric; Zheng, Huang

    2014-03-01

    Origami, the Japanese art of paper folding, is traditionally viewed as an amusing pastime and medium of artistic expression. However, in recent years, origami has begun to inspire innovations in science and engineering. For example, K. Miura led the study of a paper folding pattern in regards to deployment of solar panels to outer space, resulting in more efficient packing and unpacking of the solar panels into tightly constrained spaces. In this work, we study the geometric and mechanical properties of a twisting origami pattern. The pattern created by the fold exhibits several interesting properties, including rigid foldibility, and finely tunable helical coiling, with control over pitch, radius, and handedness of the helix. In addition, the pattern closely mimics the twist buckling patterns shown by thin materials, for example, a mobius strip. In our work, we relate the six parameters of the twisting origami pattern to generate a fully tunable graphical model of the fold. In addition, we demonstrate that the morphogenesis of such folding pattern can be modeled through finite element analysis. We hope our research into the diagonal fold brings insight into the potential scientific and engineering applications of origami and spark further research into how the traditional paper art can be applied as a simple, inexpensive model for complex problems.

  13. Conservation of polyproline II helices in homologous proteins: implications for structure prediction by model building.

    PubMed Central

    Adzhubei, A. A.; Sternberg, M. J.

    1994-01-01

    Left-handed polyproline II (PPII) helices commonly occur in globular proteins in segments of 4-8 residues. This paper analyzes the structural conservation of PPII-helices in 3 protein families: serine proteinases, aspartic proteinases, and immunoglobulin constant domains. Calculations of the number of conserved segments based on structural alignment of homologous molecules yielded similar results for the PPII-helices, the alpha-helices, and the beta-strands. The PPII-helices are consistently conserved at the level of 100-80% in the proteins with sequence identity above 20% and RMS deviation of structure alignments below 3.0 A. The most structurally important PPII segments are conserved below this level of sequence identity. These results suggest that the PPII-helices, in addition to the other 2 secondary structure classes, should be identified as part of structurally conserved regions in proteins. This is supported by similar values for the local RMS deviations of the aligned segments for the structural classes of PPII-helices, alpha-helices, and beta-strands. The PPII-helices are shown to participate in supersecondary elements such as PPII-helix/alpha-helix. The conservation of PPII-helices depends on the conservation of a supersecondary element as a whole. PPII-helices also form links, possibly flexible, in the interdomain regions. The role of the PPII-helices in model building by homology is 2-fold; they serve as additional conserved elements in the structure allowing improvement of the accuracy of a model and provide correct chain geometry for modeling of the segments equivalenced to them in a target sequence. The improvement in model building is demonstrated in 2 test studies. PMID:7756993

  14. Magnetic Helicity, Tilt, and Twist

    NASA Astrophysics Data System (ADS)

    Pevtsov, Alexei A.; Berger, Mitchell A.; Nindos, Alexander; Norton, Aimee A.; van Driel-Gesztelyi, Lidia

    2014-12-01

    Since its introduction to astro- and solar physics, the concept of helicity has proven to be useful in providing critical insights into physics of various processes from astrophysical dynamos, to magnetic reconnection and eruptive phenomena. Signature of helicity was also detected in many solar features, including orientation of solar active regions, or Joy's law. Here we provide a summary of both solar phenomena and consider mutual relationship and its importance for the evolution of solar magnetic fields.

  15. DESIGN PACKAGE 1D SYSTEM SAFETY ANALYSIS

    SciTech Connect

    L.R. Eisler

    1995-02-02

    The purpose of this analysis is to systematically identify and evaluate hazards related to the Yucca Mountain Project Exploratory Studies Facility (ESF) Design Package 1D, Surface Facilities, (for a list of design items included in the package 1D system safety analysis see section 3). This process is an integral part of the systems engineering process; whereby safety is considered during planning, design, testing, and construction. A largely qualitative approach was used since a radiological System Safety analysis is not required. The risk assessment in this analysis characterizes the accident scenarios associated with the Design Package 1D structures/systems/components in terms of relative risk and includes recommendations for mitigating all identified risks. The priority for recommending and implementing mitigation control features is: (1) Incorporate measures to reduce risks and hazards into the structure/system/component (S/S/C) design, (2) add safety devices and capabilities to the designs that reduce risk, (3) provide devices that detect and warn personnel of hazardous conditions, and (4) develop procedures and conduct training to increase worker awareness of potential hazards, on methods to reduce exposure to hazards, and on the actions required to avoid accidents or correct hazardous conditions. The scope of this analysis is limited to the Design Package 1D structures/systems/components (S/S/Cs) during normal operations excluding hazards occurring during maintenance and ''off normal'' operations.

  16. Deciphering the structural code for proteins: helical propensities in domain classes and statistical multiresidue information in alpha-helices.

    PubMed Central

    Negrete, J. A.; Viñuales, Y.; Palau, J.

    1998-01-01

    We made several statistical analyses in a large sample of nearly 4,000 helices (from 546 redundancy-controlled PDB protein subunits), which give new insights into the helical properties of globular proteins. In a first experiment, the amino acid composition of the whole sample was compared with the composition of two helical sample subgroups (the "mainly-alpha" and the "(alpha/beta)8 barrel" domain classes); we reached the conclusion that composition-based helical propensities for secondary structure prediction do not depend on the structural class. Running a five-residue window through the whole sample, the positional composition revealed that positive and negative residues are located throughout the helices and tend to neutralize the macrodipole effect. On this basis, we analyzed charged triplets using a running five-residue window. The conclusion was that only mixed charged residues [positive (+) and negative (-)] located at positions 1-2-5 and 1-4-5 are clearly favored. In these locations the most abundant are (- -..+) and (-..+ +), and this shows the existence of side chain microdipoles, which neutralize the large macrodipole of the helix. We made a systematic statistical analysis of charged, dipolar, and hydrophobic + aromatic residues, which enabled us to work out rules that should be useful for modeling and design purposes. Finally, we analyzed the relative abundance of all the different amphipathic double-arcs that are present in helices formed by octapeptides (8) and nonapeptides (18). All of the double-arcs that make up Schiffer and Edmundson's classical helical wheel are found in abundance in the sample. PMID:9655341

  17. TCTEX1D2 mutations underlie Jeune asphyxiating thoracic dystrophy with impaired retrograde intraflagellar transport.

    PubMed

    Schmidts, Miriam; Hou, Yuqing; Cortés, Claudio R; Mans, Dorus A; Huber, Celine; Boldt, Karsten; Patel, Mitali; van Reeuwijk, Jeroen; Plaza, Jean-Marc; van Beersum, Sylvia E C; Yap, Zhi Min; Letteboer, Stef J F; Taylor, S Paige; Herridge, Warren; Johnson, Colin A; Scambler, Peter J; Ueffing, Marius; Kayserili, Hulya; Krakow, Deborah; King, Stephen M; Beales, Philip L; Al-Gazali, Lihadh; Wicking, Carol; Cormier-Daire, Valerie; Roepman, Ronald; Mitchison, Hannah M; Witman, George B

    2015-01-01

    The analysis of individuals with ciliary chondrodysplasias can shed light on sensitive mechanisms controlling ciliogenesis and cell signalling that are essential to embryonic development and survival. Here we identify TCTEX1D2 mutations causing Jeune asphyxiating thoracic dystrophy with partially penetrant inheritance. Loss of TCTEX1D2 impairs retrograde intraflagellar transport (IFT) in humans and the protist Chlamydomonas, accompanied by destabilization of the retrograde IFT dynein motor. We thus define TCTEX1D2 as an integral component of the evolutionarily conserved retrograde IFT machinery. In complex with several IFT dynein light chains, it is required for correct vertebrate skeletal formation but may be functionally redundant under certain conditions. PMID:26044572

  18. TCTEX1D2 mutations underlie Jeune asphyxiating thoracic dystrophy with impaired retrograde intraflagellar transport

    PubMed Central

    Schmidts, Miriam; Hou, Yuqing; Cortés, Claudio R.; Mans, Dorus A.; Huber, Celine; Boldt, Karsten; Patel, Mitali; van Reeuwijk, Jeroen; Plaza, Jean-Marc; van Beersum, Sylvia E. C.; Yap, Zhi Min; Letteboer, Stef J. F.; Taylor, S. Paige; Herridge, Warren; Johnson, Colin A.; Scambler, Peter J.; Ueffing, Marius; Kayserili, Hulya; Krakow, Deborah; King, Stephen M.; Beales, Philip L.; Al-Gazali, Lihadh; Wicking, Carol; Cormier-Daire, Valerie; Roepman, Ronald; Mitchison, Hannah M.; Witman, George B.; Al-Turki, Saeed; Anderson, Carl; Anney, Richard; Antony, Dinu; Asimit, Jennifer; Ayub, Mohammad; Barrett, Jeff; Barroso, Inês; Bentham, Jamie; Bhattacharya, Shoumo; Blackwood, Douglas; Bobrow, Martin; Bochukova, Elena; Bolton, Patrick; Boustred, Chris; Breen, Gerome; Brion, Marie-Jo; Brown, Andrew; Calissano, Mattia; Carss, Keren; Chatterjee, Krishna; Chen, Lu; Cirak, Sebhattin; Clapham, Peter; Clement, Gail; Coates, Guy; Collier, David; Cosgrove, Catherine; Cox, Tony; Craddock, Nick; Crooks, Lucy; Curran, Sarah; Daly, Allan; Danecek, Petr; Smith, George Davey; Day-Williams, Aaron; Day, Ian; Durbin, Richard; Edkins, Sarah; Ellis, Peter; Evans, David; Farooqi, I. Sadaf; Fatemifar, Ghazaleh; Fitzpatrick, David; Flicek, Paul; Floyd, Jamie; Foley, A. Reghan; Franklin, Chris; Futema, Marta; Gallagher, Louise; Gaunt, Tom; Geschwind, Daniel; Greenwood, Celia; Grozeva, Detelina; Guo, Xiaosen; Gurling, Hugh; Hart, Deborah; Hendricks, Audrey; Holmans, Peter; Huang, Jie; Humphries, Steve E.; Hurles, Matt; Hysi, Pirro; Jackson, David; Jamshidi, Yalda; Jewell, David; Chris, Joyce; Kaye, Jane; Keane, Thomas; Kemp, John; Kennedy, Karen; Kent, Alastair; Kolb-Kokocinski, Anja; Lachance, Genevieve; Langford, Cordelia; Lee, Irene; Li, Rui; Li, Yingrui; Ryan, Liu; Lönnqvist, Jouko; Lopes, Margarida; MacArthur, Daniel G.; Massimo, Mangino; Marchini, Jonathan; Maslen, John; McCarthy, Shane; McGuffin, Peter; McIntosh, Andrew; McKechanie, Andrew; McQuillin, Andrew; Memari, Yasin; Metrustry, Sarah; Min, Josine; Moayyeri, Alireza; Morris, James; Muddyman, Dawn; Muntoni, Francesco; Northstone, Kate; O'Donovan, Michael; O'Rahilly, Stephen; Onoufriadis, Alexandros; Oualkacha, Karim; Owen, Michael; Palotie, Aarno; Panoutsopoulou, Kalliope; Parker, Victoria; Parr, Jeremy; Paternoster, Lavinia; Paunio, Tiina; Payne, Felicity; Perry, John; Pietilainen, Olli; Plagnol, Vincent; Quail, Michael A.; Quaye, Lydia; Raymond, Lucy; Rehnström, Karola; Brent Richards, J.; Ring, Sue; Ritchie, Graham R S; Savage, David B.; Schoenmakers, Nadia; Semple, Robert K.; Serra, Eva; Shihab, Hashem; Shin, So-Youn; Skuse, David; Small, Kerrin; Smee, Carol; Soler, Artigas María; Soranzo, Nicole; Southam, Lorraine; Spector, Tim; St Pourcain, Beate; St. Clair, David; Stalker, Jim; Surdulescu, Gabriela; Suvisaari, Jaana; Tachmazidou, Ioanna; Tian, Jing; Timpson, Nic; Tobin, Martin; Valdes, Ana; van Kogelenberg, Margriet; Vijayarangakannan, Parthiban; Wain, Louise; Walter, Klaudia; Wang, Jun; Ward, Kirsten; Wheeler, Ellie; Whittall, Ros; Williams, Hywel; Williamson, Kathy; Wilson, Scott G.; Wong, Kim; Whyte, Tamieka; ChangJiang, Xu; Zeggini, Eleftheria; Zhang, Feng; Zheng, Hou-Feng

    2015-01-01

    The analysis of individuals with ciliary chondrodysplasias can shed light on sensitive mechanisms controlling ciliogenesis and cell signalling that are essential to embryonic development and survival. Here we identify TCTEX1D2 mutations causing Jeune asphyxiating thoracic dystrophy with partially penetrant inheritance. Loss of TCTEX1D2 impairs retrograde intraflagellar transport (IFT) in humans and the protist Chlamydomonas, accompanied by destabilization of the retrograde IFT dynein motor. We thus define TCTEX1D2 as an integral component of the evolutionarily conserved retrograde IFT machinery. In complex with several IFT dynein light chains, it is required for correct vertebrate skeletal formation but may be functionally redundant under certain conditions. PMID:26044572

  19. Employing helicity amplitudes for resummation

    NASA Astrophysics Data System (ADS)

    Moult, Ian; Stewart, Iain W.; Tackmann, Frank J.; Waalewijn, Wouter J.

    2016-05-01

    Many state-of-the-art QCD calculations for multileg processes use helicity amplitudes as their fundamental ingredients. We construct a simple and easy-to-use helicity operator basis in soft-collinear effective theory (SCET), for which the hard Wilson coefficients from matching QCD onto SCET are directly given in terms of color-ordered helicity amplitudes. Using this basis allows one to seamlessly combine fixed-order helicity amplitudes at any order they are known with a resummation of higher-order logarithmic corrections. In particular, the virtual loop amplitudes can be employed in factorization theorems to make predictions for exclusive jet cross sections without the use of numerical subtraction schemes to handle real-virtual infrared cancellations. We also discuss matching onto SCET in renormalization schemes with helicities in 4- and d -dimensions. To demonstrate that our helicity operator basis is easy to use, we provide an explicit construction of the operator basis, as well as results for the hard matching coefficients, for p p →H +0 , 1, 2 jets, p p →W /Z /γ +0 , 1, 2 jets, and p p →2 , 3 jets. These operator bases are completely crossing symmetric, so the results can easily be applied to processes with e+e- and e-p collisions.

  20. Long polypeptide 310-helices at atomic resolution

    PubMed Central

    Bavoso, Alfonso; Benedetti, Ettore; Di Blasio, Benedetto; Pavone, Vincenzo; Pedone, Carlo; Toniolo, Claudio; Bonora, Gian Maria

    1986-01-01

    The crystal-state preferred conformation of the terminally blocked homooctapeptide from the Cα,α-dimethylated α-aminoisobutyric acid (Aib) residue, pBrBz-(Aib)8-OBut, in which pBrBz is para-bromobenzoyl and OBut is tert-butoxy, determined by x-ray diffraction analysis using direct methods, was found to be a 310-helix stabilized by six consecutive intramolecular N—H....O=C hydrogen bonds of the C10-III (or III′) type. This is the first observation at atomic resolution of a regular 310-helix longer than two complete turns. The solid-state structural analysis was extended to the terminally blocked, α-aminoisobutyric acid-rich octapeptide corresponding to the 2-9 sequence of the peptaibol antibiotics emerimicins III and IV, pBrBz-Aib3-L-Val-Gly-L-Leu-Aib2-OMe. Again, this peptide adopts a (right-handed) 310-helical structure, although slightly distorted at the level of the L-leucine residue. The role of specific amino acid sequence and peptide main-chain length in stabilizing either the 310- or the α-helical conformation and their possible implications on the nature of the channel formed by peptaibol antibiotics in the membrane are also briefly discussed. PMID:16593674

  1. Absolute Helicity Induction in Three-Dimensional Homochiral Frameworks

    PubMed Central

    Zhang, Jian; Bu, Xianhui

    2009-01-01

    Three Co(II) isomers assembled from d-, or l-, or dl-camphorate together with achiral isonicotinate exhibit a clear relationship between chirality and helicity even though chiral molecules are not in the backbone of the helix: the absolute sense of helix made of achiral components is controlled by chains of metal and enantiopure chiral ligands running perpendicular to helix in two enantiomeric forms. PMID:19099070

  2. Centrosome Positioning in 1D Cell Migration

    NASA Astrophysics Data System (ADS)

    Adlerz, Katrina; Aranda-Espinoza, Helim

    During cell migration, the positioning of the centrosome and nucleus define a cell's polarity. For a cell migrating on a two-dimensional substrate the centrosome is positioned in front of the nucleus. Under one-dimensional confinement, however, the centrosome is positioned behind the nucleus in 60% of cells. It is known that the centrosome is positioned by CDC42 and dynein for cells moving on a 2D substrate in a wound-healing assay. It is currently unknown, however, if this is also true for cells moving under 1D confinement, where the centrosome position is often reversed. Therefore, centrosome positioning was studied in cells migrating under 1D confinement, which mimics cells migrating through 3D matrices. 3 to 5 μm fibronectin lines were stamped onto a glass substrate and cells with fluorescently labeled nuclei and centrosomes migrated on the lines. Our results show that when a cell changes directions the centrosome position is maintained. That is, when the centrosome is between the nucleus and the cell's trailing edge and the cell changes direction, the centrosome will be translocated across the nucleus to the back of the cell again. A dynein inhibitor did have an influence on centrosome positioning in 1D migration and change of directions.

  3. Synthesis, structural characterization, and solid-state NMR spectroscopy of [Ga(phen)(H{sub 1.5}PO{sub 4}){sub 2}].H{sub 2}O and [Ga(phen)(HPO{sub 4})(H{sub 2}PO{sub 4})].1.5H{sub 2}O (phen=1, 10-phenanthroline), two organic-inorganic hybrid compounds with 1-D chain structures

    SciTech Connect

    Chang, W.-J.; Chang, P.-C.; Kao, H.-M.; Lii, K.-H. . E-mail: liikh@cc.ncu.edu.tw

    2005-12-15

    Two new organic-inorganic hybrid compounds, [Ga(phen)(H{sub 1.5}PO{sub 4}){sub 2}].H{sub 2}O (1) and [Ga(phen)(HPO{sub 4})(H{sub 2}PO{sub 4})].1.5H{sub 2}O (2) (phen=1,10-phenanthroline), have been synthesized by hydrothermal methods and structurally characterized by single-crystal X-ray diffraction, infrared spectroscopy, thermogravimetric analysis, and solid-state NMR spectroscopy. Their structures consist of 1-D chains of strictly alternating GaO{sub 4}N{sub 2} octahedra and phosphate tetrahedra. The phen ligands in both compounds bind in a bidentate fashion to the gallium atoms and the 1-D structures extend into 3-D supramolecular arrays via {pi}-{pi} stacking interactions of phen ligands and hydrogen bonds. {sup 2}H MAS NMR spectroscopy was applied to study the deuterated sample of 1 which contains very short hydrogen bonds with an O-O distance of 2.406(2) A. Crystal data for 1: monoclinic, space group C2/c (No. 15), a=11.077(1) A, b=21.496(2) A, c=7.9989(7) A, {beta}=127.211(2){sup o}, and Z=4. The crystal symmetry is the same for 2 as for 1 except a=27.555(2) A, b=6.3501(5) A, c=21.327(2) A, {beta}=122.498(1){sup o}, and Z=8.

  4. Selective control for helical microswimmers

    NASA Astrophysics Data System (ADS)

    Katsamba, Panayiota; Lauga, Eric

    2015-11-01

    One of the greatest aspirations for artificial microswimmers is their application in non-invasive medicine. For any practical use, adequate mechanisms enabling control of multiple artificial swimmers is of paramount importance. Here we propose a multi-helical, freely-jointed motor as a novel selective control mechanism. We show that the nonlinear step-out behavior of a magnetized helix driven by a rotating magnetic field can be exploited, when used in conjunction with other helices, to obtain a velocity profile that is non-negligible only within a chosen interval of operating frequencies. Specifically, the force balance between the competing opposite-handed helices is tuned to give no net motion at low frequencies while in the middle frequency range, the swimming velocity increases monotonically with the driving frequency if two opposite helices are used, thereby allowing speed adjustment by varying the driving frequency. We illustrate this idea in detail on a two-helix system, and demonstrate how to generalize to N helices, both numerically and theoretically. We finish by explaining how to solve the inverse problem and design an artificial swimmer with an arbitrarily-complex velocity vs. frequency relationship.

  5. 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.

  6. Transferability of different classical force fields for right and left handed α-helices constructed from enantiomeric amino acids.

    PubMed

    Biswas, Santu; Sarkar, Sujit; Pandey, Prithvi Raj; Roy, Sudip

    2016-02-21

    Amino acids can form d and l enantiomers, of which the l enantiomer is abundant in nature. The naturally occurring l enantiomer has a greater preference for a right handed helical conformation, and the d enantiomer for a left handed helical conformation. The other conformations, that is, left handed helical conformations of the l enantiomers and right handed helical conformations of the d enantiomers, are not common. The energetic differences between left and right handed alpha helical peptide chains constructed from enantiomeric amino acids are investigated using quantum chemical calculations (using the M06/6-311g(d,p) level of theory). Further, the performances of commonly used biomolecular force fields (OPLS/AA, CHARMM27/CMAP and AMBER) to represent the different helical conformations (left and right handed) constructed from enantiomeric (D and L) amino acids are evaluated. 5- and 10-mer chains from d and l enantiomers of alanine, leucine, lysine, and glutamic acid, in right and left handed helical conformations, are considered in the study. Thus, in total, 32 α-helical polypeptides (4 amino acids × 4 conformations of 5-mer and 10-mer) are studied. Conclusions, with regards to the performance of the force fields, are derived keeping the quantum optimized geometry as the benchmark, and on the basis of phi and psi angle calculations, hydrogen bond analysis, and different long range helical order parameters. PMID:26863595

  7. Transferability of different classical force fields for right and left handed α-helices constructed from enantiomeric amino acids.

    PubMed

    Biswas, Santu; Sarkar, Sujit; Pandey, Prithvi Raj; Roy, Sudip

    2016-02-21

    Amino acids can form d and l enantiomers, of which the l enantiomer is abundant in nature. The naturally occurring l enantiomer has a greater preference for a right handed helical conformation, and the d enantiomer for a left handed helical conformation. The other conformations, that is, left handed helical conformations of the l enantiomers and right handed helical conformations of the d enantiomers, are not common. The energetic differences between left and right handed alpha helical peptide chains constructed from enantiomeric amino acids are investigated using quantum chemical calculations (using the M06/6-311g(d,p) level of theory). Further, the performances of commonly used biomolecular force fields (OPLS/AA, CHARMM27/CMAP and AMBER) to represent the different helical conformations (left and right handed) constructed from enantiomeric (D and L) amino acids are evaluated. 5- and 10-mer chains from d and l enantiomers of alanine, leucine, lysine, and glutamic acid, in right and left handed helical conformations, are considered in the study. Thus, in total, 32 α-helical polypeptides (4 amino acids × 4 conformations of 5-mer and 10-mer) are studied. Conclusions, with regards to the performance of the force fields, are derived keeping the quantum optimized geometry as the benchmark, and on the basis of phi and psi angle calculations, hydrogen bond analysis, and different long range helical order parameters.

  8. Human laminin B2 chain

    SciTech Connect

    Pikkarainen, T.; Kallunki, T.; Tryggvason, K.

    1988-05-15

    The complete amino acid sequence of the human laminin B2 chains has been determined by sequencing of cDNA clones. The six overlapping clones studied cover approximately 7.5 kilobases of which 5312 nucleotides were sequenced from the 5' end. The open reading frame codes for a 33-residue signal peptide and a 1576-residue B2 chain proper, which is 189 residues less than in the highly homologous B1 chain. Computer analysis revealed that the B2 chain consists of distinct domains that contain helical structures, cysteine-rich repeats, and globular regions, as does the B1 chain. However, domain ..cap alpha.. and domain ..beta.. of the B1 chain have no counterpart in B2, and the number of cysteine-rich repeats is 12, or 1 less than in the B1 chain. The degree of homology between the two chains is highest in the cysteine repeat-containing domains III and V where 40% of the residues match. However, in helical domains I/II only 16% of residues match. The results demonstrate that the B1 and B2 chains of laminin are highly homologous proteins that are probably the products of related genes.

  9. Generalized helicity and Beltrami fields

    SciTech Connect

    Buniy, Roman V.; Kephart, Thomas W.

    2014-05-15

    We propose covariant and non-abelian generalizations of the magnetic helicity and Beltrami equation. The gauge invariance, variational principle, conserved current, energy–momentum tensor and choice of boundary conditions elucidate the subject. In particular, we prove that any extremal of the Yang–Mills action functional 1/4 ∫{sub Ω}trF{sub μν}F{sup μν}d{sup 4}x subject to the local constraint ε{sup μναβ}trF{sub μν}F{sub αβ}=0 satisfies the covariant non-abelian Beltrami equation. -- Highlights: •We introduce the covariant non-abelian helicity and Beltrami equation. •The Yang–Mills action and instanton term constraint lead to the Beltrami equation. •Solutions of the Beltrami equation conserve helicity.

  10. Use of Helical Transport Channels for Bunch Recombination

    SciTech Connect

    Neuffer, David; Yonehara, Katsuya; Yoshikawa, Cary; /MUONS Inc., Batavia

    2010-03-01

    Cooling scenarios for a high-luminosity Muon Collider require bunch recombination for optimal luminosity. In this report we note that the tunable chronicity property of a helical transport channel (HTC) makes it a desirable component of a bunch recombiner. A large chronicity HTC is desirable for the bunch recombining transport, while more isochronous transport may be preferred for rf manipulations. Scenarios for bunch recombination are presented, with initial 1-D simulations, in order to set the stage for future 3-D simulation and optimization. HTC transports may enable a very compact bunch recombiner.

  11. Brownian motion of helical flagella.

    PubMed

    Hoshikawa, H; Saito, N

    1979-07-01

    We develops a theory of the Brownian motion of a rigid helical object such as bacterial flagella. The statistical properties of the random forces acting on the helical object are discussed and the coefficients of the correlations of the random forces are determined. The averages , and are also calculated where z and theta are the position along and angle around the helix axis respectively. Although the theory is limited to short time interval, direct comparison with experiment is possible by using the recently developed cinematography technique. PMID:16997210

  12. Synthesis, characterization and crystal structure determination of Mn (II) ion based 1D polymer constructed from 2, 2′ bipyridyl and azide group, its thermal stability, magnetic properties and Hirshfeld surface analysis

    SciTech Connect

    Mudsainiyan, R.K. Jassal, Amanpreet Kaur; Chawla, S.K.

    2015-05-15

    The 1-D polymeric complex (I) is having formula [Mn(2,2′-BP).(N{sub 3}){sub 2}]{sub n}, which has been crystallized in distilled water and characterized by elemental analyses, FT-IR spectrum, powder X-ray diffraction analyses and single-crystal diffraction analysis. This polymer possesses 1D helical chains or coils where Mn–azide–Mn forms the base of the coil which is alternatively garlanded by rigid bi-pyridine rings, where coordinates are in anti-fashion. The Mn (II) ions in the repeating units are linked by two end-on azide groups which extend through the two end-to-end azide ligands to the next unit forming a 1-D polymeric chain. The present study suggests that the use of this rigid and neutral building block leads to give better arrangement of the polymeric motif with [010] chains in 2-c uninodal net. During investigation of strong or weak intermolecular interactions, X-ray diffraction analysis and Hirshfeld surface analysis give rise to comparable results but in Hirshfeld surface analysis, two-third times more results of close contacts are obtained. The fingerprint plots demonstrate that these weak non-bonding interactions are important for stabilizing the crystal packing. Magnetic properties of the complex (I) were analyzed on the basis of an alternating ferro- and antiferromagnetic Heisenberg chain of Mn (II) ions. The J-exchange parameters found are J{sub 1}=64.3 K (45.3 cm{sup −1}), and J{sub 2}=−75.7 K (−53.3 cm{sup −1}). Magnetic properties are discussed in comparison with those of other similar molecular magnets of [Mn(L–L)(N{sub 3}){sub 2}]{sub n} type. - - Highlights: • Synthesized 1-D polymeric complex of Mn (II) ions with 2, 2′ bipyridyl and azide group. • X-ray data of complex (I) is in a good agreement with TGA and other spectroscopic techniques. • DFT calculations were done and compared with the parameter of experimental and theoretical data. • Intermolecular interactions calculated by Hirshfeld surface analysis

  13. Novel electronic structures of self-organized 1D surface nanostructures

    NASA Astrophysics Data System (ADS)

    Yeom, Han Woong

    2002-03-01

    Recently we have searched for the exotic physical properties of the nanostructures formed on semiconductor surfaces by STM and photoelectron spectroscopy [1]. The major objects have been the 1D chains of metal adsorbates on Si or SiC surfaces. It now seems obvious that such (sub)nanometer-scale atomic chains possess significant technological implications for the future device technology. Furthermore those systems provide very attractive and unprecedented opportunity to study exotic physical properties of 1D electronic systems in detail, such as Peierls instability, charge density wave (CDW), electron correlation, non-Fermi liquid behavior, and interplay of defects with 1D excitations (1D solitons, 1D domain walls and etc). The present talk focuses on the recent experimental and theoretical studies for the novel electronic properties of the 1D atomic chain systems on the Si(111) surface such as Si(111)4x1-In [2], Si(111)5x2-Au [3], Si(557)5x2-Au [4], and Si(111)3x2-Ba(or Ca) [5]. These systems have well defined one dimensional electronic bands, which exhibit intriguing properties challenging our present understanding. The major points of debates right now are the origin of the periodicity-doubling phase transition of Si(111)4x1-In in relation to 1D CDW [2], the nature of the band gap (or pseudo gap) of Si(111)5x2-Au (also related to 1D CDW idea) [3], the Si(111)3x2-Ba (or Ca) surface (1D Mott-Hubbard system ?) [5], and the nature of the band dispersion of the Si(557)5x2-Au surface (any Luttinger liquid behavior ?) [4]. Some new aspects of these systems are introduced such as the doping dependence of the 1D CDW system and the transport measurements across the 1D CDW transition. References [1] For a recent review, see H. W. Yeom, J. Electron Spectro. and Rel. Phenom., 114-116, 283 (2001). [2] H.W. Yeom et al., Phys. Rev. Lett. 82, 4898 (1999); C. Kumpf et al, Phys. Rev. Lett. 85, 4916 (2001); H.W. Yeom et al., submitted; G. Le Lay et al., submitted; J.-H. Cho et al

  14. A 1-D dusty plasma photonic crystal

    SciTech Connect

    Mitu, M. L.; Ticoş, C. M.; Toader, D.; Banu, N.; Scurtu, A.

    2013-09-21

    It is demonstrated numerically that a 1-D plasma crystal made of micron size cylindrical dust particles can, in principle, work as a photonic crystal for terahertz waves. The dust rods are parallel to each other and arranged in a linear string forming a periodic structure of dielectric-plasma regions. The dispersion equation is found by solving the waves equation with the boundary conditions at the dust-plasma interface and taking into account the dielectric permittivity of the dust material and plasma. The wavelength of the electromagnetic waves is in the range of a few hundred microns, close to the interparticle separation distance. The band gaps of the 1-D plasma crystal are numerically found for different types of dust materials, separation distances between the dust rods and rod diameters. The distance between levitated dust rods forming a string in rf plasma is shown experimentally to vary over a relatively wide range, from 650 μm to about 1350 μm, depending on the rf power fed into the discharge.

  15. Mechanics of helical mesostructures from polymer-nanoparticle hybrids

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

    We describe the fabrication and mechanics of polymer and nanoparticle (NP)-based high-aspect ratio mesostructures, which we refer to as ribbons, with nm-scale cross-sections and up to cm-scale lengths. When placed into a fluid like water, interfacial tension associated with the ribbons' intrinsic geometric asymmetry balances the elastic cost of bending, turning ribbons into helices with tunable preferred curvature. This universal, elastocapillary-based mechanism enables the reversible formation of helices from a variety of polymer and NP compositions, as demonstrated with specific examples of poly(methyl methacrylate), CdSe quantum dots, and gold NPs with polystyrene-azide or undecene ligands. Using custom-designed characterization methods, we quantitatively show that helices are highly stretchable with force-displacement relationships described by a nonlinear spring of finite extensibility. At small strains, these helices generate nN forces, affording mesostructures with a stiffness similar to single polymer chains (ca. 10-6 N/m), and when fully stretched, they display properties similar to synthetic polymer nanofibers. These mesostructures offer a novel platform for engineering tunable materials with a broad range of mechanical properties and organic or inorganic functionality.

  16. Three-Dimensional Reconstruction of Helical Polymers

    PubMed Central

    Egelman, Edward H.

    2015-01-01

    The field of three-dimensional electron microscopy began more than 45 years ago with a reconstruction of a helical phage tail, and helical polymers continue to be important objects for three-dimensional reconstruction due to the centrality of helical protein and nucleoprotein polymers in all aspects of biology. We are now witnessing a fundamental revolution in this area, made possible by direct electron detectors, which has led to near-atomic resolution for a number of important helical structures. Most importantly, the possibility of achieving such resolution routinely for a vast number of helical samples is within our reach. One of the main problems in helical reconstruction, ambiguities in assigning the helical symmetry, is overcome when one reaches a resolution where secondary structure is clearly visible. However, obstacles still exist due to the intrinsic variability within many helical filaments. PMID:25912526

  17. Three-dimensional reconstruction of helical polymers.

    PubMed

    Egelman, Edward H

    2015-09-01

    The field of three-dimensional electron microscopy began more than 45years ago with a reconstruction of a helical phage tail, and helical polymers continue to be important objects for three-dimensional reconstruction due to the centrality of helical protein and nucleoprotein polymers in all aspects of biology. We are now witnessing a fundamental revolution in this area, made possible by direct electron detectors, which has led to near-atomic resolution for a number of important helical structures. Most importantly, the possibility of achieving such resolution routinely for a vast number of helical samples is within our reach. One of the main problems in helical reconstruction, ambiguities in assigning the helical symmetry, is overcome when one reaches a resolution where secondary structure is clearly visible. However, obstacles still exist due to the intrinsic variability within many helical filaments.

  18. The transport of relative canonical helicity

    SciTech Connect

    You, S.

    2012-09-15

    The evolution of relative canonical helicity is examined in the two-fluid magnetohydrodynamic formalism. Canonical helicity is defined here as the helicity of the plasma species' canonical momentum. The species' canonical helicity are coupled together and can be converted from one into the other while the total gauge-invariant relative canonical helicity remains globally invariant. The conversion is driven by enthalpy differences at a surface common to ion and electron canonical flux tubes. The model provides an explanation for why the threshold for bifurcation in counter-helicity merging depends on the size parameter. The size parameter determines whether magnetic helicity annihilation channels enthalpy into the magnetic flux tube or into the vorticity flow tube components of the canonical flux tube. The transport of relative canonical helicity constrains the interaction between plasma flows and magnetic fields, and provides a more general framework for driving flows and currents from enthalpy or inductive boundary conditions.

  19. Mycobacterial phosphatidylinositol mannoside is a natural antigen for CD1d-restricted T cells

    PubMed Central

    Fischer, Karsten; Scotet, Emmanuel; Niemeyer, Marcus; Koebernick, Heidrun; Zerrahn, Jens; Maillet, Sophie; Hurwitz, Robert; Kursar, Mischo; Bonneville, Marc; Kaufmann, Stefan H. E.; Schaible, Ulrich E.

    2004-01-01

    A group of T cells recognizes glycolipids presented by molecules of the CD1 family. The CD1d-restricted natural killer T cells (NKT cells) are primarily considered to be self-reactive. By employing CD1d-binding and T cell assays, the following structural parameters for presentation by CD1d were defined for a number of mycobacterial and mammalian lipids: two acyl chains facilitated binding, and a polar head group was essential for T cell recognition. Of the mycobacterial lipids tested, only a phosphatidylinositol mannoside (PIM) fulfilled the requirements for CD1d binding and NKT cell stimulation. This PIM activated human and murine NKT cells via CD1d, thereby triggering antigen-specific IFN-γ production and cell-mediated cytotoxicity, and PIM-loaded CD1d tetramers identified a subpopulation of murine and human NKT cells. This phospholipid, therefore, represents a mycobacterial antigen recognized by T cells in the context of CD1d. PMID:15243159

  20. Baryogenesis from decaying magnetic helicity

    NASA Astrophysics Data System (ADS)

    Kamada, Kohei; Long, Andrew J.

    2016-09-01

    As a result of the Standard Model chiral anomalies, baryon number is violated in the early Universe in the presence of a hypermagnetic field with varying helicity. We investigate whether the matter/antimatter asymmetry of the Universe can be created from the decaying helicity of a primordial (hyper)magnetic field before and after the electroweak phase transition. In this model, baryogenesis occurs without (B -L )-violation, since the (B +L ) asymmetry generated by the hypermagnetic field counteracts the washout by electroweak sphalerons. At the electroweak crossover, the hypermagnetic field becomes an electromagnetic field, which does not source (B +L ). Although the sphalerons remain in equilibrium for a time, washout is avoided since the decaying magnetic helicity sources chirality. The relic baryon asymmetry is fixed when the electroweak sphaleron freezes out. Under reasonable assumptions, a baryon asymmetry of nB/s ≃4 ×10-12 can be generated from a maximally helical, right-handed (hyper)magnetic field that has a field strength of B0≃10-14 Gauss and coherence length of λ0≃1 pc today. Relaxing an assumption that relates λ0 to B0, the model predicts nB/s ≳10-10, which could potentially explain the observed baryon asymmetry of the Universe.

  1. Note: Helical nanobelt force sensors

    SciTech Connect

    Hwang, G.; Hashimoto, H.

    2012-12-15

    We present the fabrication and characterization of helical nanobelt force sensors. These self-sensing force sensors are based on the giant piezoresistivity of helical nanobelts. The three-dimensional helical nanobelts are self-formed from 27 nm-thick n-type InGaAs/GaAs bilayers using rolled-up techniques, and assembled onto electrodes on a micropipette using nanorobotic manipulations. The helical nanobelt force sensors can be calibrated using a calibrated atomic force microscope cantilever system under scanning electron microscope. Thanks to their giant piezoresistance coefficient (515 Multiplication-Sign 10{sup -10} Pa{sup -1}), low stiffness (0.03125 N/m), large-displacement capability ({approx}10 {mu}m), and good fatigue resistance, they are well suited to function as stand-alone, compact ({approx}20 {mu}m without the plug-in support), light ({approx}5 g including the plug-in support), versatile and large range ({approx}{mu}N) and high resolution ({approx}nN) force sensors.

  2. Physical Gelation of α-Helical Copolypeptides.

    PubMed

    Vacogne, Charlotte D; Schopferer, Michael; Schlaad, Helmut

    2016-07-11

    Owing to its rod-like α-helical secondary structure, the synthetic polypeptide poly(γ-benzyl-l-glutamate) (PBlG) can form physical and thermoreversible gels in helicogenic solvents such as toluene. The versatility of PBlG can be increased by introducing functionalizable comonomers, such as allylglycine (AG). In this work we examined the secondary structure of PBlG and a series of statistical poly(γ-benzyl-l-glutamate-co-allylglycine) copolypeptides, varying in composition and chain length, by circular dichroism (CD), Fourier-transform infrared (FTIR) and Raman spectroscopy, and wide-angle X-ray scattering (WAXS). The secondary structure of PBlG and the copolypeptides presented dissimilarities that increased with increasing AG molar fraction, especially when racemic AG units were incorporated. The physical gelation behavior of these copolypeptides was analyzed by temperature-sweep (1)H NMR and rheological measurements. The study revealed that both copolypeptide composition and chain length affected secondary structure, gelation temperature, and gel stiffness. PMID:27233111

  3. Peptoid oligomers with alpha-chiral, aromatic side chains: effects of chain length on secondary structure.

    PubMed

    Wu, C W; Sanborn, T J; Zuckermann, R N; Barron, A E

    2001-04-01

    Oligomeric N-substituted glycines or "peptoids" with alpha-chiral, aromatic side chains can adopt stable helices in organic or aqueous solution, despite their lack of backbone chirality and their inability to form intrachain hydrogen bonds. Helical ordering appears to be stabilized by avoidance of steric clash as well as by electrostatic repulsion between backbone carbonyls and pi clouds of aromatic rings in the side chains. Interestingly, these peptoid helices exhibit intense circular dichroism (CD) spectra that closely resemble those of peptide alpha-helices. Here, we have utilized CD to systematically study the effects of oligomer length, concentration, and temperature on the chiral secondary structure of organosoluble peptoid homooligomers ranging from 3 to 20 (R)-N-(1-phenylethyl)glycine (Nrpe) monomers in length. We find that a striking evolution in CD spectral features occurs for Nrpe oligomers between 4 and 12 residues in length, which we attribute to a chain length-dependent population of alternate structured conformers having cis versus trans amide bonds. No significant changes are observed in CD spectra of oligomers between 13 and 20 monomers in length, suggesting a minimal chain length of about 13 residues for the formation of stable poly(Nrpe) helices. Moreover, no dependence of circular dichroism on concentration is observed for an Nrpe hexamer, providing evidence that these helices remain monomeric in solution. In light of these new data, we discuss chain length-related factors that stabilize organosoluble peptoid helices of this class, which are important for the design of helical, biomimetic peptoids sharing this structural motif.

  4. 1D fast coded aperture camera.

    PubMed

    Haw, Magnus; Bellan, Paul

    2015-04-01

    A fast (100 MHz) 1D coded aperture visible light camera has been developed as a prototype for imaging plasma experiments in the EUV/X-ray bands. The system uses printed patterns on transparency sheets as the masked aperture and an 80 channel photodiode array (9 V reverse bias) as the detector. In the low signal limit, the system has demonstrated 40-fold increase in throughput and a signal-to-noise gain of ≈7 over that of a pinhole camera of equivalent parameters. In its present iteration, the camera can only image visible light; however, the only modifications needed to make the system EUV/X-ray sensitive are to acquire appropriate EUV/X-ray photodiodes and to machine a metal masked aperture. PMID:25933861

  5. 1D fast coded aperture camera.

    PubMed

    Haw, Magnus; Bellan, Paul

    2015-04-01

    A fast (100 MHz) 1D coded aperture visible light camera has been developed as a prototype for imaging plasma experiments in the EUV/X-ray bands. The system uses printed patterns on transparency sheets as the masked aperture and an 80 channel photodiode array (9 V reverse bias) as the detector. In the low signal limit, the system has demonstrated 40-fold increase in throughput and a signal-to-noise gain of ≈7 over that of a pinhole camera of equivalent parameters. In its present iteration, the camera can only image visible light; however, the only modifications needed to make the system EUV/X-ray sensitive are to acquire appropriate EUV/X-ray photodiodes and to machine a metal masked aperture.

  6. 1D-VAR Retrieval Using Superchannels

    NASA Technical Reports Server (NTRS)

    Liu, Xu; Zhou, Daniel; Larar, Allen; Smith, William L.; Schluessel, Peter; Mango, Stephen; SaintGermain, Karen

    2008-01-01

    Since modern ultra-spectral remote sensors have thousands of channels, it is difficult to include all of them in a 1D-var retrieval system. We will describe a physical inversion algorithm, which includes all available channels for the atmospheric temperature, moisture, cloud, and surface parameter retrievals. Both the forward model and the inversion algorithm compress the channel radiances into super channels. These super channels are obtained by projecting the radiance spectra onto a set of pre-calculated eigenvectors. The forward model provides both super channel properties and jacobian in EOF space directly. For ultra-spectral sensors such as Infrared Atmospheric Sounding Interferometer (IASI) and the NPOESS Airborne Sounder Testbed Interferometer (NAST), a compression ratio of more than 80 can be achieved, leading to a significant reduction in computations involved in an inversion process. Results will be shown applying the algorithm to real IASI and NAST data.

  7. 2-D simulation of a waveguide free electron laser having a helical undulator

    SciTech Connect

    Kim, S.K.; Lee, B.C.; Jeong, Y.U.

    1995-12-31

    We have developed a 2-D simulation code for the calculation of output power from an FEL oscillator having a helical undulator and a cylindrical waveguide. In the simulation, the current and the energy of the electron beam is 2 A and 400 keV, respectively. The parameters of the permanent-magnet helical undulator are : period = 32 mm, number of periods = 20, magnetic field = 1.3 kG. The gain per pass is 10 and the output power is calculated to be higher than 10 kW The results of the 2-D simulation are compared with those of 1-D simulation.

  8. Design, Synthesis, and Functional Activity of Labeled CD1d Glycolipid Agonists

    PubMed Central

    2013-01-01

    Invariant natural killer T cells (iNKT cells) are restricted by CD1d molecules and activated upon CD1d-mediated presentation of glycolipids to T cell receptors (TCRs) located on the surface of the cell. Because the cytokine response profile is governed by the structure of the glycolipid, we sought a method for labeling various glycolipids to study their in vivo behavior. The prototypical CD1d agonist, α-galactosyl ceramide (α-GalCer) 1, instigates a powerful immune response and the generation of a wide range of cytokines when it is presented to iNKT cell TCRs by CD1d molecules. Analysis of crystal structures of the TCR−α-GalCer–CD1d ternary complex identified the α-methylene unit in the fatty acid side chain, and more specifically the pro-S hydrogen at this position, as a site for incorporating a label. We postulated that modifying the glycolipid in this way would exert a minimal impact on the TCR–glycolipid–CD1d ternary complex, allowing the labeled molecule to function as a good mimic for the CD1d agonist under investigation. To test this hypothesis, the synthesis of a biotinylated version of the CD1d agonist threitol ceramide (ThrCer) was targeted. Both diastereoisomers, epimeric at the label tethering site, were prepared, and functional experiments confirmed the importance of substituting the pro-S, and not the pro-R, hydrogen with the label for optimal activity. Significantly, functional experiments revealed that biotinylated ThrCer (S)-10 displayed behavior comparable to that of ThrCer 5 itself and also confirmed that the biotin residue is available for streptavidin and antibiotin antibody recognition. A second CD1d agonist, namely α-GalCer C20:2 4, was modified in a similar way, this time with a fluorescent label. The labeled α-GalCer C20:2 analogue (11) again displayed functional behavior comparable to that of its unlabeled substrate, supporting the notion that the α-methylene unit in the fatty acid amide chain should be a suitable site for

  9. Orientation Determination of Protein Helical Secondary Structure Using Linear and Nonlinear Vibrational Spectroscopy

    PubMed Central

    Nguyen, Khoi Tan; Le Clair, Stéphanie V.; Ye, Shuji; Chen, Zhan

    2009-01-01

    measured parameters for orientation determination, aiding in the deduction of more complicated orientation distributions. In this paper, we discussed two types of helices: the α-helix and 3–10 helix. However, the orientation determination method presented here is general, and thus can be applied to study other helices as well. The calculations of SFG amide I hyperpolarizability components for α-helical and 3–10 helical structures with different chain lengths have also been performed. It was found that when the helices reach a certain length, the number of peptide units in the helix should not alter the data analysis substantially. It was shown in the calculation, however, that when the helix chain is short, the SFG hyperpolarizability component ratios can vary substantially when the chain length is changed. Because 3–10 helical structures can be quite short in proteins, the orientation determination for a short 3–10 helix needs to take into account the number of peptide units in the helix. PMID:19650636

  10. Crystal Structures of Human TBC1D1 and TBC1D4 (AS160) RabGTPase-activating Protein (RabGAP) Domains Reveal Critical Elements for GLUT4 Translocation

    SciTech Connect

    S Park; W Jin; S Shoelson

    2011-12-31

    We have solved the x-ray crystal structures of the RabGAP domains of human TBC1D1 and human TBC1D4 (AS160), at 2.2 and 3.5 {angstrom} resolution, respectively. Like the yeast Gyp1p RabGAP domain, whose structure was solved previously in complex with mouse Rab33B, the human TBC1D1 and TBC1D4 domains both have 16 {alpha}-helices and no {beta}-sheet elements. We expected the yeast Gyp1p RabGAP/mouse Rab33B structure to predict the corresponding interfaces between cognate mammalian RabGAPs and Rabs, but found that residues were poorly conserved. We further tested the relevance of this model by Ala-scanning mutagenesis, but only one of five substitutions within the inferred binding site of the TBC1D1 RabGAP significantly perturbed catalytic efficiency. In addition, substitution of TBC1D1 residues with corresponding residues from Gyp1p did not enhance catalytic efficiency. We hypothesized that biologically relevant RabGAP/Rab partners utilize additional contacts not described in the yeast Gyp1p/mouse Rab33B structure, which we predicted using our two new human TBC1D1 and TBC1D4 structures. Ala substitution of TBC1D1 Met{sup 930}, corresponding to a residue outside of the Gyp1p/Rab33B contact, substantially reduced catalytic activity. GLUT4 translocation assays confirmed the biological relevance of our findings. Substitutions with lowest RabGAP activity, including catalytically dead RK and Met{sup 930} and Leu{sup 1019} predicted to perturb Rab binding, confirmed that biological activity requires contacts between cognate RabGAPs and Rabs beyond those in the yeast Gyp1p RabGAP/mouse Rab33B structure.

  11. Predictive supracolloidal helices from patchy particles

    PubMed Central

    Guo, Ruohai; Mao, Jian; Xie, Xu-Ming; Yan, Li-Tang

    2014-01-01

    A priori prediction of supracolloidal architectures from nanoparticle and colloidal assembly is a challenging goal in materials chemistry and physics. Despite intense research in this area, much less has been known about the predictive science of supracolloidal helices from designed building blocks. Therefore, developing conceptually new rules to construct supracolloidal architectures with predictive helicity is becoming an important and urgent task of great scientific interest. Here, inspired by biological helices, we show that the rational design of patchy arrangement and interaction can drive patchy particles to self-assemble into biomolecular mimetic supracolloidal helices. We further derive a facile design rule for encoding the target supracolloidal helices, thus opening the doors to the predictive science of these supracolloidal architectures. It is also found that kinetics and reaction pathway during the formation of supracolloidal helices offer a unique way to study supramolecular polymerization, and that well-controlled supracolloidal helices can exhibit tailorable circular dichroism effects at visible wavelengths. PMID:25387544

  12. Predictive supracolloidal helices from patchy particles

    NASA Astrophysics Data System (ADS)

    Guo, Ruohai; Mao, Jian; Xie, Xu-Ming; Yan, Li-Tang

    2014-11-01

    A priori prediction of supracolloidal architectures from nanoparticle and colloidal assembly is a challenging goal in materials chemistry and physics. Despite intense research in this area, much less has been known about the predictive science of supracolloidal helices from designed building blocks. Therefore, developing conceptually new rules to construct supracolloidal architectures with predictive helicity is becoming an important and urgent task of great scientific interest. Here, inspired by biological helices, we show that the rational design of patchy arrangement and interaction can drive patchy particles to self-assemble into biomolecular mimetic supracolloidal helices. We further derive a facile design rule for encoding the target supracolloidal helices, thus opening the doors to the predictive science of these supracolloidal architectures. It is also found that kinetics and reaction pathway during the formation of supracolloidal helices offer a unique way to study supramolecular polymerization, and that well-controlled supracolloidal helices can exhibit tailorable circular dichroism effects at visible wavelengths.

  13. Synthesis and characterization of 1D iron(II) spin crossover coordination polymers with hysteresis.

    PubMed

    Bauer, Wolfgang; Lochenie, Charles; Weber, Birgit

    2014-02-01

    Purposeful ligand design was used for the synthesis of eight new 1D iron(II) spin crossover coordination polymers aiming for cooperative spin transitions with hysteresis. The results from magnetic measurements and X-ray structure analysis show that the combination of rigid linkers and a hydrogen bond network between the 1D chains is a promising tool to reach this goal. Five of the eight new samples show a cooperative spin transition with hysteresis with up to 43 K wide hysteresis loops.

  14. An experimental superconducting helical undulator

    SciTech Connect

    Caspi, S.; Taylor, C.

    1995-12-31

    Improvements in the technology of superconducting magnets for high energy physics and recent advancements in SC materials with the artificial pinning centers (APC){sup 2}, have made a bifilar helical SC device an attractive candidate for a single-pass free electron laser (FEL){sup 3}. Initial studies have suggested that a 6.5 mm inner diameter helical device, with a 27 mm period, can generate a central field of 2-2.5 Tesla. Additional studies have also suggested that with a stored energy of 300 J/m, such a device can be made self-protecting in the event of a quench. However, since the most critical area associated with high current density SC magnets is connected with quenching and training, a short experimental device will have to be built and tested. In this paper we discuss technical issues relevant to the construction of such a device, including a conceptual design, fields, and forces.

  15. Helical screw expander evaluation project

    NASA Technical Reports Server (NTRS)

    Mckay, R.

    1982-01-01

    A one MW helical rotary screw expander power system for electric power generation from geothermal brine was evaluated. The technology explored in the testing is simple, potentially very efficient, and ideally suited to wellhead installations in moderate to high enthalpy, liquid dominated field. A functional one MW geothermal electric power plant that featured a helical screw expander was produced and then tested with a demonstrated average performance of approximately 45% machine efficiency over a wide range of test conditions in noncondensing, operation on two-phase geothermal fluids. The Project also produced a computer equipped data system, an instrumentation and control van, and a 1000 kW variable load bank, all integrated into a test array designed for operation at a variety of remote test sites. Data are presented for the Utah testing and for the noncondensing phases of the testing in Mexico. Test time logged was 437 hours during the Utah tests and 1101 hours during the Mexico tests.

  16. Cell wall glycosphingolipids of Sphingomonas paucimobilis are CD1d-specific ligands for NKT cells.

    PubMed

    Sriram, Venkataraman; Du, Wenjun; Gervay-Hague, Jacquelyn; Brutkiewicz, Randy R

    2005-06-01

    The current consensus on characterization of NKT cells is based on their reactivity to the synthetic glycolipid, alpha-galactosylceramide (alpha-GalCer) in a CD1d-dependent manner. Because of the limited availability of alpha-GalCer, there is a constant search for CD1d-presented ligands that activate NKT cells. The alpha-anomericity of the carbohydrate is considered to be an important requisite for the CD1d-specific activation of NKT cells. The gram-negative, lipopolysaccharide-free bacterium Sphingomonas paucimobilis is known to contain glycosphingolipids (GSL) with alpha-anomeric sugars attached to the lipid chain. Here, we report that GSL extracted from this bacterium are able to stimulate NKT cells in a CD1d-specific manner. In addition, soluble CD1d-Ig dimers loaded with this lipid extract specifically bind to NKT cells (but not conventional T cells). Further studies on the S. paucimobilis GSL could potentially lead to other natural sources of CD1d-specific ligands useful for NKT cell analyses and aimed at identifying novel therapies for a variety of disease states.

  17. Helical Antimicrobial Sulfono- {gamma} -AApeptides

    SciTech Connect

    Li, Yaqiong; Wu, Haifan; Teng, Peng; Bai, Ge; Lin, Xiaoyang; Zuo, Xiaobing; Cao, Chuanhai; Cai, Jianfeng

    2015-06-11

    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, are 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.

  18. 1D-1D Coulomb drag in a 6 Million Mobility Bi-layer Heterostructure

    NASA Astrophysics Data System (ADS)

    Bilodeau, Simon; Laroche, Dominique; Xia, Jian-Sheng; Lilly, Mike; Reno, John; Pfeiffer, Loren; West, Ken; Gervais, Guillaume

    We report Coulomb drag measurements in vertically-coupled quantum wires. The wires are fabricated in GaAs/AlGaAs bilayer heterostructures grown from two different MBE chambers: one at Sandia National Laboratories (1.2M mobility), and the other at Princeton University (6M mobility). The previously observed positive and negative drag signals are seen in both types of devices, demonstrating the robustness of the result. However, attempts to determine the temperature dependence of the drag signal in the 1D regime proved challenging in the higher mobility heterostructure (Princeton), in part because of difficulties in aligning the wires within the same transverse subband configuration. Nevertheless, this work, performed at the Microkelvin laboratory of the University of Florida, is an important proof-of-concept for future investigations of the temperature dependence of the 1D-1D drag signal down to a few mK. Such an experiment could confirm the Luttinger charge density wave interlocking predicted to occur in the wires. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under Contract DE-AC04-94AL8500.

  19. A Parallel Coiled-Coil Tetramer with Offset Helices

    SciTech Connect

    Liu,J.; Deng, Y.; Zheng, Q.; Cheng, C.; Kallenbach, N.; Lu, M.

    2006-01-01

    Specific helix-helix interactions are fundamental in assembling the native state of proteins and in protein-protein interfaces. Coiled coils afford a unique model system for elucidating principles of molecular recognition between {alpha} helices. The coiled-coil fold is specified by a characteristic seven amino acid repeat containing hydrophobic residues at the first (a) and fourth (d) positions. Nonpolar side chains spaced three and four residues apart are referred to as the 3-4 hydrophobic repeat. The presence of apolar amino acids at the e or g positions (corresponding to a 3-3-1 hydrophobic repeat) can provide new possibilities for close-packing of {alpha}-helices that includes examples such as the lac repressor tetramerization domain. Here we demonstrate that an unprecedented coiled-coil interface results from replacement of three charged residues at the e positions in the dimeric GCN4 leucine zipper by nonpolar valine side chains. Equilibrium circular dichroism and analytical ultracentrifugation studies indicate that the valine-containing mutant forms a discrete {alpha}-helical tetramer with a significantly higher stability than the parent leucine-zipper molecule. The 1.35 {angstrom} resolution crystal structure of the tetramer reveals a parallel four-stranded coiled coil with a three-residue interhelical offset. The local packing geometry of the three hydrophobic positions in the tetramer conformation is completely different from that seen in classical tetrameric structures yet bears resemblance to that in three-stranded coiled coils. These studies demonstrate that distinct van der Waals interactions beyond the a and d side chains can generate a diverse set of helix-helix interfaces and three-dimensional supercoil structures.

  20. Thiophene-Based Double Helices: Syntheses, X-ray Structures, and Chiroptical Properties.

    PubMed

    Zhang, Sheng; Liu, Xinming; Li, Chunli; Li, Lu; Song, Jinsheng; Shi, Jianwu; Morton, Martha; Rajca, Suchada; Rajca, Andrzej; Wang, Hua

    2016-08-10

    We demonstrate facile and efficient construction of conjugated double helical ladder oligomers from the saddle-shaped cyclooctatetrathiophene (COTh) building blocks. The key step involves deprotonation of tetra[3,4]thienylene (β,β-COTh) with n-BuLi which displays remarkably high ipsilateral selectivity. Three racemic double helical ladder oligomers, rac-DH-1, rac-DH-2, and rac-DH-3, containing two, three, and five COTh annelated moieties are efficiently synthesized by diastereoselective coupling of the racemic precursors. The X-ray crystallographic studies of rac-DH-1, rac-DH-2 and rac-DH-3 unambiguously revealed that each double helical scaffold has two single helices intertwined with each other via the C-C single bonds. Following removal of TMS groups, double helical ladder oligomer rac-DH-1-D had sufficient solubility to be resolved via chiral HPLC, thus enabling determination of its chirooptical properties such as CD spectra and optical rotation. (+)-DH-1-D has a large barrier for racemization, with lower limit of ΔG(‡) > 48 kcal mol(-1), which may be compared to DFT-computed barrier of 51 kcal mol(-1). The enantiomers of DH-1-D show 1 order of magnitude stronger chirooptical properties than the carbon-sulfur [7]helicene, as determined by the anisotropy factor g = Δε/ε = -0.039, based on Δεmax = -11 and ε = 2.8 × 10(2) L mol(-1) cm(-1) in cyclohexane at 327 nm. PMID:27440376

  1. Structural Basis of the Interaction between Tuberous Sclerosis Complex 1 (TSC1) and Tre2-Bub2-Cdc16 Domain Family Member 7 (TBC1D7).

    PubMed

    Qin, Jiayue; Wang, Zhizhi; Hoogeveen-Westerveld, Marianne; Shen, Guobo; Gong, Weimin; Nellist, Mark; Xu, Wenqing

    2016-04-15

    Mutations in TSC1 or TSC2 cause tuberous sclerosis complex (TSC), an autosomal dominant disorder characterized by the occurrence of benign tumors in various vital organs and tissues. TSC1 and TSC2, the TSC1 and TSC2 gene products, form the TSC protein complex that senses specific cellular growth conditions to control mTORC1 signaling. TBC1D7 is the third subunit of the TSC complex, and helps to stabilize the TSC1-TSC2 complex through its direct interaction with TSC1. Homozygous inactivation of TBC1D7 causes intellectual disability and megaencephaly. Here we report the crystal structure of a TSC1-TBC1D7 complex and biochemical characterization of the TSC1-TBC1D7 interaction. TBC1D7 interacts with the C-terminal region of the predicted coiled-coil domain of TSC1. The TSC1-TBC1D7 interface is largely hydrophobic, involving the α4 helix of TBC1D7. Each TBC1D7 molecule interacts simultaneously with two parallel TSC1 helices from two TSC1 molecules, suggesting that TBC1D7 may stabilize the TSC complex by tethering the C-terminal ends of two TSC1 coiled-coils.

  2. Simulations of Edge Effect in 1D Spin Crossover Compounds by Atom-Phonon Coupling Model

    NASA Astrophysics Data System (ADS)

    Linares, J.; Chiruta, D.; Jureschi, C. M.; Alayli, Y.; Turcu, C. O.; Dahoo, P. R.

    2016-08-01

    We used the atom-phonon coupling model to explain and illustrate the behaviour of a linear nano-chain of molecules. The analysis of the system's behaviour was performed using Free Energy method, and by applying Monte Carlo Metropolis (MCM) method which take into account the phonon contribution. In particular we tested both the MCM algorithm and the dynamic-matrix method and we expose how the thermal behaviour of a 1D spin crossover system varies as a function of different factors. Furthermore we blocked the edge atoms of the chain in its high spin state to study the effect on the system's behaviour.

  3. The effects of regularly spaced glutamine substitutions on alpha-helical peptide structures: A DFT/ONIOM study

    NASA Astrophysics Data System (ADS)

    Roy, Dipankar; Dannenberg, J. J.

    2011-08-01

    The side-chains of the residues of glutamine (Q) and asparagine (N) contain amide groups. These can H-bond to each other in patterns similar to those of the backbone amides in α-helices. We show that mutating multiple Q's for alanines (A's) in a polyalanine helix stabilizes the helical structure, while similar mutations with multiple N's do not. We suggest that modification of peptides by incorporating Q's in such positions can make more robust helices that can be used to test the effects of secondary structures in biochemical experiments linked to proteins with variable structures such as tau and α-synuclein.

  4. Helicity in dynamical processes in the atmosphere

    NASA Astrophysics Data System (ADS)

    Kurgansky, Michael; Maksimenkov, Leonid; Khapaev, Alexey; Chkhetiani, Otto

    2016-04-01

    In modern geophysical fluid dynamics and dynamic meteorology, a notable interest is observed to the notion of helicity ("kinetic helicity" to be distinguished from "magnetic helicity" widely used in magnetohydrodynamics, astrophysics and Solar physics), which is defined by the scalar product of 3D vectors of velocity and vorticity. In this contribution, we bring together different, both known in the literature and novel formulations of the helicity balance equation, by also taking into account the effects of air compressibility and Earth rotation. Equations and relationships are presented that are valid under different approximations customarily made in the dynamic meteorology, e.g. Boussinesq approximation, quasi-static approximation, quasi-geostrophic approximation. An emphasis is placed on the helicity budget analysis in large-scale atmospheric motions. An explicit expression is presented for the rate of helicity injection from the free atmosphere into a non-linear Ekman boundary layer. This injection is shown to be exactly balanced by the helicity viscous destruction within the boundary layer. It is conjectured that this helicity injection may characterize the intensity of atmospheric circulation in extratropical latitudes of both terrestrial hemispheres. Examples are provided based on re-analyses data. Vertical distribution of helicity and superhelicity in different Ekman boundary layers is also discussed.

  5. Probing and controlling liquid crystal helical nanofilaments.

    PubMed

    Zhu, Chenhui; Wang, Cheng; Young, Anthony; Liu, Feng; Gunkel, Ilja; Chen, Dong; Walba, David; Maclennan, Joseph; Clark, Noel; Hexemer, Alexander

    2015-05-13

    We report the first in situ measurement of the helical pitch of the helical nanofilament B4 phase of bent-core liquid crystals using linearly polarized, resonant soft X-ray scattering at the carbon K-edge. A strong, anisotropic scattering peak corresponding to the half-pitch of the twisted smectic layer structure was observed. The equilibrium helical half-pitch of NOBOW is found to be 120 nm, essentially independent of temperature. However, the helical pitch can be tuned by mixing guest organic molecules with the bent-core host, followed by thermal annealing.

  6. 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.

  7. Building blocks for subleading helicity operators

    NASA Astrophysics Data System (ADS)

    Kolodrubetz, Daniel W.; Moult, Ian; Stewart, Iain W.

    2016-05-01

    On-shell helicity methods provide powerful tools for determining scattering amplitudes, which have a one-to-one correspondence with leading power helicity operators in the Soft-Collinear Effective Theory (SCET) away from singular regions of phase space. We show that helicity based operators are also useful for enumerating power suppressed SCET operators, which encode subleading amplitude information about singular limits. In particular, we present a complete set of scalar helicity building blocks that are valid for constructing operators at any order in the SCET power expansion. We also describe an interesting angular momentum selection rule that restricts how these building blocks can be assembled.

  8. Magnetic helicity in emerging solar active regions

    SciTech Connect

    Liu, Y.; Hoeksema, J. T.; Bobra, M.; Hayashi, K.; Sun, X.; Schuck, P. W.

    2014-04-10

    Using vector magnetic field data from the Helioseismic and Magnetic Imager instrument aboard the Solar Dynamics Observatory, we study magnetic helicity injection into the corona in emerging active regions (ARs) and examine the hemispheric helicity rule. In every region studied, photospheric shearing motion contributes most of the helicity accumulated in the corona. In a sample of 28 emerging ARs, 17 follow the hemisphere rule (61% ± 18% at a 95% confidence interval). Magnetic helicity and twist in 25 ARs (89% ± 11%) have the same sign. The maximum magnetic twist, which depends on the size of an AR, is inferred in a sample of 23 emerging ARs with a bipolar magnetic field configuration.

  9. Helical tomotherapy superficial dose measurements

    SciTech Connect

    Ramsey, Chester R.; Seibert, Rebecca M.; Robison, Benjamin; Mitchell, Martha

    2007-08-15

    Helical tomotherapy is a treatment technique that is delivered from a 6 MV fan beam that traces a helical path while the couch moves linearly into the bore. In order to increase the treatment delivery dose rate, helical tomotherapy systems do not have a flattening filter. As such, the dose distributions near the surface of the patient may be considerably different from other forms of intensity-modulated delivery. The purpose of this study was to measure the dose distributions near the surface for helical tomotherapy plans with a varying separation between the target volume and the surface of an anthropomorphic phantom. A hypothetical planning target volume (PTV) was defined on an anthropomorphic head phantom to simulate a 2.0 Gy per fraction IMRT parotid-sparing head and neck treatment of the upper neck nodes. A total of six target volumes were created with 0, 1, 2, 3, 4, and 5 mm of separation between the surface of the phantom and the outer edge of the PTV. Superficial doses were measured for each of the treatment deliveries using film placed in the head phantom and thermoluminescent dosimeters (TLDs) placed on the phantom's surface underneath an immobilization mask. In the 0 mm test case where the PTV extends to the phantom surface, the mean TLD dose was 1.73{+-}0.10 Gy (or 86.6{+-}5.1% of the prescribed dose). The measured superficial dose decreases to 1.23{+-}0.10 Gy (61.5{+-}5.1% of the prescribed dose) for a PTV-surface separation of 5 mm. The doses measured by the TLDs indicated that the tomotherapy treatment planning system overestimates superficial doses by 8.9{+-}3.2%. The radiographic film dose for the 0 mm test case was 1.73{+-}0.07 Gy, as compared to the calculated dose of 1.78{+-}0.05 Gy. Given the results of the TLD and film measurements, the superficial calculated doses are overestimated between 3% and 13%. Without the use of bolus, tumor volumes that extend to the surface may be underdosed. As such, it is recommended that bolus be added for these

  10. Structure and binding kinetics of three different human CD1d-alpha-galactosylceramide-specific T cell receptors.

    PubMed

    Gadola, Stephan D; Koch, Michael; Marles-Wright, Jon; Lissin, Nikolai M; Shepherd, Dawn; Matulis, Gediminas; Harlos, Karl; Villiger, Peter M; Stuart, David I; Jakobsen, Bent K; Cerundolo, Vincenzo; Jones, E Yvonne

    2006-03-20

    Invariant human TCR Valpha24-Jalpha18+/Vbeta11+ NKT cells (iNKT) are restricted by CD1d-alpha-glycosylceramides. We analyzed crystal structures and binding characteristics for an iNKT TCR plus two CD1d-alpha-GalCer-specific Vbeta11+ TCRs that use different TCR Valpha chains. The results were similar to those previously reported for MHC-peptide-specific TCRs, illustrating the versatility of the TCR platform. Docking TCR and CD1d-alpha-GalCer structures provided plausible insights into their interaction. The model supports a diagonal orientation of TCR on CD1d and suggests that complementarity determining region (CDR)3alpha, CDR3beta, and CDR1beta interact with ligands presented by CD1d, whereas CDR2beta binds to the CD1d alpha1 helix. This docking provides an explanation for the dominant usage of Vbeta11 and Vbeta8.2 chains by human and mouse iNKT cells, respectively, for recognition of CD1d-alpha-GalCer.

  11. Helical coil thermal hydraulic model

    NASA Astrophysics Data System (ADS)

    Caramello, M.; Bertani, C.; De Salve, M.; Panella, B.

    2014-11-01

    A model has been developed in Matlab environment for the thermal hydraulic analysis of helical coil and shell steam generators. The model considers the internal flow inside one helix and its associated control volume of water on the external side, both characterized by their inlet thermodynamic conditions and the characteristic geometry data. The model evaluates the behaviour of the thermal-hydraulic parameters of the two fluids, such as temperature, pressure, heat transfer coefficients, flow quality, void fraction and heat flux. The evaluation of the heat transfer coefficients as well as the pressure drops has been performed by means of the most validated literature correlations. The model has been applied to one of the steam generators of the IRIS modular reactor and a comparison has been performed with the RELAP5/Mod.3.3 code applied to an inclined straight pipe that has the same length and the same elevation change between inlet and outlet of the real helix. The predictions of the developed model and RELAP5/Mod.3.3 code are in fairly good agreement before the dryout region, while the dryout front inside the helical pipes is predicted at a lower distance from inlet by the model.

  12. Spheromak Power and Helicity Balance

    SciTech Connect

    Thomassen, K.I.

    2000-05-18

    This note addresses the division of gun power and helicity between the open line volume and the closed flux surface volume in a steady state flux core spheromak. Our assumptions are that fine scale turbulence maintains each region close to a Taylor state, {mu}{sub o}J = {lambda}B. The gun region that feeds these two volumes surrounded by a flux conserver is shown topologically below. (The actual geometry is toroidal). Flux and current from the magnetized gun flow on open lines around the entire closed surface containing the spheromak. The gun current flows down the potential gradient, the potential difference between the two ends of each line being the gun voltage. Here, the gun voltage excludes the sheath drops at each end. When these volumes have different values of {lambda} (ratio of {mu}{sub o}B{sup -2}j {center_dot} B in each region) in the open line volume V{sub 1} and the closed spheromak volume V{sub 2} the efficiency of transferring the gun power to the spheromak to sustain the ohmic loss is the {lambda}-ratio of these regions, in the limit V{sub 1} << V{sub 2}. This result follows immediately from helicity balance in that limit. Here we give an accounting of all the gun power, and do not assume a small edge (open line) region.

  13. A semi-analytical study on helical springs made of shape memory polymer

    NASA Astrophysics Data System (ADS)

    Baghani, M.; Naghdabadi, R.; Arghavani, J.

    2012-04-01

    In this paper, the responses of shape memory polymer (SMP) helical springs under axial force are studied both analytically and numerically. In the analytical solution, we first derive the response of a cylindrical tube under torsional loadings. This solution can be used for helical springs in which both the curvature and pitch effects are negligible. This is the case for helical springs with large ratios of the mean coil radius to the cross sectional radius (spring index) and also small pitch angles. Making use of this solution simplifies the analysis of the helical springs to that of the torsion of a straight bar with circular cross section. The 3D phenomenological constitutive model recently proposed for SMPs is also reduced to the 1D shear case. Thus, an analytical solution for the torsional response of SMP tubes in a full cycle of stress-free strain recovery is derived. In addition, the curvature effect is added to the formulation and the SMP helical spring is analyzed using the exact solution presented for torsion of curved SMP tubes. In this modified solution, the effect of the direct shear force is also considered. In the numerical analysis, the 3D constitutive equations are implemented in a finite element program and a full cycle of stress-free strain recovery of an SMP (extension or compression) helical spring is simulated. Analytical and numerical results are compared and it is shown that the analytical solution gives accurate stress distributions in the cross section of the helical SMP spring besides the global load-deflection response. Some case studies are presented to show the validity of the presented analytical method.

  14. Observation of helical edge states and fractional quantum Hall effect in a graphene electron-hole bilayer

    NASA Astrophysics Data System (ADS)

    Luo, Jason Yuanhong; Sanchez-Yamagishi, Javier; Watanabe, Kenji; Taniguchi, Takashi; Jarillo-Herrero, Pablo

    1D electronic systems are common theoretical building blocks for constructing quantum circuits, motivating a search for new experimental systems where 1D edge states of different quantum numbers can be coupled to each other by design. Twisted bilayer graphene allows for the stacking of two separate 1D quantum hall edge states, thus providing a natural sandbox for studying different types of edge state interactions. Via doping to form an electron-hole bilayer at moderate magnetic fields, we can induce edge modes of opposite chiralities and spin polarizations on different layers, thereby creating helical edge states reminiscent of a two-dimensional quantum spin Hall system. We report magnetotransport measurements of high-quality twisted bilayer graphene, showing how non-local measurements allow us to elucidate the nature and robustness of the helical edge states, as well as hints of fractional edge state interactions that are observable at higher magnetic fields.

  15. Human serotonin 1D receptor is encoded by a subfamily of two distinct genes: 5-HT1D alpha and 5-HT1D beta.

    PubMed Central

    Weinshank, R L; Zgombick, J M; Macchi, M J; Branchek, T A; Hartig, P R

    1992-01-01

    The serotonin 1D (5-HT1D) receptor is a pharmacologically defined binding site and functional receptor site. Observed variations in the properties of 5-HT1D receptors in different tissues have led to the speculation that multiple receptor proteins with slightly different properties may exist. We report here the cloning, deduced amino acid sequences, pharmacological properties, and second-messenger coupling of a pair of human 5-HT1D receptor genes, which we have designated 5-HT1D alpha and 5-HT1D beta due to their strong similarities in sequence, pharmacological properties, and second-messenger coupling. Both genes are free of introns in their coding regions, are expressed in the human cerebral cortex, and can couple to inhibition of adenylate cyclase activity. The pharmacological binding properties of these two human receptors are very similar, and match closely the pharmacological properties of human, bovine, and guinea pig 5-HT1D sites. Both receptors exhibit high-affinity binding of sumatriptan, a new anti-migraine medication, and thus are candidates for the pharmacological site of action of this drug. Images PMID:1565658

  16. Alpha-turn mimetics: short peptide alpha-helices composed of cyclic metallopentapeptide modules.

    PubMed

    Kelso, Michael J; Beyer, Renée L; Hoang, Huy N; Lakdawala, Ami S; Snyder, James P; Oliver, Warren V; Robertson, Tom A; Appleton, Trevor G; Fairlie, David P

    2004-04-21

    Alpha-Helices are key structural components of proteins and important recognition motifs in biology. Short peptides (helical sequences are rarely helical away from their stabilizing protein environments. New techniques for stabilizing short peptide helices could be valuable for studying protein folding, modeling proteins, creating artificial proteins, and may aid the design of inhibitors or mimics of protein function. This study reports the facile incorporation of 3- and 4-alpha turns in 10-15 residue peptides through formation in situ of multiple cyclic metallopeptide modules [Pd(en)(H*XXXH*)](2+). The nonhelical peptides Ac-H*ELTH*H*VTDH*-NH(2) (1), Ac-H*ELTH*AVTDYH*ELTH*-NH(2) (2), and Ac-H*AAAH*HELTH*H*VTDH*-NH(2) (3) (H is histidine-methylated at imidazole-N3) react in N,N-dimethylformamide (DMF) or water with 2, 2, and 3 molar equivalents, respectively, of [Pd(en)(NO(3))(2)] to form exclusively [Pd(2)(en)(2)(Ac-H*ELTH*H*VTDH*-NH(2))](4+) (4), [Pd(2)(en)(2)(Ac-H*ELTH*AVTDYH*ELTH*-NH(2))](4+) (5), and [Pd(3)(en)(3)(Ac-H*AAAH*HELTH*H*VTDH*-NH(2))](6+) (6), characterized by mass spectrometry, 1D and 2D (1)H- and 1D (15)N-NMR spectroscopy. Despite the presence of multiple histidines and other possible metal-binding residues in these peptides, 2D (1)H NMR spectra reveal that Pd(en)(2+) is remarkably specific in coordinating to imidazole-N1 of only (i, i + 4) pairs of histidines (i.e., only those separated by three amino acids), resulting in 4-6 made up of cyclic metallopentapeptide modules ([Pd(en)(H*XXXH*)](2+))(n), n = 2, 2, 3, respectively, each cycle being a 22-membered ring. We have previously shown that a single metallopentapeptide can nucleate alpha-helicity (Kelso et al., Angew. Chem., Int. Ed. 2003, 42, 421-424.). We now demonstrate its use as an alpha-turn-mimicking module for the facile conversion of unstructured short peptides into helices of macrocycles and provide 1D and 2D NMR spectroscopic data, structure

  17. Hydrodynamic characteristics of the helical flow pump.

    PubMed

    Ishii, Kohei; Hosoda, Kyohei; Nishida, Masahiro; Isoyama, Takashi; Saito, Itsuro; Ariyoshi, Koki; Inoue, Yusuke; Ono, Toshiya; Nakagawa, Hidemoto; Sato, Masami; Hara, Sintaro; Lee, Xinyang; Wu, Sheng-Yuan; Imachi, Kou; Abe, Yusuke

    2015-09-01

    The helical flow pump (HFP) was invented to be an ideal pump for developing the TAH and the helical flow TAH (HFTAH) using two HFPs has been developed. However, since the HFP is quite a new pump, hydrodynamic characteristics inside the pump are not clarified. To analyze hydrodynamic characteristics of the HFP, flow visualization study using the particle image velocimetry and computational fluid dynamics analysis were performed. The experimental and computational models were developed to simulate the left HFP of the HFTAH and distributions of flow velocity vectors, shear stress and pressure inside the pump were examined. In distribution of flow velocity vectors, the vortexes in the vane were observed, which indicated that the HFP has a novel and quite unique working principle in which centrifugal force rotates the fluid in the helical volutes and the fluid is transferred from the inlet to the outlet helical volutes according to the helical structure. In distribution of shear stress, the highest shear stress that was considered to be occurred by the shunt flow across the impeller was found around the entrance of the inlet helical volute. However, it was not so high to cause hemolysis. This shunt flow is thought to be improved by redesigning the inlet and outlet helical volutes. In distribution of pressure, negative pressure was found near the entrance of the inlet helical volute. However, it was not high. Negative pressure is thought to be reduced with an improvement in the design of the impeller or the vane shape. PMID:25784463

  18. The AGS synchrotron with four helical magnets

    SciTech Connect

    Tsoupas N.; Huang, H.; Roser, T.; MacKay, W.W.; Trbojevic, D.

    2012-05-20

    The idea of using two partial helical magnets was applied successfully to the AGS synchrotron to preserve the proton beam polarization. In this paper we explore in details the idea of using four helical magnets placed symmetrically in the AGS ring. The placement of four helical magnets in the AGS ring provides many advantages over the present setup of the AGS which uses two partial helical magnets. First, the symmetric placement of the four helical magnets allows for a better control of the AGS optics with reduced values of the beta functions especially near beam injection, second, the vertical spin direction during beam injection and extraction is closer to vertical, and third, it provides for a larger 'spin tune gap', which allows the vertical and horizontal tunes to be placed, and prevent the horizontal and vertical intrinsic spin resonances of the AGS to occur during the acceleration cycle. Although the same spin gap can be obtained with a single or two partial helices, the required high field strength of a single helix makes its use impractical, and that of the double helix rather difficult. In this paper we will provide results on the spin tune and on the optics of the AGS with four partial helical magnets, and compare these results with the present setup of the AGS that uses two partial helical magnets.

  19. Simplified Fabrication of Helical Copper Antennas

    NASA Technical Reports Server (NTRS)

    Petro, Andrew

    2006-01-01

    A simplified technique has been devised for fabricating helical antennas for use in experiments on radio-frequency generation and acceleration of plasmas. These antennas are typically made of copper (for electrical conductivity) and must have a specific helical shape and precise diameter.

  20. 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.

  1. Quasi-1D physics in metal-organic frameworks: MIL-47(V) from first principles

    PubMed Central

    Jaeken, Jan W; De Baerdemacker, Stijn; Lejaeghere, Kurt; Van Speybroeck, Veronique

    2014-01-01

    Summary The geometric and electronic structure of the MIL-47(V) metal-organic framework (MOF) is investigated by using ab initio density functional theory (DFT) calculations. Special focus is placed on the relation between the spin configuration and the properties of the MOF. The ground state is found to be antiferromagnetic, with an equilibrium volume of 1554.70 Å3. The transition pressure of the pressure-induced large-pore-to-narrow-pore phase transition is calculated to be 82 MPa and 124 MPa for systems with ferromagnetic and antiferromagnetic chains, respectively. For a mixed system, the transition pressure is found to be a weighted average of the ferromagnetic and antiferromagnetic transition pressures. Mapping DFT energies onto a simple-spin Hamiltonian shows both the intra- and inter-chain coupling to be antiferromagnetic, with the latter coupling constant being two orders of magnitude smaller than the former, suggesting the MIL-47(V) to present quasi-1D behavior. The electronic structure of the different spin configurations is investigated and it shows that the band gap position varies strongly with the spin configuration. The valence and conduction bands show a clear V d-character. In addition, these bands are flat in directions orthogonal to VO6 chains, while showing dispersion along the the direction of the VO6 chains, similar as for other quasi-1D materials. PMID:25383285

  2. Best packing of identical helices

    NASA Astrophysics Data System (ADS)

    Huh, Youngsik; Hong, Kyungpyo; Kim, Hyoungjun; No, Sungjong; Oh, Seungsang

    2016-10-01

    In this paper we prove the unique existence of a ropelength-minimizing conformation of the θ-spun double helix in a mathematically rigorous way, and find the minimal ropelength {{{Rop}}}* (θ )=-\\tfrac{8π }{t} where t is the unique solution in [-θ ,0] of the equation 2-2\\cos (t+θ )={t}2. Using this result, the pitch angles of the standard, triple and quadruple helices are around 39.3771^\\circ , 42.8354^\\circ and 43.8351^\\circ , respectively, which are almost identical with the approximated pitch angles of the zero-twist structures previously known by Olsen and Bohr. We also find the ropelength of the standard N-helix.

  3. The quantum Hall effect helicity

    SciTech Connect

    Shrivastava, Keshav N.

    2015-04-16

    The quantum Hall effect in semiconductor heterostructures is explained by two signs in the angular momentum j=l±s and g=(2j+1)/(2l+1) along with the Landau factor (n+1/2). These modifications in the existing theories explain all of the fractional charges. The helicity which is the sign of the product of the linear momentum with the spin p.s plays an important role for the understanding of the data at high magnetic fields. In particular it is found that particles with positive sign in the spin move in one direction and those with negative sign move in another direction which explains the up and down stream motion of the particles.

  4. Thermal deformation of helical gears

    NASA Astrophysics Data System (ADS)

    Zhang, Yong; Fei, Ye-tai; Liu, Shan-lin

    2010-08-01

    The analytical equation for the thermal field of a helical gear under normal working condition in a stable thermal field is established using mathematical physics, and the thermal deformation of the gear can be computed using this equation. The variations of gear geometric parameters, such as radial dimension, tooth depth, spiral angle, pressure angle, flank clearance and etc., are investigated with respect to the temperature change. According to the analytical and computational results obtained using the equation, the thermal deformation of the gear is strongly dependent on the choice of parameters, which is also confirmed using simulation software (COMSOL Multiphysic software). This is significant for the improvement of the rotation precision and working efficiency of screw gears.

  5. Adding helicity to inflationary magnetogenesis

    SciTech Connect

    Caprini, Chiara; Sorbo, Lorenzo E-mail: sorbo@physics.umass.edu

    2014-10-01

    The most studied mechanism of inflationary magnetogenesis relies on the time-dependence of the coefficient of the gauge kinetic term F{sub μν} F{sup μν}. Unfortunately, only extremely finely tuned versions of the model can consistently generate the cosmological magnetic fields required by observations. We propose a generalization of this model, where also the pseudoscalar invariant F{sub μν}  F-tilde {sup μν} is multiplied by a time dependent function. The new parity violating term allows more freedom in tuning the amplitude of the field at the end of inflation. Moreover, it leads to a helical magnetic field that is amplified at large scales by magnetohydrodynamical processes during the radiation dominated epoch. As a consequence, our model can satisfy the observational lower bounds on fields in the intergalactic medium, while providing a seed for the galactic dynamo, if inflation occurs at an energy scale ranging from 10{sup 5} to 10{sup 10} GeV. Such energy scale is well below that suggested by the recent BICEP2 result, if the latter is due to primordial tensor modes. However, the gauge field is a source of tensors during inflation and generates a spectrum of gravitational waves that can give a sizable tensor to scalar ratio r=O(0.2) even if inflation occurs at low energies. This system therefore evades the Lyth bound. For smaller values of r, lower values of the inflationary energy scale are required. The model predicts fully helical cosmological magnetic fields and a chiral spectrum of primordial gravitational waves.

  6. Tctex1d2 associates with short-rib polydactyly syndrome proteins and is required for ciliogenesis

    PubMed Central

    Gholkar, Ankur A.; Senese, Silvia; Lo, Yu-Chen; Capri, Joseph; Deardorff, William J; Dharmarajan, Harish; Contreras, Ely; Hodara, Emmanuelle; Whitelegge, Julian P; Jackson, Peter K; Torres, Jorge Z

    2015-01-01

    Short-rib polydactyly syndromes (SRPS) arise from mutations in genes involved in retrograde intraflagellar transport (IFT) and basal body homeostasis, which are critical for cilia assembly and function. Recently, mutations in WDR34 or WDR60 (candidate dynein intermediate chains) were identified in SRPS. We have identified and characterized Tctex1d2, which associates with Wdr34, Wdr60 and other dynein complex 1 and 2 subunits. Tctex1d2 and Wdr60 localize to the base of the cilium and their depletion causes defects in ciliogenesis. We propose that Tctex1d2 is a novel dynein light chain important for trafficking to the cilium and potentially retrograde IFT and is a new molecular link to understanding SRPS pathology. PMID:25830415

  7. Tctex1d2 associates with short-rib polydactyly syndrome proteins and is required for ciliogenesis.

    PubMed

    Gholkar, Ankur A; Senese, Silvia; Lo, Yu-Chen; Capri, Joseph; Deardorff, William J; Dharmarajan, Harish; Contreras, Ely; Hodara, Emmanuelle; Whitelegge, Julian P; Jackson, Peter K; Torres, Jorge Z

    2015-01-01

    Short-rib polydactyly syndromes (SRPS) arise from mutations in genes involved in retrograde intraflagellar transport (IFT) and basal body homeostasis, which are critical for cilia assembly and function. Recently, mutations in WDR34 or WDR60 (candidate dynein intermediate chains) were identified in SRPS. We have identified and characterized Tctex1d2, which associates with Wdr34, Wdr60 and other dynein complex 1 and 2 subunits. Tctex1d2 and Wdr60 localize to the base of the cilium and their depletion causes defects in ciliogenesis. We propose that Tctex1d2 is a novel dynein light chain important for trafficking to the cilium and potentially retrograde IFT and is a new molecular link to understanding SRPS pathology.

  8. Magnetic Helicity in a Cyclic Convective Dynamo

    NASA Astrophysics Data System (ADS)

    Miesch, Mark S.; Zhang, Mei; Augustson, Kyle C.

    2016-05-01

    Magnetic helicity is a fundamental agent for magnetic self-organization in magnetohydrodynamic (MHD) dynamos. As a conserved quantity in ideal MHD, it establishes a strict topological coupling between large and small-scale magnetic fields. The generation of magnetic fields on scales larger than the velocity field is linked to an upscale transfer of magnetic helicity, either locally in spectral space as in the inverse cascade of magnetic helicity in MHD turbulence or non-locally, as in the turbulent alpha-effect of mean-field dynamo theory. Thus, understanding the generation, transport, and dissipation of magnetic helicity is an essential prerequisite to understanding manifestations of magnetic self-organization in the solar dynamo, including sunspots, the prominent dipole and quadrupole moments, and the 22-year magnetic activity cycle. We investigate the role of magnetic helicity in a convective dynamo model that exhibits regular magnetic cycles. The cycle is marked by coherent bands of toroidal field that persist within the convection zone and that are antisymmetric about the equator. When these toriodal bands interact across the equator, it initiates a global restructuring of the magnetic topology that contributes to the reversal of the dipole moment. Thus, the polar field reversals are preceeded by a brief reversal of the subsurface magnetic helicity. There is some evidence that the Sun may exhibit a similar magnetic helicity reversal prior to its polar field reversals.

  9. 1D to 3D and Chiral to Noncentrosymmetric Metal-Organic Complexes Controlled by the Amount of DEF Solvent: Photoluminescent and NLO Properties.

    PubMed

    Wen, Yuehong; Sheng, Tianlu; Zhuo, Chao; Zhu, Xiaoquan; Hu, Shengmin; Cao, Wenhai; Li, Haoran; Zhang, Hao; Wu, Xintao

    2016-05-01

    A mixture of 2D and 1D metal-organic complexes, [ZnL(H2O)2·G1·DEF·2H2O]n (1a: G1 = naphthalene-2,7-disulfonate; DEF = N,N-diethylformamide) and [ZnL(H2O)3·G1·DEF·2H2O]n (2), has been prepared from a hydrogenated Schiff base L and Zn(II) in a DEF-contained solvent system under mild conditions. The yields of 1a and 2 are equivalent; however, they can be tuned by varying the amount of DEF solvent. Increasing the use of DEF tends to form pure 1a, while decreasing it generates 2. Without DEF, another novel 3D four-connected CdSO4 (cds) framework [ZnL(H2O)2·G1·2H2O]n (3) composed of alternated right-handed and left-handed helical chains has been constructed. The amount of DEF solvent has a significant impact on the diverse coordination architectures of 1-3, which is rare in the preparation of metal-organic complexes. The photoluminescence of complexes 1-3 along with naphthalene-2,7-disulfonate has been investigated in the solid state. The luminescent emission of G1 was enhanced greatly after being confined into metal-organic networks. In addition, complexes 1-3 display second-harmonic generation efficiencies, which are approximately 0.58, 0.42, 0.32, and 0.52 times as much as that of potassium dihydrogen phosphate.

  10. 1D to 3D and Chiral to Noncentrosymmetric Metal-Organic Complexes Controlled by the Amount of DEF Solvent: Photoluminescent and NLO Properties.

    PubMed

    Wen, Yuehong; Sheng, Tianlu; Zhuo, Chao; Zhu, Xiaoquan; Hu, Shengmin; Cao, Wenhai; Li, Haoran; Zhang, Hao; Wu, Xintao

    2016-05-01

    A mixture of 2D and 1D metal-organic complexes, [ZnL(H2O)2·G1·DEF·2H2O]n (1a: G1 = naphthalene-2,7-disulfonate; DEF = N,N-diethylformamide) and [ZnL(H2O)3·G1·DEF·2H2O]n (2), has been prepared from a hydrogenated Schiff base L and Zn(II) in a DEF-contained solvent system under mild conditions. The yields of 1a and 2 are equivalent; however, they can be tuned by varying the amount of DEF solvent. Increasing the use of DEF tends to form pure 1a, while decreasing it generates 2. Without DEF, another novel 3D four-connected CdSO4 (cds) framework [ZnL(H2O)2·G1·2H2O]n (3) composed of alternated right-handed and left-handed helical chains has been constructed. The amount of DEF solvent has a significant impact on the diverse coordination architectures of 1-3, which is rare in the preparation of metal-organic complexes. The photoluminescence of complexes 1-3 along with naphthalene-2,7-disulfonate has been investigated in the solid state. The luminescent emission of G1 was enhanced greatly after being confined into metal-organic networks. In addition, complexes 1-3 display second-harmonic generation efficiencies, which are approximately 0.58, 0.42, 0.32, and 0.52 times as much as that of potassium dihydrogen phosphate. PMID:27093469

  11. Brady 1D seismic velocity model ambient noise prelim

    DOE Data Explorer

    Mellors, Robert J.

    2013-10-25

    Preliminary 1D seismic velocity model derived from ambient noise correlation. 28 Green's functions filtered between 4-10 Hz for Vp, Vs, and Qs were calculated. 1D model estimated for each path. The final model is a median of the individual models. Resolution is best for the top 1 km. Poorly constrained with increasing depth.

  12. Helical Defect Packings in a Quasi-One-Dimensional System of Cylindrically Confined Hard Spheres

    NASA Astrophysics Data System (ADS)

    Yamchi, Mahdi Zaeifi; Bowles, Richard K.

    2015-07-01

    We use a combination of analytical theory and molecular dynamics simulation to study the inherent structure landscape of a system of hard spheres confined to narrow cylindrical channels of diameter 1 +√{3 }/2 helical sections between defects become asymmetrical and are better described as a double helix with angular twists between the first and second nearest neighbors that are determined by the defect separation distance. Increasing the fraction of defects unwinds the two helical strands so that the least dense structure is a nonhelical packing of two zigzag chains. We also show that the packing effects of the helical section induce a long-range, entropically driven attraction between the defects.

  13. Enhanced helical swimming in Boger fluids

    NASA Astrophysics Data System (ADS)

    Godinez, Francisco; Mendez-Rojano, Rodrigo; Zenit, Roberto; Lauga, Eric

    2014-11-01

    We conduct experiments with force-free magnetically-driven helical swimmers in Newtonian and viscoelastic (Boger) fluids. In order assess the effect of viscoelasticity on the swimming performance, we conduct experiments for swimmers with different helical tail geometries. We use helices with the same wave length and total length but vary the angle of the helix. As previously reported by the computational study of Spagniole and collaborators, we found that the swimming performance can either increase, decrease or remain unchanged, depending on the geometry of the tail. With the right geometry, the enhancement can be up to a factor of two.

  14. Helices in the wake of precipitation fronts.

    PubMed

    Thomas, Shibi; Lagzi, István; Molnár, Ferenc; Rácz, Zoltán

    2013-08-01

    A theoretical study of the emergence of helices in the wake of precipitation fronts is presented. The precipitation dynamics is described by the Cahn-Hilliard equation and the fronts are obtained by quenching the system into a linearly unstable state. Confining the process onto the surface of a cylinder and using the pulled-front formalism, our analytical calculations show that there are front solutions that propagate into the unstable state and leave behind a helical structure. We find that helical patterns emerge only if the radius of the cylinder R is larger than a critical value R>R(c), in agreement with recent experiments. PMID:24032809

  15. Helical flux ropes in solar prominences

    NASA Technical Reports Server (NTRS)

    Martens, P. C. H.; Van Ballegooijen, A. A.

    1990-01-01

    The present numerical method for the computation of force-free, cancelling magnetic structures shows that flux cancellation at the neutral line in a sheared magnetic arcade generates helical field lines that can support a prominence's plasma. With increasing flux cancellation, the axis of the helical fields moves to greater heights; this is suggestive of a prominence eruption. Two alternative scenarios are proposed for the formation of polar crown prominences which yield the correct axial magnetic field sign. Both models are noted to retain the formation of helical flux tubes through flux cancellation as their key feature.

  16. Steering Chiral Swimmers along Noisy Helical Paths

    NASA Astrophysics Data System (ADS)

    Friedrich, Benjamin M.; Jülicher, Frank

    2009-08-01

    Chemotaxis along helical paths towards a target releasing a chemoattractant is found in sperm cells and many microorganisms. We discuss the stochastic differential geometry of the noisy helical swimming path of a chiral swimmer. A chiral swimmer equipped with a simple feedback system can navigate in a concentration gradient of chemoattractant. We derive an effective equation for the alignment of helical paths with a concentration gradient which is related to the alignment of a dipole in an external field and discuss the chemotaxis index.

  17. Two-phase induction of the nonnative alpha-helical form of beta-lactoglobulin in the presence of trifluoroethanol.

    PubMed Central

    Mendieta, J; Folqué, H; Tauler, R

    1999-01-01

    The trifluoroethanol-dependent induction of the nonnative alpha-helical form of beta-lactoglubulin has been studied by circular dichroism spectroscopy. Data analysis is performed by factor analysis and multivariate curve resolution. An intermediate form in the induction of the alpha-helical form of the beta-lactoglobulin has been identified at low TFE concentration. By application of an alternating least-squares algorithm, the CD spectrum corresponding to the intermediate form has been resolved. The deconvolution of this CD spectrum shows a secondary structure content more in agreement with the one predicted from the amino acid sequence than the secondary structure of the helical form obtained at higher TFE concentrations. The additional alpha-helical content of the form present at higher TFE concentrations could be due to nonspecific interaction of TFE with the polypeptide chain. PMID:9876157

  18. The interplay of configuration and conformation in helical perylenequinones: Insights from chirality induction in liquid crystals and calculations

    PubMed Central

    Frezza, Elisa; Pieraccini, Silvia; Mazzini, Stefania

    2012-01-01

    Summary The chirality transfer in liquid crystals induced by two helical perylenequinones (namely, the natural compounds cercosporin and phleichrome) was investigated by integrating measurements of helical twisting power with a conformational analysis by DFT calculations and with the prediction of their twisting ability by the surface-chirality method. The two quasi-enantiomeric derivatives induce oppositely handed cholesteric phases when introduced as dopants in nematic solvents. We evaluated the role of the different conformations of the chiral hydroxyalkyl side chains in determining the helical twisting power: They were found to affect the strength of the chirality transfer, although the handedness of the induced cholesteric phase is essentially determined by the axial chirality (helicity) of the core of the perylenequinones. PMID:22423282

  19. Endoplasmic Reticulum Glycoprotein Quality Control Regulates CD1d Assembly and CD1d-mediated Antigen Presentation*

    PubMed Central

    Kunte, Amit; Zhang, Wei; Paduraru, Crina; Veerapen, Natacha; Cox, Liam R.; Besra, Gurdyal S.; Cresswell, Peter

    2013-01-01

    The non-classical major histocompatibility complex (MHC) homologue CD1d presents lipid antigens to innate-like lymphocytes called natural-killer T (NKT) cells. These cells, by virtue of their broad cytokine repertoire, shape innate and adaptive immune responses. Here, we have assessed the role of endoplasmic reticulum glycoprotein quality control in CD1d assembly and function, specifically the role of a key component of the quality control machinery, the enzyme UDP glucose glycoprotein glucosyltransferase (UGT1). We observe that in UGT1-deficient cells, CD1d associates prematurely with β2-microglobulin (β2m) and is able to rapidly exit the endoplasmic reticulum. At least some of these CD1d-β2m heterodimers are shorter-lived and can be rescued by provision of a defined exogenous antigen, α-galactosylceramide. Importantly, we show that in UGT1-deficient cells the CD1d-β2m heterodimers have altered antigenicity despite the fact that their cell surface levels are unchanged. We propose that UGT1 serves as a quality control checkpoint during CD1d assembly and further suggest that UGT1-mediated quality control can shape the lipid repertoire of newly synthesized CD1d. The quality control process may play a role in ensuring stability of exported CD1d-β2m complexes, in facilitating presentation of low abundance high affinity antigens, or in preventing deleterious responses to self lipids. PMID:23615906

  20. Single-handed helical wrapping of single-walled carbon nanotubes by chiral, ionic, semiconducting polymers.

    PubMed

    Deria, Pravas; Von Bargen, Christopher D; Olivier, Jean-Hubert; Kumbhar, Amar S; Saven, Jeffery G; Therien, Michael J

    2013-10-30

    We establish the requisite design for aryleneethynylene polymers that give rise to single-handed helical wrapping of single-walled carbon nanotubes (SWNTs). Highly charged semiconducting polymers that utilize either an (R)- or (S)-1,1'-bi-2-naphthol component in their respective conjugated backbones manifest HRTEM and AFM images of single-chain-wrapped SWNTs that reveal significant preferences for the anticipated helical wrapping handedness; statistical analysis of these images, however, indicates that ∼20% of the helical structures are formed with the "unexpected" handedness. CD spectroscopic data, coupled with TDDFT-based computational studies that correlate the spectral signatures of semiconducting polymer-wrapped SWNT assemblies with the structural properties of the chiral 1,1'-binaphthyl unit, suggest strongly that two distinct binaphthalene SWNT binding modes, cisoid-facial and cisoid-side, are possible for these polymers, with the latter mode responsible for inversion of helical chirality and the population of polymer-SWNT superstructures that feature the unexpected polymer helical wrapping chirality at the nanotube surface. Analogous aryleneethynylene polymers were synthesized that feature a 2,2'-(1,3-benzyloxy)-bridged (b)-1,1'-bi-2-naphthol unit: this 1,1'-bi-2-naphthol derivative is characterized by a bridging 2,2'-1,3 benzyloxy tether that restricts the torsional angle between the two naphthalene subunits along its C1-C1' chirality axis to larger, oblique angles that facilitate more extensive van der Waals contact of the naphthyl subunits with the nanotube. Similar microscopic, spectroscopic, and computational studies determine that chiral polymers based on conformationally restricted transoid binaphthyl units direct preferential facial binding of the polymer with the SWNT and thereby guarantee helically wrapped polymer-nanotube superstructures of fixed helical chirality. Molecular dynamics simulations provide an integrated picture tying together the

  1. Interaction of environmental contaminants with zebrafish organic anion transporting polypeptide, Oatp1d1 (Slco1d1)

    SciTech Connect

    Popovic, Marta; Zaja, Roko; Fent, Karl; Smital, Tvrtko

    2014-10-01

    Polyspecific transporters from the organic anion transporting polypeptide (OATP/Oatp) superfamily mediate the uptake of a wide range of compounds. In zebrafish, Oatp1d1 transports conjugated steroid hormones and cortisol. It is predominantly expressed in the liver, brain and testes. In this study we have characterized the transport of xenobiotics by the zebrafish Oatp1d1 transporter. We developed a novel assay for assessing Oatp1d1 interactors using the fluorescent probe Lucifer yellow and transient transfection in HEK293 cells. Our data showed that numerous environmental contaminants interact with zebrafish Oatp1d1. Oatp1d1 mediated the transport of diclofenac with very high affinity, followed by high affinity towards perfluorooctanesulfonic acid (PFOS), nonylphenol, gemfibrozil and 17α-ethinylestradiol; moderate affinity towards carbaryl, diazinon and caffeine; and low affinity towards metolachlor. Importantly, many environmental chemicals acted as strong inhibitors of Oatp1d1. A strong inhibition of Oatp1d1 transport activity was found by perfluorooctanoic acid (PFOA), chlorpyrifos-methyl, estrone (E1) and 17β-estradiol (E2), followed by moderate to low inhibition by diethyl phthalate, bisphenol A, 7-acetyl-1,1,3,4,4,6-hexamethyl-1,2,3,4 tetrahydronapthalene and clofibrate. In this study we identified Oatp1d1 as a first Solute Carrier (SLC) transporter involved in the transport of a wide range of xenobiotics in fish. Considering that Oatps in zebrafish have not been characterized before, our work on zebrafish Oatp1d1 offers important new insights on the understanding of uptake processes of environmental contaminants, and contributes to the better characterization of zebrafish as a model species. - Highlights: • We optimized a novel assay for determination of Oatp1d1 interactors • Oatp1d1 is the first SLC characterized fish xenobiotic transporter • PFOS, nonylphenol, diclofenac, EE2, caffeine are high affinity Oatp1d1substrates • PFOA, chlorpyrifos

  2. Emergence of helicity in rotating stratified turbulence

    NASA Astrophysics Data System (ADS)

    Marino, Raffaele; Mininni, Pablo D.; Rosenberg, Duane; Pouquet, Annick

    2013-03-01

    We perform numerical simulations of decaying rotating stratified turbulence and show, in the Boussinesq framework, that helicity (velocity-vorticity correlation), as observed in supercell storms and hurricanes, is spontaneously created due to an interplay between buoyancy and rotation common to large-scale atmospheric and oceanic flows. Helicity emerges from the joint action of eddies and of inertia-gravity waves (with inertia and gravity with respective associated frequencies f and N), and it occurs when the waves are sufficiently strong. For N/f<3 the amount of helicity produced is correctly predicted by a quasilinear balance equation. Outside this regime, and up to the highest Reynolds number obtained in this study, namely Re≈10000, helicity production is found to be persistent for N/f as large as ≈17, and for ReFr2 and ReRo2, respectively, as large as ≈100 and ≈24000.

  3. Building blocks for subleading helicity operators

    DOE PAGES

    Kolodrubetz, Daniel W.; Moult, Ian; Stewart, Iain W.

    2016-05-24

    On-shell helicity methods provide powerful tools for determining scattering amplitudes, which have a one-to-one correspondence with leading power helicity operators in the Soft-Collinear Effective Theory (SCET) away from singular regions of phase space. We show that helicity based operators are also useful for enumerating power suppressed SCET operators, which encode subleading amplitude information about singular limits. In particular, we present a complete set of scalar helicity building blocks that are valid for constructing operators at any order in the SCET power expansion. In conclusion, we also describe an interesting angular momentum selection rule that restricts how these building blocks canmore » be assembled.« less

  4. Passive micromixers with dual helical channels

    NASA Astrophysics Data System (ADS)

    Liu, Keyin; Yang, Qing; Chen, Feng; Zhao, Yulong; Meng, Xiangwei; Shan, Chao; Li, Yanyang

    2015-02-01

    In this study, a three-dimensional (3D) micromixer with cross-linked double helical microchannels is studied to achieve rapid mixing of fluids at low Reynolds numbers (Re). The 3D micromixer takes full advantages of the chaotic advection model with helical microchannels; meanwhile, the proposed crossing structure of double helical microchannels enables two flow patterns of repelling flow and straight flow in the fluids to promote the agitation effect. The complex 3D micromixer is realized by an improved femtosecond laser wet etching (FLWE) technology embedded in fused silica. The mixing results show that cross-linked double helical microchannels can achieve excellent mixing within 3 cycles (300 μm) over a wide range of low Re (1.5×10-3~600), which compare well with the conventional passive micromixers. This highly-effective micromixer is hoped to contribute to the integration of microfluidic systems.

  5. Motion of multiple helical vortices

    NASA Astrophysics Data System (ADS)

    Velasco Fuentes, Oscar

    2015-11-01

    In 1912 Joukowsky deduced that in an unbounded ideal fluid a set of helical vortices--when these are equal, coaxial and symmetrically arranged--would translate and rotate steadily while the vortices preserve their form and relative position. Each vortex is an infinite tube whose cross-section is circular (with radius a) and whose centerline is a helix of pitch L and radius R. The motion is thus determined by three non-dimensional parameters only: the number of vortices N, the vortex radius α = a / R and the vortex pitch τ = L / 2 πR . Here, we express the linear and angular velocities of the vortices as the sum of the mutually induced velocities found by Okulov (2004) and the self-induced velocities found by Velasco Fuentes (2015). We verified that our results are accurate over the whole range of values of the vortices' pitch and radius by numerically computing the vortex motion with two smoothed versions of the Biot-Savart law. It was found that the translation velocity U grows with the number of vortices (N) but decreases as the vortices' radius and pitch (a and τ, respectively) increase; in contrast, the rotation velocity Ω grows with N and a but has a local minimum around τ = 1 for fixed values of N and a.

  6. Spheromak Power and Helicity Balance

    SciTech Connect

    Thomassen, K.I.

    2000-05-18

    This note addresses the division of gun power and helicity between the open line volume and the closed flux surface volume in a steady state flux core spheromak. Our assumptions are that fine scale turbulence maintains each region close to an axisymmetric Taylor state, {mu}{sub o}j = {lambda}B. The gun region that feeds these two volumes surrounded by a flux conserver is shown topologically below. (The actual geometry is toroidal). Flux and current from the magnetized gun flow on open lines around the entire closed surface containing the spheromak. The gun current flows down the potential gradient, the potential difference between the two ends of each line being the gun voltage. Here, the gun voltage excludes the sheath drops at each end. These volumes have different values of {lambda} in each region (open line volume V{sub 1} and closed spheromak volume V{sub 2}) and we want to calculate the efficiency of transferring the gun power to the spheromak to sustain the ohmic loss in steady state.

  7. CURRENT HELICITY OF ACTIVE REGIONS AS A TRACER OF LARGE-SCALE SOLAR MAGNETIC HELICITY

    SciTech Connect

    Zhang, H.; Gao, Y.; Xu, H.; Moss, D.; Kleeorin, N.; Rogachevskii, I.; Kuzanyan, K.; Sokoloff, D.

    2012-05-20

    We demonstrate that the current helicity observed in solar active regions traces the magnetic helicity of the large-scale dynamo generated field. We use an advanced two-dimensional mean-field dynamo model with dynamo saturation based on the evolution of the magnetic helicity and algebraic quenching. For comparison, we also studied a more basic two-dimensional mean-field dynamo model with simple algebraic alpha-quenching only. Using these numerical models we obtained butterfly diagrams both for the small-scale current helicity and also for the large-scale magnetic helicity, and compared them with the butterfly diagram for the current helicity in active regions obtained from observations. This comparison shows that the current helicity of active regions, as estimated by -A {center_dot} B evaluated at the depth from which the active region arises, resembles the observational data much better than the small-scale current helicity calculated directly from the helicity evolution equation. Here B and A are, respectively, the dynamo generated mean magnetic field and its vector potential. A theoretical interpretation of these results is given.

  8. D1/D5 dopamine receptors modulate spatial memory formation.

    PubMed

    da Silva, Weber C N; Köhler, Cristiano C; Radiske, Andressa; Cammarota, Martín

    2012-02-01

    We investigated the effect of the intra-CA1 administration of the D1/D5 receptor antagonist SCH23390 and the D1/D5 receptor agonist SKF38393 on spatial memory in the water maze. When given immediately, but not 3h after training, SCH23390 hindered long-term spatial memory formation without affecting non-spatial memory or the normal functionality of the hippocampus. On the contrary, post-training infusion of SKF38393 enhanced retention and facilitated the spontaneous recovery of the original spatial preference after reversal learning. Our findings demonstrate that hippocampal D1/D5 receptors play an essential role in spatial memory processing.

  9. 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.

  10. Duality and helicity: A symplectic viewpoint

    NASA Astrophysics Data System (ADS)

    Elbistan, M.; Duval, C.; Horváthy, P. A.; Zhang, P.-M.

    2016-10-01

    The theorem which says that helicity is the conserved quantity associated with the duality symmetry of the vacuum Maxwell equations is proved by viewing electromagnetism as an infinite dimensional symplectic system. In fact, it is shown that helicity is the moment map of duality acting as an SO (2) group of canonical transformations on the symplectic space of all solutions of the vacuum Maxwell equations.

  11. Surface binding of alamethicin stabilizes its helical structure: molecular dynamics simulations.

    PubMed Central

    Tieleman, D P; Berendsen, H J; Sansom, M S

    1999-01-01

    Alamethicin is an amphipathic alpha-helical peptide that forms ion channels. An early event in channel formation is believed to be the binding of alamethicin to the surface of a lipid bilayer. Molecular dynamics simulations are used to compare the structural and dynamic properties of alamethicin in water and alamethicin bound to the surface of a phosphatidylcholine bilayer. The bilayer surface simulation corresponded to a loosely bound alamethicin molecule that interacted with lipid headgroups but did not penetrate the hydrophobic core of the bilayer. Both simulations started with the peptide molecule in an alpha-helical conformation and lasted 2 ns. In water, the helix started to unfold after approximately 300 ps and by the end of the simulation only the N-terminal region of the peptide remained alpha-helical and the molecule had collapsed into a more compact form. At the surface of the bilayer, loss of helicity was restricted to the C-terminal third of the molecule and the rod-shaped structure of the peptide was retained. In the surface simulation about 10% of the peptide/water H-bonds were replaced by peptide/lipid H-bonds. These simulations suggest that some degree of stabilization of an amphipathic alpha-helix occurs at a bilayer surface even without interactions between hydrophobic side chains and the acyl chain core of the bilayer. PMID:10354443

  12. Fourier-Bessel reconstruction of helical assemblies.

    PubMed

    Diaz, Ruben; Rice, William J; Stokes, David L

    2010-01-01

    Helical symmetry is commonly used for building macromolecular assemblies. Helical symmetry is naturally present in viruses and cytoskeletal filaments and also occurs during crystallization of isolated proteins, such as Ca-ATPase and the nicotinic acetyl choline receptor. Structure determination of helical assemblies by electron microscopy has a long history dating back to the original work on three-dimensional (3D) reconstruction. A helix offers distinct advantages for structure determination. Not only can one improve resolution by averaging across the constituent subunits, but each helical assembly provides multiple views of these subunits and thus provides a complete 3D data set. This review focuses on Fourier methods of helical reconstruction, covering the theoretical background, a step-by-step guide to the process, and a practical example based on previous work with Ca-ATPase. Given recent results from helical reconstructions at atomic resolution and the development of graphical user interfaces to aid in the process, these methods are likely to continue to make an important contribution to the field of structural biology. PMID:20888960

  13. Gluons in glueballs: Spin or helicity?

    SciTech Connect

    Mathieu, Vincent; Buisseret, Fabien; Semay, Claude

    2008-06-01

    In the past decade, lattice QCD has been able to compute the low-lying glueball spectrum with accuracy. Like other effective approaches of QCD, potential models still have difficulties to cope with gluonic hadrons. Assuming that glueballs are bound states of valence gluons with zero current mass, it is readily understood that the use of a potential model, intrinsically noncovariant, could be problematic in this case. The main challenge for this kind of model is actually to find a way to introduce properly the more relevant degree of freedom of the gluon: spin or helicity. In this work, we use the so-called helicity formalism of Jacob and Wick to describe two-gluon glueballs. We show, in particular, that this helicity formalism exactly reproduces the J{sup PC} numbers which are observed in lattice QCD when the constituent gluons have a helicity-1, without introducing extra states as is the case in most of the potential models. These extra states appear when gluons are seen as spin-1 particles. Using a simple spinless Salpeter model with Cornell potential within the helicity formalism, we obtain a glueball mass spectrum which is in good agreement with lattice QCD predictions for helicity-1 gluons provided instanton-induced interactions are taken into account.

  14. Helicity Annihilation in Trefoil Reconnection: Simulations

    NASA Astrophysics Data System (ADS)

    Kerr, Robert M.

    2015-11-01

    The simulated evolution and self-reconnection of a perturbed trefoil vortex knot is compared to the experiment. To have a single initial reconnection, as in the experiments, the trefoil is perturbed by 4 weak vortex rings. Visualizations show that the simulations and experiments undergo similar topological changes. Quantitative comparisons using the helicity and global topological number show that both are preserved for a long period before reconnection begins, as in the experiments. Unlike the experiments, once reconnection begins, a significant fraction of the helicity is dissipated and the global topological number changes by a discrete amount in a fixed time. Helicity spectra and physical space correlations show that the change in helicity is associated with the appearance of negative helicity at lower wavenumbers and in the outer regions of the trefoil. Furthermore, using a range of Reynolds numbers, with the highest comparable to the experiments, it is demonstrated that a Reynolds number independent fraction of the initial helicity is dissipated in a finite time. This observation does not violate any current mathematics restricting the strong growth of Navier-Stokes norms as the viscosity goes to zero due to the structure of the trefoil.

  15. Alternative Methods for Field Corrections in Helical Solenoids

    SciTech Connect

    Lopes, M. L.; Krave, S. T.; Tompkins, J. C.; Yonehara, K.; Flanagan, G.; Kahn, S. A.; Melconian, K.

    2015-05-01

    Helical cooling channels have been proposed for highly efficient 6D muon cooling. Helical solenoids produce solenoidal, helical dipole, and helical gradient field components. Previous studies explored the geometric tunability limits on these main field components. In this paper we present two alternative correction schemes, tilting the solenoids and the addition of helical lines, to reduce the required strength of the anti-solenoid and add an additional tuning knob.

  16. A human serotonin 1D receptor variant (5HT1D beta) encoded by an intronless gene on chromosome 6.

    PubMed Central

    Demchyshyn, L; Sunahara, R K; Miller, K; Teitler, M; Hoffman, B J; Kennedy, J L; Seeman, P; Van Tol, H H; Niznik, H B

    1992-01-01

    An intronless gene encoding a serotonin receptor (5HT1D beta) has been cloned and functionally expressed in mammalian fibroblast cultures. Based on the deduced amino acid sequence, the gene encodes a 390-amino acid protein displaying considerable homology, within putative transmembrane domains (approximately 75% identity) to the canine and human 5HT1D receptors. Membranes prepared from CHO cells stably expressing the receptor bound [3H]serotonin with high affinity (Kd 4 nM) and displayed a pharmacological profile consistent, but not identical, with that of the characterized serotonin 5HT1D receptor. Most notably, metergoline and serotonergic piperazine derivatives, as a group, display 3- to 8-fold lower affinity for the 5HT1D beta receptor than for the 5HT1D receptor, whereas both receptors display similar affinities for tryptamine derivatives, including the antimigraine drug sumatriptan. Northern blot analysis revealed an mRNA of approximately 5.5 kilobases expressed in human and monkey frontal cortex, medulla, striatum, hippocampus and amygdala but not in cerebellum, olfactory tubercle, and pituitary. The 5HT1D beta gene maps to human chromosome 6. The existence of multiple neuronal 5HT1D-like receptors may help account for some of the complexities associated with [3H]serotonin binding patterns in native membranes. Images PMID:1351684

  17. Hierarchical amplification of macromolecular helicity of dynamic helical poly(phenylacetylene)s composed of chiral and achiral phenylacetylenes in dilute solution, liquid crystal, and two-dimensional crystal.

    PubMed

    Ohsawa, Sousuke; Sakurai, Shin-ichiro; Nagai, Kanji; Banno, Motonori; Maeda, Katsuhiro; Kumaki, Jiro; Yashima, Eiji

    2011-01-12

    Optically active poly(phenylacetylene) copolymers consisting of optically active and achiral phenylacetylenes bearing L-alanine decyl esters (1L) and 2-aminoisobutylic acid decyl esters (Aib) as the pendant groups (poly(1L(m)-co-Aib(n))) with various compositions were synthesized by the copolymerization of the optically active 1L with achiral Aib using a rhodium catalyst, and their chiral amplification of the macromolecular helicity in a dilute solution, a lyotropic liquid crystalline (LC) state, and a two-dimensional (2D) crystal on the substrate was investigated by measuring the circular dichroism of the copolymers, mesoscopic cholesteric twist in the LC state (cholesteric helical pitch), and high-resolution atomic force microscopy (AFM) images of the self-assembled 2D helix-bundles of the copolymer chains. We found that the macromolecular helicity of poly(1L(m)-co-Aib(n))s could be hierarchically amplified in the order of the dilute solution, LC state, and 2D crystal. In sharp contrast, almost no chiral amplification of the macromolecular helicity was observed for the homopolymer mixtures of 1L and Aib in the LC state and 2D crystal on graphite. PMID:21141965

  18. 60. BOILER CHAMBER No. 1, D LOOP STEAM GENERATOR AND ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    60. BOILER CHAMBER No. 1, D LOOP STEAM GENERATOR AND MAIN COOLANT PUMP LOOKING NORTHEAST (LOCATION OOO) - Shippingport Atomic Power Station, On Ohio River, 25 miles Northwest of Pittsburgh, Shippingport, Beaver County, PA

  19. 1D Nanostructures: Controlled Fabrication and Energy Applications

    SciTech Connect

    Hu, Michael Z.

    2013-01-01

    Jian Wei, Xuchun Song, Chunli Yang, and Michael Z. Hu, 1D Nanostructures: Controlled Fabrication and Energy Applications, Journal of Nanomaterials, published special issue (http://www.hindawi.com/journals/jnm/si/197254/) (2013).

  20. TBC1D24 genotype–phenotype correlation

    PubMed Central

    Balestrini, Simona; Milh, Mathieu; Castiglioni, Claudia; Lüthy, Kevin; Finelli, Mattea J.; Verstreken, Patrik; Cardon, Aaron; Stražišar, Barbara Gnidovec; Holder, J. Lloyd; Lesca, Gaetan; Mancardi, Maria M.; Poulat, Anne L.; Repetto, Gabriela M.; Banka, Siddharth; Bilo, Leonilda; Birkeland, Laura E.; Bosch, Friedrich; Brockmann, Knut; Cross, J. Helen; Doummar, Diane; Félix, Temis M.; Giuliano, Fabienne; Hori, Mutsuki; Hüning, Irina; Kayserili, Hulia; Kini, Usha; Lees, Melissa M.; Meenakshi, Girish; Mewasingh, Leena; Pagnamenta, Alistair T.; Peluso, Silvio; Mey, Antje; Rice, Gregory M.; Rosenfeld, Jill A.; Taylor, Jenny C.; Troester, Matthew M.; Stanley, Christine M.; Ville, Dorothee; Walkiewicz, Magdalena; Falace, Antonio; Fassio, Anna; Lemke, Johannes R.; Biskup, Saskia; Tardif, Jessica; Ajeawung, Norbert F.; Tolun, Aslihan; Corbett, Mark; Gecz, Jozef; Afawi, Zaid; Howell, Katherine B.; Oliver, Karen L.; Berkovic, Samuel F.; Scheffer, Ingrid E.; de Falco, Fabrizio A.; Oliver, Peter L.; Striano, Pasquale; Zara, Federico

    2016-01-01

    Objective: To evaluate the phenotypic spectrum associated with mutations in TBC1D24. Methods: We acquired new clinical, EEG, and neuroimaging data of 11 previously unreported and 37 published patients. TBC1D24 mutations, identified through various sequencing methods, can be found online (http://lovd.nl/TBC1D24). Results: Forty-eight patients were included (28 men, 20 women, average age 21 years) from 30 independent families. Eighteen patients (38%) had myoclonic epilepsies. The other patients carried diagnoses of focal (25%), multifocal (2%), generalized (4%), and unclassified epilepsy (6%), and early-onset epileptic encephalopathy (25%). Most patients had drug-resistant epilepsy. We detail EEG, neuroimaging, developmental, and cognitive features, treatment responsiveness, and physical examination. In silico evaluation revealed 7 different highly conserved motifs, with the most common pathogenic mutation located in the first. Neuronal outgrowth assays showed that some TBC1D24 mutations, associated with the most severe TBC1D24-associated disorders, are not necessarily the most disruptive to this gene function. Conclusions: TBC1D24-related epilepsy syndromes show marked phenotypic pleiotropy, with multisystem involvement and severity spectrum ranging from isolated deafness (not studied here), benign myoclonic epilepsy restricted to childhood with complete seizure control and normal intellect, to early-onset epileptic encephalopathy with severe developmental delay and early death. There is no distinct correlation with mutation type or location yet, but patterns are emerging. Given the phenotypic breadth observed, TBC1D24 mutation screening is indicated in a wide variety of epilepsies. A TBC1D24 consortium was formed to develop further research on this gene and its associated phenotypes. PMID:27281533

  1. Falling chains

    NASA Astrophysics Data System (ADS)

    Wong, Chun Wa; Yasui, Kosuke

    2006-06-01

    The one-dimensional fall of a folded chain with one end suspended from a rigid support and a chain falling from a resting heap on a table is studied. Because their Lagrangians contain no explicit time dependence, the falling chains are conservative systems. Their equations of motion are shown to contain a term that enforces energy conservation when masses are transferred between subchains. We show that Cayley's 1857 energy nonconserving solution for a chain falling from a resting heap is incorrect because it neglects the energy gained when a link leaves a subchain. The maximum chain tension measured by Calkin and March for the falling folded chain is given a simple if rough interpretation. Other aspects of the falling folded chain are briefly discussed.

  2. Designed, Helical Protein Nanotubes with Variable Diameters from a Single Building Block.

    PubMed

    Brodin, Jeffrey D; Smith, Sarah J; Carr, Jessica R; Tezcan, F Akif

    2015-08-26

    Due to their structural and mechanical properties, 1D helical protein assemblies represent highly attractive design targets for biomolecular engineering and protein design. Here we present a designed, tetrameric protein building block, Zn8R4, which assembles via Zn coordination interactions into a series of crystalline, helical nanotubes whose widths can be controlled by solution conditions. X-ray crystallography and transmission electron microscopy (TEM) measurements indicate that all classes of protein nanotubes are constructed through the same 2D arrangement of Zn8R4 tetramers held together by Zn coordination. The mechanical properties of these nanotubes are correlated with their widths. All Zn8R4 nanotubes are found to be highly flexible despite possessing crystalline order, owing to their minimal interbuilding-block interactions mediated solely by metal coordination.

  3. Facile Synthesis of Stapled, Structurally Reinforced Peptide Helices via A Photoinduced Intramolecular 1,3-Dipolar Cycloaddition Reaction†

    PubMed Central

    Madden, Michael M.; Vera, Claudia I. Rivera; Song, Wenjiao; Lin, Qing

    2009-01-01

    We report the first use of a photoinduced 1,3-dipolar cycloaddition reaction in “stapling” peptide side chains to reinforce a model peptide helical structure with moderate to excellent yields. The resulting pyrazoline “staplers” exhibit unique fluorescence useful in a cell permeability study. PMID:19753366

  4. Simulation of coherent energy transfer in an alpha-helical peptide by Fermi resonance.

    PubMed Central

    Clarke, D L; Collins, M A

    1992-01-01

    A mechanism by which NH stretching quanta are coherently transported along a chain of hydrogen bonded peptide groups is demonstrated by classical simulation of a section of the alpha-helical peptide poly(L-alanine). Vibrational motion takes place on a complex energy surface constructed from earlier ab initio and empirical surfaces. A speculative hypothesis of the biological role of this mechanism is presented, and the critical parameters governing the dynamics are identified and discussed. Images FIGURE 1 PMID:1547322

  5. The influence of helical background fields on current helicity and electromotive force of magnetoconvection

    NASA Astrophysics Data System (ADS)

    Rüdiger, G.; Küker, M.

    2016-07-01

    Motivated by the empirical finding that the known hemispheric rules for the current helicity at the solar surface are not strict, we demonstrate the excitation of small-scale current helicity by the influence of large-scale helical magnetic background fields on nonrotating magnetoconvection. This is shown within a quasilinear analytic theory of driven turbulence and by nonlinear simulations of magnetoconvection that the resulting small-scale current helicity has the same sign as the large-scale current helicity, while the ratio of both pseudoscalars is of the order of the magnetic Reynolds number of the convection. The same models do not provide finite values of the small-scale kinetic helicity. On the other hand, a turbulence-induced electromotive force is produced including the diamagnetic pumping term, as well as the eddy diffusivity but, however, no α effect. It has thus been argued that the relations for the simultaneous existence of small-scale current helicity and α effect do not hold for the model of nonrotating magnetoconvection under consideration. Calculations for various values of the magnetic Prandtl number demonstrate that, for the considered diffusivities, the current helicity increases for growing magnetic Reynolds number, which is not true for the velocity of the diamagnetic pumping, which is in agreement with the results of the quasilinear analytical approximation.

  6. Controlling Orientational Order in 1-D Assemblies of Multivalent Triangular Prisms.

    PubMed

    Kohlstedt, Kevin L; Olvera de la Cruz, Monica; Schatz, George C

    2013-01-01

    Multivalent nanostructures are becoming an increasingly important player in the self-assembly of supramolecular lattices. Understanding the role that shape plays in the coordination of the assemblies is crucial for the functional response of the material. We develop a simple design rule for the assembly of multivalent Au triangular nanoprisms into 1-D ordered arrays based on both the length of the valent DNA and the aspect ratio of the prism. Using MD simulations, we describe an order parameter that captures the short-range order of the assembly controlled by the design parameters. The order parameter shows that even short chains (N = 4) of prisms have a high degree of orientational order that transitions to no orientational order when the DNA length is similar to the prism length. Unlike isotropic polyvalent assemblies, we find that the highly oriented chains of prisms lose orientational order in discrete steps during melting as the prisms in the arrays dissociate.

  7. Helical peptide-polyamine and -polyether conjugates as synthetic ionophores.

    PubMed

    Benincasa, Monica; Francescon, Marco; Fregonese, Massimo; Gennaro, Renato; Pengo, Paolo; Rossi, Paola; Scrimin, Paolo; Tecilla, Paolo

    2015-12-01

    Two new synthetic ionophores in which the hydrophobic portion is represented by a short helical Aib-peptide (Aib=α-amino-isobutyric acid) and the hydrophilic one is a poly-amino (1a) or a polyether (1b) chain have been prepared. The two conjugates show a high ionophoric activity in phospholipid membranes being able to efficiently dissipate a pH gradient and, in the case of 1b, to transport Na(+) across the membrane. Bioactivity evaluation of the two conjugates shows that 1a has a moderate antimicrobial activity against a broad spectrum of microorganisms and it is able to permeabilize the inner and the outer membrane of Escherichia coli cells. PMID:26558517

  8. Uncharged Helical Modular Polypeptide Hydrogels for Cellular Scaffolds.

    PubMed

    Ahrens, Caroline C; Welch, M Elizabeth; Griffith, Linda G; Hammond, Paula T

    2015-12-14

    Grafted synthetic polypeptides hold appeal for extending the range of biophysical properties achievable in synthetic extracellular matrix (ECM) hydrogels. Here, N-carboxyanhydride polypeptide, poly(γ-propargyl-l-glutamate) (PPLG) macromers were generated by fully grafting the "clickable" side chains with mixtures of short polyethylene glycol (PEG) chains terminated with inert (-OH) or reactive (maleimide and/or norbornene) groups, then reacting a fraction of these groups with an RGD cell attachment motif. A panel of synthetic hydrogels was then created by cross-linking the PPLG macromers with a 4-arm PEG star molecule. Compared to well-established PEG-only hydrogels, gels containing PPLG exhibited dramatically less dependence on swelling as a function of cross-link density. Further, PPLG-containing gels, which retain an α-helical chain conformation, were more effective than standard PEG gels in fostering attachment of a human mesenchymal stem cell (hMSC) line for a given concentration of RGD in the gel. These favorable properties of PPLG-containing PEG hydrogels suggest they may find broad use in synthetic ECM.

  9. Engineered Ionizable Side Chains.

    PubMed

    Cymes, Gisela D; Grosman, Claudio

    2015-01-01

    One of the great challenges of mechanistic ion-channel biology is to obtain structural information from well-defined functional states. In the case of neurotransmitter-gated ion channels, the open-channel conformation is particularly elusive owing to its transient nature and brief mean lifetime. In this Chapter, we show how the analysis of single-channel currents recorded from mutants engineered to contain single ionizable side chains in the transmembrane region can provide specific information about the open-channel conformation without any interference from the closed or desensitized conformations. The method takes advantage of the fact that the alternate binding and unbinding of protons to and from an ionizable side chain causes the charge of the protein to fluctuate by 1 unit. We show that, in mutant muscle acetylcholine nicotinic receptors (AChRs), this fluctuating charge affects the rate of ion conduction in such a way that individual proton-transfer events can be identified in a most straightforward manner. From the extent to which the single-channel current amplitude is reduced every time a proton binds, we can learn about the proximity of the engineered side chain to the lumen of the pore. And from the kinetics of proton binding and unbinding, we can calculate the side-chain's affinity for protons (pK a), and hence, we can learn about the electrostatic properties of the microenvironment around the introduced ionizable group. The application of this method to systematically mutated AChRs allowed us to identify unambiguously the stripes of the M1, M2 and M3 transmembrane α-helices that face the pore's lumen in the open-channel conformation in the context of a native membrane. PMID:26381938

  10. Evaluation of helicity generation in the tropical storm Gonu

    NASA Astrophysics Data System (ADS)

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

    2016-06-01

    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.

  11. Fabrication and experimentation of FRP helical spring

    NASA Astrophysics Data System (ADS)

    Ekanthappa, J.; Shiva Shankar, G. S.; Amith, B. M.; Gagan, M.

    2016-09-01

    In present scenario, the automobile industry sector is showing increased interest in reducing the unsprung weight of the automobile & hence increasing the fuel Efficiency. One of the feasible sub systems of a vehicle where weight reduction may be attempted is vehicle- suspension system. Usage of composite material is a proven way to lower the component weight without any compromise in strength. The composite materials are having high specific strength, more elastic strain energy storage capacity in comparison with those of steel. Therefore, helical coil spring made of steel is replaceable by composite cylindrical helical coil spring. This research aims at preparing a re-usable mandrel (mould) of Mild steel, developing a setup for fabrication, fabrication of FRP helical spring using continuous glass fibers and Epoxy Resin (Polymer). Experimentation has been conducted on fabricated FRP helical spring to determine its strength parameters & for failure analysis. It is found that spring stiffness (K) of Glass/Epoxy helical-spring is greater than steel-coil spring with reduced weight.

  12. Thermoelectric Analysis for Helical Power Generation Systems

    NASA Astrophysics Data System (ADS)

    Meng, Xiangning; Fujisaka, Takeyuki; Suzuki, Ryosuke O.

    2014-06-01

    The performance of a three-dimensional helical thermoelectric generation (TEG) system is examined by exposing it to a temperature difference with hot and cold sources. The helical paths for the two thermal fluids give the TEG device the potential to efficiently convert thermal energy. The characteristic performance of the helical system is numerically analyzed by using the finite-volume method in a compact system. The helical system is compared with a straight system in which all the thermoelectric (TE) elements present equivalent geometry. The difference in the TE performance between the two systems is not significant when the TE surfaces are maintained at constant temperatures. Both the electromotive force and the current in the TEG system increase linearly with the temperature difference Δ T applied at the two module surfaces. The current preferentially flows through a main path determined by the geometry of the TE element. The merits of the helical design are its compactness, space saving, and smooth fluid flow due to gravity, compared with the straight system.

  13. Working member of a helical downhole motor for drilling wells

    SciTech Connect

    Kochnev, A.M.; Vshivkov, A.N.; Goldobin, V.B.

    1993-06-22

    A working member of a helical downhole motor is described for drilling wells comprising: separate tubular sections having helical teeth arranged in succession and interconnected by connecting elements, each connecting element having the form of a ring, rigidly secured at the tubular sections and having helical teeth of a pitch and a direction equal to a pitch and a direction, respectively, of the helical teeth of the tubular sections, whereas a profile of the helical teeth of the ring is equidistant to a profile of the helical teeth of the sections.

  14. Dimensional phase transition from 1D behavior to a 3D Bose-Einstein condensate

    NASA Astrophysics Data System (ADS)

    Pelster, Axel; Morath, Denis; Straßel, Dominik; Eggert, Sebastian

    The emergence of new properties from low-dimensional building blocks is a universal theme in different areas in physics. The investigation of transitions between isolated and coupled low-dimensional systems promises to reveal new phenomena and exotic phases. Interacting 1D bosons, which are coupled in a two-dimensional array, are maybe the most fundamental example of a system which illustrates the concept of a dimensional phase transition. However, recent experiments using ultracold gases have shown a surprising discrepancy between theory and experiment and it is far from obvious if the power laws from the underlying 1D theory can predict the transition temperature and order parameter correctly for all interaction strengths. Using a combination of large-scale Quantum Monte-Carlo simulations and chain mean-field calculations, we show that the behavior of the ordering temperature as a function of inter-chain coupling strength does not follow a universal powerlaw, but also depends strongly on the filling

  15. 1D self-assembly of chemisorbed thymine on Cu(110) driven by dispersion forces

    NASA Astrophysics Data System (ADS)

    Temprano, I.; Thomas, G.; Haq, S.; Dyer, M. S.; Latter, E. G.; Darling, G. R.; Uvdal, P.; Raval, R.

    2015-03-01

    Adsorption of thymine on a defined Cu(110) surface was studied using reflection-absorption infrared spectroscopy (RAIRS), temperature programmed desorption (TPD), and scanning tunnelling microscopy (STM). In addition, density functional theory (DFT) calculations were undertaken in order to further understand the energetics of adsorption and self-assembly. The combination of RAIRS, TPD, and DFT results indicates that an upright, three-point-bonded adsorption configuration is adopted by the deprotonated thymine at room temperature. DFT calculations show that the upright configuration adopted by individual molecules arises as a direct result of strong O-Cu and N-Cu bonds between the molecule and the surface. STM data reveal that this upright thymine motif self-assembles into 1D chains, which are surprisingly oriented along the open-packed [001] direction of the metal surface and orthogonal to the alignment of the functional groups that are normally implicated in H-bonding interactions. DFT modelling of this system reveals that the molecular organisation is actually driven by dispersion interactions, which cause a slight tilt of the molecule and provide the major driving force for assembly into dimers and 1D chains. The relative orientations and distances of neighbouring molecules are amenable for π-π stacking, suggesting that this is an important contributor in the self-assembly process.

  16. 1D nanocrystals with precisely controlled dimensions, compositions, and architectures

    NASA Astrophysics Data System (ADS)

    Pang, Xinchang; He, Yanjie; Jung, Jaehan; Lin, Zhiqun

    2016-09-01

    The ability to synthesize a diverse spectrum of one-dimensional (1D) nanocrystals presents an enticing prospect for exploring nanoscale size- and shape-dependent properties. Here we report a general strategy to craft a variety of plain nanorods, core-shell nanorods, and nanotubes with precisely controlled dimensions and compositions by capitalizing on functional bottlebrush-like block copolymers with well-defined structures and narrow molecular weight distributions as nanoreactors. These cylindrical unimolecular nanoreactors enable a high degree of control over the size, shape, architecture, surface chemistry, and properties of 1D nanocrystals. We demonstrate the synthesis of metallic, ferroelectric, upconversion, semiconducting, and thermoelectric 1D nanocrystals, among others, as well as combinations thereof.

  17. The GIRAFFE Archive: 1D and 3D Spectra

    NASA Astrophysics Data System (ADS)

    Royer, F.; Jégouzo, I.; Tajahmady, F.; Normand, J.; Chilingarian, I.

    2013-10-01

    The GIRAFFE Archive (http://giraffe-archive.obspm.fr) contains the reduced spectra observed with the intermediate and high resolution multi-fiber spectrograph installed at VLT/UT2 (ESO). In its multi-object configuration and the different integral field unit configurations, GIRAFFE produces 1D spectra and 3D spectra. We present here the status of the archive and the different functionalities to select and download both 1D and 3D data products, as well as the present content. The two collections are available in the VO: the 1D spectra (summed in the case of integral field observations) and the 3D field observations. These latter products can be explored using the VO Paris Euro3D Client (http://voplus.obspm.fr/ chil/Euro3D).

  18. PC-1D installation manual and user's guide

    SciTech Connect

    Basore, P.A.

    1991-05-01

    PC-1D is a software package for personal computers that uses finite-element analysis to solve the fully-coupled two-carrier semiconductor transport equations in one dimension. This program is particularly useful for analyzing the performance of optoelectronic devices such as solar cells, but can be applied to any bipolar device whose carrier flows are primarily one-dimensional. This User's Guide provides the information necessary to install PC-1D, define a problem for solution, solve the problem, and examine the results. Example problems are presented which illustrate these steps. The physical models and numerical methods utilized are presented in detail. This document supports version 3.1 of PC-1D, which incorporates faster numerical algorithms with better convergence properties than previous versions of the program. 51 refs., 17 figs., 5 tabs.

  19. Pitch-based pattern splitting for 1D layout

    NASA Astrophysics Data System (ADS)

    Nakayama, Ryo; Ishii, Hiroyuki; Mikami, Koji; Tsujita, Koichiro; Yaegashi, Hidetami; Oyama, Kenichi; Smayling, Michael C.; Axelrad, Valery

    2015-07-01

    The pattern splitting algorithm for 1D Gridded-Design-Rules layout (1D layout) for sub-10 nm node logic devices is shown. It is performed with integer linear programming (ILP) based on the conflict graph created from a grid map for each designated pitch. The relation between the number of times for patterning and the minimum pitch is shown systematically with a sample pattern of contact layer for each node. From the result, the number of times for patterning for 1D layout is fewer than that for conventional 2D layout. Moreover, an experimental result including SMO and total integrated process with hole repair technique is presented with the sample pattern of contact layer whose pattern density is relatively high among critical layers (fin, gate, local interconnect, contact, and metal).

  20. 1D nanocrystals with precisely controlled dimensions, compositions, and architectures.

    PubMed

    Pang, Xinchang; He, Yanjie; Jung, Jaehan; Lin, Zhiqun

    2016-09-16

    The ability to synthesize a diverse spectrum of one-dimensional (1D) nanocrystals presents an enticing prospect for exploring nanoscale size- and shape-dependent properties. Here we report a general strategy to craft a variety of plain nanorods, core-shell nanorods, and nanotubes with precisely controlled dimensions and compositions by capitalizing on functional bottlebrush-like block copolymers with well-defined structures and narrow molecular weight distributions as nanoreactors. These cylindrical unimolecular nanoreactors enable a high degree of control over the size, shape, architecture, surface chemistry, and properties of 1D nanocrystals. We demonstrate the synthesis of metallic, ferroelectric, upconversion, semiconducting, and thermoelectric 1D nanocrystals, among others, as well as combinations thereof. PMID:27634531

  1. Flexible Photodetectors Based on 1D Inorganic Nanostructures

    PubMed Central

    Lou, Zheng

    2015-01-01

    Flexible photodetectors with excellent flexibility, high mechanical stability and good detectivity, have attracted great research interest in recent years. 1D inorganic nanostructures provide a number of opportunities and capabilities for use in flexible photodetectors as they have unique geometry, good transparency, outstanding mechanical flexibility, and excellent electronic/optoelectronic properties. This article offers a comprehensive review of several types of flexible photodetectors based on 1D nanostructures from the past ten years, including flexible ultraviolet, visible, and infrared photodetectors. High‐performance organic‐inorganic hybrid photodetectors, as well as devices with 1D nanowire (NW) arrays, are also reviewed. Finally, new concepts of flexible photodetectors including piezophototronic, stretchable and self‐powered photodetectors are examined to showcase the future research in this exciting field. PMID:27774404

  2. The helical structure of DNA facilitates binding

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

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

  3. Nondispersive optical activity of meshed helical metamaterials.

    PubMed

    Park, Hyun Sung; Kim, Teun-Teun; Kim, Hyeon-Don; Kim, Kyungjin; Min, Bumki

    2014-11-17

    Extreme optical properties can be realized by the strong resonant response of metamaterials consisting of subwavelength-scale metallic resonators. However, highly dispersive optical properties resulting from strong resonances have impeded the broadband operation required for frequency-independent optical components or devices. Here we demonstrate that strong, flat broadband optical activity with high transparency can be obtained with meshed helical metamaterials in which metallic helical structures are networked and arranged to have fourfold rotational symmetry around the propagation axis. This nondispersive optical activity originates from the Drude-like response as well as the fourfold rotational symmetry of the meshed helical metamaterials. The theoretical concept is validated in a microwave experiment in which flat broadband optical activity with a designed magnitude of 45° per layer of metamaterial is measured. The broadband capabilities of chiral metamaterials may provide opportunities in the design of various broadband optical systems and applications.

  4. The helical structure of DNA facilitates binding

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

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

  5. Manipulation of wavefront using helical metamaterials.

    PubMed

    Yang, Zhenyu; Wang, Zhaokun; Tao, Huan; Zhao, Ming

    2016-08-01

    Helical metamaterials, a kind of 3-dimensional structure, has relatively strong coupling effect among the helical nano-wires. Therefore, it is expected to be a good candidate for generating phase shift and controlling wavefront with high efficiency. In this paper, using the finite-difference time-domain (FDTD) method, we studied the phase shift properties in the helical metamaterials. It is found that the phase shift occurs for both transmitted and reflected light waves. And the maximum of reflection coefficients can reach over 60%. In addition, the phase shift (φ) is dispersionless in the range of 600 nm to 860 nm, that is, it is only dominated by the initial angle (θ) of the helix. The relationship between them is φ = ± 2θ. Using Jones calculus we give a further explanation for these properties. Finally, by arranging the helixes in an array with a constant phase gradient, the phenomenon of anomalous refraction was also observed in a broad wavelength range.

  6. Structural Transition from Helices to Hemihelices

    PubMed Central

    Su, Tianxiang; Bertoldi, Katia; Clarke, David R.

    2014-01-01

    Helices are amongst the most common structures in nature and in some cases, such as tethered plant tendrils, a more complex but related shape, the hemihelix forms. In its simplest form it consists of two helices of opposite chirality joined by a perversion. A recent, simple experiment using elastomer strips reveals that hemihelices with multiple reversals of chirality can also occur, a richness not anticipated by existing analyses. Here, we show through analysis and experiments that the transition from a helical to a hemihelical shape, as well as the number of perversions, depends on the height to width ratio of the strip's cross-section. Our findings provides the basis for the deterministic manufacture of a variety of complex three-dimensional shapes from flat strips. PMID:24759785

  7. 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

  8. Heat Loss by Helicity Injection II

    SciTech Connect

    Fowler, T K

    2006-04-25

    Arguments are reviewed showing that helicity transport always flattens the temperature profile, yielding unit current amplification in SSPX and flat temperature profiles in RFP's whenever the dynamo is active. The argument is based on transport theory yielding a hyper-resistivity {Lambda} {approx} (c{sup 2}/{omega}{sub pc}{sup 2}){chi}{sub c} with electron thermal diffusivity {chi}{sub c}, valid for any process producing a random-walk in electron constants of motion in the unperturbed field. The theory could be tested by deriving {Lambda} from helicity transport in SSPX, by analogy with recent analysis yielding {chi}{sub c} from heat transport. If the predicted ratio {Lambda}/{chi}{sub c} is confirmed, efforts to increase current amplification in SSPX must be based on scenario scenarios consistent with slow helicity transport compared to heat s transport (pulsed reactor, multipulse, neutral beam injection).

  9. Primordial magnetic helicity from stochastic electric currents

    NASA Astrophysics Data System (ADS)

    Calzetta, Esteban; Kandus, Alejandra

    2014-04-01

    We study the possibility that primordial magnetic fields generated in the transition between inflation and reheating posses magnetic helicity, HM. The fields are induced by stochastic currents of scalar charged particles created during the mentioned transition. We estimate the rms value of the induced magnetic helicity by computing different four-point scalar quantum electrodynamics Feynman diagrams. For any considered volume, the magnetic flux across its boundaries is in principle not null, which means that the magnetic helicity in those regions is gauge dependent. We use the prescription given by Berger and Field and interpret our result as the difference between two magnetic configurations that coincide in the exterior volume. In this case, the magnetic helicity gives only the number of magnetic links inside the considered volume. We calculate a concrete value of HM for large scales and analyze the distribution of magnetic defects as a function of the scale. Those defects correspond to regular as well as random fields in the considered volume. We find that the fractal dimension of the distribution of topological defects is D=1/2. We also study if the regular fields induced on large scales are helical, finding that they are and that the associated number of magnetic defects is independent of the scale. In this case, the fractal dimension is D=0. We finally estimate the intensity of fields induced at the horizon scale of reheating and evolve them until the decoupling of matter and radiation under the hypothesis of the inverse cascade of magnetic helicity. The resulting intensity is high enough and the coherence length long enough to have an impact on the subsequent process of structure formation.

  10. GIS-BASED 1-D DIFFUSIVE WAVE OVERLAND FLOW MODEL

    SciTech Connect

    KALYANAPU, ALFRED; MCPHERSON, TIMOTHY N.; BURIAN, STEVEN J.

    2007-01-17

    This paper presents a GIS-based 1-d distributed overland flow model and summarizes an application to simulate a flood event. The model estimates infiltration using the Green-Ampt approach and routes excess rainfall using the 1-d diffusive wave approximation. The model was designed to use readily available topographic, soils, and land use/land cover data and rainfall predictions from a meteorological model. An assessment of model performance was performed for a small catchment and a large watershed, both in urban environments. Simulated runoff hydrographs were compared to observations for a selected set of validation events. Results confirmed the model provides reasonable predictions in a short period of time.

  11. Observation of Dynamical Fermionization in 1D Bose Gases

    NASA Astrophysics Data System (ADS)

    Malvania, Neel; Xia, Lin; Xu, Wei; Wilson, Joshua M.; Zundel, Laura A.; Rigol, Marcos; Weiss, David S.

    2016-05-01

    The momentum distribution of a harmonically trapped 1D Bose gases in the Tonks-Girardeau limit is expected to undergo dynamical fermionization. That is, after the harmonic trap is suddenly turned off, the momentum distribution steadily transforms into that of an ideal Fermi gas in the same initial trap. We measure 1D momentum distributions at variable times after such a quench, and observe the predicted dynamical fermionization. In addition to working in the strong coupling limit, we also perform the experiment with intermediate coupling, where theoretical calculations are more challenging.

  12. [Examination of motion artifacts for helical and non-helical scanning modes in head CT].

    PubMed

    Fujimura, Ichiro; Ichikawa, Katsuhiro; Terakawa, Shoichi; Hara, Takanori; Miura, Yohei

    2011-01-01

    For head computed tomography (CT), non-helical scanning has been recommended even in the widely used multi-slice CT (MSCT). Also, an acute stroke imaging standardization group has recommended the non-helical mode in Japan. However, no detailed comparison has been reported for current MSCT with more than 16 slices. In this study, we compared the non-helical and helical modes for head CT, focusing on temporal resolution and motion artifacts. The temporal resolution was evaluated by using temporal sensitivity profiles (TSPs) measured using a temporal impulse method. In both modes, the TSPs and temporal modulation transfer factors (MTFs) were measured for various pitch factors using 64-slice CT (Aquilion 64, Toshiba). Two motion phantoms were scanned to evaluate motion artifacts, and then quantitative analyses for motion artifacts and helical artifacts were performed by measuring multiple regions of interest (ROIs) in the phantom images. In addition, the rates of artifact occurrence for retrospective clinical cases were compared. The temporal resolution increased as the pitch factor was increased. Remarkable streak artifacts appeared in the non-helical images of the motion phantom, in spite of the equivalent effective temporal resolution. In clinical analysis, results consistent with the phantom studies were shown. These results indicated that the low pitch helical mode would be effective for emergency head CT with patient movement.

  13. Dimensional phase transition from an array of 1D Luttinger liquids to a 3D Bose-Einstein condensate.

    PubMed

    Vogler, Andreas; Labouvie, Ralf; Barontini, Giovanni; Eggert, Sebastian; Guarrera, Vera; Ott, Herwig

    2014-11-21

    We study the thermodynamic properties of a 2D array of coupled one-dimensional Bose gases. The system is realized with ultracold bosonic atoms loaded in the potential tubes of a two-dimensional optical lattice. For negligible coupling strength, each tube is an independent weakly interacting 1D Bose gas featuring Tomonaga Luttinger liquid behavior. By decreasing the lattice depth, we increase the coupling strength between the 1D gases and allow for the phase transition into a 3D condensate. We extract the phase diagram for such a system and compare our results with theoretical predictions. Because of the high effective mass across the periodic potential and the increased 1D interaction strength, the phase transition is shifted to large positive values of the chemical potential. Our results are prototypical to a variety of low-dimensional systems, where the coupling between the subsystems is realized in a higher spatial dimension such as coupled spin chains in magnetic insulators.

  14. Equilibrium calculations for helical axis stellarators

    SciTech Connect

    Hender, T.C.; Carreras, B.A.

    1984-04-01

    An average method based on a vacuum flux coordinate system is presented. This average method permits the study of helical axis stellarators with toroidally dominated shifts. An ordering is introduced, and to lowest order the toroidally averaged equilibrium equations are reduced to a Grad-Shafranov equation. Also, to lowest order, a Poisson-type equation is obtained for the toroidally varying corrections to the equilibium. By including these corrections, systems that are toroidally dominated, but with significant helical distortion to the equilibrium, may be studied. Numerical solutions of the average method equations are shown to agree well with three-dimensional calculations.

  15. 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

  16. The nature of phonons and solitary waves in alpha-helical proteins.

    PubMed Central

    Lawrence, A. F.; McDaniel, J. C.; Chang, D. B.; Birge, R. R.

    1987-01-01

    A parametric study of the Davydov model of energy transduction in alpha-helical proteins is described. Previous investigations have shown that the Davydov model predicts that nonlinear interactions between phonons and amide-I excitations can stabilize the latter and produce a long-lived combined excitation (the so-called Davydov soliton), which propagates along the helix. The dynamics of this solitary wave are approximately those of solitons described using the nonlinear Schrödinger equation. The present study extends these previous investigations by analyzing the effect of helix length and nonlinear coupling efficiency on the phonon spectrum in short and medium length alpha-helical segments. The phonon energy accompanying amide-I excitation shows periodic variation in time with fluctuations that follow three different time scales. The phonon spectrum is highly dependent upon chain length but a majority of the energy remains localized in normal mode vibrations even in the long chain alpha-helices. Variation of the phonon-exciton coupling coefficient changes the amplitudes but not the frequencies of the phonon spectrum. The computed spectra contain frequencies ranging from 200 GHz to 6 THz, and as the chain length is increased, the long period oscillations increase in amplitude. The most important prediction of this study, however, is that the dynamics predicted by the numerical calculations have more in common with dynamics described by using the Frohlich polaron model than by using the Davydov soliton. Accordingly, the relevance of the Davydov soliton model was applied to energy transduction in alpha-helical proteins is questionable. We conclude that the Raman lines that have been assigned to solitons in E. coli are either associated with low frequency normal modes or are instrumental- or fluorescence-induced artifacts. PMID:3593874

  17. Reversible supra-channel effects: 3D kagome structure and catalysis via a molecular array of 1D coordination polymers.

    PubMed

    Lee, Haeri; Noh, Tae Hwan; Jung, Ok-Sang

    2013-10-14

    Self-assembly of CuX2 (X(-) = ClO4(-) and BF4(-)) with 2,3-bis(nicotinoyloxy)naphthalene yields a 1D loop-chain skeleton. The loop-chains form an ensemble constituting a unique 3D kagome-type structure with both hexagonal and trigonal supra-channels. The unprecedented supra-channel effects on the catalytic oxidation of 3,5-di-tert-butylcatechol to 3,5-di-tert-butylbenzoquinone were investigated.

  18. Non-cooperative Brownian donkeys: A solvable 1D model

    NASA Astrophysics Data System (ADS)

    Jiménez de Cisneros, B.; Reimann, P.; Parrondo, J. M. R.

    2003-12-01

    A paradigmatic 1D model for Brownian motion in a spatially symmetric, periodic system is tackled analytically. Upon application of an external static force F the system's response is an average current which is positive for F < 0 and negative for F > 0 (absolute negative mobility). Under suitable conditions, the system approaches 100% efficiency when working against the external force F.

  19. Ab initio quantum mechanical models of peptide helices and their vibrational spectra.

    PubMed

    Bour, Petr; Kubelka, Jan; Keiderling, Timothy A

    2002-10-01

    Structural parameters for standard peptide helices (alpha, 3(10), 3(1) left-handed) were fully ab initio optimized for Ac-(L-Ala)(9)-NHMe and for Ac-(L-Pro)(9)-NHMe (poly-L-proline-PLP I and PLP II-forms), in order to better understand the relative stability and minimum energy geometries of these conformers and the dependence of the ir absorption and vibrational CD (VCD) spectra on detailed variation in these conformations. Only the 3(10)-helical Ala-based conformation was stable in vacuum for this decaamide structure, but both Pro-based conformers minimized successfully. Inclusion of solvent effects, by use of the conductor-like screening solvent model (COSMO), enabled ab initio optimizations [at the DFT/B3LYP/SV(P) level] without any constraints for the alpha- and 3(10)-helical Ala-based peptides as well as the two Pro-based peptides. The geometries obtained compare well with peptide chain torsion angles and hydrogen-bond distances found for these secondary structure types in x-ray structures of peptides and proteins. For the simulation of VCD spectra, force field and intensity response tensors were obtained ab initio for the complete Ala-based peptides in vacuum, but constrained to the COSMO optimized torsional angles, due to limitations of the solvent model. Resultant spectral patterns reproduce well many aspects of the experimental spectra and capture the differences observed for these various helical types.

  20. 1D design style implications for mask making and CEBL

    NASA Astrophysics Data System (ADS)

    Smayling, Michael C.

    2013-09-01

    At advanced nodes, CMOS logic is being designed in a highly regular design style because of the resolution limitations of optical lithography equipment. Logic and memory layouts using 1D Gridded Design Rules (GDR) have been demonstrated to nodes beyond 12nm.[1-4] Smaller nodes will require the same regular layout style but with multiple patterning for critical layers. One of the significant advantages of 1D GDR is the ease of splitting layouts into lines and cuts. A lines and cuts approach has been used to achieve good pattern fidelity and process margin to below 12nm.[4] Line scaling with excellent line-edge roughness (LER) has been demonstrated with self-aligned spacer processing.[5] This change in design style has important implications for mask making: • The complexity of the masks will be greatly reduced from what would be required for 2D designs with very complex OPC or inverse lithography corrections. • The number of masks will initially increase, as for conventional multiple patterning. But in the case of 1D design, there are future options for mask count reduction. • The line masks will remain simple, with little or no OPC, at pitches (1x) above 80nm. This provides an excellent opportunity for continual improvement of line CD and LER. The line pattern will be processed through a self-aligned pitch division sequence to divide pitch by 2 or by 4. • The cut masks can be done with "simple OPC" as demonstrated to beyond 12nm.[6] Multiple simple cut masks may be required at advanced nodes. "Coloring" has been demonstrated to below 12nm for two colors and to 8nm for three colors. • Cut/hole masks will eventually be replaced by e-beam direct write using complementary e-beam lithography (CEBL).[7-11] This transition is gated by the availability of multiple column e-beam systems with throughput adequate for high- volume manufacturing. A brief description of 1D and 2D design styles will be presented, followed by examples of 1D layouts. Mask complexity for 1

  1. 1-D Modes on Step-edges of the Putative Weak Topological Insulator BI2TeI

    NASA Astrophysics Data System (ADS)

    Avraham, Nurit; Norris, Andrew; Pan, Lin; Wu, Shu-Chun; Felser, Claudia; Yan, Binghai; Beidenkopf, Haim

    Weak topological insulators are layered materials that possess surfaces with an even number of Dirac cones and surfaces that are fully gapped. This inherent anisotropy provides them with unique properties such as sensitivity to the parity of the number of layers and absence of localization of their surface states. We use scanning tunneling microscopy to study the topological properties of stacked Bi2TeI, a promising candidate for weak topological insulator. We report the observation of the bulk energy gap on terraces perpendicular to the stacking direction and signatures of 1D intra-gap topological edge states along step-edges. The rich structure of quasi 2D terraces and Islands obtained on such cleaved Bi2TeI surfaces provides an excellent playground to explore some of the most fundamental concepts of TIs such as their Z2 classification, ``partner switching'' of Kramer's degenerate pairs, and helical modes along dislocation lines.

  2. Kinetic assembly of block copolymers in solution helical cylindrical micelles and patchy nanoparticles

    NASA Astrophysics Data System (ADS)

    Zhong, Sheng

    There is always an interest to understand how molecules behave under different conditions. One application of this knowledge is to self-assemble molecules into increasingly complex structures in a simple fashion. Self-assembly of amphiphilic block copolymer in solution has produced a large variety of nanostructures through the manipulation in polymer chemistry, assembly environment, and additives. Moreover, some reports suggest the formation of many polymeric assemblies is driven by kinetic process. The goal of this dissertation is to study the influence of kinetics on the assembly of block copolymer. The study shows kinetic control can be a very effective way to make novel polymeric nanostructures. Two examples discussed here are helical cylindrical micelles and patchy nanoparticles. Helical cylindrical micelles are made from the co-assembly of amphiphilic triblock copolymer poly(acrylic acid)-block-poly(methyl acrylate)- block-polystyrene and organoamine molecules in a mixture of tetrahydrofuran (THF) and water (H2O). This system has already shown promise of achieving many assembled structures. The unique aspects about this system are the use of amine molecules to complex with acid groups and the existence of cosolvent system. Application of amine molecules offers a convenient control over assembled morphology and the introduction of PMA-PS selective solvent, THF, promotes the mobility of the polymer chains. In this study, multivalent organoamine molecules, such as diethylenetriamine and triethylenetetramine, are used to interact with block copolymer in THF/water mixture. As expected, the assembled morphologies are dependent on the polymer architecture, selection and quantity of the organoamine molecules, and solution composition. Under the right conditions, unprecedented, multimicrometer-long, supramolecular helical cylindrical micelles are formed. Both single-stranded and double-stranded helices are found in the same system. These helical structures share

  3. Magnetic tetrastability in a spin chain

    NASA Astrophysics Data System (ADS)

    Pianet, Vivien; Urdampilleta, Matias; Colin, Thierry; Clérac, Rodolphe; Coulon, Claude

    2016-08-01

    Bistability in magnetism is extensively used, in particular for information storage. Here an alternative approach using tetrastable magnetic domains in one-dimensional (1D) spin systems is presented. Using numerical and analytical calculations, we show that a spin chain with a canting angle of π/4 possesses four energy-equivalent states. We discuss the static properties of this canted 1D system such as the profile and the energy of the domain walls as they govern the dynamics of the magnetization. The realization of this π/4 canted spin chain could enable the encoding of the information on four bits, which is a potential alternative toward the increase of storage density.

  4. A Prospective Evaluation of Helical Tomotherapy

    SciTech Connect

    Bauman, Glenn ||. E-mail: glenn.bauman@lhsc.on.ca; Yartsev, Slav; Rodrigues, George ||; Lewis, Craig; Hammond, Alex; Perera, Francisco; Ash, Robert, Dar, A. Rashid |; Venkatesan, Varagur M. |; Yu, Edward; Lock, Michael; Battista, Jerry; Van Dyk, Jake ||; Baily, Laura; Coad, Terry C; Trenka, Kris C.; Warr, Barbara; Kron, Tomas

    2007-06-01

    Purpose: To report results from two clinical trials evaluating helical tomotherapy (HT). Methods and Materials: Patients were enrolled in one of two prospective trials of HT (one for palliative and one for radical treatment). Both an HT plan and a companion three-dimensional conformal radiotherapy (3D-CRT) plan were generated. Pretreatment megavoltage computed tomography was used for daily image guidance. Results: From September 2004 to January 2006, a total of 61 sites in 60 patients were treated. In all but one case, a clinically acceptable tomotherapy plan for treatment was generated. Helical tomotherapy plans were subjectively equivalent or superior to 3D-CRT in 95% of plans. Helical tomotherapy was deemed equivalent or superior in two thirds of dose-volume point comparisons. In cases of inferiority, differences were either clinically insignificant and/or reflected deliberate tradeoffs to optimize the HT plan. Overall imaging and treatment time (median) was 27 min (range, 16-91 min). According to a patient questionnaire, 78% of patients were satisfied to very satisfied with the treatment process. Conclusions: Helical tomotherapy demonstrated clear advantages over conventional 3D-CRT in this diverse patient group. The prospective trials were helpful in deploying this technology in a busy clinical setting.

  5. Helicity as a Component of Filament Formation

    NASA Astrophysics Data System (ADS)

    Mackay, D. H.; Gaizauskas, V.

    2003-09-01

    In this paper we seek the origin of the axial component of the magnetic field in filaments by adapting theory to observations. A previous paper (Mackay, Gaizauskas, and van Ballegooijen, 2000) showed that surface flows acting on potential magnetic fields for 27 days the maximum time between the emergence of magnetic flux and the formation of large filaments between the resulting activity complexes cannot explain the chirality or inverse polarity nature of the observed filaments. We show that the inclusion of initial helicity, for which there is observational evidence, in the flux transport model results in sufficiently strong dextral fields of inverse polarity to account for the existence and length of an observed filament within the allotted time. The simulations even produce a large length of dextral chirality when just small amounts of helicity are included in the initial configuration. The modeling suggests that the axial field component in filaments can result from a combination of surface (flux transport) and sub-surface (helicity) effects acting together. Here surface effects convert the large-scale helicity emerging in active regions into a smaller-scale magnetic-field component parallel to the polarity inversion line so as to form a magnetic configuration suitable for a filament.

  6. Multislice helical CT: image temporal resolution.

    PubMed

    Hui, H; Pan, T; Shen, Y

    2000-05-01

    A multislice helical computed tomography (CT) halfscan (HS) reconstruction algorithm is proposed for cardiac applications. The imaging performances (in terms of the temporal resolution, z-axis resolution, image noise, and image artifacts) of the HS algorithm are compared to the existing algorithms using theoretical models and clinical data. A theoretical model of the temporal resolution performance (in terms of the temporal sensitivity profile) is established for helical CT, in general, i.e., for any number of detector rows and any reconstruction algorithm used. It is concluded that the HS reconstruction results in improved image temporal resolution than the corresponding 180 degrees LI (linear interpolation) reconstruction and is more immune to the inconsistent data problem induced by cardiac motions. The temporal resolution of multislice helical CT with the HS algorithm is comparable to that of single-slice helical CT with the HS algorithm. In practice, the 180 degrees LI and HS-LI algorithms can be used in parallel to generate two image sets from the same scan acquisition, one (180 degrees LI) for improved z-resolution and noises, and the other (HS-LI) for improved image temporal resolution.

  7. QCD Evolution of Helicity and Transversity TMDs

    SciTech Connect

    Prokudin, Alexei

    2014-01-01

    We examine the QCD evolution of the helicity and transversity parton distribution functions when including also their dependence on transverse momentum. Using an appropriate definition of these polarized transverse momentum distributions (TMDs), we describe their dependence on the factorization scale and rapidity cutoff, which is essential for phenomenological applications.

  8. Deformation of flexible micro helices under flow

    NASA Astrophysics Data System (ADS)

    Daieff, Marine; Lindner, Anke; Du Roure, Olivia; Morozov, Alexander; Pham, Jonathan; Crosby, Alfred

    The interaction of small helices with fluids is important because of its relevance to both fundamental science and technological applications, such as swimming microrobots or microflow sensors. Helically shaped flagella are also exploited by swimming microorganisms to move through their surrounding fluids. Here we study experimentally the deformation of flexible helical ribbons under flow in a microfluidic channel. The size of the helix is typically microscale for the diameter and nanoscale for the thickness. We focus on two different aspects: the overall shape of the helix and the viscous frictional properties. The frictional coefficients determined by our experiments are consistent with calculated values in the context of resistive force theory. Deformation of helices by viscous flow is well-described by non-linear finite extensibility. Due to the non-uniform distribution of the pitch under distributed loading, we identify both linear and nonlinear behavior along the contour length of a single helix. Utilizing our system, we explore the impact of non-Newtonian fluid properties on the mechanics of helix-fluid interactions.

  9. Phase diagram of two interacting helical states

    NASA Astrophysics Data System (ADS)

    Santos, Raul A.; Gutman, D. B.; Carr, Sam T.

    2016-06-01

    We consider two coupled time-reversal-invariant helical edge modes of the same helicity, such as would occur on two stacked quantum spin Hall insulators. In the presence of interaction, the low-energy physics is described by two collective modes, one corresponding to the total current flowing around the edge and the other one describing relative fluctuations between the two edges. We find that quite generically, the relative mode becomes gapped at low temperatures, but only when tunneling between the two helical modes is nonzero. There are two distinct possibilities for the gapped state depending on the relative size of different interactions. If the intraedge interaction is stronger than the interedge interaction, the state is characterized as a spin-nematic phase. However, in the opposite limit, when the interaction between the helical edge modes is strong compared to the interaction within each mode, a spin-density wave forms, with emergent topological properties. First, the gap protects the conducting phase against localization by weak nonmagnetic impurities; second, the protected phase hosts localized zero modes on the ends of the edge that may be created by sufficiently strong nonmagnetic impurities.

  10. Artificial, parallel, left-handed DNA helices.

    PubMed

    Tian, Cheng; Zhang, Chuan; Li, Xiang; Li, Yingmei; Wang, Guansong; Mao, Chengde

    2012-12-19

    This communication reports an engineered DNA architecture. It contains multiple domains of half-turn-long, standard B-DNA duplexes. While each helical domain is right-handed and its two component strands are antiparallel, the global architecture is left-handed and the two component DNA strands are oriented parallel to each other.

  11. Muon Beam Helical Cooling Channel Design

    SciTech Connect

    Johnson, Rolland; Ankenbrandt, Charles; Flanagan, G; Kazakevich, G M; Marhauser, Frank; Neubauer, Michael; Roberts, T; Yoshikawa, C; Derbenev, Yaroslav; Morozov, Vasiliy; Kashikhin, V S; Lopes, Mattlock; Tollestrup, A; Yonehara, Katsuya; Zloblin, A

    2013-06-01

    The Helical Cooling Channel (HCC) achieves effective ionization cooling of the six-dimensional (6d) phase space of a muon beam by means of a series of 21st century inventions. In the HCC, hydrogen-pressurized RF cavities enable high RF gradients in strong external magnetic fields. The theory of the HCC, which requires a magnetic field with solenoid, helical dipole, and helical quadrupole components, demonstrates that dispersion in the gaseous hydrogen energy absorber provides effective emittance exchange to enable longitudinal ionization cooling. The 10-year development of a practical implementation of a muon-beam cooling device has involved a series of technical innovations and experiments that imply that an HCC of less than 300 m length can cool the 6d emittance of a muon beam by six orders of magnitude. We describe the design and construction plans for a prototype HCC module based on oxygen-doped hydrogen-pressurized RF cavities that are loaded with dielectric, fed by magnetrons, and operate in a superconducting helical solenoid magnet.

  12. 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.

  13. The Effects of Spatial Smoothing on Solar Magnetic Helicity and the Hemispheric Helicity Sign Rule

    NASA Astrophysics Data System (ADS)

    Koch Ocker, Stella; Petrie, Gordon

    2016-05-01

    The hemispheric sign rule for solar magnetic helicity, which states that negative/positive helicity occurs preferentially in the northern/southern hemisphere, provides clues to the causes of twisted, flaring magnetic fields. However, previous studies on the hemisphere rule may have been significantly affected by seeing from atmospheric turbulent motions. Using Hinode/SOT-SP data spanning from 2006 to 2012, we studied the effects of two important data processing steps that imitate the effects of atmospheric seeing: noise reduction by ignoring pixel values that are weaker than the estimated noise threshold, and Gaussian spatial smoothing. We applied these processing techniques to the helicity distribution maps for active regions NOAA 11158 and NOAA 11243, along with the average helicities of 36 active regions, in order to imitate and understand the effects of seeing from atmospheric turbulence. We found that rather than changing trends in the helicity distributions, Gaussian smoothing and noise reduction enhanced existing trends by pushing outliers towards the mean or removing them altogether. We also found that, when separated for weak and strong magnetic fields, the average helicities of the 36 active regions conformed to the hemisphere rule for weak field helicities and breached the rule for strong field helicities. In general, we found that data processing did not affect whether the hemisphere rule held for data taken from space-based instruments, and thus that seeing from atmospheric turbulence did not significantly affect previous studies' ground-based results on the hemisphere rule. This work was carried out through the National Solar Observatory Research Experiences for Undergraduates (REU) Program, which is funded by the National Science Foundation (NSF). The National Solar Observatory is operated by the Association of Universities for Research in Astronomy, Inc. (AURA) under cooperative agreement with the NSF.

  14. Solid Phase Synthesis of Helically Folded Aromatic Oligoamides.

    PubMed

    Dawson, S J; Hu, X; Claerhout, S; Huc, I

    2016-01-01

    Aromatic amide foldamers constitute a growing class of oligomers that adopt remarkably stable folded conformations. The folded structures possess largely predictable shapes and open the way toward the design of synthetic mimics of proteins. Important examples of aromatic amide foldamers include oligomers of 7- or 8-amino-2-quinoline carboxylic acid that have been shown to exist predominantly as well-defined helices, including when they are combined with α-amino acids to which they may impose their folding behavior. To rapidly iterate their synthesis, solid phase synthesis (SPS) protocols have been developed and optimized for overcoming synthetic difficulties inherent to these backbones such as low nucleophilicity of amine groups on electron poor aromatic rings and a strong propensity of even short sequences to fold on the solid phase during synthesis. For example, acid chloride activation and the use of microwaves are required to bring coupling at aromatic amines to completion. Here, we report detailed SPS protocols for the rapid production of: (1) oligomers of 8-amino-2-quinolinecarboxylic acid; (2) oligomers containing 7-amino-8-fluoro-2-quinolinecarboxylic acid; and (3) heteromeric oligomers of 8-amino-2-quinolinecarboxylic acid and α-amino acids. SPS brings the advantage to quickly produce sequences having varied main chain or side chain components without having to purify multiple intermediates as in solution phase synthesis. With these protocols, an octamer could easily be synthesized and purified within one to two weeks from Fmoc protected amino acid monomer precursors. PMID:27586338

  15. Numerical simulations of heavily polluted fine-grained sediment remobilization using 1D, 1D+, and 2D channel schematization.

    PubMed

    Kaiglová, Jana; Langhammer, Jakub; Jiřinec, Petr; Janský, Bohumír; Chalupová, Dagmar

    2015-03-01

    This article used various hydrodynamic and sediment transport models to analyze the potential and the limits of different channel schematizations. The main aim was to select and evaluate the most suitable simulation method for fine-grained sediment remobilization assessment. Three types of channel schematization were selected to study the flow potential for remobilizing fine-grained sediment in artificially modified channels. Schematization with a 1D cross-sectional horizontal plan, a 1D+ approach, splitting the riverbed into different functional zones, and full 2D mesh, adopted in MIKE by the DHI modeling suite, was applied to the study. For the case study, a 55-km stretch of the Bílina River, in the Czech Republic, Central Europe, which has been heavily polluted by the chemical and coal mining industry since the mid-twentieth century, was selected. Long-term exposure to direct emissions of toxic pollutants including heavy metals and persistent organic pollutants (POPs) resulted in deposits of pollutants in fine-grained sediments in the riverbed. Simulations, based on three hydrodynamic model schematizations, proved that for events not exceeding the extent of the riverbed profile, the 1D schematization can provide comparable results to a 2D model. The 1D+ schematization can improve accuracy while keeping the benefits of high-speed simulation and low requirements of input DEM data, but the method's suitability is limited by the channel properties. PMID:25687259

  16. TCTEX1D4, a novel protein phosphatase 1 interactor: connecting the phosphatase to the microtubule network

    PubMed Central

    Korrodi-Gregório, Luís; Vieira, Sandra I.; Esteves, Sara L. C.; Silva, Joana V.; Freitas, Maria João; Brauns, Ann-Kristin; Luers, Georg; Abrantes, Joana; Esteves, Pedro J.; da Cruz e Silva, Odete A. B.; Fardilha, Margarida; da Cruz e Silva, Edgar F.

    2013-01-01

    Summary Reversible phosphorylation plays an important role as a mechanism of intracellular control in eukaryotes. PPP1, a major eukaryotic Ser/Thr-protein phosphatase, acquires its specificity by interacting with different protein regulators, also known as PPP1 interacting proteins (PIPs). In the present work we characterized a physiologically relevant PIP in testis. Using a yeast two-hybrid screen with a human testis cDNA library, we identified a novel PIP of PPP1CC2 isoform, the T-complex testis expressed protein 1 domain containing 4 (TCTEX1D4) that has recently been described as a Tctex1 dynein light chain family member. The overlay assays confirm that TCTEX1D4 interacts with the different spliced isoforms of PPP1CC. Also, the binding domain occurs in the N-terminus, where a consensus PPP1 binding motif (PPP1BM) RVSF is present. The distribution of TCTEX1D4 in testis suggests its involvement in distinct functions, such as TGFβ signaling at the blood–testis barrier and acrosome cap formation. Immunofluorescence in human ejaculated sperm shows that TCTEX1D4 is present in the flagellum and in the acrosome region of the head. Moreover, TCTEX1D4 and PPP1 co-localize in the microtubule organizing center (MTOC) and microtubules in cell cultures. Importantly, the TCTEX1D4 PPP1BM seems to be relevant for complex formation, for PPP1 retention in the MTOC and movement along microtubules. These novel results open new avenues to possible roles of this dynein, together with PPP1. In essence TCTEX1D4/PPP1C complex appears to be involved in microtubule dynamics, sperm motility, acrosome reaction and in the regulation of the blood–testis barrier. PMID:23789093

  17. 1-D Numerical Analysis of ABCC Engine Performance

    NASA Technical Reports Server (NTRS)

    Holden, Richard

    1999-01-01

    ABCC engine combines air breathing and rocket engine into a single engine to increase the specific impulse over an entire flight trajectory. Except for the heat source, the basic operation of the ABCC is similar to the basic operation of the RBCC engine. The ABCC is intended to have a higher specific impulse than the RBCC for single stage Earth to orbit vehicle. Computational fluid dynamics (CFD) is a useful tool for the analysis of complex transport processes in various components in ABCC propulsion system. The objective of the present research was to develop a transient 1-D numerical model using conservation of mass, linear momentum, and energy equations that could be used to predict flow behavior throughout a generic ABCC engine following a flight path. At specific points during the development of the 1-D numerical model a myriad of tests were performed to prove the program produced consistent, realistic numbers that follow compressible flow theory for various inlet conditions.

  18. Phase diagram of a bulk 1d lattice Coulomb gas

    NASA Astrophysics Data System (ADS)

    Démery, V.; Monsarrat, R.; Dean, D. S.; Podgornik, R.

    2016-01-01

    The exact solution, via transfer matrix, of the simple one-dimensional lattice Coulomb gas (1d LCG) model can reproduce peculiar features of ionic liquid capacitors, such as overscreening, layering, and camel- and bell-shaped capacitance curves. Using the same transfer matrix method, we now compute the bulk properties of the 1d LCG in the constant voltage ensemble. We unveil a phase diagram with rich structure exhibiting low-density disordered and high-density ordered phases, separated by a first-order phase transition at low temperature; the solid state at full packing can be ordered or not, depending on the temperature. This phase diagram, which is strikingly similar to its three-dimensional counterpart, also sheds light on the behaviour of the confined system.

  19. 1D Josephson quantum interference grids: diffraction patterns and dynamics

    NASA Astrophysics Data System (ADS)

    Lucci, M.; Badoni, D.; Corato, V.; Merlo, V.; Ottaviani, I.; Salina, G.; Cirillo, M.; Ustinov, A. V.; Winkler, D.

    2016-02-01

    We investigate the magnetic response of transmission lines with embedded Josephson junctions and thus generating a 1D underdamped array. The measured multi-junction interference patterns are compared with the theoretical predictions for Josephson supercurrent modulations when an external magnetic field couples both to the inter-junction loops and to the junctions themselves. The results provide a striking example of the analogy between Josephson phase modulation and 1D optical diffraction grid. The Fiske resonances in the current-voltage characteristics with voltage spacing {Φ0}≤ft(\\frac{{\\bar{c}}}{2L}\\right) , where L is the total physical length of the array, {Φ0} the magnetic flux quantum and \\bar{c} the speed of light in the transmission line, demonstrate that the discrete line supports stable dynamic patterns generated by the ac Josephson effect interacting with the cavity modes of the line.

  20. Morphodynamics and sediment tracers in 1-D (MAST-1D): 1-D sediment transport that includes exchange with an off-channel sediment reservoir

    NASA Astrophysics Data System (ADS)

    Lauer, J. Wesley; Viparelli, Enrica; Piégay, Hervé

    2016-07-01

    Bed material transported in geomorphically active gravel bed rivers often has a local source at nearby eroding banks and ends up sequestered in bars not far downstream. However, most 1-D numerical models for gravel transport assume that gravel originates from and deposits on the channel bed. In this paper, we present a 1-D framework for simulating morphodynamic evolution of bed elevation and size distribution in a gravel-bed river that actively exchanges sediment with its floodplain, which is represented as an off-channel sediment reservoir. The model is based on the idea that sediment enters the channel at eroding banks whose elevation depends on total floodplain sediment storage and on the average elevation of the floodplain relative to the channel bed. Lateral erosion of these banks occurs at a specified rate that can represent either net channel migration or channel widening. Transfer of material out of the channel depends on a typical bar thickness and a specified lateral exchange rate due either to net channel migration or narrowing. The model is implemented using an object oriented framework that allows users to explore relationships between bank supply, bed structure, and lateral change rates. It is applied to a ∼50-km reach of the Ain River, France, that experienced significant reduction in sediment supply due to dam construction during the 20th century. Results are strongly sensitive to lateral exchange rates, showing that in this reach, the supply of sand and gravel at eroding banks and the sequestration of gravel in point bars can have strong influence on overall reach-scale sediment budgets.

  1. The structure of aquaporin-1 at 4.5-A resolution reveals short alpha-helices in the center of the monomer.

    PubMed

    Mitsuoka, K; Murata, K; Walz, T; Hirai, T; Agre, P; Heymann, J B; Engel, A; Fujiyoshi, Y

    1999-12-01

    Aquaporin-1 is a water channel found in mammalian red blood cells that is responsible for high water permeability of its membrane. Our electron crystallographic analysis of the three-dimensional structure of aquaporin-1 at 4.5-A resolution confirms the previous finding that each subunit consists of a right-handed bundle of six highly tilted transmembrane helices that surround a central X-shaped structure. In our new potential map, the rod-like densities for the transmembrane helices show helically arranged protrusions, indicating the positions of side chains. Thus, in addition to the six transmembrane helices, observation of helically arranged side-chain densities allowed the identification of two short alpha-helices representing the two branches of the central X-shaped structure that extend to the extracellular and cytoplasmic membrane surfaces. The other two branches are believed to be loops connecting the short alpha-helix to a neighboring transmembrane helix. A pore found close to the center of the aquaporin-1 monomer is suggested to be the course of water flow with implications for the water selectivity. PMID:10600556

  2. Enhancing Solar Cell Efficiencies through 1-D Nanostructures

    PubMed Central

    2009-01-01

    The current global energy problem can be attributed to insufficient fossil fuel supplies and excessive greenhouse gas emissions resulting from increasing fossil fuel consumption. The huge demand for clean energy potentially can be met by solar-to-electricity conversions. The large-scale use of solar energy is not occurring due to the high cost and inadequate efficiencies of existing solar cells. Nanostructured materials have offered new opportunities to design more efficient solar cells, particularly one-dimensional (1-D) nanomaterials for enhancing solar cell efficiencies. These 1-D nanostructures, including nanotubes, nanowires, and nanorods, offer significant opportunities to improve efficiencies of solar cells by facilitating photon absorption, electron transport, and electron collection; however, tremendous challenges must be conquered before the large-scale commercialization of such cells. This review specifically focuses on the use of 1-D nanostructures for enhancing solar cell efficiencies. Other nanostructured solar cells or solar cells based on bulk materials are not covered in this review. Major topics addressed include dye-sensitized solar cells, quantum-dot-sensitized solar cells, and p-n junction solar cells.

  3. Constructing 3D interaction maps from 1D epigenomes

    PubMed Central

    Zhu, Yun; Chen, Zhao; Zhang, Kai; Wang, Mengchi; Medovoy, David; Whitaker, John W.; Ding, Bo; Li, Nan; Zheng, Lina; Wang, Wei

    2016-01-01

    The human genome is tightly packaged into chromatin whose functional output depends on both one-dimensional (1D) local chromatin states and three-dimensional (3D) genome organization. Currently, chromatin modifications and 3D genome organization are measured by distinct assays. An emerging question is whether it is possible to deduce 3D interactions by integrative analysis of 1D epigenomic data and associate 3D contacts to functionality of the interacting loci. Here we present EpiTensor, an algorithm to identify 3D spatial associations within topologically associating domains (TADs) from 1D maps of histone modifications, chromatin accessibility and RNA-seq. We demonstrate that active promoter–promoter, promoter–enhancer and enhancer–enhancer associations identified by EpiTensor are highly concordant with those detected by Hi-C, ChIA-PET and eQTL analyses at 200 bp resolution. Moreover, EpiTensor has identified a set of interaction hotspots, characterized by higher chromatin and transcriptional activity as well as enriched TF and ncRNA binding across diverse cell types, which may be critical for stabilizing the local 3D interactions. PMID:26960733

  4. Constructing 3D interaction maps from 1D epigenomes.

    PubMed

    Zhu, Yun; Chen, Zhao; Zhang, Kai; Wang, Mengchi; Medovoy, David; Whitaker, John W; Ding, Bo; Li, Nan; Zheng, Lina; Wang, Wei

    2016-01-01

    The human genome is tightly packaged into chromatin whose functional output depends on both one-dimensional (1D) local chromatin states and three-dimensional (3D) genome organization. Currently, chromatin modifications and 3D genome organization are measured by distinct assays. An emerging question is whether it is possible to deduce 3D interactions by integrative analysis of 1D epigenomic data and associate 3D contacts to functionality of the interacting loci. Here we present EpiTensor, an algorithm to identify 3D spatial associations within topologically associating domains (TADs) from 1D maps of histone modifications, chromatin accessibility and RNA-seq. We demonstrate that active promoter-promoter, promoter-enhancer and enhancer-enhancer associations identified by EpiTensor are highly concordant with those detected by Hi-C, ChIA-PET and eQTL analyses at 200 bp resolution. Moreover, EpiTensor has identified a set of interaction hotspots, characterized by higher chromatin and transcriptional activity as well as enriched TF and ncRNA binding across diverse cell types, which may be critical for stabilizing the local 3D interactions. PMID:26960733

  5. Development of 1D Liner Compression Code for IDL

    NASA Astrophysics Data System (ADS)

    Shimazu, Akihisa; Slough, John; Pancotti, Anthony

    2015-11-01

    A 1D liner compression code is developed to model liner implosion dynamics in the Inductively Driven Liner Experiment (IDL) where FRC plasmoid is compressed via inductively-driven metal liners. The driver circuit, magnetic field, joule heating, and liner dynamics calculations are performed at each time step in sequence to couple these effects in the code. To obtain more realistic magnetic field results for a given drive coil geometry, 2D and 3D effects are incorporated into the 1D field calculation through use of correction factor table lookup approach. Commercial low-frequency electromagnetic fields solver, ANSYS Maxwell 3D, is used to solve the magnetic field profile for static liner condition at various liner radius in order to derive correction factors for the 1D field calculation in the code. The liner dynamics results from the code is verified to be in good agreement with the results from commercial explicit dynamics solver, ANSYS Explicit Dynamics, and previous liner experiment. The developed code is used to optimize the capacitor bank and driver coil design for better energy transfer and coupling. FRC gain calculations are also performed using the liner compression data from the code for the conceptual design of the reactor sized system for fusion energy gains.

  6. “Size-selectivity” in the template-directed assembly of dinuclear triple-stranded helicates

    PubMed Central

    Albrecht, Markus; Blau, Oliver; Fröhlich, Roland

    2002-01-01

    The self-assembly of supramolecular structures depends on a subtle interplay of a series of different control mechanisms. The geometric as well as electronic complementarity of the molecular building blocks is crucial for the specific formation of defined supramolecular species. In addition, secondary effects, like templating, also have an important function. The templating ability of different cations in the formation of triple-stranded helicate-type complexes from alkyl-bridged di(8-hydroxyquinoline) ligands is investigated by introduction of alkyl chains of different length as ligand spacers. Hereby a “size-selectivity” between the cations and the dinuclear helicate-type complexes {(ligand)3M2} is observed. Large cations support the formation of big dinuclear complexes, whereas small cations are able to template the formation of small complexes. PMID:11959938

  7. Modeling helical polymer brushes using self-consistent field theory (SCFT)

    NASA Astrophysics Data System (ADS)

    Mahalik, Jyoti; Sumpter, Bobby; Kumar, Rajeev

    We investigate structure of helical polymer brushes in terms of segment density distribution and local helical ordering using SCFT. A flexible chain model with vector potential was used to model liquid crystalline-like ordering in the brushes. The effects of surface grafting density, polymer molecular weight and the solvent quality on the brush structure were investigated. For densely grafted polymer brushes or the brushes made up of high molecular weight polymers, immersed in good quality solvent, stronger orientational ordering was found near the edge of the brushes (i.e., far from the grafting surface). Furthermore, an increase in the orientational ordering near the grafted end was found with decrease in solvent quality or decrease in molecular weight and decrease in surface grafting density. Computer Science and Mathematics Division, Oak Ridge National Laboratory.

  8. Tailor-made designer helical peptides that induce mitochondrion-mediated cell death without necrosis.

    PubMed

    Nogami, Kagayaki; Takahama, Kentaro; Okushima, Ayako; Oyoshi, Takanori; Fujimoto, Kazuhisa; Inouye, Masahiko

    2014-11-24

    Managing protein-protein interactions is essential for resolving unknown biological events at the molecular level and developing drugs. We have designed and synthesized a side-chain-crosslinked helical peptides based on the binding domain of a pro-apoptotic protein (Bad) that induces programmed cell death. The peptide showed high helical content and bound to its target, Bcl-XL, more strongly than its non-crosslinked counterparts. When HeLa cells were incubated with the crosslinked peptide, the peptide entered the cytosol across the plasma membrane. The peptide formed a stable complex with Bcl-XL localized at the outer mitochondrial membrane, and this binding event caused the release of cytochrome c from the intermembrane space of mitochondria into the cytosol. This activated the caspase cascade: 70% of HeLa cells died by the apoptosis pathway (without evidence of necrosis).

  9. Molecular characterization of zebrafish Oatp1d1 (Slco1d1), a novel organic anion-transporting polypeptide.

    PubMed

    Popovic, Marta; Zaja, Roko; Fent, Karl; Smital, Tvrtko

    2013-11-22

    The organic anion-transporting polypeptide (OATP/Oatp) superfamily includes a group of polyspecific transporters that mediate transport of large amphipathic, mostly anionic molecules across cell membranes of eukaryotes. OATPs/Oatps are involved in the disposition and elimination of numerous physiological and foreign compounds. However, in non-mammalian species, the functional properties of Oatps remain unknown. We aimed to elucidate the role of Oatp1d1 in zebrafish to gain insights into the functional and structural evolution of the OATP1/Oatp1 superfamily. We show that diversification of the OATP1/Oatp1 family occurs after the emergence of jawed fish and that the OATP1A/Oatp1a and OATP1B/Oatp1b subfamilies appeared at the root of tetrapods. The Oatp1d subfamily emerged in teleosts and is absent in tetrapods. The zebrafish Oatp1d1 is similar to mammalian OATP1A/Oatp1a and OATP1B/Oatp1b members, with the main physiological role in transport and balance of steroid hormones. Oatp1d1 activity is dependent upon pH gradient, which could indicate bicarbonate exchange as a mode of transport. Our analysis of evolutionary conservation and structural properties revealed that (i) His-79 in intracellular loop 3 is conserved within OATP1/Oatp1 family and is crucial for the transport activity; (ii) N-glycosylation impacts membrane targeting and is conserved within the OATP1/Oatp1 family with Asn-122, Asn-133, Asn-499, and Asn-512 residues involved; (iii) the evolutionarily conserved cholesterol recognition interaction amino acid consensus motif is important for membrane localization; and (iv) Oatp1d1 is present in dimeric and possibly oligomeric form in the cell membrane. In conclusion, we describe the first detailed characterization of a new Oatp transporter in zebrafish, offering important insights into the functional evolution of the OATP1/Oatp1 family and the physiological role of Oatp1d1.

  10. Helical localized wave solutions of the scalar wave equation.

    PubMed

    Overfelt, P L

    2001-08-01

    A right-handed helical nonorthogonal coordinate system is used to determine helical localized wave solutions of the homogeneous scalar wave equation. Introducing the characteristic variables in the helical system, i.e., u = zeta - ct and v = zeta + ct, where zeta is the coordinate along the helical axis, we can use the bidirectional traveling plane wave representation and obtain sets of elementary bidirectional helical solutions to the wave equation. Not only are these sets bidirectional, i.e., based on a product of plane waves, but they may also be broken up into right-handed and left-handed solutions. The elementary helical solutions may in turn be used to create general superpositions, both Fourier and bidirectional, from which new solutions to the wave equation may be synthesized. These new solutions, based on the helical bidirectional superposition, are members of the class of localized waves. Examples of these new solutions are a helical fundamental Gaussian focus wave mode, a helical Bessel-Gauss pulse, and a helical acoustic directed energy pulse train. Some of these solutions have the interesting feature that their shape and localization properties depend not only on the wave number governing propagation along the longitudinal axis but also on the normalized helical pitch.

  11. Helical localized wave solutions of the scalar wave equation.

    PubMed

    Overfelt, P L

    2001-08-01

    A right-handed helical nonorthogonal coordinate system is used to determine helical localized wave solutions of the homogeneous scalar wave equation. Introducing the characteristic variables in the helical system, i.e., u = zeta - ct and v = zeta + ct, where zeta is the coordinate along the helical axis, we can use the bidirectional traveling plane wave representation and obtain sets of elementary bidirectional helical solutions to the wave equation. Not only are these sets bidirectional, i.e., based on a product of plane waves, but they may also be broken up into right-handed and left-handed solutions. The elementary helical solutions may in turn be used to create general superpositions, both Fourier and bidirectional, from which new solutions to the wave equation may be synthesized. These new solutions, based on the helical bidirectional superposition, are members of the class of localized waves. Examples of these new solutions are a helical fundamental Gaussian focus wave mode, a helical Bessel-Gauss pulse, and a helical acoustic directed energy pulse train. Some of these solutions have the interesting feature that their shape and localization properties depend not only on the wave number governing propagation along the longitudinal axis but also on the normalized helical pitch. PMID:11488494

  12. 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

  13. 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.

  14. A Helical Polyphenylacetylene Having Amino Alcohol Moieties Without Chiral Side Groups as a Chiral Ligand for the Asymmetric Addition of Diethylzinc to Benzaldehyde.

    PubMed

    Liu, Lijia; Long, Qing; Aoki, Toshiki; Zhang, Geng; Kaneko, Takashi; Teraguchi, Masahiro; Zhang, Chunhong; Wang, Yudan

    2015-08-01

    One-handed helical polyphenylacetylenes having achiral amino alcohol moieties, but no chiral side groups, were synthesized by the helix-sense-selective copolymerization of an achiral phenylacetylene having an amino alcohol side group with a phenylacetylene having two hydroxyl groups. Since the resulting helical copolymers were successfully utilized as chiral ligands for the enantioselective alkylation of benzaldehyde with diethylzinc, we can conclude that the main-chain chirality based on the one-handed helical conformation is useful for the chiral catalysis of an asymmetric reaction for the first time. The enantioselectivities of the reaction were controlled by the optical purities of the helical polymer ligands. In addition, the polymer ligands could be easily recovered by precipitation after the reaction.

  15. Polychalcogenophosphate flux synthesis of 1D-KInP 2Se 6 and 1D and 3D-NaCrP 2S 6

    NASA Astrophysics Data System (ADS)

    Coste, Servane; Kopnin, Evgeni; Evain, Michel; Jobic, Stéphane; Brec, Raymond; Chondroudis, Konstantinos; Kanatzidis, Mercouri G.

    2002-04-01

    Three new chalcogenophosphates, 1D-KInP 2Se 6 ( I), 1D-NaCrP 2S 6 ( II) and 3D-NaCrP 2S 6 ( III), have been synthesized and their structure determined from single crystal diffraction analysis. ( I) and ( II) crystallize in the monoclinic system (space group P2 1/n, No. 14) with cell parameters a=7.5112(11), b=6.4861(5), c=22.789(2) Å and β=98.912(16)° ( V=1096.9(2) Å 3), Z=4 and R/ Rw( F2)=0.0234/0.0387 (for 900 observed reflections and 92 refined parameters) for ( I) and a=7.0279(5), b=5.8797(2), c=21.2578(14) Å and β=92.110(3)° ( V=877.82(9) Å 3), Z=4 and R/ Rw( F2)=0.0572/0.1151 (for 1455 observed reflections and 92 refined parameters) for ( II). Both materials exhibit 1/ ∞[MP 2Q 6] - chains built upon [MQ 6] octahedra (M=In, Cr; Q=Se, S) sharing edges to define 1/ ∞[MQ 4] 5- zigzag fibers which are capped by tetradentate ethane-like [P 2Q 6] groups. ( III) crystallizes in the orthorhombic system (space group Fdd2, No. 43) with cell parameters a=10.9742(7), b=7.9828(6), c=20.8590(19) Å ( V=1827.3(4) Å 3), Z=8 and R/ Rw=0.0184/0.0378 (for 967 observed reflections and 47 refined parameters), and displays a three-dimensional framework arrangement. Its structure is similar to that of TiP 2S 6 where titanium atoms are substituted for the chromium, the sodium atoms being inserted in the empty tunnels to ensure the charge balance. The exfoliation properties of 1D-NaCrP 2S 6 in polar solvents are reported.

  16. Revisiting the Anderson Model with Power-Law Correlated Disorder in 1D and 2D

    NASA Astrophysics Data System (ADS)

    Petersen, Greg; Sandler, Nancy

    2011-03-01

    The dimensionality of a disordered system directly affects the critical energy where a localization/delocalization transition occurs. In non-interacting systems with uncorrelated disorder, it is widely known that all states in one-dimension are localized. However, for some correlations there exist transition energies similar to mobility edges or small subsets of extended states that are robust against disorder. In this talk, we will present results on the diffusion of a wavepacket in a power-law correlated random potential of the form < V (r) V (0) > =1/(a + r)α . We also report results for the participation ratio Pr =1/N 2 < |ai |4 > . Preliminary results for 1D chains support the existence of a mobility edge near the band center. Square and graphene lattices will also be discussed. This work has been supported by the NSF-PIRE mwn/ciam and NSF Grant DMR-0710581.

  17. Three 2D Ag(I)-framework isomers with helical structures controlled by the chirality of camphor-10-sulfonic acid.

    PubMed

    Guo, Peng

    2011-02-28

    Three 2D Ag(I)-framework isomers were constructed from enantiopure camphor-10-sulfonic acids or racemic camphor-10-sulfonic acids, together with achiral 4-aminobenzoic acids. In complex 1, (+)-camphor-10-sulfonic acids bridge the single left-handed helices that are made up of Ag ions and 4-aminobenzoic acids, generating a homochiral 2D layer. In such a structure, the interweaving of triple left-handed homohelices was also found. It is worth noting that the helicity of complex 2 could be controlled by the handedness of the camphor-10-sulfonic acid. In complex 2, there are right-handed helical structures, including single right-handed and triple right-handed helical structures connected by (-)-camphor-10-sulfonic acids. For a comparative study, (±)-camphor-10-sulfonic acids were utilized to synthesize complex 3, in which equal numbers of right-handed or left-handed double-helical chains are created. All the complexes were characterized by single-crystal X-ray structure determination, powder X-ray diffraction, IR, TGA and element analysis. Circular dichroism spectra of complexes 1 and 2 were been studied to confirm the fact that enantiopure bridging ligands do not racemize. PMID:21264423

  18. Three 2D Ag(I)-framework isomers with helical structures controlled by the chirality of camphor-10-sulfonic acid.

    PubMed

    Guo, Peng

    2011-02-28

    Three 2D Ag(I)-framework isomers were constructed from enantiopure camphor-10-sulfonic acids or racemic camphor-10-sulfonic acids, together with achiral 4-aminobenzoic acids. In complex 1, (+)-camphor-10-sulfonic acids bridge the single left-handed helices that are made up of Ag ions and 4-aminobenzoic acids, generating a homochiral 2D layer. In such a structure, the interweaving of triple left-handed homohelices was also found. It is worth noting that the helicity of complex 2 could be controlled by the handedness of the camphor-10-sulfonic acid. In complex 2, there are right-handed helical structures, including single right-handed and triple right-handed helical structures connected by (-)-camphor-10-sulfonic acids. For a comparative study, (±)-camphor-10-sulfonic acids were utilized to synthesize complex 3, in which equal numbers of right-handed or left-handed double-helical chains are created. All the complexes were characterized by single-crystal X-ray structure determination, powder X-ray diffraction, IR, TGA and element analysis. Circular dichroism spectra of complexes 1 and 2 were been studied to confirm the fact that enantiopure bridging ligands do not racemize.

  19. Universal low-energy physics in 1D strongly repulsive multi-component Fermi gases

    NASA Astrophysics Data System (ADS)

    Jiang, Yuzhu; He, Peng; Guan, Xi-Wen

    2016-04-01

    It has been shown (Yang and You 2011 Chin. Phys. Lett. 28 020503) that at zero temperature the ground state of the one-dimensional (1D) w-component Fermi gas coincides with that of the spinless Bose gas in the limit ω \\to ∞ . This behavior was experimentally evidenced through quasi-1D tightly trapping ultracold 173Yb atoms in a recent paper (Pagano et al 2014 Nat. Phys. 10 198). However, understanding of low-temperature behavior of Fermi gases with a repulsive interaction requires spin-charge separated conformal field theories of an effective Tomonaga-Luttinger liquid and an antiferromagnetic SU(w) Heisenberg spin chain. Here we analytically derive universal thermodynamics of 1D strongly repulsive fermionic gases with SU(w) symmetry via the Yang-Yang thermodynamic Bethe ansatz method. The analytical free energy and magnetic properties of the systems at low temperature in a weak magnetic field are obtained through the Wiener-Hopf method. In particular, the free energy essentially manifests the spin-charge separated conformal field theories for high-symmetry systems with arbitrary repulsive interaction strength. We also find that the sound velocity of the Fermi gases in the large w limit coincides with that for the spinless Bose gas, whereas the spin velocity vanishes quickly as w becomes large. This indicates strong suppression of the Fermi exclusion statistics by the commutativity feature among the w-component fermions with different spin states in the Tomonaga-Luttinger liquid phase. Moreover, the equations of state and critical behavior of physical quantities at finite temperature are analytically derived in terms of the polylogarithm functions in the quantum critical region.

  20. Vacuum systems for the ILC helical undulator

    SciTech Connect

    Malyshev, O. B.; Scott, D. J.; Bailey, I. R.; Barber, D. P.; Baynham, E.; Bradshaw, T.; Brummitt, A.; Carr, S.; Clarke, J. A.; Cooke, P.; Dainton, J. B.; Ivanyushenkov, Y.; Malysheva, L. I.; Moortgat-Pick, G. A.; Rochford, J.; Department of Physics, University of Liverpool Oxford St. Liverpool L69 7ZE; Cockcroft Institute, Warrington WA4 4AD

    2007-07-15

    The International Linear Collider (ILC) positron source uses a helical undulator to generate polarized photons of {approx}10 MeV at the first harmonic. Unlike many undulators used in synchrotron radiation sources, the ILC helical undulator vacuum chamber will be bombarded by photons, generated by the undulator, with energies mostly below that of the first harmonic. Achieving the vacuum specification of {approx}100 nTorr in a narrow chamber of 4-6 mm inner diameter, with a long length of 100-200 m, makes the design of the vacuum system challenging. This article describes the vacuum specifications and calculations of the flux and energy of photons irradiating the undulator vacuum chamber and considers possible vacuum system design solutions for two cases: cryogenic and room temperature.

  1. Properties of dc helicity injected tokamak plasmas

    SciTech Connect

    Darrow, D.S.; Ono, M.; Forest, C.B.; Greene, G.J.; Hwang, Y.S.; Park, H.K. ); Taylor, R.J.; Pribyl, P.A.; Evans, J.D.; Lai, K.F.; Liberati, J.R. )

    1990-06-01

    Several dc helicity injection experiments using an electron beam technique have been conducted on the Current Drive Experiment (CDX) (Phys. Rev. Lett. {bold 59}, 2165 (1987)) and the Continuous Current Tokamak (CCT) (Phys. Rev. Lett. {bold 63}, 2365 (1989)). The data strongly suggest that tokamak plasmas are being formed and maintained by this method. The largest currents driven to date are 1 kA in CDX ({ital q}{sub {ital a}} =5) and 6 kA in CCT ({ital q}{sub {ital a}} =3.5). An initial comparison of discharge properties with helicity theory indicates rough agreement. Current drive energy efficiencies are 9% and 23% of Ohmic efficiency in two cases analyzed. Strong radial electric fields are observed in these plasmas that cause poloidal rotation and, possibly, improved confinement.

  2. Helical Muon Beam Cooling Channel Engineering Design

    SciTech Connect

    Kashikhin, V.S.; Lopes, M.L.; Romanov, G.V.; Tartaglia, M.A.; Yonehara, K.; Yu, M.; Zlobin, A.V.; Flanagan, G.; Johnson, R.P.; Kazakevich, G.M.; Marhauser, F.; /MUONS Inc., Batavia

    2012-05-01

    The Helical Cooling Channel (HCC), a novel technique for six-dimensional (6D) ionization cooling of muon beams, has shown considerable promise based on analytic and simulation studies. However, the implementation of this revolutionary method of muon cooling requires new techniques for the integration of hydrogen-pressurized, high-power RF cavities into the low-temperature superconducting magnets of the HCC. We present the progress toward a conceptual design for the integration of 805 MHz RF cavities into a 10 T Nb{sub 3}Sn based HCC test section. We include discussions on the pressure and thermal barriers needed within the cryostat to maintain operation of the magnet at 4.2 K while operating the RF and energy absorber at a higher temperature. Additionally, we include progress on the Nb{sub 3}Sn helical solenoid design.

  3. Viscosity of Sheared Helical filament Suspensions

    NASA Astrophysics Data System (ADS)

    Sartucci, Matthew; Urbach, Jeff; Blair, Dan; Schwenger, Walter

    The viscosity of suspensions can be dramatically affected by high aspect ratio particles. Understanding these systems provides insight into key biological functions and can be manipulated for many technological applications. In this talk, the viscosity as a function of shear rate of suspensions of helical filaments is compared to that of suspensions of straight rod-like filaments. Our goal is to determine the impact of filament geometry on low volume fraction colloidal suspensions in order to identify strategies for altering viscosity with minimal volume fraction. In this research, the detached flagella of the bacteria Salmonella Typhimurium are used as a model system of helical filaments and compared to mutated straight flagella of the Salmonella. We compare rheological measurements of the suspension viscosity in response to shear flow and use a combination of the rheology and fluorescence microscopy to identify the microstructural changes responsible for the observed rheological response.

  4. Helicity of a toroidal vortex with swirl

    NASA Astrophysics Data System (ADS)

    Bannikova, E. Yu.; Kontorovich, V. M.; Poslavsky, S. A.

    2016-04-01

    Based on the solutions of the Bragg-Hawthorne equation, we discuss the helicity of a thin toroidal vortex in the presence of swirl, orbital motion along the torus directrix. The relation between the helicity and circulations along the small and large linked circumferences (the torus directrix and generatrix) is shown to depend on the azimuthal velocity distribution in the core of the swirling ring vortex. In the case of nonuniform swirl, this relation differs from the well-known Moffat relation, viz., twice the product of such circulations multiplied by the number of linkages. The results can find applications in investigating the vortices in planetary atmospheres and the motions in the vicinity of active galactic nuclei.

  5. A Helical Magnet Design for RHIC^*.

    NASA Astrophysics Data System (ADS)

    Willen, E.; Gupta, R.; Kelly, E.; Muratore, J.

    1997-05-01

    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. The project requires 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 design restraint is that the magnets operate at relatively low current (less than 500 amperes) in order to minimize the heat load from the current leads. A magnet has been developed that uses a small diameter superconducting cable wound into helical grooves machined into a thick-walled aluminum cylinder. The design and test results of this prototype magnet will be described. ^*Work supported by the U.S. Department of Energy.

  6. Guided wave helical ultrasonic tomography of pipes.

    PubMed

    Leonard, Kevin R; Hinders, Mark K

    2003-08-01

    Ultrasonic guided waves have been used for a wide variety of ultrasonic inspection techniques. We describe here a new variation called helical ultrasound tomography (HUT) that uses guided ultrasonic waves along with tomographic reconstruction algorithms that have been developed by seismologists for what they call "cross borehole" tomography. In HUT, the Lamb-like guided waves travel the various helical criss-cross paths between two parallel circumferential transducer arrays instead of the planar criss-cross seismic paths between two boreholes. Although the measurement itself is fairly complicated, the output of the tomographic reconstruction is a readily interpretable map of a quantity of interest such as pipe wall thickness. In this paper we demonstrate HUT via laboratory scans on steel pipe segments into which controlled thinnings have been introduced.

  7. Coherent electron transport in a helical nanotube

    NASA Astrophysics Data System (ADS)

    Liang, Guo-Hua; Wang, Yong-Long; Du, Long; Jiang, Hua; Kang, Guang-Zhen; Zong, Hong-Shi

    2016-09-01

    The quantum dynamics of carriers bound to helical tube surfaces is investigated in a thin-layer quantization scheme. By numerically solving the open-boundary Schrödinger equation in curvilinear coordinates, geometric effect on the coherent transmission spectra is analysed in the case of single propagating mode as well as multimode. It is shown that, the coiling endows the helical nanotube with different transport properties from a bent cylindrical surface. Fano resonance appears as a purely geometric effect in the conductance, the corresponding energy of quasibound state is obviously influenced by the torsion and length of the nanotube. We also find new plateaus in the conductance. The transport of double-degenerate mode in this geometry is reminiscent of the Zeeman coupling between the magnetic field and spin angular momentum in quasi-one-dimensional structure.

  8. Helical Tomotherapy for Parotid Gland Tumors

    SciTech Connect

    Lee, Tae Kyu; Rosen, Isaac I.; Gibbons, John P.; Fields, Robert S.; Hogstrom, Kenneth R.

    2008-03-01

    Purpose: To investigate helical tomotherapy (HT) intensity-modulated radiotherapy (IMRT) as a postoperative treatment for parotid gland tumors. Methods and Materials: Helical tomotherapy plans were developed for 4 patients previously treated with segmental multileaf collimator (SMLC) IMRT. A primary planning target volume (PTV64) and two secondary PTVs (PTV60, PTV54) were defined. The clinical goals from the SMLC plans were applied as closely as possible to the HT planning. The SMLC plans included bolus, whereas HT plans did not. Results: In general, the HT plans showed better target coverage and target dose homogeneity. The minimum doses to the desired coverage volume were greater, on average, in the HT plans for all the targets. Minimum PTV doses were larger, on average, in the HT plans by 4.6 Gy (p = 0.03), 4.8 Gy (p = 0.06), and 4.9 Gy (p = 0.06) for PTV64, PTV60, and PTV54, respectively. Maximum PTV doses were smaller, on average, by 2.9 Gy (p = 0.23), 3.2 Gy (p = 0.02), and 3.6 Gy (p = 0.03) for PTV64, PTV60, and PTV54, respectively. Average dose homogeneity index was statistically smaller in the HT plans, and conformity index was larger for PTV64 in 3 patients. Tumor control probabilities were higher for 3 of the 4 patients. Sparing of normal structures was comparable for the two techniques. There were no significant differences between the normal tissue complication probabilities for the HT and SMLC plans. Conclusions: Helical tomotherapy treatment plans were comparable to or slightly better than SMLC plans. Helical tomotherapy is an effective alternative to SMLC IMRT for treatment of parotid tumors.

  9. Automatic generation of tree level helicity amplitudes

    NASA Astrophysics Data System (ADS)

    Stelzer, T.; Long, W. F.

    1994-11-01

    The program MadGraph is presented which automatically generates postscript Feynman diagrams and Fortran code to calculate arbitrary tree level helicity amplitudes by calling HELAS[1] subroutines. The program is written in Fortran and is available in Unix and VMS versions. MadGraph currently includes standard model interactions of QCD and QFD, but is easily modified to include additional models such as supersymmetry.

  10. Automatic generation of tree level helicity amplitudes

    NASA Astrophysics Data System (ADS)

    Stelzer, T.; Long, W. F.

    1994-07-01

    The program MadGraph is presented which automatically generates postscript Feynman diagrams and Fortran code to calculate arbitrary tree level helicity amplitudes by calling HELAS[1] subroutines. The program is written in Fortran and is available in Unix and VMS versions. MadGraph currently includes standard model interactions of QCD and QFD, but is easily modified to include additional models such as supersymmetry.

  11. Field of a helical Siberian Snake

    SciTech Connect

    Luccio, A.

    1995-02-01

    To preserve the spin polarization of a beam of high energy protons in a circular accelerator, magnets with periodic magnetic field, called Siberian Snakes are being used. Recently, it was proposed to build Siberian Snakes with superconducting helical dipoles. In a helical, or twisted dipole, the magnetic field is perpendicular to the axis of the helix and rotates around it as one proceeds along the magnet. In an engineering study of a 4 Tesla helical snake, the coil geometry is derived, by twisting, from the geometry of a cosine superconducting dipole. While waiting for magnetic measurement data on such a prototype, an analytical expression for the field of the helice is important, to calculate the particle trajectories and the spin precession in the helix. This model will also allow to determine the optical characteristics of the snake, as an insertion in the lattice of the accelerator. In particular, one can calculate the integrated multipoles through the magnet and the equivalent transfer matrix. An expression for the field in the helix body, i.e., excluding the fringe field was given in a classical paper. An alternate expression can be found by elaborating on the treatment of the field of a transverse wiggler obtained under the rather general conditions that the variables are separable. This expression exactly satisfies Maxwell`s div and curl equations for a stationary field, {del} {center_dot} B = 0, {del} x B = 0. This approach is useful in that it will allow one to use much of the work already done on the problem of inserting wigglers and undulators in the lattice of a circular accelerator.

  12. Bacteria that glide with helical tracks

    PubMed Central

    Nan, Beiyan; McBride, Mark J.; Chen, Jing; Zusman, David R.; Oster, George

    2014-01-01

    Many bacteria glide smoothly on surfaces, but with no discernable propulsive organelles on their surface. Recent experiments with Myxococcus xanthus and Flavobacterium johnsoniae show that both distantly related bacterial species glide utilizing proteins that move in helical tracks, albeit with significantly different motility mechanisms. Both species utilize proton motive force for movement. However, the motors that power gliding in M. xanthus have been identified, while the F. johnsoniae motors remain to be discovered. PMID:24556443

  13. Helical Cerenkov effect, a novel radiation source

    SciTech Connect

    Soln, J. )

    1994-10-01

    The observability of the helical Cerenkov effect as a novel radiation source is discussed. Depending on the value of the index of refraction of the medium, the strength of the uniform magnetic field, and the electron beam energy, helical Cerenkov radiation can occur in the same spectral regions as the ordinary Cerenkov effect, that is, from microwave to visible wavelengths. From the kinematics point of view, the author argues that for a microwave wavelength of 10[sup [minus]1] cm this effect should be observable in a medium with an index of refraction of 1.4, with a beam energy of 3 MeV, and a uniform magnetic field of 4 T. On the specific level, however, for the sake of simplicity, he discusses the observability of this effect for visible light with the central wavelength of 5 [times] 10[sup [minus]5] cm which can be achieved with 2 MeV in beam energy, silica aerogel as a medium (with an index of refraction of 1.075), and uniform magnetic fields from 5 to 10 T. For a 10-T magnetic field, he calculates that in the visible region of 250 to 750 nm an electron will produce a photon per 10 cm of traveled length. As to the stimulated helical Cerenkov emission, the author estimates that respectable gains are possible even if the beam passes close to the dielectric rather than through it. In addition to being potentially a new radiation source, the helical Cerenkov effect could possibly be used as a detector of radiation by energetic electrons that are trapped in a medium by strong magnetic fields.

  14. Overview of the Helicity Injected Torus Program

    NASA Astrophysics Data System (ADS)

    Nelson, B. A.; Jarboe, T. R.; Hamp, W. T.; Izzo, V. A.; O'Neill, R. G.; Redd, A. J.; Sieck, P. E.; Smith, R. J.

    2004-11-01

    The Helicity Injected Torus with Steady Inductive Helicity Injection (SIHI) spheromak experiment (HIT-SI) [Jarboe, Fus. Tech., (36)1, p.85, 1999] addresses critical issues for spheromaks, including current drive, operation at high beta, and confinement. HIT-SI features an optimal high-beta plasma shape and current profile, steady-state operation, minimal plasma-wall interaction, and injected power always flowing into the plasma. HIT-SI has a ``bow-tie'' shaped 1 cm thick Cu flux conserver with major radius R = 0.33 m and axial extent of 0.57 m. A half torus helicity injector at each end of the flux conserver produces conjugate sinusoidal flux (4 MW peak) and loop voltages (20 MW peak) at 5 kHz by IGBT-based switching power amplifiers. Injector flux and loop voltages are phase controlled to maintain power flow always inward. Insulating breaks for the oscillating flux and loop voltage are provided by a novel double viton o-ring system. HIT-SI uses the diagnostic suite previously used by the HIT-II experiment, (presented in an accompanying poster.) Results and 3D MHD simulations will be presented.

  15. Magnetic Helical Microswimmers in Poiseuille Flow

    NASA Astrophysics Data System (ADS)

    Acemoglu, Alperen; Yesilyurt, Serhat

    2014-11-01

    We analyze the motion of artificial magnetic microswimmers which mimic the swimming of natural organisms at low Reynolds numbers. Artificial magnetic microswimmers consist of a rigidly connected helical tail and a magnetic head. Magnetic swimmers are actuated with three orthogonal electromagnetic coil pairs. The swimmer motion is examined in the laminar flow which is introduced to channel with syringe pump. We recorded videos for forward (pusher-like swimming / in the head direction) and backward (puller-like swimming / in the tail direction) motion of swimmers. Swimmers have non-stable helical trajectories for forward motion and stable straight trajectories for backward motion. The flow effects on trajectories are observed for swimmers with different geometric parameters in the circular channels. Experiment results show that helical wavelengths of the trajectories are affected with the flow. Additionally, the flow has more pronounced effect on the trajectories of the swimmers in wide channels. Moreover, circular confinement in narrow channels leads to more stable trajectories; in wide channels swimmers follow complex trajectories. A CFD model is used to compare experiments with simulations and to analyze the effects of hydrodynamic interactions.

  16. Helical swimming in viscoelastic and porous media

    NASA Astrophysics Data System (ADS)

    Liu, Bin

    2012-02-01

    Many bacteria swim by rotating helical flagella. These cells often live in polymer suspensions, which are viscoelastic. Recently there have been several theoretical and experimental studies showing that viscoelasticity can either enhance or suppress propulsion, depending on the details of the microswimmer. To help clarify this situation, we study experimentally the motility of the flagellum using a scaled-up model system - a motorized helical coil that rotates along its axial direction. A free-swimming speed is obtained when the net force on the helix is zero. When the helix is immersed in a viscoelastic (Boger) fluid, we find an increase in the force-free swimming speed as compared with the Newtonian case. The enhancement is maximized at a Deborah number of approximately one, and the magnitude depends not only on the elasticity of the fluid but also on the geometry of the helix. In the second part of my talk, I will discuss how spatial confinements, such as a porous medium, affect the flagellated swimming. For clarity, the porous media are modeled as cylindrical cavities with solid walls. A modified boundary element method allows us to investigate a situation that the helical flagella are very close to the wall, with high spatial resolution and relatively low computational cost. To our surprise, at fixed power consumption, a highly coiled flagellum swims faster in narrower confinements, while an elongated flagellum swims faster in a cavity with a wider opening. We try understanding these effects with simple physical pictures.

  17. Mechanical Resonances of Helically Coiled Carbon Nanowires

    NASA Astrophysics Data System (ADS)

    Saini, D.; Behlow, H.; Podila, R.; Dickel, D.; Pillai, B.; Skove, M. J.; Serkiz, S. M.; Rao, A. M.

    2014-07-01

    Despite their wide spread applications, the mechanical behavior of helically coiled structures has evaded an accurate understanding at any length scale (nano to macro) mainly due to their geometrical complexity. The advent of helically coiled micro/nanoscale structures in nano-robotics, nano-inductors, and impact protection coatings has necessitated the development of new methodologies for determining their shear and tensile properties. Accordingly, we developed a synergistic protocol which (i) integrates analytical, numerical (i.e., finite element using COMSOL®) and experimental (harmonic detection of resonance; HDR) methods to obtain an empirically validated closed form expression for the shear modulus and resonance frequency of a singly clamped helically coiled carbon nanowire (HCNW), and (ii) circumvents the need for solving 12th order differential equations. From the experimental standpoint, a visual detection of resonances (using in situ scanning electron microscopy) combined with HDR revealed intriguing non-planar resonance modes at much lower driving forces relative to those needed for linear carbon nanotube cantilevers. Interestingly, despite the presence of mechanical and geometrical nonlinearities in the HCNW resonance behavior the ratio of the first two transverse modes f2/f1 was found to be similar to the ratio predicted by the Euler-Bernoulli theorem for linear cantilevers.

  18. Helical antimicrobial polypeptides with radial amphiphilicity

    PubMed Central

    Xiong, Menghua; Lee, Michelle W.; Mansbach, Rachael A.; Song, Ziyuan; Bao, Yan; Peek, Richard M.; Yao, Catherine; Chen, Lin-Feng; Ferguson, Andrew L.; Wong, Gerard C. L.; Cheng, Jianjun

    2015-01-01

    α-Helical antimicrobial peptides (AMPs) generally have facially amphiphilic structures that may lead to undesired peptide interactions with blood proteins and self-aggregation due to exposed hydrophobic surfaces. Here we report the design of a class of cationic, helical homo-polypeptide antimicrobials with a hydrophobic internal helical core and a charged exterior shell, possessing unprecedented radial amphiphilicity. The radially amphiphilic structure enables the polypeptide to bind effectively to the negatively charged bacterial surface and exhibit high antimicrobial activity against both gram-positive and gram-negative bacteria. Moreover, the shielding of the hydrophobic core by the charged exterior shell decreases nonspecific interactions with eukaryotic cells, as evidenced by low hemolytic activity, and protects the polypeptide backbone from proteolytic degradation. The radially amphiphilic polypeptides can also be used as effective adjuvants, allowing improved permeation of commercial antibiotics in bacteria and enhanced antimicrobial activity by one to two orders of magnitude. Designing AMPs bearing this unprecedented, unique radially amphiphilic structure represents an alternative direction of AMP development; radially amphiphilic polypeptides may become a general platform for developing AMPs to treat drug-resistant bacteria. PMID:26460016

  19. Mechanical Resonances of Helically Coiled Carbon Nanowires

    PubMed Central

    Saini, D.; Behlow, H.; Podila, R.; Dickel, D.; Pillai, B.; Skove, M. J.; Serkiz, S. M.; Rao, A. M.

    2014-01-01

    Despite their wide spread applications, the mechanical behavior of helically coiled structures has evaded an accurate understanding at any length scale (nano to macro) mainly due to their geometrical complexity. The advent of helically coiled micro/nanoscale structures in nano-robotics, nano-inductors, and impact protection coatings has necessitated the development of new methodologies for determining their shear and tensile properties. Accordingly, we developed a synergistic protocol which (i) integrates analytical, numerical (i.e., finite element using COMSOL®) and experimental (harmonic detection of resonance; HDR) methods to obtain an empirically validated closed form expression for the shear modulus and resonance frequency of a singly clamped helically coiled carbon nanowire (HCNW), and (ii) circumvents the need for solving 12th order differential equations. From the experimental standpoint, a visual detection of resonances (using in situ scanning electron microscopy) combined with HDR revealed intriguing non-planar resonance modes at much lower driving forces relative to those needed for linear carbon nanotube cantilevers. Interestingly, despite the presence of mechanical and geometrical nonlinearities in the HCNW resonance behavior the ratio of the first two transverse modes f2/f1 was found to be similar to the ratio predicted by the Euler-Bernoulli theorem for linear cantilevers. PMID:24986377

  20. Manipulation of wavefront using helical metamaterials.

    PubMed

    Yang, Zhenyu; Wang, Zhaokun; Tao, Huan; Zhao, Ming

    2016-08-01

    Helical metamaterials, a kind of 3-dimensional structure, has relatively strong coupling effect among the helical nano-wires. Therefore, it is expected to be a good candidate for generating phase shift and controlling wavefront with high efficiency. In this paper, using the finite-difference time-domain (FDTD) method, we studied the phase shift properties in the helical metamaterials. It is found that the phase shift occurs for both transmitted and reflected light waves. And the maximum of reflection coefficients can reach over 60%. In addition, the phase shift (φ) is dispersionless in the range of 600 nm to 860 nm, that is, it is only dominated by the initial angle (θ) of the helix. The relationship between them is φ = ± 2θ. Using Jones calculus we give a further explanation for these properties. Finally, by arranging the helixes in an array with a constant phase gradient, the phenomenon of anomalous refraction was also observed in a broad wavelength range. PMID:27505790

  1. Total scalp irradiation using helical tomotherapy

    SciTech Connect

    Orton, Nigel . E-mail: nporton@facstaff.wisc.edu; Jaradat, Hazim; Welsh, James; Tome, Wolfgang

    2005-09-30

    Homogeneous irradiation of the scalp poses technical and dosimetric challenges due to the extensive, superficial, curved treatment volume. Conventional treatments on a linear accelerator use multiple matched electron fields or a combination of electron and photon fields. Problems with these techniques include dose heterogeneity in the target due to varying source-to-skin distance (SSD) and angle of beam incidence, significant dose to the brain, and the potential for overdose or underdose at match lines between the fields. Linac-based intensity-modulated radiation therapy (IMRT) plans have similar problems. This work presents treatment plans for total scalp irradiation on a helical tomotherapy machine. Helical tomotherapy is well-suited for scalp irradiation because it has the ability to deliver beamlets that are tangential to the scalp at all points. Helical tomotherapy also avoids problems associated with field matching and use of more than one modality. Tomotherapy treatment plans were generated and are compared to plans for treatment of the same patient on a linac. The resulting tomotherapy plans show more homogeneous target dose and improved critical structure dose when compared to state-of-the-art linac techniques. Target equivalent uniform dose (EUD) for the best tomotherapy plan was slightly higher than for the linac plan, while the volume of brain tissue receiving over 30 Gy was reduced by two thirds. Furthermore, the tomotherapy plan can be more reliably delivered than linac treatments, because the patient is aligned prior to each treatment based on megavoltage computed tomography (MVCT)

  2. Nuclear design of Helical Cruciform Fuel rods

    SciTech Connect

    Shirvan, K.; Kazimi, M. S.

    2012-07-01

    In order to increase the power density of current and new light water reactor designs, the Helical Cruciform Fuel (HCF) rods are proposed. The HCF rods are equivalent to a cylindrical rod, with the fuel in a cruciform shaped, twisted axially. The HCF rods increase the surface area to volume ratio and inter-subchannel mixing behavior due to their cruciform and helical shapes, respectively. In a previous study, the HCF rods have shown the potential to up-rate existing PWRs by 50% and BWRs by 25%. However, HCF rods do display different neutronics modeling and performance. The cruciform cross section of HCF rods creates radially asymmetric heat generation and temperature distribution. The nominal HCF rod's beginning of life reactivity is reduced, compared to a cylindrical rod with the same fuel volume, by 500 pcm, due to increase in absorption in cladding. The rotation of these rods accounts for reactivity changes, which depends on the H/HM ratio of the pin cell. The HCF geometry shows large sensitivities to U{sup 235} or gadolinium enrichments compared to a cylindrical geometry. In addition, the gadolinium-containing HCF rods show a stronger effect on neighboring HCF rods than in case of cylindrical rods, depending on the orientation of the HCF rods. The helical geometry of the rods introduces axial shadowing of about 600 pcm, not seen in typical cylindrical rods. (authors)

  3. Quantifying foot deformation using finite helical angle.

    PubMed

    Pothrat, Claude; Goislard de Monsabert, Benjamin; Vigouroux, Laurent; Viehweger, Elke; Berton, Eric; Rao, Guillaume

    2015-10-15

    Foot intrinsic motion originates from the combination of numerous joint motions giving this segment a high adaptive ability. Existing foot kinematic models are mostly focused on analyzing small scale foot bone to bone motions which require both complex experimental methodology and complex interpretative work to assess the global foot functionality. This study proposes a method to assess the total foot deformation by calculating a helical angle from the relative motions of the rearfoot and the forefoot. This method required a limited number of retro-reflective markers placed on the foot and was tested for five different movements (walking, forefoot impact running, heel impact running, 90° cutting, and 180° U-turn) and 12 participants. Overtime intraclass correlation coefficients were calculated to quantify the helical angle pattern repeatability for each movement. Our results indicated that the method was suitable to identify the different motions as different amplitudes of helical angle were observed according to the flexibility required in each movement. Moreover, the results showed that the repeatability could be used to identify the mastering of each motion as this repeatability was high for well mastered movements. Together with existing methods, this new protocol could be applied to fully assess foot function in sport or clinical contexts.

  4. 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.

  5. Extended-Range Ultrarefractive 1D Photonic Crystal Prisms

    NASA Technical Reports Server (NTRS)

    Ting, David Z.

    2007-01-01

    A proposal has been made to exploit the special wavelength-dispersive characteristics of devices of the type described in One-Dimensional Photonic Crystal Superprisms (NPO-30232) NASA Tech Briefs, Vol. 29, No. 4 (April 2005), page 10a. A photonic crystal is an optical component that has a periodic structure comprising two dielectric materials with high dielectric contrast (e.g., a semiconductor and air), with geometrical feature sizes comparable to or smaller than light wavelengths of interest. Experimental superprisms have been realized as photonic crystals having three-dimensional (3D) structures comprising regions of amorphous Si alternating with regions of SiO2, fabricated in a complex process that included sputtering. A photonic crystal of the type to be exploited according to the present proposal is said to be one-dimensional (1D) because its contrasting dielectric materials would be stacked in parallel planar layers; in other words, there would be spatial periodicity in one dimension only. The processes of designing and fabricating 1D photonic crystal superprisms would be simpler and, hence, would cost less than do those for 3D photonic crystal superprisms. As in 3D structures, 1D photonic crystals may be used in applications such as wavelength-division multiplexing. In the extended-range configuration, it is also suitable for spectrometry applications. As an engineered structure or artificially engineered material, a photonic crystal can exhibit optical properties not commonly found in natural substances. Prior research had revealed several classes of photonic crystal structures for which the propagation of electromagnetic radiation is forbidden in certain frequency ranges, denoted photonic bandgaps. It had also been found that in narrow frequency bands just outside the photonic bandgaps, the angular wavelength dispersion of electromagnetic waves propagating in photonic crystal superprisms is much stronger than is the angular wavelength dispersion obtained

  6. Non-linearity in Bayesian 1-D magnetotelluric inversion

    NASA Astrophysics Data System (ADS)

    Guo, Rongwen; Dosso, Stan E.; Liu, Jianxin; Dettmer, Jan; Tong, Xiaozhong

    2011-05-01

    This paper applies a Bayesian approach to examine non-linearity for the 1-D magnetotelluric (MT) inverse problem. In a Bayesian formulation the posterior probability density (PPD), which combines data and prior information, is interpreted in terms of parameter estimates and uncertainties, which requires optimizing and integrating the PPD. Much work on 1-D MT inversion has been based on (approximate) linearized solutions, but more recently fully non-linear (numerical) approaches have been applied. This paper directly compares results of linearized and non-linear uncertainty estimation for 1-D MT inversion; to do so, advanced methods for both approaches are applied. In the non-linear formulation used here, numerical optimization is carried out using an adaptive-hybrid algorithm. Numerical integration applies Metropolis-Hastings sampling, rotated to a principal-component parameter space for efficient sampling of correlated parameters, and employing non-unity sampling temperatures to ensure global sampling. Since appropriate model parametrizations are generally not known a priori, both under- and overparametrized approaches are considered. For underparametrization, the Bayesian information criterion is applied to determine the number of layers consistent with the resolving power of the data. For overparametrization, prior information is included which favours simple structure in a manner similar to regularized inversion. The data variance and/or trade-off parameter regulating data and prior information are treated in several ways, including applying fixed optimal estimates (an empirical Bayesian approach) or including them as hyperparameters in the sampling (hierarchical Bayesian). The latter approach has the benefit of accounting for the uncertainty in the hyperparameters in estimating model parameter uncertainties. Non-linear and linearized inversion results are compared for synthetic test cases and for the measured COPROD1 MT data by considering marginal probability

  7. Viscous behavior in a quasi-1D fractal cluster glass.

    PubMed

    Etzkorn, S J; Hibbs, Wendy; Miller, Joel S; Epstein, A J

    2002-11-11

    The spin glass transition of a quasi-1D organic-based magnet ([MnTPP][TCNE]) is explored using both ac and dc measurements. A scaling analysis of the ac susceptibility shows a spin glass transition near 4 K, with a viscous decay of the thermoremanent magnetization recorded above 4 K. We propose an extension to a fractal cluster model of spin glasses that determines the dimension of the spin clusters (D) ranging from approximately 0.8 to over 1.5 as the glass transition is approached. Long-range dipolar interactions are suggested as the origin of this low value for the apparent lower critical dimension.

  8. Practical variational tomography for critical 1D systems

    NASA Astrophysics Data System (ADS)

    Lee, Jong Yeon; Landon-Cardinal, Olivier

    2015-03-01

    We further investigate a recently introduced efficient quantum state reconstruction procedure targeted to states well-approximated by the multi-scale entanglement renormalization ansatz (MERA). First, we introduce an improved optimization scheme that can be easily generalized for MERA states with larger bond dimension. Second, we provide a detailed analysis of the error propagation and quantify how it affects the distance between the experimental state and the reconstructed state. Third, we explain how to bound this distance using local data, providing an efficient scalable certification method. Fourth, we examine the performance of MERA tomography on the ground states of several 1D critical models.

  9. Structural stability of a 1D compressible viscoelastic fluid model

    NASA Astrophysics Data System (ADS)

    Huo, Xiaokai; Yong, Wen-An

    2016-07-01

    This paper is concerned with a compressible viscoelastic fluid model proposed by Öttinger. Although the model has a convex entropy, the Hessian matrix of the entropy does not symmetrize the system of first-order partial differential equations due to the non-conservative terms in the constitutive equation. We show that the corresponding 1D model is symmetrizable hyperbolic and dissipative and satisfies the Kawashima condition. Based on these, we prove the global existence of smooth solutions near equilibrium and justify the compatibility of the model with the Navier-Stokes equations.

  10. Deconvolution/identification techniques for 1-D transient signals

    SciTech Connect

    Goodman, D.M.

    1990-10-01

    This paper discusses a variety of nonparametric deconvolution and identification techniques that we have developed for application to 1-D transient signal problems. These methods are time-domain techniques that use direct methods for matrix inversion. Therefore, they are not appropriate for large data'' problems. These techniques involve various regularization methods and permit the use of certain kinds of a priori information in estimating the unknown. These techniques have been implemented in a package using standard FORTRAN that should make the package readily transportable to most computers. This paper is also meant to be an instruction manual for the package. 25 refs., 17 figs., 1 tab.

  11. Coherent thermal conductance of 1-D photonic crystals

    NASA Astrophysics Data System (ADS)

    Tschikin, Maria; Ben-Abdallah, Philippe; Biehs, Svend-Age

    2012-10-01

    We present an exact calculation of coherent thermal conductance in 1-D multilayer photonic crystals using the S-matrix method. In particular, we study the thermal conductance in a bilayer structure of Si/vacuum or Al2O3/vacuum slabs by means of the exact radiative heat flux expression. Based on the results obtained for the Al2O3/vacuum structure we show by comparison with previous works that the material losses and (localized) surface modes supported by the inner layers play a fundamental role and cannot be omitted in the definition of thermal conductance. Our results could have significant implications in the conception of efficient thermal barriers.

  12. ICPP: Results from Helical Axis Stellarators

    NASA Astrophysics Data System (ADS)

    Blackwell, B. D.

    2000-10-01

    Helical axis stellarators produce magnetic surfaces of high rotational transform and moderate shear solely by means of external currents, with the promise of high β. Several machines with quite different toroidal, helical, and ``bumpy'' Fourier components of magnetic field are now operating. The H-1 Heliac (1m, 1Tesla: Canberra, Australia), an M=3, low aspect ratio flexible heliac has been operated up to 0.5 Tesla with RF heating up to Ti ~ 100eV. Confinement transitions observed in this plasma exhibit many features of improved confinement regimes in tokamaks obtained at much larger power. ECH at 28GHz is being commissioned, and results from a suite of scattering, scalar and vector tomographic and multipoint probe and optical measurements will be presented. The M=4 Flexible Heliac ``TJ-II'' (1.5m, 1.2T: CIEMAT, Madrid) has accumulated a database of ECH plasma (1T) for a variety of configurations, (iota ~ 1.3--2.24) and a comprehensive set of diagnostics. Temperatures up to 2keV were measured by Thomson scattering/ECE. Observations include stored energy dependence, evidence of internal transport barriers, ELM-like bursts of magnetic activity and E×B sheared flows near rational surfaces in the plasma boundary. A new advanced configuration, the helical-axis heliotron, ``Heliotron J'' (1.2m, 1.5T: IAE, Kyoto University), the successor to Heliotron E, uses a ``bumpy'' magnetic component to improve high-energy particle confinement and reduce neoclassical transport. A combination of toroidal and helical coils produces a range of configurations. First plasma was successfully produced on December 1999, by ECH at 53GHz(2ω_ce). Following field mapping and final installation of diagnostics, the full experiment will start July 2000. The Helically Symmetric Experiment, ``HSX'' (Univ. Wisconsin, Madison) employs computer optimized non-planar coils to exploit a quasi-symmetry that minimizes toroidal magnetic field harmonics, confirmed by recent mapping of the drift orbits

  13. MH2c: Characterization of major histocompatibility α-helices - an information criterion approach

    NASA Astrophysics Data System (ADS)

    Hischenhuber, B.; Frommlet, F.; Schreiner, W.; Knapp, B.

    2012-07-01

    Major histocompatibility proteins share a common overall structure or peptide binding groove. Two binding groove domains, on the same chain for major histocompatibility class I or on two different chains for major histocompatibility class II, contribute to that structure that consists of two α-helices (“wall”) and a sheet of eight anti-parallel beta strands (“floor”). Apart from the peptide presented in the groove, the major histocompatibility α-helices play a central role for the interaction with the T cell receptor. This study presents a generalized mathematical approach for the characterization of these helices. We employed polynomials of degree 1 to 7 and splines with 1 to 2 nodes based on polynomials of degree 1 to 7 on the α-helices projected on their principal components. We evaluated all models with a corrected Akaike Information Criterion to determine which model represents the α-helices in the best way without overfitting the data. This method is applicable for both the stationary and the dynamic characterization of α-helices. By deriving differential geometric parameters from these models one obtains a reliable method to characterize and compare α-helices for a broad range of applications. Catalogue identifier: AELX_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AELX_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 327 565 No. of bytes in distributed program, including test data, etc.: 17 433 656 Distribution format: tar.gz Programming language: Matlab Computer: Personal computer architectures Operating system: Windows, Linux, Mac (all systems on which Matlab can be installed) RAM: Depends on the trajectory size, min. 1 GB (Matlab) Classification: 2.1, 4.9, 4.14 External routines: Curve Fitting Toolbox and Statistic Toolbox of

  14. Synthesis, crystal structure, and properties of a 1-D terbium-substituted monolacunary Keggin-type polyoxotungstate.

    PubMed

    Ma, Pengtao; Si, Yanan; Wan, Rong; Zhang, Shaowei; Wang, Jingping; Niu, Jingyang

    2015-03-01

    A new 1-D linear chainlike terbium-substituted polyoxometalate [Tb(H2O)2(α-PW11O39)](4-) (1) has been synthesized in aqueous solution and characterized by elemental analysis, inductively coupled plasma atomic emission spectrometry (ICP-AES), X-ray powder diffraction (XRPD), IR spectrum, thermal analysis, electrospray ionization mass spectrometry (ESI-MS), and X-ray single-crystal diffraction. X-ray structural analysis reveals that 1 displays a 1-D linear chain containing [Tb(H2O)2(α-PW11O39)](4-) moieties. The Tb(III) cation incorporated into the monolacunary Keggin-type [α-PW11O39](7-) unit resides in a distorted monocapped triangular prismatic geometry and acts as a linker to join two adjacent [α-PW11O39](7-) units to form a 1-D chain structure. Solid-state photoluminescent property of 1 has been investigated at room temperature and the photoluminescent emission mainly results from the synergistic effect of the Tb(III) cation and the Na7[α-PW11O39] precursor. The ESI-MS spectrum of 1 confirms that the polyanion [Tb(H2O)(HPW11O39)](3-) is stable in aqueous solution.

  15. 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.

  16. Faraday signature of magnetic helicity from reduced depolarization

    SciTech Connect

    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. 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.

  17. Evolution of field line helicity during magnetic reconnection

    NASA Astrophysics Data System (ADS)

    Russell, A. J. B.; Yeates, A. R.; Hornig, G.; Wilmot-Smith, A. L.

    2015-03-01

    We investigate the evolution of field line helicity for magnetic fields that connect two boundaries without null points, with emphasis on localized finite-B magnetic reconnection. Total (relative) magnetic helicity is already recognized as an important topological constraint on magnetohydrodynamic processes. Field line helicity offers further advantages because it preserves all topological information and can distinguish between different magnetic fields with the same total helicity. Magnetic reconnection changes field connectivity and field line helicity reflects these changes; the goal of this paper is to characterize that evolution. We start by deriving the evolution equation for field line helicity and examining its terms, also obtaining a simplified form for cases where dynamics are localized within the domain. The main result, which we support using kinematic examples, is that during localized reconnection in a complex magnetic field, the evolution of field line helicity is dominated by a work-like term that is evaluated at the field line endpoints, namely, the scalar product of the generalized field line velocity and the vector potential. Furthermore, the flux integral of this term over certain areas is very small compared to the integral of the unsigned quantity, which indicates that changes of field line helicity happen in a well-organized pairwise manner. It follows that reconnection is very efficient at redistributing helicity in complex magnetic fields despite having little effect on the total helicity.

  18. Evolution of field line helicity during magnetic reconnection

    SciTech Connect

    Russell, A. J. B. Hornig, G.; Wilmot-Smith, A. L.; Yeates, A. R.

    2015-03-15

    We investigate the evolution of field line helicity for magnetic fields that connect two boundaries without null points, with emphasis on localized finite-B magnetic reconnection. Total (relative) magnetic helicity is already recognized as an important topological constraint on magnetohydrodynamic processes. Field line helicity offers further advantages because it preserves all topological information and can distinguish between different magnetic fields with the same total helicity. Magnetic reconnection changes field connectivity and field line helicity reflects these changes; the goal of this paper is to characterize that evolution. We start by deriving the evolution equation for field line helicity and examining its terms, also obtaining a simplified form for cases where dynamics are localized within the domain. The main result, which we support using kinematic examples, is that during localized reconnection in a complex magnetic field, the evolution of field line helicity is dominated by a work-like term that is evaluated at the field line endpoints, namely, the scalar product of the generalized field line velocity and the vector potential. Furthermore, the flux integral of this term over certain areas is very small compared to the integral of the unsigned quantity, which indicates that changes of field line helicity happen in a well-organized pairwise manner. It follows that reconnection is very efficient at redistributing helicity in complex magnetic fields despite having little effect on the total helicity.

  19. 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. PMID:27572732

  20. Differential Recognition of CD1d-[alpha]-Galactosyl Ceramide by the V[beta]8.2 and V[beta]7 Semi-invariant NKT T Cell Receptors

    SciTech Connect

    Pellicci, Daniel G.; Patel, Onisha; Kjer-Nielsen, Lars; Pang, Siew Siew; Sullivan, Lucy C.; Kyparissoudis, Konstantinos; Brooks, Andrew G.; Reid, Hugh H.; Gras, Stephanie; Lucet, Isabelle S.; Koh, Ruide; Smyth, Mark J.; Mallevaey, Thierry; Matsuda, Jennifer L.; Gapin, Laurent; McCluskey, James; Godfrey, Dale I.; Rossjohn, Jamie; PMCI-A; Monash; UCHSC; Melbourne

    2009-09-02

    The semi-invariant natural killer T cell receptor (NKT TCR) recognizes CD1d-lipid antigens. Although the TCR{alpha} chain is typically invariant, the {beta} chain expression is more diverse, where three V{beta} chains are commonly expressed in mice. We report the structures of V{alpha}14-V{beta}8.2 and V{alpha}14-V{beta}7 NKT TCRs in complex with CD1d-{alpha}-galactosylceramide ({alpha}-GalCer) and the 2.5 {angstrom} structure of the human NKT TCR-CD1d-{alpha}-GalCer complex. Both V{beta}8.2 and V{beta}7 NKT TCRs and the human NKT TCR ligated CD1d-{alpha}-GalCer in a similar manner, highlighting the evolutionarily conserved interaction. However, differences within the V{beta} domains of the V{beta}8.2 and V{beta}7 NKT TCR-CD1d complexes resulted in altered TCR{beta}-CD1d-mediated contacts and modulated recognition mediated by the invariant {alpha} chain. Mutagenesis studies revealed the differing contributions of V{beta}8.2 and V{beta}7 residues within the CDR2{beta} loop in mediating contacts with CD1d. Collectively we provide a structural basis for the differential NKT TCR V{beta} usage in NKT cells.

  1. SMART Observation of Magnetic Helicity in Solar Filaments

    NASA Astrophysics Data System (ADS)

    Hagino, M.; Kitai, R.; Shibata, K.

    2006-08-01

    We examined the magnetic helicity of solar filaments from their structure in the chromosphere and corona. The H-alpha telescope of the Solar Magnetic Activity Research Telescope (SMART) observed 239 intermediate filaments from 2005 July 1 to 2006 May 15. The intermediate filament usually locates between two active regions. Using these images, we identified the filament spine and its barbs, and determined the chromospheric filament helicity from the mean angle between each barbs and a spine. We found that 71% (78 of 110) of intermediate filaments in the northern hemisphere are negative helicity and 67% (87 of 129) of filaments in the southern hemisphere are positive, which agreed with the well-known hemispheric tendency of the magnetic helicity. Additionally, we studied the coronal helicity of intermediate filaments. The coronal filament helicity is defined as the crossing angle of threads formed a filament. The helicity pattern of coronal filaments obtained with EIT/SOHO 171A also shows the helicity hemispheric tendency. Namely, 65% (71 of 110) of coronal filaments in the northern hemisphere exhibit negative helicity and the 65% (84 of 129) of filaments in the southern hemisphere show negative helicity. These data were observed in the same day with the SMART H-alpha data. Moreover, we found 12 filament eruptions in our data. The 7 of 12 filaments show the clear opposite sign of the hemispheric tendency of the magnetic helicity. The helicity seems to be change during temporal evolution. This results suggest that filament instability may be driven by the opposite sign helicity injection from the foot point of the barb.

  2. New Exact Relations for Helicities in Hall Magnetohydrodynamic Turbulence

    NASA Astrophysics Data System (ADS)

    Banerjee, Supratik; Galtier, Sebastien

    2016-04-01

    Hall magnetohydrodynamics is a mono-fluid plasma model appropriate for probing Final{some of the} physical processes (other than pure kinetic effects) at length scales smaller than the scales of standard MHD. In sub-ionic space plasma turbulence (e.g. the solar wind) this fluid model has been proved to be useful. Three-dimensional incompressible Hall magnetohydrodynamics (MHD) possesses three inviscid invariants which are the total energy, the magnetic helicity and the generalized helicity. In this presentation, we would like to discuss new exact relations for helicities (magnetic helicities and generalized helicities) which are derived for homogeneous stationary (not necessarily isotropic) Hall MHD turbulence (and also for its inertialess electron MHD limit) in the asymptotic limit of large Reynolds numbers. The universal laws are written only in terms of mixed second-order structure functions, i.e. the scalar product of two different increments and are written simply as ηM = di < δ ( {b} × {j}) \\cdot δ {b} >, with ηM the average magnetic helicity flux rate, {b} the magnetic field, {j} the current and ± ηG = < δ ( {v} × {Ω} ) \\cdot δ {Ω} > , with ηM the average generalized helicity flux rate, {v} the fluid velocity and {Ω} = {b} + dI {ω} being the generalized helicity where ω is simply the fluid vorticity ( = nabla × {v}). It provides, therefore, a direct measurement of the dissipation rates for the corresponding helicities even in case of an anisotropic plasma turbulence. This study shows that the generalized helicity cascade is strongly linked to the left polarized fluctuations while the magnetic helicity cascade is linked to the right polarized fluctuations. The newly derived relations also show that like energy, a non-zero helicity flux can only be associated to a departure of Beltrami flow state. {Reference} S. Banerjee & S. Galtier, {Chiral Exact Relations for Helicities in Hall Magnetohydrodynamic Turbulence} (submitted).

  3. Helical muon beam cooling channel engineering design

    SciTech Connect

    Johnson, Rolland

    2015-08-07

    The Helical Cooling Channel (HCC) achieves effective ionization cooling of the six-dimensional (6d) phase space of a muon beam by means of a series of 21st century inventions. In the HCC, hydrogen-pressurized RF cavities enable high RF gradients in strong external magnetic fields. The theory of the HCC, which requires a magnetic field with solenoid, helical dipole, and helical quadrupole components, demonstrates that dispersion in the gaseous hydrogen energy absorber provides effective emittance exchange to enable longitudinal ionization cooling. The 10-year development of a practical implementation of a muon-beam cooling device has involved a series of technical innovations and experiments that imply that an HCC of less than 300 m length can cool the 6d emittance of a muon beam by six orders of magnitude. We describe the design and construction plans for a prototype HCC module based on oxygen-doped hydrogen-pressurized RF cavities that are loaded with dielectric, fed by magnetrons, and operate in a superconducting helical solenoid magnet. The first phase of this project saw the development of a conceptual design for the integration of 805 MHz RF cavities into a 10 T Nb3Sn-based HS test section. Two very novel ideas are required to realize the design. The first idea is the use of dielectric inserts in the RF cavities to make them smaller for a given frequency so that the cavities and associated plumbing easily fit inside the magnet cryostat. Calculations indicate that heat loads will be tolerable, while RF breakdown of the dielectric inserts will be suppressed by the pressurized hydrogen gas. The second new idea is the use of a multi-layer Nb3Sn helical solenoid. The technology demonstrations for the two aforementioned key components of a 10T, 805 MHz HCC were begun in this project. The work load in the Fermilab Technical Division made it difficult to test a multi-layer Nb3Sn solenoid as originally planned. Instead, a complementary

  4. Fast Optimal Load Balancing Algorithms for 1D Partitioning

    SciTech Connect

    Pinar, Ali; Aykanat, Cevdet

    2002-12-09

    One-dimensional decomposition of nonuniform workload arrays for optimal load balancing is investigated. The problem has been studied in the literature as ''chains-on-chains partitioning'' problem. Despite extensive research efforts, heuristics are still used in parallel computing community with the ''hope'' of good decompositions and the ''myth'' of exact algorithms being hard to implement and not runtime efficient. The main objective of this paper is to show that using exact algorithms instead of heuristics yields significant load balance improvements with negligible increase in preprocessing time. We provide detailed pseudocodes of our algorithms so that our results can be easily reproduced. We start with a review of literature on chains-on-chains partitioning problem. We propose improvements on these algorithms as well as efficient implementation tips. We also introduce novel algorithms, which are asymptotically and runtime efficient. We experimented with data sets from two different applications: Sparse matrix computations and Direct volume rendering. Experiments showed that the proposed algorithms are 100 times faster than a single sparse-matrix vector multiplication for 64-way decompositions on average. Experiments also verify that load balance can be significantly improved by using exact algorithms instead of heuristics. These two findings show that exact algorithms with efficient implementations discussed in this paper can effectively replace heuristics.

  5. A simple quasi-1D model of Fibonacci anyons

    NASA Astrophysics Data System (ADS)

    Aasen, David; Mong, Roger; Clarke, David; Alicea, Jason; Fendley, Paul

    2015-03-01

    There exists various ways of understanding the topological properties of Ising anyons--from simple free-fermion toy models to formal topological quantum field theory. For other types of anyons simple toy models rarely exist; their properties have to be obtained using formal self-consistency relations. We explore a family of gapped 1D local bosonic models that in a certain limit become trivial to solve and provide an intuitive picture for Fibonacci anyons. One can interpret this model as a quasi-1D wire that forms the building block of a 2D topological phase with Fibonacci anyons. With this interpretation all topological properties of the Fibonacci anyons become manifest including ground state degeneracy and braid relations. We conjecture that the structure of the model is protected by an emergent symmetry analogous to fermion parity. 1) NSF Grant DMR-1341822 2) Institute for Quantum Information and Matter, an NSF physics frontier center with support from the Moore Foundation. 3) NSERC-PGSD.

  6. A 1D analysis of two high order MOC methods

    SciTech Connect

    Everson, M. S.; Forget, B.

    2012-07-01

    The work presented here provides two different methods for evaluating angular fluxes along long characteristics. One is based off a projection of the 1D transport equation onto a complete set of Legendre polynomials, while the other uses the 1D integral transport equation to evaluate the angular flux values at specific points along each track passing through a cell. The Moment Long Characteristic (M-LC) method is shown to provide 2(P+1) spatial convergence and significant gains in accuracy with the addition of only a few spatial degrees of freedom. The M-LC method, though, is shown to be ill-conditioned at very high order and for optically thin geometries. The Point Long Characteristic (P-LC) method, while less accurate, significantly improves stability to problems with optically thin cells. The P-LC method is also more flexible, allowing for extra angular flux evaluations along a given track to give a more accurate representation of the shape along each track. This is at the expense of increasing the degrees of freedom of the system, though, and requires an increase in memory storage. This work concludes that both may be used simultaneously within the same geometry to provide the best mix of accuracy and stability possible. (authors)

  7. Engineered atom-light interactions in 1D photonic crystals

    NASA Astrophysics Data System (ADS)

    Martin, Michael J.; Hung, Chen-Lung; Yu, Su-Peng; Goban, Akihisa; Muniz, Juan A.; Hood, Jonathan D.; Norte, Richard; McClung, Andrew C.; Meenehan, Sean M.; Cohen, Justin D.; Lee, Jae Hoon; Peng, Lucas; Painter, Oskar; Kimble, H. Jeff

    2014-05-01

    Nano- and microscale optical systems offer efficient and scalable quantum interfaces through enhanced atom-field coupling in both resonators and continuous waveguides. Beyond these conventional topologies, new opportunities emerge from the integration of ultracold atomic systems with nanoscale photonic crystals. One-dimensional photonic crystal waveguides can be engineered for both stable trapping configurations and strong atom-photon interactions, enabling novel cavity QED and quantum many-body systems, as well as distributed quantum networks. We present the experimental realization of such a nanophotonic quantum interface based on a nanoscale photonic crystal waveguide, demonstrating a fractional waveguide coupling of Γ1 D /Γ' of 0 . 32 +/- 0 . 08 , where Γ1 D (Γ') is the atomic emission rate into the guided (all other) mode(s). We also discuss progress towards intra-waveguide trapping of ultracold Cs. This work was supported by the IQIM, an NSF Physics Frontiers Center with support from the Moore Foundation, the DARPA ORCHID program, the AFOSR QuMPASS MURI, the DoD NSSEFF program, NSF, and the Kavli Nanoscience Institute (KNI) at Caltech.

  8. Reactions of HO2 with carbon monoxide and nitric oxide and of O/1 D/ with water.

    NASA Technical Reports Server (NTRS)

    Simonaitis, R.; Heicklen, J.

    1973-01-01

    Investigation of the reactions of the hydroperoxyl radical with carbon monoxide and nitric oxide in a static system, and reexamination of the reaction of O(1 D) with water. The HO2 radicals were generated by the photolysis of N2O at 2139 A in the presence of excess H2O or H2 and smaller amounts of CO and O2. The O(1 D) atoms produced from the photolysis of N2O react with H2O or with H2 to give OH radicals in the case of H2O or OH radicals and H atoms in the case of H2. With H2O, two OH radicals are produced for each O(1 D) removed at low pressures, but the OH yield drops as the pressure is raised. This drop is attributed to an insertion reaction which removes from 10 to 30% of the O(1 D) atoms at about 650 torr of H2O at 200 F. The OH radicals generated can react with either CO or H2 to produce H atoms, which then add to O2 to produce HO2. In the absence of NO, the HO2 radicals could react by two routes, while with NO present NO2 is produced in a long chain process.

  9. Rotatoelectricity in cholesteric side-chain liquid single crystal elastomers.

    PubMed

    Menzel, Andreas M; Brand, Helmut R

    2006-11-21

    We analyze the phenomenon of rotatoelectricity which is characteristic of cholesteric side-chain liquid single crystal elastomers. Using a linearized macroscopic continuum description and our previous work we show that if such a material is exposed to a static external electric field oriented parallel to the cholesteric helical axis, the director of the liquid crystalline phase will rotate around the helical axis. The material considered is assumed to be a perfect electric insulator. We propose an experiment in which the effect of rotatoelectricity should be directly observable and from which the ratio of the material parameters involved will be accessible.

  10. Resistive Interchange Modes Destabilized by Helically Trapped Energetic Ions in a Helical Plasma

    NASA Astrophysics Data System (ADS)

    Du, X. D.; Toi, K.; Osakabe, M.; Ohdachi, S.; Ido, T.; Tanaka, K.; Yokoyama, M.; Yoshinuma, M.; Ogawa, K.; Watanabe, K. Y.; Isobe, M.; Nagaoka, K.; Ozaki, T.; Sakakibara, S.; Seki, R.; Shimizu, A.; Suzuki, Y.; Tsuchiya, H.

    2015-04-01

    A new bursting m =1 /n =1 instability (m ,n : poloidal and toroidal mode numbers) with rapid frequency chirping down has been observed for the first time in a helical plasma with intense perpendicular neutral beam injection. This is destabilized in the plasma peripheral region by resonant interaction between helically trapped energetic ions and the resistive interchange mode. A large radial electric field is induced near the edge due to enhanced radial transport of the trapped energetic ions by the mode, and leads to clear change in toroidal plasma flow, suppression of microturbulence, and triggering an improvement of bulk plasma confinement.

  11. Theoretical modeling of peptide α-helical circular dichroism in aqueous solution.

    PubMed

    Kaminský, Jakub; Kubelka, Jan; Bour, Petr

    2011-03-10

    Reliable modeling of protein and peptide circular dichroism (CD) spectra in the far UV presents a challenge for current theoretical approaches. In this study, the time-dependent density functional theory (TDDFT), configuration interaction with single excitation (CIS), and transition dipole coupling (TDC) were used to assess the most important factors contributing to the CD spectra of the α-helical secondary structure. The dependence on the peptide chain length and also the role of the flexibility and solvent environment were investigated with a model oligopeptide Ac-(Ala)(N)-NH-Me, (N = 1, ..., 18). Both the TDDFT and TDC-like methods suggest that the CD curve typical for the α-helix arises gradually, but its basic characteristic is discernible already for peptides with 4-5 amino acid residues. The calculated dependence was in a qualitative agreement with experimental spectra of short α-helices stabilized by the histidine-metal binding. The TDDFT computations of the CD were found to be unusually sensitive to the basis set and solvent model. Explicit hydration and temperature fluctuations of the peptide geometry, simulated with the aid of molecular dynamics (MD), significantly influenced the CD and absorption spectral shapes. An extensive averaging over MD configurations is thus required to obtain a converged spectral profile in cluster simulations. On the other hand, both the TDDFT and TDC models indicate only a minor influence of the alanine side chains. The CIS and TDC calculations also point toward a relatively small effect of the helix-helix interaction on the CD spectral profiles. For a model system of two helices, the CIS method predicted larger changes in the spectra than TDC. This suggests other than interactions between peptide chains, such as mutual polarization, can have a minor, but measurable, effect on the CD spectrum.

  12. Mouse and Human CD1d-Self-Lipid Complexes Are Recognized Differently by Murine Invariant Natural Killer T Cell Receptors

    PubMed Central

    Guo, Tingxi; Chamoto, Kenji; Nakatsugawa, Munehide; Ochi, Toshiki; Yamashita, Yuki; Anczurowski, Mark; Butler, Marcus O.; Hirano, Naoto

    2016-01-01

    Invariant natural killer T (iNKT) cells recognize self-lipids presented by CD1d through characteristic TCRs, which mainly consist of the invariant Vα14-Jα18 TCRα chain and Vβ8.2, 7 or 2 TCRβ chains with hypervariable CDR3β sequences in mice. The iNKT cell-CD1d axis is conserved between humans and mice, and human CD1d reactivity of murine iNKT cells have been described. However, the detailed differences between the recognition of human and mouse CD1d bound to various self-lipids by mouse iNKT TCRs are largely unknown. In this study, we generated a de novo murine iNKT TCR repertoire with a wider range of autoreactivity compared with that of naturally occurring peripheral iNKT TCRs. Vβ8.2 mouse iNKT TCRs capable of recognizing the human CD1d-self-lipid tetramer were identified, although such clones were not detectable in the Vβ7 or Vβ2 iNKT TCR repertoire. In line with previously reports, clonotypic Vβ8.2 iNKT TCRs with unique CDR3β loops did not discriminate among lipids presented by mouse CD1d. Unexpectedly, however, these iNKT TCRs showed greater ligand selectivity toward human CD1d presenting the same lipids. Our findings demonstrated that the recognition of mouse and human CD1d-self-lipid complexes by murine iNKT TCRs is not conserved, thereby further elucidating the differences between cognate and cross-species reactivity of self-antigens by mouse iNKT TCRs. PMID:27213277

  13. Coordination chemistry strategies for dynamic helicates: time-programmable chirality switching with labile and inert metal helicates.

    PubMed

    Miyake, Hiroyuki; Tsukube, Hiroshi

    2012-11-01

    'Chirality switching' is one of the most important chemical processes controlling many biological systems. DNAs and proteins often work as time-programmed functional helices, in which specific external stimuli alter the helical direction and tune the time scale of subsequent events. Although a variety of organic foldamers and their hybrids with natural helices have been developed, we highlight coordination chemistry strategies for development of structurally and functionally defined metal helicates. These metal helicates have characteristic coordination geometries, redox reactivities and spectroscopic/magnetic properties as well as complex chiralities. Several kinds of inert metal helicates maintain rigid helical structures and their stereoisomers are separable by optical resolution techniques, while labile metal helicates offer dynamic inversion of their helical structures via non-covalent interactions with external chemical signals. The latter particularly have dynamically ordered helical structures, which are controlled by the combinations of metal centres and chiral ligands. They further function as time-programmable switches of chirality-derived dynamic rotations, translations, stretching and shape flipping, which are useful applications in nanoscience and related technology.

  14. Deuterium NMR of 2HCO-Val1. gramicidin A and 2HCO-Val1-D-Leu2. gramicidin A in oriented DMPC bilayers

    SciTech Connect

    Hing, A.W.; Adams, S.P.; Silbert, D.F.; Norberg, R.E. )

    1990-05-01

    Deuterium NMR is used to study the structure and dynamics of the formyl C-2H bond in selectively deuterated gramicidin molecules. Specifically, the functionally different analogues 2HCO-Val1...gramicidin A and 2HCO-Val1-D-Leu2...gramicidin A are studied by 2H NMR so that any conformational or dynamical differences between the two analogues can be correlated with their difference in lifetime. These analogues are first synthesized, purified, and characterized and then incorporated into oriented bilayers of dimyristoylphosphatidylcholine sandwiched between glass coverslips. Phosphorous NMR line shapes obtained from these samples are consistent with the presence of the bilayer phase and indicate that the disorder exhibited by the lipid matrix is approximately of the same type and degree for both analogues. Deuterium NMR line shapes obtained from these samples indicate that the motional axis of the formyl group of gramicidin is parallel to the coverslip normal, that the distribution of motional axis orientations has a width of 7-9 degrees, and that a similar, major conformational and dynamical state exists for the formyl C-2H bond of both analogues. In this state, if the only motion present is fast axial rotation, then the experimentally derived angle between the formyl C-2H bond and the motional axis is consistent with the presence of a right-handed, single-stranded, beta 6.3 helical dimer but is not consistent with the presence of a left-handed, single-stranded, beta 6.3 helical dimer. However, if fast axial rotation is not the only motion present, then the left-handed, single-stranded, beta 6.3 helical dimer cannot be absolutely excluded as a possibility. Also, a second, minor conformational and dynamical state appears to be present in the spectrum of 2HCO-Val1-D-Leu2...gramicidin A but is not observed in the spectrum of 2HCO-Val1...gramicidin A.

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

    NASA Astrophysics Data System (ADS)

    Li, Lin; Liu, Chong-Bo; Yang, Gao-Shan; Xiong, Zhi-Qiang; Liu, Hong; Wen, Hui-Liang

    2015-11-01

    Hydrothermal reactions of 2,2‧-[hexafluoroisopropylidenebis(p-phenyleneoxy)]diacetic acid (H2L) and zinc ions in the presence of N-donor ancillary ligands afford four novel coordination polymers, namely, [Zn2(μ2-OH)(μ4-O)0.5(L)]·0.5H2O (1), [Zn(L)(2,2‧-bipy)(H2O)] (2), [Zn3(L)3(phen)2]·H2O (3) and [Zn2(L)2(4,4‧-bipy)] (4) (2,2‧-bipy=2,2‧-bipyridine; 4,4‧-bipy=4,4‧-bipyridine; phen=1,10-phenanthroline). Their structures have been determined by single-crystal X-ray diffraction analyses, elemental analyses, IR spectra, powder X-ray diffraction (PXRD), and thermogravimetric (TG) analyses. Complex 1 shows a 3-D clover framework consisting of [Zn4(μ4-O)(μ2-OH)2]4+ clusters, and exhibits a novel (3,8)-connected topological net with the Schläfli symbol of {3·4·5}2{34·44·52·66·710·82}, and contains double-stranded and two kinds of meso-helices. 2 displays a helical chain structure, which is further extended via hydrogen bonds into a 3-D supramolecular structure with meso-helix chains. 3 displays a 2-D {44·62} parallelogram structure, which is further extended via hydrogen bonds into a 3-D supramolecular structure with single-stranded helical chains. 4 shows a 2-D {44·62} square structure with left- and right-handed helical chains. Moreover, the luminescent properties of 1-4 have been investigated.

  16. Helical growth in plant organs: mechanisms and significance.

    PubMed

    Smyth, David R

    2016-09-15

    Many plants show some form of helical growth, such as the circular searching movements of growing stems and other organs (circumnutation), tendril coiling, leaf and bud reversal (resupination), petal arrangement (contortion) and leaf blade twisting. Recent genetic findings have revealed that such helical growth may be associated with helical arrays of cortical microtubules and of overlying cellulose microfibrils. An alternative mechanism of coiling that is based on differential contraction within a bilayer has also recently been identified and underlies at least some of these growth patterns. Here, I provide an overview of the genes and cellular processes that underlie helical patterning. I also discuss the diversity of helical growth patterns in plants, highlighting their potential adaptive significance and comparing them with helical growth patterns in animals. PMID:27624832

  17. Dispersion phenomena in helical flow in a concentric annulus.

    PubMed

    Song, Young Seok; Brenner, Howard

    2009-12-14

    We examined dispersion phenomena of solutes in helical flow in a concentric annulus through a multiscale approach. The helical flow was developed by the combination of the Poiseuille flow and Couette flow. Here, we present an analytic model that can address the multidimensional Taylor dispersion in the helical flow under a lateral field of thermophoresis (or thermal diffusion) in the gapwise direction. Macroscopic parameters including the average solute velocity and dispersivity were analyzed using relevant microscopic physicochemical properties. The mathematically obtained results were validated by the numerical simulation carried out in this study. The findings show that macrotransport processes are robust and straightforward to handle multidimensional dispersion phenomena of solutes in helical flow. This study is expected to provide a theoretical platform for applications of helical flow such as tube exchangers, oil drilling, and multidimensional field flow fractionations (e.g., helical flow field flow fractionation). PMID:20001025

  18. Dispersion phenomena in helical flow in a concentric annulus

    NASA Astrophysics Data System (ADS)

    Song, Young Seok; Brenner, Howard

    2009-12-01

    We examined dispersion phenomena of solutes in helical flow in a concentric annulus through a multiscale approach. The helical flow was developed by the combination of the Poiseuille flow and Couette flow. Here, we present an analytic model that can address the multidimensional Taylor dispersion in the helical flow under a lateral field of thermophoresis (or thermal diffusion) in the gapwise direction. Macroscopic parameters including the average solute velocity and dispersivity were analyzed using relevant microscopic physicochemical properties. The mathematically obtained results were validated by the numerical simulation carried out in this study. The findings show that macrotransport processes are robust and straightforward to handle multidimensional dispersion phenomena of solutes in helical flow. This study is expected to provide a theoretical platform for applications of helical flow such as tube exchangers, oil drilling, and multidimensional field flow fractionations (e.g., helical flow field flow fractionation).

  19. Dispersion phenomena in helical flow in a concentric annulus.

    PubMed

    Song, Young Seok; Brenner, Howard

    2009-12-14

    We examined dispersion phenomena of solutes in helical flow in a concentric annulus through a multiscale approach. The helical flow was developed by the combination of the Poiseuille flow and Couette flow. Here, we present an analytic model that can address the multidimensional Taylor dispersion in the helical flow under a lateral field of thermophoresis (or thermal diffusion) in the gapwise direction. Macroscopic parameters including the average solute velocity and dispersivity were analyzed using relevant microscopic physicochemical properties. The mathematically obtained results were validated by the numerical simulation carried out in this study. The findings show that macrotransport processes are robust and straightforward to handle multidimensional dispersion phenomena of solutes in helical flow. This study is expected to provide a theoretical platform for applications of helical flow such as tube exchangers, oil drilling, and multidimensional field flow fractionations (e.g., helical flow field flow fractionation).

  20. Helicity Inferences Stemming from a Mean-Field Solar Dynamo

    NASA Astrophysics Data System (ADS)

    Pipin, Valery

    The global magnetic field of the Sun is generated by dynamo instability that stems from interactions of magnetic field with the large and small-scale flows. Theoretically, it is expected that such interactions produce a helical magnetic field which evolves following to magnetic helicity conservation law. We discuss some consequences of magnetic helicity conservation for the mean-field solar dynamo. We also discuss the observational aspect of the problem including the recent results about observations of the current helicity of solar active regions, the magnetic helicity of the global magnetic field as revealed by SOHO/MDI observations, and the problem of magnetic helicity transport from the solar convection zone to the outer atmosphere.

  1. Density of states of helically symmetric boron carbon nitride nanotubes.

    PubMed

    Carvalho, A C M; Bezerra, C G; Lawlor, J A; Ferreira, M S

    2014-01-01

    Motivated by the existence of helical wrapping patterns in composite nanotube systems, in this work we study the effects of the helical incorporation of carbon atoms in boron nitride nanotubes. We consider the substitutional carbon atoms distributed in stripes forming helical patterns along the nanotube axis. The density of states and energy band gap were calculated adopting Green function formalism by using the Rubio-Sancho technique in order to solve the matrix Dyson equation. We report the effects of the helical atomic distribution of carbon atoms on the behaviour of the density of states and the energy band gap. In particular, we show that the electronic energy band gap displays a non-monotonical dependence on the helical pattern, oscillating as a function of the helical angle θ.

  2. Ionic α-Helical Polypeptides towards Non-Viral Gene Delivery

    PubMed Central

    Zhang, Rujing; Song, Ziyuan; Yin, Lichen; Zheng, Nan; Tang, Haoyu; Lu, Hua; Gabrielson, Nathan P.; Lin, Yao; Kim, Kyung; Cheng, Jianjun

    2014-01-01

    The advent of polymeric materials has significantly promoted the development and rapid growth of various technologies in biomedical applications, such as tissue engineering and controlled drug and gene delivery. Water-soluble polypeptides bearing functional side chains and adopting stable secondary structures are a new class of functional polymeric materials of potentially broad applications in medicine and biotechnology. In this article, we summarize our recent effort on the design and synthesis of the water-soluble α-helical ionic polypeptides originally developed in our laboratory and highlight their applications in cell membrane penetration and non-viral gene/siRNA delivery. PMID:25377262

  3. Single-Layered Hybrid Materials Based on 1D Associated Metalorganic Nanoribbons for Controlled Release of Pheromones.

    PubMed

    Moreno, José María; Navarro, Ismael; Díaz, Urbano; Primo, Jaime; Corma, Avelino

    2016-09-01

    A new family of stable layered organic-inorganic materials has been prepared, in one-step solvothermal process. They are based on an ordered nickel cluster-type nanoribbons separated from each other by specific alkyl (heptyl- or dodecyl-) arylic mono-carboxylate moieties acting as molecular spacers, perpendicular to the 1D inorganic chains. These organic spacers contain hydrocarbon tails with different length which control the separation level between inorganic 1D sub-units, inhibiting the 3D growth of conventional DUT-8-type metal-organic frameworks (MOFs). The lamellar nature of the materials formed was studied and confirmed by different characterization techniques, showing the structural location of individual organic and inorganic building units. They have been successfully used as a long-lasting biodegradable and water-proof materials for controlled release of chemicals, such as pheromones for sustainable treatment of insect plagues. PMID:27444798

  4. Chain Gang

    NASA Technical Reports Server (NTRS)

    2006-01-01

    6 August 2006 This Mars Global Surveyor (MGS) Mars Orbiter Camera (MOC) image shows a chain of clustered and battered craters. These were formed by secondary impact. That is, somewhere to the south (beyond the bottom of this image), a large impact crater formed. When this occurred, material ejected from the crater was thrown tens to hundreds of kilometers away. This material then impacted the martian surface, forming clusters and chains of smaller craters.

    Location near: 15.8oN, 35.6oW Image width: 3 km (1.9 mi) Illumination from: upper left Season: Northern Spring

  5. Non-Kolmogorov cascade of helicity-driven turbulence.

    PubMed

    Kessar, Mouloud; Plunian, Franck; Stepanov, Rodion; Balarac, Guillaume

    2015-09-01

    We solve the Navier-Stokes equations with two simultaneous forcings. One forcing is applied at a given large scale and it injects energy. The other forcing is applied at all scales belonging to the inertial range and it injects helicity. In this way we can vary the degree of turbulence helicity from nonhelical to maximally helical. We find that increasing the rate of helicity injection does not change the energy flux. On the other hand, the level of total energy is strongly increased and the energy spectrum gets steeper. The energy spectrum spans from a Kolmogorov scaling law k^{-5/3} for a nonhelical turbulence, to a non-Kolmogorov scaling law k^{-7/3} for a maximally helical turbulence. In the latter case we find that the characteristic time of the turbulence is not the turnover time but a time based on the helicity injection rate. We also analyze the results in terms of helical modes decomposition. For a maximally helical turbulence one type of helical mode is found to be much more energetic than the other one, by several orders of magnitude. The energy cascade of the most energetic type of helical mode results from the sum of two fluxes. One flux is negative and can be understood in terms of a decimated model. This negative flux, however, is not sufficient to lead an inverse energy cascade. Indeed, the other flux involving the least energetic type of helical mode is positive and the largest. The least energetic type of helical mode is then essential and cannot be neglected.

  6. On the Origin of Magnetic Helicity in the Solar Corona

    NASA Astrophysics Data System (ADS)

    Tian, Lirong; Alexander, David

    2008-01-01

    Twenty-three active regions associated with pronounced sigmoidal structure in Yohkoh soft X-ray observations are selected to investigate the origin of magnetic helicity in the solar corona. We calculate the radial magnetic flux of each polarity, the rate of magnetic helicity injection, and total flux of the helicity injection (Δ HLCT) over 4-5 days using MDI 96 minute line-of-sight magnetograms and a local correlation tracking technique. We also estimate the contribution from differential rotation to the overall helicity budget (Δ Hrot). It is found that of the seven active regions for which the flux emergence exceeds 1.0 × 1022 Mx, six exhibited a helicity flux injection exceeding 1.0 × 1043 Mx2 (i.e., Δ H = Δ HLCT - Δ Hrot). Moreover, the rate of helicity injection and the total helicity flux are larger (smaller) during periods of more (less) increase of magnetic flux. Of the remaining 16 active regions, with flux emergence less than 1022 Mx, only 4 had significant injection of helicity, exceeding 1043 Mx2. Typical contributions from differential rotation over the same period were 2-3 times smaller than that of the strong magnetic field emergence. These statistical results signify that the strong emergence of magnetic field is the most important origin of the coronal helicity, while horizontal motions and differential rotation are insufficient to explain the measured helicity injection flux. Furthermore, the study of the helicity injection in nineteen newly emerging active regions confirms the result on the important role played by strong magnetic flux emergence in controlling the injection of magnetic helicity into the solar corona.

  7. Ureterolithiasis: classical and atypical findings on unenhanced helical computed tomography.

    PubMed

    Vaswani, Kuldeep K; El-Dieb, Adam; Vitellas, Kenneth M; Bennett, William F; Bova, James G

    2002-03-01

    Evaluation of patients with acute flank pain using helical computed tomography (CT) is a well-accepted, rapid, and safe procedure in the emergency setting. Various primary and secondary signs are described in the literature for evaluation of these patients. Our purpose is to demonstrate both the classical findings associated with ureteral calculi on unenhanced helical CT and atypical findings and potential pitfalls. We also provide readers with a systematic approach to interpreting unenhanced helical CT scans performed for acute flank pain.

  8. Scaling Behavior in Twisted, Helical and Undulating Lysozyme Amyloid Fibrils

    NASA Astrophysics Data System (ADS)

    Mezzenga, Raffaele; Lara, Cecile; Adamcik, Jozef; Usov, Ivan; Jordens, Sophia

    2012-02-01

    We combine atomic force microscopy single-molecule statistical analysis with polymer physics concepts to study the molecular conformations of lysozyme amyloid fibrils. We use different denaturation conditions to yield amyloid fibrils of different types. At 90 C and pH2, highly laminated twisted and helical ribbons are found, in which as many as 17 protofilaments pack laterally for a total width approaching 180 nm. In the case of 60 C and pH2, we find thin, wavy fibrils, in which the scaling behavior varies at multiple length scales. We use bond and pair correlation functions, end-to-end distribution and worm-like chain model to identify 3 characteristic length scales. At short length scales there is a first bending transition of the fibrils, corresponding to a bending length Lb. At slightly larger length scales (>2Lb), the fibrils become pseudoperiodic and start to undulate. Finally, at length scales larger than the persistence length Lp, the fibrils become flexible and are well described by a 2D self-avoiding random walk. We interpret these results in terms of the periodic fluctuations of the cross-section orientation of the fibrils (twisting) and the impact these have on the area moment of inertia and the corresponding propensity of the fibrils to bend.

  9. Structure of Human Ferritin L Chain

    SciTech Connect

    Wang,Z.; Li, C.; Ellenburg, M.; Soistman, E.; Ruble, J.; Wright, B.; Ho, J.; Carter, D.

    2006-01-01

    Ferritin is the major iron-storage protein present in all cells. It generally contains 24 subunits, with different ratios of heavy chain (H) to light chain (L), in the shape of a hollow sphere hosting up to 4500 ferric Fe atoms inside. H-rich ferritins catalyze the oxidation of iron(II), while L-rich ferritins promote the nucleation and storage of iron(III). Several X-ray structures have been determined, including those of L-chain ferritins from horse spleen (HoSF), recombinant L-chain ferritins from horse (HoLF), mouse (MoLF) and bullfrog (BfLF) as well as recombinant human H-chain ferritin (HuHF). Here, structures have been determined of two crystal forms of recombinant human L-chain ferritin (HuLF) obtained from native and perdeuterated proteins. The structures show a cluster of acidic residues at the ferrihydrite nucleation site and at the iron channel along the threefold axis. An ordered Cd{sup 2+} structure is observed within the iron channel, offering further insight into the route and mechanism of iron transport into the capsid. The loop between helices D and E, which is disordered in many other L-chain structures, is clearly visible in these two structures. The crystals generated from perdeuterated HuLF will be used for neutron diffraction studies.

  10. Axion string dynamics I: 2+1D

    NASA Astrophysics Data System (ADS)

    Fleury, Leesa M.; Moore, Guy D.

    2016-05-01

    If the axion exists and if the initial axion field value is uncorrelated at causally disconnected points, then it should be possible to predict the efficiency of cosmological axion production, relating the axionic dark matter density to the axion mass. The main obstacle to making this prediction is correctly treating the axion string cores. We develop a new algorithm for treating the axionic string cores correctly in 2+1 dimensions. When the axionic string cores are given their full physical string tension, axion production is about twice as efficient as in previous simulations. We argue that the string network in 2+1 dimensions should behave very differently than in 3+1 dimensions, so this result cannot be simply carried over to the physical case. We outline how to extend our method to 3+1D axion string dynamics.

  11. 1D-transport properties of single superconducting lead nanowires

    NASA Astrophysics Data System (ADS)

    Michotte, S.; Mátéfi-Tempfli, S.; Piraux, L.

    2003-09-01

    We report on the transport properties of single superconducting lead nanowires grown by an electrodeposition technique, embedded in a nanoporous track-etched polymer membrane. The nanowires are granular, have uniform diameter of ∼40 nm and a very large aspect ratio (∼500). The diameter of the nanowire is small enough to ensure a 1D superconducting regime in a wide temperature range below Tc. The non-zero resistance in the superconducting state and its variation caused by fluctuations of the superconducting order parameter were measured versus temperature, magnetic field, and applied DC current (or voltage). The current induced breakdowns in the V- I characteristics may be explained by the formation of phase slip centers. Moreover, DC voltage driven measurements reveal the existence of a new S-shape behavior near the formation of these phase slip centers.

  12. Microlens Masses from 1-D Parallaxes and Heliocentric Proper Motions

    NASA Astrophysics Data System (ADS)

    Gould, Andrew

    2014-12-01

    One-dimensional (1-D) microlens parallaxes can be combined with heliocentric lens-source relative proper motion measurements to derive the lens mass and distance, as suggested by Ghosh et al. (2004). Here I present the first mathematical anlysis of this procedure, which I show can be represented as a quadratic equation. Hence, it is formally subject to a two-fold degeneracy. I show that this degeneracy can be broken in many cases using the relatively crude 2-D parallax information that is often available for microlensing events. I also develop an explicit formula for the region of parameter space where it is more difficult to break this degeneracy. Although no mass/distance measurements have yet been made using this technique, it is likely to become quite common over the next decade.

  13. Quadratic Finite Element Method for 1D Deterministic Transport

    SciTech Connect

    Tolar, Jr., D R; Ferguson, J M

    2004-01-06

    In the discrete ordinates, or SN, numerical solution of the transport equation, both the spatial ({und r}) and angular ({und {Omega}}) dependences on the angular flux {psi}{und r},{und {Omega}}are modeled discretely. While significant effort has been devoted toward improving the spatial discretization of the angular flux, we focus on improving the angular discretization of {psi}{und r},{und {Omega}}. Specifically, we employ a Petrov-Galerkin quadratic finite element approximation for the differencing of the angular variable ({mu}) in developing the one-dimensional (1D) spherical geometry S{sub N} equations. We develop an algorithm that shows faster convergence with angular resolution than conventional S{sub N} algorithms.

  14. Effective theory of black holes in the 1/D expansion

    NASA Astrophysics Data System (ADS)

    Emparan, Roberto; Shiromizu, Tetsuya; Suzuki, Ryotaku; Tanabe, Kentaro; Tanaka, Takahiro

    2015-06-01

    The gravitational field of a black hole is strongly localized near its horizon when the number of dimensions D is very large. In this limit, we can effectively replace the black hole with a surface in a background geometry (e.g. Minkowski or Anti-deSitter space). The Einstein equations determine the effective equations that this `black hole surface' (or membrane) must satisfy. We obtain them up to next-to-leading order in 1/ D for static black holes of the Einstein-(A)dS theory. To leading order, and also to next order in Minkowski backgrounds, the equations of the effective theory are the same as soap-film equations, possibly up to a redshift factor. In particular, the Schwarzschild black hole is recovered as a spherical soap bubble. Less trivially, we find solutions for `black droplets', i.e. black holes localized at the boundary of AdS, and for non-uniform black strings.

  15. Connected components of irreducible maps and 1D quantum phases

    NASA Astrophysics Data System (ADS)

    Szehr, Oleg; Wolf, Michael M.

    2016-08-01

    We investigate elementary topological properties of sets of completely positive (CP) maps that arise in quantum Perron-Frobenius theory. We prove that the set of primitive CP maps of fixed Kraus rank is path-connected and we provide a complete classification of the connected components of irreducible CP maps at given Kraus rank and fixed peripheral spectrum in terms of a multiplicity index. These findings are then applied to analyse 1D quantum phases by studying equivalence classes of translational invariant matrix product states that correspond to the connected components of the respective CP maps. Our results extend the previously obtained picture in that they do not require blocking of physical sites, they lead to analytic paths, and they allow us to decompose into ergodic components and to study the breaking of translational symmetry.

  16. Glycolipid antigen processing for presentation by CD1d molecules.

    PubMed

    Prigozy, T I; Naidenko, O; Qasba, P; Elewaut, D; Brossay, L; Khurana, A; Natori, T; Koezuka, Y; Kulkarni, A; Kronenberg, M

    2001-01-26

    The requirement for processing glycolipid antigens in T cell recognition was examined with mouse CD1d-mediated responses to glycosphingolipids (GSLs). Although some disaccharide GSL antigens can be recognized without processing, the responses to three other antigens, including the disaccharide GSL Gal(alpha1-->2)GalCer (Gal, galactose; GalCer, galactosylceramide), required removal of the terminal sugars to permit interaction with the T cell receptor. A lysosomal enzyme, alpha-galactosidase A, was responsible for the processing of Gal(alpha1-->2)GalCer to generate the antigenic monosaccharide epitope. These data demonstrate a carbohydrate antigen processing system analogous to that used for peptides and an ability of T cells to recognize processed fragments of complex glycolipids.

  17. Helical structure of Bordetella pertussis fimbriae.

    PubMed Central

    Steven, A C; Bisher, M E; Trus, B L; Thomas, D; Zhang, J M; Cowell, J L

    1986-01-01

    The helical structures of Bordetella pertussis fimbriae of serotypes 2 and 6 were determined by optical diffraction analysis of electron micrographs of negatively stained paracrystalline bundles of purified fimbriae. The fimbrial structure is based on an axial repeat of 13 nm that contains five repeating units in two complete turns of a single-start helix. This structure was confirmed by direct measurements of mass per unit length for individual fimbriae performed by dark-field scanning transmission electron microscopy of unstained specimens. These data further established that the helically repeating unit is a monomer of fimbrial protein (Mr congruent to 22,000 for type 2 and Mr congruent to 21,500 for type 6). Radial density profiles calculated from the scanning transmission electron micrographs showed that the fimbria has peak density at its center, i.e., no axial channel, consistent with the results of conventional negative-staining electron microscopy. The radial profile gives an outermost diameter of approximately 7.5 nm, although the peripheral density is, on average, diffuse, allowing sufficient intercalation between adjacent fimbriae to give a center-to-center spacing of approximately 5.5 nm in the paracrystals. Despite serological and biochemical differences between type 2 and type 6 fimbriae, the packing arrangements of their fimbrial subunits are identical. From this observation, we infer that the respective subunits may have in common conserved regions whose packing dictates the helical geometry of the fimbria. It is plausible that a similar mechanism may underlie the phenomenon of phase variations in other systems of bacterial fimbriae. Images PMID:2875062

  18. The helical decomposition and the instability assumption

    NASA Technical Reports Server (NTRS)

    Waleffe, Fabian A.

    1993-01-01

    Direct numerical simulations show that the triadic transfer function T(k,p,q) peaks sharply when q (or p) is much smaller than k. The triadic transfer function T(k,p,q) gives the rate of energy input into wave number k from all interactions with modes of wave number p and q, where k, p, q form a triangle. This observation was thought to suggest that energy is cascaded downscale through non-local interactions with local transfer and that there was a strong connection between large and small scales. Both suggestions were in contradiction with the classical Kolmogorov picture of the energy cascade. The helical decomposition was found useful in distinguishing between kinematically independent interactions. That analysis has gone beyond the question of non-local interaction with local transfer. In particular, an assumption about the statistical direction of triadic energy transfer in any kinematically independent interaction was introduced (the instability assumption). That assumption is not necessary for the conclusions about non-local interactions with local transfer recalled above. In the case of turbulence under rapid rotation, the instability assumption leads to the prediction that energy is transferred in spectral space from the poles of the rotation axis toward the equator. The instability assumption is thought to be of general validity for any type of triad interactions (e.g. internal waves). The helical decomposition and the instability assumption offer detailed information about the homogeneous statistical dynamics of the Navier-Stokes equations. The objective was to explore the validity of the instability assumption and to study the contributions of the various types of helical interactions to the energy cascade and the subgrid-scale eddy-viscosity. This was done in the context of spectral closures of the Direct Interaction or Quasi-Normal type.

  19. Helical Poly(5-alkyl-2,3-thiophene)s: Controlled Synthesis and Structure Characterization

    DOE PAGES

    Zhang, Hong-Hai; Ma, Chuanxu; Bonnesen, Peter V.; Zhu, Jiahua; Sumpter, Bobby G.; Carrillo, Jan-Michael Y.; Yin, Panchao; Wang, Yangyang; Li, An-Ping; Hong, Kunlun

    2016-07-12

    Whereas Poly(3-alkyl-2,5-thiophene)s (P3AT), with many potential applications, have been extensively investigated, their ortho-connected isomers, poly(5-alkyl-2,3-thiophene)s (P5AT), have never been reported because of the difficulty in their syntheses. We herein present the first synthesis of regioregular P5AT via controlled Suzuki cross-coupling polymerization with PEPPSI-IPr as catalyst, affording the polymers with tunable molecular weight, narrow polydispersity (PDI) and well-defined functional end groups at the gram scale. The helical geometry of P5AT was studied by a combination of NMR, small angle x-ray scattering (SAXS) and scanning tunneling microscopy (STM). Particularly, the single polymer chain of poly(5- 2 butyl-2,3-thiophene) (P5BT) on highly oriented pyrolyticmore » graphite (HOPG) substrates with either M or P helical conformation was directly observed by STM. The comparison of UV-vis absorption between poly(5-hexyl-2,3-thiophene) (P5HT) (λ = 345 nm) and poly(3-hexyl-2,5- thiophene) (P3HT) (λ = 450 nm) indicated that the degree of conjugation of the backbone in P5HT is less than in P3HT, which may be a consequence of the helical geometry of the former compared to the more planar geometry of the latter. Moreover, we found that P5HT can emit green fluorescence under UV (λ = 360 nm) irradiation« less

  20. Alamethicin helices in a bilayer and in solution: molecular dynamics simulations.

    PubMed Central

    Tieleman, D P; Sansom, M S; Berendsen, H J

    1999-01-01

    Alamethicin is an alpha-helical channel-forming peptide, which inserts into lipid bilayers in a voltage-dependent, asymmetrical fashion. Nanosecond molecular dynamics simulations have been used to compare alamethicin conformation and dynamics in three different environments: 1) in water; 2) in methanol; and 3) inserted into a lipid (palmitoyl-oleoyl-phosphatidylcholine) bilayer to form a transmembrane helix. In the bilayer and in methanol, there was little change (Calpha RMSD approximately 0.2 nm over 2 ns and 1 ns) from the initial helical conformation of the peptide. In water there were substantial changes (Calpha RMSD approximately 0.4 nm over 1 ns), especially in the C-terminal segment of the peptide, which lost its alpha-helical conformation. In the bilayer and in methanol, the alamethicin molecule underwent hinge-bending motion about its central Gly-X-X-Pro sequence motif. Analysis of H-bonding interactions revealed that the polar C-terminal side chains of alamethicin provided an "anchor" to the bilayer/water interface via formation of multiple H-bonds that persisted throughout the simulation. This explains why the preferred mode of helix insertion into the bilayer is N-terminal, which is believed to underlie the asymmetry of voltage activation of alamethicin channels. PMID:9876121

  1. Helical Magnetic Fields from Sphaleron Decay and Baryogenesis

    SciTech Connect

    Copi, Craig J.; Ferrer, Francesc; Vachaspati, Tanmay; Achucarro, Ana

    2008-10-24

    Many models of baryogenesis rely on anomalous particle physics processes to give baryon number violation. By numerically evolving the electroweak equations on a lattice, we show that baryogenesis in these models creates helical cosmic magnetic fields, though the helicity created is smaller than earlier analytical estimates. After a transitory period, electroweak dynamics is found to conserve the Chern-Simons number and the total electromagnetic helicity. We argue that baryogenesis could lead to magnetic fields of nano-Gauss strength today on astrophysical length scales. In addition to being astrophysically relevant, such helical magnetic fields can provide an independent probe of baryogenesis and CP violation in particle physics.

  2. Helical Magnetic Fields from Sphaleron Decay and Baryogenesis

    NASA Astrophysics Data System (ADS)

    Copi, Craig J.; Ferrer, Francesc; Vachaspati, Tanmay; Achúcarro, Ana

    2008-10-01

    Many models of baryogenesis rely on anomalous particle physics processes to give baryon number violation. By numerically evolving the electroweak equations on a lattice, we show that baryogenesis in these models creates helical cosmic magnetic fields, though the helicity created is smaller than earlier analytical estimates. After a transitory period, electroweak dynamics is found to conserve the Chern-Simons number and the total electromagnetic helicity. We argue that baryogenesis could lead to magnetic fields of nano-Gauss strength today on astrophysical length scales. In addition to being astrophysically relevant, such helical magnetic fields can provide an independent probe of baryogenesis and CP violation in particle physics.

  3. Applying of helicity in an analysis of a severe sandstorm

    NASA Astrophysics Data System (ADS)

    Tao, Jian-hong; Wang, Jin-song; Feng, Jian-ying; Chang, Yue; Liu, Xiao-li

    2005-08-01

    The helicity of a severe sandstorm happened in Northwest China was analyzed by using global reanalysis grid data of NCEP/NCAR for 4 times a day. As an important physical parameter in analyzing and predicting severe convective weather, the helicity also has good indication in the forecasting of sandstorm. The distribution of helicity over the sandstorm area was negative at higher levels and positive at lower levels. There was definite relationship between the evolvement of helicity's negative value at higher levels and the occurrence of sandstorm.

  4. The global distribution of magnetic helicity in the solar corona

    NASA Astrophysics Data System (ADS)

    Yeates, A. R.; Hornig, G.

    2016-10-01

    By defining an appropriate field line helicity, we apply the powerful concept of magnetic helicity to the problem of global magnetic field evolution in the Sun's corona. As an ideal-magnetohydrodynamic invariant, the field line helicity is a meaningful measure of how magnetic helicity is distributed within the coronal volume. It may be interpreted, for each magnetic field line, as a magnetic flux linking with that field line. Using magneto-frictional simulations, we investigate how field line helicity evolves in the non-potential corona as a result of shearing by large-scale motions on the solar surface. On open magnetic field lines, the helicity injected by the Sun is largely output to the solar wind, provided that the coronal relaxation is sufficiently fast. But on closed magnetic field lines, helicity is able to build up. We find that the field line helicity is non-uniformly distributed, and is highly concentrated in twisted magnetic flux ropes. Eruption of these flux ropes is shown to lead to sudden bursts of helicity output, in contrast to the steady flux along the open magnetic field lines. Movies are available at http://www.aanda.org

  5. The formation of helical mesoporous silica nanotubes

    NASA Astrophysics Data System (ADS)

    Wan, Xiaobing; Pei, Xianfeng; Zhao, Huanyu; Chen, Yuanli; Guo, Yongmin; Li, Baozong; Hanabusa, Kenji; Yang, Yonggang

    2008-08-01

    Three chiral cationic gelators were synthesized. They can form translucent hydrogels in pure water. These hydrogels become highly viscous liquids under strong stirring. Mesoporous silica nanotubes with coiled pore channels in the walls were prepared using the self-assemblies of these gelators as templates. The mechanism of the formation of this hierarchical nanostructure was studied using transmission electron microscopy at different reaction times. The results indicated that there are some interactions between the silica source and the gelator. The morphologies of the self-assemblies of gelators changed gradually during the sol-gel transcription process. It seems that the silica source directed the organic self-assemblies into helical nanostructures.

  6. Spin transport in helical biological systems

    SciTech Connect

    Díaz, Elena; Gutierrez, Rafael

    2014-08-20

    Motivated by the recent experimental demonstration of spin selective effects in monolayers of double-stranded DNA oligomers, our work presents a minimal model to describe electron transmission through helical fields. Our model highlight that the lack of inversion symmetry due to the chirality of the potential is a key factor which will lead to a high spin-polarization (SP). We also study the stability of the SP against fluctuations of the electronic structure induced by static disorder affecting the on-site energies. In the energy regions where the spin-filtering occurs, our results remain stable against moderate disorders although the SP is slightly reduced.

  7. Helicon wave excitation with helical antennas

    SciTech Connect

    Light, M.; Chen, F.F.

    1995-04-01

    Components of the wave magnetic field in a helicon discharge have been measured with a single-turn, coaxial magnetic probe. Left- and right-handed helical antennas, as well as plane-polarized antennas, were used; and the results were compared with the field patterns computed for a nonuniform plasma. The results show that the right-hand circularly polarized mode is preferentially excited with all antennas, even those designed to excite the left-hand mode. For right-hand excitation, the radial amplitude profiles are in excellent agreement with computations. {copyright} {ital 1995} {ital American} {ital Institute} {ital of} {ital Physics}.

  8. Generalized unitarity and six-dimensional helicity

    SciTech Connect

    Bern, Zvi; Dennen, Tristan; Huang, Yu-tin; Ita, Harald; Carrasco, John Joseph

    2011-04-15

    We combine the unitarity method with the six-dimensional helicity formalism of Cheung and O'Connell to construct loop-level scattering amplitudes. As a first example, we construct dimensionally regularized QCD one-loop four-point amplitudes. As a nontrivial multiloop example, we confirm that the recently constructed four-loop four-point amplitude of N=4 super-Yang-Mills theory, including nonplanar contributions, is valid for dimensions D{<=}6. We comment on the connection of our approach to the recently discussed Higgs infrared regulator and on dual conformal properties in six dimensions.

  9. [Helical CT of urinary tract: clinical applications].

    PubMed

    Roy, C; Tuchmann, C; Guth, S; Lang, H; Saussine, C; Jacqmin, D

    2000-09-01

    Helical CT is the most useful imaging modality to evaluate kidney diseases. Different imaging protocols are used to assess the correct diagnosis in each clinical situation. The nephrographic phase (between 90 and 100 s of delay after injection) is more accurate than the cortical phase (between 30 and 40 s of delay) to depict and characterise small renal masses. Multiplanar and 3D reconstruction are useful to plan partial kidney surgery or percutaneous surgery of lithiasis. In emergency, spiral CT, if available, is suitable to assess renal colic. Spiral CT is the best modality to evaluate traumatic kidney.

  10. Inverse moments equilibria for helical anisotropic systems

    NASA Astrophysics Data System (ADS)

    Cooper, W. A.; Hirshman, S. P.; Depassier, M. C.

    1987-11-01

    An energy functional is devised for magnetic confinement schemes that have anisotropic plasma pressure. The minimization of this energy functional is demonstrated to reproduce components of the magnetohydrodynamic (MHD) force balance relation in systems with helical symmetry. An iterative steepest descent procedure is applied to the Fourier moments of the inverse magnetic flux coordinates to minimize the total energy and thus generate anisotropic pressure MHD equilibria. Applications to straight ELMO Snaky Torus (NTIS Document No. DE-84002406) configurations that have a magnetic well on the outermost flux surfaces have been obtained.

  11. Helical Luttinger liquid in topological insulator nanowires.

    PubMed

    Egger, R; Zazunov, A; Yeyati, A Levy

    2010-09-24

    We derive and analyze the effective low-energy theory for interacting electrons in a cylindrical nanowire made of a strong topological insulator. Three different approaches provide a consistent picture for the band structure, where surface states forming inside the bulk gap correspond to one-dimensional bands indexed by total angular momentum. When a half-integer magnetic flux pierces the nanowire, we find a strongly correlated helical Luttinger liquid topologically protected against weak disorder. We describe how transport experiments can detect this state.

  12. Dissipation of Energy, Cross Helicity, and Magnetic Helicity in Ideal MHD

    NASA Astrophysics Data System (ADS)

    Aluie, Hussein; Eyink, Gregory L.; Vishniac, Ethan T.

    2007-11-01

    The ``invariants'' of ideal MHD--energy, cross helicity, and magnetic helicity--need not be conserved in the limit of zero viscosity and resistivity if the solution fields become singular. This is observed to occur in MHD turbulence, where the effective dissipation is due to nonlinear cascade of the invariants to small-scales. We study the large-scale balances of the three invariants via a ``coarse-graining'' approach related to Wilson-Kadanoff renormalization group. The ideal dissipation in this framework is due to ``turbulent stress'' and ``turbulent EMF'' generated by eliminated plasma motions below the coarse-graining length. We derive upper bounds on these turbulent contributions to the MHD equations and improve the necessary conditions of [1] for ideal dissipation. In particular, we show that the conditions for turbulent dissipation/forward cascade of magnetic helicity are so severe--infinite 3rd-order moments of the velocity & magnetic fields!--that they are unlikely to ever naturally occur. We also establish local balance equations in space-time of the three invariants, both for measurable ``coarsed-grained'' variables and also for ``bare'' fields. On this basis we give physical interpretations of the turbulent cascades, in terms of work concepts for energy and in terms of topological linkage [2] for the two helicities. [1] Caflisch et al. 1997 Comm. Math. Phys. 184, 443-455 [2] Moffatt, H. K. 1969 J. Fluid Mech. 35, 117-129.

  13. Electronic transport in single-helical protein molecules: Effects of multiple charge conduction pathways and helical symmetry

    NASA Astrophysics Data System (ADS)

    Kundu, Sourav; Karmakar, S. N.

    2016-07-01

    We propose a tight-binding model to investigate electronic transport properties of single helical protein molecules incorporating both the helical symmetry and the possibility of multiple charge transfer pathways. Our study reveals that due to existence of both the multiple charge transfer pathways and helical symmetry, the transport properties are quite rigid under influence of environmental fluctuations which indicates that these biomolecules can serve as better alternatives in nanoelectronic devices than its other biological counterparts e.g., single-stranded DNA.

  14. Roles of TBC1D1 and TBC1D4 in insulin- and exercise-stimulated glucose transport of skeletal muscle

    PubMed Central

    Cartee, Gregory D.

    2014-01-01

    This review focuses on two paralogue Rab GTPase activating proteins known as TBC1D1 Tre-2/BUB2/cdc 1 domain family (TBC1D) 1 and TBC1D4 (also called Akt Substrate of 160 kDa, AS160) and their roles in controlling skeletal muscle glucose transport in response to the independent and combined effects of insulin and exercise. Convincing evidence implicates Akt2-dependent TBC1D4 phosphorylation on T642 as a key part of the mechanism for insulin-stimulated glucose uptake by skeletal muscle. TBC1D1 phosphorylation on several insulin-responsive sites (including T596, a site corresponding to T642 in TBC1D4) does not appear to be essential for in vivo insulin-stimulated glucose uptake by skeletal muscle. In vivo exercise or ex vivo contraction of muscle result in greater TBC1D1 phosphorylation on S237 that is likely to be secondary to increased AMP-activated protein kinase activity and potentially important for contraction-stimulated glucose uptake. Several studies that evaluated both normal and insulin-resistant skeletal muscle stimulated with a physiological insulin concentration after a single exercise session found that greater post-exercise insulin-stimulated glucose uptake was accompanied by greater TBC1D4 phosphorylation on several sites. In contrast, enhanced post-exercise insulin sensitivity was not accompanied by greater insulin-stimulated TBC1D1 phosphorylation. The mechanism for greater TBC1D4 phosphorylation in insulin-stimulated muscles after acute exercise is uncertain, and a causal link between enhanced TBC1D4 phosphorylation and increased post-exercise insulin sensitivity has yet to be established. In summary, TBC1D1 and TBC1D4 have important, but distinct roles in regulating muscle glucose transport in response to insulin and exercise. PMID:25280670

  15. Helicity of the Solar Magnetic Field

    NASA Astrophysics Data System (ADS)

    Tiwari, Sanjiv Kumar

    2009-11-01

    Magnetic helicity is a physical quantity that measures the degree of linkages and twistedness in the field lines. It is given by a volume integral over the scalar product of magnetic field B and its vector potential A. Direct computation of magnetic helicity in the solar atmosphere is not possible due to two reasons. First, we do not have the observations at different heights in the solar atmosphere to compute the volume integral. Second, the vector potential A is non-unique owing to gauge variance. Many researchers incorrectly inferred twist, a component of magnetic helicity, from the force-free parameter α. We clarified the physical meaning of α and its relation with the magnetic helicity. Also, a direct method is proposed for the computation of global α values of sunspots. An analytical bipole was generated to study the effect of polarimetric noise on the estimation of various magnetic parameters. We find that the effect of polarimetric noise, present in the recent vector magnetograms e.g., from Hinode (Solar Optical Telescope/Spectro- Polarimeter (SOT/SP)), on the magnetic parameters like α and magnetic energy, is negligible. We examined the fine structures of local current and α in the sunspots. Local α patches of opposite signs are present in the umbra of each sunspot. The amplitude of the spatial variation of local α in the umbra is typically of the order of the global α of the sunspot. We find that the local α and current are distributed as alternately positive and negative filaments in the penumbra. The amplitude of azimuthal variation of the local α in the penumbra is approximately an order of magnitude larger than that in the umbra. The contributions of the local positive and negative currents and α in the penumbra cancel each other giving almost no contribution for their global values for whole sunspot. We have introduced the concept of signed shear angle (SSA) for sunspots and establish its importance for non force

  16. Gyrotron beam generation with helical magnetic fields

    NASA Astrophysics Data System (ADS)

    Jackson, R. H.; Sedlak, C. A.

    1983-08-01

    This report presents the results of an investigation into the basic properties of a new type of electron gun for generating high transverse velocity beams, the bifilar helix - Pierce gun or H-gun. The H-gun differs significantly from presently used magnetron injection guns (MIGs) in that first a laminar, low transverse velocity beam is formed and then transverse velocity is imparted by propagating the beam through the magnetic field of a bifilar helix. In order to evaluate the H-gun, an analytic and computational study was conducted to examine the relationships between the magnetic fields (axial and helical), and the beam properties after existing the helical field. The effects of the helix field entrance profile, the helix-axial field gyroresonance, and helix field gradients have been taken into account in the investigation. Based on the results of this research, conditions have been specified which will produce a high transverse velocity beam with low axial velocity spread. In particular, it has been found that an adiabatic helix entrance profile can provide a flexible means of generating high quality beams for gyro-devices.

  17. Determining How Magnetic Helicity Injection Really Works

    SciTech Connect

    Paul M. Bellan

    2001-10-09

    OAK-B135 The goal of the Caltech program is to determine how helicity injection works by investigating the actual dynamics and topological evolution associated with magnetic relaxation. A new coaxial helicity injection source has been constructed and brought into operation. The key feature of this source is that it has maximum geometric simplicity. Besides being important for fusion research, this work also has astrophysical implications. Photos obtained using high-speed cameras show a clear sequence of events in the formation process. In particular, they show initial merging/reconnection processes, jet-like expansion, kinking, and separation of the plasma from the source. Various diagnostics have been developed, including laser induced fluorescence and soft x-ray detection using high speed diodes. Gas valves have been improved and a patent disclosure relating to puffed gas valves has been filed. Presentations on this work have been given in the form of invited talks at several university physics departments that were previously unfamiliar with laboratory plasma experiments.

  18. Cosmic acceleration and the helicity-0 graviton

    SciTech Connect

    Rham, Claudia de; Heisenberg, Lavinia; Gabadadze, Gregory; Pirtskhalava, David

    2011-05-15

    We explore cosmology in the decoupling limit of a nonlinear covariant extension of Fierz-Pauli massive gravity obtained recently in arXiv:1007.0443. In this limit the theory is a scalar-tensor model of a unique form defined by symmetries. We find that it admits a self-accelerated solution, with the Hubble parameter set by the graviton mass. The negative pressure causing the acceleration is due to a condensate of the helicity-0 component of the massive graviton, and the background evolution, in the approximation used, is indistinguishable from the {Lambda}CDM model. Fluctuations about the self-accelerated background are stable for a certain range of parameters involved. Most surprisingly, the fluctuation of the helicity-0 field above its background decouples from an arbitrary source in the linearized theory. We also show how massive gravity can remarkably screen an arbitrarily large cosmological constant in the decoupling limit, while evading issues with ghosts. The obtained static solution is stable against small perturbations, suggesting that the degravitation of the vacuum energy is possible in the full theory. Interestingly, however, this mechanism postpones the Vainshtein effect to shorter distance scales. Hence, fifth force measurements severely constrain the value of the cosmological constant that can be neutralized, making this scheme phenomenologically not viable for solving the old cosmological constant problem. We briefly speculate on a possible way out of this issue.

  19. Microwave Studies of Perfluoropentane and its Helicity

    NASA Astrophysics Data System (ADS)

    Fournier, Joseph A.; Bohn, Robert K.; Montgomery, John A.; , Jr.

    2009-06-01

    Unlike hydrocarbons, fluorocarbons are helical in their all-trans most stable conformations. A definitive experimental determination of the helical angle has not been accomplished because single crystal X-ray studies are not available due to the lack of suitable crystallization solvents, but a value of 17^° from exactly trans is generally accepted from X-ray fiber studies. Using a pulsed-jet Fourier Transform microwave spectrometer, we have observed and assigned the rotational spectra of the lowest energy all-anti C_2 symmetry form of perfluoro-n-pentane and all three of its ^{13}C isotopomers. A, B, and C values of the parent species are 990.6394(4) MHz, 314.00020(14) MHz, and 304.37034(14) MHz, respectively. A range of effective r_0 structures incorporating various model constraints are consistent with about 16^° torsion and a Kraitchman analysis of the parent and ^{13}C species gives 13.3^°. Ab initio calculations are consistent with the experimental results.

  20. Neutrino helicity reversal and fundamental symmetries

    NASA Astrophysics Data System (ADS)

    Jentschura, U. D.; Wundt, B. J.

    2014-07-01

    A rather elusive helicity reversal occurs in a gedanken experiment in which a massive left-handed Dirac neutrino, traveling at a velocity u < c, is overtaken on a highway by a speeding vehicle (traveling at velocity v with u < v < c). Namely, after passing the neutrino, looking back, one would see a right-handed neutrino (which has never been observed in nature). The Lorentz-invariant mass of the right-handed neutrino is still the same as before the passing. The gedanken experiment thus implies the existence of right-handed, light neutrinos, which are not completely sterile. Furthermore, overtaking a bunch of massive right-handed Dirac neutrinos leads to gradual de-sterilization. We discuss the helicity reversal and the concomitant sterilization and de-sterilization mechanisms by way of an illustrative example calculation, with a special emphasis on massive Dirac and Majorana neutrinos. We contrast the formalism with a modified Dirac neutrino described by a Dirac equation with a pseudoscalar mass term proportional to the fifth current.

  1. Quantification of a Helical Origami Fold

    NASA Astrophysics Data System (ADS)

    Dai, Eric; Han, Xiaomin; Chen, Zi

    2015-03-01

    Origami, the Japanese art of paper folding, is traditionally viewed as an amusing pastime and medium of artistic expression. However, in recent years, origami has served as a source of inspiration for innovations in science and engineering. Here, we present the geometric and mechanical properties of a twisting origami fold. The origami structure created by the fold exhibits several interesting properties, including rigid foldibility, local bistability and finely tunable helical coiling, with control over pitch, radius and handedness of the helix. In addition, the pattern generated by the fold closely mimics the twist buckling patterns shown by thin materials, for example, a mobius strip. We use six parameters of the twisting origami pattern to generate a fully tunable graphical model of the fold. Finally, we present a mathematical model of the local bistability of the twisting origami fold. Our study elucidates the mechanisms behind the helical coiling and local bistability of the twisting origami fold, with potential applications in robotics and deployable structures. Acknowledgment to Branco Weiss Fellowship for funding.

  2. Transport of helical gyrotactic swimmers in channels

    NASA Astrophysics Data System (ADS)

    Alqarni, M. S.; Bearon, R. N.

    2016-07-01

    We develop a mechanistic model that describes the transport of gyrotactic cells with propulsive force and propulsive torque that are not parallel. In sufficiently weak shear this yields helical swimming trajectories, whereas in stronger shear cells can attain a stable equilibrium orientation. We obtain the stable equilibrium solution for cell orientation as a function of the shear strength and determine the feasibility region for equilibrium solutions. We compute numerically the trajectories of cells in two dimensional vertical channel flow where the shear is non-uniform. Depending on the parameter values, we show that helical swimmers may display classical gyrotactic focussing towards the centre of the channel or can display a new phenomenon of focussing away from the centre of the channel. This result can be explained by consideration of the equilibrium solution for cell orientation. In this study we consider only dilute suspensions where there is no feedback from cell swimming on the hydrodynamics, and both cell-wall and cell-cell interactions are neglected.

  3. CURRENT AND KINETIC HELICITY OF LONG-LIVED ACTIVITY COMPLEXES

    SciTech Connect

    Komm, Rudolf; Gosain, Sanjay

    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%, 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.

  4. Magnetic Relaxation and Coercivity of Finite-size Single Chain Magnets

    NASA Astrophysics Data System (ADS)

    Gredig, Thomas; Byrne, Matthew; Vindigni, Alessandro

    2015-03-01

    The magnetic coercivity of hysteresis loops for iron phthalocyanine thin films depends on the iron chain length and the measurement sweep speed below 5 K. The average one-dimensional (1D) iron chain length in samples is controlled during deposition. These 1D iron chains can be tuned over one order of magnitude with the shortest chain having 100 elements. We show that the coercivity strongly increases with the average length of the iron chains, which self-assemble parallel to the substrate surface. Magnetic relaxation and sweep speed data suggest spin dynamics play an important role. Implementing Glauber dynamics with a finite-sized 1D Ising model provides qualitative agreement with experimental data. This suggests that iron phthalocyanine thin films act as single chain magnets and provide a solid test system for tunable finite-sized magnetic chains. This research has been supported with the NSF-DMR 0847552 grant.

  5. Evaluation of the Transport of Natural Radioactive Materials in Large Lysimeters Using Hydrus-1D

    NASA Astrophysics Data System (ADS)

    Pontedeiro, E.; Cipriani, M.; van Genuchten, M.; Simunek, J.

    2007-12-01

    The mining industry in Brazil often uses raw materials that contain relatively high concentrations of naturally occurring radioactive materials (referred to as NORM). Ores of relatively low grade typically are used to produce refined metals of high purity (e.g., Nb, Ta, Sn, and Au) using pyrometallurgic processes. The final waste is a slag rich in natural radioactive contaminants (the U and Th decay series), which are then usually deposited in industrial landfills. To study the long-term fate and transport of radionuclides leached from the NORM wastes, several large (3 m deep) lysimeters were constructed at the Pocos de Caldas Laboratory of the Brazilian Nuclear Energy Commision (CNEN). The lysimeters were packed with surface soils and slags from one of the mining sites in South East Brazil. Main purpose of our lysimeter experiments was to follow the dissolution and transport of radionuclides from the slags under natural climatic conditions. Leaching rates and radionuclide concentrations of the effluent were observed during a three-year time period. A variety of physical and chemical properties of the soils and slags (including laboratory batch equilibrium sorption values) were also determined. The data were analyzed using several computer software packages, including the STANMOD code for analytical modeling of decay chain transport during steady flow, the HYDRUS-1D code for variably-saturated flow and the transport of multiple solutes, and the HP1 code for a more comprehensive analysis of the geochemistry involved. In this presentation we describe the experimental setup and provide preliminary results of the theoretical analyses, especially those using HYDRUS-1D.

  6. 1-D and 2-D Probabilistic Inversions of Fault Zone Guided Waves

    NASA Astrophysics Data System (ADS)

    Gulley, A.; Eccles, J. D.; Kaipio, J. P.; Malin, P. E.

    2015-12-01

    Fault Zone Guided Waves (FZGWs) are seismic coda that are trapped by the low velocity damage zone of faults. Inversions of these phases can be carried out using their measured dispersion and a Bayesian probability approach. This method utilises a Markov chain Monte Carlo which allows uncertainties and trade-offs to be quantified. Accordingly we have developed a scheme that estimates the dispersion curve and amplitude response variability from a FZGW record. This method allows the computation of both the point estimates and the covariance of the dispersion curve. The subsequent estimation of fault zone parameters is then based on a Gaussian model for the dispersion curve. We then show that inversions using FZGW dispersion data can only resolve fault zone velocity contrast and fault zone width - it leaves densities, absolute country rock velocities and the earthquake location unresolved. We show that they do however significantly affect the estimated fault zone velocities and widths. As these parameters cannot be resolved, we allow for their effects on the estimates of fault zone width and velocity contrast by using the Bayesian approximation error method. We show that using this method reduces computational time from days to minutes and the associated loss of accuracy is insignificant compared to carrying out the inversion on all parameters. We have extended our scheme to 2-D using 1-D slices. The Bayesian approximation error methodology is further employed to provide a 'correction term' with uncertainty for the 1-D slice approximation. We investigate these features with both synthetic data and FZGW data from the Alpine Fault of New Zealand.

  7. 1D X-ray Beam Compressing Monochromators

    SciTech Connect

    Korytar, D.; Dobrocka, E.; Konopka, P.; Zaprazny, Z.; Ferrari, C.; Mikulik, P.; Vagovic, P.; Ac, V.; Erko, A.; Abrosimov, N.

    2010-04-06

    A total beam compression of 5 and 10 corresponding to the asymmetry angles of 9 deg. and 12 deg. is achieved with V-5 and V-10 monochromators, respectively, in standard single crystal pure germanium (220) X-ray beam compressing (V-shaped) monochromators for CuKalpha{sub 1} radiation. A higher 1D compression of X-ray beam is possible using larger angles of asymmetry, however it is achieved at the expense of the total intensity, which is decreased due to the refraction effect. To increase the monochromator intensity, several ways are considered both theoretically and experimentally. Linearly graded germanium rich Ge{sub x}Si{sub (1-x)} single crystal was used to prepare a V-21 single crystal monochromator with 15 deg. asymmetry angles (compression factor of 21). Its temperature gradient version is discussed for CuKalpha{sub 1} radiation. X-ray diffraction measurements on the graded GeSi monochromator showed more than 3-times higher intensity at the output compared with that of a pure Ge monochromator.

  8. 1-D Numerical Analysis of RBCC Engine Performance

    NASA Technical Reports Server (NTRS)

    Han, Samuel S.

    1998-01-01

    An RBCC engine combines air breathing and rocket engines into a single engine to increase the specific impulse over an entire flight trajectory. Considerable research pertaining to RBCC propulsion was performed during the 1960's and these engines were revisited recently as a candidate propulsion system for either a single-stage-to-orbit (SSTO) or two-stage-to-orbit (TSTO) launch vehicle. There are a variety of RBCC configurations that had been evaluated and new designs are currently under development. However, the basic configuration of all RBCC systems is built around the ejector scramjet engine originally developed for the hypersonic airplane. In this configuration, a rocket engine plays as an ejector in the air-augmented initial acceleration mode, as a fuel injector in scramjet mode and the rocket in all rocket mode for orbital insertion. Computational fluid dynamics (CFD) is a useful tool for the analysis of complex transport processes in various components in RBCC propulsion systems. The objective of the present research was to develop a transient 1-D numerical model that could be used to predict flow behavior throughout a generic RBCC engine following a flight path.

  9. Dynamic decoupling in the presence of 1D random walk

    NASA Astrophysics Data System (ADS)

    Chakrabarti, Arnab; Chakraborty, Ipsita; Bhattacharyya, Rangeet

    2016-05-01

    In the recent past, many dynamic decoupling sequences have been proposed for the suppression of decoherence of spins connected to thermal baths of various natures. Dynamic decoupling schemes for suppressing decoherence due to Gaussian diffusion have also been developed. In this work, we study the relative performances of dynamic decoupling schemes in the presence of a non-stationary Gaussian noise such as a 1D random walk. Frequency domain analysis is not suitable to determine the performances of various dynamic decoupling schemes in suppressing decoherence due to such a process. Thus, in this work, we follow a time domain calculation to arrive at the following conclusions: in the presence of such a noise, we show that (i) the traditional Carr–Purcell–Meiboom–Gill (CPMG) sequence outperforms Uhrig’s dynamic decoupling scheme, (ii) CPMG remains the optimal sequence for suppression of decoherence due to random walk in the presence of an external field gradient. Later, the theoretical predictions are experimentally verified by using nuclear magnetic resonance spectroscopy on spin 1/2 particles diffusing in a liquid medium.

  10. Control and imaging of O(1D2) precession

    NASA Astrophysics Data System (ADS)

    Wu, Shiou-Min; Radenovic, Dragana Č.; van der Zande, Wim J.; Groenenboom, Gerrit C.; Parker, David H.; Vallance, Claire; Zare, Richard N.

    2011-01-01

    Larmor precession of a quantum mechanical angular momentum vector about an applied magnetic field forms the basis for a range of magnetic resonance techniques, including nuclear magnetic resonance spectroscopy and magnetic resonance imaging. We have used a polarized laser pump-probe scheme with velocity-map imaging detection to visualize, for the first time, the precessional motion of a quantum mechanical angular momentum vector. Photodissociation of O2 at 157 nm provides a clean source of fast-moving O(1D2) atoms, with their electronic angular momentum vector strongly aligned perpendicular to the recoil direction. In the presence of an external magnetic field, the distribution of atomic angular momenta precesses about the field direction, and polarization-sensitive images of the atomic scattering distribution recorded as a function of field strength yield ‘time-lapse-photography’ style movies of the precessional motion. We present movies recorded in various experimental geometries, and discuss potential consequences and applications in atmospheric chemistry and reaction dynamics.

  11. Helical grip for the cable cars of San Francisco

    NASA Technical Reports Server (NTRS)

    Peyran, R. J.

    1979-01-01

    A helical cable car grip to minimize high maintenance costs of San Francisco's cable car operation is presented. The grip establishes a rolling contact between the cable and grip to reduce sliding friction and associated cable wear. The design, development, and testing of the helical cable car grip are described.

  12. Experimental investigation of solar powered diaphragm and helical pumps

    Technology Transfer Automated Retrieval System (TEKTRAN)

    For several years, many types of solar powered water pumping systems were evaluated, and in this paper, diaphragm and helical solar photovoltaic (PV) powered water pumping systems are discussed. Data were collected on diaphragm and helical pumps which were powered by different solar PV arrays at mul...

  13. 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.

  14. Water tuned the helical nanostructures and supramolecular chirality in organogels.

    PubMed

    Liu, Changxia; Jin, Qingxian; Lv, Kai; Zhang, Li; Liu, Minghua

    2014-04-11

    Water was found to tune the self-assembled nanostructures of a cationic amphiphile in organic solvents from nanofibers to helical tapes, helical tubes and chiral nanotwists with various pitch lengths depending on water content. Inversion of CD spectra was observed in the water-triggered polar and non-polar solvent gels.

  15. Helical channel design and technology for cooling of muon beams

    SciTech Connect

    Yonehara, K; Derbenev, Y.S.; Johnson, R.P.; /MUONS Inc., Batavia

    2010-08-01

    Novel magnetic helical channel designs for capture and cooling of bright muon beams are being developed using numerical simulations based on new inventions such as helical solenoid (HS) magnets and hydrogen-pressurized RF (HPRF) cavities. We are close to the factor of a million six-dimensional phase space (6D) reduction needed for muon colliders. Recent experimental and simulation results are presented.

  16. Computing magnetic energy and helicity fluxes from series of magnetograms .

    NASA Astrophysics Data System (ADS)

    Démoulin, P.; Pariat, E.

    Magnetic energy and helicity fluxes can now be derived from measurements of the photospheric magnetic and velocity fields. We show that only photospheric flux-tube motions are needed to estimate the full fluxes. The derived maps of flux densities permit to localize where energy and helicity input occurs in active regions (ARs). The precision of the energy flux density is dominantly limited by the precision obtained on the transverse component of the magnetic field. On the contrary, the helicity flux density requires only the measurement of the vertical component of the magnetic field. Previously, the magnetic helicity maps were strongly affected by a false definition of the helicity flux density involving the magnetic vector potential. Applied to observations, this approach introduces important fake polarities. We define a better helicity flux density; it reduces the fake polarities by more than an order of magnitude. The spatial distribution of helicity injected into the studied ARs is much more coherent than previously thought, and presents a dominant sign in each AR. Finally, the correct helicity flux density could be derived from magnetograms if coronal connectivities are known.

  17. The magnetic helicity spectrum from solar vector magnetograms

    NASA Astrophysics Data System (ADS)

    Brandenburg, Axel; Zhang, Hongqi; Sokoloff, Dmitry

    2016-05-01

    The gauge-invariant (or relative) magnetic helicity is often measured to characterize the degree of magnetic complexity of active regions. However, magnetic helicity is expected to have different signs on different length scales that can be identified with the large- and small-scale fields used in dynamo theory. To address this, it is important to determine magnetic helicity spectra as functions of wavenumber. These spectra are defined such that the integral over all wavenumbers gives the usual magnetic helicity density in a particular patch of interest. Using vector magnetograms from the Helioseismic and Magnetic Imager on board the Solar Dynamics Observatory for active region NOAA 11515, which was on the southern hemisphere, we show that the magnetic helicity spectrum has positive sign on scales below 30 Mm, but negative sign on larger scales. This active region was rather complex and its magnetic helicity was within 26% of its theoretical maximum value. This is much more than that of NOAA 11158, which was also rather complex, but only within 5% of its theoretical maximum value. Since the contribution of larger length scales turned out to be important in the case of NOAA 11515, its total magnetic helicity is dominated by the negative values from large length scales, which explains the unusual sign for the southern hemisphere. Measuring magnetic helicity spectra with DKIST may become an important tool to learn about the workings of the underlying dynamo.

  18. Single amino acid mutation in alpha-helical peptide affect second harmonic generation hyperpolarizability

    NASA Astrophysics Data System (ADS)

    Wei, Jing; Wang, Jin-Yun; Zhang, Min-Yi; Chai, Guo-Liang; Lin, Chen-Sheng; Cheng, Wen-Dan

    2013-01-01

    We investigate the effect of side chain on the first-order hyperpolarizability in α-helical polyalanine peptide with the 10th alanine mutation (Acetyl(ala)9X(ala)7NH2). Structures of various substituted peptides are optimized by ONIOM (DFT: AM1) scheme, and then linear and nonlinear optical properties are calculated by SOS//CIS/6-31G∗ method. The polarizability and first-order hyperpolarizability increase obviously only when 'X' represents phenylalanine, tyrosine and tryptophan. We also discuss the origin of nonlinear optical response and determine what caused the increase of first-order hyperpolarizability. Our results strongly suggest that side chains containing benzene, phenol and indole have important contributions to first-order hyperpolarizability.

  19. Absolute rate constant determinations for the deactivation of O/1D/ by time resolved decay of O/1D/ yields O/3P/ emission

    NASA Technical Reports Server (NTRS)

    Davidson, J. A.; Sadowski, C. M.; Schiff, H. I.; Howard, C. J.; Schmeltekopf, A. L.; Jennings, D. A.; Streit, G. E.

    1976-01-01

    Absolute rate constants for the deactivation of O(1D) atoms by some atmospheric gases have been determined by observing the time-resolved emission of O(1D) at 630 nm. O(1D) atoms were produced by the dissociation of ozone via repetitive laser pulses at 266 nm. Absolute rate constants for the relaxation of O(1D) at 298 K are reported for N2, O2, CO2, O3, H2, D2, CH4, HCl, NH3, H2O, N2O, and Ne. The results obtained are compared with previous relative and absolute measurements reported in the literature.

  20. Accumulation of heavy particles around a helical vortex filament

    NASA Astrophysics Data System (ADS)

    IJzermans, Rutger H. A.; Hagmeijer, Rob; van Langen, Pieter J.

    2007-10-01

    The motion of small heavy particles near a helical vortex filament in incompressible flow is investigated. Both the configurations of a helical vortex filament in free space and a helical vortex filament in a concentric pipe are considered, and the corresponding helically symmetric velocity fields are expressed in terms of a stream function. Particle motion is assumed to be driven by Stokes drag, and the flow fields are assumed to be independent from the motion of particles. Numerical results show that heavy particles may be attracted to helical trajectories. The stability of these attraction trajectories is demonstrated by linear stability analysis. In addition, the correlation between the attraction trajectories and the streamline topologies is investigated.

  1. Chiral exact relations for helicities in Hall magnetohydrodynamic turbulence.

    PubMed

    Banerjee, Supratik; Galtier, Sébastien

    2016-03-01

    Besides total energy, three-dimensional incompressible Hall magnetohydrodynamics (MHD) possesses two inviscid invariants, which are the magnetic helicity and the generalized helicity. Exact relations are derived for homogeneous (nonisotropic) stationary Hall MHD turbulence (and also for its inertialess electron MHD limit) with nonzero helicities and in the asymptotic limit of large Reynolds numbers. The universal laws are written only in terms of mixed second-order structure functions, i.e., the scalar product of two different increments. It provides, therefore, a direct measurement of the dissipation rates for the corresponding invariant flux. This study shows that the generalized helicity cascade is strongly linked to the left polarized fluctuations, while the magnetic helicity cascade is linked to the right polarized fluctuations. PMID:27078460

  2. 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. PMID:26367106

  3. 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.

  4. Chiral exact relations for helicities in Hall magnetohydrodynamic turbulence.

    PubMed

    Banerjee, Supratik; Galtier, Sébastien

    2016-03-01

    Besides total energy, three-dimensional incompressible Hall magnetohydrodynamics (MHD) possesses two inviscid invariants, which are the magnetic helicity and the generalized helicity. Exact relations are derived for homogeneous (nonisotropic) stationary Hall MHD turbulence (and also for its inertialess electron MHD limit) with nonzero helicities and in the asymptotic limit of large Reynolds numbers. The universal laws are written only in terms of mixed second-order structure functions, i.e., the scalar product of two different increments. It provides, therefore, a direct measurement of the dissipation rates for the corresponding invariant flux. This study shows that the generalized helicity cascade is strongly linked to the left polarized fluctuations, while the magnetic helicity cascade is linked to the right polarized fluctuations.

  5. Hierarchical Helical Order in the Twisted Growth of Plant Organs

    NASA Astrophysics Data System (ADS)

    Wada, Hirofumi

    2012-09-01

    The molecular and cellular basis of left-right asymmetry in plant morphogenesis is a fundamental issue in biology. A rapidly elongating root or hypocotyl of twisting mutants of Arabidopsis thaliana exhibits a helical growth with a handedness opposite to that of the underlying cortical microtubule arrays in epidermal cells. However, how such a hierarchical helical order emerges is currently unknown. We propose a model for investigating macroscopic chiral asymmetry in Arabidopsis mutants. Our elastic model suggests that the helical pattern observed is a direct consequence of the simultaneous presence of anisotropic growth and tilting of cortical microtubule arrays. We predict that the root helical pitch angle is a function of the microtubule helical angle and elastic moduli of the tissues. The proposed model is versatile and is potentially important for other biological systems ranging from protein fibrous structures to tree trunks.

  6. 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.

  7. Signal transmission through the CXC chemokine receptor 4 (CXCR4) transmembrane helices.

    PubMed

    Wescott, Melanie P; Kufareva, Irina; Paes, Cheryl; Goodman, Jason R; Thaker, Yana; Puffer, Bridget A; Berdougo, Eli; Rucker, Joseph B; Handel, Tracy M; Doranz, Benjamin J

    2016-08-30

    The atomic-level mechanisms by which G protein-coupled receptors (GPCRs) transmit extracellular ligand binding events through their transmembrane helices to activate intracellular G proteins remain unclear. Using a comprehensive library of mutations covering all 352 residues of the GPCR CXC chemokine receptor 4 (CXCR4), we identified 41 amino acids that are required for signaling induced by the chemokine ligand CXCL12 (stromal cell-derived factor 1). CXCR4 variants with each of these mutations do not signal properly but remain folded, based on receptor surface trafficking, reactivity to conformationally sensitive monoclonal antibodies, and ligand binding. When visualized on the structure of CXCR4, the majority of these residues form a continuous intramolecular signaling chain through the transmembrane helices; this chain connects chemokine binding residues on the extracellular side of CXCR4 to G protein-coupling residues on its intracellular side. Integrated into a cohesive model of signal transmission, these CXCR4 residues cluster into five functional groups that mediate (i) chemokine engagement, (ii) signal initiation, (iii) signal propagation, (iv) microswitch activation, and (v) G protein coupling. Propagation of the signal passes through a "hydrophobic bridge" on helix VI that coordinates with nearly every known GPCR signaling motif. Our results agree with known conserved mechanisms of GPCR activation and significantly expand on understanding the structural principles of CXCR4 signaling. PMID:27543332

  8. Self-assembly of Janus particles into helices with tunable pitch

    NASA Astrophysics Data System (ADS)

    Fernández, M. Sobrino; Misko, V. R.; Peeters, F. M.

    2015-10-01

    Janus particles present an important class of building blocks for directional assembly. These are compartmentalized colloids with two different hemispheres. In this work we consider a three-dimensional model of Janus spheres that contain one hydrophobic and one charged hemisphere. Using molecular dynamics simulations, we study the morphology of these particles when confined in a channel-like environment. The interplay between the attractive and repulsive forces on each particle gives rise to a rich phase space where the relative orientation of each particle plays a dominant role in the formation of large-scale clusters. The interest in this system is primarily due to the fact that it could give a better understanding of the mechanisms of the formation of polar membranes. A variety of ordered membranelike morphologies is found consisting of single and multiple connected chain configurations. The helicity of these chains can be chosen by simply changing the salt concentration of the solution. Special attention is given to the formation of Bernal spirals. These helices are composed of regular tetrahedra and are known to exhibit nontrivial translational and rotational symmetry.

  9. Evidence of α-helical coiled coils and β-sheets in hornet silk.

    PubMed

    Kameda, Tsunenori; Nemoto, Takashi; Ogawa, Tetsuya; Tosaka, Masatoshi; Kurata, Hiroki; Schaper, Andreas K

    2014-03-01

    α-Helical coiled coil and β-sheet complexes are essential structural building elements of silk proteins produced by different species of the Hymenoptera. Beside X-ray scattering at wide and small angles we applied cryo-electron diffraction and microscopy to demonstrate the presence and the details of such structures in silk of the giant hornet Vespa mandarinia japonica. Our studies on the assembly of the fibrous silk proteins and their internal organization in relation to the primary chain structure suggest a 172 Å pitch supercoil consisting of four intertwined alanine-rich α-helical strands. The axial periodicity may adopt even multiples of the pitch value. Coiled coil motifs form the largest portion of the hornet silk structure and are aligned nearly parallel to the cocoon fiber axis in the same way as the membrane-like parts of the cocoon are molecularly orientated in the spinning direction. Supercoils were found to be associated with β-crystals, predominantly localized in the l-serine-rich chain sequences terminating each of the four predominant silk proteins. Such β-sheet blocks are considered resulting from transformation of random coil molecular sequences due to the action of elongational forces during the spinning process. PMID:24345346

  10. Rings and ribbons in protein structures: Characterization using helical parameters and Ramachandran plots for repeating dipeptides.

    PubMed

    Hayward, Steven; Leader, David P; Al-Shubailly, Fawzia; Milner-White, E James

    2014-02-01

    Helical parameters displayed on a Ramachandran plot allow peptide structures with successive residues having identical main chain conformations to be studied. We investigate repeating dipeptide main chain conformations and present Ramachandran plots encompassing the range of possible structures. Repeating dipeptides fall into the categories: rings, ribbons, and helices. Partial rings occur in the form of "nests" and "catgrips"; many nests are bridged by an oxygen atom hydrogen bonding to the main chain NH groups of alternate residues, an interaction optimized by the ring structure of the nest. A novel recurring feature is identified that we name unpleated β, often situated at the ends of a β-sheet strand. Some are partial rings causing the polypeptide to curve gently away from the sheet; some are straight. They lack β-pleat and almost all incorporate a glycine. An example is the first glycine in the GxxxxGK motif of P-loop proteins. Ribbons in repeating dipeptides can be either flat, as seen in repeated type II and type II' β-turns, or twisted, as in multiple type I and type I' β-turns. Hexa- and octa-peptides in such twisted ribbons occur frequently in proteins, predominantly with type I β-turns, and are the same as the "β-bend ribbons" hitherto identified only in short peptides. One is seen in the GTPase-activating protein for Rho in the active, but not the inactive, form of the enzyme. It forms a β-bend ribbon, which incorporates the catalytic arginine, allowing its side chain guanidino group to approach the active site and enhance enzyme activity.

  11. 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.

  12. Local order and mobility of water molecules around ambivalent helices.

    PubMed

    Bhattacharjee, Nicholus; Biswas, Parbati

    2011-10-27

    Water on a protein surface plays a key role in determining the structure and dynamics of proteins. Compared to the properties of bulk water, many aspects of the structure and dynamics of the water surrounding the proteins are less understood. It is interesting therefore to explore how the properties of the water within the solvation shell around the peptide molecule depend on its specific secondary structure. In this work we investigate the orientational order and residence times of the water molecules to characterize the structure, energetics, and dynamics of the hydration shell water around ambivalent peptides. Ambivalent sequences are identical sequences which display multiple secondary structures in different proteins. Molecular dynamics simulations of representative proteins containing variable helix, variable nonhelix, and conserved helix are also used to explore the local structure and mobility of water molecules in their vicinity. The results, for the first time, depict a different water distribution pattern around the conserved and variable helices. The water molecules surrounding the helical segments in variable helices are found to possess a less locally ordered structure compared to those around their corresponding nonhelical counterparts and conserved helices. The long conserved helices exhibit extremely high local residence times compared to the helical conformations of the variable helices, whereas the residence times of the nonhelical conformations of the variable helices are comparable to those of the short conserved helices. This differential pattern of the structure and dynamics of water molecules in the vicinity of conserved/variable helices may lend valuable insights for understanding the role of solvent effects in determining sequence ambivalency and help in improving the accuracy of water models used in the simulations of proteins.

  13. Construction of the Helicity Injected Torus with Steady Inductive Helicity Injection (HIT-SI)

    NASA Astrophysics Data System (ADS)

    Sieck, P. E.; Gu, P.; Hamp, W. T.; Izzo, V. A.; Jarboe, T. R.; Nelson, B. A.; Rogers, J. A.

    2001-10-01

    HIT-SI is a ``bow tie'' spheromak designed to implement Steady Inductive Helicity Injection (SIHI). The engineering requirements of SIHI lead to several unique design features, including a multiply connected electrically insulating o-ring seal and a close-fitting passive flux conserver that is electrically insulated from the plasma. Prototype tests have been performed to verify the performance of the o-ring seal and the plasma sprayed zirconia insulation. An engineering test of the new HIT-SI front end will be done before it replaces the present HIT-II front end on HIT. Startup and one millisecond of sustainment will be done to test breakdown and verify power supply requirements. The power supplies and external coils are designed to provide 20 MW at 5 kHz to 50 kHz for 1 ms to the helicity injection circuits for this test. Progress in the construction and assembly of HIT-SI will be presented.

  14. Role of glycosaminoglycans in determining the helicity of paired helical filaments.

    PubMed Central

    Arrasate, M.; Pérez, M.; Valpuesta, J. M.; Avila, J.

    1997-01-01

    It is known from previous work that tau is the main component of paired helical filaments (PHFs) and that it can assemble in vitro into polymers resembling PHFs when high concentrations of protein are used. In the search for molecules that can facilitate tau polymerization, a component of neurofibrillary tangles, heparan sulfate (or its more sulfated form, heparin), and other glycosaminoglycans have been tested. Glycosaminoglycans, in the sulfated but not in the unsulfated form, facilitate not only tau assembly but also the formation of polymers resembling PHFs. Conversely, PHFs were found to contain heparan sulfate and chondroitin sulfate. Heparinase or chondroitinase treatment of PHFs results in the formation of straight structures. All of these results suggest a role for sulfated glycosaminoglycans in determining the helicity of PHFs. Images Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 Figure 6 PMID:9327745

  15. Structure-based design of novel Chlamydomonas reinhardtii D1-D2 photosynthetic proteins for herbicide monitoring

    PubMed Central

    Rea, Giuseppina; Polticelli, Fabio; Antonacci, Amina; Scognamiglio, Viviana; Katiyar, Prashant; Kulkarni, Sudhir A; Johanningmeier, Udo; Giardi, Maria Teresa

    2009-01-01

    The D1-D2 heterodimer in the reaction center core of phototrophs binds the redox plastoquinone cofactors, QA and QB, the terminal acceptors of the photosynthetic electron transfer chain in the photosystem II (PSII). This complex is the target of the herbicide atrazine, an environmental pollutant competitive inhibitor of QB binding, and consequently it represents an excellent biomediator to develop biosensors for pollutant monitoring in ecosystems. In this context, we have undertaken a study of the Chlamydomonas reinhardtii D1-D2 proteins aimed at designing site directed mutants with increased affinity for atrazine. The three-dimensional structure of the D1 and D2 proteins from C. reinhardtii has been homology modeled using the crystal structure of the highly homologous Thermosynechococcus elongatus proteins as templates. Mutants of D1 and D2 were then generated in silico and the atrazine binding affinity of the mutant proteins has been calculated to predict mutations able to increase PSII affinity for atrazine. The computational approach has been validated through comparison with available experimental data and production and characterization of one of the predicted mutants. The latter analyses indicated an increase of one order of magnitude of the mutant sensitivity and affinity for atrazine as compared to the control strain. Finally, D1-D2 heterodimer mutants were designed and selected which, according to our model, increase atrazine binding affinity by up to 20 kcal/mol, representing useful starting points for the development of high affinity biosensors for atrazine. PMID:19693932

  16. Insulin-induced tyrosine dephosphorylation of paxillin and focal adhesion kinase requires active phosphotyrosine phosphatase 1D.

    PubMed Central

    Ouwens, D M; Mikkers, H M; van der Zon, G C; Stein-Gerlach, M; Ullrich, A; Maassen, J A

    1996-01-01

    Insulin stimulation of fibroblasts rapidly induces the tyrosine dephosphorylation of proteins of 68 kDa and 125 kDa, in addition to the tyrosine phosphorylation of the insulin receptor beta-chain, insulin receptor substrates 1 and 2, and Shc. Using specific antibodies, the 68 kDa and 125 kDa proteins were identified as paxillin and focal adhesion kinase (pp125FAK) respectively. We have examined whether dephosphorylation of paxillin and pp125FAK requires interaction of the cells with the extracellular matrix. For this, cells were grown on poly(L-lysine) plates, and the tyrosine phosphorylation of pp125FAK and paxillin was increased by addition of lysophosphatidic acid. Under these conditions, insulin still induced the complete dephosphorylation of pp125FAK and paxillin, indicating that this process can occur independently of the interaction of integrins with extracellular matrix proteins. We also studied whether dephosphorylation of pp125FAK and paxillin results from the action of a phosphotyrosine phosphatase. It was found that phenylarsine oxide, a phosphotyrosine phosphatase inhibitor, prevented the insulin-induced dephosphorylation of pp125FAK and paxillin. Furthermore, this insulin-induced dephosphorylation was also impaired in cells expressing a dominant-negative mutant of phosphotyrosine phosphatase 1D (PTP 1D). Thus we have identified paxillin as a target for dephosphorylation by insulin. In addition, we have obtained evidence that the insulin-mediated dephosphorylation of paxillin and pp125FAK requires active PTP 1D. PMID:8809054

  17. Landau Theory of Helical Fermi Liquids.

    PubMed

    Lundgren, Rex; Maciejko, Joseph

    2015-08-01

    We construct a phenomenological Landau theory for the two-dimensional helical Fermi liquid found on the surface of a three-dimensional time-reversal invariant topological insulator. In the presence of rotation symmetry, interactions between quasiparticles are described by ten independent Landau parameters per angular momentum channel, by contrast with the two (symmetric and antisymmetric) Landau parameters for a conventional spin-degenerate Fermi liquid. We project quasiparticle states onto the Fermi surface and obtain an effectively spinless, projected Landau theory with a single projected Landau parameter per angular momentum channel that captures the spin-momentum locking or nontrivial Berry phase of the Fermi surface. As a result of this nontrivial Berry phase, projection to the Fermi surface can increase or lower the angular momentum of the quasiparticle interactions. We derive equilibrium properties, criteria for Fermi surface instabilities, and collective mode dispersions in terms of the projected Landau parameters. We briefly discuss experimental means of measuring projected Landau parameters.

  18. Chaotic coordinates for the Large Helical Device

    SciTech Connect

    Hudson, S. R.; Suzuki, Y.

    2014-10-15

    The theory of quadratic-flux-minimizing (QFM) surfaces is reviewed, and numerical techniques that allow high-order QFM surfaces to be efficiently constructed for experimentally relevant, non-integrable magnetic fields are described. As a practical example, the chaotic edge of the magnetic field in the Large Helical Device (LHD) is examined. A precise technique for finding the boundary surface is implemented, the hierarchy of partial barriers associated with the near-critical cantori is constructed, and a coordinate system, which we call chaotic coordinates, that is based on a selection of QFM surfaces is constructed that simplifies the description of the magnetic field, so that flux surfaces become “straight” and islands become “square.”.

  19. Cool and hot flux ropes, their helicity

    NASA Astrophysics Data System (ADS)

    Nindos, Alexander

    2016-07-01

    We will review recent indirect and direct evidence for the existence of magnetic flux ropes in the solar atmosphere. Magnetic flux ropes may appear as S-shaped or reverse S-shaped (sigmoidal) structures in regions that are likely to erupt, and may also show in nonlinear force-free field extrapolations that use data from photospheric vector magnetograms as boundary condition. The availability of high sensitivity data recorded with unprecedented spatial and temporal resolution in hot EUV wavelengths by the Atmospheric Imaging Assembly (AIA) onboard the Solar Dynamics Observatory (SDO) has revealed the existence of coherent structures identified as hot flux ropes. In this presentation, we will review the properties of both cool and hot flux ropes with an emphasis on the frequency of their occurrence in large flares and on their magnetic helicity content.

  20. Helical Membrane Protein Conformations and their Environment

    PubMed Central

    Cross, Timothy A.; Murray, Dylan T.; Watts, Anthony

    2013-01-01

    Evidence that membrane proteins respond conformationally and functionally to their environment is gaining pace. Structural models, by necessity, have been characterized in preparations where the protein has been removed from its native environment. Different structural methods have used various membrane mimetics that have recently included lipid bilayers as a more native-like environment. Structural tools applied to lipid bilayer-embedded integral proteins are informing us about important generic characteristics of how membrane proteins respond to the lipid environment as compared with their response to other non-lipid environments. Here, we review the current status of the field, with specific reference to observations of some well-studied α-helical membrane proteins, as a starting point to aid the development of possible generic principals for model refinement. PMID:23996195

  1. Conditioner for a helically transported electron beam

    SciTech Connect

    Wang, Changbiao.

    1992-05-01

    The kinetic theory is developed to investigate a conditioner for a helically transported electron beam. Linear expressions for axial velocity spread are derived. Numerical simulation is used to check the theoretical results and examine nonlinear aspects of the conditioning process. The results show that in the linear regime the action of the beam conditioner on a pulsed beam mainly depends on the phase at which the beam enters the conditioner and depends only slightly on the operating wavelength. In the nonlinear regime, however, the action of the conditioner strongly depends on the operating wavelength and only slightly upon the entrance phase. For a properly chosen operating wavelength, a little less than the electron's relativistic cyclotron wavelength, the conditioner can decrease the axial velocity spread of a pulsed beam down to less than one-third of its initial value.

  2. Conditioner for a helically transported electron beam

    SciTech Connect

    Wang, Changbiao

    1992-05-01

    The kinetic theory is developed to investigate a conditioner for a helically transported electron beam. Linear expressions for axial velocity spread are derived. Numerical simulation is used to check the theoretical results and examine nonlinear aspects of the conditioning process. The results show that in the linear regime the action of the beam conditioner on a pulsed beam mainly depends on the phase at which the beam enters the conditioner and depends only slightly on the operating wavelength. In the nonlinear regime, however, the action of the conditioner strongly depends on the operating wavelength and only slightly upon the entrance phase. For a properly chosen operating wavelength, a little less than the electron`s relativistic cyclotron wavelength, the conditioner can decrease the axial velocity spread of a pulsed beam down to less than one-third of its initial value.

  3. Helicity evolution at small-x

    DOE PAGES

    Kovchegov, Yuri V.; Pitonyak, Daniel; Sievert, Matthew D.

    2016-01-13

    We construct small-x evolution equations which can be used to calculate quark and anti-quark helicity TMDs and PDFs, along with the g1 structure function. These evolution equations resum powers of αs ln2(1/x) in the polarization-dependent evolution along with the powers of αs ln(1/x) in the unpolarized evolution which includes saturation efects. The equations are written in an operator form in terms of polarization-dependent Wilson line-like operators. While the equations do not close in general, they become closed and self-contained systems of non-linear equations in the large-Nc and large-Nc & Nf limits. As a cross-check, in the ladder approximation, our equationsmore » map onto the same ladder limit of the infrared evolution equations for g1 structure function derived previously by Bartels, Ermolaev and Ryskin.« less

  4. Novel Design of Superconducting Helical Dipole Magnet

    NASA Astrophysics Data System (ADS)

    Meinke, R.; Senti, M.; Stelzer, G.

    1997-05-01

    Superconducting helical dipole magnets with a nominal field of 4 Tesla are needed for the spin physics program at the Relativistic Heavy Ion Collider (RHIC) at Brookhaven National Laboratory. The magnets are required to operate at a relatively low current of 400 A since many of these magnets have to be independently controlled. The Advanced Magnet Lab, Inc., in Palm Bay, FL has designed and built two prototype magnets using advanced computer controlled coil winding technology. The AML design is extremely cost effective since it avoids magnet specific tooling despite the required complex coil pattern and any precision machined inserts or spacers. It is the first time an accelerator magnet of this technology has reached a field above 4 Tesla. Results from the prototype testing at BNL are presented.

  5. Conditioner for a helically transported electron beam

    SciTech Connect

    Wang, C.

    1992-05-01

    The kinetic theory is developed to investigate a conditioner for a helically imported electron beam. Linear expressions for axial velocity spread are derived. Numerical simulation is used to check the theoretical results and examine nonlinear aspects of the conditioning process. The results show that in the linear regime the action of the beam conditioner on a pulsed beam mainly depends on the phase at which the beam enters the conditioner and depends only slightly on the operating wavelength. In the nonlinear regime, however, the action of the conditioner strongly depends on the operating wavelength and only slightly upon the entrance phase. For a properly chosen operating wavelength, a little less than the electron's relativistic cyclotron wavelength, the conditioner can decrease the axial velocity spread of a pulsed beam down to less than one-third of its initial value.

  6. Conditioner for a helically transported electron beam

    SciTech Connect

    Wang, C.

    1992-05-01

    The kinetic theory is developed to investigate a conditioner for a helically imported electron beam. Linear expressions for axial velocity spread are derived. Numerical simulation is used to check the theoretical results and examine nonlinear aspects of the conditioning process. The results show that in the linear regime the action of the beam conditioner on a pulsed beam mainly depends on the phase at which the beam enters the conditioner and depends only slightly on the operating wavelength. In the nonlinear regime, however, the action of the conditioner strongly depends on the operating wavelength and only slightly upon the entrance phase. For a properly chosen operating wavelength, a little less than the electron`s relativistic cyclotron wavelength, the conditioner can decrease the axial velocity spread of a pulsed beam down to less than one-third of its initial value.

  7. Evidence against dopamine D1/D2 receptor heteromers

    PubMed Central

    Frederick, Aliya L.; Yano, Hideaki; Trifilieff, Pierre; Vishwasrao, Harshad D.; Biezonski, Dominik; Mészáros, József; Sibley, David R.; Kellendonk, Christoph; Sonntag, Kai C.; Graham, Devon L.; Colbran, Roger J.; Stanwood, Gregg D.; Javitch, Jonathan A.

    2014-01-01

    Hetero-oligomers of G-protein-coupled receptors have become the subject of intense investigation because their purported potential to manifest signaling and pharmacological properties that differ from the component receptors makes them highly attractive for the development of more selective pharmacological treatments. In particular, dopamine D1 and D2 receptors have been proposed to form hetero-oligomers that couple to Gαq proteins, and SKF83959 has been proposed to act as a biased agonist that selectively engages these receptor complexes to activate Gαq and thus phospholipase C. D1/D2 heteromers have been proposed as relevant to the pathophysiology and treatment of depression and schizophrenia. We used in vitro bioluminescence resonance energy transfer (BRET), ex vivo analyses of receptor localization and proximity in brain slices, and behavioral assays in mice to characterize signaling from these putative dimers/oligomers. We were unable to detect Gαq or Gα11 protein coupling to homomers or heteromers of D1 or D2 receptors using a variety of biosensors. SKF83959-induced locomotor and grooming behaviors were eliminated in D1 receptor knockout mice, verifying a key role for D1-like receptor activation. In contrast, SKF83959-induced motor responses were intact in D2 receptor and Gαq knockout mice, as well as in knock-in mice expressing a mutant Ala286-CaMKIIα, that cannot autophosphorylate to become active. Moreover, we found that in the shell of the nucleus accumbens, even in neurons in which D1 and D2 receptor promoters are both active, the receptor proteins are segregated and do not form complexes. These data are not compatible with SKF83959 signaling through Gαq or through a D1–D2 heteromer and challenge the existence of such a signaling complex in the adult animals that we used for our studies. PMID:25560761

  8. Dynamical functions of a 1D correlated quantum liquid

    NASA Astrophysics Data System (ADS)

    Carmelo, J. M. P.; Bozi, D.; Penc, K.

    2008-10-01

    The dynamical correlation functions in one-dimensional electronic systems show power-law behaviour at low energies and momenta close to integer multiples of the charge and spin Fermi momenta. These systems are usually referred to as Tomonaga-Luttinger liquids. However, near well defined lines of the (k,ω) plane the power-law behaviour extends beyond the low-energy cases mentioned above, and also appears at higher energies, leading to singular features in the photoemission spectra and other dynamical correlation functions. The general spectral-function expressions derived in this paper were used in recent theoretical studies of the finite-energy singular features in photoemission of the organic compound tetrathiafulvalene-tetracyanoquinodimethane (TTF-TCNQ) metallic phase. They are based on a so-called pseudofermion dynamical theory (PDT), which allows us to systematically enumerate and describe the excitations in the Hubbard model starting from the Bethe ansatz, as well as to calculate the charge and spin object phase shifts appearing as exponents of the power laws. In particular, we concentrate on the spin-density m\\rightarrow 0 limit and on effects in the vicinity of the singular border lines, as well as close to half filling. Our studies take into account spectral contributions from types of microscopic processes that do not occur for finite values of the spin density. In addition, the specific processes involved in the spectral features of TTF-TCNQ are studied. Our results are useful for the further understanding of the unusual spectral properties observed in low-dimensional organic metals and also provide expressions for the one- and two-atom spectral functions of a correlated quantum system of ultracold fermionic atoms in a 1D optical lattice with on-site two-atom repulsion.

  9. Structure and dynamics of the lipid modifications of a transmembrane α-helical peptide determined by ²H solid-state NMR spectroscopy.

    PubMed

    Penk, Anja; Müller, Matthias; Scheidt, Holger A; Langosch, Dieter; Huster, Daniel

    2011-03-01

    The fusion of biological membranes is mediated by integral membrane proteins with α-helical transmembrane segments. Additionally, those proteins are often modified by the covalent attachment of hydrocarbon chains. Previously, a series of de novo designed α-helical peptides with mixed Leu/Val sequences was presented, mimicking fusiogenically active transmembrane segments in model membranes (Hofmann et al., Proc. Natl. Acad. Sci. USA 101 (2004) 14776-14781). From this series, we have investigated the peptide LV16 (KKKW LVLV LVLV LVLV LVLV KKK), which was synthesized featuring either a free N-terminus or a saturated N-acylation of 2, 8, 12, or 16 carbons. We used ²H and ³¹P NMR spectroscopy to investigate the structure and dynamics of those peptide lipid modifications in POPC and DLPC bilayers and compared them to the hydrocarbon chains of the surrounding membrane. Except for the C2 chain, all peptide acyl chains were found to insert well into the membrane. This can be explained by the high local lipid concentrations the N-terminal lipid chains experience. Further, the insertion of these peptides did not influence the membrane structure and dynamics as seen from the ²H and ³¹P NMR data. In spite of the fact that the longer acyl chains insert into the membrane, they do not adapt their lengths to the thickness of the bilayer. Even the C16 lipid chain on the peptide, which could match the length of the POPC palmitoyl chain, exhibited lower order parameters in the upper chain, which get closer and finally reach similar values in the lower chain region. ²H NMR square law plots reveal motions of slightly larger amplitudes for the peptide lipid chains compared to the surrounding phospholipids. In spite of the significantly different chain lengths of the acylations, the fraction of gauche defects in the inserted chains is constant.

  10. New approach for designing single-chain magnets: organization of chains via hydrogen bonding between nucleobases.

    PubMed

    Zhang, Wei-Xiong; Shiga, Takuya; Miyasaka, Hitoshi; Yamashita, Masahiro

    2012-04-25

    Two one-dimensional (1D) manganese complexes, [Mn(2)(naphtmen)(2)(L)](ClO(4))·2Et(2)O·2MeOH·H(2)O (1) and [Mn(2)(naphtmen)(2)(HL)](ClO(4))(2)·MeOH (2), were synthesized by using a bridging ligand with a nucleobase moiety, 6-amino-9-β-carboxyethylpurine, and a salen-type manganese(III) dinuclear complex, [Mn(2)(naphtmen)(2)(H(2)O)(2)](ClO(4))(2) (naphtmen(2-) = N,N'-(1,1,2,2-tetramethylethylene)bis(naphthylideneiminato) dianion). In 1 and 2, the carboxylate-bridged Mn(III) dinuclear units are alternately linked by two kinds of weak Mn···O interactions into 1D chains. As a result, canted antiferromagnetic and ferromagnetic interactions are alternately present along the chains, leading to a 1D chain with non-cancellation of anisotropic spins. Since the chains connected via H-bonds between nucleobase moieties are magnetically isolated, both 1 and 2 act as single-chain magnets (SCMs). More importantly, this result shows the smaller canting angles hinder long-range ordering in favor of SCM dynamics.

  11. Synthesis, characterization, and physical properties of 1D nanostructures

    NASA Astrophysics Data System (ADS)

    Marley, Peter Mchael

    The roster of materials exhibiting metal---insulator transitions with sharply discontinuous switching of electrical conductivity close to room temperature remains rather sparse despite the fundamental interest in the electronic instabilities manifested in such materials and the plethora of potential technological applications, ranging from frequency-agile metamaterials to electrochromic coatings and Mott field-effect transistors. Vanadium oxide bronzes with the general formula MxV2O 5, provide a wealth of compositions and frameworks where strong electron correlation can be systematically (albeit thus far only empirically) tuned. Charge fluctuations along the quasi-1D frameworks of MxV 2O5 bronzes have evinced much recent interest owing to the manifestation of colossal metal---insulator transitions and superconductivity. We start with a general review on the phase transitions, both electronic and structural, of vanadium oxide bronzes in Chapter 1. In Chapter 2, we demonstrate an unprecedented reversible transformation between double-layered (delta) and tunnel (beta) quasi-1D geometries for nanowires of a divalent vanadium bronze CaxV2O5 (x ˜0.23) upon annealing-induced dehydration and hydrothermally-induced hydration. Such a facile hydration/dehydration-induced interconversion between two prominent quasi-1D structures (accompanied by a change in charge ordering motifs) has not been observed in the bulk and is posited to result from the ease of propagation of crystallographic slip processes across the confined nanowire widths for the delta→beta conversion and the facile diffusion of water molecules within the tunnel geometries for the beta→delta reversion. We demonstrate in Chapter 3 unprecedented pronounced metal-insulator transitions induced by application of a voltage for nanowires of a vanadium oxide bronze with intercalated divalent cations, beta-PbxV 2O5 (x ˜0.33). The induction of the phase transition through application of an electric field at room

  12. Synthesis, characterization, and physical properties of 1D nanostructures

    NASA Astrophysics Data System (ADS)

    Marley, Peter Mchael

    The roster of materials exhibiting metal---insulator transitions with sharply discontinuous switching of electrical conductivity close to room temperature remains rather sparse despite the fundamental interest in the electronic instabilities manifested in such materials and the plethora of potential technological applications, ranging from frequency-agile metamaterials to electrochromic coatings and Mott field-effect transistors. Vanadium oxide bronzes with the general formula MxV2O 5, provide a wealth of compositions and frameworks where strong electron correlation can be systematically (albeit thus far only empirically) tuned. Charge fluctuations along the quasi-1D frameworks of MxV 2O5 bronzes have evinced much recent interest owing to the manifestation of colossal metal---insulator transitions and superconductivity. We start with a general review on the phase transitions, both electronic and structural, of vanadium oxide bronzes in Chapter 1. In Chapter 2, we demonstrate an unprecedented reversible transformation between double-layered (delta) and tunnel (beta) quasi-1D geometries for nanowires of a divalent vanadium bronze CaxV2O5 (x ˜0.23) upon annealing-induced dehydration and hydrothermally-induced hydration. Such a facile hydration/dehydration-induced interconversion between two prominent quasi-1D structures (accompanied by a change in charge ordering motifs) has not been observed in the bulk and is posited to result from the ease of propagation of crystallographic slip processes across the confined nanowire widths for the delta→beta conversion and the facile diffusion of water molecules within the tunnel geometries for the beta→delta reversion. We demonstrate in Chapter 3 unprecedented pronounced metal-insulator transitions induced by application of a voltage for nanowires of a vanadium oxide bronze with intercalated divalent cations, beta-PbxV 2O5 (x ˜0.33). The induction of the phase transition through application of an electric field at room

  13. SCCRO3 (DCUN1D3) Antagonizes the Neddylation and Oncogenic Activity of SCCRO (DCUN1D1)*

    PubMed Central

    Huang, Guochang; Stock, Cameron; Bommeljé, Claire C.; Weeda, Víola B.; Shah, Kushyup; Bains, Sarina; Buss, Elizabeth; Shaha, Manish; Rechler, Willi; Ramanathan, Suresh Y.; Singh, Bhuvanesh

    2014-01-01

    The activity of cullin-RING type ubiquitination E3 ligases is regulated by neddylation, a process analogous to ubiquitination that culminates in covalent attachment of the ubiquitin-like protein Nedd8 to cullins. As a component of the E3 for neddylation, SCCRO/DCUN1D1 plays a key regulatory role in neddylation and, consequently, cullin-RING ligase activity. The essential contribution of SCCRO to neddylation is to promote nuclear translocation of the cullin-ROC1 complex. The presence of a myristoyl sequence in SCCRO3, one of four SCCRO paralogues present in humans that localizes to the membrane, raises questions about its function in neddylation. We found that although SCCRO3 binds to CAND1, cullins, and ROC1, it does not efficiently bind to Ubc12, promote cullin neddylation, or conform to the reaction processivity paradigms, suggesting that SCCRO3 does not have E3 activity. Expression of SCCRO3 inhibits SCCRO-promoted neddylation by sequestering cullins to the membrane, thereby blocking its nuclear translocation. Moreover, SCCRO3 inhibits SCCRO transforming activity. The inhibitory effects of SCCRO3 on SCCRO-promoted neddylation and transformation require both an intact myristoyl sequence and PONY domain, confirming that membrane localization and binding to cullins are required for in vivo functions. Taken together, our findings suggest that SCCRO3 functions as a tumor suppressor by antagonizing the neddylation activity of SCCRO. PMID:25349211

  14. Correlation between inter-spin interaction and molecular dynamics of organic radicals in organic 1D nanochannels

    SciTech Connect

    Kobayashi, Hirokazu

    2015-12-31

    One-dimensional (1D) molecular chains of 4-substituted-2,2,6,6-tetramethyl-1-piperidinyloxyl (4-X-TEMPO) radicals were constructed in the crystalline 1D nanochannels of 2,4,6-tris(4-chlorophenoxy)-1,3,5-triazine (CLPOT) used as a template. The ESR spectra of CLPOT inclusion compounds (ICs) using 4-X-TEMPO were examined on the basis of spectral simulation using EasySpin program package for simulating and fitting ESR spectra. The ESR spectra of [(CLPOT){sub 2}-(TEMPO){sub 1.0}] IC were isotropic in the total range of temperatures. The peak-to-peak line width (ΔB{sub pp}) became monotonically narrower from 2.8 to 1.3 mT with increase in temperature in the range of 4.2–298 K. The effect of the rotational diffusion motion of TEMPO radicals in the CLPOT nanochannels for the inter-spin interaction of the [(CLPOT){sub 2}-(TEMPO){sub 1.0}] IC was found to be smaller than the case of [(TPP){sub 2}−(TEMPO){sub 1.0}] IC (TPP = tris(o-phenylenedioxy)cyclotriphosphazene) reported in our previous study. The ΔB{sub pp} of the [(CLPOT){sub 2}-(TEMPO){sub 1.0}] IC in the whole range of temperatures was much narrower than the estimation to be based on the Van Vleck’s formula for the second moment of the rigid lattice model where the electron spin can be considered as fixed; 11 mT of Gaussian line-width component. This suggests the possibility of exchange narrowing in the 1D organic-radical chains of the [(CLPOT){sub 2}-(TEMPO){sub 1.0}] IC. On the other hand, the ESR spectra of [(CLPOT){sub 2}-(MeO-TEMPO){sub 0.41}] IC (MeO-TEMPO = 4-methoxy-TEMPO) were reproduced by a superposition of major broad isotropic adsorption line and minor temperature-dependent modulated triplet component. This suggests that the IC has the part of 1D organic-radical chains and MeO-TEMPO molecules isolated in the CLPOT nanochannels.

  15. Correlation between inter-spin interaction and molecular dynamics of organic radicals in organic 1D nanochannels

    NASA Astrophysics Data System (ADS)

    Kobayashi, Hirokazu

    2015-12-01

    One-dimensional (1D) molecular chains of 4-substituted-2,2,6,6-tetramethyl-1-piperidinyloxyl (4-X-TEMPO) radicals were constructed in the crystalline 1D nanochannels of 2,4,6-tris(4-chlorophenoxy)-1,3,5-triazine (CLPOT) used as a template. The ESR spectra of CLPOT inclusion compounds (ICs) using 4-X-TEMPO were examined on the basis of spectral simulation using EasySpin program package for simulating and fitting ESR spectra. The ESR spectra of [(CLPOT)2-(TEMPO)1.0] IC were isotropic in the total range of temperatures. The peak-to-peak line width (ΔBpp) became monotonically narrower from 2.8 to 1.3 mT with increase in temperature in the range of 4.2-298 K. The effect of the rotational diffusion motion of TEMPO radicals in the CLPOT nanochannels for the inter-spin interaction of the [(CLPOT)2-(TEMPO)1.0] IC was found to be smaller than the case of [(TPP)2-(TEMPO)1.0] IC (TPP = tris(o-phenylenedioxy)cyclotriphosphazene) reported in our previous study. The ΔBpp of the [(CLPOT)2-(TEMPO)1.0] IC in the whole range of temperatures was much narrower than the estimation to be based on the Van Vleck's formula for the second moment of the rigid lattice model where the electron spin can be considered as fixed; 11 mT of Gaussian line-width component. This suggests the possibility of exchange narrowing in the 1D organic-radical chains of the [(CLPOT)2-(TEMPO)1.0] IC. On the other hand, the ESR spectra of [(CLPOT)2-(MeO-TEMPO)0.41] IC (MeO-TEMPO = 4-methoxy-TEMPO) were reproduced by a superposition of major broad isotropic adsorption line and minor temperature-dependent modulated triplet component. This suggests that the IC has the part of 1D organic-radical chains and MeO-TEMPO molecules isolated in the CLPOT nanochannels.

  16. Synthesis, characterization and comparison of polyaniline 1D-structure controlled by poly(L-lactide) and poly(D-lactide)

    NASA Astrophysics Data System (ADS)

    Gu, Zhou-Jie; Shen, Qing

    2016-01-01

    1D-structural polyaniline (PANI) was controllably synthesized by utilizing the poly(L-lactide) (PLLA) and poly(D-lactide) (PDLA) as controllers. FESEM images showed that the morphology of 1D-structural PANI controlled by PDLA likes a joint obviously unlike PLLA controlled vertebra structure reported previously. To set the ratio of ANI/PLLA (ml/g) at 0.45/0.135, 0.45/0.270 and 0.45/0.540, the formed PANI 1D structure was changed in the cross-section as four round leaves, four non-round leaves and four sharp leaves, respectively. FTIR and XRD analysis indicated that the PLLA and PDLA both were doped in PANI chains while the PLLA was strongly in the electrons delocalization than that of the PDLA due probably to the L-type stronger in crystal polymorphism than that of the D-type.

  17. 1-D Tremor Streaks: Implications for a Streak Source Model

    NASA Astrophysics Data System (ADS)

    Houston, H.; Ghosh, A.; Vidale, J. E.

    2009-12-01

    Recent observations of non-volcanic tremor in Cascadia and Japan show “streaks” of tremor moving up and down dip in a convergence-parallel direction at “driving velocities” (i.e., 30 to 120 km/hr). Streak lengths of 30 to 40 km are occasionally observed. We explore the implications of these observations for a source model and spectrum of tremor. Key elements involve the extreme geometry and slow “rupture velocity” implied by the streaks. The source spectrum of tremor and other ETS seismic radiation exhibits a spectral falloff roughly as the inverse of frequency (1/f) in contrast to that of earthquakes, which follow a spectral falloff of 1/f squared above a corner frequency. Nevertheless, several observations suggest that the deformation that generates tremor is shear slip in the plate convergence direction. A fundamental question, then, has been what slip source could produce such an observed 1/f falloff over a wide frequency range. We propose a kinematic model, consistent with the 1-D geometry of the tremor streaks, in which fault displacement and width are strongly limited and rupture growth occurs only along fault length, which is oriented in a convergence-parallel direction (up or down dip). This is a version of the well-known Haskell model in which the durations of the two boxcars are very different. A 1/f spectral falloff holds between the corner frequencies associated with the two durations. Thus, the frequency range of the observed 1/f spectral falloff of tremor provides constraints on the durations of the boxcars. Further constraints involve the maximum likely displacement in an ETS event, the rupture velocities of the streaks, and the moment release rate. The narrow streak geometry implies fairly high strain and stress drops, in contrast to the low overall stress drops inferred from tidal modulation of tremor and the low strain across the entire ETS region. The observation of tremor streaks migrating at 10's of km/hour, in conjunction with the

  18. Monomers, Dimers, and Helices: Complexities of Cerium and Plutonium Phenanthrolinecarboxylates.

    PubMed

    Cary, Samantha K; Ferrier, Maryline G; Baumbach, Ryan E; Silver, Mark A; Lezama Pacheco, Juan; Kozimor, Stosh A; La Pierre, Henry S; Stein, Benjamin W; Arico, Alexandra A; Gray, Danielle L; Albrecht-Schmitt, Thomas E

    2016-05-01

    The reaction of Ce(III) or Pu(III) with 1,10-phenanthroline-2,9-dicarboxylic acid (PDAH2) results in the formation of new f-element coordination complexes. In the case of cerium, Ce(PDA)(H2O)2Cl·H2O (1) or [Ce(PDAH)(PDA)]2[Ce(PDAH)(PDA)] (2) was isolated depending on the Ce/ligand ratio in the reaction. The structure of 2 is composed of two distinct substructures that are constructed from the same monomer. This monomer is composed of a Ce(III) cation bound by one PDA(2-) dianionic ligand and one PDAH(-) monoanionic ligand, both of which are tetradentate. Bridging by the carboxylate moieties leads to either [Ce(PDAH)(PDA)]2 dimers or [Ce(PDAH)(PDA)]1∞ helical chains. For plutonium, Pu(PDA)2 (3) was the only product isolated regardless of the Pu/ligand ratio employed in the reaction. During the reaction of plutonium with PDAH2, Pu(III) is oxidized to Pu(IV), generating 3. This assignment is consistent with structural metrics and the optical absorption spectrum. Ambiguity in the assignment of the oxidation state of cerium in 1 and 2 from UV-vis-near-IR spectra invoked the use of Ce L3,2-edge X-ray absorption near-edge spectroscopy, magnetic susceptibility, and heat capacity measurements. These experiments support the assignment of Ce(III) in both compounds. The bond distances and coordination numbers are also consistent with these assignments. 3 contains 8-coordinate Pu(IV), whereas the cerium centers in 1 and 2 are 9- and/or 10-coordinate, which correlates with the increased size of Ce(III) versus Pu(IV). Taken together, these data provide an example of a system where the differences in the redox behavior between these f elements creates more complex chemistry with cerium than with plutonium. PMID:27070401

  19. A drift-magnetohydrodynamical fluid model of helical magnetic island equilibria in the pedestals of H-mode tokamak plasmas

    SciTech Connect

    Fitzpatrick, R.; Waelbroeck, F. L.

    2010-06-15

    A drift-magnetohydrodynamical (MHD) fluid model is developed for an isolated, steady-state, helical magnetic island chain, embedded in the pedestal of a large aspect ratio, low-beta, circular cross section, H-mode tokamak plasma, to which an externally generated, multiharmonic, static magnetic perturbation whose amplitude is sufficiently large to fully relax the pedestal toroidal ion flow is applied. The model is based on a set of single helicity, reduced, drift-MHD fluid equations which take into account neoclassical poloidal and toroidal flow damping, the perturbed bootstrap current, diamagnetic flows, anomalous cross-field diffusion, average magnetic-field line curvature, and coupling to drift-acoustic waves. These equations are solved analytically in a number of different ordering regimes by means of a systematic expansion in small quantities. For the case of a freely rotating island chain, the main aims of the calculation are to determine the chain's phase velocity, and the sign and magnitude of the ion polarization term appearing in its Rutherford radial width evolution equation. For the case of a locked island chain, the main aims of the calculation are to determine the sign and magnitude of the polarization term.

  20. HELICITY CONSERVATION IN NONLINEAR MEAN-FIELD SOLAR DYNAMO

    SciTech Connect

    Pipin, V. V.; Sokoloff, D. D.; Zhang, H.; Kuzanyan, K. M.

    2013-05-01

    It is believed that magnetic helicity conservation is an important constraint on large-scale astrophysical dynamos. In this paper, we study a mean-field solar dynamo model that employs two different formulations of the magnetic helicity conservation. In the first approach, the evolution of the averaged small-scale magnetic helicity is largely determined by the local induction effects due to the large-scale magnetic field, turbulent motions, and the turbulent diffusive loss of helicity. In this case, the dynamo model shows that the typical strength of the large-scale magnetic field generated by the dynamo is much smaller than the equipartition value for the magnetic Reynolds number 10{sup 6}. This is the so-called catastrophic quenching (CQ) phenomenon. In the literature, this is considered to be typical for various kinds of solar dynamo models, including the distributed-type and the Babcock-Leighton-type dynamos. The problem can be resolved by the second formulation, which is derived from the integral conservation of the total magnetic helicity. In this case, the dynamo model shows that magnetic helicity propagates with the dynamo wave from the bottom of the convection zone to the surface. This prevents CQ because of the local balance between the large-scale and small-scale magnetic helicities. Thus, the solar dynamo can operate in a wide range of magnetic Reynolds numbers up to 10{sup 6}.

  1. Deducing the symmetry of helical assemblies: Applications to membrane proteins.

    PubMed

    Coudray, Nicolas; Lasala, Ralph; Zhang, Zhening; Clark, Kathy M; Dumont, Mark E; Stokes, David L

    2016-08-01

    Helical reconstruction represents a convenient and powerful approach for structure determination of macromolecules that assemble into helical arrays. In the case of membrane proteins, formation of tubular crystals with helical symmetry represents an attractive alternative, especially when their small size precludes the use of single-particle analysis. An essential first step for helical reconstruction is to characterize the helical symmetry. This process is often daunting, due to the complexity of helical diffraction and to the low signal-to-noise ratio in images of individual assemblies. Furthermore, the large diameters of the tubular crystals produced by membrane proteins exacerbates the innate ambiguities that, if not resolved, will produce incorrect structures. In this report, we describe a set of tools that can be used to eliminate ambiguities and to validate the choice of symmetry. The first approach increases the signal-to-noise ratio along layer lines by incoherently summing data from multiple helical assemblies, thus producing several candidate indexing schemes. The second approach compares the layer lines from images with those from synthetic models built with the various candidate schemes. The third approach uses unit cell dimensions measured from collapsed tubes to distinguish between these candidate schemes. These approaches are illustrated with tubular crystals from a boron transporter from yeast, Bor1p, and a β-barrel channel from the outer membrane of E. coli, OmpF.

  2. Helicity transport from solar convection zone to interplanetary space

    NASA Astrophysics Data System (ADS)

    Zhang, Mei

    2013-07-01

    Magnetic helicity is a physical quantity that describes field topology. It is also a conserved quantity as Berger in 1984 demonstrated that the total magnetic helicity is still conserved in the corona even when there is a fast magnetic reconnection. It is generally believed that solar magnetic fields, together with their helicity, are created in the convection zone by various dynamo processes. These fields and helicity are transported into the corona through solar photosphere and finally released into the interplanetary space via various processes such as coronal mass ejections (CMEs) and solar winds. Here I will give a brief review on our recent works, first on helicity observations on the photosphere and how to understand these observations via dynamo models. Mostly, I will talk about what are the possible consequences of magnetic helicity accumulation in the corona, namely, the formation of magnetic flux ropes, CMEs taking place as an unavoidable product of coronal evolution, and flux emergences as a trigger of CMEs. Finally, I will address on in what a form magnetic field in the interplanetary space would accommodate a large amount of magnetic helicity that solar dynamo processes have been continuously producing.

  3. What is the Most Important Origin of the Coronal Helicity?

    NASA Astrophysics Data System (ADS)

    Tian, L.

    23 active regions (ARs) with well-defined SXR sigmoids are selected to study which is the more important origin of the coronal helicity -- the emergence of magnetic fields or photospheric horizontal motions. The radial magnetic flux of each polarity, the helicity injection rate, and total helicity flux (Δ Hlct) are calculated using local correlation tracking technique and {MDI 96m} line-of-sight magnetograms, and the helicity budget of the differential rotation (Δ Hrot) is also estimated. It is found that six ARs inject helicity flux greater than 1.0× 1043 {Mx}^2 (Δ H=Δ Hlct-Δ Hrot), in a sample of seven ARs with emerging magnetic flux greater than 1.0× 1022 Mx. On the other hand, in sixteen ARs with emerging magnetic flux less than 1.0× 1022 Mx, only four ARs inject helicity flux greater than 1.0× 1043 Mx^2, which denotes the main contribution of the horizontal motions. The statistical results suggest that the horizontal motions are not important to the coronal helicity injection when there is little magnetic field emergence.

  4. Extreme Helicity and Intense Convective Towers in Hurricane Bonnie

    NASA Technical Reports Server (NTRS)

    Molinari, John; Vollaro, David

    2008-01-01

    Helicity was calculated in Hurricane Bonnie (1998) using tropospheric-deep dropsonde soundings from the NASA Convection and Moisture Experiment. Large helicity existed downshear of the storm center with respect to the ambient vertical wind shear. It was associated with veering, semicircular hodographs created by strong, vortex-scale, radial-vertical flow induced by the shear. The most extreme values of helicity, among the largest ever reported in the literature, occurred in the vicinity of deep convective cells in the downshear-left quadrant. These cells reached as high as 17.5 km and displayed the temporal and spatial scales of supercells. Convective available potential energy (CAPE) averaged 861 J/kg downshear, but only about one-third as large upshear. The soundings nearest the deep cells were evaluated using two empirical supercell parameters that make use of CAPE, helicity, and/or shear. These parameters supported the possible existence of supercells as a consequence of the exceptional helicity combined with moderate but sufficient CAPE. Ambient vertical wind shear exceeded 12 m/s for 30 h, yet the hurricane maintained 50 m/s maximum winds. It is hypothesized that the long-lived convective cells enabled the storm to resist the negative impact of the shear. Supercells in large-helicity, curved-hodograph environments appear to provide a useful conceptual model for intense convection in the hurricane core. Helicity calculations might also give some insight into the behavior of vortical hot towers, which share some characteristics with supercells.

  5. Pool-cooled superconducting magnet design of large helical device

    NASA Astrophysics Data System (ADS)

    Suzuki, S.; Miyazawa, H.; Saito, R.; Iida, F.; Ogata, H.; Yamazaki, Y.; Motojima, Osamu; Yamamoto, Junya; Fujiwara, Masami; Takeo, M.

    1990-03-01

    The Large Helical Device is the next generation in helical equipment for nuclear fusion. The large scale superconducting magnets are going to be applied to these coils. The major and minor radius of the helical coil system are 4 and 0.96 m respectively and the magnetic field is 4 T at the plasma center and 8 T at the coil surface. The coil system stores about 2 GJ of total energy. The superconductor of the helical coil is pure aluminum stabilized Nb-Ti compacted strand cable with copper housing. The coils have a stainless-steel helium can that is filled with liquid helium. This pool-cooled superconducting helical coil system satisfies the fully stabilized condition. The superconducting poloidal coils are composed of six (three pairs) circular coils and use forced-cooled superconductors to reduce the eddy current losses by the field changing operation. The helical and poloidal coil system are built in the large bell-jar (vacuum vessel for thermal insulation) with outer diameter of 13 m. Conductor design and stability of superconducting magnets for helical and poloidal coil systems are described.

  6. Helicity, topology, and Kelvin waves in reconnecting quantum knots

    NASA Astrophysics Data System (ADS)

    Clark di Leoni, P.; Mininni, P. D.; Brachet, M. E.

    2016-10-01

    Helicity is a topological invariant that measures the linkage and knottedness of lines, tubes, and ribbons. As such, it has found myriads of applications in astrophysics, fluid dynamics, atmospheric sciences, and biology. In quantum flows, where topology-changing reconnection events are a staple, helicity appears as a key quantity to study. However, the usual definition of helicity is not well posed in quantum vortices, and its computation based on counting links and crossings of centerline vorticity can be downright impossible to apply in complex and turbulent scenarios. We present a definition of helicity which overcomes these problems and which gives the expected result in the large-scale limit. With it, we show that certain reconnection events can excite Kelvin waves and other complex motions of the centerline vorticity, which slowly deplete helicity as they interact nonlinearly, thus linking the theory of vortex knots with observations of quantum fluids. This process also results in the depletion of helicity in a fully turbulent quantum flow, in a way reminiscent of the decay of helicity in classical fluids.

  7. Deducing the symmetry of helical assemblies: Applications to membrane proteins.

    PubMed

    Coudray, Nicolas; Lasala, Ralph; Zhang, Zhening; Clark, Kathy M; Dumont, Mark E; Stokes, David L

    2016-08-01

    Helical reconstruction represents a convenient and powerful approach for structure determination of macromolecules that assemble into helical arrays. In the case of membrane proteins, formation of tubular crystals with helical symmetry represents an attractive alternative, especially when their small size precludes the use of single-particle analysis. An essential first step for helical reconstruction is to characterize the helical symmetry. This process is often daunting, due to the complexity of helical diffraction and to the low signal-to-noise ratio in images of individual assemblies. Furthermore, the large diameters of the tubular crystals produced by membrane proteins exacerbates the innate ambiguities that, if not resolved, will produce incorrect structures. In this report, we describe a set of tools that can be used to eliminate ambiguities and to validate the choice of symmetry. The first approach increases the signal-to-noise ratio along layer lines by incoherently summing data from multiple helical assemblies, thus producing several candidate indexing schemes. The second approach compares the layer lines from images with those from synthetic models built with the various candidate schemes. The third approach uses unit cell dimensions measured from collapsed tubes to distinguish between these candidate schemes. These approaches are illustrated with tubular crystals from a boron transporter from yeast, Bor1p, and a β-barrel channel from the outer membrane of E. coli, OmpF. PMID:27255388

  8. Human CD1d knock-in mouse model demonstrates potent antitumor potential of human CD1d-restricted invariant natural killer T cells

    PubMed Central

    Wen, Xiangshu; Rao, Ping; Carreño, Leandro J.; Kim, Seil; Lawrenczyk, Agnieszka; Porcelli, Steven A.; Cresswell, Peter; Yuan, Weiming

    2013-01-01

    Despite a high degree of conservation, subtle but important differences exist between the CD1d antigen presentation pathways of humans and mice. These differences may account for the minimal success of natural killer T (NKT) cell-based antitumor therapies in human clinical trials, which contrast strongly with the powerful antitumor effects in conventional mouse models. To develop an accurate model for in vivo human CD1d (hCD1d) antigen presentation, we have generated a hCD1d knock-in (hCD1d-KI) mouse. In these mice, hCD1d is expressed in a native tissue distribution pattern and supports NKT cell development. Reduced numbers of invariant NKT (iNKT) cells were observed, but at an abundance comparable to that in most normal humans. These iNKT cells predominantly expressed mouse Vβ8, the homolog of human Vβ11, and phenotypically resembled human iNKT cells in their reduced expression of CD4. Importantly, iNKT cells in hCD1d knock-in mice exert a potent antitumor function in a melanoma challenge model. Our results show that replacement of mCD1d by hCD1d can select a population of functional iNKT cells closely resembling human iNKT cells. These hCD1d knock-in mice will allow more accurate in vivo modeling of human iNKT cell responses and will facilitate the preclinical assessment of iNKT cell-targeted antitumor therapies. PMID:23382238

  9. Membrane-induced helical conformation of an active candidacidal fragment of salivary histatins.

    PubMed

    Raj, P A; Soni, S D; Levine, M J

    1994-04-01

    The conformational preference of the candidacidal C-terminal 16 residue fragment (9-24; G-Y-K-R-K-F-H-E-K-H-H-S-H-R-G-Y) of salivary histatin 5 was examined in water, methanol, and dimethyl sulfoxide solutions using 500 MHz two-dimensional-NMR. Fourier transform infrared and CD spectroscopy were used to delineate its membrane-bound conformation in lipid vesicles. The peptide backbone and side-chain proton resonance assignments were accomplished by two-dimensional total correlated and nuclear Overhauser effect (NOE) spectra. The coupling constant (JNH-C alpha H) values determined from the double quantum-filtered correlated spectra, temperature coefficients of NH chemical shifts (d delta/dT), 1H/2H exchange rates on amide resonances, and the set of NOE connectivities were used to delineate backbone conformational features. The high JNH-C alpha H values (> or = 7.4 Hz), absence of any characteristic NH-NH (i, i + 1) or C alpha H-C beta H (i, i + 3) NOE connectivities, high d delta/dT values (> or = 0.004), and the fast 1H/2H amide exchange suggest that the histatin peptide favors unfolded random conformations in aqueous solution at pH 3.8. In contrast, the JNH-C alpha H values (< or = 6.5 Hz), slow 1H/2H exchange, low d delta/dT values (< or = 0.003) observed for amide resonances of residues 5-16, and the characteristic NH-NH (i, i + 1), C alpha H-C beta H (i, i + 3) NOE connectivities, provide evidence for the presence of largely alpha-helical conformations in dimethyl sulfoxide, which mimics the polar aprotic membrane environment. In methanolic solutions, 3(10)-helical conformations could exist as a minor population together with the major alpha-helical conformations. Fourier transform infrared spectroscopy and CD data indicate that lipid environments such as dimyristoylphosphatidylcholine vesicles could induce the peptide to fold into predominantly alpha-helical conformation. The results suggest that in dimethyl sulfoxide and dimyristoylphosphatidylcholine vesicles

  10. Majority-Rules-Type Helical Poly(quinoxaline-2,3-diyl)s as Highly Efficient Chirality-Amplification Systems for Asymmetric Catalysis.

    PubMed

    Ke, Yuan-Zhen; Nagata, Yuuya; Yamada, Tetsuya; Suginome, Michinori

    2015-08-01

    A highly efficient majority-rules effect of poly(quinoxaline-2,3-diyl)s (PQXs) bearing 2-butoxymethyl chiral side chains at the 6- and 7-positions was established and attributed to large ΔG(h) values (0.22-0.41 kJ mol(-1)), which are defined as the energy difference between P- and M-helical conformations per chiral unit. A PQX copolymer prepared from a monomer derived from (R)-2-octanol (23% ee) and a monomer bearing a PPh2 group adopted a single-handed helical structure (>99%) and could be used as a highly enantioselective chiral ligand in palladium-catalyzed asymmetric reactions (products formed with up to 94% ee), in which the enantioselectivity could be switched by solvent-dependent inversion of the helical PQX backbone.

  11. Multipinhole SPECT helical scan parameters and imaging volume

    SciTech Connect

    Yao, Rutao Deng, Xiao; Wei, Qingyang; Dai, Tiantian; Ma, Tianyu; Lecomte, Roger

    2015-11-15

    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 evaluated 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.

  12. Crystal Structures of Lys-63-linked tri- and di-ubiquitin Reveal a Highly Extended Chain Architecture

    SciTech Connect

    Weeks, S.; Grasty, K; Hernandez-Cuebas, L; Loll, P

    2009-01-01

    The covalent attachment of different types of poly-ubiquitin chains signal different outcomes for the proteins so targeted. For example, a protein modified with Lys-48-linked poly-ubiquitin chains is targeted for proteasomal degradation, whereas Lys-63-linked chains encode nondegradative signals. The structural features that enable these different types of chains to encode different signals have not yet been fully elucidated. We report here the X-ray crystal structures of Lys-63-linked tri- and di-ubiquitin at resolutions of 2.3 and 1.9 {angstrom}, respectively. The tri- and di-ubiquitin species adopt essentially identical structures. In both instances, the ubiquitin chain assumes a highly extended conformation with a left-handed helical twist; the helical chain contains four ubiquitin monomers per turn and has a repeat length of {approx}110 {angstrom}. Interestingly, Lys-48 ubiquitin chains also adopt a left-handed helical structure with a similar repeat length. However, the Lys-63 architecture is much more open than that of Lys-48 chains and exposes much more of the ubiquitin surface for potential recognition events. These new crystal structures are consistent with the results of solution studies of Lys-63 chain conformation, and reveal the structural basis for differential recognition of Lys-63 versus Lys-48 chains.

  13. Triheptanoin for glucose transporter type I deficiency (G1D): Modulation of human ictogenesis, cerebral metabolic rate and cognitive indices by a food supplement

    PubMed Central

    Pascual, Juan M.; Liu, Peiying; Mao, Deng; Kelly, Dorothy; Hernandez, Ana; Sheng, Min; Good, Levi B.; Ma, Qian; Marin-Valencia, Isaac; Zhang, Xuchen; Park, Jason Y.; Hynan, Linda S.; Stavinoha, Peter; Roe, Charles R.; Lu, Hanzhang

    2015-01-01

    Objective G1D is commonly associated with electrographic spike-wave and - less-noticeably – with absence seizures. The G1D syndrome has long been attributed to energy (i.e., ATP-synthetic) failure, as have experimental, toxic-rodent epilepsies to impaired brain metabolism and tricarboxylic acid (TCA) cycle intermediate depletion. Indeed, a (seldom-acknowledged) function of glucose and other substrates is the generation of brain TCAs via carbon-donor reactions collectively named anaplerosis. However, TCAs are preserved in murine G1D. This renders inferences about energy failure premature and suggests a different hypothesis, also grounded on our findings, that consumption of alternate TCA precursors is stimulated, potentially detracting from other functions. Second, common ketogenic diets can ameliorate G1D seizures, but lead to a therapeutically-counterintuitive reduction in blood glucose available to the brain, and they can prove ineffective in 1/3 of cases. While developing G1D treatments, all of this motivated us to: a) uphold (rather than attenuate) the residual brain glucose flux that all G1D patients possess; and b) stimulate the TCA cycle, including anaplerosis. Therefore, we tested the medium-chain triglyceride triheptanoin, a widely-used medical food supplement that can fulfill both of these metabolic roles. The rationale is that ketone bodies derived from ketogenic diets are not anaplerotic, in contrast with triheptanoin metabolites, as we have shown in the G1D mouse brain. Design We supplemented the regular diet of a case series of G1D patients with food-grade triheptanoin. First we confirmed that, despite their frequent electroencephalographic (EEG) presence as spike-waves, most seizures are rarely visible, such that perceptions by patients or others are inadequate for treatment evaluation. Thus, we used EEG, quantitative neuropsychological, blood analytical, and MRI cerebral metabolic rate measurements as main outcomes. Setting Academic and

  14. Self-organization of protein with helical domains

    NASA Astrophysics Data System (ADS)

    Frenkel, Zakhar M.; Melker, Alexander I.

    2002-02-01

    In this contribution, we report on a study of the self- organization of isolated polypeptides. The process is computer simulated by the method of molecular dynamics. We observed that the helical structures have a very impotent role in the protein self-organization. We have found conditions under which such structures to be stable. The process and result of self-organization under these conditions were sharply different from others, unable to maintain the helical structures. The structures obtained have a strong resemblance to the native conformations of the corresponding real proteins in a case of proteins composed by helical domains.

  15. Neoclassical Transport in the Helical Reversed-Field Pinch

    NASA Astrophysics Data System (ADS)

    Gobbin, M.; Spizzo, G.; Marrelli, L.; White, R. B.

    2010-11-01

    Test particle evaluation of the diffusion coefficient in a fusion plasma in the reversed-field pinch (RFP) configuration shows distinct similarities with stellarators when the plasma spontaneously evolves towards a helical shape. The almost total absence of superbanana particles at the levels of helical deformation seen in experiment (Bh/B=10%) causes transport to be proportional to collision frequency (at low collisions). This fact excludes the possibility that the minimum conceivable transport could be inversely proportional to collision frequency, which is typical of unoptimized stellarators. This result strengthens the perspectives of the helical RFP as a fusion configuration.

  16. Josephson junction through a disordered topological insulator with helical magnetization

    NASA Astrophysics Data System (ADS)

    Zyuzin, Alexander; Alidoust, Mohammad; Loss, Daniel

    2016-06-01

    We study supercurrent and proximity vortices in a Josephson junction made of disordered surface states of a three-dimensional topological insulator with a proximity induced in-plane helical magnetization. In a regime where the rotation period of helical magnetization is larger than the junction width, we find supercurrent 0 -π crossovers as a function of junction thickness, magnetization strength, and parameters inherent to the helical modulation and surface states. The supercurrent reversals are associated with proximity induced vortices, nucleated along the junction width, where the number of vortices and their locations can be manipulated by means of the superconducting phase difference and the parameters mentioned above.

  17. Tailoring chiro-optical effects by helical nanowire arrangement

    NASA Astrophysics Data System (ADS)

    Esposito, Marco; Tasco, Vittorianna; Todisco, Francesco; Benedetti, Alessio; Tarantini, Iolena; Cuscunà, Massimo; Dominici, Lorenzo; de Giorgi, Milena; Passaseo, Adriana

    2015-10-01

    In this work, we experimentally investigate the chiro-optical properties of 3D metallic helical systems at optical frequencies. Both single and triple-nanowire geometries have been studied. In particular, we found that in single-helical nanostructures, the enhancement of chiro-optical effects achievable by geometrical design is limited, especially with respect to the operation wavelength and the circular polarization conversion purity. Conversely, in the triple-helical nanowire configuration, the dominant interaction is the coupling among the intertwined coaxial helices which is driven by a symmetric spatial arrangement. Consequently, a general improvement in the g-factor, extinction ratio and signal-to-noise-ratio is achieved in a broad spectral range. Moreover, while in single-helical nanowires a mixed linear and circular birefringence results in an optical activity strongly dependent on the sample orientation and wavelength, in the triple-helical nanowire configuration, the obtained purely circular birefringence leads to a large optical activity up to 8°, independent of the sample angle, and extending in a broad band of 500 nm in the visible range. These results demonstrate a strong correlation between the configurational internal interactions and the chiral feature designation, which can be effectively exploited for nanoscale chiral device engineering.In this work, we experimentally investigate the chiro-optical properties of 3D metallic helical systems at optical frequencies. Both single and triple-nanowire geometries have been studied. In particular, we found that in single-helical nanostructures, the enhancement of chiro-optical effects achievable by geometrical design is limited, especially with respect to the operation wavelength and the circular polarization conversion purity. Conversely, in the triple-helical nanowire configuration, the dominant interaction is the coupling among the intertwined coaxial helices which is driven by a symmetric spatial

  18. Helical Spin Order from Topological Dirac and Weyl Semimetals

    SciTech Connect

    Sun, Xiao-Qi; Zhang, Shou-Cheng; Wang, Zhong

    2015-08-14

    In this paper, we study dynamical mass generation and the resultant helical spin orders in topological Dirac and Weyl semimetals, including the edge states of quantum spin Hall insulators, the surface states of weak topological insulators, and the bulk materials of Weyl semimetals. In particular, the helical spin textures of Weyl semimetals manifest the spin-momentum locking of Weyl fermions in a visible manner. Finally, the spin-wave fluctuations of the helical order carry electric charge density; therefore, the spin textures can be electrically controlled in a simple and predictable manner.

  19. Proteasome-mediated degradation antagonizes critical levels of the apoptosis-inducing C1D protein

    PubMed Central

    Rothbarth, Karsten; Stammer, Hermann; Werner, Dieter

    2002-01-01

    The C1D gene is expressed in a broad spectrum of mammalian cells and tissues but its product induces apoptotic cell death when exceeding a critical level. Critical levels are achieved in a fraction of cells by transient transfection with EGFP-tagged C1D expression constructs. However, transfected cells expressing sub-critical levels of C1D(EGFP) escape apoptotic cell death by activation of a proteasome-mediated rescue mechanism. Inhibition of the proteasome-dependent degradation of the C1D(EGFP) protein results in a parallel increase of the intracellular C1D level and in the fraction of apoptotic cells. PMID:12379155

  20. Anion-dependent construction of a series of fluorescent coordination polymers based on 1D zinc∩4,4‧-bis(imidazol-1-yl)-biphenyl substrates

    NASA Astrophysics Data System (ADS)

    Zou, Kang-Yu; Zou, Qian; Han, Tong; Liu, Yi-Chen; Wang, Jun-Jie; Zhang, Xue; Li, Zuo-Xi

    2016-03-01

    In this work, the rod-like ligand 4,4‧-bis(imidazol-1-yl)-biphenyl (bibp) has been utilized as a building block to carry out counterion effects on the structural diversities of coordination polymers. A series of new zinc complexes, [Zn(trans-bibp)Cl2]∞ (1), [Zn(trans-bibp)Br2]∞ (2), {[Zn(cis-bibp)(Ac)2]·(H2O)}∞ (3), [Zn(trans-bibp)SO4]∞ (4), {[Zn2(cis-bibp)2(ipa)2]·(H2O)}∞ (5, H2ipa=isophthalic acid) and {[Zn(trans-bibp)(cis-bibp)]·(ClO4)2(CHCl3)2(CH3OH)}∞ (6) have been successfully synthesized. Complexes 1 and 2 are iso-structural, which show a 1D W-type chain [Zn(trans-bibp)]∞. Complex 3 exhibits a 2D wave-like layer formed by the hydrogen bond among the 1D linear chain [Zn(cis-bibp)]∞. Complex 4 displays a 2D fish-bone lattice, which is generated from connecting the 1D W-type chain [Zn(trans-bibp)]∞ by the μ2-SO42- . Complex 5 presents an interesting 2D-3D 65·8 architecture, including two 1D chains [Zn(ipa)]∞ and [Zn(cis-bibp)]∞. Complex 6 demonstrates a 2D wave-like layer [Zn(trans-bibp)(cis-bibp)]∞. The structural diversities among 1-6 have been carefully discussed, and the role of counterion in the self-assembly of coordination polymer have also been well documented from the coordination affinity and bridging mode. Furthermore, the solid-state fluorescence properties of 1-6 at room temperature have been studied.