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Sample records for 1d helical chains

  1. Molecular tectonics: from 1-D interwoven racemic chains to quadruple-stranded helices.

    PubMed

    Lin, Mei-Jin; Jouaiti, Abdelaziz; Kyritsakas, Nathalie; Hosseini, Mir Wais

    2010-01-07

    The combination of two positional isomers tectons 1 and 2, based on a racemic 1,1'-spirobi(indane) scaffold bearing two pyridine units, with HgCl(2) affords doubly interwoven and quadruple-stranded helical architectures, respectively.

  2. Molecular cable-like 1-D iodic spiral chains covered with triple helices stabilized in guest-included chiral porous framework.

    PubMed

    Tadokoro, Makoto; Tanaka, Yasuko; Noguchi, Khoichiro; Sugaya, Tomoaki; Isoda, Kyosuke

    2012-07-21

    The supramolecular crystal {[Pr(DMFA)](3)[Ni(II)(Hbim)(3)](2)I}(n) with intricate chiral networks of [Ni(II)(Hbim)(3)](-) molecules is reported. It includes a cationic architecture as a guest, constructed from chiral nanotubes that penetrate I(-) chains with spiral channels wrapped by triple helices. The I(-) chains have AC conductivity in crystals like a molecular cable.

  3. Helical Floquet Channels in 1D Lattices

    NASA Astrophysics Data System (ADS)

    Budich, Jan Carl; Hu, Ying; Zoller, Peter

    2017-03-01

    We show how dispersionless channels exhibiting perfect spin-momentum locking can arise in a 1D lattice model. While such spectra are forbidden by fermion doubling in static 1D systems, here we demonstrate their appearance in the stroboscopic dynamics of a periodically driven system. Remarkably, this phenomenon does not rely on any adiabatic assumptions, in contrast to the well known Thouless pump and related models of adiabatic spin pumps. The proposed setup is shown to be experimentally feasible with state-of-the-art techniques used to control ultracold alkaline earth atoms in optical lattices.

  4. Heat Capacity of 1D Molecular Chains

    NASA Astrophysics Data System (ADS)

    Bagatskii, M. I.; Barabashko, M. S.; Sumarokov, V. V.; Jeżowski, A.; Stachowiak, P.

    2017-04-01

    The heat capacity of 1D chains of nitrogen and methane molecules (adsorbed in the outer grooves of bundles of closed-cap single-walled carbon nanotubes) has been studied in the temperature ranges 2-40 and 2-60 K, respectively. The temperature dependence of the heat capacity of 1D chains of nitrogen molecules below 3 K is close to a linear. It was found that the rotational heat capacity of methane molecules is a significant part of the total heat capacity of the chains throughout the whole investigated temperature range, whereas in the case of nitrogen, the librations are significant only above 15 K. The dependence of the heat capacity for methane below 10 K indicates the presence of a Schottky anomaly caused by the tunneling between the lowest energy levels of the CH4 molecule rotational spectra. Characteristic features observed in the temperature dependence of the heat capacity of 1D methane crystals are also discussed.

  5. Formation of helical ion chains

    NASA Astrophysics Data System (ADS)

    Nigmatullin, R.; del Campo, A.; De Chiara, G.; Morigi, G.; Plenio, M. B.; Retzker, A.

    2016-01-01

    We study the nonequilibrium dynamics of the linear-to-zigzag structural phase transition exhibited by an ion chain confined in a trap with periodic boundary conditions. The transition is driven by reducing the transverse confinement at a finite quench rate, which can be accurately controlled. This results in the formation of zigzag domains oriented along different transverse planes. The twists between different domains can be stabilized by the topology of the trap, and under laser cooling the system has a chance to relax to a helical chain with nonzero winding number. Molecular dynamics simulations are used to obtain a large sample of possible trajectories for different quench rates. The scaling of the average winding number with different quench rates is compared to the prediction of the Kibble-Zurek theory, and a good quantitative agreement is found.

  6. Weakly-coupled quasi-1D helical modes in disordered 3D topological insulator quantum wires

    PubMed Central

    Dufouleur, J.; Veyrat, L.; Dassonneville, B.; Xypakis, E.; Bardarson, J. H.; Nowka, C.; Hampel, S.; Schumann, J.; Eichler, B.; Schmidt, O. G.; Büchner, B.; Giraud, R.

    2017-01-01

    Disorder remains a key limitation in the search for robust signatures of topological superconductivity in condensed matter. Whereas clean semiconducting quantum wires gave promising results discussed in terms of Majorana bound states, disorder makes the interpretation more complex. Quantum wires of 3D topological insulators offer a serious alternative due to their perfectly-transmitted mode. An important aspect to consider is the mixing of quasi-1D surface modes due to the strong degree of disorder typical for such materials. Here, we reveal that the energy broadening γ of such modes is much smaller than their energy spacing Δ, an unusual result for highly-disordered mesoscopic nanostructures. This is evidenced by non-universal conductance fluctuations in highly-doped and disordered Bi2Se3 and Bi2Te3 nanowires. Theory shows that such a unique behavior is specific to spin-helical Dirac fermions with strong quantum confinement, which retain ballistic properties over an unusually large energy scale due to their spin texture. Our result confirms their potential to investigate topological superconductivity without ambiguity despite strong disorder. PMID:28374744

  7. Rigid dimers formed through strong interdigitated H-bonds yield compact 1D supramolecular helical polymers.

    PubMed

    Ciesielski, Artur; Stefankiewicz, Artur R; Hanke, Felix; Persson, Mats; Lehn, Jean-Marie; Samorì, Paolo

    2011-02-07

    Hierarchical self-assembly of small abiotic molecular modules interacting through noncovalent forces is increasingly being used to generate functional structures and materials for electronic, catalytic, and biomedical applications. The greatest control over the geometry in H-bond supramolecular architectures, especially in H-bonded supramolecular polymers, can be achieved by using conformationally rigid molecular modules undergoing self-assembly through strong H-bonds. Their binding strength depends on the multiplicity of the H-bonds, the nature of donor/acceptor pairs and their secondary attractive/repulsive interactions. Here a functionalized molecular module is described, which is capable of self-associating through self-complementary H-bonding patterns comprising four strong and two medium-strength H-bonds to form dimers. The self-association of these phenylpyrimidine-based dimers through directional H-bonding between two lateral pyridin-2(1H)-one units of neighboring molecules allows the formation of highly compact 1D supramolecular polymers by self-assembly on graphite. A concentration-dependent study by scanning tunneling microscopy at the solid-liquid interface, corroborated by dispersion-corrected density functional studies, reveals the controlled generation of either linear supramolecular 2D arrays, or long helical supramolecular polymers with a high shape persistence.

  8. Discovering side-chain correlation in {alpha}-Helices

    SciTech Connect

    Klinger, T.M.; Brutlag, D.L.

    1994-12-31

    Using a new representation for interactions in protein sequences based on correlations between pairs of amino acids, we have examined {alpha}-helical segments from known protein structures for important interactions. Traditional techniques for representing protein sequences usually make an explicit assumption of conditional independence of residues in the sequences. Protein structure analyses, however, have repeatedly demonstrated the importance of amino acid interactions for structural stability. We have developed an automated program for discovering sequence correlations in sets of aligned protein sequences using standard statistical tests and for representing them with Bayesian networks. In this paper, we demonstrate the power of our discovery program and representation by analyzing pairs of residues from {alpha}-helices. The sequence correlations we find represent physical and chemical interactions among amino-acid side chains in helical structures. Furthermore, these local interactions are likely to be important for stabilizing and packing {alpha}-helices. Lastly, we have also detect correlations in side-chain conformations that indicate important structural interactions but which don`t appear as sequence correlations.

  9. Nanojet-induced modes in 1D chains of microspheres

    NASA Astrophysics Data System (ADS)

    Kapitonov, A. M.; Astratov, V. N.

    2007-02-01

    We report on the light transport phenomena in linear chains composed of several tens of touching spherical microcavities. A new optical mode type, namely nanojet-induced modes (NIMs) is observed. These modes result from the optical coupling of microspheres acting as a series of micro-lenses, which periodically focus propagating wave into photonic nanojets. Theoretically, formation of periodic nanojets has been predicted in Z. Chen et al., Opt. Lett. 31, 389 (2006). The chains were produced by means of the self-assembly directed by micro-flows of water suspension of polystyrene microspheres. The mean size of spheres was varied in the 2-10 micron range. To couple light to NIMs we used built-in emission sources formed by several locally excited dye-doped microcavities from the same chain. Conversion of modes emitted by the light source into the NIMs results in losses of several dB per sphere in the vicinity (first few tens of spheres) of such sources. At longer distances we found an attenuation rate as small as 0.5 dB per sphere that reveals low intrinsic propagation loss for NIMs. The NIMs have potential applications for coupling and guiding of light in compact arrays of spherical cavities with extremely high quality (Q) whispering gallery modes.

  10. Package of double helical bromine chains inside single-walled carbon nanotubes

    NASA Astrophysics Data System (ADS)

    Yao, Zhen; Liu, Chun Jian; Lv, Hang; Yang, Xi Bao

    2016-10-01

    The helicity of stable double helical bromine chains inside single-walled carbon nanotubes (SWCNTs) was studied through the calculation of systematic interaction energy, using the van der Waals interaction potential. The results presented clear images of stable double helical structures inside SWCNTs. The optimal helical radius and helical angle of chain structure increase and decrease, respectively, with the increase of tube radius. The detailed analysis indicated that some metastable structures in SWCNTs may also co-exist with the optimal structures, but not within the same tubes. In addition, a detailed simulation of X-ray diffraction patterns was performed for the obtained optimal helical structures.

  11. 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.

  12. 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.

  13. Chiral symmetry breaking of a double-stranded helical chain through bend-writhe coupling

    NASA Astrophysics Data System (ADS)

    Yanao, Tomohiro; Yoshikawa, Kenichi

    2014-06-01

    This paper explores asymmetric elasticity of a double-stranded helical chain, which serves as a minimal model of biopolymers. The model consists of two elastic chains that mutually intertwine in a right-handed manner, forming a double-stranded helix. A simple numerical experiment for structural relaxation, which reduces the total elastic energy of the model monotonically without thermal fluctuations, reveals possible asymmetric elasticity inherent in the helical chain. It is first shown that a short segment of the double-stranded helical chain has a tendency to unwind when it is bent. It is also shown that a short segment of the helical chain has a tendency to writhe in the left direction upon bending. This tendency gives rise to a propensity for a longer segment of the chain to form a left-handed superhelix spontaneously upon bending. Finally, this propensity of the helical chain to form a left-handed superhelix is proposed to be a possible origin of the uniform left-handed wrapping of DNA around nucleosome core particles in nature. The results presented here could provide deeper insights into the roles and significance of helical chirality of biopolymers.

  14. A novel coordination polymer containing both interdigitated 1D chains and interpenetrated 2D grids.

    PubMed

    Ayyappan, Ponnaiyan; Evans, Owen R; Lin, Wenbin

    2002-07-01

    A hydro(solvo)thermal reaction between zinc perchlorate and ethyl ester of a new pyridinecarboxylate bridging ligand of approximately 17.6 A in length yields a unique coordination polymer which contains both interdigitated infinite 1D chains and interpenetrated 2D rhombohedral grids [Zn(2.5)(L)(4)(mu(3)-OH)] x (H(2)O)(5), 1, where L is 3-[[4-(4-pyridylethenyl)phenyl]ethenyl]benzoate. The 1D chains contain mu(3)-bridged hydroxy groups and have a [Zn(4)(mu(3)-OH)(2)(L)(6)] stoichiometry, while the 2D grids have a Zn(L)(2) formula and diagonal distances of 31.7 and 25.2 A. Crystal data for 1: monoclinic space group P2/c, a = 15.686(2) A, b = 12.6103(16) A, c = 38.999(5) A, beta = 98.397(2) degrees, and Z = 4.

  15. Magnetic properties driven by local structure in quasi-1D Ising chain system cobaltate system

    NASA Astrophysics Data System (ADS)

    Kim, Bongjae; Kim, Beom Hyun; Kim, Kyoo; Choi, Hong Chul; Park, Sang-Yeon; Jeong, Y.-H.; Min, B. I.

    2012-02-01

    Using ab-initio band structure method and the microscopic model calculation, the origins of the large orbital magnetic moment and unique magnetic anisotropy in the quasi-1D magnetic cobaltate, α-CoV2O6, is investigated. Unique crystal electric field effect in α-CoV2O6 is combined with the strong spin-orbit coupling, results in intriguing magnetic properties of the system. Based on the estimated strengths of the intra- and the inter-chain exchange interaction, experimentally found 1/3 magnetization plateau in the MH curve can be attributed to spin-flop mechanism. Origin of the reduced magnetic entropy behavior is found to be the strong uniaxial magnetic anisotropy in the quasi-1D Ising chain system.

  16. Self-assembled 1D magnetic Ising chains: epitaxial islands of Co/Ru(0001)

    NASA Astrophysics Data System (ADS)

    Li, Dongqi; Yu, Chengtao; Pearson, John; Bader, Samuel

    2002-03-01

    We have self-assembled magnetic Co dot chains via epitaxial island decoration of grooved Ru(0001) to create a model 1D system. Co wedge-like structures of 0-60 nm thick were deposited onto flat and grooved Ru(0001) substrates via molecular beam epitaxy at 350¢ªC and characterized ex-situ with atomic force and the magnetic force microscopy (MFM), and magneto-optic Kerr effect. The grooved substrate has a saw-tooth profile with spacing of order of 1 um, due to residual polishing scratches / step bunching. Co forms strain-induced, quasi-hexagonal dots of 70-500 nm in diameter and 1-20 nm high, depending on nominal dosage. On grooved substrate, the dots self align into chains along the groove near the top and bottom of the saw-tooth structure.[1] The dots are ferromagnetically coupled along the chain and exhibit magnetic single-domains with in-plane uniaxial anisotropy along the grooves. The inter-dot magnetic pair correlation was deduced from the MFM images of the dot-chains, and can be understood in terms of the classic 1D Ising model. * Work supported by DOE BES-MS under #W-31-109-ENG-38. 1. Chengtao Yu, Dongqi Li, J. Pearson, and S.D. Bader, Appl. Phys. Lett. 78, 1228 (2001); ibid. 79, 3848 (2001).

  17. Formation of Gd coordination polymer with 1D chains mediated by Bronsted acidic ionic liquids

    NASA Astrophysics Data System (ADS)

    Luo, Qianqian; Han, Ying; Lin, Hechun; Zhang, Yuanyuan; Duan, Chungang; Peng, Hui

    2017-03-01

    One dimensional coordination polymer Gd[(SO4)(NO3)(C2H6SO)2] (1) is prepared through the mediation of Bronsted acid ionic liquid, which crystallized in the monoclinic space of C2/c. In this polymer, adjacent Gd atoms are linked by two SO42- ions to generate a 1-D chain, and all oxygen atoms in SO42- groups are connected to three nearest Gd atoms in μ3:η1:η1:η2 fashion. Gd, S and N from SO42- and NO3- are precisely coplanar. The planar is coordinated by a pair of DMSO molecules, which is parallel and linked by hydrogen bonding to form a three-dimensional supramolecular network. Magnetic susceptibility measurement of 1 reveals weak antiferromagnetic interactions between the Gd (III) ions. It exhibits relatively large magneto-caloric effect with -ΔSm=28.8 J Kg-1 K-1 for ΔH=7 T.

  18. Helical Inversion of Gel Fibrils by Elongation of Perfluoroalkyl Chains as Studied by Vibrational Circular Dichroism.

    PubMed

    Sato, Hisako; Yajima, Tomoko; Yamagishi, Akihiko

    2016-05-01

    Vibrational circular dichroism (VCD) spectroscopy was applied to gelation by a chiral low-molecular mass weight gelator, N,N'-diperfluoroalkanoyl-1,2-trans-diaminocyclohexane. Attention was focused on the winding effects of (-CF2 )n chains on the gelating ability. For this purpose, a series of gelators were synthesized with perfluoroalkyl chains of different length (n = 6-8). When gelation was studied using acetonitrile as a solvent, the fibrils took different morphologies, depending on the chain length: twisted saddle-like ribbon or helical ribbon from fibril (n = 6) and a helical ribbon from platelet (n = 8). The signs of VCD peaks assigned to the couplet of C=O stretching and to the C-F stretching were also dependent on n, indicating that a gelator molecule changed conformation on elongating perfluoroalkyl chains. A model is proposed for the aggregation modes in fibrils. Chirality 28:361-364, 2016. © 2016 Wiley Periodicals, Inc.

  19. 2D warp-and-woof interwoven networks constructed by helical chains with different chirality.

    PubMed

    Feng, Yuhua; Guo, Yang; OuYang, Yan; Liu, Zhanquan; Liao, Daizheng; Cheng, Peng; Yan, Shiping; Jiang, Zonghui

    2007-09-21

    Two unprecedented 2D entangled layers of warp-and-woof threads interwoven by left- and right-handed helical chains, {[Mn(salen)Au(CN)2]4(H2O)}n (salen = N,N'-ethylenebis(salicylideneaminato)) and {Mn(acacen)Ag(CN)2}n (acacen = N,N'-ethylenebis(acetylacetonylideneiminate)) 2, have been synthesized and characterized.

  20. 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.

  1. Propagation of the Ultra-Short Laser Pulses Through the Helical 1D Photonic Crystal Structure with Twist Defect

    NASA Astrophysics Data System (ADS)

    Antonov, Dmitrii V.; Iegorov, Roman

    2016-02-01

    The presence of the photonic band-gap is a featured property of the cholesteric liquid crystals (CLC). It can be practically realized for almost any reasonable wavelengths with very high degree of tunability. We have investigated theoretically the influence of the twist defect of the CLC helical structure onto the bandwidth-limited ultra-short laser pulse propagating inside the photonic band-gap. The changes of both pulse duration and peak power with defect angle were observed together with pulse acceleration and retardation for a case of normal incidence of the light.

  2. A novel cryogenic magnetic refrigerant metal-organic framework based on 1D gadolinium(III) chain

    NASA Astrophysics Data System (ADS)

    Tang, Qun; Li, Peng-Fei; Zou, Zhi-Ming; Liu, Zheng; Liu, Shu-Xia

    2017-02-01

    A metal-organic framework (MOF) based on gadolinium ion (Gd3+) and tricarboxylate ligand, [Gd(BTPCA)(H2O)]·2DMF·3H2O (Gd-BTPCA) (H3BTPCA =1,1‧,1‧-(benzene-1,3,5-triyl)tripiperidine-4-carboxylic acid; DMF=dimethylformamide), was synthesized and structurally characterized. The adjacent Gd3+ ions are intraconnected by the carboxylate groups of the BTPCA3- ligands to form a 1D Gd3+ ion chain. The 1D Gd3+ ion chains are interconnected by the BTPCA3- ligands, giving rise to a 3D framework with 1D open channel. The magnetic studies indicate that Gd-BTPCA exhibits weak ferromagnetic interactions, and acts as a cryogenic magnetic refrigerant having the magnetic entropy change (-ΔSm) of 20.40 J kg-1 K-1 for ΔH =7 T at 3 K.

  3. 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.

  4. 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.

  5. Role of side-chain interactions on the formation of α -helices in model peptides

    NASA Astrophysics Data System (ADS)

    Mahmoudinobar, Farbod; Dias, Cristiano L.; Zangi, Ronen

    2015-03-01

    The role played by side-chain interactions on the formation of α -helices is studied using extensive all-atom molecular dynamics simulations of polyalanine-like peptides in explicit TIP4P water. The peptide is described by the OPLS-AA force field except for the Lennard-Jones interaction between Cβ-Cβ atoms, which is modified systematically. We identify values of the Lennard-Jones parameter that promote α -helix formation. To rationalize these results, potentials of mean force (PMF) between methane-like molecules that mimic side chains in our polyalanine-like peptides are computed. These PMF exhibit a complex distance dependence where global and local minima are separated by an energy barrier. We show that α -helix propensity correlates with values of these PMF at distances corresponding to Cβ-Cβ of i -i +3 and other nearest neighbors in the α -helix. In particular, the set of Lennard-Jones parameters that promote α -helices is characterized by PMF that exhibit a global minimum at distances corresponding to i -i +3 neighbors in α -helices. Implications of these results are discussed.

  6. Role of side-chain interactions on the formation of α-helices in model peptides.

    PubMed

    Mahmoudinobar, Farbod; Dias, Cristiano L; Zangi, Ronen

    2015-03-01

    The role played by side-chain interactions on the formation of α-helices is studied using extensive all-atom molecular dynamics simulations of polyalanine-like peptides in explicit TIP4P water. The peptide is described by the OPLS-AA force field except for the Lennard-Jones interaction between Cβ-Cβ atoms, which is modified systematically. We identify values of the Lennard-Jones parameter that promote α-helix formation. To rationalize these results, potentials of mean force (PMF) between methane-like molecules that mimic side chains in our polyalanine-like peptides are computed. These PMF exhibit a complex distance dependence where global and local minima are separated by an energy barrier. We show that α-helix propensity correlates with values of these PMF at distances corresponding to Cβ-Cβ of i-i+3 and other nearest neighbors in the α-helix. In particular, the set of Lennard-Jones parameters that promote α-helices is characterized by PMF that exhibit a global minimum at distances corresponding to i-i+3 neighbors in α-helices. Implications of these results are discussed.

  7. 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.

  8. Helical structures in vertically aligned dust particle chains in a complex plasma.

    PubMed

    Hyde, Truell W; Kong, Jie; Matthews, Lorin S

    2013-05-01

    Self-assembly of structures from vertically aligned, charged dust particle bundles within a glass box placed on the lower, powered electrode of a Gaseous Electronics Conference rf reference cell were produced and examined experimentally. Self-organized formation of one-dimensional vertical chains, two-dimensional zigzag structures, and three-dimensional helical structures of triangular, quadrangular, pentagonal, hexagonal, and heptagonal symmetries are shown to occur. System evolution is shown to progress from a one-dimensional chain structure, through a zigzag transition to a two-dimensional, spindlelike structure, and then to various three-dimensional, helical structures exhibiting multiple symmetries. Stable configurations are found to be dependent upon the system confinement, γ(2)=(ω(0h)/ω(0v))(2) (where ω(0h,v) are the horizontal and vertical dust resonance frequencies), the total number of particles within a bundle, and the rf power. For clusters having fixed numbers of particles, the rf power at which structural phase transitions occur is repeatable and exhibits no observable hysteresis. The critical conditions for these structural phase transitions as well as the basic symmetry exhibited by the one-, two-, and three-dimensional structures that subsequently develop are in good agreement with the theoretically predicted configurations of minimum energy determined employing molecular dynamics simulations for charged dust particles confined in a prolate, spheroidal potential as presented theoretically by Kamimura and Ishihara [Kamimura and Ishihara, Phys. Rev. E 85, 016406 (2012)].

  9. A strategy for tuning achiral main-chain polymers into helical assemblies and chiral memory systems.

    PubMed

    Yang, Dong; Zhao, Yin; Lv, Kai; Wang, Xiufeng; Zhang, Wei; Zhang, Li; Liu, Minghua

    2016-01-28

    A general strategy to tune the achiral main chain polymers into helical nanoassemblies was proposed based on the co-gelation approach. As an example, two achiral main chain polymers, PCz8 and PSi8, were selected, and their co-assembly with an amphiphilic l- or d-glutamide gelator was investigated. Although the polymers could not form gels individually, they could form co-gels with the gelator and the resultant gels exhibited macroscopic supramolecular chirality, which could be confirmed by CD spectra and SEM observations. Moreover, the supramolecular chirality can be memorized even after the gelator molecules were removed. Remarkably, either the gelator-containing or gelator-free chiral polymer assemblies showed circularly polarized luminescence (CPL), which is usually inherent to intrinsic chiral polymers. It was suggested that during the co-gelation, the chirality of the gelator was transferred to and memorized by the achiral polymers. The approach seems to be general and we provided the first example to tune the achiral polymers into helical assemblies through the co-gelation.

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

    SciTech Connect

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

    2016-07-15

    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)]·2H_2O}{sub n} (1), {[Zn(bib)(atbip)]·H_2O}{sub n} (2), {[Zn(bib)(2,2′-tda)]}{sub n} (3) and {[Zn(bib)(5-tbipa)]·EtOH}{sub n} (4), (H{sub 2}atibdc=5-amino-2,4,6-triiodoisophthalic acid, H{sub 2}atbip=5-amino-2,4,6-tribromoisophthalic acid, 2,2′-H{sub 2}tad=2,2′-thiodiacetic acid, 5-H{sub 2}tbipa=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 (E{sub 1}=209.658 kJ·mol{sup −1}, E{sub 2}=250.037 kJ mol{sup −1}, E{sub 3}=225.300 kJ mol{sup −1}, E{sub 4}=186.529 kJ·mol{sup −1}) demonstrates that the reaction rate of the melting decomposition is slow. The thermodynamic parameters (ΔH{sup ‡}, ΔG{sup ‡} and ΔS{sup ‡}) at the peak temperatures of the DTG curves were also calculated. ΔG{sup ‡}>0 indicates that the skeleton collapse is not spontaneous. ΔH{sub d}>0 suggests that the skeleton collapse is endothermic, corresponding to the intense endothermic peak of the DSC curve. The

  11. 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.

  12. A bridge between pillared-layer and helical structures: a series of three-dimensional pillared coordination polymers with multiform helical chains.

    PubMed

    Xiao, Dong-Rong; Wang, En-Bo; An, Hai-Yan; Li, Yang-Guang; Su, Zhong-Min; Sun, Chun-Yan

    2006-08-25

    Rational self-assembly of a long V-shaped 3,3',4,4'-benzophenonetetracarboxylate (bptc) ligand and metal salts in the presence of linear bidentate ligand yield a series of novel pillared helical-layer complexes, namely, [Cu2(bptc)(bpy)2] (1), [M3(Hbptc)2(bpy)3(H2O)4].2 H2O (M = Fe(2) and Ni(3)), [Co2(bptc)(bpy)(H2O)].0.5 bpy (4), [Cd2(bptc)(bpy)(H2O)2].H2O (5), [Mn2(bptc)(bpy)1.5(H2O)3] (6) and [M2(bptc)(bpy)0.5(H2O)5].0.5 bpy (M = Mn(7), Mg(8) and Co(9), bpy=4,4'-bipyridine). Their structures were determined by single-crystal X-ray diffraction analyses and further characterized by elemental analyses, IR spectra, and thermogravimetric (TG) analyses. The structure of 1 consists of two types of chiral layers, one left-handed and the other right-handed, which are connected by bpy pillars to generate a novel 3D open framework featuring four distinct helical chains. Compounds 2 and 3 are isostructural and feature 3D structures formed from the interconnection of arm-shaped helical layers with bpy pillars. Compound 4 is a pillared helical double-layer complex containing four different types of helices, among which the nine-fold interwoven helices constructed from triple-stranded helical motifs are unprecedented. Compound 5 exhibits a novel 3D covalent framework which features nanosized tubular channels. These channels are built from helical layers pillared by bptc ligands. The structure of 6 is constructed from {Mn(bptc)(H2O)}n2n- layers, which consist of left- and right-handed helical chains, pillared by [Mn2(bpy)3(H2O)4]4+ complexes into a 3D framework. To the best of our knowledge, compounds 1-6 are the first examples of pillared helical-layer coordination polymers. Compounds 7-9 are isostructural and exhibit interesting 2D helical double-layer structures, which are constructed from {M(bptc)(H2O)2}n2n- ribbons cross-linked by [M2(bpy)(H2O)6]4+ complexes. Furthermore, the 3D supramolecular structures of 7-9 are similar to the 3D structure of 6, and the 2D structure of 7

  13. Crystal structures of bovine CD1d reveal altered αGalCer presentation and a restricted A' pocket unable to bind long-chain glycolipids.

    PubMed

    Wang, Jing; Guillaume, Joren; Pauwels, Nora; Van Calenbergh, Serge; Van Rhijn, Ildiko; Zajonc, Dirk M

    2012-01-01

    NKT cells play important roles in immune surveillance. They rapidly respond to pathogens by detecting microbial glycolipids when presented by the non-classical MHC I homolog CD1d. Previously, ruminants were considered to lack NKT cells due to the lack of a functional CD1D gene. However, recent data suggest that cattle express CD1d with unknown function. In an attempt to characterize the function of bovine CD1d, we assessed the lipid binding properties of recombinant Bos taurus CD1d (boCD1d) in vitro. BoCD1d is able to bind glycosphingolipids (GSLs) with fatty acid chain lengths of C₁₈, while GSLs with fatty acids of C₂₄ do not bind. Crystal structures of boCD1d bound to a short-chain C₁₂-di-sulfatide antigen, as well as short-chain C₁₆-αGalCer revealed that the Á pocket of boCD1d is restricted in size compared to that of both mouse and human CD1d, explaining the inability of long chain GSL's to bind to boCD1d. Moreover, while di-sulfatide is presented similarly compared to the presentation of sulfatide by mouse CD1d, αGalCer is presented differently at the cell surface, due to an amino acid Asp151Asn substitution that results in loss of intimate contacts between the αGalCer headgroup and CD1d. The altered αGalCer presentation by boCD1d also explains its lack of cross-activation of mouse iNKT cells and raises the interesting question of the nature and function of bovine lipid-reactive T cells.

  14. Crystal Structures of Bovine CD1d Reveal Altered αGalCer Presentation and a Restricted A’ Pocket Unable to Bind Long-Chain Glycolipids

    PubMed Central

    Wang, Jing; Guillaume, Joren; Pauwels, Nora; Van Calenbergh, Serge; Van Rhijn, Ildiko; Zajonc, Dirk M.

    2012-01-01

    NKT cells play important roles in immune surveillance. They rapidly respond to pathogens by detecting microbial glycolipids when presented by the non-classical MHC I homolog CD1d. Previously, ruminants were considered to lack NKT cells due to the lack of a functional CD1D gene. However, recent data suggest that cattle express CD1d with unknown function. In an attempt to characterize the function of bovine CD1d, we assessed the lipid binding properties of recombinant Bos taurus CD1d (boCD1d) in vitro. BoCD1d is able to bind glycosphingolipids (GSLs) with fatty acid chain lengths of C18, while GSLs with fatty acids of C24 do not bind. Crystal structures of boCD1d bound to a short-chain C12-di-sulfatide antigen, as well as short-chain C16-αGalCer revealed that the Á pocket of boCD1d is restricted in size compared to that of both mouse and human CD1d, explaining the inability of long chain GSL’s to bind to boCD1d. Moreover, while di-sulfatide is presented similarly compared to the presentation of sulfatide by mouse CD1d, αGalCer is presented differently at the cell surface, due to an amino acid Asp151Asn substitution that results in loss of intimate contacts between the αGalCer headgroup and CD1d. The altered αGalCer presentation by boCD1d also explains its lack of cross-activation of mouse iNKT cells and raises the interesting question of the nature and function of bovine lipid-reactive T cells. PMID:23110152

  15. 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.

  16. Two unprecedented 1D coordination polymer chains based on tetranuclear copper(II) building blocks

    SciTech Connect

    Li Gaijuan; Xing Yan Song Shuyan; Xu Ning; Liu Xianchun; Su Zhongmin

    2008-09-15

    The reaction of copper(II) sulfate with pyridine in DMF or methanol yield two unprecedented Cu(II) coordination polymers {l_brace}[Cu{sub 4}({mu}{sub 4}-O)(py){sub 4}(SO{sub 4}){sub 4}][{mu}-Cu(py)(DMF){sub 2}]{r_brace}{sub n}(1) and {l_brace}[Cu{sub 4}({mu}{sub 4}-O)(py){sub 4}(SO{sub 4}){sub 4}][{mu}-Cu(py){sub 4}]{r_brace}{sub n}(2), respectively. Single-crystal X-ray diffraction indicated that compound 1 crystallizes in the monoclinic system, space group p2(1)/n, a=14.542(5) A, b=16.359(5) A, c=18.951(5) A, {beta}=92.047(5){sup o}, V=4505(2) A{sup 3}, Z=4 while 2 is monoclinic C2/c, a=23.078(5) A, b=10.214(5) A, c=23.142(5) A, {beta}=115.471(5){sup o}, V=4925(3) A{sup 3}, Z=4. Both of the two compounds consist of tetrahedral tetranuclear [Cu{sub 4}({mu}{sub 4}-O)(py){sub 4}(SO{sub 4}){sub 4}] clusters that are bridged by pentacoordinated Cu atom for 1 or hexacoordinated Cu atoms for 2 through the sulfate oxygen to form the infinite one-dimensional polymer chains. - Graphical abstract: Two unprecedented Cu(II) coordination polymers have been prepared by using solvothermal method; they consist of tetrahedral tetranuclear clusters that are bridged by unique Cu(II) atom through the sulfate oxygen to form the infinite one-dimensional polymer chains (a) for complex 1 and (b) for complex 2.

  17. 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.

  18. Force responses of strongly intrinsically curved DNA helices deviate from worm-like chain predictions

    NASA Astrophysics Data System (ADS)

    Tompitak, M.; Schiessel, H.; Barkema, G. T.

    2016-12-01

    DNA sequences with nontrivial intrinsic curvature are of interest for a range of biological and artificial DNA systems. We design both intrinsically strongly curved and intrinsically straight sequences. We find that such sequences with opposing curvatures can be designed even under constraints that would naively lead one to assume that those sequences would be highly similar in their mechanical properties. We then characterize the force response of those sequences and find that their force-extension curves deviate significantly in the low-force regime, and that the standard worm-like chain description is inadequate to describe the low-force response of the strongly bent sequences. We propose a modified description that takes the intrinsic curvature into account, making the DNA act, in the low-force regime, like a nanoscale helical spring. We find strongly improved agreement between the model and the simulated force-extension curves.

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

    PubMed

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

    2015-01-12

    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 (R3) 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.

  20. Two-step spin transition in a 1D Fe(II) 1,2,4-triazole chain compound.

    PubMed

    Dîrtu, Marinela M; Schmit, France; Naik, Anil D; Rusu, Ionela; Rotaru, Aurelian; Rackwitz, Sergej; Wolny, Juliusz A; Schünemann, Volker; Spinu, Leonard; Garcia, Yann

    2015-04-07

    A thermochromic 1D spin crossover coordination (SCO) polymer [Fe(βAlatrz)3](BF4)2⋅2 H2O (1⋅2 H2O), whose precursor βAlatrz, (1,2,4-triazol-4-yl-propionate) has been tailored from a β-amino acid ester is investigated in detail by a set of superconducting quantum interference device (SQUID), (57)Fe Mössbauer, differential scanning calorimetry, infrared, and Raman measurements. An hysteretic abrupt two-step spin crossover (T1/2(↓) = 230 K and T1/2(↑) = 235 K, and T1/2(↓) = 172 K and T1/2(↑) = 188 K, respectively) is registered for the first time for a 1,2,4-triazole-based Fe(II) 1D coordination polymer. The two-step SCO configuration is observed in a 1:2 ratio of low-spin/high-spin in the intermediate phase for a 1D chain. The origin of the stepwise transition was attributed to a distribution of chains of different lengths in 1⋅2 H2O after First Order Reversal Curves (FORC) analyses. A detailed DFT analysis allowed us to propose the normal mode assignment of the Raman peaks in the low-spin and high-spin states of 1⋅2 H2O. Vibrational spectra of 1⋅2 H2O reveal that the BF4(-) anions and water molecules play no significant role on the vibrational properties of the [Fe(βAlatrz)3](2+) polymeric chains, although non-coordinated water molecules have a dramatic influence on the emergence of a step in the spin transition curve. The dehydrated material [Fe(βAlatrz)3](BF4)2 (1) reveals indeed a significantly different magnetic behavior with a one-step SCO which was also investigated.

  1. Functional CD1d and/or NKT cell invariant chain transcript in horse, pig, African elephant and guinea pig, but not in ruminants

    PubMed Central

    Looringh van Beeck, Frank A.; Reinink, Peter; Hermsen, Roel; Zajonc, Dirk M.; Laven, Marielle J.; Fun, Axel; Troskie, Milana; Schoemaker, Nico J.; Morar, Darshana; Lenstra, Johannes A.; Vervelde, Lonneke; Rutten, Victor P.M.G.; van Eden, Willem; Van Rhijn, Ildiko

    2009-01-01

    CD1d-restricted invariant natural killer T cells (NKT cells) have been well characterized in humans and mice, but it is unknown whether they are present in other species. Here we describe the invariant TCR α chain and the full length CD1d transcript of pig and horse. Molecular modeling predicts that porcine (po) invariant TCR α chain/poCD1d/α-GalCer and equine (eq) invariant TCR α chain/eqCD1d/α-GalCer form complexes that are highly homologous to the human complex. Since a prerequisite for the presence of NKT cells is the expression of CD1d protein, we performed searches for CD1D genes and CD1d transcripts in multiple species. Previously, cattle and guinea pig have been suggested to lack CD1D genes. The CD1D genes of European taurine cattle (Bos taurus) are known to be pseudogenes because of disrupting mutations in the start codon and in the donor splice site of the first intron. Here we show that the same mutations are found in six other ruminants: African buffalo, sheep, bushbuck, bongo, N’Dama cattle, and roe deer. In contrast, intact CD1d transcripts were found in guinea pig, African elephant, horse, rabbit, and pig. Despite the discovery of a highly homologous NKT/CD1d system in pig and horse, our data suggest that functional CD1D and CD1d-restricted NKT cells are not universally present in mammals. PMID:19185921

  2. 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.

  3. 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

  4. 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

  5. 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.

  6. Unique microporous NbO-type Co{sup II}/Zn{sup II} MOFs from double helical chains: Sorption and luminescent properties

    SciTech Connect

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

    2016-06-15

    Under solvothermal conditions, the reactions of Co{sup II}/Zn{sup II} 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}{sub n} (guest=H{sub 2}O, M=Co{sup II} (1), Zn{sup II} (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 N{sub 2}, CO{sub 2} and H{sub 2} uptake capacities, while compound 2 displays the strong luminescent emission with obvious red shift. - Graphical abstract: Two 2-fold interpenetrated NbO-type MOFs with 1D nanochannel were synthesized. Compound 1 exhibits improved N{sub 2}, CO{sub 2} and H{sub 2} uptake capacities, while compound 2 displays the strong fluorescent emission with obvious red shift. Display Omitted.

  7. 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

  8. Quantum soliton in 1D Heisenberg spin chains with Dzyaloshinsky-Moriya and next-nearest-neighbor interactions

    NASA Astrophysics Data System (ADS)

    Djoufack, Z. I.; Tala-Tebue, E.; Nguenang, J. P.; Kenfack-Jiotsa, A.

    2016-10-01

    We report in this work, an analytical study of quantum soliton in 1D Heisenberg spin chains with Dzyaloshinsky-Moriya Interaction (DMI) and Next-Nearest-Neighbor Interactions (NNNI). By means of the time-dependent Hartree approximation and the semi-discrete multiple-scale method, the equation of motion for the single-boson wave function is reduced to the nonlinear Schrödinger equation. It comes from this present study that the spectrum of the frequencies increases, its periodicity changes, in the presence of NNNI. The antisymmetric feature of the DMI was probed from the dispersion curve while changing the sign of the parameter controlling it. Five regions were identified in the dispersion spectrum, when the NNNI are taken into account instead of three as in the opposite case. In each of these regions, the quantum model can exhibit quantum stationary localized and stable bright or dark soliton solutions. In each region, we could set up quantum localized n-boson Hartree states as well as the analytical expression of their energy level, respectively. The accuracy of the analytical studies is confirmed by the excellent agreement with the numerical calculations, and it certifies the stability of the stationary quantum localized solitons solutions exhibited in each region. In addition, we found that the intensity of the localization of quantum localized n-boson Hartree states increases when the NNNI are considered. We also realized that the intensity of Hartree n-boson states corresponding to quantum discrete soliton states depend on the wave vector.

  9. Quantum soliton in 1D Heisenberg spin chains with Dzyaloshinsky-Moriya and next-nearest-neighbor interactions.

    PubMed

    Djoufack, Z I; Tala-Tebue, E; Nguenang, J P; Kenfack-Jiotsa, A

    2016-10-01

    We report in this work, an analytical study of quantum soliton in 1D Heisenberg spin chains with Dzyaloshinsky-Moriya Interaction (DMI) and Next-Nearest-Neighbor Interactions (NNNI). By means of the time-dependent Hartree approximation and the semi-discrete multiple-scale method, the equation of motion for the single-boson wave function is reduced to the nonlinear Schrödinger equation. It comes from this present study that the spectrum of the frequencies increases, its periodicity changes, in the presence of NNNI. The antisymmetric feature of the DMI was probed from the dispersion curve while changing the sign of the parameter controlling it. Five regions were identified in the dispersion spectrum, when the NNNI are taken into account instead of three as in the opposite case. In each of these regions, the quantum model can exhibit quantum stationary localized and stable bright or dark soliton solutions. In each region, we could set up quantum localized n-boson Hartree states as well as the analytical expression of their energy level, respectively. The accuracy of the analytical studies is confirmed by the excellent agreement with the numerical calculations, and it certifies the stability of the stationary quantum localized solitons solutions exhibited in each region. In addition, we found that the intensity of the localization of quantum localized n-boson Hartree states increases when the NNNI are considered. We also realized that the intensity of Hartree n-boson states corresponding to quantum discrete soliton states depend on the wave vector.

  10. 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.

  11. Foldamers to nanotubes: influence of amino acid side chains in the hierarchical assembly of α,γ(4)-hybrid peptide helices.

    PubMed

    Jadhav, Sandip V; Misra, Rajkumar; Gopi, Hosahudya N

    2014-12-08

    Supramolecular assembly of various artificially folded 12-helical architectures composed of γ(4) -Val, γ(4) -Leu and γ(4) -Phe residues is investigated. In contrast to the 12-helices composed of γ(4) -Val and γ(4) -Leu residues, the helices with γ(4) -Phe residues displayed unique elongated nanotubular architectures. The elongated nanotube assembly was further explored as a template for biomineralization of silver ions to silver nanowires. A comparative study using an analogous α-peptide helix reveals the importance of the spatial arrangement of aromatic side chains along the helical cylinder in a 12-helix. These results suggested that the proteolytically and structurally stable α,γ(4) -hybrid peptide 12-helices may serve as a new generation of potential templates in the design of functional biomaterials.

  12. A New Carbon Allotrope with Six-Fold Helical Chains in all-sp2 Bonding Networks

    PubMed Central

    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 () symmetry that comprises six-fold helical chains with alternating sp2-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. PMID:24614093

  13. Linear polynuclear helicates as a link between discrete supramolecular complexes and programmed infinite polymetallic chains.

    PubMed

    Dalla-Favera, Natalia; Hamacek, Josef; Borkovec, Michal; Jeannerat, Damien; Gumy, Frédéric; Bünzli, Jean-Claude G; Ercolani, Gianfranco; Piguet, Claude

    2008-01-01

    The contribution of the solvation energies to the assembly of polynuclear helicates reduces the free energy of intermetallic repulsion, DeltaE(MM), in condensed phase to such an extent that stable D(3)-symmetrical tetranuclear lanthanide-containing triple-stranded helicates [Ln(4)(L4)(3)](12+) are quantitatively produced at millimolar concentrations, despite the twelve positive charge borne by these complexes. A detailed modelling of the formation constants using statistical factors, adapted to self-assembly processes involving intra- and intermolecular connections, provides a set of five microscopic parameters, which can be successfully used for rationalizing the stepwise generation of linear bi-, tri- and tetranuclear analogues. Photophysical studies of [Eu(4)(L4)(3)](12+) confirm the existence of two different binding sites producing differentiated metal-centred emission at low temperature, which transforms into single site luminescence at room temperature because of intramolecular energy funelling processes.

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

    PubMed Central

    Grechko, Maksim; Zanni, Martin T.

    2012-01-01

    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. PMID:23163364

  15. 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.

  16. 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

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

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

    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.

  18. Dynamics of helical worm-like chains. VIII. Higher-order subspace approximations to dielectric and magnetic relaxation and fluorescence depolarization for flexible chains

    NASA Astrophysics Data System (ADS)

    Yamakawa, Hiromi; Yoshizaki, Takenao; Fujii, Motoharu

    1986-04-01

    Following the general scheme developed in the preceding paper (paper VII), dielectric and magnetic relaxation and fluorescence depolarization for flexible chain polymers in dilute solution are reinvestigated on the basis of the discrete helical worm-like chain in the higher-order subspace approximation. A comparison of theory with experiment is made with respect to the dielectric correlation time τD, the spin-lattice relaxation time T1, the spin-spin relaxation time T2, the nuclear Overhauser enhancement (NOE), the fluorescence emission anisotropy r(t), the average fluorescence anisotropy r¯, and the fluorescence correlation time τF. It is found that there is agreement between the diameters of the chains determined from these dynamic properties and those from chemical structures, better than in the previous crude subspace approximation, indicating that the theory is remarkably improved in the present approximation. The magnetic correlation time τM is in general not an observable, and therefore an empirical equation to be used for its determination from the observed T1 is constructed. It is then found that there is good correlation between the dynamic chain stiffness τX/τ0X and the static chain stiffness λ-1, where τ0X is the correlation time of the isolated subbody (monomer unit) with X=D, M, and F; τX/τ0X is a monotonically increasing function of λ-1 nearly independent of X as far as perpendicular dipoles are concerned. An explanation of this result is given. However, the dependence of τX on temperature cannot be explained very satisfactorily.

  19. 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.

  20. Snorkeling of lysine side chains in transmembrane helices: how easy can it get?

    PubMed

    Strandberg, Erik; Killian, J Antoinette

    2003-06-05

    Transmembrane segments of proteins are often flanked by lysine residues. The side chains of these residues may snorkel, i.e. they may bury themselves with their aliphatic part in the hydrophobic region of the lipid bilayer, while positioning the charged amino group in the more polar interface. Here we estimate the free energy cost of snorkeling from thermodynamical calculations based on studies with synthetic transmembrane peptides [Strandberg et al. (2002) Biochemistry 41, 7190-7198]. The value is estimated to be between 0.07 and 0.7 kcal mol(-1) for a lysine side chain. This very low value indicates that snorkeling may be a common process, which should be taken into consideration both in experimental and in theoretical studies on protein-lipid interactions.

  1. Rings, chains and helices: new antimicrobial silver coordination compounds with (iso-)nicotinic acid derivatives.

    PubMed

    Chevrier, Inès; Sagué, Jorge L; Brunetto, Priscilla S; Khanna, Nina; Rajacic, Zarko; Fromm, Katharina M

    2013-01-07

    Complexes with silver ions have great potential for applications in medicine. Appropriate bidentate ligands, binding to silver ions, are able to generate coordination polymers as well as molecular entities as a function of ligand flexibility, conformation and length. Here we present the continuation of our previous studies in this field with ligands based on oligomers of polyethylene glycol, functionalized at both ends with either nicotinic or isonicotinic acid. The structures of three ligands and nine new coordination compounds are presented. A large variety of structures are obtained as a function of counterion, solvent and ligand-to-metal ratio, such as isolated rings, offset stacked rings, parallel chains and entangled chains, and their antimicrobial properties as well as biocompatibility are assessed.

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

    PubMed

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

    2015-03-07

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

  3. Helical jump motions of poly(L-lactic acid) chains in the α phase as revealed by solid-state NMR.

    PubMed

    Chen, Wei; Reichert, Detlef; Miyoshi, Toshikazu

    2015-03-26

    The molecular dynamics of Poly(L-lactic Acid) (PLLA) chains in the α phase was investigated by Solid-State NMR spectroscopy. (13)C high-resolution NMR clearly indicates that the crystalline signals split into 2, 3, and 4 signals for the CH3, CH and CO groups, respectively at 25 °C, while the amorphous signals give a broad component at the bottom of the crystalline signals. (13)C NMR spectra show that the crystalline line shape changes with increasing temperatures well above the glass transition temperature (Tg) and imply the presence of the molecular dynamics in the crystalline region. Comparisons of the evolution-time dependence of CODEX data and simulation results based on reorientation of chemical shift anisotropy (CSA) indicate that the chains in the α phase perform helical jump motions in the slow dynamic range at temperatures above 115 °C. The mixing-time dependence of the CODEX data yields an activation energy of Ea of (95 ± 8) kJ/mol for the helical jump motions. Moreover, two-dimensional exchange NMR with highly resolved signals for the CO group provides cross peaks among four well resolved signals due to the helical jumps. Comparison of 2D buildup curves of the cross peaks and calculated data determines that helical jump motions prefer largely uncorrelated random back-and-forth motions between the neighboring sites, possibly enabling large-scale chain diffusion in the crystalline regions.

  4. A novel 1D chain of azido bridged copper(II) with a salen-type di-Schiff base ligand

    NASA Astrophysics Data System (ADS)

    Biswas, Saptarshi; Ghosh, Ashutosh

    2012-07-01

    One new complex of Cu(II), [(CuL)2Cu3(N3)6]n (1) has been synthesized by reacting the "ligand complex", [CuL] with copper acetate and sodium azide (NaN3) in methanol-water where the di-Schiff base ligand H2L = N,N‧-bis(α-methylsalicylidene)-1,3-propanediamine. The X-ray single crystal structural analysis shows that complex 1 consists of an incomplete face-sharing double cube of four Cu(II) ions with the formula of [(CuL)2Cu2(N3)2]2+ which are connected by [Cu(N3)4]2- unit to form a novel 1D chain.

  5. 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.

  6. A Series of Lanthanide Metal-Organic Frameworks with Interesting Adjustable Photoluminescence Constructed by Helical Chains.

    PubMed

    Liu, Ying; Zhang, Yu; Hu, Gong Hao; Zhou, Shuai; Fan, Ruiqing; Yang, Yulin; Xu, Yan

    2015-07-13

    Based on the isonicotinic acid (HIN=pyridine-4-carboxylic acid), seven lanthanide metal-organic frameworks (MOFs) with the formula [Ln(IN)2 L] (Ln=Eu (1), Tb (2), Er (3), Dy (4), Ho (5), Gd (6), La (7), L=OCH2 CH2 OH) have been synthesized by mixing Ln2 O3 with HIN under solvothermal conditions, and characterized by single-crystal X-ray diffraction, powder X-ray diffraction, infrared spectroscopy, and fluorescence spectroscopy. Crystal structural analysis shows that compounds 1-6 are isostructural, crystallize in a chiral space group P21 21 21 , whereas compound 7 crystallizes in space group C2/c. Nevertheless, they all consist of new intertwined chains. Simultaneously, on the basis of the above-mentioned compounds, we have realized a rational design strategy to form the doped Ln MOFs [(Eux Tb1-x )(IN)2 L] (x=0.35 (8), x=0.19 (9), x=0.06 (10)) by utilizing Tb(III) as the second "rare-earth metal". Interestingly, the photoluminescence of [(Eux Tb1-x )(IN)2 L] are not only adjustable by the ratios of Eu/Tb, but also temperature or excitation wavelength.

  7. Probing alpha-helical secondary structure at a specific site in model peptides via restriction of tryptophan side-chain rotamer conformation.

    PubMed Central

    Willis, K J; Neugebauer, W; Sikorska, M; Szabo, A G

    1994-01-01

    The relationship between alpha-helical secondary structure and the fluorescence properties of an intrinsic tryptophan residue were investigated. A monomeric alpha-helix forming peptide and a dimeric coiled-coil forming peptide containing a central tryptophan residue were synthesized. The fluorescence parameters of the tryptophan residue were determined for these model systems at a range of fractional alpha-helical contents. The steady-state emission maximum was independent of the fractional alpha-helical content. A minimum of three exponential decay times was required to fully describe the time-resolved fluorescence data. Changes were observed in the decay times and more significantly, in their relative contributions that could be correlated with alpha-helix content. The results were also shown to be consistent with a model in which the decay times were independent of both alpha-helix content and emission wavelength. In this model the relative contributions of the decay time components were directly proportional to the alpha-helix content. Data were also analyzed according to a continuous distribution of exponential decay time model, employing global analysis techniques. The recovered distributions had "widths" that were both poorly defined and independent of peptide conformation. We propose that the three decay times are associated with the three ground-state chi 1 rotamers of the tryptophan residue and that the changes in the relative contributions of the decay times are the result of conformational constraints, imposed by the alpha-helical main-chain, on the chi 1 rotamer populations. PMID:8061211

  8. 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.

  9. Self-assembly of silver(I) coordination polymers from aminopyrimidyl derivatives and malonate acid: From 1D chain to 2D layer

    NASA Astrophysics Data System (ADS)

    Sun, Di; Zhang, Na; Xu, Qin-Juan; Luo, Geng-Geng; Huang, Rong-Bin; Zheng, Lan-Sun

    2010-04-01

    Two new silver(I) coordination polymers (CPs) of the formula [Ag 2(dmapym) 4(mal)·H 2O] n ( 1) and [Ag 3(apym) 3(mal)NO 3] n ( 2) (dmapym = 2-amino-4,6-dimethylprimidine, apym = 2-aminopyrimidine, H 2mal = malonate) have been synthesized by reactions of AgNO 3 and 2-aminopyrimidyl ligands with malonate under the ammoniacal condition. Both complexes have been characterized by element analysis, IR and single-crystal X-ray diffraction. The monodentate dmapym and tridentate mal ligands link Ag(I) ions to give complex 1 a one-dimensional (1D) H-shaped chain structure. The complex 2 is a two-dimensional (2D) double sheet structure constructed by (4, 4) single sheet. Additionally, the hydrogen-bonding and C-H⋯π interactions also direct the self-assembly of supramolecular architectures. The photoluminescence properties of the 1 and 2 were investigated in the solid state at room temperature.

  10. Molecular analogs of the hemihelix: A computational study of chain molecules containing left- and right-handed helices

    NASA Astrophysics Data System (ADS)

    Pichierri, Fabio

    2014-08-01

    Using density functional theory (DFT) we design two novel chain molecules containing a left-handed (thia)helicene unit connected to a right-handed (thia)helicene unit via a phosphoroussbnd phosphorous (Psbnd P) bond. These chains represent the molecular analogs of the novel hemihelix structure recently discovered by a group of Harvard University scientists. The HOMO and LUMO levels of the heterochiral chains, termed hemihelicenes, are localized on the left- and right-handed blocks, respectively. In contrast, the frontier orbitals of the chains containing homochiral (thia)helicenes connected by a Psbnd P bond are delocalized all over the chain.

  11. Stable polyglutamine dimers can contain β-hairpins with interdigitated side chains-but not α-helices, β-nanotubes, β-pseudohelices, or steric zippers.

    PubMed

    Miettinen, Markus S; Monticelli, Luca; Nedumpully-Govindan, Praveen; Knecht, Volker; Ignatova, Zoya

    2014-04-15

    A common thread connecting nine fatal neurodegenerative protein aggregation diseases is an abnormally expanded polyglutamine tract found in the respective proteins. Although the structure of this tract in the large mature aggregates is increasingly well described, its structure in the small early aggregates remains largely unknown. As experimental evidence suggests that the most toxic species along the aggregation pathway are the small early ones, developing strategies to alleviate disease pathology calls for understanding the structure of polyglutamine peptides in the early stages of aggregation. Here, we present a criterion, grounded in available experimental data, that allows for using kinetic stability of dimers to assess whether a given polyglutamine conformer can be on the aggregation path. We then demonstrate that this criterion can be assessed using present-day molecular dynamics simulations. We find that although the α-helical conformer of polyglutamine is very stable, dimers of α-helices lack the kinetic stability necessary to support further oligomerization. Dimers of steric zipper, β-nanotube, and β-pseudohelix conformers are also too short-lived to initiate aggregation. The β-hairpin-containing conformers, instead, invariably form very stable dimers when their side chains are interdigitated. Combining these findings with the implications of recent solid-state NMR data on mature fibrils, we propose a possible pathway for the initial stages of polyglutamine aggregation, in which β-hairpin-containing conformers act as templates for fibril formation.

  12. Molecular tectonics: self-complementary supramolecular Se...N synthons directing assembly of 1D silver chains into 3D porous molecular architectures.

    PubMed

    Zhou, Ai-Ju; Zheng, Shao-Liang; Fang, Yue; Tong, Ming-Liang

    2005-06-27

    Reaction of 2,1,3-benzoselenadiazole (bsd) with AgNO3 results in the formation of a novel model example of a Se...N synthon directed molecular network of different polymorphs at different temperatures. Alpha-[Ag(bsd)2(NO3)] x 0.5bsd formed at ambient temperature, has a 3D porous molecular network constructed with monomeric [Ag(bsd)2(NO3)] motif, and has 1D channels that are encapsulated with 1D arrays of two-fold-disordered dimeric (bsd)2 guests aggregated by the self-complementary nonbonded Se...N interactions. This is the first molecular net directed by supramolecular Se...N synthons. The second polymorph, beta-[Ag(bsd)2(NO3)] x 0.5bsd, formed from an analogous reaction at 50 degrees C, contains a similar 3D molecular network constructed with tetrameric [Ag4(bsd)8(NO3)4] motif and 1D arrays of well-ordered dimeric (bsd)2 guests are encapsulated in the channels. Such ordered (bsd)2 dimers provide an excellent simplified dimeric model for MO calculations of intermolecular nonbonded Se...N interactions.

  13. Non-native side chain IR probe in peptides: ab initio computation and 1D and 2D IR spectral simulation.

    PubMed

    Zheng, Michael L; Zheng, David C; Wang, Jianping

    2010-02-18

    Infrared frequency region of 2000-2600 cm(-1) (i.e., ca. 4-5 microm in wavelength) is a well-known open spectral window for peptides and proteins. In this work, six unnatural amino acids (unAAs) were designed to have characteristic absorption bands located in this region. Key chemical groups that served as side chains in these unAAs are C[triple bond]C, Phe-C[triple bond]C, N=C=O, N=C=S, P-H, and Si-H, respectively. Cysteine (a natural AA having S-H in side chain) was also studied for comparison. The anharmonic vibrational properties, including frequencies, anharmonicities, and intermode couplings, were examined using the density functional theory. Broadband linear infrared (IR) and two-dimensional (2D) IR spectra were simulated for each molecule. It is found that all of the side chain modes have significant overtone diagonal anharmonicities. All have moderate transition dipole strengths except the C[triple bond]C and S-H stretching modes, in comparison with the C=O stretching mode. In each case, a collection of 2D IR cross peaks were predicted to appear due to the presence of the side chain groups, whose strengths are closely related to the intramolecular anharmonic interactions, and to the transition dipole strengths of the coupled vibrators. Further, potential energy distribution analysis and high-order anharmonic constant computation showed that these IR probes possess a varying degree of mode localization. The results suggest that these IR probes are potentially useful in complementing the well-studied amide-I mode, to investigate structures and dynamics of peptides and proteins.

  14. Effects of magnetic site disorder of the 1-D Ising spin chain compounds Ca3(Co,Mn)2O6 with dilute doping

    NASA Astrophysics Data System (ADS)

    Casas, Brian; Lampen, Paula; Phan, Manh-Huong; Srikanth, Hariharan; Kovak, Jozef; Skorvanek, Ivan

    2015-03-01

    The spin chain compound Ca3Co2O6 has been extensively studied due to a number of unusual properties originating from geometrically frustrated Ising-like spin chains arranged in a triangular lattice. These quasi one dimensional structures provide an ideal environment to study dilute magnetic disorder in spin-glass like systems. Disorder controlled via chemical doping has been observed to weaken the spin glass behavior and disrupt a number of metamagnetic transitions found in pristine Ca3Co2O6. We report a systematic study of the effects of dilute Mn doping (x = 0.05 - 0.50) in Ca3Co2-xMnxO6 synthesized via a sol-gel method. Detailed AC and DC magnetization measurements performed on a SQUID magnetometer reveal the suppression of the step-like metamagnetic transitions by a doping of x = 0.25. The relaxation time is found to decrease with increasing Mn content, showing the destruction of the spin-glass like behavior. Our observations yield new insight into the role of site disorder on the glassy behavior in spin chain systems. Research was supported by the U.S. Department of Energy, Office of Basic Energy Sciences, Division of Materials Sciences and Engineering under Award No. DE-FG02-07ER46438.

  15. 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.

  16. Structural Modulation from 1D Chain to 3D Framework: Improved Thermostability, Insensitivity, and Energies of Two Nitrogen-Rich Energetic Coordination Polymers.

    PubMed

    Guo, Zhaoqi; Wu, Yunlong; Deng, Chongqing; Yang, Guoping; Zhang, Jiangong; Sun, Zhihua; Ma, Haixia; Gao, Chao; An, Zhongwei

    2016-11-07

    Two new energetic coordination polymers (CPs) [Pb(BT)(H2O)3]n (1) and [Pb3(DOBT)3(H2O)2]n·(4H2O)n (2) with 1D and 3D structures were synthesized by employing two rational designed ligands, 1H,1'H-5,5'-bitetrazole (H2BT) and 1H,1'H-[5,5'-bitetrazole]-1,1'-diol ligands (DHBT), respectively. Thermal analyses and sensitivity tests show that the 3D architecture reinforces the network of 2 which has higher thermal stability and lower sensitivity than that of 1. Through oxygen-bomb combustion calorimetry the molar enthalpy of formation of 2 is derived to be much higher than that of 1 as well as the reported CPs. Herein, more importantly, the heats of detonation (ΔHdet) were calculated according to the decomposition products of TG-DSC-MS-FTIR simultaneous analyses for the first time. The calculated results show that ΔHdet of 2 is 23% higher than that of 1. This research demonstrates that 3D energetic CP with outstanding energetic properties can be obtained through efficient and reasonable design.

  17. 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.

  18. 1D μ-glycine-briged copper (II) chain in complex [Cu(μ-Gly)Im(ClO4)]n and ferromagnetic interactions among copper (II)

    NASA Astrophysics Data System (ADS)

    Pan, Lu; Lv, Xue-Chuan; Luo, Guan-Hua; Gao, Xiao-Han; Tan, Zhi-Cheng

    2016-12-01

    Complex [Cu(μ-Gly)Im(ClO4)]n(Im = imidazole, and Gly = glycine) with μ-glycine-briged copper (II) chain, containing six-coordination distorted elongated octahedron, was synthesized and characterized. The complex belongs to space group P 21/c measured by X-ray single crystal diffraction. In the cluster, each Cu2+ ion are six-coordination by one nitrogen atom and two oxygen atoms of glycine, one nitrogen atoms of imidazole, and two of oxygen atoms of two perchlorate. Each Cu2+ ion has an N2O4 donor set, which forms the distorted elongated octahedron due to the Jahn-Teller (JT) effect. The magnetic and thermodynamic properties were researched. Magnetic susceptibilities of the complex showed that ferromagnetic interactions occurred between the Cu (II) atoms. The Curie-Weiss constant C = 0.565 cm3 K·mol-1 and the Weiss constant θ = 1.0585 K were given by the Curie-Weiss law The ferromagnetic nature of the interaction could be deduced as the exchange pathway of Cusbnd Osbnd Csbnd Osbnd Cu, which involved an equatorial position at one copper (II) ion and an axial position of the nearest copper (II). The complex decomposed from 511 to 538 K as two steps.

  19. Self-assembly of 1-D n-type nanostructures based on naphthalene diimide-appended dipeptides.

    PubMed

    Shao, Hui; Nguyen, Tuan; Romano, Natalie C; Modarelli, David A; Parquette, Jon R

    2009-11-18

    n-Type 1D nanostructures are formed from the beta-sheet assembly of dipeptides bearing a 1,4,5,8-naphthalenetetracarboxylic acid diimide (NDI) side chain into either helical nanofibers or twisted nanoribbons. Amyloid-like 1-D helical nanofibers and twisted nanoribbons assemble in an aqueous solution depending on the placement of the NDI group. beta-Sheet-type hydrogen bonding and pi-pi association play important roles in directing the assembly process. A delicate balance between electrostatic repulsion and hydrophobic interactions is critical for self-assembly. Fluorescence lifetime and anisotropy experiments indicate that the nature of the intermolecular organization and packing within the nanostructures critically impacts intermolecular energy migration pi-electron delocalization.

  20. 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.

  1. Enhanced ion anisotropy by nonconventional coordination geometry: single-chain magnet behavior for a [{Fe(II)L}2{Nb(IV)(CN)8}] helical chain compound designed with heptacoordinate Fe(II).

    PubMed

    Venkatakrishnan, Thengarai S; Sahoo, Shaon; Bréfuel, Nicolas; Duhayon, Carine; Paulsen, Carley; Barra, Anne-Laure; Ramasesha, S; Sutter, Jean-Pascal

    2010-05-05

    Nonconventional heptacoordination in combination with efficient magnetic exchange coupling is shown to yield a 1-D heteronuclear {Fe(II)Nb(IV)} compound with remarkable magnetic features when compared to other Fe(II)-based single chain magnets (SCM). Cyano-bridged heterometallic {3d-4d} and {3d-5d} chains are formed upon assembling Fe(II) bearing a pentadentate macrocycle as the blocking ligand with octacyano metallates, [M(CN)(8)](4-) (M = Nb(IV), Mo(IV), W(IV)). X-ray diffraction (single-crystal and powder) measurements reveal that the [{(H(2)O)Fe(L(1))}{M(CN)(8)}{Fe(L(1))}](infinity) architectures consist of isomorphous 1-D polymeric structures based on the alternation of {Fe(L(1))}(2+) and {M(CN)(8)}(4-) units (L(1) stands for the pentadentate macrocycle). Analysis of the magnetic susceptibility behavior revealed cyano-bridged {Fe-Nb} exchange interaction to be antiferromagnetic with J = -20 cm(-1) deduced from fitting an Ising model taking into account the noncollinear spin arrangement. For this ferrimagnetic chain a slow relaxation of its magnetization is observed at low temperature revealing a SCM behavior with Delta/k(B) = 74 K and tau(0) = 4.6 x 10(-11) s. The M versus H behavior exhibits a hysteresis loop with a coercive field of 4 kOe at 1 K and reveals at 380 mK magnetic avalanche processes, i.e., abrupt reversals in magnetization as H is varied. The origin of these characteristics is attributed to the combination of efficient {Fe-Nb} exchange interaction and significant anisotropy of the {Fe(L(1))} unit. High field EPR and magnetization experiments have revealed for the parent compound [Fe(L(1))(H(2)O)(2)]Cl(2) a negative zero field splitting parameter of D approximately = -17 cm(-1). The crystal structure, magnetic behavior, and Mossbauer data for [Fe(L(1))(H(2)O)(2)]Cl(2) are also reported.

  2. 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.

  3. 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.

  4. A unified convention for biological assemblies with helical symmetry.

    PubMed

    Tsai, Chung Jung; Nussinov, Ruth

    2011-08-01

    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(1), n(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.

  5. The effect of branched side chains on the relative stability of α- and π-helices: a combination of the enveloping distribution sampling and one-step perturbation methods†

    NASA Astrophysics Data System (ADS)

    Lin, Zhixiong; van Gunsteren, Wilfred F.

    2013-08-01

    The method of enveloping distribution sampling (EDS) to efficiently obtain free enthalpy differences between different molecular systems from a single simulation can also be used to compute free enthalpy differences between two different conformations of a system. A combination (EDS-OSP) of EDS and the one-step perturbation (OSP) method that yields many free enthalpy differences from a single simulation allows for rapid prediction of conformational free enthalpy differences for many not too different molecular systems from a single simulation. Here, we applied EDS-OSP to predict the free enthalpy differences between a π-helix and an α-helix for a set of four deca-peptides with as fifth residue Ala, Val, Leu, or Ile in aqueous solution. First, an EDS simulation of a designed soft-core reference-state Hamiltonian was carried out to sample both helices in a single simulation. Then the soft-core atoms are perturbed into real atoms of each of the four peptides. Thus, the free enthalpy differences between the π-helix and the α-helix for all four perturbed-state, real peptides can be predicted with only one simulation using EDS-OSP. EDS-OSP and the original EDS method gave very similar free enthalpy values, i.e., the average absolute deviation between the two methods for the four peptides is 0.8 kJ mol-1, while EDS-OSP required almost four times less computational effort. Side chains branched at the C β -position were found to slightly decrease the stability of the α-helical conformation with respect to the π-helical one.

  6. 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.

  7. 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.

  8. An α-Helical Signal in the Cytosolic Domain of the Interleukin 2 Receptor β Chain Mediates Sorting Towards Degradation after Endocytosis

    PubMed Central

    Subtil, Agathe; Delepierre, Muriel; Dautry-Varsat, Alice

    1997-01-01

    High-affinity IL2 receptors consist of three components, the α, β, and γ chains that are associated in a noncovalent manner. Both the β and γ chains belong to the cytokine receptor superfamily. Interleukin 2 (IL2) binds to high-affinity receptors on the cell surface and IL2-receptor complexes are internalized. After endocytosis, the components of this multimolecular receptor have different intracellular fates: one of the chains, α, recycles to the plasma membrane, while the others, β and γ, are routed towards late endocytic compartments and are degraded. We show here that the cytosolic domain of the β chain contains a 10–amino acid sequence which codes for a sorting signal. When transferred to a normally recycling receptor, this sequence diverts it from recycling. The structure of a 17–amino acid segment of the β chain including this sequence has been studied by nuclear magnetic resonance and circular dichroism spectroscopy, which revealed that the 10 amino acids corresponding to the sorting signal form an amphipathic α helix. This work thus describes a novel, highly structured signal, which is sufficient for sorting towards degradation compartments after endocytosis. PMID:9024689

  9. A unified convention for biological assemblies with helical symmetry

    PubMed Central

    Tsai, Chung-Jung; Nussinov, Ruth

    2011-01-01

    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 1, n 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. PMID:21795813

  10. 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

  11. Mn4 single-molecule-magnet-based polymers of a one-dimensional helical chain and a three-dimensional network: syntheses, crystal structures, and magnetic properties.

    PubMed

    Tsai, Hui-Lien; Yang, Chen-I; Wernsdorfer, Wolfgang; Huang, Siang-Hua; Jhan, Siang-Yu; Liu, Ming-Hsuan; Lee, Gene-Hsiang

    2012-12-17

    Two Mn(4) single-molecule-magnet (SMM)-based coordination polymers, {[Mn(4)O(salox)(3)(N(3))(3)(DMF)(2)(H(2)O)(dpp)]·0.5MeOH}(n) (1·0.5MeOH; H(2)salox = salicylaldoxime; dpp = 1,3-di-4-pyridylpropane; DMF = N,N-dimethylformamide) and {[Mn(4)O(Me-salox)(3)(N(3))(3)(dpp)(1.5)]·1.5Et(2)O}(n) (2·1.5Et(2)O; Me-H(2)salox = hydroxyphenylethanone oxime), are self-assembled from Mn(ClO(4))(2)·6H(2)O/H(2)salox and Mn(ClO(4))(2)·6H(2)O/Me-H(2)salox systems with dpp and NaN(3) in DMF/MeOH, respectively. Both compounds comprise a mixed-valence tetranuclear manganese core, [Mn(II)Mn(III)(3)O](9+), which serves as a building unit for subsequent assembly via oximate and azido ligands. The flexible dpp ligand links with a Mn(4) unit, leading to the formation of a one-dimensional helical structure in 1·0.5MeOH and a three-dimensional pcu network in 2·1.5Et(2)O. The magnetic data analysis shows that antiferromagnetic interactions within the Mn(4) units resulted in S = (3)/(2) and (7)/(2) ground states for 1·0.5MeOH and 2·1.5Et(2)O, respectively. Both compounds show SMM behavior, as evidenced by frequency-dependent out-of-phase signals in alternating-current magnetic susceptibility and magnetic hysteresis loop studies with an energy barrier of U(eff) = 37 K for 2·1.5Et(2)O.

  12. Axial-bundle phases--new modes of 2D, 3D, and helical columnar self-assembly in liquid crystalline phases of bolaamphiphiles with swallow tail lateral chains.

    PubMed

    Prehm, Marko; Liu, Feng; Zeng, Xiangbing; Ungar, Goran; Tschierske, Carsten

    2011-04-06

    Two series of polyphilic molecules composed of a rigid and linear p-terphenyl core, terminated at both ends with polar glycerol groups capable of hydrogen bonding, and two branched swallow tail-type lateral chains, composed of a fluorinated and a nonfluorinated branch or two fluorinated branches, were synthesized and investigated by differential scanning calorimetry, polarizing microscopy, and X-ray diffraction (XRD) with respect to their self-assembly in thermotropic liquid crystalline (LC) phases. Hexagonal columnar phases were formed by all molecules, at least at the highest temperature. In these phases the columns are composed of a core of aromatic rods and an aliphatic shell. The aromatic rods form bundles which are rotationally averaged and lie parallel to the column long axis. This unique organization is proven by different optical and XRD methods. The aromatic and glycerol groups inside the rod bundles are segregated into alternating segments. Depending on temperature and molecular structure, long-range intercolumnar correlation of this periodicity could take place, leading to a 3D-ordered LC phase with rhombohedral R ̄3m symmetry. The bundles are embedded in the matrix of the lateral chains, which is divided into fluoroalkyl- and aliphatic-rich regions. In the 2D columnar phase the fluorinated regions take the form of either straight columns running along the edges of the hexagonal Voronoi cells or, for compounds with a higher degree of fluorination, fuse to a hexagonal honeycomb enclosing the aromatic cores. In the R ̄3m phase the fluorine-rich chains are preferentially found along right- and left-handed helices wound around the 3(1) screw axes between the main aromatic columns.

  13. 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.

  14. Helicity Within and Among Macromolecules

    NASA Astrophysics Data System (ADS)

    Green, Mark M.

    2004-03-01

    There are several classes of helical polymers and supramolecular arrays in which the left and right helical senses are of equal probability and as well in dynamic equilibrium. One example of this class of materials is a polymer first created at Dupont as a commercial fiber candidate almost fifty years ago but which did not rise to the level necessary for commercial use. The polymer, nylon 1, widely known as a polyisocyanate, did become a focal point of research for polymer physics because of its stiff archetypical wormlike nature. An array of research tools was able to elucidate the conformational characteristics of this polymer and therefore reveal in quantitative detail both the source of its stiffness and the limit to this characteristic. Further effort explored the nature of the expected lyotropic liquid crystal properties with similar success. As part of these studies, chiral experiments, which were introduced to determine how to favor one helical sense, played a key role. Statistical physical analysis of these chiral experiments first by Shneior Lifson for uniform chiral fields and later by Jonathan Selinger for quenched random chiral fields gave insight into the cooperative characteristics by which the chiral information influenced the helical senses in these polymers. These kinds of experiments finding parallels to the behavior of sergeants and soldiers and to majority rule were later applied widely in the literature offering insight into the cooperative nature of helical polymers and arrays in general. Moreover, the interplay between the character of the single chains and the liquid crystals that arise in concentrated solutions from the polyisocyanates yielded new kinds of information about the cholesteric state formed by lyotropic liquid crystals in general and even led to new phenomena connecting liquid crystal behavior to temperature.

  15. Bilinear forms and soliton solutions for a fourth-order variable-coefficient nonlinear Schrödinger equation in an inhomogeneous Heisenberg ferromagnetic spin chain or an alpha helical protein

    NASA Astrophysics Data System (ADS)

    Yang, Jin-Wei; Gao, Yi-Tian; Wang, Qi-Min; Su, Chuan-Qi; Feng, Yu-Jie; Yu, Xin

    2016-01-01

    In this paper, a fourth-order variable-coefficient nonlinear Schrödinger equation is studied, which might describe a one-dimensional continuum anisotropic Heisenberg ferromagnetic spin chain with the octuple-dipole interaction or an alpha helical protein with higher-order excitations and interactions under continuum approximation. With the aid of auxiliary function, we derive the bilinear forms and corresponding constraints on the variable coefficients. Via the symbolic computation, we obtain the Lax pair, infinitely many conservation laws, one-, two- and three-soliton solutions. We discuss the influence of the variable coefficients on the solitons. With different choices of the variable coefficients, we obtain the parabolic, cubic, and periodic solitons, respectively. We analyse the head-on and overtaking interactions between/among the two and three solitons. Interactions between a bound state and a single soliton are displayed with different choices of variable coefficients. We also derive the quasi-periodic formulae for the three cases of the bound states.

  16. From 1D chain to 3D network: a new family of inorganic-organic hybrid semiconductors MO3(L)(x) (M = Mo, W; L = organic linker) built on perovskite-like structure modules.

    PubMed

    Zhang, Xiao; Hejazi, Mehdi; Thiagarajan, Suraj J; Woerner, William R; Banerjee, Debasis; Emge, Thomas J; Xu, Wenqian; Teat, Simon J; Gong, Qihan; Safari, Ahmad; Yang, Ronggui; Parise, John B; Li, Jing

    2013-11-20

    MO3 (M = Mo, W) or VI-VI binary compounds are important semiconducting oxides that show great promise for a variety of applications. In an effort to tune and enhance their properties in a systematic manner we have applied a designing strategy to deliberately introduce organic linker molecules in these perovskite-like crystal lattices. This approach has led to a wealth of new hybrid structures built on one-dimensional (1D) and two-dimensional (2D) VI-VI modules. The hybrid semiconductors exhibit a number of greatly improved properties and new functionality, including broad band gap tunability, negative thermal expansion, largely reduced thermal conductivity, and significantly enhanced dielectric constant compared to their MO3 parent phases.

  17. 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.

  18. Discrete hexamer water clusters and 2D water layer trapped in three luminescent Ag/tetramethylpyrazine/benzene-dicarboxylate hosts: 1D chain, 2D layer and 3D network

    NASA Astrophysics Data System (ADS)

    Mei, Hong-Xin; Zhang, Ting; Huang, Hua-Qi; Huang, Rong-Bin; Zheng, Lan-Sun

    2016-03-01

    Three mix-ligand Ag(I) coordination compounds, namely, {[Ag10(tpyz) 5(L1) 5(H2 O)2].(H2 O)4}n (1, tpyz = 2,3,4,5-tetramethylpyrazine, H2 L1 = phthalic acid), [Ag4(tpyz) 2(L2) 2(H2 O)].(H2 O)5}n (2, H2 L2 = isophthalic acid) {[Ag2(tpyz) 2(L3) (H2 O)4].(H2 O)8}n (3, H2 L3 = terephthalic acid), have been synthesized and characterized by elemental analysis, IR, PXRD and X-ray single-crystal diffraction. 1 exhibits a 2D layer which can be simplified as a (4,4) net. 2 is a 3D network which can be simplified as a (3,3)-connected 2-nodal net with a point symbol of {102.12}{102}. 3 consists of linear [Ag(tpyz) (H2 O)2]n chain. Of particular interest, discrete hexamer water clusters were observed in 1 and 2, while a 2D L10(6) water layer exists in 3. The results suggest that the benzene dicarboxylates play pivotal roles in the formation of the different host architectures as well as different water aggregations. Moreover, thermogravimetric analysis (TGA) and emissive behaviors of these compounds were investigated.

  19. Emerging double helical nanostructures.

    PubMed

    Zhao, Meng-Qiang; Zhang, Qiang; Tian, Gui-Li; Wei, Fei

    2014-08-21

    As one of the most important and land-mark structures found in nature, a double helix consists of two congruent single helices with the same axis or a translation along the axis. This double helical structure renders the deoxyribonucleic acid (DNA) the crucial biomolecule in evolution and metabolism. DNA-like double helical nanostructures are probably the most fantastic yet ubiquitous geometry at the nanoscale level, which are expected to exhibit exceptional and even rather different properties due to the unique organization of the two single helices and their synergistic effect. The organization of nanomaterials into double helical structures is an emerging hot topic for nanomaterials science due to their promising exceptional unique properties and applications. This review focuses on the state-of-the-art research progress for the fabrication of double-helical nanostructures based on 'bottom-up' and 'top-down' strategies. The relevant nanoscale, mesoscale, and macroscopic scale fabrication methods, as well as the properties of the double helical nanostructures are included. Critical perspectives are devoted to the synthesis principles and potential applications in this emerging research area. A multidisciplinary approach from the scope of nanoscience, physics, chemistry, materials, engineering, and other application areas is still required to the well-controlled and large-scale synthesis, mechanism, property, and application exploration of double helical nanostructures.

  20. A Helical Stairway Project

    ERIC Educational Resources Information Center

    Farmer, Tom

    2008-01-01

    We answer a geometric question that was raised by the carpenter in charge of erecting helical stairs in a 10-story hospital. The explanation involves the equations of lines, planes, and helices in three-dimensional space. A brief version of the question is this: If A and B are points on a cylinder and the line segment AB is projected radially onto…

  1. Unusually Stable Helical Coil Allotrope of Phosphorus.

    PubMed

    Liu, Dan; Guan, Jie; Jiang, Jingwei; Tománek, David

    2016-12-14

    We have identified an unusually stable helical coil allotrope of phosphorus. Our ab initio density functional theory calculations indicate that the uncoiled, isolated straight one-dimensional chain is equally stable as a monolayer of black phosphorus dubbed phosphorene. The coiling tendency and the attraction between adjacent coil segments add an extra stabilization energy of ∼12 meV/atom to the coil allotrope, similar in value to the ∼16 meV/atom interlayer attraction in bulk black phosphorus. Thus, the helical coil structure is essentially as stable as black phosphorus, the most stable phosphorus allotrope known to date. With an optimum radius of 2.4 nm, the helical coil of phosphorus may fit well and even form inside wide carbon nanotubes.

  2. 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.

  3. Squeezed helical elastica.

    PubMed

    Bouzar, Lila; Müller, Martin Michael; Gosselin, Pierre; Kulić, Igor M; Mohrbach, Hervé

    2016-11-01

    We theoretically study the conformations of a helical semi-flexible filament confined to a flat surface. This squeezed helix exhibits a variety of unexpected shapes resembling circles, waves or spirals depending on the material parameters. We explore the conformation space in detail and show that the shapes can be understood as the mutual elastic interaction of conformational quasi-particles. Our theoretical results are potentially useful to determine the material parameters of such helical filaments in an experimental setting.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. Helical spring holder assembly

    NASA Technical Reports Server (NTRS)

    Newman, Wyatt S. (Inventor)

    1987-01-01

    A helically-threaded spring holder on which a helically wound spring is mounted has a groove formed in one side of the thread at the end where the spring engages the spring holder. The groove relieves the portion of the side in which it is formed from restricting the spring against axial movement during deflection of the spring. The circumferential length of this groove is chosen to establish the number of spring coils which can be deflected without contacting the side of the thread. The end of the thread is also made rigid to prevent flexing thereof during maximal elongation of the spring.

  9. 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.

  10. The Helicity of Vortex Filaments.

    NASA Astrophysics Data System (ADS)

    Petrich, Dean; Tao, Louis

    1996-03-01

    The helicity, defined by H = int dV v \\cdot nabla × v, is a conserved quantity of the three-dimensional Euler equations. Traditionally the helicity has been viewed as a measure of the topology of vortex lines, but it is shown that the helicity measures their geometry as well as their topology (J.D. Bekenstein, Physics Letters B), 282 (1992) 44-49.. The existence of helicity-preserving reconnection events is discussed.

  11. 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.

  12. On the energy density of helical proteins.

    PubMed

    Barros, Manuel; Ferrández, Angel

    2014-12-01

    We solve the problem of determining the energy actions whose moduli space of extremals contains the class of Lancret helices with a prescribed slope. We first see that the energy density should be linear both in the total bending and in the total twisting, such that the ratio between the weights of them is the prescribed slope. This will give an affirmative answer to the conjecture stated in Barros and Ferrández (J Math Phys 50:103529, 2009). Then, we normalize to get the best choice for the helical energy. It allows us to show that the energy, for instance of a protein chain, does not depend on the slope and is invariant under homotopic changes of the cross section which determines the cylinder where the helix is lying. In particular, the energy of a helix is not arbitrary, but it is given as natural multiples of some basic quantity of energy.

  13. Helically Coiled Graphene Nanoribbons.

    PubMed

    Daigle, Maxime; Miao, Dandan; Lucotti, Andrea; Tommasini, Matteo; Morin, Jean-François

    2017-03-07

    Graphene is a zero-gap, semiconducting 2D material that exhibits outstanding charge-transport properties. One way to open a band gap and make graphene useful as a semiconducting material is to confine the electron delocalization in one dimension through the preparation of graphene nanoribbons (GNR). Although several methods have been reported so far, solution-phase, bottom-up synthesis is the most promising in terms of structural precision and large-scale production. Herein, we report the synthesis of a well-defined, helically coiled GNR from a polychlorinated poly(m-phenylene) through a regioselective photochemical cyclodehydrochlorination (CDHC) reaction. The structure of the helical GNR was confirmed by (1) H NMR, FT-IR, XPS, TEM, and Raman spectroscopy. This Riemann surface-like GNR has a band gap of 2.15 eV and is highly emissive in the visible region, both in solution and the solid state.

  14. Analysis of Helical Waveguide.

    DTIC Science & Technology

    1985-12-23

    tube Efficiency Helix structure Backward wave oscillation Gain 19. ABSTRACT (Continue on reverse if necessary and identofy by block number) The...4,vailabilitY CCdes -vai aidIorDist spec a ." iii "- -. .5- S.. . ANALYSIS OF HELICAL WAVEGUIDE I. INTRODUCTION High power (- 10 kW) and broadband ...sys- tems. The frequency range of interest is 60-100 GHz. In this frequency range, the conventional slow wave circuits such as klystrons and TWTs have

  15. 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.

  16. A rational route to SCM materials based on a 1-D cobalt selenocyanato coordination polymer.

    PubMed

    Boeckmann, Jan; Näther, Christian

    2011-07-07

    Thermal annealing of a discrete complex with terminal SeCN anions and monodentate coligands enforces the formation of a 1D cobalt selenocyanato coordination polymer that shows slow relaxation of the magnetization. Therefore, this approach offers a rational route to 1D materials that might show single chain magnetic behaviour.

  17. Magnetic helicity in astrophysical dynamos

    NASA Astrophysics Data System (ADS)

    Candelaresi, Simon

    2012-09-01

    The broad variety of ways in which magnetic helicity affects astrophysical systems, in particular dynamos, is discussed. The so-called alpha effect is responsible for the growth of large-scale magnetic fields. The conservation of magnetic helicity, however, quenches the alpha effect, in particular for high magnetic Reynolds numbers. Predictions from mean-field theories state particular power law behavior of the saturation strength of the mean fields, which we confirm in direct numerical simulations. The loss of magnetic helicity in the form of fluxes can alleviate the quenching effect, which means that large-scale dynamo action is regained. Physically speaking, galactic winds or coronal mass ejections can have fundamental effects on the amplification of galactic and solar magnetic fields. The gauge dependence of magnetic helicity is shown to play no effect in the steady state where the fluxes are represented in form of gauge-independent quantities. This we demonstrate in the Weyl-, resistive- and pseudo Lorentz-gauge. Magnetic helicity transport, however, is strongly affected by the gauge choice. For instance the advecto-resistive gauge is more efficient in transporting magnetic helicity into small scales, which results in a distinct spectrum compared to the resistive gauge. The topological interpretation of helicity as linking of field lines is tested with respect to the realizability condition, which imposes a lower bound for the spectral magnetic energy in presence of magnetic helicity. It turns out that the actual linking does not affect the relaxation process, unlike the magnetic helicity content. Since magnetic helicity is not the only topological variable, I conduct a search for possible others, in particular for non-helical structures. From this search I conclude that helicity is most of the time the dominant restriction in field line relaxation. Nevertheless, not all numerical relaxation experiments can be described by the conservation of magnetic helicity

  18. Position of helical kinks in membrane protein crystal structures and the accuracy of computational prediction.

    PubMed

    Hall, Spencer E; Roberts, Kyle; Vaidehi, Nagarajan

    2009-01-01

    The structural features of helical transmembrane (TM) proteins, such as helical kinks, tilts, and rotational orientations are important in modulation of their function and these structural features give rise to functional diversity in membrane proteins with similar topology. In particular, the helical kinks caused by breaking of the backbone hydrogen bonds lead to hinge bending flexibility in these helices. Therefore it is important to understand the nature of the helical kinks and to be able to reproduce these kinks in structural models of membrane proteins. We have analyzed the position and extent of helical kinks in the transmembrane helices of all the crystal structures of membrane proteins taken from the MPtopo database, which are about 405 individual helices of length between 19 and 35 residues. 44% of the crystal structures of TM helices showed a significant helical kink, and 35% of these kinks are caused by prolines. Many of the non-proline helical kinks are caused by other residues like Ser and Gly that are located at the center of helical kinks. The side chain of Ser makes a hydrogen bond with the main chain carbonyl of the i - 4th or i + 4th residue thus making a kink. We have also studied how well molecular dynamics (MD) simulations on isolated helices can reproduce the position of the helical kinks in TM helices. Such a method is useful for structure prediction of membrane proteins. We performed MD simulations, starting from a canonical helix for the 405 TM helices. 1 ns of MD simulation results show that we can reproduce about 79% of the proline kinks, only 59% of the vestigial proline kinks and 18% of the non-proline helical kinks. We found that similar results can be obtained from choosing the lowest potential energy structure from the MD simulation. 4-14% more of the vestigial prolines were reproduced by replacing them with prolines before performing MD simulations, and changing the amino acid back to proline after the MD simulations. From these

  19. Helical edge states and fractional quantum Hall effect in a graphene electron-hole bilayer

    NASA Astrophysics Data System (ADS)

    Sanchez-Yamagishi, Javier D.; Luo, Jason Y.; Young, Andrea F.; Hunt, Benjamin M.; Watanabe, Kenji; Taniguchi, Takashi; Ashoori, Raymond C.; Jarillo-Herrero, Pablo

    2016-10-01

    Helical 1D electronic systems are a promising route towards realizing circuits of topological quantum states that exhibit non-Abelian statistics. Here, we demonstrate a versatile platform to realize 1D systems made by combining quantum Hall (QH) edge states of opposite chiralities in a graphene electron-hole bilayer at moderate magnetic fields. Using this approach, we engineer helical 1D edge conductors where the counterpropagating modes are localized in separate electron and hole layers by a tunable electric field. These helical conductors exhibit strong non-local transport signals and suppressed backscattering due to the opposite spin polarizations of the counterpropagating modes. Unlike other approaches used for realizing helical states, the graphene electron-hole bilayer can be used to build new 1D systems incorporating fractional edge states. Indeed, we are able to tune the bilayer devices into a regime hosting fractional and integer edge states of opposite chiralities, paving the way towards 1D helical conductors with fractional quantum statistics.

  20. Electronic, bonding, and optical properties of 1d [CuCN]n (n = 1-10) chains, 2d [CuCN]n (n = 2-10) nanorings, and 3d [Cun (CN)n ]m (n = 4, m = 2, 3; n = 10, m = 2) tubes studied by DFT/TD-DFT methods.

    PubMed

    Tsipis, Athanassios C; Stalikas, Alexandros V

    2015-06-30

    The electronic, bonding, and photophysical properties of one-dimensional [CuCN](n) (n = 1-10) chains, 2-D [CuCN](n) (n = 2-10) nanorings, and 3-D [Cu(n)(CN)(n)](m) (n = 4, m = 2, 3; n = 10, m = 2) tubes are investigated by means of a multitude of computational methodologies using density functional theory (DFT) and time-dependent-density-functional theory (TD-DFT) methods. The calculations revealed that the 2-D [CuCN](n) (n = 2-10) nanorings are more stable than the respective 1-D [CuCN](n) (n = 2-10) linear chains. The 2-D [CuCN](n) (n = 2-10) nanorings are predicted to form 3-D [Cun (CN)(n)](m) (n = 4, m = 2, 3; n = 10, m = 2) tubes supported by weak stacking interactions, which are clearly visualized as broad regions in real space by the 3D plots of the reduced density gradient. The bonding mechanism in the 1-D [CuCN](n) (n = 1-10) chains, 2-D [CuCN](n) (n = 2-10) nanorings, and 3-D [Cu(n)(CN)(n)](m) (n = 4, m = 2, 3; n = 10, m = 2) tubes are easily recognized by a multitude of electronic structure calculation approaches. Particular emphasis was given on the photophysical properties (absorption and emission spectra) of the [CuCN](n) chains, nanorings, and tubes which were simulated by TD-DFT calculations. The absorption and emission bands in the simulated TD-DFT absorption and emission spectra have thoroughly been analyzed and assignments of the contributing principal electronic transitions associated to individual excitations have been made.

  1. 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.

  2. 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.

  3. 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.

  4. Prediction of buried helices in multispan alpha helical membrane proteins.

    PubMed

    Adamian, Larisa; Liang, Jie

    2006-04-01

    Analysis of a database of structures of membrane proteins shows that membrane proteins composed of 10 or more transmembrane (TM) helices often contain buried helices that are inaccessible to phospholipids. We introduce a method for identifying TM helices that are least phospholipid accessible and for prediction of fully buried TM helices in membrane proteins from sequence information alone. Our method is based on the calculation of residue lipophilicity and evolutionary conservation. Given that the number of buried helices in a membrane protein is known, our method achieves an accuracy of 78% and a Matthew's correlation coefficient of 0.68. A server for this tool (RANTS) is available online at http://gila.bioengr.uic.edu/lab/.

  5. Crystal Engineering of Hand-Twisted Helical Crystals.

    PubMed

    Saha, Subhankar; Desiraju, Gautam R

    2017-02-08

    A strategy is outlined for the design of hand-twisted helical crystals. The starting point in the exercise is the one-dimensional (1D) plastic crystal, 1,4-dibromobenzene, which is then changed to a 1D elastic crystal, exemplified by 4-bromophenyl 4'-chlorobenzoate, by introduction of a molecular synthon -O-CO- in lieu of the supramolecular synthon Br···Br in the precursor. The 1D elastic crystals are next modified to two-dimensional (2D) elastic crystals, of the type 4-bromophenyl 4'-nitrobenzoate where the halogen bonding and C-H···O hydrogen bonding are well-matched. Finally, varying the interaction strengths in these 2D elastic crystals gives plastic crystals with two pairs of bendable faces but without slip planes. Typical examples are 4-chlorophenyl and 4-bromophenyl 4'-nitrobenzoate. This type of 2D plasticity represents a new type of bendable crystals in which plastic behavior is seen with a fair degree of isotropic character in the crystal packing. The presence of two sets of bendable faces, generally orthogonal to each other, allows for the possibility of hand-twisting of the crystals to give grossly helical morphologies. Accordingly, we propose the name hand-twisted helical crystals for these substances.

  6. Helical phases in superconductors

    NASA Astrophysics Data System (ADS)

    Sandhu, Raminder P. Kaur

    In conventional superconductors, the Cooper pairs are formed from quasiparticles with opposite momentum and spins because of the degeneracy of the quasiparticles under time reversal and inversion. The absence of any of these symmetries will have pronounced effects on superconducting states. Time reversal symmetry can be broken in the presence of magnetic impurities or by the application of a magnetic field. Similarly, the dislocation of crystal ions from their higher symmetric positions can cause broken inversion symmetry. We studied the effects of broken time reversal and inversion symmetries on unconventional superconductors, such as high temperature cuprates, Sr2RuO 4, and CePt3Si. In the cuprates, the superconducting state exists near the antiferromagnetic order. Sr2RuO4 and CePt3Si do not have spatial inversion, and the superconducting states coexist with magnetic order. In cuprates, the broken time reversal symmetry has been reported in the pseudogap phase which will effect the d-wave superconducting state of underdoped regime. On the basis of symmetry analysis we found that a mixture of spin-singlet and -triplet state, d+ip, which is shown to give rise to a helical superconducting phase. Consequences of this d+ip state on Josephson experiments are also discussed. Sr2RuO 4 is known to be another broken time reversal superconductor with spin triplet superconductivity. The widely believed superconducting state, the chiral p wave state, has been extensively studied through Ginzburg Landau theory, but the predictions for this state contradict some experimental observations like anisotropy in the upper critical field, and the existence of a second vortex state. We have formalize quasiclassical theory to find the origin of these contradictions, and also extended the theory to study other possible super-conducting states. Surprisingly, we find that a superconducting state corresponding to freely rotating in-plane d-vector explains the existing experimental results

  7. 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.

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

    PubMed

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

    2013-05-21

    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.

  9. Helical Nanofilament Phases

    SciTech Connect

    L Hough; H Jung; D Kruerke; M Heberling; M Nakata; C Jones; D Chen; D Link; N Clark; et al.

    2011-12-31

    In the formation of chiral crystals, the tendency for twist in the orientation of neighboring molecules is incompatible with ordering into a lattice: Twist is expelled from planar layers at the expense of local strain. We report the ordered state of a neat material in which a local chiral structure is expressed as twisted layers, a state made possible by spatial limitation of layering to a periodic array of nanoscale filaments. Although made of achiral molecules, the layers in these filaments are twisted and rigorously homochiral - a broken symmetry. The precise structural definition achieved in filament self-assembly enables collective organization into arrays in which an additional broken symmetry - the appearance of macroscopic coherence of the filament twist-produces a liquid crystal phase of helically precessing layers.

  10. Mixing in Helical Pipes

    NASA Astrophysics Data System (ADS)

    Gratton, Michael B.; Bernoff, Andrew J.

    2001-11-01

    We consider advection and diffusion of a passive scalar in a helical pipe. By assuming that the curvature and torsion are small (equivalent to small Dean number) and the Reynolds number is moderate, we can use a closed form approximation, due to Dean (1927) and Germano (1982), for the induced recirculation. We investigate the problem numerically using a split-step particle method for a variety of localized initial conditions. The problem is governed by two parameters: a nondimensional diffusion constant D (typically small), and the scaled ratio of torsion to curvature λ. At small times, the longitudinal width of the particle distribution, σ, is governed by diffusive effects (σ ∝ √Dt). At large times, Taylor diffusion dominates (σ ∝ √t/D). However, at intermediate times, a ballistic region exists where the width spreads linearly, as postulated by Mezic & Wiggins (1994). We also discuss how these various behaviors scale with the parameters D and λ.

  11. Helical Emg Effective Resistance

    NASA Astrophysics Data System (ADS)

    Chernyshev, V. K.; Zharinov, E. I.; Busin, V. N.; Grinevich, B. E.; Sokolova, O. V.; Smirnova, G. N.; Klimushkin, K. N.

    2004-11-01

    The efficiency of explosive-magnetic system operation depends on the magnetic flux losses produced under circuit deformation. Losses primarily arise from circuit ohmic resistance and flux pocketing due to the disturbed continuity of helix wires deformation. This is because of technological faults in fabrication and potential electric breakdowns resulting from the voltage overload in the generator circuit. Since it is rather difficult to identify each type of loss mentioned, all soles are expressed as the effective resistance of the circuit, Reff. The EMG-160 multi-sectional helical generator with a 760 mm long helix having an inner diameter of 160 mm is considered as an example. EMG-160 initial conductance was 34 μH and the final inductance was 25 nH. The effective resistance of the circuit was calculated for this experiment. The method of determining the effective resistance allows estimation of EMG efficiency at all stages of generator operation.

  12. Helical Siberian snakes

    SciTech Connect

    Courant, E.D.

    1988-01-01

    To eliminate spin resonances in circular accelerators ''Siberian Snakes'' may be inserted at one or more azimuths in such a way that the overall spin precession tune ..nu../sub s/ equals 1/2. A snake is a sequence of horizontal and vertical deflection magnets whose overall effect is to rotate the spin by ..pi.. about an axis in the plane of the orbit, either longitudinal or transverse or any angle /var phi/ in between. At the same time the magnets of the snake should be arranged so as to produce zero net deflection and displacement of the particle orbit. We investigate here how the orbit deflections can be made small by using helical deflecting magnets rather than discrete horizontal and vertical deflectors.

  13. 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.

  14. EMODEL_1D v. 1.0

    SciTech Connect

    Aldridge, David F.

    2016-07-06

    Program EMODEL_1D is an electromagnetic earth model construction utility designed to generate a three-dimensional (3D) uniformly-gridded representation of one-dimensional (1D) layered earth model. Each layer is characterized by the isotropic EM properties electric permittivity ?, magnetic permeability ?, and current conductivity ?. Moreover, individual layers of the model may possess a linear increase/decrease of any or all of these properties with depth.

  15. Nonlocal order parameters for the 1D Hubbard model.

    PubMed

    Montorsi, Arianna; Roncaglia, Marco

    2012-12-07

    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 U(c)=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 U(c). The behavior of the parity correlators is captured by an effective free spinless fermion model.

  16. 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.

  17. Plasma driven by helical electrodes

    NASA Astrophysics Data System (ADS)

    Akcay, Cihan; Finn, John; Nebel, Richard; Barnes, Daniel

    2016-10-01

    A novel plasma state, obtained by applying a helical voltage at the wall with a uniform axial magnetic field, is studied by means of zero-pressure resistive MHD simulations in a periodic cylinder. The radial magnetic field at the wall is taken to be zero. For a small helical electrode voltage, the helical perturbation in the plasma is small and localized to the edge. Beyond a critical electrode voltage, there is a bifurcation to the newly discovered state, which is a single-helicity Ohmic equilibrium with the same helicity as the electrodes, i.e., the fields depend only on radius and mθ - nφ , where θ and φ = z / R are the poloidal and toroidal angles. For electrostatic driving with m = 1 , the mean magnetic field (m = n = 0) has field line safety factor q(r) equal to the pitch of the electrodes m / n = 1 / n except near the edge, where it monotonically increases an amount of order unity. The plasma is force-free in the interior. Near the edge, however, the current crosses the field lines to enter and exit through the helical electrodes. A large helical plasma flow related Pfirsch-Schlüter-like currents exist in this edge vicinity. Applications to current drive in tokamaks, as well as to straight plasmas with endcap electrodes are discussed.

  18. Chiral Sulfoxide-Induced Single Turn Peptide α-Helicity

    PubMed Central

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

    2016-01-01

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

  19. Local and macroscopic electrostatic interactions in single α-helices

    PubMed Central

    Baker, Emily G.; Bartlett, Gail J.; Crump, Matthew P.; Sessions, Richard B.; Linden, Noah; Faul, Charl F. J.; Woolfson, Derek N.

    2015-01-01

    The non-covalent forces that stabilise protein structures are not fully understood. One way to address this is to study equilibria between unfolded states and α-helices in peptides. For these, electrostatic forces are believed to contribute, including interactions between: side chains; the backbone and side chains; and side chains and the helix macrodipole. Here we probe these experimentally using designed peptides. We find that both terminal backbone-side chain and certain side chain-side chain interactions (i.e., local effects between proximal charges, or interatomic contacts) contribute much more to helix stability than side chain-helix macrodipole electrostatics, which are believed to operate at larger distances. This has implications for current descriptions of helix stability, understanding protein folding, and the refinement of force fields for biomolecular modelling and simulations. In addition, it sheds light on the stability of rod-like structures formed by single α-helices that are common in natural proteins including non-muscle myosins. PMID:25664692

  20. Twist Helicity in Classical Vortices

    NASA Astrophysics Data System (ADS)

    Scheeler, Martin W.; Kedia, Hridesh; Kleckner, Dustin; Irvine, William T. M.

    2015-11-01

    Recent experimental work has demonstrated that a partial measure of fluid Helicity (the sum of linking and writhing of vortex tubes) is conserved even as those vortices undergo topology changing reconnections. Measuring the total Helicity, however, requires additional information about how the vortex lines are locally twisted inside the vortex core. To bridge this gap, we have developed a novel technique for experimentally measuring twist Helicity. Using this method, we are able to measure the production and eventual decay of twist for a variety of vortex evolutions. Remarkably, we observe twist dynamics capable of conserving total Helicity even in the presence of rapidly changing writhe. This work was supported by the NSF MRSEC shared facilities at the University of Chicago (DMR-0820054) and an NSF CAREER award (DMR-1351506). W.T.M.I. further acknowledges support from the A.P. Sloan Foundation and the Packard Foundation.

  1. 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

  2. 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

  3. 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

  4. 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.

  5. 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.

  6. 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.

  7. Molecular dynamics modeling of polymer crystallization; from simple polymers to helical ones.

    PubMed

    Yamamoto, Takashi; Orimi, Naohiko; Urakami, Naohiko; Sawada, Kaoru

    2005-01-01

    Crystallization of helical polymers is a very big challenge for molecular simulation. It involves many significant issues, such as folding in biomolecules and molecular recognition during crystal growth. Though direct molecular simulations of the process still involve very difficult problems, we here report our recent efforts toward better understanding of the crystallization in helical polymers. We begin with a brief review of our former studies on simple polyethylene-like polymers, and then we introduce several helical polymer models which are systematically made more complicated. We have already reported that a simple polyethylene-like polymer crystallizes very fast into chain folded lamellae from the melt. A slight modification of this simple polymer model by introducing proper bond angle and dihedral angle potentials gives one of the present models of the helical polymer. This helical polymer model is devised to be relatively rigid but mobile, to show easy helix-reversals, and to have a definite preference for gauche bonds. We find that this highly mobile helical polymer shows quick chain folded crystallization and forms approximate 4/1 helical structure. The intra- and the intermolecular order grow quite simultaneously suggesting highly cooperative nature of the phenomena. Further elaboration of the helical model, giving pendant side groups and higher energy barrier to the helix reversals, leads us to a realistic united atom model of iPP. The conventional and the multi-canonical Monte Carlo simulations are applied to find probable modes of chain folding and the ground state conformations. Though a very short chain readily forms a regular 3/1 helix of alternating trans and gauche bonds, much longer chains of 30- and 50-propylene units are not found to have energetic ground states in the regularly folded conformations.

  8. Folding of polyglutamine chains

    NASA Astrophysics Data System (ADS)

    Chopra, Manan; Reddy, Allam S.; Abbott, N. L.; de Pablo, J. J.

    2008-10-01

    Long polyglutamine chains have been associated with a number of neurodegenerative diseases. These include Huntington's disease, where expanded polyglutamine (PolyQ) sequences longer than 36 residues are correlated with the onset of symptoms. In this paper we study the folding pathway of a 54-residue PolyQ chain into a β-helical structure. Transition path sampling Monte Carlo simulations are used to generate unbiased reactive pathways between unfolded configurations and the folded β-helical structure of the polyglutamine chain. The folding process is examined in both explicit water and an implicit solvent. Both models reveal that the formation of a few critical contacts is necessary and sufficient for the molecule to fold. Once the primary contacts are formed, the fate of the protein is sealed and it is largely committed to fold. We find that, consistent with emerging hypotheses about PolyQ aggregation, a stable β-helical structure could serve as the nucleus for subsequent polymerization of amyloid fibrils. Our results indicate that PolyQ sequences shorter than 36 residues cannot form that nucleus, and it is also shown that specific mutations inferred from an analysis of the simulated folding pathway exacerbate its stability.

  9. Multiply-Twisted Helices of Various Inter-Round Couplings

    NASA Astrophysics Data System (ADS)

    Ugajin, R.; Watanabe, Y.; Mori, Y.

    Multiply-twisted helices in which a helical chain of components, i.e. atoms or nanoclusters, is twisted, producing a doubly-twisted helix, which if itself is twisted produces a triply-twisted helix, and so on, are characterized by inter-round couplings, through which electrons in the structure transit between adjacent rounds. The multiply-twisted helix of inter-round couplings via a chain of sites and that of inter-round couplings through a single site are compared with that of the direct inter-round couplings previously reported by R. Ugajin [J. Nanosci. Nanotechnol. 1, 227 (2001)]. Monte Carlo simulations of classical spins suggest that the multiply-twisted helix of inter-round couplings through a single site, in which the Curie temperature of ferromagnetic transition is robust against the change of a basal helix, might be critical among these three types.

  10. Analysis of the rotational structure in the high-resolution infrared spectra of trans-hexatriene-1,1-d2 and -cis-1-d1

    NASA Astrophysics Data System (ADS)

    Craig, Norman C.; Fuson, Hannah A.; Tian, Hengfeng; Blake, Thomas A.

    2012-09-01

    Mixtures of trans-hexatriene-1,1-d2, -cis-1-d1, and -trans-1-d1 have been synthesized. Anharmonic frequencies and harmonic intensities were predicted with the B3LYP/cc-pVTZ model for the out-of-plane (a″) modes of the three isotopologues. Assignments are proposed for most of the a″ vibrational modes above 500 cm-1. Ground state (GS) rotational constants have been determined for the 1,1-d2 and cis-1-d1 species from the analysis of rotational structure of C-type bands in the high-resolution (0.0015 cm-1) infrared spectra in a mixture of the three isotopologues. The GS constants for the 1,1-d2 species are A0 = 0.8018850(6), B0 = 0.0418540(6), and C0 = 0.0397997(4) cm-1. The GS constants for the cis-1-d1 species are A0 = 0.809388(1), B0 = 0.043532(2), and C0 = 0.041320(1) cm-1. Small inertial defects confirm planarity for both species. These ground state rotational constants are intended for use in determining a semiexperimental equilibrium structure and evaluating the influence of chain length on π-electron delocalization in polyenes.

  11. 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

  12. Calibration of a 1D/1D urban flood model using 1D/2D model results in the absence of field data.

    PubMed

    Leandro, J; Djordjević, S; Chen, A S; Savić, D A; Stanić, M

    2011-01-01

    Recently increased flood events have been prompting researchers to improve existing coupled flood-models such as one-dimensional (1D)/1D and 1D/two-dimensional (2D) models. While 1D/1D models simulate sewer and surface networks using a one-dimensional approach, 1D/2D models represent the surface network by a two-dimensional surface grid. However their application raises two issues to urban flood modellers: (1) stormwater systems planning/emergency or risk analysis demands for fast models, and the 1D/2D computational time is prohibitive, (2) and the recognized lack of field data (e.g. Hunter et al. (2008)) causes difficulties for the calibration/validation of 1D/1D models. In this paper we propose to overcome these issues by calibrating a 1D/1D model with the results of a 1D/2D model. The flood-inundation results show that: (1) 1D/2D results can be used to calibrate faster 1D/1D models, (2) the 1D/1D model is able to map the 1D/2D flood maximum extent well, and the flooding limits satisfactorily in each time-step, (3) the 1D/1D model major differences are the instantaneous flow propagation and overestimation of the flood-depths within surface-ponds, (4) the agreement in the volume surcharged by both models is a necessary condition for the 1D surface-network validation and (5) the agreement of the manholes discharge shapes measures the fitness of the calibrated 1D surface-network.

  13. Origins of the helical wrapping of phenyleneethynylene polymers about single-walled carbon nanotubes.

    PubMed

    Von Bargen, Christopher D; MacDermaid, Christopher M; Lee, One-Sun; Deria, Pravas; Therien, Michael J; Saven, Jeffery G

    2013-10-24

    The highly charged, conjugated polymer poly[p-{2,5-bis(3-propoxysulfonicacidsodiumsalt)}phenylene]ethynylene (PPES) has been shown to wrap single-wall carbon nanotubes (SWNTs), adopting a robust helical superstructure. Surprisingly, PPES adopts a helical rather than a linear conformation when adhered to SWNTs. The complexes formed by PPES and related polymers upon helical wrapping of a SWNT are investigated using atomistic molecular dynamics (MD) simulations in the presence and absence of aqueous solvent. In simulations of the PPES/SWNT system in an aqueous environment, PPES spontaneously takes on a helical conformation. A potential of mean force, ΔA(ξ), is calculated as a function of ξ, the component of the end-to-end vector of the polymer chain projected on the SWNT axis; ξ is a monotonic function of the polymer's helical pitch. ΔA(ξ) provides a means to quantify the relative free energies of helical conformations of the polymer when wrapped about the SWNT. The aqueous system possesses a global minimum in ΔA(ξ) at the experimentally observed value of the helical pitch. The presence of this minimum is associated with preferred side chain conformations, where the side chains adopt conformations that provide van der Waals contact between the tubes and the aliphatic components of the side chains, while exposing the anionic sulfonates for aqueous solvation. The simulations provide a free energy estimate of a 0.2 kcal/mol/monomer preference for the helical over the linear conformation of the PPES/SWNT system in an aqueous environment.

  14. MH(2)c: Characterization of major histocompatibility α-helices - an information criterion approach.

    PubMed

    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.

  15. 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.

  16. Helical CT in emergency radiology.

    PubMed

    Novelline, R A; Rhea, J T; Rao, P M; Stuk, J L

    1999-11-01

    Today, a wide range of traumatic and nontraumatic emergency conditions are quickly and accurately diagnosed with helical computed tomography (CT). Many traditional emergency imaging procedures have been replaced with newer helical CT techniques that can be performed in less time and with greater accuracy, less patient discomfort, and decreased cost. The speed of helical technology permits CT examination of seriously ill patients in the emergency department, as well as patients who might not have been taken to CT previously because of the length of the examinations of the past. Also, helical technology permits multiple, sequential CT scans to be quickly obtained in the same patient, a great advance for the multiple-trauma patient. Higher quality CT examinations result from decreased respiratory misregistration, enhanced intravenous contrast material opacification of vascular structures and parenchymal organs, greater flexibility in image reconstruction, and improved multiplanar and three-dimensional reformations. This report summarizes the role and recommended protocols for the helical CT diagnosis of thoracic aortic trauma; aortic dissection; pulmonary embolism; acute conditions of the neck soft tissues; abdominal trauma; urinary tract stones; appendicitis; diverticulitis; abdominal aortic aneurysm; fractures of the face, spine, and extremities; and acute stroke.

  17. 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.

  18. Glass-based 1-D dielectric microcavities

    NASA Astrophysics Data System (ADS)

    Chiasera, Alessandro; Scotognella, Francesco; Valligatla, Sreeramulu; Varas, Stefano; Jasieniak, Jacek; Criante, Luigino; Lukowiak, Anna; Ristic, Davor; Gonçalves, Rogeria Rocha; Taccheo, Stefano; Ivanda, Mile; Righini, Giancarlo C.; Ramponi, Roberta; Martucci, Alessandro; Ferrari, Maurizio

    2016-11-01

    We have developed a reliable RF sputtering techniques allowing to fabricate glass-based one dimensional microcavities, with high quality factor. This property is strongly related to the modification of the density of states due to the confinement of the gain medium in a photonic band gap structure. In this short review we present some of the more recent results obtained by our team exploiting these 1D microcavities. In particular we present: (1) Er3+ luminescence enhancement of the 4I13/2 → 4I15/2 transition; (2) broad band filters based on disordered 1-D photonic structures; (3) threshold defect-mode lasing action in a hybrid structure.

  19. 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.

  20. 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.

  1. Helical axis stellarator equilibrium model

    SciTech Connect

    Koniges, A.E.; Johnson, J.L.

    1985-02-01

    An asymptotic model is developed to study MHD equilibria in toroidal systems with a helical magnetic axis. Using a characteristic coordinate system based on the vacuum field lines, the equilibrium problem is reduced to a two-dimensional generalized partial differential equation of the Grad-Shafranov type. A stellarator-expansion free-boundary equilibrium code is modified to solve the helical-axis equations. The expansion model is used to predict the equilibrium properties of Asperators NP-3 and NP-4. Numerically determined flux surfaces, magnetic well, transform, and shear are presented. The equilibria show a toroidal Shafranov shift.

  2. 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.

  3. On steady kinematic helical dynamos

    NASA Astrophysics Data System (ADS)

    Eltayeb, I. A.; Loper, D. E.

    The equations governing steady kinematic helical dynamos are studied, using the formalism of Benton (1979), when the flow has no radial component (in cylindrical coordinates). It is shown that all solutions must decay exponentially to zero at large distances, s, from the axis of the helix. When the flow depends on s only it is shown that a necessary condition for dynamo action is that the flow possesses components along both the primary and secondary helices. It is also found that periodic motion of one mode along the primary helix cannot support dynamo action even if the field is composed of mean and periodic parts.

  4. Better understanding of tubular helical buckling

    SciTech Connect

    Wu, J.

    1996-09-01

    Tubular buckling is a significant problem within the oil industry. Although it has been studied for many years, methods to analyze tubular helical buckling continues to appear in the literature. Several criteria have been derived and presented leading to confusion in understanding and correctly predicting tubular helical buckling. The prediction of tubular helical buckling is complicated by the fact that the tubular is confined within the wellbore. The tubular initially buckles sinusoidally, and then changes into the shape of a helix (helical buckling) as the axial load increases. Different approaches in modeling the helical buckling process and the use of energy methods resulted in those different helical buckling criteria. Helical buckling criteria proposed in the literature, as well as their derivations are discussed in this paper, to help better understand and effectively predict tubular helical buckling in engineering operations.

  5. 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.

  6. 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

  7. Conservation of magnetic helicity during plasma relaxation

    SciTech Connect

    Ji, H.; Prager, S.C.; Sarff, J.S.

    1994-07-01

    Decay of the total magnetic helicity during the sawtooth relaxation in the MST Reversed-Field Pinch is much larger than the MHD prediction. However, the helicity decay (3--4%) is smaller than the magnetic energy decay (7--9%), modestly supportive of the helicity conservation hypothesis in Taylor`s relaxation theory. Enhanced fluctuation-induced helicity transport during the relaxation is observed.

  8. Note: Helical nanobelt force sensors

    NASA Astrophysics Data System (ADS)

    Hwang, G.; Hashimoto, H.

    2012-12-01

    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 × 10-10 Pa-1), low stiffness (0.03125 N/m), large-displacement capability (˜10 μm), and good fatigue resistance, they are well suited to function as stand-alone, compact (˜20 μm without the plug-in support), light (˜5 g including the plug-in support), versatile and large range (˜μN) and high resolution (˜nN) force sensors.

  9. Hybrid helical snakes and rotators for RHIC

    SciTech Connect

    Courant, E.D.

    1995-06-13

    The spin rotators and Siberian snakes presently envisaged for RHIC utilize helical dipole magnets. The snakes and the rotators each consist of four helices, each with a full twist (360{degrees}) of the field. Here we investigate an alternate layout, namely combinations of helical and pure bending magnet, and show that this may have advantages.

  10. 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.

  11. Tctex1d2 Is a Negative Regulator of GLUT4 Translocation and Glucose Uptake.

    PubMed

    Shimoda, Yoko; Okada, Shuichi; Yamada, Eijiro; Pessin, Jeffrey E; Yamada, Masanobu

    2015-10-01

    Tctex1d2 (Tctex1 domain containing 2) is an open reading frame that encodes for a functionally unknown protein that contains a Tctex1 domain found in dynein light chain family members. Examination of gene expression during adipogenesis demonstrated a marked increase in Tctex1d2 protein expression that was essentially undetectable in preadipocytes and markedly induced during 3T3-L1 adipocyte differentiation. Tctex1d2 overexpression significantly inhibited insulin-stimulated glucose transporter 4 (GLUT4) translocation and 2-deoxyglucose uptake. In contrast, Tctex1d2 knockdown significantly increased insulin-stimulated GLUT4 translocation and 2-deoxyglucose uptake. However, acute insulin stimulation (up to 30 min) in 3T3-L1 adipocytes with overexpression or knockdown of Tctex1d2 had no effect on Akt phosphorylation, a critical signal transduction target required for GLUT4 translocation. Although overexpression of Tctex1d2 had no significant effect on GLUT4 internalization, Tctex1d2 was found to associate with syntaxin 4 in an insulin-dependent manner and inhibit Doc2b binding to syntaxin 4. In addition, glucose-dependent insulinotropic polypeptide rescued the Tctex1d2 inhibition of insulin-stimulated GLUT4 translocation by suppressing the Tctex1d2-syntaxin 4 interaction and increasing Doc2b-Synatxin4 interactions. Taking these results together, we hypothesized that Tctex1d2 is a novel syntaxin 4 binding protein that functions as a negative regulator of GLUT4 plasma membrane translocation through inhibition of the Doc2b-syntaxin 4 interaction.

  12. 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.

  13. 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.

  14. 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

  15. 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.

  16. Contemporary strategies for the stabilization of peptides in the alpha-helical conformation.

    PubMed

    Henchey, Laura K; Jochim, Andrea L; Arora, Paramjit S

    2008-12-01

    Herein we review contemporary synthetic and protein design strategies to stabilize the alpha-helical motif in short peptides and miniature proteins. Advances in organometallic catalyst design, specifically for the olefin metathesis reaction, enable the use of hydrocarbon bridges to either crosslink side chains of specific residues or mimic intramolecular hydrogen bonds with carbon-carbon bonds. The resulting hydrocarbon-stapled and hydrogen bond surrogate alpha-helices provide unique synthetic ligands for targeting biomolecules. In the protein design realm, several classes of miniature proteins that display stable helical domains have been engineered and manipulated with powerful in vitro selection technologies to yield libraries of sequences that retain their helical folds. Rational re-design of these scaffolds provide distinctive reagents for the modulation of protein-protein interactions.

  17. Analysis of Rotational Structure in the High-Resolution Infrared Spectra of the TRANS-HEXATRIENE-1,1-D2 and -CIS-1-D1 Species

    NASA Astrophysics Data System (ADS)

    Craig, Norman C.; Fuson, Hannah A.; Tian, Hengfeng; Blake, Thomas A.

    2011-06-01

    Hexatriene-1,1-D2 with some admixture of the cis-1-D1 and trans-1-D1 species was synthesized by reaction of 2,4-pentadienal and (methyl-D3)-triphenylphosphonium iodide (Wittig reagent). The trans isomer was isolated by preparative gas chromatography, and the high-resolution (0.0015 Cm-1) infrared spectrum was recorded on a Bruker IFS 125HR instrument. The rotational structure in two C-type bands for the 1,1-D2 species was analyzed. For this species the bands at 902.043 and 721.864 Cm-1 yielded composite ground state rotational constants of A0 = 0.801882(1), B0 = 0.041850(2), and C0 = 0.039804(1) Cm-1. For the cis-1-D1 species the C-type band at 803.018 Cm-1 gave A0 = 0.809384(2), B0 = 0.043530(3), and C0 = 0.041321(2) Cm-1. By iodine-catalyzed isomerization, we have obtained some of the much less favored cis isomer and hope to obtain microwave spectra for its three deuterium-substituted species. The rotational constants reported here contribute to data needed for determining a semi-experimental structure for trans-hexatriene, which should show that the structural consequences of pi-electron delocalization increase with the chain length of polyenes.

  18. 75 FR 27411 - Airworthiness Directives; Turbomeca Arriel 1B, 1D, 1D1, and 1S1 Turboshaft Engines

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-05-17

    ... (that incorporate Turbomeca Modification (mod) TU 148), Arriel 1D, 1D1, and 1S1 turboshaft engines that do not incorporate mod TU 347. That AD also requires initial and repetitive replacements of 2nd stage... incorporate mod TU 148), 1D, 1D1, and 1S1 turboshaft engines that do not incorporate mod TU 347. We...

  19. Helical screw expander evaluation project

    NASA Astrophysics Data System (ADS)

    McKay, R.

    1982-03-01

    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.

  20. 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.

  1. 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.

  2. Topology of modified helical gears

    NASA Technical Reports Server (NTRS)

    Litvin, F. L.; Zhang, J.; Handschuh, R. F.; Coy, J. J.

    1989-01-01

    The topology of several types of modified surfaces of helical gears is proposed. The modified surfaces allow absorption of a linear or almost linear function of transmission errors. These errors are caused by gear misalignment and an improvement of the contact of gear tooth surfaces. Principles and corresponding programs for computer aided simulation of meshing and contact of gears have been developed. The results of this investigation are illustrated with numerical examples.

  3. Emulsification-Induced Homohelicity in Racemic Helical Polymer for Preparing Optically Active Helical Polymer Nanoparticles.

    PubMed

    Zhao, Biao; Deng, Jinrui; Deng, Jianping

    2016-04-01

    Optically active nano- and microparticles have constituted a significant category of advanced functional materials. However, constructing optically active particles derived from synthetic helical polymers still remains as a big challenge. In the present study, it is attempted to induce a racemic helical polymer (containing right- and left-handed helices in equal amount) to prefer one predominant helicity in aqueous media by using emulsifier in the presence of chiral additive (emulsification process). Excitingly, the emulsification process promotes the racemic helical polymer to unify the helicity and directly provides optically active nanoparticles constructed by chirally helical polymer. A possible mechanism is proposed to explain the emulsification-induced homohelicity effect. The present study establishes a novel strategy for preparing chirally helical polymer-derived optically active nanoparticles based on racemic helical polymers.

  4. Design, synthesis, and functional activity of labeled CD1d glycolipid agonists.

    PubMed

    Jervis, Peter J; Polzella, Paolo; Wojno, Justyna; Jukes, John-Paul; Ghadbane, Hemza; Garcia Diaz, Yoel R; Besra, Gurdyal S; Cerundolo, Vincenzo; Cox, Liam R

    2013-04-17

    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 attaching

  5. 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

  6. Structures of N-termini of helices in proteins.

    PubMed Central

    Doig, A. J.; MacArthur, M. W.; Stapley, B. J.; Thornton, J. M.

    1997-01-01

    We have surveyed 393 N-termini of alpha-helices and 156 N-termini of 3(10)-helices in 85 high resolution, non-homologous protein crystal structures for N-cap side-chain rotamer preferences, hydrogen bonding patterns, and solvent accessibilities. We find very strong rotamer preferences that are unique to N-cap sites. The following rules are generally observed for N-capping in alpha-helices: Thr and Ser N-cap side chains adopt the gauche - rotamer, hydrogen bond to the N3 NH and have psi restricted to 164 +/- 8 degrees. Asp and Asn N-cap side chains either adopt the gauche - rotamer and hydrogen bond to the N3 NH with psi = 172 +/- 10 degrees, or adopt the trans rotamer and hydrogen bond to both the N2 and N3 NH groups with psi = 1-7 +/- 19 degrees. With all other N-caps, the side chain is found in the gauche + rotamer so that the side chain does not interact unfavorably with the N-terminus by blocking solvation and psi is unrestricted. An i, i + 3 hydrogen bond from N3 NH to the N-cap backbone C = O in more likely to form at the N-terminus when an unfavorable N-cap is present. In the 3(10)-helix Asn and Asp remain favorable N-caps as they can hydrogen bond to the N2 NH while in the trans rotamer; in contrast, Ser and Thr are disfavored as their preferred hydrogen bonding partner (N3 NH) is inaccessible. This suggests that Ser is the optimum choice of N-cap when alpha-helix formation is to be encouraged while 3(10)-helix formation discouraged. The strong energetic and structural preferences found for N-caps, which differ greatly from positions within helix interiors, suggest that N-caps should be treated explicitly in any consideration of helical structure in peptides or proteins. PMID:9007987

  7. Helicity comparison among three magnetographs

    NASA Astrophysics Data System (ADS)

    Xu, Haiqing; Gao, Yu; Zhang, Hongqi; Sakurai, T.; Pevtsov, A. A.; Sokoloff, D.

    We compare vector magnetograms of 228 active regions observed by Solar Magnetic Field Telescope (SMFT) at Huairou (HR) Solar Observing Station and the Solar Flare Telescope (SFT) at Mitaka (MTK) of the National Astronomical Observatory of Japan from 1992 to 2005 and 55 active regions observed by SFT and Haleakala Stokes Polarimeter (HSP) at Mees Solar Observatory, University of Hawaii from 1997 to 2000. Two helicity parameters, current helicity density hc and αff coefficient of linear force free field are calculated. From this comparison we conclude: (1) the mean azimuthal angle differences of transverse fields between HR and MTK data are systematic smaller than that between MTK and Mees data; (2) there are 83.8% of hc and 78.1% of αff for 228 active regions observed at HR and MTK agree in sign, and the Pearson linear correlation coefficient between these two data sets is 0.72 for hc and 0.56 for αff. There are 61.8% of hc and 58.2% of αff for 55 active regions observed at MTK and Mees agree in sign, and the Pearson linear correlation coefficient between these two data sets is 0.34 for hc and 0.31 for αff; (3) there is a basic agreement on time variation of helicity parameters in active regions observed at HR, Mees, and MTK.

  8. Helically twisted photonic crystal fibres.

    PubMed

    Russell, P St J; Beravat, R; Wong, G K L

    2017-02-28

    Recent theoretical and experimental work on helically twisted photonic crystal fibres (PCFs) is reviewed. Helical Bloch theory is introduced, including a new formalism based on the tight-binding approximation. It is used to explore and explain a variety of unusual effects that appear in a range of different twisted PCFs, including fibres with a single core and fibres with N cores arranged in a ring around the fibre axis. We discuss a new kind of birefringence that causes the propagation constants of left- and right-spinning optical vortices to be non-degenerate for the same order of orbital angular momentum (OAM). Topological effects, arising from the twisted periodic 'space', cause light to spiral around the fibre axis, with fascinating consequences, including the appearance of dips in the transmission spectrum and low loss guidance in coreless PCF. Discussing twisted fibres with a single off-axis core, we report that optical activity in a PCF is opposite in sign to that seen in a step-index fibre. Fabrication techniques are briefly described and emerging applications reviewed. The analytical results of helical Bloch theory are verified by an extensive series of 'numerical experiments' based on finite-element solutions of Maxwell's equations in a helicoidal frame.This article is part of the themed issue 'Optical orbital angular momentum'.

  9. Helically twisted photonic crystal fibres

    PubMed Central

    Beravat, R.; Wong, G. K. L.

    2017-01-01

    Recent theoretical and experimental work on helically twisted photonic crystal fibres (PCFs) is reviewed. Helical Bloch theory is introduced, including a new formalism based on the tight-binding approximation. It is used to explore and explain a variety of unusual effects that appear in a range of different twisted PCFs, including fibres with a single core and fibres with N cores arranged in a ring around the fibre axis. We discuss a new kind of birefringence that causes the propagation constants of left- and right-spinning optical vortices to be non-degenerate for the same order of orbital angular momentum (OAM). Topological effects, arising from the twisted periodic ‘space’, cause light to spiral around the fibre axis, with fascinating consequences, including the appearance of dips in the transmission spectrum and low loss guidance in coreless PCF. Discussing twisted fibres with a single off-axis core, we report that optical activity in a PCF is opposite in sign to that seen in a step-index fibre. Fabrication techniques are briefly described and emerging applications reviewed. The analytical results of helical Bloch theory are verified by an extensive series of ‘numerical experiments’ based on finite-element solutions of Maxwell's equations in a helicoidal frame. This article is part of the themed issue ‘Optical orbital angular momentum’. PMID:28069771

  10. Helically twisted photonic crystal fibres

    NASA Astrophysics Data System (ADS)

    Russell, P. St. J.; Beravat, R.; Wong, G. K. L.

    2017-02-01

    Recent theoretical and experimental work on helically twisted photonic crystal fibres (PCFs) is reviewed. Helical Bloch theory is introduced, including a new formalism based on the tight-binding approximation. It is used to explore and explain a variety of unusual effects that appear in a range of different twisted PCFs, including fibres with a single core and fibres with N cores arranged in a ring around the fibre axis. We discuss a new kind of birefringence that causes the propagation constants of left- and right-spinning optical vortices to be non-degenerate for the same order of orbital angular momentum (OAM). Topological effects, arising from the twisted periodic `space', cause light to spiral around the fibre axis, with fascinating consequences, including the appearance of dips in the transmission spectrum and low loss guidance in coreless PCF. Discussing twisted fibres with a single off-axis core, we report that optical activity in a PCF is opposite in sign to that seen in a step-index fibre. Fabrication techniques are briefly described and emerging applications reviewed. The analytical results of helical Bloch theory are verified by an extensive series of `numerical experiments' based on finite-element solutions of Maxwell's equations in a helicoidal frame. This article is part of the themed issue 'Optical orbital angular momentum'.

  11. 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.

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

    PubMed

    Bauer, Wolfgang; Lochenie, Charles; Weber, Birgit

    2014-02-07

    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.

  13. On the origin of multi-step spin transition behaviour in 1D nanoparticles

    NASA Astrophysics Data System (ADS)

    Chiruta, Daniel; Jureschi, Catalin-Maricel; Linares, Jorge; Dahoo, Pierre Richard; Garcia, Yann; Rotaru, Aurelian

    2015-09-01

    To investigate the spin state switching mechanism in spin crossover (SCO) nanoparticles, a special attention is given to three-step thermally induced SCO behavior in 1D chains. An additional term is included in the standard Ising-like Hamiltonian to account for the border interaction between SCO molecules and its local environment. It is shown that this additional interaction, together with the short range interaction, drives the multi-steps thermal hysteretic behavior in 1D SCO systems. The relation between a polymeric matrix and this particular multi-step SCO phenomenon is discussed accordingly. Finally, the environmental influence on the SCO system's size is analyzed as well.

  14. The Helical Liquid and the Edge of Quantum Spin Hall Systems

    NASA Astrophysics Data System (ADS)

    Wu, Congjun; Bernevig, B. Andrei; Zhang, Shou-Cheng

    2006-03-01

    The edge states of the recently proposed quantum spin Hall systems constitute a new symmetry class of one-dimensional liquids dubbed the ``helical liquid,'' where the spin orientation is determined by the direction of electron motion. We prove a no-go theorem which states that a helical liquid with an odd number of components cannot be constructed in a purely 1D lattice system. In a helical liquid with an odd number of components, a uniform gap in the ground state can only appear when the time-reversal (TR) symmetry is spontaneously broken by interactions. On the other hand, a correlated two-particle backscattering term by an impurity can become relevant while keeping the TR invariance. We further study the Kondo effect in such a liquid which exhibits new features in the structure of the screening cloud.

  15. 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.

  16. Helicity fluctuations in incompressible turbulent flows

    NASA Technical Reports Server (NTRS)

    Rogers, Michael M.; Moin, Parviz

    1987-01-01

    Results from direct numerical simulations of several homogeneous flows and fully developed turbulent channel flow indicate that the probability distribution function (pdf) of relative helicity density exhibits at most a 20 percent deviation from a flat distribution. Isotropic flows exhibit a slight helical nature but the presence of mean strain in homogeneous turbulence suppresses helical behavior. All the homogeneous turbulent flows studied show no correlation between relative helicity density and the dissipation of turbulent kinetic energy. The channel flow simulations indicate that, except for low-dissipation regions near the outer edge of the buffer layer, there is no tendency for the flow to be helical. The strong peaks in the relative helicity density pdf and the association of these peaks with regions of low dissipation found in previous simulations by Pelz et al.(1985) are not observed.

  17. 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.

  18. Building blocks for subleading helicity operators

    SciTech Connect

    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 can be assembled.

  19. 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.

  20. 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.

  1. 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.

  2. Higher helicity invariants and solar dynamo

    NASA Astrophysics Data System (ADS)

    Sokolov, D. D.; Illarionov, E. A.; Akhmet'ev, P. M.

    2017-01-01

    Modern models of nonlinear dynamo saturation in celestial bodies (specifically, on the Sun) are largely based on the consideration of the balance of magnetic helicity. This physical variable has also a topological meaning: it is associated with the linking coefficient of magnetic tubes. In addition to magnetic helicity, magnetohydrodynamics has a number of topological integrals of motion (the so-called higher helicity moments). We have compared these invariants with magnetic helicity properties and concluded that they can hardly serve as nonlinear constraints on dynamo action.

  3. 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

  4. Neutrino helicity asymmetries in leptogenesis

    SciTech Connect

    Bento, Luis; Santos, Francisco C.

    2005-05-01

    It is pointed out that the heavy singlet neutrinos characteristic of leptogenesis develop asymmetries in the abundances of the two helicity states as a result of the same mechanism that generates asymmetries in the standard lepton sector. Neutrinos and standard leptons interchange asymmetries in collisions with each other. It is shown that an appropriate quantum number, B-L{sup '}, combining baryon, lepton and neutrino asymmetries, is not violated as fast as the standard B-L. This suppresses the washout effects relevant for the derivation of the final baryon asymmetry. One presents detailed calculations for the period of neutrino thermal production in the framework of the singlet seesaw mechanism.

  5. 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.

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

    PubMed Central

    Woolf, T B

    1997-01-01

    Understanding the role of the lipid bilayer in membrane protein structure and dynamics is needed for tertiary structure determination methods. However, the molecular details are not well understood. Molecular dynamics computer calculations can provide insight into these molecular details of protein:lipid interactions. This paper reports on 10 simulations of individual alpha-helices in explicit lipid bilayers. The 10 helices were selected from the bacteriorhodopsin structure as representative alpha-helical membrane folding components. The bilayer is constructed of dimyristoyl phosphatidylcholine molecules. The only major difference between simulations is the primary sequence of the alpha-helix. The results show dramatic differences in motional behavior between alpha-helices. For example, helix A has much smaller root-mean-squared deviations than does helix D. This can be understood in terms of the presence of aromatic residues at the interface for helix A that are not present in helix D. Additional motions are possible for the helices that contain proline side chains relative to other amino acids. The results thus provide insight into the types of motion and the average structures possible for helices within the bilayer setting and demonstrate the strength of molecular simulations in providing molecular details that are not directly visualized in experiments. Images FIGURE 3 FIGURE 4 FIGURE 5 FIGURE 6 Figure 6 PMID:9370432

  7. 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.

  8. 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.

  9. Segregation of helicity in inertial wave packets

    NASA Astrophysics Data System (ADS)

    Ranjan, A.

    2017-03-01

    Inertial waves are known to exist in the Earth's rapidly rotating outer core and could be important for the dynamo generation. It is well known that a monochromatic inertial plane wave traveling parallel to the rotation axis (along positive z ) has negative helicity while the wave traveling antiparallel (negative z ) has positive helicity. Such a helicity segregation, north and south of the equator, is necessary for the α2-dynamo model based on inertial waves [Davidson, Geophys. J. Int. 198, 1832 (2014), 10.1093/gji/ggu220] to work. The core is likely to contain a myriad of inertial waves of different wave numbers and frequencies. In this study, we investigate whether this characteristic of helicity segregation also holds for an inertial wave packet comprising waves with the same sign of Cg ,z, the z component of group velocity. We first derive the polarization relations for inertial waves and subsequently derive the resultant helicity in wave packets forming as a result of superposition of two or more waves. We find that the helicity segregation does hold for an inertial wave packet unless the wave numbers of the constituent waves are widely separated. In the latter case, regions of opposite color helicity do appear, but the mean helicity retains the expected sign. An illustration of this observation is provided by (a) calculating the resultant helicity for a wave packet formed by superposition of four upward-propagating inertial waves with different wave vectors and (b) conducting the direct numerical simulation of a Gaussian eddy under rapid rotation. Last, the possible effects of other forces such as the viscous dissipation, the Lorentz force, buoyancy stratification, and nonlinearity on helicity are investigated and discussed. The helical structure of the wave packet is likely to remain unaffected by dissipation or the magnetic field, but can be modified by the presence of linearly stable stratification and nonlinearity.

  10. Hydrothermal synthesis of two copper helical coordination polymers with acentric three-dimensional framework constructing from mixed pyridine carboxylates

    SciTech Connect

    Zhang Shuai; Cao Yanning; Zhang Hanhui Chai Xiaochuan; Chen Yiping

    2008-03-15

    Two copper helical coordination polymers, [Cu(2-pc)(3-pc)]{sub n}1 and [Cu(2-pc)(4-pc)]{sub n}2 (2-pc=2-pyridine carboxylate, 3-pc=3-pyridine carboxylate, 4-pc=4-pyridine carboxylate) have been hydrothermally synthesized directly from pyridine carboxylic acids and copper nitrate. The crystal structure were determined by single-crystal X-ray diffraction with the following data: compound 1, orthorhombic, P2{sub 1}2{sub 1}2{sub 1}, a=6.591(3) A, b=8.692(5) A, c=20.548(9) A, V=1177.2(9) A{sup 3}, Z=4; compound 2, orthorhombic, Pna2{sub 1}, a=21.160(10) A, b=9.095(5) A, c=6.401(3) A, V=1231.9(11) A{sup 3}, Z=4. The acentric three-dimensional (3D) framework of 1 is constructed from right-handed helical Cu(2-pc) chains and left-handed Cu(3-pc) helices. As for 2, Cu(2-pc) helical chains, in which left- and right-handed helices are coexisting, and Cu(4-pc) zigzag chains combined together to form acentric 3D architecture of 2 as well. Additionally, besides general spectral characterization, we first introduce generalized 2D correlation spectroscopy to explore the coordination polymers and ascertain the stretching vibration location of carboxylate groups of compounds 1 and 2. -- Abstract: Two copper helical coordination polymers, [Cu(2-pc)(3-pc)]{sub n}1 and [Cu(2-pc)(4-pc)]{sub n}2 have been obtained by hydrothermal synthesis. Both two compounds crystallized in non-centrosymmetric space groups, P2{sub 1}2{sub 1}2{sub 1} and Pna2{sub 1}, respectively. The 3D framework of 1 is constructed from right-handed helical Cu(2-pc) chains and left-handed Cu(3-pc) helices. As for 2, Cu(2-pc) helical chains, in which left- and right-handed helices are coexisting, and Cu(4-pc) zigzag chains combined together to form 3D architecture of 2 as well.

  11. Peptide-Directed Assembly of Single-Helical Gold Nanoparticle Superstructures Exhibiting Intense Chiroptical Activity.

    PubMed

    Merg, Andrea D; Boatz, Jennifer C; Mandal, Abhishek; Zhao, Gongpu; Mokashi-Punekar, Soumitra; Liu, Chong; Wang, Xianting; Zhang, Peijun; van der Wel, Patrick C A; Rosi, Nathaniel L

    2016-10-11

    Chiral nanoparticle assemblies are an interesting class of materials whose chiroptical properties make them attractive for a variety of applications. Here, C18-(PEPAu(M-ox))2 (PEPAu(M-ox) = AYSSGAPPM(ox)PPF) is shown to direct the assembly of single-helical gold nanoparticle superstructures that exhibit exceptionally strong chiroptical activity at the plasmon frequency with absolute g-factor values up to 0.04. Transmission electron microscopy (TEM) and cryogenic electron tomography (cryo-ET) results indicate that the single helices have a periodic pitch of approximately 100 nm and consist of oblong gold nanoparticles. The morphology and assembled structure of C18-(PEPAu(M-ox))2 are studied using TEM, atomic force microscopy (AFM), Fourier transform infrared (FTIR) spectroscopy, circular dichroism (CD) spectroscopy, X-ray diffraction (XRD), and solid-state nuclear magnetic resonance (ssNMR) spectroscopy. TEM and AFM reveal that C18-(PEPAu(M-ox))2 assembles into linear amyloid-like 1D helical ribbons having structural parameters that correlate to those of the single-helical gold nanoparticle superstructures. FTIR, CD, XRD, and ssNMR indicate the presence of cross-β and polyproline II secondary structures. A molecular assembly model is presented that takes into account all experimental observations and that supports the single-helical nanoparticle assembly architecture. This model provides the basis for the design of future nanoparticle assemblies having programmable structures and properties.

  12. 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.

  13. 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.

  14. 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.

  15. Elliptical Muon Helical Cooling Channel Coils

    SciTech Connect

    Kahn, S. A.; Flanagan, G.; Lopes, M. L.; Yonehara, K.

    2013-09-01

    A helical cooling channel (HCC) consisting of a pressurized gas absorber imbedded in a magnetic channel that provides solenoid, helical dipole and helical quadrupole fields has shown considerable promise in providing six-dimensional phase space reduction for muon beams. The most effective approach to implementing the desired magnetic field is a helical solenoid (HS) channel composed of short solenoid coils arranged in a helical pattern. The HS channel along with an external solenoid allows the B$_z$ and B$_{\\phi}$ components along the reference orbit to be set to any desired values. To set dB$_{\\phi}$/dr to the desired value for optimum focusing requires an additional variable to tune. We shall show that using elliptical shaped coils in the HS channel allows the flexibility to achieve the desired dB$_{\\phi}$/dr on the reference orbit without significant change to B$_z$ and B$_{\\phi}$.

  16. 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.

  17. Kinked structures of isolated nicotinic receptor M2 helices: a molecular dynamics study.

    PubMed

    Sankararamakrishnan, R; Samsom, M S

    1994-12-01

    The pore-lining M2 helix of the nicotinic acetylcholine receptor exhibits a pronounced kink when the corresponding ion channel is in a closed conformation [N. Unwin (1993) Journal of Molecular Biology, Vol. 229, pp. 1101-1124]. We have performed molecular dynamics simulations of isolated 22-residue M2 helices in order to identify a possible molecular origin of this kink. In order to sample a wide range of conformational space, a simulated annealing protocol was used to generate five initial M2 helix structures, each of which was subsequently used as the basis of 300 ps MD simulations. Two helix sequences (M2 alpha and M2 delta) were studied in this manner, resulting in a total of ten 300 ps trajectories. Kinked helices present in the trajectories were identified and energy minimized to yield a total of five different stable kinked structures. For comparison, a similar molecular dynamics simulation of a Leu23 helix yielded no stable kinked structures. In four of the five kinked helices, the kink was stabilized by H bonds between the helix backbone and polar side-chain atoms. Comparison with data from the literature on site-directed mutagenesis of M2 residues suggests that such polar side-chain to main-chain H bonds may also contribute to kinking of M2 helices in the intact channel protein.

  18. Solvent-induced collapse of a helical semiflexible polymer

    NASA Astrophysics Data System (ADS)

    Varshney, Vikas

    2005-03-01

    It has been stated that ``the class of materials richest in the occurrence of phase transitions are polymers'' (E. A. Di Marzio, Prog. Polym. Sci. 24, 329 (1999)). This wealth of phase transitions is unique to polymers and is a consequence of the myriad of possible ways of coupling the basic ten classes of polymeric phase transitions into pairs, triplets and so forth. Two of these transitions are the helix-coil and coil-globule transitions. In this talk we explore the coupling of these two transitions, its molecular origins and physical consequences. For this purpose, we extend a recently developed model of helical polymers to describe the effect of solvent quality and solve it using Monte Carlo simulations based on the Wang and Landau algorithm. We find a very rich phase diagram consisting of 6 phases characterized by very specific conformations of the chain, i.e., a perfect helix, a random coil, a globule or other globular states with residual helical strands. We study the phase boundaries and provide further insight into the physics of the problem with a detailed analysis of the conformational and thermodynamic properties of the polymer chain.

  19. Competing interactions contributing to alpha-helical stability in aqueous solution.

    PubMed Central

    Bodkin, M. J.; Goodfellow, J. M.

    1995-01-01

    The stability of a 15-residue peptide has been investigated using CD spectroscopy and molecular simulation techniques. The sequence of the peptide was designed to include key features that are known to stabilize alpha-helices, including ion pairs, helix dipole capping, peptide bond capping, and aromatic interactions. The degree of helicity has been determined experimentally by CD in three solvents (aqueous buffer, methanol, and trifluoroethanol) and at two temperatures. Simulations of the peptide in the aqueous system have been performed over 500 ps at the same two temperatures using a fully explicit solvent model. Consistent with the CD data, the degree of helicity is decreased at the higher temperature. Our analysis of the simulation results has focused on competition between different side-chain/side-chain and side-chain/main-chain interactions, which can, in principle, stabilize the helix. The unfolding in aqueous solution occurs at the amino terminus because the side-chain interactions are insufficient to stabilize both the helix dipole and the peptide hydrogen bonds. Loss of capping of the peptide backbone leads to water insertion within the first peptide hydrogen bond and hence unfolding. In contrast, the carboxy terminus of the alpha-helix is stable in both simulations because the C-terminal lysine residue stabilizes the helix dipole, but at the expense of an ion pair. PMID:7613460

  20. Solubilization and fractionation of paired helical filaments.

    PubMed

    González, P J; Correas, I; Avila, J

    1992-09-01

    Paired helical filaments isolated from brains of two different patients with Alzheimer's disease were extensively treated with the ionic detergent, sodium dodecyl sulphate. Filaments were solubilized at different extents, depending on the brain examined, thus suggesting the existence of two types of paired helical filaments: sodium dodecyl sulphate-soluble and insoluble filaments. In the first case, the number of structures resembling paired helical filaments greatly decreased after the detergent treatment, as observed by electron microscopy. Simultaneously, a decrease in the amount of sedimentable protein was also observed upon centrifugation of the sodium dodecyl sulfate-treated paired helical filaments. A sodium dodecyl sulphate-soluble fraction was isolated as a supernatant after low-speed centrifugation of the sodium dodecyl sulphate-treated paired helical filaments. The addition of the non-ionic detergent Nonidet-P40 to this fraction resulted in the formation of paired helical filament-like structures. When the sodium dodecyl sulphate-soluble fraction was further fractionated by high-speed centrifugation, three subfractions were observed: a supernatant, a pellet and a thin layer between these two subfractions. No paired helical filaments were observed in any of these subfractions, even after addition of Nonidet P-40. However, when they were mixed back together, the treatment with Nonidet P-40 resulted in the visualization of paired helical filament-like structures. These results suggest that at least two different components are needed for the reconstitution of paired helical filaments as determined by electron microscopy. The method described here may allow the study of the components involved in the formation of paired helical filaments and the identification of possible factors capable of blocking this process.

  1. 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.

  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. Helicity Evolution at Small x

    NASA Astrophysics Data System (ADS)

    Sievert, Michael; Kovchegov, Yuri; Pitonyak, Daniel

    2017-01-01

    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 ln2(1 / x) in the polarization-dependent evolution along with the powers of ln(1 / x) in the unpolarized evolution which includes saturation effects. 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. After solving the large-Nc equations numerically we obtain the following small- x asymptotics for the flavor-singlet g1 structure function along with quarks hPDFs and helicity TMDs (in absence of saturation effects): g1S(x ,Q2) ΔqS(x ,Q2) g1L S(x ,kT2) (1/x) > αh (1/x) 2.31√{αsNc/2 π. We also give an estimate of how much of the proton's spin may be at small x and what impact this has on the so-called ``spin crisis.'' Work supported by the U.S. DOE, Office of Science, Office of Nuclear Physics under Award Number DE-SC0004286 (YK), the RIKEN BNL Research Center, and TMD Collaboration (DP), and DOE Contract No. DE-SC0012704 (MS).

  4. Structural insight for chain selection and stagger control in collagen

    PubMed Central

    Boudko, Sergei P.; Bächinger, Hans Peter

    2016-01-01

    Collagen plays a fundamental role in all known metazoans. In collagens three polypeptides form a unique triple-helical structure with a one-residue stagger to fit every third glycine residue in the inner core without disturbing the poly-proline type II helical conformation of each chain. There are homo- and hetero-trimeric types of collagen consisting of one, two or three distinct chains. Thus there must be mechanisms that control composition and stagger during collagen folding. Here, we uncover the structural basis for both chain selection and stagger formation of a collagen molecule. Three distinct chains (α1, α2 and α3) of the non-collagenous domain 2 (NC2) of type IX collagen are assembled to guide triple-helical sequences in the leading, middle and trailing positions. This unique domain opens the door for generating any fragment of collagen in its native composition and stagger. PMID:27897211

  5. 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

  6. Nonlinear electrical conductivity in a 1D granular medium

    NASA Astrophysics Data System (ADS)

    Falcon, E.; Castaing, B.; Creyssels, M.

    2004-04-01

    We report on observations of the electrical transport within a chain of metallic beads (slightly oxidized) under an applied stress. A transition from an insulating to a conductive state is observed as the applied current is increased. The voltage-current ( U- I) characteristics are nonlinear and hysteretic, and saturate to a low voltage per contact (0.4 V). Our 1D experiment allows us to understand phenomena (such as the “Branly effect”) related to this conduction transition by focusing on the nature of the contacts instead of the structure of the granular network. We show that this transition comes from an electro-thermal coupling in the vicinity of the microcontacts between each bead - the current flowing through these contact points generates their local heating which leads to an increase of their contact areas, and thus enhances their conduction. This current-induced temperature rise (up to 1050 ^{circ}C) results in the microsoldering of the contact points (even for voltages as low as 0.4 V). Based on this self-regulated temperature mechanism, an analytical expression for the nonlinear U- I back trajectory is derived, and is found to be in very good agreement with the experiments. In addition, we can determine the microcontact temperature with no adjustable parameters. Finally, the stress dependence of the resistance is found to be strongly non-hertzian due to the presence of the surface films. This dependence cannot be usually distinguished from the one due to the disorder of the granular contact network in 2D or 3D experiments.

  7. Helicity within the vortex filament model

    PubMed Central

    Hänninen, R.; Hietala, N.; Salman, H.

    2016-01-01

    Kinetic helicity is one of the invariants of the Euler equations that is associated with the topology of vortex lines within the fluid. In superfluids, the vorticity is concentrated along vortex filaments. In this setting, helicity would be expected to acquire its simplest form. However, the lack of a core structure for vortex filaments appears to result in a helicity that does not retain its key attribute as a quadratic invariant. By defining a spanwise vector to the vortex through the use of a Seifert framing, we are able to introduce twist and henceforth recover the key properties of helicity. We present several examples for calculating internal twist to illustrate why the centreline helicity alone will lead to ambiguous results if a twist contribution is not introduced. Our choice of the spanwise vector can be expressed in terms of the tangential component of velocity along the filament. Since the tangential velocity does not alter the configuration of the vortex at later times, we are able to recover a similar equation for the internal twist angle to that of classical vortex tubes. Our results allow us to explain how a quasi-classical limit of helicity emerges from helicity considerations for individual superfluid vortex filaments. PMID:27883029

  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. Helicity within the vortex filament model

    NASA Astrophysics Data System (ADS)

    Hänninen, R.; Hietala, N.; Salman, H.

    2016-11-01

    Kinetic helicity is one of the invariants of the Euler equations that is associated with the topology of vortex lines within the fluid. In superfluids, the vorticity is concentrated along vortex filaments. In this setting, helicity would be expected to acquire its simplest form. However, the lack of a core structure for vortex filaments appears to result in a helicity that does not retain its key attribute as a quadratic invariant. By defining a spanwise vector to the vortex through the use of a Seifert framing, we are able to introduce twist and henceforth recover the key properties of helicity. We present several examples for calculating internal twist to illustrate why the centreline helicity alone will lead to ambiguous results if a twist contribution is not introduced. Our choice of the spanwise vector can be expressed in terms of the tangential component of velocity along the filament. Since the tangential velocity does not alter the configuration of the vortex at later times, we are able to recover a similar equation for the internal twist angle to that of classical vortex tubes. Our results allow us to explain how a quasi-classical limit of helicity emerges from helicity considerations for individual superfluid vortex filaments.

  10. Hydrodynamic interaction between two helical swimmers

    NASA Astrophysics Data System (ADS)

    Ruiz Esparza, Alejandro; Godinez, Francisco; Lauga, Eric; Zenit, Roberto

    2016-11-01

    Many motile bacteria, such as E. coli, possess several helical flagellar filaments that bundle together to form a coherent helical element for propulsion. In order to understand the process of bundling, we study the interaction between two identical helical magnetic swimmers that self propel in a highly viscous Newtonian fluid due to the rotation of an external magnetic field. Our experiments reveal that hydrodynamic interactions lead to nontrivial collective and relative effects, both in translation and rotation. We will present our experimental results and discuss the physical mechanisms responsible for our observations.

  11. Helicity oscillations of Dirac and Majorana neutrinos

    NASA Astrophysics Data System (ADS)

    Dobrynina, Alexandra; Kartavtsev, Alexander; Raffelt, Georg

    2016-06-01

    The helicity of a Dirac neutrino with mass m evolves under the influence of a B field because it has a magnetic dipole moment proportional to m . Moreover, it was recently shown that a polarized or anisotropic medium engenders the same effect for both Dirac and Majorana neutrinos. Because a B field polarizes a background medium, it instigates helicity oscillations even for Majorana neutrinos unless the medium is symmetric between matter and antimatter. Motivated by these observations, we review the impact of a B field and of an anisotropic or polarized medium on helicity oscillations for Dirac and Majorana neutrinos from the common perspective of in-medium dispersion.

  12. Polymorphic transformation of helical flagella of bacteria

    NASA Astrophysics Data System (ADS)

    Lim, Sookkyung; Howard Berg Collaboration; William Ko Collaboration; Yongsam Kim Collaboration; Wanho Lee Collaboration; Charles Peskin Collaboration

    2016-11-01

    Bacteria such as E. coli swim in an aqueous environment by utilizing the rotation of flagellar motors and alternate two modes of motility, runs and tumbles. Runs are steady forward swimming driven by bundles of flagellar filaments whose motors are turning CCW; tumbles involve a reorientation of the direction of swimming triggered by motor reversals. During tumbling, the helical flagellum undergoes polymorphic transformations, which is a local change in helical pitch, helical radius, and handedness. In this work, we investigate the underlying mechanism of structural conformation and how this polymorphic transition plays a role in bacterial swimming. National Science Foundation.

  13. Thermally activated helicity reversals of skyrmions

    NASA Astrophysics Data System (ADS)

    Yu, X. Z.; Shibata, K.; Koshibae, W.; Tokunaga, Y.; Kaneko, Y.; Nagai, T.; Kimoto, K.; Taguchi, Y.; Nagaosa, N.; Tokura, Y.

    2016-04-01

    Magnetic bubbles with winding number S =1 are topologically equivalent to skyrmions. Here we report the discovery of helicity (in-plane magnetization-swirling direction) reversal of skyrmions, while keeping their hexagonal lattice form, at above room temperature in a thin hexaferrite magnet. We have observed that the frequency of helicity reversals dramatically increases with temperature in a thermally activated manner, revealing that the generation energy of a kink-soliton pair for switching helicity on a skyrmion rapidly decreases towards the magnetic transition temperature.

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

    PubMed

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

    2016-11-01

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

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

    PubMed Central

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

    2016-01-01

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

  16. Distinctions in early stage unwinding mechanisms of zwitterionic, capped, and neutral forms of different α-helical homopolymeric peptides.

    PubMed

    Pandey, Prithvi Raj; Roy, Sudip

    2012-04-26

    Molecular dynamics simulations of α-helical polyalanine, polyleucine, polylysine, and poly(glutamic acid) with different forms of terminal groups in water at 300 K showed sharp distinctions in their unwinding mechanisms. Zwitterionic, capped, and neutral forms of polyalanine, polyleucine, and polylysine have been explored to elucidate their unwinding mechanism at very early stage, e.g., initial time window. Role of water in the unwinding mechanisms of the various helices has been envisaged. Also, it is evident from our calculations that the short- and long-range nonbonded interactions among the side chains is an important factor determining the unwinding mechanisms of the various homopolymeric α-helices. These findings can be helpful in constructing predictive models for understanding of the unwinding of α-helical proteins and peptides.

  17. TREN (Tris(2-aminoethyl)amine): an effective scaffold for the assembly of triple helical collagen mimetic structures.

    PubMed

    Kwak, Juliann; De Capua, Antonia; Locardi, Elsa; Goodman, Murray

    2002-11-27

    A new scaffold, TREN-(suc-OH)(3) where TREN is tris(2-aminoethyl)amine and suc is the succinic acid spacers, was incorporated to assemble triple helices composed of Gly-Nleu-Pro sequences (Nleu denotes N-isobutylglycine). Extensive biophysical studies which include denaturation studies, CD and NMR spectroscopy, and molecular modeling demonstrated that TREN-[suc-(Gly-Nleu-Pro)(n)-NH(2)](3) (n = 5 and 6) form stable triple helical structures in solution. A comparative analysis of TREN-assembled and KTA-assembled collagen mimetics (KTA denotes Kemp triacid, 1,3,5-trimethylcyclohexane-1,3,5-tricarboxylic acid) indicates that the flexibility of the TREN scaffold is superior to the KTA scaffold in inducing triple helicity. This effect most likely arises from the flexibility of the TREN scaffold which allows the three peptide chains to adjust their register for a tighter triple helical packing.

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

    PubMed

    Frezza, Elisa; Pieraccini, Silvia; Mazzini, Stefania; Ferrarini, Alberta; Spada, Gian Piero

    2012-01-01

    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.

  20. Brady 1D seismic velocity model ambient noise prelim

    SciTech Connect

    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.

  1. 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

  2. Chromatographic enantioseparation by poly(biphenylylacetylene) derivatives with memory of both axial chirality and macromolecular helicity.

    PubMed

    Ishidate, Ryoma; Ikai, Tomoyuki; Kanoh, Shigeyoshi; Yashima, Eiji; Maeda, Katsuhiro

    2017-03-29

    Novel poly(biphenylylacetylene) derivatives bearing two acetyloxy groups at the 2- and 2'-positions and an alkoxycarbonyl group at the 4'-position of the biphenyl pendants (poly-Ac's) were synthesized by the polymerization of the corresponding biphenylylacetylenes using a rhodium catalyst. The obtained stereoregular (cis-transoidal) poly-Ac's folded into a predominantly one-handed helical conformation accompanied by a preferred-handed axially twisted conformation of the biphenyl pendants through noncovalent interactions with a chiral alcohol and both the induced main-chain helicity and the pendant axial chirality were maintained, that is, memorized, after complete removal of the chiral alcohol. The stability of the helicity memory of the poly-Ac's in a solution was lower than that of the analogous poly(biphenylylacetylene)s bearing two methoxymethoxy groups at the 2- and 2'-positions of the biphenyl pendants (poly-MOM's). In the solid state, however, the helicity memory of the poly-Ac's was much more stable and showed a better chiral recognition ability toward several racemates than that of the previously reported poly-MOM when used as a chiral stationary phase for high-performance liquid chromatography. In particular, the poly-Ac-based CSP with a helicity memory efficiently separated racemic benzoin derivatives into enantiomers.

  3. Discontinuous membrane helices in transport proteins and their correlation with function.

    PubMed

    Screpanti, Emanuela; Hunte, Carola

    2007-08-01

    Alpha-helical bundles and beta-barrel proteins represent the two basic types of architecture known for integral membrane proteins. Irregular structural motifs have been revealed with the growing number of structures determined. "Discontinuous" helices are present in membrane proteins that actively transport ions. In the Ca(2+)-ATPase, a primary active transporter, and in the secondary transporters NhaA, LeuT(Aa), ClC H(+)/Cl(-) exchanger and Glt(Ph), the helical structure of two membrane segments is interrupted and the interjacent polypeptide chain forms an extended peptide. The discontinuous helices are integrated in the membrane either as transmembrane-spanning or hairpin-type segments. In addition, the secondary transporters have inverted internal duplication domains, which are only weakly correlated with their amino acid sequence. The symmetry comprises either parts of or the complete molecule, but always includes the discontinuous helices. The helix-peptide-helix motif is correlated with the ion translocation function. The extended peptides with their backbone atoms, the helix termini and the polar/charged amino acid residues in close vicinity provide the basis for ion recognition, binding and translocation.

  4. Scaling laws in decaying helical hydromagnetic turbulence

    NASA Astrophysics Data System (ADS)

    Christensson, M.; Hindmarsh, M.; Brandenburg }%, A.

    2005-07-01

    We study the evolution of growth and decay laws for the magnetic field coherence length ξ, energy E_M and magnetic helicity H in freely decaying 3D MHD turbulence. We show that with certain assumptions, self-similarity of the magnetic power spectrum alone implies that ξ σm t1/2. This in turn implies that magnetic helicity decays as Hσm t-2s, where s=(ξ_diff/ξH)2, in terms of ξ_diff, the diffusion length scale, and ξ_H, a length scale defined from the helicity power spectrum. The relative magnetic helicity remains constant, implying that the magnetic energy decays as E_M σm t-1/2-2s. The parameter s is inversely proportional to the magnetic Reynolds number Re_M, which is constant in the self-similar regime.

  5. Helical vortices: viscous dynamics and instability

    NASA Astrophysics Data System (ADS)

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

    2014-11-01

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

  6. Helical Microfilaments with Alternating Imprinted Intrinsic Curvatures.

    PubMed

    Silva, Pedro Emanuel Santos; Godinho, Maria Helena

    2017-03-01

    There has been an intense research for developing techniques that can produce filaments with helical shapes, given the widespread of potential applications. In this work, how helices with different curvatures can be precisely imprinted in microfilaments is shown. It is also shown that using this technique, it is possible to produce, in a single fiber, helices with different curvatures. This striking and innovative behavior is observed when one side of the stretched filaments is irradiated with UV light, modifying the mechanical properties at surface. Upon release, the regions with higher curvature start to curl first, while regions with lower intrinsic curvature remain stretched until start to curl later. The results presented here can be important to understand why structures adopt a helical shape in general, which can be of interest in nanotechnology, biomolecular science, or even to understand why plant filaments curl.

  7. 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

  8. Helical modes in boundary layer transition

    NASA Astrophysics Data System (ADS)

    Bose, Rikhi; Durbin, Paul A.

    2016-11-01

    Observations are presented to show that in an adverse pressure gradient boundary layer, beneath free-stream turbulence, the interaction between Klebanoff streaks and naturally arising instability waves leads to helical disturbances which break down to form turbulent spots. This occurs under low to moderate levels, 1%-2%, of free-stream turbulence. At high levels of free-stream turbulence, conventional bypass mechanisms are seen. The helical structures are clearly identifiable in visualizations of isosurfaces of streamwise perturbation velocity. A direct numerical simulation also was performed in zero pressure gradient, with a time-periodic Tollmien-Schlichting wave eigenfunction at the inlet. Again, under a moderate level of free-stream turbulence, helices were observed, and found to trigger transition. Their wave speed is on the order of 1/2 U∞ , so helical breakdown can be viewed as a type of inner mode, secondary instability.

  9. 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.

  10. Shielding requirements in helical tomotherapy

    NASA Astrophysics Data System (ADS)

    Baechler, S.; Bochud, F. O.; Verellen, D.; Moeckli, R.

    2007-08-01

    Helical tomotherapy is a relatively new intensity-modulated radiation therapy (IMRT) treatment for which room shielding has to be reassessed for the following reasons. The beam-on-time needed to deliver a given target dose is increased and leads to a weekly workload of typically one order of magnitude higher than that for conventional radiation therapy. The special configuration of tomotherapy units does not allow the use of standard shielding calculation methods. A conventional linear accelerator must be shielded for primary, leakage and scatter photon radiations. For tomotherapy, primary radiation is no longer the main shielding issue since a beam stop is mounted on the gantry directly opposite the source. On the other hand, due to the longer irradiation time, the accelerator head leakage becomes a major concern. An analytical model based on geometric considerations has been developed to determine leakage radiation levels throughout the room for continuous gantry rotation. Compared to leakage radiation, scatter radiation is a minor contribution. Since tomotherapy units operate at a nominal energy of 6 MV, neutron production is negligible. This work proposes a synthetic and conservative model for calculating shielding requirements for the Hi-Art II TomoTherapy unit. Finally, the required concrete shielding thickness is given for different positions of interest.

  11. Shielding requirements in helical tomotherapy.

    PubMed

    Baechler, S; Bochud, F O; Verellen, D; Moeckli, R

    2007-08-21

    Helical tomotherapy is a relatively new intensity-modulated radiation therapy (IMRT) treatment for which room shielding has to be reassessed for the following reasons. The beam-on-time needed to deliver a given target dose is increased and leads to a weekly workload of typically one order of magnitude higher than that for conventional radiation therapy. The special configuration of tomotherapy units does not allow the use of standard shielding calculation methods. A conventional linear accelerator must be shielded for primary, leakage and scatter photon radiations. For tomotherapy, primary radiation is no longer the main shielding issue since a beam stop is mounted on the gantry directly opposite the source. On the other hand, due to the longer irradiation time, the accelerator head leakage becomes a major concern. An analytical model based on geometric considerations has been developed to determine leakage radiation levels throughout the room for continuous gantry rotation. Compared to leakage radiation, scatter radiation is a minor contribution. Since tomotherapy units operate at a nominal energy of 6 MV, neutron production is negligible. This work proposes a synthetic and conservative model for calculating shielding requirements for the Hi-Art II TomoTherapy unit. Finally, the required concrete shielding thickness is given for different positions of interest.

  12. The motion of helical vortices

    NASA Astrophysics Data System (ADS)

    Velasco Fuentes, Oscar

    2014-11-01

    We study the motion of a helical vortex in an inviscid, incompressible fluid of infinite extent. The vortex is a thin tube, of circular cross section and uniform vorticity, whose centerline is a helix of uniform pitch. Ever since Joukowsky (1912) deduced that this vortex is a steady solution of the Euler equations, numerous attempts have been made to compute its self-induced velocity. Here we use Hardin's (1982) solution for the velocity field in order to compute, for any pitch value, the linear and angular velocities of the vortex. Our formulas were verified by direct numerical integration of both the Biot-Savart and Helmholtz equations, and were also found to compare favourably with previous theoretical results. In terms of the vortex capacity to transport fluid, we identified three regimes: a helix of large pitch moves slowly, carrying a large mass of fluid; a thin helix of small pitch moves fast, carrying a small mass of fluid; and a fat helix of small pitch is a moderate carrier itself but it pushes fluid forward along its axis.

  13. 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.

  14. Decay of helical and nonhelical magnetic knots

    NASA Astrophysics Data System (ADS)

    Candelaresi, Simon; Brandenburg, Axel

    2011-07-01

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

  15. Helical rotary screw expander power system

    NASA Technical Reports Server (NTRS)

    Mckay, R. A.; Sprankle, R. S.

    1974-01-01

    An energy converter for the development of wet steam geothermal fields is described. A project to evaluate and characterize a helical rotary screw expander for geothermal applications is discussed. The helical screw expander is a positive displacement machine which can accept untreated corrosive mineralized water of any quality from a geothermal well. The subjects of corrosion, mineral deposition, the expansion process, and experience with prototype devices are reported.

  16. 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

  17. Hierarchical formation of helical supramolecular polymers via stacking of hydrogen-bonded pairs in water.

    PubMed

    Brunsveld, L; Vekemans, J A J M; Hirschberg, J H K K; Sijbesma, R P; Meijer, E W

    2002-04-16

    Bifunctional ureido-s-triazines provided with penta(ethylene oxide) side chains are able to self assemble in water, leading to helical columns via cooperative stacking of the hydrogen-bonded pairs (DADA array). Monofunctional ureido-s-triazines do not form such helical architectures. The presence of a linker, covalently connecting the two ureido-s-triazine units, is essential as it generates a high local concentration of aromatic units, favorable for stacking interactions. This hydrophobic stacking of the aromatic units occurs at concentrations as low as 5 x 10(-6) M and can be visualized by using fluorescence spectroscopy. The stacking generates a hydrophobic microenvironment that allows intermolecular hydrogen bonding to occur at higher concentrations because the hydrogen bonds are shielded from competitive hydrogen bonding with water. This hierarchical process results in the formation of a helical self-assembled polymer in water at concentrations above 10(-4) M. Chiral side chains attached to the ureido-s-triazine units bias the helicity of these columns as concluded from CD spectroscopy and "Sergeants and Soldiers" experiments.

  18. Template-Tethered Collagen Mimetic Peptides for Studying Heterotrimeric Triple-Helical Interactions

    PubMed Central

    Li, Yang; Mo, Xiao; Kim, Daniel

    2010-01-01

    Collagen mimetic peptides (CMPs) have been used to elucidate the structure and stability of the triple helical conformation of collagen molecules. Although CMP homotrimers have been widely studied, very little work has been reported regarding CMP heterotrimers because of synthetic difficulties. Here we present the synthesis and characterization of homotrimers and ABB type heterotrimers comprising natural and synthetic CMP sequences that are covalently tethered to a template, a tris(2-aminoethyl) amine (TREN) succinic acid derivative. Various tethered heterotrimers comprising synthetic CMPs [(ProHypGly)6, (ProProGly)6] and CMPs representing specific domains of type I collagen were synthesized and characterized in terms of triple helical structure, thermal melting behavior and refolding kinetics. The results indicated that CMPs derived from natural type I collagen sequence can form stable heterotrimeric helical complexes with artificial CMPs and that the thermal stability and the folding rate increase with the increasing number of helical stabilizing amino acids (e.g. Hyp) in the peptide chains. Covalent tethering enhanced the thermal stability and refolding kinetics of all CMPs; however their relative values were not affected suggesting that the tethered system can be used for comparative study of heterotrimeric CMP's folding behavior in regards to chain composition and for characterization of thermally unstable CMPs. PMID:20740489

  19. Influence of initial mean helicity on homogeneous turbulent shear flow.

    PubMed

    Jacobitz, Frank G; Schneider, Kai; Bos, Wouter J T; Farge, Marie

    2011-11-01

    Helicity statistics are studied in homogeneous turbulent shear flow. Initial mean helicity is imposed on an isotropic turbulence field using a decomposition of the flow into complex-valued helical waves. The initial decay of the turbulent kinetic energy is weakened in the presence of strong mean helicity, consistent with an analytic analysis of the spectral tensor of velocity correlations. While exponential growth of the mean turbulent kinetic energy is obtained, the mean helicity decays. Probability distribution functions (PDFs) of helicity are skewed and show that the imposed mean helicity prevails throughout the simulations. A wavelet-based scale-dependent analysis shows a trend to two dimensionalization for large scales of motion and a preference for helical motion at small scales. The magnitude of the skewness of the PDFs decreases for smaller scales. Joint PDFs indicate a strong correlation of the signs of both, helicity and superhelicity, for all cases. This correlation supports the conjecture that superhelicity dissipates helicity.

  20. Bioinspired helical microswimmers based on vascular plants.

    PubMed

    Gao, Wei; Feng, Xiaomiao; Pei, Allen; Kane, Christopher R; Tam, Ryan; Hennessy, Camille; Wang, Joseph

    2014-01-08

    Plant-based bioinspired magnetically propelled helical microswimmers are described. The helical microstructures are derived from spiral water-conducting vessels of different plants, harnessing the intrinsic biological structures of nature. Geometric variables of the spiral vessels, such as the helix diameter and pitch, can be controlled by mechanical stretching for the precise fabrication and consistent performance of helical microswimmers. Xylem vessels of a wide variety of different plants have been evaluated for the consistency and reproducibility of their helical parameters. Sequential deposition of thin Ti and Ni layers directly on the spiral vessels, followed by dicing, leads to an extremely simple and cost-efficient mass-production of functional helical microswimmers. The resulting plant-based magnetic microswimmers display efficient propulsion, with a speed of over 250 μm/s, as well as powerful locomotion in biological media such as human serum. The influence of actuation frequencies on the swimming velocity is investigated. Such use of plant vessels results in significant savings in the processing costs and provides an extremely simple, cost-effective fabrication route for the large-scale production of helical magnetic swimmers.

  1. The AGS with four helical magnets

    SciTech Connect

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

    2010-02-25

    The idea of using multiple 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. This modification provides many advantages over the present setup of the AGS that uses two partial helical magnets. First, it provides a larger 'spin tune gap' for the placement of the vertical betatron tune of the AGS during acceleration, second, the vertical spin direction during the beam injection and extraction is closer to vertical, third, the symmetric placement of the snakes allows for a better control of the AGS optics, and for reduced values of the beta and eta functions, especially near injection, fourth, the optical properties of the helical magnets also favor the placement of the horizontal betatron tune in the 'spin tune gap', thus eliminating the horizontal spin resonances. In this paper we provide results on the spin tune and on the optics of the AGS with four partial helical magnets, and we compare these results with the present setup of the AGS that uses two partial helical magnets.

  2. FILAMENT CHANNEL FORMATION VIA MAGNETIC HELICITY CONDENSATION

    SciTech Connect

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

    2015-08-20

    A major unexplained feature of the solar atmosphere is the accumulation of magnetic shear in the form of filament channels at photospheric polarity inversion lines (PILs). In addition to free energy, this shear represents magnetic helicity, which is conserved under reconnection. In this paper we address the problem of filament channel formation and show how filaments acquire their shear and magnetic helicity. The results of three-dimensional (3D) simulations using the Adaptively Refined Magnetohydrodynamics Solver are presented. Our findings support the model of filament channel formation by magnetic helicity condensation that was developed by Antiochos. We consider the small-scale photospheric twisting of a quasi-potential flux system that is bounded by a PIL and contains a coronal hole (CH). The magnetic helicity injected by the small-scale photospheric motions is shown to inverse cascade up to the largest allowable scales that define the closed flux system: the PIL and the CH. This process produces field lines that are both sheared and smooth, and are sheared in opposite senses at the PIL and the CH. The accumulated helicity and shear flux are shown to be in excellent quantitative agreement with the helicity condensation model. We present a detailed analysis of the simulations, including comparisons of our analytical and numerical results, and discuss their implications for observations.

  3. 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

  4. 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.

  5. 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.

  6. Spontaneous Helicity of a Polymer with Side Loops Confined to a Cylinder

    NASA Astrophysics Data System (ADS)

    Chaudhuri, Debasish; Mulder, Bela M.

    2012-06-01

    Inspired by recent experiments on the spatial organization of bacterial chromosomes, we consider a type of “bottle-brush” polymer consisting of a flexible backbone chain, to which flexible side loops are connected. We show that such a model with an open linear backbone spontaneously adopts a helical structure with a well-defined pitch when confined to small cylindrical volume. This helicity persists over a range of sizes and aspect ratios of the cylinder, provided the packing fraction of the chain is suitably large. We analyze these results in terms of the interplay between the effective stiffness and actual intrachain packing effects caused by the side loops in response to the confinement.

  7. Light-directing chiral liquid crystal nanostructures: from 1D to 3D.

    PubMed

    Bisoyi, Hari Krishna; Li, Quan

    2014-10-21

    Endowing external, remote, and dynamic control to self-organized superstructures with desired functionalities is a principal driving force in the bottom-up nanofabrication of molecular devices. Light-driven chiral molecular switches or motors in liquid crystal (LC) media capable of self-organizing into optically tunable one-dimensional (1D) and three-dimensional (3D) superstructures represent such an elegant system. As a consequence, photoresponsive cholesteric LCs (CLCs), i.e., self-organized 1D helical superstructures, and LC blue phases (BPs), i.e., self-organized 3D periodic cubic lattices, are emerging as a new generation of multifunctional supramolecular 1D and 3D photonic materials in their own right because of their fundamental academic interest and technological significance. These smart stimuli-responsive materials can be facilely fabricated from achiral LC hosts by the addition of a small amount of a light-driven chiral molecular switch or motor. The photoresponsiveness of these materials is a result of both molecular interaction and geometry changes in the chiral molecular switch upon light irradiation. The doped photoresponsive CLCs undergo light-driven pitch modulation and/or helix inversion, which has many applications in color filters, polarizers, all-optical displays, optical lasers, sensors, energy-saving smart devices, and so on. Recently, we have conceptualized and rationally synthesized different light-driven chiral molecular switches that have very high helical twisting powers (HTPs) and exhibit large changes in HTP in different states, thereby enabling wide phototunability of the systems by the addition of very small amounts of the molecular switches into commercially available achiral LCs. The light-driven chiral molecular switches are based on well-recognized azobenzene, dithienylcyclopentene, and spirooxazine derivatives. We have demonstrated high-resolution and lightweight photoaddressable displays without patterned electronics on

  8. 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

  9. 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.

  10. Helical buckling of pipes in extended reach and horizontal wells -- Part 1: Preventing helical buckling

    SciTech Connect

    Wu, J.; Juvkam-Wold, H.C.; Lu, R. . Petroleum Engineering Dept.)

    1993-09-01

    This paper studies the helical buckling of pipes (drillstring and tubing) in extended reach and horizontal wells, theoretically and experimentally, resulting in new equations to correctly predict and effectively prevent the helical buckling of pipes in such wells. The theoretically study shows that the so-called helical buckling load that appears in the current literature is only the average axial load in the helical buckling development process. The laboratory experiments confirm the theoretical analysis. The new helical buckling load equations are formulated by combining the theoretical analysis and the experimental results, thereby resolving the existing assumption-and-result inconsistency in the current literature. The new equation predicts the true helical buckling load to be about 1.3 times the so-called helical buckling load in the current literature, and about 1.8 times the critical buckling load that predicts the onset of sinusoidal buckling. Consequently, larger bit weights or packer setting loads can be applied to increase the drilling rate or to ensure a proper seal, before the helical buckling of the pipes can occur.

  11. Helical Spin Texture and Interference of Majorana Bound States in One-Dimensional Topological Superconductor

    NASA Astrophysics Data System (ADS)

    Kawakami, Takuto; Hu, Xiao

    2016-01-01

    We investigate one-dimensional (1D) Majorana bound states (MBSs) realized in terms of the helical edge states of a 2D quantum spin-Hall insulator in a heterostructure with a superconducting substrate and two ferromagnetic insulators (FIs). By means of Bogoliubov-de Gennes approach we demonstrate that there is a helical spin texture in the MBS wave function with a pitch proportional to the Fermi momentum. Moreover, simultaneous detection on local density of states by scanning tunneling microscopy and spectroscopy at a position close to one FI edge and at the midpoint between the two FIs can not only map out the energy spectrum ±E cos(ϕ/2) where ϕ is the relative angle between the magnetizations of two FIs, but also prove experimentally that the two quasiparticle excitations do not mix with each other as protected by the parity conservation associated with the MBSs.

  12. 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.

  13. 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

  14. Helicity, assembly, and circularly polarised luminesence of chiral AIEgens

    NASA Astrophysics Data System (ADS)

    Li, Hongkun; Li, Bing Shi; Tang, Ben Zhong

    2016-09-01

    As opposed to most fluorophores that suffer from aggregation-caused quenching (ACQ), aggregation-induced emissive luminogens (AIEgens) possess very weak fluorescence in solution, but show strong emission upon aggregation due to restriction of intramolecular motion (RIM). Since AIEgens are often comprised of propeller-shaped structures, i.e. polyphenylsiloles or tetraphenylethylene (TPE), the attachment of chiral units has recently proven a powerful tool to fabricate chiral AIEgens exhibiting strong circularly-polarized luminescence (CPL) signal upon aggregation. Different chiral moieties lead to various assembled structures, such as helical nanoribbons, superhelical ropes, hollow and solid micro-/nanospheres. Generally, these structures exhibit enhanced chiroptical properties when compared to their monomeric counterpart. In this context, we report on the tetraphenylsilole and TPE derivatives with side-chains bearing an enantiomerically pure chiral units readily assembled into superhelical ropes upon aggregation, which displayed large CPL dissymmetry factors (gem) of -0.32 - a record for purely organic chiral materials.

  15. Consensus Prediction of Charged Single Alpha-Helices with CSAHserver.

    PubMed

    Dudola, Dániel; Tóth, Gábor; Nyitray, László; Gáspári, Zoltán

    2017-01-01

    Charged single alpha-helices (CSAHs) constitute a rare structural motif. CSAH is characterized by a high density of regularly alternating residues with positively and negatively charged side chains. Such segments exhibit unique structural properties; however, there are only a handful of proteins where its existence is experimentally verified. Therefore, establishing a pipeline that is capable of predicting the presence of CSAH segments with a low false positive rate is of considerable importance. Here we describe a consensus-based approach that relies on two conceptually different CSAH detection methods and a final filter based on the estimated helix-forming capabilities of the segments. This pipeline was shown to be capable of identifying previously uncharacterized CSAH segments that could be verified experimentally. The method is available as a web server at http://csahserver.itk.ppke.hu and also a downloadable standalone program suitable to scan larger sequence collections.

  16. Hydrogels of Superlong Helices to Synthesize Hybrid Ag-Helical Nanomaterials.

    PubMed

    Li, Guihua; Wang, Yitong; Wang, Ling; Song, Aixin; Hao, Jingcheng

    2016-11-22

    The gelation behavior of mixtures of sodium deoxycholate (NaDC) and glutathione (GSH) in water is investigated. The system exhibits a structural transition of self-assembled hydrogels from nanofibers to nanohelix structures, and then to helical ribbons with increasing GSH concentration. Superlong helical nanofibers with left- and right-handed orientations are produced by tuning the concentration of GSH at a fixed concentration of NaDC. Random coil and β-sheet structures are significant for the formation of the helical structures, and are indicated by circular dichroism (CD) and Fourier transform infrared (FT-IR) spectra. The mechanical strength of the "weak" hydrogels is enhanced by the introduction of appropriate suitable amount of AgNO3. Furthermore, the controlled growth of Ag nanoparticles at spatially arranged locations along the nanohelices (hybrid Ag-helical nanomaterial) is readily achieved by UV reduction of Ag (I) ions on the supramolecular helical templates.

  17. DNS of helicity-induced stratified turbulent flow

    NASA Astrophysics Data System (ADS)

    Chandy, Abhilash J.; Rahimi, Abbas

    2013-11-01

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

  18. Tensile mechanics of alanine-based helical polypeptide: force spectroscopy versus computer simulations.

    PubMed

    Afrin, Rehana; Takahashi, Ichiro; Shiga, Kazuki; Ikai, Atsushi

    2009-02-01

    In nature, an alpha-helix is commonly used to build thermodynamically stable and mechanically rigid protein conformations. In view of growing interest in the mechanical rigidity of proteins, we measured the tensile profile of an alanine-based alpha-helical polypeptide on an atomic-force microscope to investigate the basic mechanics of helix extension with minimal interference from side-chain interactions. The peptide was extended to its maximum contour length with much less force than in reported cases of poly-L-Glu or poly-L-Lys, indicating that chain stiffness strongly depended on the physicochemical properties of side chains, such as their bulkiness. The low tensile-force extension originated presumably in locally unfolded parts because of spontaneous structural fluctuations. In 50% trifluoroethanol, the well-known helix-promoting agent, the rigidity of the sample polypeptide was markedly increased. Computer simulations of the peptide-stretching process showed that a majority of constituent residues underwent a transition from an alpha-helical to an extended conformation by overcoming an energy barrier around psi approximately 0 degrees on the Ramachandran plot. The observed lability of an isolated helix signified the biological importance of the lateral bundling of helices to maintain a rigid protein structure.

  19. 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.

  20. 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.

  1. TURBULENT DYNAMOS WITH SHEAR AND FRACTIONAL HELICITY

    SciTech Connect

    Kaepylae, Petri J.; Brandenburg, Axel

    2009-07-10

    Dynamo action owing to helically forced turbulence and large-scale shear is studied using direct numerical simulations. The resulting magnetic field displays propagating wave-like behavior. This behavior can be modeled in terms of an {alpha}{omega} dynamo. In most cases super-equipartition fields are generated. By varying the fraction of helicity of the turbulence the regeneration of poloidal fields via the helicity effect (corresponding to the {alpha}-effect) is regulated. The saturation level of the magnetic field in the numerical models is consistent with a linear dependence on the ratio of the fractional helicities of the small and large-scale fields, as predicted by a simple nonlinear mean-field model. As the magnetic Reynolds number (Re{sub M}) based on the wavenumber of the energy-carrying eddies is increased from 1 to 180, the cycle frequency of the large-scale field is found to decrease by a factor of about 6 in cases where the turbulence is fully helical. This is interpreted in terms of the turbulent magnetic diffusivity, which is found to be only weakly dependent on the Re{sub M}.

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

    PubMed

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

    2013-01-03

    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.

  3. Rab28 is a TBC1D1/TBC1D4 substrate involved in GLUT4 trafficking.

    PubMed

    Zhou, Zhou; Menzel, Franziska; Benninghoff, Tim; Chadt, Alexandra; Du, Chen; Holman, Geoffrey D; Al-Hasani, Hadi

    2017-01-01

    The Rab-GTPase-activating proteins (GAPs) TBC1D1 and TBC1D4 play important roles in the insulin-stimulated translocation of the glucose transporter GLUT4 from intracellular vesicles to the plasma membrane in muscle cells and adipocytes. We identified Rab28 as a substrate for the GAP domains of both TBC1D1 and TBC1D4 in vitro. Rab28 is expressed in adipose cells and skeletal muscle, and its GTP-binding state is acutely regulated by insulin. We found that in intact isolated mouse skeletal muscle, siRNA-mediated knockdown of Rab28 decreases basal glucose uptake. Conversely, in primary rat adipose cells, overexpression of Rab28-Q72L, a constitutively active mutant, increases basal cell surface levels of an epitope-tagged HA-GLUT4. Our results indicate that Rab28 is a novel GTPase involved in the intracellular retention of GLUT4 in insulin target cells.

  4. 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.

  5. A helically distorted MHD flux rope model

    NASA Technical Reports Server (NTRS)

    Theobald, Michael L.; Montgomery, David

    1990-01-01

    A flux rope model is proposed which has a variable degree of helical distortion from axisymmetry. The basis for this suggestion is a series of numerical and analytical investigations of magnetohydrodynamic states which result when an axial electric current is directed down on dc magnetic field. The helically distorted states involve a flow velocity and seem to be favored because of their lower rate of energy dissipation. Emphasis is on the magnetometer and particle energy analyzer traces that might be characteristic of such flux ropes. It is shown that even a fractionally small helical distortion may considerably alter the traces in minimum-variance coordinates. In short, what may be fairly common MHD processes can render a flux rope almost unrecognizable under standard diagnostics, even if the departures from axisymmetry are not great.

  6. 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

  7. Helical motion of chiral liquid crystal droplets

    NASA Astrophysics Data System (ADS)

    Yamamoto, Takaki; Sano, Masaki

    Artificial swimmers have been intensively studied to understand the mechanism of the locomotion and collective behaviors of cells and microorganisms. Among them, most of the artificial swimmers are designed to move along the straight path. However, in biological systems, chiral dynamics such as circular and helical motion are quite common because of the chirality of their bodies, which are made of chiral biomolecules. To understand the role of the chirality in the physics of microswimmers, we designed chiral artificial swimmers and the theoretical model for the chiral motion. We found that chiral liquid crystal droplets, when dispersed in surfactant solutions, swim in the helical path induced by the Marangoni effect. We will discuss the mechanism of the helical motion with our phenomenological model. This work is supported by Grant-in-Aid for JSPS Fellows (Grant No. 26.9814), and MEXT KAKENHI Grant No. 25103004.

  8. Generation of acoustic helical wavefronts using metasurfaces

    NASA Astrophysics Data System (ADS)

    Esfahlani, Hussein; Lissek, Herve; Mosig, Juan R.

    2017-01-01

    It has been shown that acoustic waves with helical wavefronts can carry angular momentum, which can be transmitted towards a propagating medium. Such a wave field can be achieved by using a planar array of electroacoustic transducers, forming a given spatial distribution of phased sound sources which produce the desired helical wavefronts. Here, we introduce a technique to generate acoustic vortices, based on the passive acoustic metasurface concept. The proposed metasurface is composed of space-coiled cylindrical unit cells transmitting sound pressure with a controllable phase shift, which are arranged in a discretized circular configuration, and thus passively transforming an incident plane wavefront into the desired helical wavefront. This method presents the advantage of overcoming the restrictions on using many acoustic sources, and it is implemented with a transmitting metasurface which can be easily three-dimensionally printed. The proposed straightforward design principle can be adopted for easy production of acoustic angular momentum with minimum complexity and using a single source.

  9. 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

  10. Large-scale dynamics of magnetic helicity

    NASA Astrophysics Data System (ADS)

    Linkmann, Moritz; Dallas, Vassilios

    2016-11-01

    In this paper we investigate the dynamics of magnetic helicity in magnetohydrodynamic (MHD) turbulent flows focusing at scales larger than the forcing scale. Our results show a nonlocal inverse cascade of magnetic helicity, which occurs directly from the forcing scale into the largest scales of the magnetic field. We also observe that no magnetic helicity and no energy is transferred to an intermediate range of scales sufficiently smaller than the container size and larger than the forcing scale. Thus, the statistical properties of this range of scales, which increases with scale separation, is shown to be described to a large extent by the zero flux solutions of the absolute statistical equilibrium theory exhibited by the truncated ideal MHD equations.

  11. Polar discontinuities and 1D interfaces in monolayered materials

    NASA Astrophysics Data System (ADS)

    Martinez-Gordillo, Rafael; Pruneda, Miguel

    2015-12-01

    Interfaces are the birthplace of a multitude of fascinating discoveries in fundamental science, and have enabled modern electronic devices, from transistors, to lasers, capacitors or solar cells. These interfaces between bulk materials are always bi-dimensional (2D) 'surfaces'. However the advent of graphene and other 2D crystals opened up a world of possibilities, as in this case the interfaces become one-dimensional (1D) lines. Although the properties of 1D nanoribbons have been extensively discussed in the last few years, 1D interfaces within infinite 2D systems had remained mostly unexplored until very recently. These include grain boundaries in polycrystalline samples, or interfaces in hybrid 2D sheets composed by segregated domains of different materials (as for example graphene/BN hybrids, or chemically different transition metal dichalcogenides). As for their 2D counterparts, some of these 1D interfaces exhibit polar characteristics, and can give rise to fascinating new physical properties. Here, recent experimental discoveries and theoretical predictions on the polar discontinuities that arise at these 1D interfaces will be reviewed, and the perspectives of this new research topic, discussed.

  12. Ion-sensing properties of 1D vanadium pentoxide nanostructures

    PubMed Central

    2012-01-01

    The application of one-dimensional (1D) V2O5·nH2O nanostructures as pH sensing material was evaluated. 1D V2O5·nH2O nanostructures were obtained by a hydrothermal method with systematic control of morphology forming different nanostructures: nanoribbons, nanowires and nanorods. Deposited onto Au-covered substrates, 1D V2O5·nH2O nanostructures were employed as gate material in pH sensors based on separative extended gate FET as an alternative to provide FET isolation from the chemical environment. 1D V2O5·nH2O nanostructures showed pH sensitivity around the expected theoretical value. Due to high pH sensing properties, flexibility and low cost, further applications of 1D V2O5·nH2O nanostructures comprise enzyme FET-based biosensors using immobilized enzymes. PMID:22709724

  13. Helicity and nuclear β decay correlations

    NASA Astrophysics Data System (ADS)

    Hong, Ran; Sternberg, Matthew G.; Garcia, Alejandro

    2017-01-01

    We present simple derivations of nuclear β-decay correlations with an emphasis on the special role of helicity. This topic provides a good opportunity to teach students about helicity and chirality in particle physics with exercises that use simple aspects of quantum mechanics. In addition, this paper serves as an introduction to nuclear β-decay correlations from both a theoretical and experimental perspective. This article can be used to introduce students to ongoing experiments searching for hints of new physics in the low-energy precision frontier.

  14. Helical Lattice Vibrational Modes in DNA.

    DTIC Science & Technology

    1988-03-10

    VIBRATIONAL MODES IN DNA(U) PURDUE UNIV l’ LAFAYETTE IND DEPT OF PHYSICS V V PRRGHU ET AL. UNCLR~~lll’ 16I MAR *6 N99914...Initiative Organization 1400014-86-K-0252 Washinton, D.C. 20301-7100 %0 %0 .0 Helical Lattixce Vibrational ’ Modes in DNA V.V. Prabhu, ’.,.K. Sclhrol!, L.L...8217+"+ " ’. % " " % ") . " ". ".",°. " . % % . . ,.-. -.-. -. ,, . . - . -]. o % % % o. -.-. , .%** %-N% Revised version Helical Lattice Vibrational Modes in DNA 1 A recent

  15. Mechanism of helix induction in poly(4-carboxyphenyl isocyanide) with chiral amines and memory of the macromolecular helicity and its helical structures.

    PubMed

    Hase, Yoko; Nagai, Kanji; Iida, Hiroki; Maeda, Katsuhiro; Ochi, Noriaki; Sawabe, Kyoichi; Sakajiri, Koichi; Okoshi, Kento; Yashima, Eiji

    2009-08-05

    helix as the most possible helical structure, which is in good agreement with the XRD results. Furthermore, the persistence length measurements revealed that these structural changes accompany a significant change in the main-chain stiffness. The mechanism of helix induction in poly-1-H and the memory of the macromolecular helicity are discussed on the basis of these results.

  16. EVOLUTION OF RELATIVE MAGNETIC HELICITY AND CURRENT HELICITY IN NOAA ACTIVE REGION 11158

    SciTech Connect

    Jing, Ju; Liu, Chang; Lee, Jeongwoo; Xu, Yan; Deng, Na; Wang, Haimin; Park, Sung-Hong; Wiegelmann, Thomas E-mail: chang.liu@njit.edu E-mail: na.deng@njit.edu E-mail: freemler@kasi.re.kr E-mail: wiegelmann@linmpi.mpg.de

    2012-06-10

    Both magnetic and current helicities are crucial ingredients for describing the complexity of active-region magnetic structure. In this Letter, we present the temporal evolution of these helicities contained in NOAA active region 11158 during five days from 2011 February 12 to 16. The photospheric vector magnetograms of the Helioseismic and Magnetic Imager on board the Solar Dynamic Observatory were used as the boundary conditions for the coronal field extrapolation under the assumption of nonlinear force-free field, from which we calculated both relative magnetic helicity and current helicity. We construct a time-altitude diagram in which altitude distribution of the magnitude of current helicity density is displayed as a function of time. This diagram clearly shows a pattern of upwardly propagating current helicity density over two days prior to the X2.2 flare on February 15 with an average propagation speed of {approx}36 m s{sup -1}. The propagation is synchronous with the emergence of magnetic flux into the photosphere, and indicative of a gradual energy buildup for the X2.2 flare. The time profile of the relative magnetic helicity shows a monotonically increasing trend most of the time, but a pattern of increasing and decreasing magnetic helicity above the monotonic variation appears prior to each of two major flares, M6.6 and X2.2, respectively. The physics underlying this bump pattern is not fully understood. However, the fact that this pattern is apparent in the magnetic helicity evolution but not in the magnetic flux evolution makes it a useful indicator in forecasting major flares.

  17. 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).

  18. 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

  19. 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.

  20. 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

  1. 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.

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

    PubMed

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

    2007-09-15

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

  3. Proline-induced hinges in transmembrane helices: possible roles in ion channel gating.

    PubMed

    Tieleman, D P; Shrivastava, I H; Ulmschneider, M R; Sansom, M S

    2001-08-01

    A number of ion channels contain transmembrane (TM) alpha-helices that contain proline-induced molecular hinges. These TM helices include the channel-forming peptide alamethicin (Alm), the S6 helix from voltage-gated potassium (Kv) channels, and the D5 helix from voltage-gated chloride (CLC) channels. For both Alm and KvS6, experimental data implicate hinge-bending motions of the helix in an aspect of channel gating. We have compared the hinge-bending motions of these TM helices in bilayer-like environments by multi-nanosecond MD simulations in an attempt to describe motions of these helices that may underlie possible modes of channel gating. Alm is an alpha-helical channel-forming peptide, which contains a central kink associated with a Gly-x-x-Pro motif in its sequence. Simulations of Alm in a TM orientation for 10 ns in an octane slab indicate that the Gly-x-x-Pro motif acts as a molecular hinge. The S6 helix from Shaker Kv channels contains a Pro-Val-Pro motif. Modeling studies and recent experimental data suggest that the KvS6 helix may be kinked in the vicinity of this motif. Simulations (10 ns) of an isolated KvS6 helix in an octane slab and in a POPC bilayer reveal hinge-bending motions. A pattern-matching approach was used to search for possible hinge-bending motifs in the TM helices of other ion channel proteins. This uncovered a conserved Gly-x-Pro motif in TM helix D5 of CLC channels. MD simulations of a model of hCLC1-D5 spanning an octane slab suggest that this channel also contains a TM helix that undergoes hinge-bending motion. In conclusion, our simulations suggest a model in which hinge-bending motions of TM helices may play a functional role in the gating mechanisms of several different families of ion channels.

  4. 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

  5. Morphology-controlled synthesis of SnO(2) nanotubes by using 1D silica mesostructures as sacrificial templates and their applications in lithium-ion batteries.

    PubMed

    Ye, Jianfeng; Zhang, Huijuan; Yang, Rong; Li, Xingguo; Qi, Limin

    2010-01-01

    SnO(2) nanotubes with controllable morphologies are successfully synthesized by using a variety of one-dimensional (1D) silica mesostructures as effective sacrificial templates. Firstly, 1D silica mesostructures with different morphologies, such as chiral nanorods, nonchiral nanofibers, and helical nanotubes, are readily synthesized in aqueous solution by using the triblock copolymer Pluronic F127 and the cationic surfactant cetyltrimethylammonium bromide as binary templates. Subsequently, the obtained 1D silica mesostructures are used as sacrificial templates to synthesize SnO(2) nanotubes with preserved morphologies via a simple hydrothermal route, resulting in the formation of well-defined SnO(2) nanotubes with different lengths and unique helical SnO(2) nanotubes with a wealth of conformations. It is revealed that both of the short and long SnO(2) nanotubes showed much better performance as anode materials in lithium-ion batteries than normal SnO(2) nanopowders, which might be related to the hollow structure of the nanotubes that could alleviate the volume changes and mechanical stress during charging/discharging cycling. Moreover, the capacity and cycling performance of short nanotubes, which showed a specific discharge capacity of 468 mAh g(-1) after 30 cycles, are considerably better than those of long nanotubes because of the more robust structure of the short nanotubes.

  6. 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.

  7. Dynamics of helical states in MST

    NASA Astrophysics Data System (ADS)

    Munaretto, Stefano; Auriemma, F.; Brower, D.; Chapman, B. E.; den Hartog, D. J.; Ding, W. X.; Duff, J.; Franz, P.; Goetz, J. A.; Holly, D.; Lin, L.; McCollam, K. J.; McGarry, M.; Morton, L.; Nornberg, M. D.; Parke, E.; Sarff, J. S.

    2014-10-01

    The thermal and the magnetic dynamics of quasi-single-helicity (QSH) plasmas evolve independently during the formation and sustainment of the core helical structure. At higher plasma current (and Lundquist number) MST plasmas transition from an axisymmetric multi-helicity state to a QSH state characterized by a strong core helical mode and reduced secondary mode amplitudes. Plasmas in the QSH state tend to wall-lock, often in an orientation that is unfavorable for optimized measurements of the 3D structure using MST's advanced diagnostics. Recently a technique to control the locking position through an applied resonant magnetic perturbation has been developed. Using this technique it is possible to adjust the 3D phase more optimally for specific diagnostics, to study the dynamics of the QSH structure and thermal features. The multi-chord FIR interferometer shows the presence of a density structure for the duration of the QSH state. Measurements of the time evolution of the electron temperature profile using the Thomson Scattering diagnostic reveal that the transition to QSH allows the presence of a 3D thermal structure, but this structure is intermittent. Understanding the mechanism(s) driving these dynamics is the goal of this work. Work supported by the US DOE and NSF.

  8. 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.

  9. Coulomb drag between helical Luttinger liquids

    NASA Astrophysics Data System (ADS)

    Kainaris, N.; Gornyi, I. V.; Levchenko, A.; Polyakov, D. G.

    2017-01-01

    We theoretically study Coulomb drag between two helical edges with broken spin-rotational symmetry, such as would occur in two capacitively coupled quantum spin Hall insulators. For the helical edges, Coulomb drag is particularly interesting because it specifically probes the inelastic interactions that break the conductance quantization for a single edge. Using the kinetic equation formalism, supplemented by bosonization, we find that the drag resistivity ρD exhibits a nonmonotonic dependence on the temperature T . In the limit of low T ,ρD vanishes with decreasing T as a power law if intraedge interactions are not too strong. This is in stark contrast to Coulomb drag in conventional quantum wires, where ρD diverges at T →0 irrespective of the strength of repulsive interactions. Another unusual property of Coulomb drag between the helical edges concerns higher T for which, unlike in the Luttinger liquid model, drag is mediated by plasmons. The special type of plasmon-mediated drag can be viewed as a distinguishing feature of the helical liquid—because it requires peculiar umklapp scattering only available in the presence of a Dirac point in the electron spectrum.

  10. Helical Gears Modified To Decrease Transmission Errors

    NASA Technical Reports Server (NTRS)

    Handschuh, R. F.; Coy, J. J.; Litvin, F. L.; Zhang, J.

    1993-01-01

    Tooth surfaces of helical gears modified, according to proposed design concept, to make gears more tolerant of misalignments and to improve distribution of contact stresses. Results in smaller transmission errors, with concomitant decreases in vibrations and noise and, possibly, increases in service lives.

  11. 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.

  12. 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.

  13. Synthesis of stabilized alpha-helical peptides.

    PubMed

    Bernal, Federico; Katz, Samuel G

    2014-01-01

    Stabilized alpha-helical (SAH) peptides are valuable laboratory tools to explore important protein-protein interactions. Whereas most peptides lose their secondary structure when isolated from the host protein, stapled peptides incorporate an all-hydrocarbon "staple" that reinforces their natural alpha-helical structure. Thus, stapled peptides retain their functional ability to bind their native protein targets and serve multiple experimental uses. First, they are useful for structural studies such as NMR or crystal structures that map and better define binding sites. Second, they can be used to identify small molecules that specifically target that interaction site. Third, stapled peptides can be used to test the importance of specific amino acid residues or posttranslational modifications to the binding. Fourth, they can serve as structurally competent bait to identify novel binding partners to specific alpha-helical motifs. In addition to markedly improved alpha-helicity, stapled peptides also display resistance to protease cleavage and enhanced cell permeability. Most importantly, they are useful for intracellular experiments that explore the functional consequences of blocking particular protein interactions. Because of their remarkable stability, stapled peptides can be applied to whole-animal, in vivo studies. Here we describe a protocol for the synthesis of a peptide that incorporates an all-hydrocarbon "staple" employing a ring-closing olefin metathesis reaction. With proper optimization, stapled peptides can be a fundamental, accurate laboratory tool in the modern chemical biologist's armory.

  14. Helical mode breakdown in transitional boundary layers

    NASA Astrophysics Data System (ADS)

    Bose, Rikhi; Durbin, Paul

    2016-11-01

    Results of direct numerical simulation of transition to turbulence in adverse pressure gradient boundary layers beneath free-stream turbulence will be presented. Instability waves are excited spontaneously and may be identified when intensity of free-stream turbulence (Tu) is sufficiently low. At very low Tu 0 . 1 % , secondary instability of the TS waves and at high Tu > 2 % , conventional bypass mechanisms trigger turbulent spot formation. At low Tu 1 % transition proceeds through formation of helical modes. Helical structures as in n = 1 instability modes of axisymmetric wakes and jets are clearly identifiable in visualizations of isosurfaces of stream-wise perturbation velocity. Helical modes also trigger transition at same level of Tu in zero pressure gradient boundary layers as well, provided that the inlet disturbances include a low amplitude time-periodic unstable TS wave. This indicates that these secondary instability modes might arise due to interaction of Klebanoff streaks and instability waves. Characteristically, the helical modes are inner instability modes. This work was supported by NSF Grant CBET-1228195. Computer time was provided by the Extreme Science and Engineering Discovery Environment (XSEDE).

  15. On statistical equilibrium in helical fluid flows

    NASA Astrophysics Data System (ADS)

    Kurgansky, M. V.

    2006-06-01

    The statistical mechanics of 3-D helical flows is re-examined for a continuum truncated at a top wavenumber. Based on the principle of equipartition of the flow enstrophy between helical modes, the emerging (i) energy spectrum law "-2" and (ii) formal mathematical analogy between the helicity and the thermodynamic entropy are discussed. It is noted that the "-2" scaling law is consistent with both spectral equilibrium and spectral cascade paradigms. In an attempt to apply the obtained results to a turbulent flow regime within the Earth's outer liquid core, where the net helicity of a turbulent flow component is presumably explained by Earth's rotation, it has been noticed that it is the energy spectral law "-1", but not "-2", which is likely realized there and within the logarithmic accuracy corresponds to the case of the velocity structure function [u(l)]2 independency on the spatial scale l, the latter is consistent with observations. It is argued that the "-1" scaling law can also be interpreted in terms of the spectral equilibrium and it is emphasized that the causes of the likely dominance of the spectral law "-1" over the spectral law "-2" in this geophysical application deserve further investigation and clarification.

  16. Magnetic stripes and skyrmions with helicity reversals

    PubMed Central

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

    2012-01-01

    It was recently realized that topological spin textures do not merely have mathematical beauty but can also give rise to unique functionalities of magnetic materials. An example is the skyrmion—a nano-sized bundle of noncoplanar spins—that by virtue of its nontrivial topology acts as a flux of magnetic field on spin-polarized electrons. Lorentz transmission electron microscopy recently emerged as a powerful tool for direct visualization of skyrmions in noncentrosymmetric helimagnets. Topologically, skyrmions are equivalent to magnetic bubbles (cylindrical domains) in ferromagnetic thin films, which were extensively explored in the 1970s for data storage applications. In this study we use Lorentz microscopy to image magnetic domain patterns in the prototypical magnetic oxide–M-type hexaferrite with a hint of scandium. Surprisingly, we find that the magnetic bubbles and stripes in the hexaferrite have a much more complex structure than the skyrmions and spirals in helimagnets, which we associate with the new degree of freedom—helicity (or vector spin chirality) describing the direction of spin rotation across the domain walls. We observe numerous random reversals of helicity in the stripe domain state. Random helicity of cylindrical domain walls coexists with the positional order of magnetic bubbles in a triangular lattice. Most unexpectedly, we observe regular helicity reversals inside skyrmions with an unusual multiple-ring structure. PMID:22615354

  17. Helical Pulse Line Structures for Ion Acceleration

    SciTech Connect

    Briggs, R.J.; Reginato, L.L.; Waldron, W.L.

    2005-05-01

    The basic concept of the ''Pulse Line Ion Accelerator'' is presented, where pulse power sources create a ramped traveling wave voltage pulse on a helical pulse line. Ions can surf on this traveling wave and achieve energy gains much larger than the peak applied voltage. Tapered and untapered lines are compared, and a transformer coupling technique for launching the wave is described.

  18. Magnetic stripes and skyrmions with helicity reversals.

    PubMed

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

    2012-06-05

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

  19. 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.

  20. 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.

  1. Amide-I characteristics of helical β-peptides by linear infrared measurement and computations.

    PubMed

    Zhao, Juan; Shi, Jipei; Wang, Jianping

    2014-01-09

    In this work, we have examined the amide-I characteristics of three β-peptide oligomers in typical helical conformations (two in 14-helix and one in 12/10-helix), solvated in water, methanol, and chloroform, respectively. Local-mode frequencies and their distributions were computed using a molecular-mechanics force field based frequency map that was constructed on the basis of molecular dynamics simulations. The local-mode frequencies were found to be determined primarily by peptide backbone and side chain, rather by solvent, suggesting their local structural sensitivities. Intermode vibrational couplings computed using a transition dipole scheme were found to be very sensitive to peptide conformation, with their signs and magnitudes varying periodically along the peptide chain. Linear infrared absorption spectra of the three peptides, simulated using a frequency-frequency time-correlation function method, were found to be in fair agreement with experimental results. Normalized potential energy distribution analysis indicated that the amide-I mode can delocalize over a few amide units. However, the IR band structure appears to be more sophisticated in helical β-peptides than in helical α-peptides.

  2. 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.

  3. Plasmonic Excitations of 1D Metal-Dielectric Interfaces in 2D Systems: 1D Surface Plasmon Polaritons

    NASA Astrophysics Data System (ADS)

    Mason, Daniel R.; Menabde, Sergey G.; Yu, Sunkyu; Park, Namkyoo

    2014-04-01

    Surface plasmon-polariton (SPP) excitations of metal-dielectric interfaces are a fundamental light-matter interaction which has attracted interest as a route to spatial confinement of light far beyond that offered by conventional dielectric optical devices. Conventionally, SPPs have been studied in noble-metal structures, where the SPPs are intrinsically bound to a 2D metal-dielectric interface. Meanwhile, recent advances in the growth of hybrid 2D crystals, which comprise laterally connected domains of distinct atomically thin materials, provide the first realistic platform on which a 2D metal-dielectric system with a truly 1D metal-dielectric interface can be achieved. Here we show for the first time that 1D metal-dielectric interfaces support a fundamental 1D plasmonic mode (1DSPP) which exhibits cutoff behavior that provides dramatically improved light confinement in 2D systems. The 1DSPP constitutes a new basic category of plasmon as the missing 1D member of the plasmon family: 3D bulk plasmon, 2DSPP, 1DSPP, and 0D localized SP.

  4. 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

  5. Synthesis and biological applications of collagen-model triple-helical peptides.

    PubMed

    Fields, Gregg B

    2010-03-21

    Triple-helical peptides (THPs) have been utilized as collagen models since the 1960s. The original focus for THP-based research was to unravel the structural determinants of collagen. In the last two decades, virtually all aspects of collagen structural biochemistry have been explored with THP models. More specifically, secondary amino acid analogs have been incorporated into THPs to more fully understand the forces that stabilize triple-helical structure. Heterotrimeric THPs have been utilized to better appreciate the contributions of chain sequence diversity on collagen function. The role of collagen as a cell signaling protein has been dissected using THPs that represent ligands for specific receptors. The mechanisms of collagenolysis have been investigated using THP substrates and inhibitors. Finally, THPs have been developed for biomaterial applications. These aspects of THP-based research are overviewed herein.

  6. 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.

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

    NASA Astrophysics Data System (ADS)

    Braun, Gregory; Tierney, Dennis; Schmitzer, Heidrun

    2011-03-01

    Rosalind Franklin, a chemical physicist (1920-1958), used x-ray diffraction to determine the structure of DNA. What exactly could she read out from her x-ray pattern, shown in Fig. 1? In lecture notes dated November 1951, R. Franklin wrote the following: "The results suggest a helical structure (which must be very closely packed) containing 2, 3 or 4 co-axial nucleic acid chains per helical unit, and having the phosphate groups near the outside."2 This was 16 months before J. D. Watson and F. Crick published their description of DNA, which was based on R. Franklin's x-ray photos. How they gained access to her x-ray photos is a fascinating tale of clashing personalities and male chauvinism.2,3

  8. 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.

  9. Magnetic helicity balance in the Sustained Spheromak Plasma Experiment

    NASA Astrophysics Data System (ADS)

    Stallard, B. W.; Hooper, E. B.; Woodruff, S.; Bulmer, R. H.; Hill, D. N.; McLean, H. S.; Wood, R. D.

    2003-07-01

    The magnetic helicity balance between the helicity input injected by a magnetized coaxial gun, the rate-of-change in plasma helicity content, and helicity dissipation in electrode sheaths and Ohmic losses have been examined in the Sustained Spheromak Plasma Experiment (SSPX) [E. B. Hooper, L. D. Pearlstein, and R. H. Bulmer, Nucl. Fusion 39, 863 (1999)]. Helicity is treated as a flux function in the mean-field approximation, allowing separation of helicity drive and losses between closed and open field volumes. For nearly sustained spheromak plasmas with low fluctuations, helicity balance analysis implies a decreasing transport of helicity from the gun input into the spheromak core at higher spheromak electron temperature. Long pulse discharges with continuously increasing helicity and larger fluctuations show higher helicity coupling from the edge to the spheromak core. The magnitude of the sheath voltage drop, inferred from cathode heating and a current threshold dependence of the gun voltage, shows that sheath losses are important and reduce the helicity injection efficiency in SSPX.

  10. 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

  11. Autonomously folded α-helical lockers promote RNAi.

    PubMed

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

    2016-10-10

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

  12. 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.

  13. Multipole Expansion for a Single Helical Current Conductor

    NASA Astrophysics Data System (ADS)

    Tominaka, T.; Hatanaka, K.; Katayama, T.

    1997-05-01

    The purpose of this paper is to give the expression of the multipole expansion for a single helical current conductor. This analytical expression will be useful for the electromagnetic analysis of various helical coils such as helical dipoles, multifilamentary superconductors and superconducting strands. The present treatment of the multipole expansion for a single helical current conductor is derived as the extension of the case for a single straight current conductor. In addition, the comparison between the analytical and numerical calculations is presented for a single helical current conductor. As a result, the agreement between the analytical and numerical calculations is quite good, except the region near the radius of a single helical current conductor. Then, for the sum of the multipole expansion for a single helical current conductor, the Cesaro's method of summation are adopted.

  14. Stabilization of Helical Macromolecular Phases by Confined Bending

    NASA Astrophysics Data System (ADS)

    Williams, Matthew J.; Bachmann, Michael

    2015-07-01

    By means of extensive replica-exchange simulations of generic coarse-grained models for helical polymers, we systematically investigate the structural transitions into all possible helical phases for flexible and semiflexible elastic polymers with self-interaction under the influence of torsion barriers. The competing interactions lead to a variety of conformational phases including disordered helical arrangements, single helices, and ordered, tertiary helix bundles. Most remarkably, we find that a bending restraint entails a clear separation and stabilization of the helical phases. This aids in understanding why semiflexible polymers such as double-stranded DNA tend to form pronounced helical structures and proteins often exhibit an abundance of helical structures, such as helix bundles, within their tertiary structure.

  15. 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.

  16. 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.

  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. Ultrahigh-Q nanocavity with 1D photonic gap.

    PubMed

    Notomi, M; Kuramochi, E; Taniyama, H

    2008-07-21

    Recently, various wavelength-sized cavities with theoretical Q values of approximately 10(8) have been reported, however, they all employ 2D or 3D photonic band gaps to realize strong light confinement. Here we numerically demonstrate that ultrahigh-Q (2.0x10(8)) and wavelength-sized (V(eff) approximately 1.4(lambda/n)3) cavities can be achieved by employing only 1D periodicity.

  19. Nonreciprocity of edge modes in 1D magnonic crystal

    NASA Astrophysics Data System (ADS)

    Lisenkov, I.; Kalyabin, D.; Osokin, S.; Klos, J. W.; Krawczyk, M.; Nikitov, S.

    2015-03-01

    Spin waves propagation in 1D magnonic crystals is investigated theoretically. Mathematical model based on plane wave expansion method is applied to different types of magnonic crystals, namely bi-component magnonic crystal with symmetric/asymmetric boundaries and ferromagnetic film with periodically corrugated top surface. It is shown that edge modes in magnonic crystals may exhibit nonreciprocal behaviour at much lower frequencies than in homogeneous films.

  20. Iterative Assembly of Helical Proteins by Optimal Hydrophobic Packing

    PubMed Central

    Wu, G. Albert; Coutsias, Evangelos A.; Dill, Ken A.

    2008-01-01

    SUMMARY We present a method for the computer-based iterative assembly of native-like tertiary structures of helical proteins from alpha-helical fragments. For any pair of helices, our method, called MATCHSTIX, first generates an ensemble of possible relative orientations of the helices with various ways to form hydrophobic contacts between them. Those conformations having steric clashes, or a large radius of gyration of hydrophobic residues, or with helices too far separated to be connected by the intervening linking region, are discarded. Then, we attempt to connect the two helical fragments by using a robotics-based loop-closure algorithm. When loop closure is feasible, the algorithm generates an ensemble of viable interconnecting loops. After energy minimization and clustering, we use a representative set of conformations for further assembly with the remaining helices, adding one helix at a time. To efficiently sample the conformational space, the order of assembly generally proceeds from the pair of helices connected by the shortest loop, followed by joining one of its adjacent helices, always proceeding with the shorter connecting loop. We tested MATCHSTIX on 28 helical proteins each containing up to 5 helices and found it to heavily sample native-like conformations. The average RMSD of the best conformations for the 17 helix-bundle proteins that have 2 or 3 helices is less than 2 Å; errors increase somewhat for proteins containing more helices. Native-like states are even more densely sampled when disulfide bonds are known and imposed as restraints. We conclude that, at least for helical proteins, if the secondary structures are known, this rapid rigid-body maximization of hydrophobic interactions can lead to small ensembles of highly native-like structures. It may be useful for protein structure prediction. PMID:18682227

  1. The stability of 1-D soliton in transverse direction

    NASA Astrophysics Data System (ADS)

    Verma, Deepa; Bera, Ratan Kumar; Das, Amita; Kaw, Predhiman

    2016-12-01

    The complete characterization of the exact 1-D solitary wave solutions (both stationary and propagating) for light plasma coupled system have been studied extensively in the parameter space of light frequency and the group speed [Poornakala et al., Phys. Plasmas 9(5), 1820 (2002)]. It has been shown in 1-D that solutions with single light wave peak and paired structures are stable and hence long lived. However, solutions having multiple peaks of light wave are unstable due to Raman scattering instability [Saxena et al., Phys. Plasmas 14, 072307 (2007)]. Here, we have shown with the help of 2-D fluid simulation that single peak and paired solutions too get destabilized by the transverse filamentation instability. The numerical growth rates obtained from simulations is seen to compare well with the analytical values. It is also shown that multiple peaks solitons first undergo the regular 1-D forward Raman scattering instability. Subsequently, they undergo a distinct second phase of destabilization through transverse filamentation instability. This is evident from the structure as well as the plot of the perturbed energy which shows a second phase of growth after saturating initially. The growth rate of the filamentation instability being comparatively slower than the forward Raman instability this phase comes quite late and is clearly distinguishable.

  2. Examining Prebiotic Chemistry Using O(^1D) Insertion Reactions

    NASA Astrophysics Data System (ADS)

    Hays, Brian M.; Laas, Jacob C.; Weaver, Susanna L. Widicus

    2013-06-01

    Aminomethanol, methanediol, and methoxymethanol are all prebiotic molecules expected to form via photo-driven grain surface chemistry in the interstellar medium (ISM). These molecules are expected to be precursors for larger, biologically-relevant molecules in the ISM such as sugars and amino acids. These three molecules have not yet been detected in the ISM because of the lack of available rotational spectra. A high resolution (sub)millimeter spectrometer coupled to a molecular source is being used to study these molecules using O(^1D) insertion reactions. The O(^1D) chemistry is initiated using an excimer laser, and the products of the insertion reactions are adiabatically cooled using a supersonic expansion. Experimental parameters are being optimized by examination of methanol formed from O(^1D) insertion into methane. Theoretical studies of the structure and reaction energies for aminomethanol, methanediol, and methoxymethanol have been conducted to guide the laboratory studies once the methanol experiment has been optimized. The results of the calculations and initial experimental results will be presented.

  3. 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.

  4. 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.

  5. Broadband optical isolator based on helical metamaterials.

    PubMed

    Cao, Hu; Yang, ZhenYu; Zhao, Ming; Wu, Lin; Zhang, Peng

    2015-05-01

    Based on helical metamaterials, a new broadband optical isolator with a triple-helix structure is proposed in this paper. The right-handed circularly polarized light can transmit through the isolator with its polarization unchanged. The reverse propagating light, which is caused by the reflection of the latter optical devices, is converted into left-handed circularly polarized light that is suppressed by the proposed isolator because of absorption. Our design has some unprecedented advantages such as broad frequency ranges and a compact structure; moreover, neither polarizers nor adscititious magnetic fields are required. Properties of the isolator are investigated using the finite-difference time-domain method, and this phenomenon is studied by the mechanism of helical antenna theory.

  6. Instabilities of a rotating helical rod

    NASA Astrophysics Data System (ADS)

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

    2016-11-01

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

  7. Spheromak Formation by Steady Inductive Helicity Injection

    SciTech Connect

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

    2006-09-15

    A spheromak is formed for the first time using a new steady state inductive helicity injection method. Using two inductive injectors with odd symmetry and oscillating at 5.8 kHz, a steady state spheromak with even symmetry is formed and sustained through nonlinear relaxation. A spheromak with about 13 kA of toroidal current is formed and sustained using about 3 MW of power. This is a much lower power threshold for spheromak production than required for electrode-based helicity injection. Internal magnetic probe data, including oscillations driven by the injectors, agree with the plasma being in the Taylor state. The agreement is remarkable considering the only fitting parameter is the amplitude of the spheromak component of the state.

  8. Helical propulsion in shear-thinning fluids

    NASA Astrophysics Data System (ADS)

    Gómez, Saúl; Godínez, Francisco A.; Lauga, Eric; Zenit, Roberto

    2017-02-01

    Swimming microorganisms often have to propel in complex, non-Newtonian fluids. We carry out experiments with self-propelling helical swimmers driven by an externally rotating magnetic field in shear-thinning, inelastic fluids. Similarly to swimming in a Newtonian fluid, we obtain for each fluid a locomotion speed which scales linearly with the rotation frequency of the swimmer, but with a prefactor which depends on the power index of the fluid. The fluid is seen to always increase the swimming speed of the helix, up to 50% faster and thus the strongest of such type reported to date. The maximum relative increase for a fluid power index of around 0.6. Using simple scalings, we argue that the speed increase is not due to the local decrease of the flow viscosity around the helical filament but hypothesise instead that it originates from confinement-like effect due to viscosity stratification around the swimmer.

  9. 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.

  10. SUPERCONDUCTING HELICAL SNAKE MAGNETS: CONSTRUCTION AND MEASUREMENTS.

    SciTech Connect

    MACKAY,W.W.

    1999-05-17

    In order to collide polarized protons, the RHIC project will have two snakes in each ring and four rotators around each of two interaction regions. Two snakes on opposite sides of each ring can minimize depolarization during acceleration by keeping the spin tune at a half. Since the spin direction is normally along the vertical direction in a flat ring, spin rotators must be used around an interaction point to have longitudinal polarization in a collider experiment. Each snake or rotator will be composed of four helical dipoles to provide the required rotation of spin with minimal transverse orbit excursions in a compact length of 10m. The basic helical dipole is a superconducting magnet producing a transverse dipole field which is twisted about the magnet axis through 360{degree} in a length of 2.4 m. The design and construction of the magnets is described in this paper.

  11. Patterns of helicity in solar active regions

    NASA Technical Reports Server (NTRS)

    Pevtsov, Alexei A.; Canfield, Richard C.; Metcalf, Thomas R.

    1994-01-01

    Using 46 vector magnetograms from the Stokes Polarimeter of Mees Solar Observatory (MSO), we studied patterns of local helicity in three diverse solar active regions. From these magnetograms we computed maps of the local helicity parameter alpha = J(sub z)/B(sub z). Although such maps are noisy, we found patterns at the level approximately 2 to 3 sigma(sub J(sub z)), which repeat in successive magnetograms for up to several days. Typically, the alpha maps of any given active region contain identifiable patches with both positive and negative values of alpha. Even within a single sunspot complex, several such alpha patches can often be seen. We followed 68 alpha patches that could be identified on at least two successive alpha maps. We found that the persistence fraction of such patches decrease exponentially, with a characteristic time approximately 27 hr.

  12. 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.

  13. 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.

  14. 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.

  15. Solar flares controlled by helicity conservation

    NASA Technical Reports Server (NTRS)

    Gliner, Erast B.; Osherovich, Vladimir A.

    1995-01-01

    The energy release in a class of solar flares is studied on the assumption that during burst events in highly conducting plasma the magnetic helicity of plasma is approximately conserved. The available energy release under a solar flare controlled by the helicity conservation is shown to be defined by the magnetic structure of the associated prominence. The approach throws light on some solar flare enigmas: the role of the associated prominence. The approach throws light on some solar flare enigmas: the role of the associated prominences; the discontinuation of the reconnection of magnetic lines long before the complete reconnection of participated fields occurs; the existence of quiet prominences which, in spite of their usual optical appearance, do not initiate any flare events; the small energy release under a solar flare in comparison with the stockpile of magnetic energy in surrounding fields. The predicted scale of the energy release is in a fair agreement with observations.

  16. 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.

  17. Inductance Calculations of Variable Pitch Helical Inductors

    DTIC Science & Technology

    2015-08-01

    Electromagnetic Phenomena. July 2003;3:392–396. 2. Snow C. Formulas for computing capacitance and inductance . In: National bu- reau of standards circular 544...ARL-TR-7380 ● AUG 2015 US Army Research Laboratory Inductance Calculations of Variable Pitch Helical Inductors by Peter T...report when it is no longer needed. Do not return it to the originator. ARL-TR-7380 ● AUG 2015 US Army Research Laboratory Inductance

  18. 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.

  19. 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.

  20. 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

  1. Amyloid-like hierarchical helical fibrils and conformational reversibility in functional polyesters based on L-amino acids.

    PubMed

    Anantharaj, Santhanaraj; Jayakannan, Manickam

    2015-03-09

    The present investigation reports one of the first examples of synthetic polymers that capable of undergoing reversible conformation transformation and also self-assembled to hierarchical helical amyloid-like fibrils. A new temperature selective melt polycondensation reaction was developed for amino acid monomers L-aspartic acid and L-glutamic acid to produce high molecular weight linear functional polyesters. These new polyesters have hydrogen bonded urethane (or carbamate) units that are in-built in each repeating unit. The polymer chains have adapted expanded chain conformation through β-sheet hydrogen bonding interactions and produced twisted ribbon-like assemblies. These twisted ribbons have subsequently undergone interchain folding for making double helical structures. The double helical fibrils aligned together to produce amyloid-like fibrils of few micrometer in length. Upon chemical deprotection of the pendent urethane units; the resultant cationic functional polyester adapted coil-like conformation and exhibited spherical charged nanoparticles of 200 ± 20 nm in size. Dynamic light scattering and zeta potential measurements revealed that both the charge and size of the spherical structures could be varied by altering the diol segment length in the polymer backbone. The coil-like chains in the charged spherical particles could be reversibly expanded into amyloid-like fibrils via fluorophore chemical substitution using dansyl chloride. The dansyl-substituted polymer exhibited helical fibrils and strong fluorescence. Thus, the L-amino acid based polyesters exhibited complete reversible conformational changes from hierarchical helical amyloid-like fibrils to charged nanoparticles in a single polymer system. These new nonpeptide polyester analogues, their amyloid fibrils, cationic polymer assemblies and fluorescent fibrils are very new based on l-amino acids, which may be useful for a wide range of biomedical applications.

  2. 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

  3. Propulsion by Helical Strips in Circular Channels

    NASA Astrophysics Data System (ADS)

    Yesilyurt, Serhat; Demir, Ebru

    2016-11-01

    Progress in manufacturing techniques avails the production of artificial micro swimmers (AMS) in various shapes and sizes. There are numerous studies on the generation of efficient locomotion by means of helical tails with circular cross-sections. This work focuses on locomotion with helical strips in circular channels. A CFD model is used to analyze the effects of geometric parameters and the radius of the channel on swimming velocity of infinite helical-strips in circular channels. Results show that there is an optimum wavelength that depends on thickness to channel radius ratio, suggesting that these parameters need to be optimized simultaneously. With constant torque, thinner strips swim faster, whereas under constant angular velocity application, thicker strips (in radial direction) prevail. As width approaches the wavelength, velocity decreases under both conditions, unless a magnetically coated tail is simulated, for which width has an optimum value. Increasing channel radius to helix amplitude ratio increases the velocity up to a maximum and after a slight drop, saturation occurs as bulk swimming conditions are approached.

  4. Mechanical resonances of helically coiled carbon nanowires.

    PubMed

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

    2014-07-02

    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.

  5. 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.

  6. 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)

  7. Double tube helical coil steam generator

    SciTech Connect

    Garabedian, G.; De Luca, R.A.

    1987-02-24

    A steam generator is described comprising a container having a closed lower end, divided into longitudinally arranged sections including an uppermost disengaging chamber, an upper plenum, and a lower plenum. The upper plenum is above the lower plenum and contains a multiplicity of double tube helical coils, wherein each of the double tube helical coils is comprised of an inner tube individually enclosed for at least a portion of its length by an outer tube to form a double tube portion and thereby define an annular gap which is outside the inner tube but enclosed by the outer tube; the inner tube being attached at one end to a feedwater inlet, and the inner tube being attached at the other end to a steam outlet; the outer tube being in open communication at both ends with the disengaging chamber; the double tube portion being in the configuration of a helix for part of its length; the upper plenum having no communication with the disengaging chamber and having restricted communication with the lower plenum such that liquid metal entering the upper plenum and flowing to the lower plenum closely contacts at least a portion of the double tube helical coils; and the annular gap being at least partially filled with liquid metal.

  8. 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.

  9. The infrared dichroism of transmembrane helical polypeptides.

    PubMed Central

    Axelsen, P H; Kaufman, B K; McElhaney, R N; Lewis, R N

    1995-01-01

    Polarized attenuated total internal reflectance techniques were applied to study the infrared dichroism of the amide I transition moment in two membrane-bound peptides that are known to form oriented transmembrane helices: gramicidin A in a supported phospholipid monolayer and Ac-Lys2-Leu24-Lys2-amide (L24) in oriented multibilayers. These studies were performed to test the ability of these techniques to determine the orientation of these peptides, to verify the value of optical parameters used to calculate electric field strengths, to examine the common assumptions regarding the amide I transition moment orientation, and to ascertain the effect of surface imperfections on molecular disorder. The two peptides exhibit marked differences in the shape and frequency of their amide I absorption bands. Yet both peptides are highly ordered and oriented with their helical axes perpendicular to the membrane surface. In the alpha-helix formed by L24, there is evidence for a mode with type E1 symmetry contributing to amide I, and the amide I transition moment must be more closely aligned with the peptide C=O (< 34 degrees) than earlier studies have suggested. These results indicate that long-standing assumptions about the orientation of amide I in a peptide require some revision, but that in general, infrared spectroscopy yields reliable information about the orientation of membrane-bound helical peptides. Images FIGURE 1 PMID:8599683

  10. 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.

  11. Internal packing of helical membrane proteins

    PubMed Central

    Eilers, Markus; Shekar, Srinivasan C.; Shieh, Ted; Smith, Steven O.; Fleming, Patrick J.

    2000-01-01

    Helix packing is important in the folding, stability, and association of membrane proteins. Packing analysis of the helical portions of 7 integral membrane proteins and 37 soluble proteins show that the helices in membrane proteins have higher packing values (0.431) than in soluble proteins (0.405). The highest packing values in integral membrane proteins originate from small hydrophobic (G and A) and small hydroxyl-containing (S and T) amino acids, whereas in soluble proteins large hydrophobic and aromatic residues have the highest packing values. The highest packing values for membrane proteins are found in the transmembrane helix–helix interfaces. Glycine and alanine have the highest occurrence among the buried amino acids in membrane proteins, whereas leucine and alanine are the most common buried residue in soluble proteins. These observations are consistent with a shorter axial separation between helices in membrane proteins. The tight helix packing revealed in this analysis contributes to membrane protein stability and likely compensates for the lack of the hydrophobic effect as a driving force for helix–helix association in membranes. PMID:10823938

  12. 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.

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

    NASA Astrophysics Data System (ADS)

    Koch Ocker, Stella; Petrie, Gordon

    2016-12-01

    The hemispheric preference for negative/positive helicity to occur in the northern/southern solar hemisphere provides clues to the causes of twisted, flaring magnetic fields. Previous studies on the hemisphere rule may have been affected by seeing from atmospheric turbulence. Using Hinode/SOT-SP data spanning 2006-2013, we studied the effects of two spatial smoothing tests that imitate atmospheric seeing: noise reduction by ignoring pixel values weaker than the estimated noise threshold, and Gaussian spatial smoothing. We studied in detail the effects of atmospheric seeing on the helicity distributions across various field strengths for active regions (ARs) NOAA 11158 and NOAA 11243, in addition to studying the average helicities of 179 ARs with and without smoothing. We found that, rather than changing trends in the helicity distributions, spatial smoothing modified existing trends by reducing random noise and by regressing outliers toward the mean, or removing them altogether. Furthermore, the average helicity parameter values of the 179 ARs did not conform to the hemisphere rule: independent of smoothing, the weak-vertical-field values tended to be negative in both hemispheres, and the strong-vertical-field values tended to be positive, especially in the south. We conclude that spatial smoothing does not significantly affect the overall statistics for space-based data, and thus seeing from atmospheric turbulence seems not to have significantly affected previous studies’ ground-based results on the hemisphere rule.

  14. Development of helix-stabilized cell-penetrating peptides containing cationic α,α-disubstituted amino acids as helical promoters.

    PubMed

    Yamashita, Hiroko; Misawa, Takashi; Oba, Makoto; Tanaka, Masakazu; Naito, Mikihiko; Kurihara, Masaaki; Demizu, Yosuke

    2017-03-15

    Cell-penetrating peptides (CPP) have attracted many scientists' attention as intracellular delivery tools due to their high cargo molecule transportation efficiency and low cytotoxicity. Therefore, in many research fields CPP, such as HIV-Tat and oligoarginine (Rn), are used to deliver hydrophilic drugs and biomolecules, including proteins, DNA, and RNA. We designed four types of CPP that contained cationic α,α-disubstituted amino acids (Api(C2Gu) and Api(C4Gu)) as helical promoters; i.e., 1-4 [FAM-β-Ala-(l-Arg-l-Arg-Xaa)3-(Gly)3-NH2 (1: Xaa=Api(C2Gu), 2: Xaa=Api(C4Gu)), 3: FAM-β-Ala-(l-Arg)8-Api(C2Gu)-(Gly)3-NH2, and 4: FAM-β-Ala-(l-Arg)5-Api(C2Gu)-(l-Arg)2-Api(C2Gu)-(Gly)3-NH2], and investigated their preferred secondary structures and cell membrane-penetrating ability. As a result, we found that the permeation efficiency of the CPP was affected by the number of helical promoters in their sequences. Specially, peptide 1, which contained three Api(C2Gu) residues, formed a stable helical structure and passed through the cell membrane more efficiently than the other peptides. Moreover, it was demonstrated that the spatial arrangement of the peptides' side chains also influenced their permeability and the helical stabilization of their main chains.

  15. Natural Outbreak of BVDV-1d-Induced Mucosal Disease Lacking Intestinal Lesions.

    PubMed

    Bianchi, M V; Konradt, G; de Souza, S O; Bassuino, D M; Silveira, S; Mósena, A C S; Canal, C W; Pavarini, S P; Driemeier, D

    2017-03-01

    Bovine viral diarrhea virus (BVDV) belongs to the Pestivirus genus, which is further divided into subgenotypes (1a-1u and 2a-c). When persistent infection occurs, the calf will be immunotolerant to BVDV and possibly develop mucosal disease. This study describes an outbreak of BVDV-1d-induced mucosal disease lacking intestinal lesions. Eleven calves presented with anorexia, sialorrhea, lameness, recumbency, and death. Three calves were necropsied, showing ulceration of the interdigital skin and the oral and nasal mucosa; linear ulcers in the tongue, esophagus, and rumen; and rounded ulcers in the abomasum. Microscopically, mucosa and skin had superficial necrosis, with single-cell necrosis and vacuolation in epithelial cells, and severe parakeratosis. Immunohistochemistry (IHC) showed BVDV antigen in the cytoplasm of epithelial cells in skin and mucosa. All 11 dead calves were positive upon reverse transcription-polymerase chain reaction (RT-PCR) for the detection of Pestivirus along with another 11 live calves from the herd, which were positive again by RT-PCR and IHC after a 4-week interval. Sequencing of the 5' untranslated region and N-terminal protease showed that viruses from these 22 calves were homologous and of subgenotype BVDV-1d. Cytopathic BVDV was isolated from 8 of 11 dead calves, but only noncytopathic BVDV was isolated from the 11 live animals. The findings indicate that this was an outbreak of mucosal disease caused by BVDV-1d, with high morbidity, and lesions restricted to the upper alimentary system and skin and absent from intestine. Thus, the epidemiological and pathological features in this form of mucosal disease may be similar to vesicular diseases, including foot and mouth disease.

  16. 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.

  17. 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.

  18. 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.

  19. 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).

  20. 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

  1. Locomotion of Helical Bodies in Viscoelastic Fluids: Enhanced Swimming at Large Helical Amplitudes

    NASA Astrophysics Data System (ADS)

    Spagnolie, Saverio E.; Liu, Bin; Powers, Thomas R.

    2013-08-01

    The motion of a rotating helical body in a viscoelastic fluid is considered. In the case of force-free swimming, the introduction of viscoelasticity can either enhance or retard the swimming speed and locomotive efficiency, depending on the body geometry, fluid properties, and the body rotation rate. Numerical solutions of the Oldroyd-B equations show how previous theoretical predictions break down with increasing helical radius or with decreasing filament thickness. Helices of large pitch angle show an increase in swimming speed to a local maximum at a Deborah number of order unity. The numerical results show how the small-amplitude theoretical calculations connect smoothly to the large-amplitude experimental measurements.

  2. 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

  3. ESO science data product standard for 1D spectral products

    NASA Astrophysics Data System (ADS)

    Micol, Alberto; Arnaboldi, Magda; Delmotte, Nausicaa A. R.; Mascetti, Laura; Retzlaff, Joerg

    2016-07-01

    The ESO Phase 3 process allows the upload, validation, storage, and publication of reduced data through the ESO Science Archive Facility. Since its introduction, 2 million data products have been archived and published; 80% of them are one-dimensional extracted and calibrated spectra. Central to Phase3 is the ESO science data product standard that defines metadata and data format of any product. This contribution describes the ESO data standard for 1d-spectra, its adoption by the reduction pipelines of selected instrument modes for in-house generation of reduced spectra, the enhanced archive legacy value. Archive usage statistics are provided.

  4. 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.

  5. Breakdown of 1D water wires inside charged carbon nanotubes

    NASA Astrophysics Data System (ADS)

    Pant, Shashank

    2016-11-01

    Using molecular dynamics approach we investigated the structure and dynamics of water confined inside pristine and charged 6,6 carbon nanotubes (CNTs). This study reports the breakdown of 1D water wires and the emergence of triangular faced water on incorporating charges in 6,6 CNTs. Incorporation of charges results in high potential barriers to flipping of water molecules due to the formation of large number of hydrogen bonds. The PMF analyses show the presence of ∼2 kcal/mol barrier for the movement of water inside pristine CNT and almost negligible barrier in charged CNTs.

  6. Spatial coherence of polaritons in a 1D channel

    SciTech Connect

    Savenko, I. G.; Iorsh, I. V.; Kaliteevski, M. A.; Shelykh, I. A.

    2013-01-15

    We analyze time evolution of spatial coherence of a polariton ensemble in a quantum wire (1D channel) under constant uniform resonant pumping. Using the theoretical approach based on the Lindblad equation for a one-particle density matrix, which takes into account the polariton-phonon and excitonexciton interactions, we study the behavior of the first-order coherence function g{sup 1} for various pump intensities and temperatures in the range of 1-20 K. Bistability and hysteresis in the dependence of the first-order coherence function on the pump intensity is demonstrated.

  7. Nanofluidic sustainable energy conversion using a 1D nanofluidic network.

    PubMed

    Kim, Sang Hui; Kwak, Seungmin; Han, Sung Il; Chun, Dong Won; Lee, Kyu Hyoung; Kim, Jinseok; Lee, Jeong Hoon

    2014-05-01

    We propose a 1-dimensional (1D) nanofluidic energy conversion device by implementing a surface-patterned Nafion membrane for the direct energy conversion of the pressure to electrical power. By implementing a -200-nm-thick nano-bridge with a 5-nm pore size between two microfluidic channels, we acquired an effective streaming potential of 307 mV and output power of 94 pW with 0.1 mM KCI under pressure difference of 45 MPa. The experimental results show both the effects of applied pressure differences and buffer concentrations on the effective streaming potential, and are consistent with the analytical prediction.

  8. 1-D blood flow modelling in a running human body.

    PubMed

    Szabó, Viktor; Halász, Gábor

    2017-04-10

    In this paper an attempt was made to simulate blood flow in a mobile human arterial network, specifically, in a running human subject. In order to simulate the effect of motion, a previously published immobile 1-D model was modified by including an inertial force term into the momentum equation. To calculate inertial force, gait analysis was performed at different levels of speed. Our results show that motion has a significant effect on the amplitudes of the blood pressure and flow rate but the average values are not effected significantly.

  9. Selective DNA Recognition and Cytotoxicity of Water-Soluble Helical Metallosupramolecular Polymers.

    PubMed

    Rana, Utpal; Chakraborty, Chanchal; Pandey, Rakesh K; Hossain, Md Delwar; Nagano, Reiko; Morita, Hiromi; Hattori, Shinya; Minowa, Takashi; Higuchi, Masayoshi

    2016-10-19

    Water-soluble helical Fe(II)-based metallosupramolecular polymers ((P)- and (M)-polyFe) were synthesized by 1:1 complexation of Fe(II) ions and bis(terpyridine)s bearing a (R)- and (S)-BINOL spacer, respectively. The binding affinity to calf thymus DNA (ct-DNA) was investigated by titration measurements. (P)-PolyFe with the same helicity as B-DNA showed 40-fold higher binding activity (Kb = 13.08 × 10(7) M(-1)) to ct-DNA than (M)-polyFe. The differences in binding affinity were supported by electrochemical impedance spectroscopy analysis. The charge-transfer resistance (Rct) of (P)-polyFe increased from 2.5 to 3.9 kΩ upon DNA binding, while that of (M)-polyFe was nearly unchanged. These results indicate that ionically strong binding of (P)-polyFe to DNA chains decreased the mobility of ions in the conjugate. Unique rod-like images were obtained by atomic force microscopy measurement of the DNA conjugate with (P)-polyFe, likely because of the rigid binding between DNA chains and the polymer. Differences in polymer chirality lead to significantly different cytotoxicity levels in A549 cells. (P)-PolyFe showed higher binding affinity to B-DNA and much higher cytotoxicity than (M)-polyFe. The helicity in metallosupramolecular polymer chains was important not only for chiral recognition of DNA but also for coordination to a biological target in the cellular environment.

  10. Chain Sampling

    DTIC Science & Technology

    1972-08-01

    35609 Advanced Techniques Branch Plans and Programs Analysis Division Directorate for Product Assurance U. S. Army Missile Command Redstone Arsenal...Ray Heathcock Advanced Techniques Branch Plans and Programs Analysis Division Directorate for Product Assurance U. S. Army Missile Command...for Product Assurance has established a rather unique computer program for handling a variety of chain sampling schemes and is available for

  11. 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

    2015-03-05

    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.

  12. Density of states of helically symmetric boron carbon nitride nanotubes.

    PubMed

    Carvalho, A C M; Bezerra, C G; Lawlor, J A; Ferreira, M S

    2014-01-08

    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.

  13. Alpha Helices Are More Robust to Mutations than Beta Strands

    PubMed Central

    Abrusán, György

    2016-01-01

    The rapidly increasing amount of data on human genetic variation has resulted in a growing demand to identify pathogenic mutations computationally, as their experimental validation is currently beyond reach. Here we show that alpha helices and beta strands differ significantly in their ability to tolerate mutations: helices can accumulate more mutations than strands without change, due to the higher numbers of inter-residue contacts in helices. This results in two patterns: a) the same number of mutations causes less structural change in helices than in strands; b) helices diverge more rapidly in sequence than strands within the same domains. Additionally, both helices and strands are significantly more robust than coils. Based on this observation we show that human missense mutations that change secondary structure are more likely to be pathogenic than those that do not. Moreover, inclusion of predicted secondary structure changes shows significant utility for improving upon state-of-the-art pathogenicity predictions. PMID:27935949

  14. 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).

  15. 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.

  16. Blood flow quantification using 1D CFD parameter identification

    NASA Astrophysics Data System (ADS)

    Brosig, Richard; Kowarschik, Markus; Maday, Peter; Katouzian, Amin; Demirci, Stefanie; Navab, Nassir

    2014-03-01

    Patient-specific measurements of cerebral blood flow provide valuable diagnostic information concerning cerebrovascular diseases rather than visually driven qualitative evaluation. In this paper, we present a quantitative method to estimate blood flow parameters with high temporal resolution from digital subtraction angiography (DSA) image sequences. Using a 3D DSA dataset and a 2D+t DSA sequence, the proposed algorithm employs a 1D Computational Fluid Dynamics (CFD) model for estimation of time-dependent flow values along a cerebral vessel, combined with an additional Advection Diffusion Equation (ADE) for contrast agent propagation. The CFD system, followed by the ADE, is solved with a finite volume approximation, which ensures the conservation of mass. Instead of defining a new imaging protocol to obtain relevant data, our cost function optimizes the bolus arrival time (BAT) of the contrast agent in 2D+t DSA sequences. The visual determination of BAT is common clinical practice and can be easily derived from and be compared to values, generated by a 1D-CFD simulation. Using this strategy, we ensure that our proposed method fits best to clinical practice and does not require any changes to the medical work flow. Synthetic experiments show that the recovered flow estimates match the ground truth values with less than 12% error in the mean flow rates.

  17. Tunability and Sensing Properties of Plasmonic/1D Photonic Crystal

    NASA Astrophysics Data System (ADS)

    Shaban, Mohamed; Ahmed, Ashour M.; Abdel-Rahman, Ehab; Hamdy, Hany

    2017-02-01

    Gold/one-dimensional photonic crystal (Au/1D-PC) is fabricated and applied for sensitive sensing of glucose and different chemical molecules of various refractive indices. The Au layer thickness is optimized to produce surface plasmon resonance (SPR) at the right edge of the photonic band gap (PBG). As the Au deposition time increased to 60 sec, the PBG width is increased from 46 to 86 nm in correlation with the behavior of the SPR. The selectivity of the optimized Au/1D-PC sensor is tested upon the increase of the environmental refractive index of the detected molecules. The resonance wavelength and the PBG edges increased linearly and the transmitted intensity increased nonlinearly as the environment refractive index increased. The SPR splits to two modes during the detection of chloroform molecules based on the localized capacitive coupling of Au particles. Also, this structure shows high sensitivity at different glucose concentrations. The PBG and SPR are shifted to longer wavelengths, and PBG width is decreased linearly with a rate of 16.04 Å/(μg/mm3) as the glucose concentration increased. The proposed structure merits; operation at room temperature, compact size, and easy fabrication; suggest that the proposed structure can be efficiently used for the biomedical and chemical application.

  18. Tunability and Sensing Properties of Plasmonic/1D Photonic Crystal

    PubMed Central

    Shaban, Mohamed; Ahmed, Ashour M.; Abdel-Rahman, Ehab; Hamdy, Hany

    2017-01-01

    Gold/one-dimensional photonic crystal (Au/1D-PC) is fabricated and applied for sensitive sensing of glucose and different chemical molecules of various refractive indices. The Au layer thickness is optimized to produce surface plasmon resonance (SPR) at the right edge of the photonic band gap (PBG). As the Au deposition time increased to 60 sec, the PBG width is increased from 46 to 86 nm in correlation with the behavior of the SPR. The selectivity of the optimized Au/1D-PC sensor is tested upon the increase of the environmental refractive index of the detected molecules. The resonance wavelength and the PBG edges increased linearly and the transmitted intensity increased nonlinearly as the environment refractive index increased. The SPR splits to two modes during the detection of chloroform molecules based on the localized capacitive coupling of Au particles. Also, this structure shows high sensitivity at different glucose concentrations. The PBG and SPR are shifted to longer wavelengths, and PBG width is decreased linearly with a rate of 16.04 Å/(μg/mm3) as the glucose concentration increased. The proposed structure merits; operation at room temperature, compact size, and easy fabrication; suggest that the proposed structure can be efficiently used for the biomedical and chemical application. PMID:28176799

  19. 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.

  20. Constitutive modeling and control of 1D smart composite structures

    NASA Astrophysics Data System (ADS)

    Briggs, Jonathan P.; Ostrowski, James P.; Ponte-Castaneda, Pedro

    1998-07-01

    Homogenization techniques for determining effective properties of composite materials may provide advantages for control of stiffness and strain in systems using hysteretic smart actuators embedded in a soft matrix. In this paper, a homogenized model of a 1D composite structure comprised of shape memory alloys and a rubber-like matrix is presented. With proportional and proportional/integral feedback, using current as the input state and global strain as an error state, implementation scenarios include the use of tractions on the boundaries and a nonlinear constitutive law for the matrix. The result is a simple model which captures the nonlinear behavior of the smart composite material system and is amenable to experiments with various control paradigms. The success of this approach in the context of the 1D model suggests that the homogenization method may prove useful in investigating control of more general smart structures. Applications of such materials could include active rehabilitation aids, e.g. wrist braces, as well as swimming/undulating robots, or adaptive molds for manufacturing processes.

  1. Tunability and Sensing Properties of Plasmonic/1D Photonic Crystal.

    PubMed

    Shaban, Mohamed; Ahmed, Ashour M; Abdel-Rahman, Ehab; Hamdy, Hany

    2017-02-08

    Gold/one-dimensional photonic crystal (Au/1D-PC) is fabricated and applied for sensitive sensing of glucose and different chemical molecules of various refractive indices. The Au layer thickness is optimized to produce surface plasmon resonance (SPR) at the right edge of the photonic band gap (PBG). As the Au deposition time increased to 60 sec, the PBG width is increased from 46 to 86 nm in correlation with the behavior of the SPR. The selectivity of the optimized Au/1D-PC sensor is tested upon the increase of the environmental refractive index of the detected molecules. The resonance wavelength and the PBG edges increased linearly and the transmitted intensity increased nonlinearly as the environment refractive index increased. The SPR splits to two modes during the detection of chloroform molecules based on the localized capacitive coupling of Au particles. Also, this structure shows high sensitivity at different glucose concentrations. The PBG and SPR are shifted to longer wavelengths, and PBG width is decreased linearly with a rate of 16.04 Å/(μg/mm(3)) as the glucose concentration increased. The proposed structure merits; operation at room temperature, compact size, and easy fabrication; suggest that the proposed structure can be efficiently used for the biomedical and chemical application.

  2. Observation of the helical structure of the bacterial polysaccharide acetan by atomic force microscopy.

    PubMed Central

    Kirby, A R; Gunning, A P; Morris, V J; Ridout, M J

    1995-01-01

    A method has been developed that has been found to give reproducible images of uncoated polysaccharides by Atomic Force Microscopy (AFM). Aqueous solutions of the polysaccharide are deposited as drops onto freshly cleaved mica surfaces, air dried, and then imaged under butanol. The method has been used to obtain images of the bacterial polysaccharide acetan. In regions within the deposited sample, where the molecules are aligned side-by-side, it has been possible to observe a periodic structure along the polysaccharide chain, attributable to the helical structure of acetan. Images FIGURE 1 FIGURE 3 FIGURE 4 PMID:7711262

  3. Decay of magnetic helicity producing polarized Alfven waves

    SciTech Connect

    Yoshida, Z.; Mahajan, S.M.

    1994-02-01

    When a super-Alfvenic electron beam propagates along an ambient magnetic field, the left-hand circularly polarized Alfven wave is Cherenkov-emitted (two stream instability). This instability results in a spontaneous conversion of the background plasma helicity to the wave helicity. The background helicity induces a frequency (energy) shift in the eigenmodes, which changes the critical velocity for Cherenkov emission, and it becomes possible for a sub-Alfvenic electron beam to excite a nonsingular Alfven mode.

  4. Swimming and pumping of helical structures in viscous fluids

    NASA Astrophysics Data System (ADS)

    Li, Lei; Spagnolie, Saverio

    2014-11-01

    Many flagellated microorganisms including E. coli swim by rotating slender helical flagella, while ciliated organisms like Paramecia swim by passing helical waves along their surfaces. We will discuss a framework for studying such problems where the Stokes equations describing viscous flow are written in helical coordinates. Analytical predictions match well with full numerical simulations, and suggest optimal geometries. This work may also aid designs in microfluidic manipulation, microswimmer engineering, and the mixing of viscous fluids.

  5. Helicity Injection by Knotted Antennas into Electron Magnetohydrodynamical Plasmas

    NASA Astrophysics Data System (ADS)

    Rousculp, C. L.; Stenzel, R. L.

    1997-08-01

    A fully three-dimensional computer simulation of an ideal electron magnetohydrodynamical plasma is performed. By introducing various pulsed inductive antenna sources, magnetic helicity ( H = A˙B dV) injection is studied. Confirming experimental results, a simple loop provides no net helicity injection. Linked and knotted antennas, however, do inject helicity and preferentially radiate whistler wave packets parallel or antiparallel to the ambient magnetic field. Relative efficiencies of these antennas are reported as well as their unique directional properties.

  6. Bidirectional uncoating of the genomic RNA of a helical virus.

    PubMed Central

    Wu, X; Shaw, J

    1996-01-01

    An essential step in the initiation of a virus infection is the release of the viral genome from the other constituents of the virus particle, a process referred to as uncoating. We have used reverse transcription and polymerase chain reaction amplification procedures to determine the rate and direction of in vivo uncoating of the rod-shaped tobacco mosaic virus. The virus particles contain a single 6.4-kb RNA molecule that lies between successive turns of a helical arrangement of coat protein subunits. When the particles are introduced into plant cells, the subunits are removed via a bidirectional uncoating mechanism. Within 2-3 min, the part of the viral RNA from the 5' end to a position >70% toward the 3' end has been freed of coat protein subunits. This is followed by removal of subunits from the 3' end of the RNA and sequential uncoating of the RNA in a 3'-to-5' direction. An internal region of the viral RNA is the final part to be uncoated. Progeny virus particles are detected in the cells 35-40 min after inoculation. Images Fig. 1 Fig. 2 Fig. 3 Fig. 4 Fig. 5 PMID:8610154

  7. Insertion of short transmembrane helices by the Sec61 translocon.

    PubMed

    Jaud, Simon; Fernández-Vidal, Mónica; Nilsson, Ingmarie; Meindl-Beinker, Nadja M; Hübner, Nadja C; Tobias, Douglas J; von Heijne, Gunnar; White, Stephen H

    2009-07-14

    The insertion efficiency of transmembrane (TM) helices by the Sec61 translocon depends on helix amino acid composition, the positions of the amino acids within the helix, and helix length. We have used an in vitro expression system to examine systematically the insertion efficiency of short polyleucine segments (L(n), n = 4 ... 12) flanked at either end by 4-residue sequences of the form XXPX-L(n)-XPXX with X = G, N, D, or K. Except for X = K, insertion efficiency (p) is <10% for n < 8, but rises steeply to 100% for n = 12. For X = K, p is already close to 100% for n = 10. A similar pattern is observed for synthetic peptides incorporated into oriented phospholipid bilayer arrays, consistent with the idea that recognition of TM segments by the translocon critically involves physical partitioning of nascent peptide chains into the lipid bilayer. Molecular dynamics simulations suggest that insertion efficiency is determined primarily by the energetic cost of distorting the bilayer in the vicinity of the TM helix. Very short lysine-flanked leucine segments can reduce the energetic cost by extensive hydrogen bonding with water and lipid phosphate groups (snorkeling) and by partial unfolding.

  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. 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.

  10. 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

  11. Active region helicity evolution and related coronal mass ejection activity.

    NASA Astrophysics Data System (ADS)

    Green, L.; Mandrini, C.; van Driel-Gesztelyi, L.; Demoulin, P.

    The computation of magnetic helicity has become increasingly important in the studies of solar activity. Observations of helical structures in the solar atmosphere, and their subsequent ejection into the interplanetary medium, have resulted in considerable interest to find the link between the amount of helicity in the coronal magnetic field and the origin of coronal mass ejections (CMEs). This is reinforced by theory which shows magnetic helicity to be a well preserved quantity (Berger, 1984), and so with a continued injection into the corona an endless accumulation will occur. CMEs therefore provide a natural method to remove helicity from the corona. Recent works (DeVore, 2000, Chae, 2001, Chae et al., 2001, Demoulin et al., 2002, Green et al., 2002) have endeavoured to find the source of helicity in the corona to explain the observed CME activity in specific cases. The main candidates being differential rotation, shear motions or a transfer of helicity from below the photosphere into the corona. In order to establish a confident relation between CMEs and helicity, these works needs to be expanded to include CME source regions with different characteristics. A study of a very different active region will be presented and the relationship between helicity content and CME activity will be discussed in the framework of the previous studies.

  12. The Writhe of Helical Structures in the Solar Corona

    DTIC Science & Technology

    2010-04-23

    2010 The writhe of helical structures in the solar corona T. Török1,2, M. A. Berger2,3, and B. Kliem2,4,5 1 LESIA, Observatoire de Paris, CNRS, UPMC...2009; accepted ... ABSTRACT 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

  13. Superposition of helical beams by using a Michelson interferometer.

    PubMed

    Gao, Chunqing; Qi, Xiaoqing; Liu, Yidong; Weber, Horst

    2010-01-04

    Orbital angular momentum (OAM) of a helical beam is of great interests in the high density optical communication due to its infinite number of eigen-states. In this paper, an experimental setup is realized to the information encoding and decoding on the OAM eigen-states. A hologram designed by the iterative method is used to generate the helical beams, and a Michelson interferometer with two Porro prisms is used for the superposition of two helical beams. The experimental results of the collinear superposition of helical beams and their OAM eigen-states detection are presented.

  14. 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.

  15. Large-scale flow generation by inhomogeneous helicity.

    PubMed

    Yokoi, N; Brandenburg, A

    2016-03-01

    The effect of kinetic helicity (velocity-vorticity correlation) on turbulent momentum transport is investigated. The turbulent kinetic helicity (pseudoscalar) enters the Reynolds stress (mirror-symmetric tensor) expression in the form of a helicity gradient as the coupling coefficient for the mean vorticity and/or the angular velocity (axial vector), which suggests the possibility of mean-flow generation in the presence of inhomogeneous helicity. This inhomogeneous helicity effect, which was previously confirmed at the level of a turbulence- or closure-model simulation, is examined with the aid of direct numerical simulations of rotating turbulence with nonuniform helicity sustained by an external forcing. The numerical simulations show that the spatial distribution of the Reynolds stress is in agreement with the helicity-related term coupled with the angular velocity, and that a large-scale flow is generated in the direction of angular velocity. Such a large-scale flow is not induced in the case of homogeneous turbulent helicity. This result confirms the validity of the inhomogeneous helicity effect in large-scale flow generation and suggests that a vortex dynamo is possible even in incompressible turbulence where there is no baroclinicity effect.

  16. Energy and helicity injection in solar quiet regions

    NASA Astrophysics Data System (ADS)

    Tziotziou, K.; Park, S.-H.; Tsiropoula, G.; Kontogiannis, I.

    2015-09-01

    Aims: We investigate the free magnetic energy and relative magnetic helicity injection in solar quiet regions. Methods: We use the DAVE4VM method to infer the photospheric velocity field and calculate the free magnetic energy and relative magnetic helicity injection rates in 16 quiet-Sun vector magnetograms sequences. Results: We find that there is no dominant sense of helicity injection in quiet-Sun regions, and that both helicity and energy injections are mostly due to surface shuffling motions that dominate the respective emergence by factors slightly larger than two. We, furthermore, estimate the helicity and energy rates per network unit area as well as the respective budgets over a complete solar cycle. Conclusions: Derived helicity and energy budgets over the entire solar cycle are similar to respective budgets derived in a recent work from the instantaneous helicity and free magnetic energy budgets and higher than previously reported values that relied on similar approaches to this analysis. Free-energy budgets, mostly generated like helicity at the network, are high enough to power the dynamics of fine-scale structures residing at the network, such as mottles and spicules, while corresponding estimates of helicity budgets are provided, pending future verification from high-resolution magneto-hydrodynamic simulations and/or observations.

  17. 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

  18. Helical Poly(5-alkyl-2,3-thiophene)s: Controlled Synthesis and Structure Characterization

    SciTech Connect

    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 pyrolytic 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

  19. Helical Poly(5-alkyl-2,3-thiophene)s: Controlled Synthesis and Structure Characterization

    DOE PAGES

    Zhang, Hong-Hai; Ma, Chuanxu; Bonnesen, Peter V.; ...

    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. 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.

  1. Study of Zγ Helicity Distributions at CMS

    NASA Astrophysics Data System (ADS)

    Chakaberia, Irakli; CMS Collaboration

    2011-04-01

    Measurement of the production of electroweak gauge bosons (γ, W, Z) provides important tests of the standard model. The production of a diboson final state at the Large Hadron Collider (LHC) can occur by quark-antiquark annihilation (t-channel) or by boson self-interaction (s-channel). The s-channel production provides a unique probe of triple gauge boson couplings (TGC) and the effects of new physics on these couplings. I present a study of the helicity angle distributions in the Zγ production process at the CMS experiment at the CERN LHC and an examination of the sensitivity of these distributions to new physics.

  2. Helical Disruptions in Small Loops of DNA

    NASA Astrophysics Data System (ADS)

    Zoli, Marco

    2015-01-01

    The thermodynamical stability of DNA minicircles is investigated by means of path integral techniques. Hydrogen bonds between base pairs on complementary strands can be broken by thermal fluctuations and temporary fluctuational openings along the double helix are essential to biological functions such as transcription and replication of the genetic information. Helix unwinding and bubble formation patterns are computed in circular sequences with variable radius in order to analyze the interplay between molecule size and appearance of helical disruptions. The latter are found in minicircles with < 100 base pairs and appear as a strategy to soften the stress due to the bending and torsion of the helix.

  3. Landau theory for helical nematic phases

    NASA Astrophysics Data System (ADS)

    Kats, E. I.; Lebedev, V. V.

    2014-09-01

    We propose Landau phenomenology for the phase transition from the conventional nematic into the conical helical orientationally non-uniform structure recently identified in liquid crystals formed by "banana"-shaped molecules. The mean field predictions are mostly in agreement with experimental data. Based on the analogy with de Gennes model, we argue that fluctuations of the order parameter turn the transition to the first order phase transition rather than continuous one predicted by the mean-field theory. This conclusion is in agreement with experimental observations. We discuss the new Goldstone mode to be observed in the low-temperature phase.

  4. The Extended Family of CD1d-Restricted NKT Cells: Sifting through a Mixed Bag of TCRs, Antigens, and Functions

    PubMed Central

    Macho-Fernandez, Elodie; Brigl, Manfred

    2015-01-01

    Natural killer T (NKT) cells comprise a family of specialized T cells that recognize lipid antigens presented by CD1d. Based on their T cell receptor (TCR) usage and antigen specificities, CD1d-restricted NKT cells have been divided into two main subsets: type I NKT cells that use a canonical invariant TCR α-chain and recognize α-galactosylceramide (α-GalCer), and type II NKT cells that use a more diverse αβ TCR repertoire and do not recognize α-GalCer. In addition, α-GalCer-reactive NKT cells that use non-canonical αβ TCRs and CD1d-restricted T cells that use γδ or δ/αβ TCRs have recently been identified, revealing further diversity among CD1d-restricted T cells. Importantly, in addition to their distinct antigen specificities, functional differences are beginning to emerge between the different members of the CD1d-restricted T cell family. In this review, while using type I NKT cells as comparison, we will focus on type II NKT cells and the other non-invariant CD1d-restricted T cell subsets, and discuss our current understanding of the antigens they recognize, the formation of stimulatory CD1d/antigen complexes, the modes of TCR-mediated antigen recognition, and the mechanisms and consequences of their activation that underlie their function in antimicrobial responses, anti-tumor immunity, and autoimmunity. PMID:26284062

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

    SciTech Connect

    Li, Lin; Liu, Chong-Bo; Yang, Gao-Shan; Xiong, Zhi-Qiang; Liu, Hong; Wen, Hui-Liang

    2015-11-15

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

  6. Chain stiffness of elastin-like polypeptides

    PubMed Central

    Fluegel, Sabine; Fischer, Karl; McDaniel, Jonathan R.; Chilkoti, Ashutosh; Schmidt, Manfred

    2010-01-01

    The hydrodynamic radii of a series of genetically engineered monodisperse elastin like polypeptides (ELP) was determined by dynamic light scattering in aqueous solution as function of molar mass. Utilizing the known theoretical expression for the hydrodynamic radius of wormlike chains, the Kuhn statistical segment length was determined to be lk = 2.1 nm, assuming that the length of the peptide repeat unit was b = 0.365 nm, a value derived for a coiled conformation of ELP. The resulting chain stiffness is significantly larger than previously reported by force-distance curve analysis (lk < 0.4 nm). The possible occurrence of superstructures, such as hairpins or helices, would reduce the contour length of the ELP, further increasing lk. Accordingly, the value lk = 2.1 nm reported here represents a lower limit of the chain stiffness for ELP. PMID:20961120

  7. 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

  8. Spiral Bevel and Circular Arc Helical Gears: Tooth Contact Analysis and the Effect of Misalignment on Circular Arc Helical Gears.

    DTIC Science & Technology

    1985-01-01

    AD-AI59 738 SPIRAL BEVEL AND CIRCULAR ARC HELICAL BEARS: TOOTH Loll CONTACT ANALYSIS AND T..(U) NATIONAL AERONAUTICS AND SPACE ADMINISTRATION...STANDARDS -1963A -_L177- 7 7 71 7 -777 , AD-A 158 738 NASA USAAVSCOM Technical Memorandum 87013 Technical Report 85-C-6 Spiral Bevel and Circular Arc Helical ...this paper cover the generation of (1) spiral bevel gears with almost zero kinematic errors, and (2) helical gears with circular arc teeth

  9. 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.

  10. Single‐Layered Hybrid Materials Based on 1D Associated Metalorganic Nanoribbons for Controlled Release of Pheromones

    PubMed Central

    Moreno, José María; Navarro, Ismael; Díaz, Urbano; Primo, Jaime

    2016-01-01

    Abstract 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

  11. 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.

  12. A series of novel 1D coordination polymers constructed from metal?quinolone complex fragments linked by aromatic dicarboxylate ligands

    NASA Astrophysics Data System (ADS)

    He, Jiang-Hong; Xiao, Dong-Rong; Yan, Shi-Wei; Sun, Dian-Zhen; Chen, Hai-Yan; Wang, Xin; Yang, Juan; Ye, Zhong-Li; Yuan, Ruo; Wang, En-Bo

    2012-08-01

    Self-assembly of quinolones with metal salts in the presence of aromatic dicarboxylate ligands affords a series of novel 1D metal-quinolone complexes, namely [Mn(Hppa)(oba)]·3H2O (1), [Co(Hppa)(oba)]·3.25H2O (2), [Zn(Hppa)(sdba)]·1.5H2O (3), [Mn(Hcf)(bpda)(H2O)]·2H2O (4), [Mn(Hppa)2(bpdc)] (5) and [Mn(Hlome)2(bpdc)]·4H2O (6) (Hppa = Pipemidic acid, Hcf = ciprofloxacin, Hlome = lomefloxacin). The structures of compounds 1-3 consist of novel polymeric chains spanning two different directions, which display an intriguing 1D → 3D inclined polycatenation of supramolecular ladders. Compound 4 exhibits a chain compound formed from the interconnection of [Mn2(Hcf)2(μ-CO2)2] dimers with bpda ligands. Compounds 5 and 6 are similar chain compounds constructed from [Mn(Hppa)2] (or [Mn(Hlome)2]) fragments linked by bpdc ligands. The magnetic properties of 4 have been studied, which indicate the existence of antiferromagnetic interactions. Furthermore, the luminescent properties of compound 3 are discussed.

  13. 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.

  14. 1-D ELECTRO-OPTIC BEAM STEERING DEVICE.

    PubMed

    Wang, Wei-Chih; Tsui, Chi Leung

    2011-06-05

    In this paper, we present the design and fabrication of a 1D beam steering device based on planar electro-optic thermal-plastic prisms and a collimator lens array. With the elimination of moving parts, the proposed device is able to overcome the mechanical limitations of present scanning devices, such as fatigue and low operating frequency, while maintaining a small system footprint (~0.5mm×0.5mm). From experimental data, our prototype device is able to achieve a maximum deflection angle of 5.6° for a single stage prism design and 29.2° for a cascaded three prisms stage design. The lens array shows a 4µm collimated beam diameter.

  15. Combinatorial approach to exactly solve the 1D Ising model

    NASA Astrophysics Data System (ADS)

    Seth, Swarnadeep

    2017-01-01

    The Ising model is a well known statistical model which can be solved exactly by various methods. The most familiar one is the transfer matrix method. Sometimes it can be difficult to approach the open boundary case rather than periodic boundary ones in higher dimensions. But physically it is more intuitive to study the open boundary case, as it gives a closer view of the real system. We have introduced a new method called the pairing method to determine the exact partition function for the simplest case, a 1D Ising lattice. This method simplifies the problem's complexities and reduces it to a pure combinatorial problem. The study also reveals that it is possible to apply this pairing method in the case of a 2D square lattice. The obtained results agree perfectly with the values in the literature and this new approach provides an algorithmic insight to deal with such problems.

  16. Statistical analysis of 1D HRR target features

    NASA Astrophysics Data System (ADS)

    Gross, David C.; Schmitz, James L.; Williams, Robert L.

    2000-08-01

    Automatic target recognition (ATR) and feature-aided tracking (FAT) algorithms that use one-dimensional (1-D) high range resolution (HRR) profiles require unique or distinguishable target features. This paper explores the use of statistical measures to quantify the separability and stability of ground target features found in HRR profiles. Measures of stability, such as the mean and variance, can be used to determine the stability of a target feature as a function of the target aspect and elevation angle. Statistical measures of feature predictability and separability, such as the Fisher and Bhattacharyya measures, demonstrate the capability to adequately predict the desired target feature over a specified aspect angular region. These statistical measures for separability and stability are explained in detail and their usefulness is demonstrated with measured HRR data.

  17. Axion string dynamics I: 2+1D

    SciTech Connect

    Fleury, Leesa M.; Moore, Guy D.

    2016-05-03

    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.

  18. 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.

  19. Uniform Propagation of Chaos for Kac's 1D Particle System

    NASA Astrophysics Data System (ADS)

    Cortez, Roberto

    2016-12-01

    In this paper we study Kac's 1D particle system, consisting of the velocities of N particles colliding at constant rate and randomly exchanging energies. We prove uniform (in time) propagation of chaos in Wasserstein distance with explicit polynomial rates in N, for both the squared (i.e., the energy) and non-squared particle system. These rates are of order N^{-1/3} (almost, in the non-squared case), assuming that the initial distribution of the limit nonlinear equation has finite moments of sufficiently high order (4+ɛ is enough when using the 2-Wasserstein distance). The proof relies on a convenient parametrization of the collision recently introduced by Hauray, as well as on a coupling technique developed by Cortez and Fontbona.

  20. 1-D ELECTRO-OPTIC BEAM STEERING DEVICE

    PubMed Central

    Wang, Wei-Chih; Tsui, Chi Leung

    2011-01-01

    In this paper, we present the design and fabrication of a 1D beam steering device based on planar electro-optic thermal-plastic prisms and a collimator lens array. With the elimination of moving parts, the proposed device is able to overcome the mechanical limitations of present scanning devices, such as fatigue and low operating frequency, while maintaining a small system footprint (~0.5mm×0.5mm). From experimental data, our prototype device is able to achieve a maximum deflection angle of 5.6° for a single stage prism design and 29.2° for a cascaded three prisms stage design. The lens array shows a 4µm collimated beam diameter. PMID:22199458

  1. Lanczos diagonalizations of the 1-D Peierls-Hubbard model

    SciTech Connect

    Loh, E.Y.; Campbell, D.K.; Gammel, J.T.

    1989-01-01

    In studies of interacting electrons in reduced dimensions'' one is trapped between the Scylla of exponential growth of the number of states in any exact many-body basis and the Charybdis of the failure of mean-field theories to capture adequately the effects of interactions. In the present article we focus on one technique -- the Lanczos method -- which, at least in the case of the 1-D Peierls-Hubbard model, appears to allow us to sail the narrow channel between these two hazards. In contrast to Quantum Monte Carlo methods, which circumvent the exponential growth of states by statistical techniques and importance sampling, the Lanczos approach attacks this problem head-on by diagonalizing the full Hamiltonian. Given the restrictions of present computers, this approach is thus limited to studying finite clusters of roughly 12--14 sites. Fortunately, in one dimension, such clusters are usually sufficient for extracting many of the properties of the infinite system provided that one makes full use of the ability to vary the boundary conditions. In this article we shall apply the Lanczos methodology and novel phase randomization'' techniques to study the 1-D Peierls-Hubbard model, with particular emphasis on the optical absorption properties, including the spectrum of absorptions as a function of photon energy. Despite the discreteness of the eigenstates in our finite clusters, we are able to obtain optical spectra that, in cases where independent tests can be made, agree well with the known exact results for the infinite system. Thus we feel that this combination of techniques represents an important and viable means of studying many interesting novel materials involving strongly correlated electrons. 26 refs., 6 figs.

  2. Evaluating 1d Seismic Models of the Lunar Interior

    NASA Astrophysics Data System (ADS)

    Yao, Y.; Thorne, M. S.; Weber, R. C.; Schmerr, N. C.

    2012-12-01

    A four station seismic network was established on the Moon from 1969 to 1977 as part of the Apollo Lunar Surface Experiment Package (ALSEP). A total of nine 1D seismic velocity models were generated using a variety of different techniques. In spite of the fact that these models were generated from the same data set, significant differences exist between them. We evaluate these models by comparing predicted travel-times to published catalogs of lunar events. We generate synthetic waveform predictions for 1D lunar models using a modified version of the Green's Function of the Earth by Minor Integration (GEMINI) technique. Our results demonstrate that the mean square errors between predicted and measured P-wave travel times are smaller than those for S-wave travel times in all cases. Moreover, models fit travel times for artificial and meteoroid impacts better than for shallow and deep moonquakes. Overall, models presented by Nakamura [Nakamura, 1983] and Garcia et al. [Garcia et al., 2011] predicted the observed travel times better than all other models and were comparable in their explanation of travel-times. Nevertheless, significant waveform differences exist between these models. In particular, the seismic velocity structure of the lunar crust and regolith strongly affect the waveform characteristics predicted by these models. Further complexity is added by possible mantle discontinuity structure that exists in a subset of these models. We show synthetic waveform predictions for these models demonstrating the role that crustal structure has in generating long duration seismic coda inherent in the lunar waveforms.

  3. Quality assurance of a helical tomotherapy machine

    NASA Astrophysics Data System (ADS)

    Fenwick, J. D.; Tomé, W. A.; Jaradat, H. A.; Hui, S. K.; James, J. A.; Balog, J. P.; DeSouza, C. N.; Lucas, D. B.; Olivera, G. H.; Mackie, T. R.; Paliwal, B. R.

    2004-07-01

    Helical tomotherapy has been developed at the University of Wisconsin, and 'Hi-Art II' clinical machines are now commercially manufactured. At the core of each machine lies a ring-gantry-mounted short linear accelerator which generates x-rays that are collimated into a fan beam of intensity-modulated radiation by a binary multileaf, the modulation being variable with gantry angle. Patients are treated lying on a couch which is translated continuously through the bore of the machine as the gantry rotates. Highly conformal dose-distributions can be delivered using this technique, which is the therapy equivalent of spiral computed tomography. The approach requires synchrony of gantry rotation, couch translation, accelerator pulsing and the opening and closing of the leaves of the binary multileaf collimator used to modulate the radiation beam. In the course of clinically implementing helical tomotherapy, we have developed a quality assurance (QA) system for our machine. The system is analogous to that recommended for conventional clinical linear accelerator QA by AAPM Task Group 40 but contains some novel components, reflecting differences between the Hi-Art devices and conventional clinical accelerators. Here the design and dosimetric characteristics of Hi-Art machines are summarized and the QA system is set out along with experimental details of its implementation. Connections between this machine-based QA work, pre-treatment patient-specific delivery QA and fraction-by-fraction dose verification are discussed.

  4. 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.

  5. Electromagnetic Propagationg of Waves in Helical Stochastic

    NASA Astrophysics Data System (ADS)

    Adrian, Reyes; Mendez, David

    2012-02-01

    We develop a model for studying the axial propagation of elliptically polarized electromagnetic waves in a spatially random helical media. We start by writing Maxwell equations for a structurally chiral medium whose helical angle contains both a stochastic contribution and a deterministic one, this latter corresponding to an uniform rotation. We write the electromagnetic equations into Marcuvitz Schwigner representation to transform them afterward by using the Oseen transformation. We exhibit that in the Oseen frame, Marcuvitz Schwigner equations turns out to be a linear vectorial stochastic system of equations with multiplicative noise. From this result and utilizing a well known formalism for treating stochastic differential equations, we find the governing equations for the first and second moments of the field amplitudes for a general correlation model for the slope angles, and calculate their corresponding band structure for a particular spectral noise density. We show that the average resulting electromagnetic fields exhibit dissipation and the appearance of a new reflection band whose chirality is the opposite of the one obtained for a simple cholesteric liquid crystals.

  6. 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.

  7. 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.

  8. Chiral separation by a terminal chirality triggered P-helical quinoline oligoamide foldamer.

    PubMed

    Noguchi, Hiroki; Takafuji, Makoto; Maurizot, Victor; Huc, Ivan; Ihara, Hirotaka

    2016-03-11

    A P-helical quinoline oligoamide foldamer was grafted on silica and applied as an HPLC stationary phase for chiral separation. The P-handedness of the quinoline oligoamide foldamer was induced by a (1S)-camphanyl group, which was introduced at the N-terminus of a tetrameric quinoline oligoamide foldamer (Cmp-Q4). To immobilize the foldamer on porous silica particles, a trimethoxysilyl group was introduced at the opposing end of the foldamer. Elemental analysis indicated that the amount of foldamer on the silica surface was 0.57μmol/m(2). Circular dichroism and vibrational CD spectra of Cmp-Q4 and Cmp-Q4-immobilized silica (Sil-Q4-Cmp) suggested that the helical structure of Cmp-Q4 was altered on the silica surface whilst retaining a chiral structure. The chiral recognition ability of Sil-Q4-Cmp was evaluated with various aromatic enantiomers. Sil-Q4-Cmp showed enantio-selectivity for axially chiral molecules (e.g., αTrigger's base=1.26 and αBinaphthol=1.07). Sil-Q4-Cmp showed remarkable recognition of helical octameric quinoline oligoamides with isobutoxy and triethylene glycol side chains (α=10.35 and 14.98, respectively). In contrast, an (1S)-camphanyl group-immobilized porous silica showed no chiral recognition for any enantiomers tested in this study. To elucidate the chiral separation mechanism of Sil-Q4-Cmp, thermodynamic parameters were calculated using van't Hoff plots. HPLC results and thermodynamic parameters suggested that the chiral recognition of Sil-Q4-Cmp is based on the helical structure of Cmp-Q4 and other thermally dependent interactions such as hydrophobic effects associated with aromatic stacking. This work represents the first known application of aromatic foldamers in chiral separation.

  9. Measurements of Magnetic Helicity within Two Interacting Flux Ropes

    NASA Astrophysics Data System (ADS)

    Dehaas, Timothy; Gekelman, Walter

    2016-10-01

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

  10. 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.

  11. Geometric principles in the assembly of α-helical bundles.

    PubMed

    Pratap, J V; Luisi, B F; Calladine, C R

    2013-06-28

    α-Helical coiled coils are usually stabilized by hydrophobic interfaces between the two constituent α-helices, in the form of 'knobs-into-holes' packing of non-polar residues arranged in repeating heptad patterns. Here we examine the corresponding 'hydrophobic cores' that stabilize bundles of four α-helices. In particular, we study three different kinds of bundle, involving four α-helices of identical sequence: two pack in a parallel and one in an anti-parallel orientation. We point out that the simplest way of understanding the packing of these 4-helix bundles is to use Crick's original idea that the helices are held together by 'hydrophobic stripes', which are readily visualized on the cylindrical surface lattice of the α-helices; and that the 'helix-crossing angle'--which determines, in particular, whether supercoiling is left- or right-handed--is fixed by the slope of the lattice lines that contain the hydrophobic residues. In our three examples the constituent α-helices have hydrophobic repeat patterns of 7, 11 and 4 residues, respectively; and we associate the different overall conformations with 'knobs-into-holes' packing along the 7-, 11- and 4-start lines, respectively, of the cylindrical surface lattices of the constituent α-helices. For the first two examples, all four interfaces between adjacent helices are geometrically equivalent; but in the third, one of the four interfaces differs significantly from the others. We provide a geometrical explanation for this non-equivalence in terms of two different but equivalent ways of assembling this bundle, which may possibly constitute a bistable molecular 'switch' with a coaxial throw of about 12 Å. The geometrical ideas that we deploy in this paper provide the simplest and clearest description of the structure of helical bundles. In an appendix, we describe briefly a computer program that we have devised in order to search for 'knobs-into-holes' packing between α-helices in proteins.

  12. 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.

  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. Helical polymers based on intramolecularly hydrogen-bonded aromatic polyamides.

    PubMed

    Lu, Yi-Xuan; Shi, Zhu-Ming; Li, Zhan-Ting; Guan, Zhibin

    2010-12-21

    Inspired by arylamide-based oligomeric foldermers that are stabilized by intramolecular hydrogen bonding, a series of polyamides with intramolecular hydrogen-bonding motifs were synthesized via polycondensation reactions. These polymers can fold into helical conformation different from their linear control. The chirality of helical conformation can further be tuned via acid-base complexation using chiral residues.

  15. Domain boundary formation in helical multishell gold nanowire

    NASA Astrophysics Data System (ADS)

    Hoshi, Takeo; Fujiwara, Takeo

    2009-03-01

    Helical multishell gold nanowire (Y. Kondo and K. Takayanagi, Science 289, 606 (2000)) is studied by molecular dynamics simulation with electronic structure (``ELSES'' http://www.elses.jp/), so as to explore formation mechanism of helical domain boundary. We have proposed a model for the formation of helical multishell gold nanowires with molecular dynamics simulation with electronic structure (Y. Iguchi, T. Hoshi, T. Fujiwara PRL 99, 125507 (2007)). In this paper, we show simulation results with lager samples, of which the rod length is more than 10 nm and the number of rod atoms is more than one thousand. Unlike the results of shorter rods in the previous paper, a well-defined domain boundary between helical and (non-)helical regions appears, when an atom moves from a inner shell into rod surface. The inserted atoms on the rod surface causes a surface reconstruction on rod surface and introduces a helical region with a domain boundary. Such an inserted atom is a possible candidate of mechanism for forming a helical rod from an ideal (non-helical) one.

  16. 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...

  17. Solar cycle-dependent helicity transport by magnetic clouds

    NASA Astrophysics Data System (ADS)

    Lynch, B. J.; Gruesbeck, J. R.; Zurbuchen, T. H.; Antiochos, S. K.

    2005-08-01

    Magnetic clouds observed with the Wind and ACE spacecraft are fit with the static, linear force-free cylinder model to obtain estimates of the chirality, fluxes, and magnetic helicity of each event. The fastest magnetic clouds (MCs) are shown to carry the most flux and helicity. We calculate the net cumulative helicity which measures the difference in right- and left-handed helicity contained in MCs over time. The net cumulative helicity does not average to zero; rather, a strong left-handed helicity bias develops over the solar cycle, dominated by the largest events of cycle 23: Bastille Day 2000 and 28 October 2003. The majority of MCs ("slow" events, < 500 km/s) have a net cumulative helicity profile that appears to be modulated by the solar activity cycle. This is far less evident for "fast" MC events ( ≥ 500 km/s), which were disproportionately left-handed over our data set. A brief discussion about the various solar sources of CME helicity and their implication for dynamo processes is included.

  18. Patterned helical metallic ribbon for continuous edge winding applications

    SciTech Connect

    Frischmann, P.G.; Liebermann, H.H.; Rosenberry, G.M.

    1983-04-19

    Metallic ribbon having cutout patterns therein is provided in continuous helical form. The cutout patterns may be situated to intersect either or both of the ribbon edges or may be situated entirely within the ribbon. The helical ribbon with the cutout patterns may additionally have a nesting, or self-stacking, feature.

  19. Helical dipole magnets for polarized protons in RHIC

    SciTech Connect

    Syphers, M.; Courant, E.; Fischer, W.

    1997-07-01

    Superconducting helical dipole magnets will be used in the Brookhaven Relativistic Heavy Ion Collider (RHIC) to maintain polarization of proton beams and to perform localized spin rotations at the two major experimental detector regions. Requirements for the helical dipole system are discussed, and magnet prototype work is reported.

  20. Helical Channel Design and Technology for Cooling of Muon Beams

    NASA Astrophysics Data System (ADS)

    Yonehara, K.; Derbenev, Y. S.; Johnson, R. P.

    2010-11-01

    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.

  1. 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.

  2. Flare Activity and Magnetic Helicity Injection By Photospheric Horizontal Motions

    NASA Astrophysics Data System (ADS)

    Moon, Y.-J.; Chae, J.; Choe, G.; Wang, H.; Park, Y. D.; Yun, H. S.; Yurchyshyn, V.; Goode, P. R.

    2002-05-01

    We present observational evidence that the occurrence of homologous flares in an active region is physically related to the injection of magnetic helicity by horizontal photospheric motions. We have analyzed a set of 1 minute cadence magnetograms of NOAA AR 8100 taken over a period of 6.5 hours by Michelson Doppler Imager (MDI) on board Solar and Heliospheric Observatory (SOHO). During this observing time span, seven homologous flares took place in the active region. We have computed the magnetic helicity injection rate into the solar atmosphere by photospheric shearing motions, and found that a significant amount of magnetic helicity was injected during the observing period. In a strong M4.1 flare, the magnetic helicity injection rate impulsively increased and peaked at the same time as the X-ray flux did. The flare X-ray flux integrated over the X-ray emission time strongly correlates with the magnetic helicity injected during the flaring interval. The integrated X-ray flux is found to be a logarithmically increasing function of the injected magnetic helicity. Our results suggest that injection of helicity and abrupt increase of helicity magnitude play a significant role in flare triggering. This work has been supported by NASA grants NAG5-10894 and NAG5-7837, by MURI grant of AFOSR, by the US-Korea Cooperative Science Program (NSF INT-98-16267), by NRL M10104000059-01J000002500 of the Korean government, and by the BK 21 project of the Korean government.

  3. Hierarchically controlled helical graphite films prepared from iodine-doped helical polyacetylene films using morphology-retaining carbonization.

    PubMed

    Matsushita, Satoshi; Kyotani, Mutsumasa; Akagi, Kazuo

    2011-11-09

    One-handed helical graphite films with a hierarchically controlled morphology were prepared from iodine-doped helical polyacetylene (H-PA) films using the recently developed morphology-retaining carbonization method. Results from scanning electron microscopy indicate that the hierarchical helical morphology of the H-PA film remains unchanged even after carbonization at 800 °C. The weight loss of the film due to carbonization was very small; only 10-29% of the weight of the film before doping was lost. Furthermore, the graphite film prepared by subsequent heating at 2600 °C retained the same morphology as that of the original H-PA film and that of the helical carbon film prepared at 800 °C. The screwed direction, twisted degree, and vertical or horizontal alignment of the helical graphite film were well controlled by changing the helical sense, helical pitch, and orientation state of the chiral nematic liquid crystal (N*-LC) used as an asymmetric LC reaction field. X-ray diffraction and Raman scattering measurements showed that graphitic crystallization proceeds in the carbon film during heat treatment at 2600 °C. Transmission electron microscopy measurements indicate that ultrasonication of the helical graphite film in ethanol for several hours gives rise to a single helical graphite fibril. The profound potentiality of the present graphite films is exemplified in their electrical properties. The horizontally aligned helical graphite film exhibits an enhancement in electrical conductivity and an evolution of electrical anisotropy in which conductivity parallel to the helical axis of the fibril bundle is higher than that perpendicular to the axis.

  4. A new cohomological formula for helicity in R2 reveals the effect of a diffeomorphism on helicity

    NASA Astrophysics Data System (ADS)

    Cantarella, Jason; Parsley, Jason

    2010-09-01

    The helicity of a vector field is a measure of the average linking of pairs of integral curves of the field. Computed by a six-dimensional integral, it is widely useful in the physics of fluids. For a divergence-free field tangent to the boundary of a domain in 3-space, helicity is known to be invariant under volume-preserving diffeomorphisms of the domain that are homotopic to the identity. We give a new construction of helicity for closed (k+1)-forms on a domain in (2k+1)-space that vanish when pulled back to the boundary of the domain. Our construction expresses helicity in terms of a cohomology class represented by the form when pulled back to the compactified configuration space of pairs of points in the domain. We show that our definition is equivalent to the standard one. We use our construction to give a new formula for computing helicity by a four-dimensional integral. We provide a Biot-Savart operator that computes a primitive for such forms; utilizing it, we obtain another formula for helicity. As a main result, we find a general formula for how much the value of helicity changes when the form is pushed forward by a diffeomorphism of the domain; it relies upon understanding the effect of the diffeomorphism on the homology of the domain and the de Rham cohomology class represented by the form. Our formula allows us to classify the helicity-preserving diffeomorphisms on a given domain, finding new helicity-preserving diffeomorphisms on the two-holed solid torus and proving that there are no new helicity-preserving diffeomorphisms on the standard solid torus. We conclude by defining helicities for forms on submanifolds of Euclidean space. In addition, we provide a detailed exposition of some standard 'folk' theorems about the cohomology of the boundary of domains in R.

  5. Binding Strength and Dynamics of Invariant Natural Killer Cell T Cell Receptor/CD1d-Glycosphingolipid Interaction on Living Cells by Single Molecule Force Spectroscopy*

    PubMed Central

    Bozna, Bianca L.; Polzella, Paolo; Rankl, Christian; Zhu, Rong; Salio, Mariolina; Shepherd, Dawn; Duman, Memed; Cerundolo, Vincenzo; Hinterdorfer, Peter

    2011-01-01

    Invariant natural killer T (iNKT) cells are a population of T lymphocytes that play an important role in regulating immunity to infection and tumors by recognizing endogenous and exogenous CD1d-bound lipid molecules. Using soluble iNKT T cell receptor (TCR) molecules, we applied single molecule force spectroscopy for the investigation of the iNKT TCR affinity for human CD1d molecules loaded with glycolipids differing in the length of the phytosphingosine chain using either recombinant CD1d molecules or lipid-pulsed THP1 cells. In both settings, the dissociation of the iNKT TCR from human CD1d molecules loaded with the lipid containing the longer phytosphingosine chain required higher unbinding forces compared with the shorter phytosphingosine lipid. Our findings are discussed in the context of previous results obtained by surface plasmon resonance measurements. We present new insights into the energy landscape and the kinetic rate constants of the iNKT TCR/human CD1d-glycosphingolipid interaction and emphasize the unique potential of single molecule force spectroscopy on living cells. PMID:21454514

  6. Binding strength and dynamics of invariant natural killer cell T cell receptor/CD1d-glycosphingolipid interaction on living cells by single molecule force spectroscopy.

    PubMed

    Bozna, Bianca L; Polzella, Paolo; Rankl, Christian; Zhu, Rong; Salio, Mariolina; Shepherd, Dawn; Duman, Memed; Cerundolo, Vincenzo; Hinterdorfer, Peter

    2011-05-06

    Invariant natural killer T (iNKT) cells are a population of T lymphocytes that play an important role in regulating immunity to infection and tumors by recognizing endogenous and exogenous CD1d-bound lipid molecules. Using soluble iNKT T cell receptor (TCR) molecules, we applied single molecule force spectroscopy for the investigation of the iNKT TCR affinity for human CD1d molecules loaded with glycolipids differing in the length of the phytosphingosine chain using either recombinant CD1d molecules or lipid-pulsed THP1 cells. In both settings, the dissociation of the iNKT TCR from human CD1d molecules loaded with the lipid containing the longer phytosphingosine chain required higher unbinding forces compared with the shorter phytosphingosine lipid. Our findings are discussed in the context of previous results obtained by surface plasmon resonance measurements. We present new insights into the energy landscape and the kinetic rate constants of the iNKT TCR/human CD1d-glycosphingolipid interaction and emphasize the unique potential of single molecule force spectroscopy on living cells.

  7. Snorkeling preferences foster an amino acid composition bias in transmembrane helices.

    PubMed

    Chamberlain, Aaron K; Lee, Yohan; Kim, Sanguk; Bowie, James U

    2004-05-28

    By analyzing transmembrane (TM) helices in known structures, we find that some polar amino acids are more frequent at the N terminus than at the C terminus. We propose the asymmetry occurs because most polar amino acids are better able to snorkel their polar atoms away from the membrane core at the N terminus than at the C terminus. Two findings lead us to this proposition: (1) side-chain conformations are influenced strongly by the N or C-terminal position of the amino acid in the bilayer, and (2) the favored snorkeling direction of an amino acid correlates well with its N to C-terminal composition bias. Our results suggest that TM helix predictions should incorporate an N to C-terminal composition bias, that rotamer preferences of TM side-chains are position-dependent, and that the ability to snorkel influences the evolutionary selection of amino acids for the helix N and C termini.

  8. Role of hydrophobicity and solvent-mediated charge-charge interactions in stabilizing alpha-helices.

    PubMed Central

    Vila, J A; Ripoll, D R; Villegas, M E; Vorobjev, Y N; Scheraga, H A

    1998-01-01

    A theoretical study to identify the conformational preferences of lysine-based oligopeptides has been carried out. The solvation free energy and free energy of ionization of the oligopeptides have been calculated by using a fast multigrid boundary element method that considers the coupling between the conformation of the molecule and the ionization equilibria explicitly, at a given pH value. It has been found experimentally that isolated alanine and lysine residues have somewhat small intrinsic helix-forming tendencies; however, results from these simulations indicate that conformations containing right-handed alpha-helical turns are energetically favorable at low values of pH for lysine-based oligopeptides. Also, unusual patterns of interactions among lysine side chains with large hydrophobic contacts and close proximity (5-6 A) between charged NH3+ groups are observed. Similar arrangements of charged groups have been seen for lysine and arginine residues in experimentally determined structures of proteins available from the Protein Data Bank. The lowest-free-energy conformation of the sequence Ac-(LYS)6-NMe from these simulations showed large pKalpha shifts for some of the NH3+ groups of the lysine residues. Such large effects are not observed in the lowest-energy conformations of oligopeptide sequences with two, three, or four lysine residues. Calculations on the sequence Ac-LYS-(ALA)4-LYS-NMe also reveal low-energy alpha-helical conformations with interactions of one of the LYS side chains with the helix backbone in an arrangement quite similar to the one described recently by (Proc. Natl. Acad. Sci. U.S.A. 93:4025-4029). The results of this study provide a sound basis with which to discuss the nature of the interactions, such as hydrophobicity, charge-charge interaction, and solvent polarization effects, that stabilize right-handed alpha-helical conformations. PMID:9826588

  9. Influence of glutamic acid residues and pH on the properties of transmembrane helices.

    PubMed

    Rajagopalan, Venkatesan; Greathouse, Denise V; Koeppe, Roger E

    2017-03-01

    Negatively charged side chains are important for the function of particular ion channels and certain other membrane proteins. To investigate the influence of single glutamic acid side chains on helices that span lipid-bilayer membranes, we have employed GWALP23 (acetyl-GGALW(5)LALALALALALALW(19)LAGA-amide) as a favorable host peptide framework. We substituted individual Leu residues with Glu residues (L12E or L14E or L16E) and incorporated specific (2)H-labeled alanine residues within the core helical region or near the ends of the sequence. Solid-state (2)H NMR spectra reveal little change for the core labels in GWALP23-E12, -E14 and -E16 over a pH range of 4 to 12.5, with the spectra being broader for samples in DOPC compared to DLPC bilayers. The spectra for samples with deuterium labels near the helix ends on alanines 3 and 21 show modest pH-dependent changes in the extent of unwinding of the helix terminals in DLPC and DOPC bilayers. The combined results indicate minor overall responses of these transmembrane helices to changes in pH, with the most buried residue E12 showing no pH dependence. While the Glu residues E14 and E16 may have high pKa values in the lipid bilayer environment, it is also possible that a paucity of helix response is masking the pKa values. Interestingly, when E16 is present, spectral changes at high pH report significant local unwinding of the core helix. Our results are consistent with the expectation that buried carboxyl groups aggressively hold their protons and/or waters of hydration.

  10. CD1d Expression in Paneth Cells and Rat Exocrine Pancreas Revealed by Novel Monoclonal Antibodies Which Differentially Affect NKT Cell Activation

    PubMed Central

    Monzon-Casanova, Elisa; Steiniger, Birte; Schweigle, Stefanie; Clemen, Holger; Zdzieblo, Daniela; Starick, Lisa; Müller, Ingrid; Wang, Chyung-Ru; Rhost, Sara; Cardell, Susanna; Pyz, Elwira; Herrmann, Thomas

    2010-01-01

    Background CD1d is a nonpolymorphic MHC class I-like molecule which presents nonpeptide ligands, e.g. glycolipids, to NKT cells. These cells are known to have multiple effects on innate and adaptive immune responses and on the development of pathological conditions. In order to analyze CD1d expression and function in the rat, the first rat CD1d-specific monoclonal antibodies (mAbs) were generated. Methodology/Principal Findings Two mAbs, WTH-1 and WTH-2, were generated which bound equally well to cell surface-expressed rat and mouse CD1d. Their non-overlapping epitopes were mapped to the CD1d heavy chain. Flow cytometry and immunohistological analyses revealed a nearly identical degree and pattern of CD1d expression for hematopoieitic cells of both species. Notable is also the detection of CD1d protein in mouse and rat Paneth cells as well as the extremely high CD1d expression in acinar exocrine cells of the rat pancreas and the expression of CD4 on rat marginal zone B cells. Both mAbs blocked α-galactosylceramide recognition by primary rat and mouse NKT cells. Interestingly, the two mAbs differed in their impact on the activation of various autoreactive T cell hybridomas, including the XV19.2 hybridoma whose activation was enhanced by the WTH-1 mAb. Conclusions/Significance The two novel monoclonal antibodies described in this study, allowed the analysis of CD1d expression and CD1d-restricted T cell responses in the rat for the first time. Moreover, they provided new insights into mechanisms of CD1d-restricted antigen recognition. While CD1d expression by hematopoietic cells of mice and rats was extremely similar, CD1d protein was detected at not yet described sites of non-lymphatic tissues such as the rat exocrine pancreas and Paneth cells. The latter is of special relevance given the recently reported defects of Paneth cells in CD1d−/− mice, which resulted in an altered composition of the gut flora. PMID:20927351

  11. 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.

  12. 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.

  13. Determining how magnetic helicity injection really works. Annual progress report

    SciTech Connect

    Bellan, P.M.

    1998-10-21

    Magnetic helicity injection is the essential process underlying both spheromak formation and helicity injection toroidal current drive in tokamaks (e.g., HIT and NSTX). The dynamical details of the helicity injection process are poorly understood because existing models avoid a dynamic description. In particular, Taylor relaxation, the main model motivating helicity injection efforts, is an argument that predicts the state to which a turbulent magnetic configuration relaxes after all dynamics are over. The goal of the Caltech experiment is to investigate the actual dynamics and topological evolution associated with relaxation and so determine how helicity injection really works. Although the global relaxation model (i.e., Taylor model) typically invokes axisymmetry, simple physical arguments (Cowling`s theorem) show that the detailed dynamics must involve topologically complex, non-axisymmetric processes. Progress for this project is given here.

  14. 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.

  15. Spatio-temporal modification of collagen scaffolds mediated by triple helical propensity.

    PubMed

    Wang, Allen Y; Foss, Catherine A; Leong, Shirley; Mo, Xiao; Pomper, Martin G; Yu, Seungju M

    2008-07-01

    Functionalized collagen that incorporates exogenous compounds may offer new and improved biomaterials applications, especially in drug-delivery, multifunctional implants, and tissue engineering. To that end, we developed a specific and reversible collagen modification technique utilizing associative chain interactions between synthetic collagen mimetic peptide (CMP) [(ProHypGly) chi; Hyp = hydroxyproline] and type I collagen. Here we show temperature-dependent collagen binding and subsequent release of a series of CMPs with varying chain lengths indicating a triple helical propensity driven binding mechanism. The binding took place when melted, single-strand CMPs were allowed to fold while in contact with reconstituted type I collagens. The binding affinity is highly specific to collagen as labeled CMP bound to nanometer scale periodic positions on type I collagen fibers and could be used to selectively image collagens in ex vivo human liver tissue. When heated to physiological temperature, bound CMPs discharged from the collagen at a sustained rate that correlated with CMP's triple helical propensity, suggesting that sustainability is mediated by dynamic collagen-CMP interactions. We also report on the spatially defined modification of collagen film with linear and multi-arm poly(ethylene glycol)-CMP conjugates; at 37 degrees C, these PEG-CMP conjugates exhibited temporary cell repelling activity lasting up to 9 days. These results demonstrate new opportunities for targeting pathologic collagens for diagnostic or therapeutic applications and for fabricating multifunctional collagen coatings and scaffolds that can temporally and spatially control the behavior of cells associated with the collagen matrices.

  16. DPD Simulation of Protein Conformations: From α-Helices to β-Structures.

    PubMed

    Vishnyakov, Aleksey; Talaga, David S; Neimark, Alexander V

    2012-11-01

    We suggest a coarse-grained model for DPD simulations of polypeptides in solutions. The model mimics hydrogen bonding that stabilizes α-helical and β-structures using dissociable Morse bonds between quasiparticles representing the peptide groups amenable to hydrogen bonding. We demonstrate the capabilities of the model by simulating transitions between coil-like, globular, α-helical, and β-hairpin configurations of model peptides, varying Morse potential parameters, the hydrophobicities of residue side chains, and pH, which determines the charges of residue side chains. We construct a model triblock polypeptide mimicking the sequence of residues α-synuclein at two different pHs. The conformations of this model polypeptide depend on pH similarly to the behavior observed experimentally. The suggested approach to accounting for hydrogen bond formation within the general DPD framework may make the DPD method a competitive alternative to CGMD for modeling equilibrium and dynamic properties of proteins and polypeptides, especially during their transport in confined environments.

  17. Signal transmission through the CXC chemokine receptor 4 (CXCR4) transmembrane helices

    PubMed Central

    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.

    2016-01-01

    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

  18. 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.

  19. 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.

  20. Lipid shape is a key factor for membrane interactions of amphipathic helical peptides.

    PubMed

    Strandberg, Erik; Tiltak, Deniz; Ehni, Sebastian; Wadhwani, Parvesh; Ulrich, Anne S

    2012-07-01

    The membrane alignment of the amphiphilic alpha-helical model peptide MSI-103 (sequence [KIAGKIA]3-NH2) was examined by solid state 2H-NMR in different lipid systems by systematically varying the acyl chain length and degree of saturation, the lipid head group type, and the peptide-to-lipid molar ratio. In liquid crystalline phosphatidylcholine (PC) lipids with saturated chains, the amphiphilic helix changes its orientation from a surface-bound "S-state" to a tilted "T-state" with increasing peptide concentration. In PC lipids with unsaturated chains, on the other hand, the S-state is found throughout all concentrations. Using phosphatidylethanolamine lipids with a small head group or by addition of lyso-lipids with only one acyl chain, the spontaneous curvature of the bilayer was purposefully changed. In the first case with a negative curvature only the S-state was found, whereas in systems with a positive curvature the peptide preferred the obliquely immersed T-state at high concentration. The orientation of MSI-103 thus correlates very well with the shape of the lipid molecules constituting the membrane. Lipid charge, on the other hand, was found to affect only the initial electrostatic attraction to the membrane surface but not the alignment preferences. In bilayers that are "sealed" with 20% cholesterol, MSI-103 cannot bind in a well-oriented manner and forms immobilized aggregates instead. We conclude that the curvature properties of a membrane are a key factor in the interactions of amphiphilic helical peptides in general, whose re-alignment and immersion preferences may thus be inferred in a straightforward manner from the lipid-shape concept.

  1. 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.

  2. 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.

  3. 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.

  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. 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.

  6. 1-D Modeling of Massive Particle Injection (MPI) in Tokamaks

    NASA Astrophysics Data System (ADS)

    Wu, W.; Parks, P. B.; Izzo, V. A.

    2008-11-01

    A 1-D Fast Current Quench (FCQ) model is developed to study current evolution and runaway electron suppression under massive density increase. The model consists of coupled toroidal electric field and energy equations, and it is solved numerically for DIII-D and ITER operating conditions. Simulation results suggest that fast shutdown by D2 liquid jet/pellet injection is in principle achievable for the desired plasma cooling time (˜15 ms for DIII-D and ˜50 ms for ITER) under ˜150x or higher densification. The current density and pressure profile are practically unaltered during the initial phase of jet propagation when dilution cooling dominates. With subsequent radiation cooling, the densified discharge enters the strongly collisional regime where Pfirsch-Schluter thermal diffusion can inhibit current contraction on the magnetic axis. Often the 1/1 kink instability, addressed by Kadomtsev's magnetic reconnection model, can be prevented. Our results are compared with NIMROD simulations in which the plasma is suddenly densified by ˜100x and experiences instantaneous dilution cooling, allowing for use of actual (lower) Lundquist numbers.

  7. Energy eigenfunctions of the 1D Gross-Pitaevskii equation

    NASA Astrophysics Data System (ADS)

    Marojević, Želimir; Göklü, Ertan; Lämmerzahl, Claus

    2013-08-01

    We developed a new and powerful algorithm by which numerical solutions for excited states in a gravito-optical surface trap have been obtained. They represent solutions in the regime of strong nonlinearities of the Gross-Pitaevskii equation. In this context we also briefly review several approaches which allow, in principle, for calculating excited state solutions. It turns out that without modifications these are not applicable to strongly nonlinear Gross-Pitaevskii equations. The importance of studying excited states of Bose-Einstein condensates is also underlined by a recent experiment of Bücker et al. in which vibrational state inversion of a Bose-Einstein condensate has been achieved by transferring the entire population of the condensate to the first excited state. Here we focus on demonstrating the applicability of our algorithm for three different potentials by means of numerical results for the energy eigenstates and eigenvalues of the 1D Gross-Pitaevskii-equation. We compare the numerically found solutions and find out that they completely agree with the case of known analytical solutions.

  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. Control and imaging of O(1D2) precession.

    PubMed

    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 O(2) at 157 nm provides a clean source of fast-moving O((1)D(2)) 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.

  10. Cavitation Influence in 1D Part-load Vortex Models

    NASA Astrophysics Data System (ADS)

    Dörfler, P. K.

    2016-11-01

    Residual swirl in the draft tube of Francis turbines may cause annoying low- frequency pulsation of pressure and power output, in particular during part-load operation. A 1D analytical model for these dynamic phenomena would enable simulation by some conventional method for computing hydraulic transients. The proper structure of such a model has implications for the prediction of prototype behaviour based on laboratory tests. The source of excitation as well as the dynamic transmission behaviour of the draft tube flow may both be described either by lumped or distributed parameters. The distributed version contains more information and, due to limited possibilities of identification, some data must be estimated. The distributed cavitation compliance is an example for this dilemma. In recent publications, the customary assumption of a constant wave speed has produced dubious results. The paper presents a more realistic model for distributed compressibility. The measured influence of the Thoma number is applied with the local cavitation factor. This concept is less sensitive to modelling errors and explains both the Thoma and Froude number influence. The possible effect of the normally unknown non-condensable gas content in the vortex cavity is shortly commented. Its measurement in future tests is recommended. It is also recommended to check the available analytical vortex models for possible dispersion effects.

  11. The Helical Alanine Controversy: An (Ala)6 Insertion Dramatically Increases Helicity

    PubMed Central

    Lin, Jasper C.; Barua, Bipasha

    2013-01-01

    Employing chemical shift melts and hydrogen/deuterium exchange NMR techniques, we have determined the stabilization of the Trp-cage miniprotein due to multiple alanine insertions within the N-terminal α-helix. Alanine is shown to be uniquely helix-stabilizing and this stabilization is reflected in the global fold stability of the Trp-cage. The associated free energy change per alanine can be utilized to calculate the alanine propagation value. From the Lifson–Roig formulation, the calculated value (wAla = 1.6) is comparable to those obtained for short, solubilized, alanine-rich helices and is much larger than the values obtained by prior host–guest techniques or in N-terminally templated helices and peptides bearing long contiguous strings of alanines with no capping or solubilizing units present. PMID:15493925

  12. 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.”.

  13. Landau Theory of Helical Fermi Liquids.

    PubMed

    Lundgren, Rex; Maciejko, Joseph

    2015-08-07

    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.

  14. 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

  15. 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.

  16. 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.

  17. 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.

  18. Microinstability Studies for the Large Helical Device

    SciTech Connect

    G. Rewoldt; L.-P. Ku; W.M. Tang; H. Sugama; N. Nakajima; K.Y. Watanabe; S. Murakami; H. Yamada; W.A. Cooper

    2002-01-28

    Fully kinetic assessments of the stability properties of toroidal drift modes have been obtained for cases for the Large Helical Device (LHD). This calculation employs the comprehensive linear microinstability code FULL, as recently extended for nonaxisymmetric systems. The code retains the important effects in the linearized gyrokinetic equation, using the lowest-order ''ballooning representation'' for high toroidal mode number instabilities in the electrostatic limit. These effects include trapped particles, FLR, transit and bounce and magnetic drift frequency resonances, etc., for any number of plasma species. Results for toroidal drift waves destabilized by trapped electrons and ion temperature gradients are presented, using numerically-calculated three-dimensional MHD equilibria. These are reconstructed from experimental measurements. Quasilinear fluxes of particles and energy for each species are also calculated. Pairs of LHD discharges with different magnetic axis positions and with and without pellet injection are compared.

  19. Helical glasses near ferromagnetic quantum criticality

    NASA Astrophysics Data System (ADS)

    Thomson, S. J.; Krüger, F.; Green, A. G.

    2013-06-01

    We study the effects of quenched charge disorder on the phase reconstruction near itinerant ferromagnetic quantum critical points in three spatial dimensions. Combining a Replica-disorder average with a fermionic version of the quantum order-by-disorder mechanism, we show that weak disorder destabilizes the ferromagnetic state and enhances the susceptibility towards incommensurate, spiral magnetic ordering. The Goldstone modes of the spiral phase are governed by a 3d-XY model. The induced disorder in the pitch of the spiral generates a random anisotropy for the Goldstone modes, inducing vortex lines in the phase of the helical order and rendering the magnetic correlations short ranged with a strongly anisotropic correlation length.

  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