WorldWideScience

Sample records for stable helical structure

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

    Energy Technology Data Exchange (ETDEWEB)

    Yao, Zhen [College of Science, Liaoning University of Technology, Jinzhou, Liaoning, 121001 (China); Liu, Chun-Jian [College of Mathematics and Physics, Bohai University, Jinzhou, Liaoning, 121000 (China); Lv, Hang [Institute of New Energy, Bohai University, Jinzhou, Liaoning, 121000 (China); Liu, Bing-Bing, E-mail: liubb@jlu.edu.cn [State Key Laboratory of Superhard Materials, Jilin University, Changchun, 130012 (China)

    2016-08-12

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

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

    International Nuclear Information System (INIS)

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

    2016-01-01

    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. (paper)

  3. From plasma crystals and helical structures towards inorganic living matter

    International Nuclear Information System (INIS)

    Tsytovich, V N; Morfill, G E; Fortov, V E; Gusein-Zade, N G; Klumov, B A; Vladimirov, S V

    2007-01-01

    Complex plasmas may naturally self-organize themselves into stable interacting helical structures that exhibit features normally attributed to organic living matter. The self-organization is based on non-trivial physical mechanisms of plasma interactions involving over-screening of plasma polarization. As a result, each helical string composed of solid microparticles is topologically and dynamically controlled by plasma fluxes leading to particle charging and over-screening, the latter providing attraction even among helical strings of the same charge sign. These interacting complex structures exhibit thermodynamic and evolutionary features thought to be peculiar only to living matter such as bifurcations that serve as 'memory marks', self-duplication, metabolic rates in a thermodynamically open system, and non-Hamiltonian dynamics. We examine the salient features of this new complex 'state of soft matter' in light of the autonomy, evolution, progenity and autopoiesis principles used to define life. It is concluded that complex self-organized plasma structures exhibit all the necessary properties to qualify them as candidates for inorganic living matter that may exist in space provided certain conditions allow them to evolve naturally

  4. Stable, streamlined and helical cavity formation by the impact of Leidenfrost spheres

    Science.gov (United States)

    Mansoor, Mohammad; Vakarelski, Ivan; Marston, Jeremy; Truscott, Tadd; Thoroddsen, Sigurdur

    2016-11-01

    This work reports results from an experimental study on the formation of stable-streamlined and helical cavity wakes following the free-surface impact of Leidenfrost spheres. The Leidenfrost effect encapsulates the sphere by a vapor layer to prevent any physical contact with the surrounding liquid. This phenomenon is essential for the pacification of acoustic rippling along the cavity interface to result in a stable-streamlined cavity wake. Such a streamlined configuration experiences drag coefficients an order of magnitude lower than those acting on room temperature spheres. A striking observation is the formation of helical cavities which occur for impact Reynolds numbers Re0 >= 1 . 4 ×105 and are characterized by multiple interfacial ridges, stemming from and rotating synchronously about an evident contact line around the sphere equator. This helical configuration has 40 - 55 % smaller overall force coefficients than those obtained in the formation of stable cavity wakes.

  5. The Enhanced Intramolecular Energy Transfer and Strengthened ff Luminescence of a Stable Helical Eu Complex in Ionic Liquids.

    Science.gov (United States)

    Hasegawa, Yuki; Ishii, Ayumi; Inazuka, Yudai; Yajima, Naho; Kawaguchi, Shogo; Sugimoto, Kunihisa; Hasegawa, Miki

    2018-01-24

    The luminescence of a Eu complex (EuL) is enhanced by stabilization of the coordination structure in highly viscous ionic liquids. The EuL was found to maintain a stable single helical structure both in organic solvents and in the ionic liquids [BMIM][PF₆] and [EMIM][PF₆]. A colorless solution of EuL dissolved in [BMIM][PF₆] exhibits bright red luminescence with a quantum yield of 32.3%, a value that is much higher than that in acetonitrile (12%). Estimated rate constants for the energy relaxation pathway indicate that the energy transfer efficiency is enhanced in [BMIM][PF₆] as a result of the suppression of molecular fluctuations in the ligands. Additionally, a highly luminescent helical structure is preserved in [EMIM][PF₆] up to 120 °C.

  6. Dynamic Behavior of Helical Structure in Ferroelectric Liquid Crystals

    Science.gov (United States)

    Katayama, Takashi; Uehara, Hiroyuki; Furue, Hirokazu; Hatano, Jun

    2004-09-01

    Ferroelectric liquid crystals (FLCs) take a helical structure which can be unwound by the application of an electric field. Although the static orientational process of FLC molecules is well known, the dynamic modification process of the helical structure is not clearly understood. We formulated equations for simulating the dynamic response in terms of the elastic free-energy density based on the continuum theory, and subsequently was solved the dynamic equations numerically. Furthermore, the conoscopic image was simulated by a 4× 4 matrix method. We investigated the effect of spontaneous polarization and dielectric anisotropy on the dynamic behavior of the helical structure in FLC.

  7. Distribution and evolution of stable single α-helices (SAH domains in myosin motor proteins.

    Directory of Open Access Journals (Sweden)

    Dominic Simm

    Full Text Available Stable single-alpha helices (SAHs are versatile structural elements in many prokaryotic and eukaryotic proteins acting as semi-flexible linkers and constant force springs. This way SAH-domains function as part of the lever of many different myosins. Canonical myosin levers consist of one or several IQ-motifs to which light chains such as calmodulin bind. SAH-domains provide flexibility in length and stiffness to the myosin levers, and may be particularly suited for myosins working in crowded cellular environments. Although the function of the SAH-domains in human class-6 and class-10 myosins has well been characterised, the distribution of the SAH-domain in all myosin subfamilies and across the eukaryotic tree of life remained elusive. Here, we analysed the largest available myosin sequence dataset consisting of 7919 manually annotated myosin sequences from 938 species representing all major eukaryotic branches using the SAH-prediction algorithm of Waggawagga, a recently developed tool for the identification of SAH-domains. With this approach we identified SAH-domains in more than one third of the supposed 79 myosin subfamilies. Depending on the myosin class, the presence of SAH-domains can range from a few to almost all class members indicating complex patterns of independent and taxon-specific SAH-domain gain and loss.

  8. Stable Conic-Helical Orbits of Planets around Binary Stars: Analytical Results

    Science.gov (United States)

    Oks, E.

    2015-05-01

    Studies of planets in binary star systems are especially important because it was estimated that about half of binary stars are capable of supporting habitable terrestrial planets within stable orbital ranges. One-planet binary star systems (OBSS) have a limited analogy to objects studied in atomic/molecular physics: one-electron Rydberg quasimolecules (ORQ). Specifically, ORQ, consisting of two fully stripped ions of the nuclear charges Z and Z‧ plus one highly excited electron, are encountered in various plasmas containing more than one kind of ion. Classical analytical studies of ORQ resulted in the discovery of classical stable electronic orbits with the shape of a helix on the surface of a cone. In the present paper we show that despite several important distinctions between OBSS and ORQ, it is possible for OBSS to have stable planetary orbits in the shape of a helix on a conical surface, whose axis of symmetry coincides with the interstellar axis; the stability is not affected by the rotation of the stars. Further, we demonstrate that the eccentricity of the stars’ orbits does not affect the stability of the helical planetary motion if the center of symmetry of the helix is relatively close to the star of the larger mass. We also show that if the center of symmetry of the conic-helical planetary orbit is relatively close to the star of the smaller mass, a sufficiently large eccentricity of stars’ orbits can switch the planetary motion to the unstable mode and the planet would escape the system. We demonstrate that such planets are transitable for the overwhelming majority of inclinations of plane of the stars’ orbits (i.e., the projections of the planet and the adjacent start on the plane of the sky coincide once in a while). This means that conic-helical planetary orbits at binary stars can be detected photometrically. We consider, as an example, Kepler-16 binary stars to provide illustrative numerical data on the possible parameters and the

  9. THE ROLE OF MAGNETIC HELICITY IN STRUCTURING THE SOLAR CORONA

    Energy Technology Data Exchange (ETDEWEB)

    Knizhnik, K. J. [Department of Physics and Astronomy, The Johns Hopkins University, Baltimore, MD 21287 (United States); Antiochos, S. K.; DeVore, C. R. [Heliophysics Science Division, NASA Goddard Space Flight Center, Greenbelt, MD 20771 (United States)

    2017-01-20

    Two of the most widely observed and striking features of the Sun's magnetic field are coronal loops, which are smooth and laminar, and prominences or filaments, which are strongly sheared. Loops are puzzling because they show little evidence of tangling or braiding, at least on the quiet Sun, despite the chaotic nature of the solar surface convection. Prominences are mysterious because the origin of their underlying magnetic structure—filament channels—is poorly understood at best. These two types of features would seem to be quite unrelated and wholly distinct. We argue that, on the contrary, they are inextricably linked and result from a single process: the injection of magnetic helicity into the corona by photospheric motions and the subsequent evolution of this helicity by coronal reconnection. In this paper, we present numerical simulations of the response of a Parker (1972) corona to photospheric driving motions that have varying degrees of helicity preference. We obtain four main conclusions: (1) in agreement with the helicity condensation model of Antiochos (2013), the inverse cascade of helicity by magnetic reconnection in the corona results in the formation of filament channels localized about polarity inversion lines; (2) this same process removes most complex fine structure from the rest of the corona, resulting in smooth and laminar coronal loops; (3) the amount of remnant tangling in coronal loops is inversely dependent on the net helicity injected by the driving motions; and (4) the structure of the solar corona depends only on the helicity preference of the driving motions and not on their detailed time dependence. We discuss the implications of our results for high-resolution observations of the corona.

  10. Variation in the helical structure of native collagen.

    Directory of Open Access Journals (Sweden)

    Joseph P R O Orgel

    Full Text Available The structure of collagen has been a matter of curiosity, investigation, and debate for the better part of a century. There has been a particularly productive period recently, during which much progress has been made in better describing all aspects of collagen structure. However, there remain some questions regarding its helical symmetry and its persistence within the triple-helix. Previous considerations of this symmetry have sometimes confused the picture by not fully recognizing that collagen structure is a highly complex and large hierarchical entity, and this affects and is effected by the super-coiled molecules that make it. Nevertheless, the symmetry question is not trite, but of some significance as it relates to extracellular matrix organization and cellular integration. The correlation between helical structure in the context of the molecular packing arrangement determines which parts of the amino acid sequence of the collagen fibril are buried or accessible to the extracellular matrix or the cell. In this study, we concentrate primarily on the triple-helical structure of fibrillar collagens I and II, the two most predominant types. By comparing X-ray diffraction data collected from type I and type II containing tissues, we point to evidence for a range of triple-helical symmetries being extant in the molecules native environment. The possible significance of helical instability, local helix dissociation and molecular packing of the triple-helices is discussed in the context of collagen's supramolecular organization, all of which must affect the symmetry of the collagen triple-helix.

  11. Cryogenic structural material and design of support structures for the Large Helical Device

    International Nuclear Information System (INIS)

    Nishimura, Arata; Imagawa, Shinsaku; Tamura, Hitoshi

    1997-01-01

    This paper describes a short history of material selection for the cryogenic support structures for the Large Helical Device (LHD) which has superconducting coils. Since the support structures are cooled down to 4.4 K together with the coils, SUS 316 was chosen because of its stable austenitic phase, sufficient mechanical properties at cryogenic temperature and good weldability. Also, outlines of the design and fabrication processes of the support structures are summarized. On the design of the support structures, a deformation analysis was carried out to maintain the proper magnetic field during operation. Afterwards, a stress analysis was performed. During machining and assembling, tolerance was noticed to keep coil positions accurate. Special welding grooves and fabrication processes were considered and achieved successfully. Finally, a cryogenic supporting post which sustains the cryogenic structures and superconducting coils is presented. CFRP was used in this specially developed supporting post to reduce the heat conduction from ambient 300 K structures. (author)

  12. The generic geometry of helices and their close-packed structures

    DEFF Research Database (Denmark)

    Olsen, Kasper; Bohr, Jakob

    2010-01-01

    with values from the literature for helical polypeptide backbone structures, the alpha-, pi-. 3-10-, and gamma-helices. The alpha-helices are close to being optimally packed in the sense of efficient use of space, i.e. close-packed. They are more densely packed than the other three types of helices...

  13. Variation in the Helical Structure of Native Collagen

    Science.gov (United States)

    2014-02-24

    2211 collagen, molecular structure, variability, xray diffraction REPORT DOCUMENTATION PAGE 11. SPONSOR/MONITOR’S REPORT NUMBER(S) 10. SPONSOR...indicates the triple-helix begins to associate at the (GPO)5 region as suggested previously [29,30], but must transition from the non-helical

  14. Assembly of alginate microfibers to form a helical structure using micromanipulation with a magnetic field

    International Nuclear Information System (INIS)

    Sun, Tao; Huang, Qiang; Shi, Qing; Wang, Huaping; Li, Pengyun; Fukuda, Toshio; Hu, Chengzhi; Nakajima, Masahiro

    2016-01-01

    Helical structures assembled using alginate microfibers have a promising spatial architecture mimicking in vivo vessels for culturing vascular cells. However, the helical structure can only be assembled at the macroscale, since a microassembly-based approach has not yet been developed. In this paper, we propose a magnetic-field-based micromanipulation method to fabricate a helical microstructure. By microfluidic spinning, alginate microfibers encapsulating magnetic nanoparticles are synthesized to enable the control of an electromagnetic needle (EMN). We developed a microrobotic system to actuate a micropipette to fix a free end of the microfiber, and then move the EMN to reel the microfiber around a micropillar. The motion of the EMN is guided using an upright microscope and a side-view camera. Because of the limitation of operation space, a spacer sleeve was designed to keep the tip of the EMN attracted to the microfiber, and simultaneously to keep the other part of the EMN isolated from the microfiber. To ensure the availability of the microfiber for continuously coiling, we enable the EMN tip to slide on the surface of the microfiber without changing the tensioning of the microfiber for positioning control. Furthermore, stable and repeatable micromanipulation was achieved to form multi-turn microfiber coils based on the motion planning of the EMN. Finally, we successfully fabricated a helical microstructure that can be applied in vascular tissue engineering in the future. (paper)

  15. Structures and related properties of helical, disulfide-stabilized peptides

    Energy Technology Data Exchange (ETDEWEB)

    Pagel, Mark D. [Univ. of California, Berkeley, CA (United States). Dept. of Chemistry

    1993-11-01

    The three dimensional structure of several peptides were determined by NMR spectroscopy and distance geometry calculations. Each peptide formed a predictable, rigid structure, consisting of an α-helix, a "scaffold" region which packed along one face of the helix, and two disulfide bridges which covalently connect the helix and scaffold regions. The peptide Apa-M5 was designed to constrain the M5 peptide from MLCK in a helical geometry using the apamin disulfide scaffold. This scaffold constrains the N- terminal end of the helix with two disulfide bridges and a reverse turn. Like the M5 peptide, Apa-M5 was found to bind calmodulin in a Ca2+-dependent 1:1 stoichiometry. However, the dissociation constant of the (Apa-M5)-calmodulin complex, 107 nM, was 100-fold higher than the dissociation constant of the M5-calmodulin complex. This difference was due to a putative steric overlap between the Apa-M5 scaffold and calmodulin. The peptide Apa-Cro was designed to replace the large structural protein matrix of λ Cro with the apamin disulfide scaffold. However, Apa-Cro did not bind the consensus DNA operator half-site of λ Cro, probably due to a steric overlap between the Apa-Cro disulfide framework and the DNA. The amino acid sequence of the scaffold-disulfide bridge arrangement of the peptide Max was derived from the core sequence of scyllatoxin, which contains an α-helix constrained at the C-terminal end by two disulfide bridges and a two-stranded βsheet scaffold. Max was shown to fold with >84% yield to form a predictable, stable structure that is similar to scyllatoxin. The folding and stability properties of Max make this scaffold and disulfide bridge arrangement an ideal candidate for the development of hybrid sequence peptides. The dynamics of a fraying C-terminal end of the helix of the peptide Apa-AlaN was determined by analysis of 15N NMR relaxation properties.

  16. Light scattering measurements supporting helical structures for chromatin in solution.

    Science.gov (United States)

    Campbell, A M; Cotter, R I; Pardon, J F

    1978-05-01

    Laser light scattering measurements have been made on a series of polynucleosomes containing from 50 to 150 nucleosomes. Radii of gyration have been determined as a function of polynucleosome length for different ionic strength solutions. The results suggest that at low ionic strength the chromatin adopts a loosely helical structure rather than a random coil. The helix becomes more regular on increasing the ionic strength, the dimension resembling those proposed by Finch and Klug for their solenoid model.

  17. Determining the helicity structure of third generation resonances

    International Nuclear Information System (INIS)

    Papaefstathiou, Andreas

    2011-11-01

    We examine methods that have been proposed for determining the helicity structure of decays of new resonances to third generation quarks and/or leptons. We present analytical and semi-analytical predictions and assess the applicability of the relevant variables in realistic reconstruction scenarios using Monte Carlo-generated events, including the effects of QCD radiation and multiple parton interactions, combinatoric ambiguities and fast detector simulation. (orig.)

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

    Science.gov (United States)

    André, Ingemar

    2018-01-01

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

  19. Micro helical polymeric structures produced by variable voltage direct electrospinning

    NARCIS (Netherlands)

    Shariatpanahi, S.P.; Iraji zad, A.; Abdollahzadeh, I.; Shirsavar, R.; Bonn, D.; Ejtehadi, R.

    2011-01-01

    Direct near field electrospinning is used to produce very long helical polystyrene microfibers in water. The pitch length of helices can be controlled by changing the applied voltage, allowing the production of both microsprings and microchannels. Using a novel high frequency variable voltage

  20. Right- and Left-Handed Helices, What is in between? Interconversion of Helical Structures of Alternating Pyridinedicarboxamide/m-(phenylazo)azobenzene Oligomers.

    Science.gov (United States)

    Tao, Peng; Parquette, Jon R; Hadad, Christopher M

    2012-12-11

    Some unnatural polymers/oligomers have been designed to adopt a well-defined, compact, three-dimensional folding capability. Azobenzene units are common linkages in these oligomer designs. Two alternating pyridinedicarboxamide/m-(phenylazo)azobenzene oligomers that can fold into both right- and left-handed helices were studied computationally in order to understand their dynamical properties. Helical structures were shown to be the global minima among the many different conformations generated from the Monte Carlo simulations, and extended conformations have higher potential energies than compact ones. To understand the interconversion process between right- and left-handed helices, replica-exchange molecular dynamic (REMD) simulations were performed on both oligomers, and with this method, both right- and left-handed helices were successfully sampled during the simulations. REMD trajectories revealed twisted conformations as intermediate structures in the interconversion pathway between the two helical forms of these azobenzene oligomers. This mechanism was observed in both oligomers in current study and occurred locally in the larger oligomer. This discovery indicates that the interconversion between helical structures with different handedness goes through a compact and partially folded structure instead of globally unfold and extended structure. This is also verified by the nudged elastic band (NEB) calculations. The temperature weighted histogram analysis method (T-WHAM) was applied on the REMD results to generate contour maps of the potential of mean force (PMF). Analysis showed that right- and left-handed helices are equally sampled in these REMD simulations. In large oligomers, both right- and left-handed helices can be adopted by different parts of the molecule simultaneously. The interconversion between two helical forms can occur in the middle of the helical structure and not necessarily at the termini of the oligomer.

  1. Structural Health Monitoring in Cylindrical Structures Using Helical Guided Wave Propagation

    Science.gov (United States)

    Baltazar, A.; Rojas, E.; Mijarez, R.

    Defect detection and characterization are critical tasks for structural health monitoring of pipe-like engineering structures. Propagation and detection of ultrasonic helical Lamb waves using macro fiber composite (MFC) sensors is studied. Experiments for defect detection and characterization on an aluminum hollow cylinder (114 mm in outer-diameter and 6 mm of wall thickness) were carried out. An experimental setup using MFC sensors coupled to the cylinder's surface in a pitch-catch configuration is presented. Time-frequency representation (TFR) using wavelets is employed to accurately perform mode identification of the ultrasonic captured signals. The initial results indicate that the use of helical waves could allow the monitoring of damage in difficult to access critical areas by locating the sensors only on a small region of the periphery of the cylindrical structure under inspection.

  2. Atomic structure and electronic properties of A2B2XY (A = Si-Pb, B = Cl-I, and XY = PN and SiS) inorganic double helices: first principles calculations.

    Science.gov (United States)

    Bijoy, T K; Murugan, P; Kumar, Vijay

    2018-03-05

    We study the structural stability and electronic properties of new classes of DNA-like inorganic double helices of the type A 2 B 2 XY (A = Si-Pb, B = Cl-I, and XY = PN and SiS) by employing first principles density functional theory (DFT) calculations including van der Waals interactions. In these quaternary double helices PN or SiS forms the inner helix while the AB helix wraps around the inner helix and the two are interconnected. We find that the bromides and iodides of Ge, Sn, and Pb as well as Pb 2 Cl 2 PN form structurally stable double helices while Ge 2 I 2 SiS as well as bromides and iodides of Sn and Pb have stable double helices. The atomic structures of different double helices have been analyzed in detail to understand the stability of these systems as there is up to about 80% difference in the interatomic distances in the two helices which is remarkable. Also in these new classes of double helices there is polar covalent bonding in the inner helix due to heteroatoms. We have calculated the DDEC6 partial atomic charges and bond orders which suggest strong covalent bonding in the inner helix. The electronic structure reveals that these double helices are semiconducting and in many cases the band gap is direct. Furthermore, we have studied the effects of doping and found that hole doping is the most appropriate way to tuning their electronic properties.

  3. Structure of acid-stable carmine.

    Science.gov (United States)

    Sugimoto, Naoki; Kawasaki, Yoko; Sato, Kyoko; Aoki, Hiromitsu; Ichi, Takahito; Koda, Takatoshi; Yamazaki, Takeshi; Maitani, Tamio

    2002-02-01

    Acid-stable carmine has recently been distributed in the U.S. market because of its good acid stability, but it is not permitted in Japan. We analyzed and determined the structure of the major pigment in acid-stable carmine, in order to establish an analytical method for it. Carminic acid was transformed into a different type of pigment, named acid-stable carmine, through amination when heated in ammonia solution. The features of the structure were clarified using a model compound, purpurin, in which the orientation of hydroxyl groups on the A ring of the anthraquinone skeleton is the same as that of carminic acid. By spectroscopic means and the synthesis of acid-stable carmine and purpurin derivatives, the structure of the major pigment in acid-stable carmine was established as 4-aminocarminic acid, a novel compound.

  4. Circular intensity differential scattering of light by helical structures. II. Applications

    Energy Technology Data Exchange (ETDEWEB)

    Bustamante, C.; Maestre, M.F.; Tinoco, I. Jr.

    1980-12-15

    Analysis and numerical calculations were made of the total scattering and differential scattering of circularly polarized light by helices as models of chiral structures. The differential scattering patterns are much more sensitive than the total scattering to helical parameters. For large helices the angular dependence of these patterns show lobes which alternate in sign. The number of lobes and the positions of the zeros directly measure the ratios of radius and pitch to wavelength. The signs depend on the sense of the helix. The results are compared with measured circular intensity differential scattering of membranes from the bacterium Spirillum serpens. Good qualitative agreement is obtained.

  5. Structure determination of helical filaments by solid-state NMR spectroscopy

    Science.gov (United States)

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

    2016-01-01

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

  6. An unprecedented 3D POM-Ag architecture with intertwined and homological helical structures.

    Science.gov (United States)

    Sha, Jing-Quan; Li, Meng-Ting; Sun, Jing-Wen; Zhang, Yu-Nan; Yan, Peng-Fei; Li, Guang-Ming

    2013-06-07

    A new hybrid compound, Na[Ag6(pyttz)2(H2O)][PMo12O40] (pyttz = 3-(pyrid-3-yl)-5-(1H-1,2,4-triazol-3-yl)-1,2,4-triazolyl), has been hydrothermally synthesized and structurally characterized by routine techniques. X-ray diffraction analysis reveals that the title compound is constructed by the 2D Ag-pyttz coordination polymer and 3D Ag-POM architecture with helix. A fascinating structural feature is the assembling fashion of the right- and left-helical chain, namely, the helical chains with different orientations are intertwined with each other forming intertwined double helical layers along the c-axis, and the identical left- or right-handed helical chains are fused together in a hand-by-hand mode generating another homological helical layer along the a-axis. As a result, these helical layers intersect each other obtaining an unprecedented 3D POM-Ag inorganic architecture. Note that the 3D framework with a helix constructed by POMs and metal ions has never been observed up to date. Additionally, its photocatalytic degradation of RhB was also investigated.

  7. Interactions between Radial Electric Field, Transport and Structure in Helical Plasmas

    International Nuclear Information System (INIS)

    Ida, Katsumi and others

    2006-01-01

    Control of the radial electric field is considered to be important in helical plasmas, because the radial electric field and its shear are expected to reduce neoclassical and anomalous transport, respectively. Particle and heat transport, that determines the radial structure of density and electron profiles, sensitive to the structure of radial electric field. On the other hand, the radial electric field itself is determined by the plasma parameters. In general, the sign of the radial electric field is determined by the plasma collisionality, while the magnitude of the radial electric field is determined by the temperature and/or density gradients. Therefore the structure of radial electric field and temperature and density are strongly coupled through the particle and heat transport and formation mechanism of radial electric field. Interactions between radial electric field, transport and structure in helical plasmas is discussed based on the experiments on Large Helical Device

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

    Science.gov (United States)

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

    2018-02-28

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

  9. Density filament and helical field line structures in three dimensional Weibel-mediated collisionless shocks

    International Nuclear Information System (INIS)

    Moritaka, Toseo; Kuramitsu, Yasuhiro; Sakawa, Youichi; Yamaura, Yuta; Ishikawa, Taishi; Takabe, Hideaki; Morita, Taichi

    2016-01-01

    Collisionless shocks mediated by Weibel instability are attracting attention for their relevance to experimental demonstrations of astrophysical shocks in high-intensity laser facilities. The three dimensional structure of Weibel-mediated shocks is investigated through a fully kinetic particle-in-cell simulation. The structures obtained are characterized by the following features: (i) helical magnetic field lines elongated in the direction upstream of the shock region, (ii) high and low density filaments inside the helical field lines. These structures originate from the interaction between counter-streaming plasma flow and magnetic vortexes caused by Weibel instability, and potentially affect the shock formation mechanism. (paper)

  10. Atomic structure governed diversity of exchange-driven spin helices in Fe nanoislands: Experiment and theory

    Science.gov (United States)

    Fischer, Jeison A.; Sandratskii, Leonid M.; Phark, Soo-hyon; Sander, Dirk; Parkin, Stuart

    2017-10-01

    We combine spin-polarized scanning tunneling microscopy (SP-STM) and first-principles calculations to demonstrate the control of the wavelength of helical spin textures in Fe nanoislands by varying their atomic structure. We make use of the complexity of submonolayer growth of Fe on Cu(111) to prepare nanoislands characterized by different thickness and in-plane atomic structure. SP-STM results reveal that the magnetic states of different nanoislands are spin helices. The wavelength of the spin helices varies strongly. Calculations performed for Fe films with different thickness and in-plane atomic structure explain the strong variation of the wavelength by a subtle balance in the competition between ferromagnetic and antiferromagnetic exchange interactions. We identify the crucial role of the effectively enhanced weak antiferromagnetic exchange interactions between distant atoms.

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

    Science.gov (United States)

    Braun, Gregory; Tierney, Dennis; Schmitzer, Heidrun

    2011-01-01

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

  12. Magnetic field structure near the plasma boundary in helical systems and divertor tokamaks

    International Nuclear Information System (INIS)

    Nagasaki, Kazunobu; Itoh, Kimitaka

    1990-02-01

    Magnetic field structure of the scrape off layer (SOL) region in both helical systems and divertor tokamaks is studied numerically by using model fields. The connection length of the field line to the wall is calculated. In helical systems, the connection length, L, has a logarithmic dependence on the distance from the outermost magnetic surface or that from the residual magnetic islands. The effect of axisymmetric fields on the field structure is also determined. In divertor tokamaks, the connection length also has logarithmic properties near the separatrix. Even when the perturbations, which resonate to rational surfaces near the plasma boundary, are added, logarithmic properties still remain. We compare the connection length of torsatron/helical-heliotron systems with that of divertor tokamaks. It is found that the former is shorter than the latter by one order magnitude with similar aspect ratio. (author)

  13. High Voltage Operation of Helical Pulseline Structures for Ion Acceleration

    CERN Document Server

    Waldron, William; Reginato, Lou

    2005-01-01

    The basic concept for the acceleration of heavy ions using a helical pulseline requires the launching of a high voltage traveling wave with a waveform determined by the beam transport physics in order to maintain stability and acceleration.* This waveform is applied to the front of the helix, creating over the region of the ion bunch a constant axial acceleration electric field that travels down the line in synchronism with the ions. Several methods of driving the helix have been considered. Presently, the best method of generating the waveform and also maintaining the high voltage integrity appears to be a transformer primary loosely coupled to the front of the helix, generating the desired waveform and achieving a voltage step-up from primary to secondary (the helix). This can reduce the drive voltage that must be brought into the helix enclosure through the feedthroughs by factors of 5 or more. The accelerating gradient is limited by the voltage holding of the vacuum insulator, and the material and helix g...

  14. Helicity in proton–proton elastic scattering and the spin structure of the pomeron

    Directory of Open Access Journals (Sweden)

    Carlo Ewerz

    2016-12-01

    Full Text Available We discuss different models for the spin structure of the nonperturbative pomeron: scalar, vector, and rank-2 symmetric tensor. The ratio of single-helicity-flip to helicity-conserving amplitudes in polarised high-energy proton–proton elastic scattering, known as the complex r5 parameter, is calculated for these models. We compare our results to experimental data from the STAR experiment. We show that the spin-0 (scalar pomeron model is clearly excluded by the data, while the vector pomeron is inconsistent with the rules of quantum field theory. The tensor pomeron is found to be perfectly consistent with the STAR data.

  15. Chirality and helicity of poly-benzyl-L-glutamate in liquid crystals and a wave structure that mimics collagen helicity in crimp

    Directory of Open Access Journals (Sweden)

    Vidal Benedicto de Campos

    2001-01-01

    Full Text Available Ideal biocompatible polymers must show a mimetic superstructure with biological supra-organization. Collagen-rich structures like tendons and ligaments are materials with various levels of order, from molecules to bundles of fibers, which affect their biomechanical properties and cellular interactions. Poly-benzyl-L-glutamate (PBLG displaying helicity was used here to test the development of wave-like structures as those occurring in collagen fibers. Birefringence of PBLG under various crystallization conditions was studied with a lambda/4 compensator according to Sénarmont. Qualitative observations were plainly sufficient to conclude that the PBLG fibrils were supra-organized helically as a chiral object. During crystallization stretched PBLG formed a helical superstructure with characteristic striation resembling waves (crimp. Supported by optical anisotropy findings, a twisted grain boundary liquid crystal type is proposed as a transition phase in the formation of the PBLG chiral object. A similarity with the wavy organization (crimp of collagen bundles is proposed.

  16. Exploring the Changes in the Structure of α-Helical Peptides ...

    Indian Academy of Sciences (India)

    sathish

    peptides based on alanine. • Validation of the results with respect to different force fields. • Interaction of long α-helical peptides derived from X-ray crystal structure with CNT. • Assessment of role of different interactions in the stabilization of CNT-peptide complex. K. Balamurugan, R. Gopalakrishnan, S. Sundar Raman, and ...

  17. Chemical signals turn on guest binding through structural reconfiguration of triangular helicates

    DEFF Research Database (Denmark)

    Sørensen, Anne; Castilla, Ana M.; Ronson, Tanya K.

    2013-01-01

    Be my guest: The function of a system based on self-assembled Zn(II) complexes can be controlled by external chemical stimuli. The complexes are based on a C3 -symmetric ligand that forms a unique triangular triple helicate structure 1. Upon subcomponent substitution, 1 is able to transform into ...

  18. Synthesis of Stable and Soluble One-Handed Helical Homopoly(substituted acetylenes without the Coexistence of Any Other Chiral Moieties via Two-Step Polymer Reactions in Membrane State: Molecular Design of the Starting Monomer

    Directory of Open Access Journals (Sweden)

    Takashi Kaneko

    2012-01-01

    Full Text Available A soluble and stable one-handed helical poly(substituted phenylacetylene without the coexistence of any other chiral moieties was successfully synthesized by asymmetric-induced polymerization of a chiral monomer followed by two-step polymer reactions in membrane state: (1 removing the chiral groups (desubstitution; and (2 introduction of achiral long alkyl groups at the same position as the desubstitution to enhance the solubility of the resulting one-handed helical polymer (resubstitution. The starting chiral monomer should have four characteristic substituents: (i a chiral group bonded to an easily hydrolyzed spacer group; (ii two hydroxyl groups; (iii a long rigid hydrophobic spacer between the chiral group and the polymerizing group; (iv a long achiral group near the chiral group. As spacer group a carbonate ester was selected. The two hydroxyl groups formed intramolecular hydrogen bonds stabilizing a one-handed helical structure in solution before and after the two-step polymer reactions in membrane state. The rigid long hydrophobic spacer, a phenylethynylphenyl group, enhanced the solubility of the starting polymer, and realized effective chiral induction from the chiral side groups to the main chain in the asymmetric-induced polymerization. The long alkyl group near the chiral group avoided shrinkage of the membrane and kept the reactivity of resubstitution in membrane state after removing the chiral groups. The g value (g = ([θ]/3,300/ε for the CD signal assigned to the main chain in the obtained final polymer was almost the same as that of the starting polymer in spite of the absence of any other chiral moieties. Moreover, since the one-handed helical structure was maintained by the intramolecular hydrogen bonds in a solution, direct observation of the one-handed helicity of the final homopolymer has been realized in CD for the solution for the first time.

  19. ALS-causing profilin-1-mutant forms a non-native helical structure in membrane environments.

    Science.gov (United States)

    Lim, Liangzhong; Kang, Jian; Song, Jianxing

    2017-11-01

    Despite having physiological functions completely different from superoxide dismutase 1 (SOD1), profilin 1 (PFN1) also carries mutations causing amyotrophic lateral sclerosis (ALS) with a striking similarity to that triggered by SOD1 mutants. Very recently, the C71G-PFN1 has been demonstrated to cause ALS by a gain of toxicity and the acceleration of motor neuron degeneration preceded the accumulation of its aggregates. Here by atomic-resolution NMR determination of conformations and dynamics of WT-PFN1 and C71G-PFN1 in aqueous buffers and in membrane mimetics DMPC/DHPC bicelle and DPC micelle, we deciphered that: 1) the thermodynamic destabilization by C71G transforms PFN1 into coexistence with the unfolded state, which is lacking of any stable tertiary/secondary structures as well as restricted ps-ns backbone motions, thus fundamentally indistinguishable from ALS-causing SOD1 mutants. 2) Most strikingly, while WT-PFN1 only weakly interacts with DMPC/DHPC bicelle without altering the native structure, C71G-PFN1 acquires abnormal capacity in strongly interacting with DMPC/DHPC bicelle and DPC micelle, energetically driven by transforming the highly disordered unfolded state into a non-native helical structure, similar to what has been previously observed on ALS-causing SOD1 mutants. Our results imply that one potential mechanism for C71G-PFN1 to initiate ALS might be the abnormal interaction with membranes as recently established for SOD1 mutants. Copyright © 2017 Elsevier B.V. All rights reserved.

  20. Analysis on sliding helices and strands in protein structural ...

    Indian Academy of Sciences (India)

    PRAKASH KUMAR

    2007-06-16

    Jun 16, 2007 ... The quality of the structural alignments plays an important role in such studies. Several structural comparison algorithms have been developed over the last few decades and some ... for superposition of distantly related multiple protein ... protein kinase [1O6L, (Yang et al 2002)], protein kinase C θ. [1XJD ...

  1. Spirulina-templated metal microcoils with controlled helical structures for THz electromagnetic responses.

    Science.gov (United States)

    Kamata, Kaori; Piao, Zhenzi; Suzuki, Soichiro; Fujimori, Takahiro; Tajiri, Wataru; Nagai, Keiji; Iyoda, Tomokazu; Yamada, Atsushi; Hayakawa, Toshiaki; Ishiwara, Mitsuteru; Horaguchi, Satoshi; Belay, Amha; Tanaka, Takuo; Takano, Keisuke; Hangyo, Masanori

    2014-05-12

    Microstructures in nature are ultrafine and ordered in biological roles, which have attracted material scientists. Spirulina forms three-dimensional helical microstructure, one of remarkable features in nature beyond our current processing technology such as lithography in terms of mass-productivity and structural multiplicity. Spirulina varies its diameter, helical pitch, and/or length against growing environment. This unique helix is suggestive of a tiny electromagnetic coil, if composed of electro-conductive metal, which brought us main concept of this work. Here, we describe the biotemplating process onto Spirulina surface to fabricate metal microcoils. Structural parameters of the microcoil can be controlled by the cultivation conditions of Spirulina template and also purely one-handed microcoil can be fabricated. A microcoil dispersion sheet exhibited optically active response attributed to structural resonance in terahertz-wave region.

  2. Assembly, maturation and three-dimensional helical structure of the teratogenic rubella virus.

    Directory of Open Access Journals (Sweden)

    Vidya Mangala Prasad

    2017-06-01

    Full Text Available Viral infections during pregnancy are a significant cause of infant morbidity and mortality. Of these, rubella virus infection is a well-substantiated example that leads to miscarriages or severe fetal defects. However, structural information about the rubella virus has been lacking due to the pleomorphic nature of the virions. Here we report a helical structure of rubella virions using cryo-electron tomography. Sub-tomogram averaging of the surface spikes established the relative positions of the viral glycoproteins, which differed from the earlier icosahedral models of the virus. Tomographic analyses of in vitro assembled nucleocapsids and virions provide a template for viral assembly. Comparisons of immature and mature virions show large rearrangements in the glycoproteins that may be essential for forming the infectious virions. These results present the first known example of a helical membrane-enveloped virus, while also providing a structural basis for its assembly and maturation pathway.

  3. Assembly, maturation and three-dimensional helical structure of the teratogenic rubella virus.

    Science.gov (United States)

    Mangala Prasad, Vidya; Klose, Thomas; Rossmann, Michael G

    2017-06-01

    Viral infections during pregnancy are a significant cause of infant morbidity and mortality. Of these, rubella virus infection is a well-substantiated example that leads to miscarriages or severe fetal defects. However, structural information about the rubella virus has been lacking due to the pleomorphic nature of the virions. Here we report a helical structure of rubella virions using cryo-electron tomography. Sub-tomogram averaging of the surface spikes established the relative positions of the viral glycoproteins, which differed from the earlier icosahedral models of the virus. Tomographic analyses of in vitro assembled nucleocapsids and virions provide a template for viral assembly. Comparisons of immature and mature virions show large rearrangements in the glycoproteins that may be essential for forming the infectious virions. These results present the first known example of a helical membrane-enveloped virus, while also providing a structural basis for its assembly and maturation pathway.

  4. Spirulina-Templated Metal Microcoils with Controlled Helical Structures for THz Electromagnetic Responses

    Science.gov (United States)

    Kamata, Kaori; Piao, Zhenzi; Suzuki, Soichiro; Fujimori, Takahiro; Tajiri, Wataru; Nagai, Keiji; Iyoda, Tomokazu; Yamada, Atsushi; Hayakawa, Toshiaki; Ishiwara, Mitsuteru; Horaguchi, Satoshi; Belay, Amha; Tanaka, Takuo; Takano, Keisuke; Hangyo, Masanori

    2014-05-01

    Microstructures in nature are ultrafine and ordered in biological roles, which have attracted material scientists. Spirulina forms three-dimensional helical microstructure, one of remarkable features in nature beyond our current processing technology such as lithography in terms of mass-productivity and structural multiplicity. Spirulina varies its diameter, helical pitch, and/or length against growing environment. This unique helix is suggestive of a tiny electromagnetic coil, if composed of electro-conductive metal, which brought us main concept of this work. Here, we describe the biotemplating process onto Spirulina surface to fabricate metal microcoils. Structural parameters of the microcoil can be controlled by the cultivation conditions of Spirulina template and also purely one-handed microcoil can be fabricated. A microcoil dispersion sheet exhibited optically active response attributed to structural resonance in terahertz-wave region.

  5. Diastereomeric Right- and Left-Handed Helical Structures with Fourteen (R)-Chiral Centers.

    Science.gov (United States)

    Eto, Ryo; Oba, Makoto; Ueda, Atsushi; Uku, Tsubasa; Doi, Mitsunobu; Matsuo, Yosuke; Tanaka, Takashi; Demizu, Yosuke; Kurihara, Masaaki; Tanaka, Masakazu

    2017-12-22

    The relationship between chiral centers and the helical-screw control of their peptides has already been reported, but it has yet to be elucidated in detail. A chiral four-membered ring α,α-disubstituted α-amino acid with a (R,R)-butane-2,3-diol acetal moiety at the γ-position, but no α-chiral carbon, was synthesized. X-ray crystallographic analysis unambiguously revealed that its homo-chiral heptapeptide formed right-handed (P) and left-handed (M) 3 10 -helical structures at a ratio of 1:1. They appeared to be enantiomeric at the peptide backbone, but diastereomeric with fourteen (R)-configuration chiral centers. Conformational analyses of homopeptides in solution also indicated that diastereomeric (P) and (M) helices existed at approximately equal amounts, with a slight preference toward right-handedness, and they quickly interchanged at room temperature. The circumstances of chiral centers are important for the control of their helical-screw direction. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. Structure and Dynamics of DNA and RNA Double Helices Obtained from the GGGGCC and CCCCGG Hexanucleotide Repeats That Are the Hallmark of C9FTD/ALS Diseases.

    Science.gov (United States)

    Zhang, Yuan; Roland, Christopher; Sagui, Celeste

    2017-03-15

    A (GGGGCC) hexanucleotide repeat (HR) expansion in the C9ORF72 gene, and its associated antisense (CCCCGG) expansion, are considered the major cause behind frontotemporal dementia and amyotrophic lateral sclerosis. We have performed molecular dynamics simulations to characterize the conformation and dynamics of the 12 duplexes that result from the three different reading frames in sense and antisense HRs for both DNA and RNA. These duplexes display atypical structures relevant not only for a molecular level understanding of these diseases but also for enlarging the repertoire of nucleic-acid structural motifs. G-rich helices share common features. The inner G-G mismatches stay inside the helix in G syn -G anti conformations and form two hydrogen bonds (HBs) between the Watson-Crick edge of G anti and the Hoogsteen edge of G syn . In addition, G syn in RNA forms a base-phosphate HB. Inner G-G mismatches cause local unwinding of the helix. G-rich double helices are more stable than C-rich helices due to better stacking and HBs of G-G mismatches. C-rich helix conformations vary wildly. C mismatches flip out of the helix in DNA but not in RNA. Least (most) stable C-rich RNA and DNA helices have single (double) mismatches separated by two (four) Watson-Crick basepairs. The most stable DNA structure displays an "e-motif" where mismatched bases flip toward the minor groove and point in the 5' direction. There are two RNA conformations, where the orientation and HB pattern of the mismatches is coupled to bending of the helix.

  7. The α-Helical Structure of Prodomains Promotes Translocation of Intrinsically Disordered Neuropeptide Hormones into the Endoplasmic Reticulum*

    Science.gov (United States)

    Dirndorfer, Daniela; Seidel, Ralf P.; Nimrod, Guy; Miesbauer, Margit; Ben-Tal, Nir; Engelhard, Martin; Zimmermann, Richard; Winklhofer, Konstanze F.; Tatzelt, Jörg

    2013-01-01

    Different neuropeptide hormones, which are either too small to adopt a stable conformation or are predicted to be intrinsically disordered, are synthesized as larger precursors containing a prodomain in addition to an N-terminal signal peptide. We analyzed the biogenesis of three unstructured neuropeptide hormones and observed that translocation of these precursors into the lumen of the endoplasmic reticulum (ER) is critically dependent on the presence of the prodomain. The hormone domains could be deleted from the precursors without interfering with ER import and secretion, whereas constructs lacking the prodomain remained in the cytosol. Domain-swapping experiments revealed that the activity of the prodomains to promote productive ER import resides in their ability to adopt an α-helical structure. Removal of the prodomain from the precursor did not interfere with co-translational targeting of the nascent chain to the Sec61 translocon but with its subsequent productive translocation into the ER lumen. Our study reveals a novel function of prodomains to enable import of small or intrinsically disordered secretory proteins into the ER based on their ability to adopt an α-helical conformation. PMID:23532840

  8. From random coil polymers to helical structures induced by carbon nanotubes and supramolecular interactions.

    Science.gov (United States)

    Huang, Kai-Wei; Wu, Yu-Rong; Jeong, Kwang-Un; Kuo, Shiao-Wei

    2013-10-01

    A simple method is reported for the preparation of double-helical structures through a series of achiral random and block copolymers poly(styrene-co-4-vinylbenzyl triazolylmethyl methylthymine) (PS-co-PVBT) with various T units on the side chains through click reactions of poly(styrene-co-4-vinylbenzyl azide) (PS-co-PVBN(3)) with propargyl thymine (PT) and also the synthesis of the A-appended pyrene derivative (A-Py) through click chemistry. This double-helical structure is observed from achiral random-coil polystyrene (PS) main chains, stabilized through the combination of multiple A-T hydrogen bonds, and π-π stacking between pyrene units and single-walled carbon nanotubes (SWCNTs). © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. Buckwheat trypsin inhibitor with helical hairpin structure belongs to a new family of plant defence peptides.

    Science.gov (United States)

    Oparin, Peter B; Mineev, Konstantin S; Dunaevsky, Yakov E; Arseniev, Alexander S; Belozersky, Mikhail A; Grishin, Eugene V; Egorov, Tsezi A; Vassilevski, Alexander A

    2012-08-15

    A new peptide trypsin inhibitor named BWI-2c was obtained from buckwheat (Fagopyrum esculentum) seeds by sequential affinity, ion exchange and reversed-phase chromatography. The peptide was sequenced and found to contain 41 amino acid residues, with four cysteine residues involved in two intramolecular disulfide bonds. Recombinant BWI-2c identical to the natural peptide was produced in Escherichia coli in a form of a cleavable fusion with thioredoxin. The 3D (three-dimensional) structure of the peptide in solution was determined by NMR spectroscopy, revealing two antiparallel α-helices stapled by disulfide bonds. Together with VhTI, a trypsin inhibitor from veronica (Veronica hederifolia), BWI-2c represents a new family of protease inhibitors with an unusual α-helical hairpin fold. The linker sequence between the helices represents the so-called trypsin inhibitory loop responsible for direct binding to the active site of the enzyme that cleaves BWI-2c at the functionally important residue Arg(19). The inhibition constant was determined for BWI-2c against trypsin (1.7×10(-1)0 M), and the peptide was tested on other enzymes, including those from various insect digestive systems, revealing high selectivity to trypsin-like proteases. Structural similarity shared by BWI-2c, VhTI and several other plant defence peptides leads to the acknowledgement of a new widespread family of plant peptides termed α-hairpinins.

  10. Tensile Characterization of Single-Walled Carbon Nanotubes with Helical Structural Defects.

    Science.gov (United States)

    Jhon, Young I; Kim, Chulki; Seo, Minah; Cho, Woon Jo; Lee, Seok; Jhon, Young Min

    2016-02-04

    Recently, evidence was presented that certain single-walled carbon nanotubes (SWNTs) possess helical defective traces, exhibiting distinct cleaved lines, yet their mechanical characterization remains a challenge. On the basis of the spiral growth model of SWNTs, here we present atomic details of helical defects and investigate how the tensile behaviors of SWNTs change with their presence using molecular dynamics simulations. SWNTs have exhibited substantially lower tensile strength and strain than theoretical results obtained from a seamless tubular structure, whose physical origin cannot be explained either by any known SWNT defects so far. We find that this long-lasting puzzle could be explained by assuming helical defects in SWNTs, exhibiting excellent agreement with experimental observation. The mechanism of this tensile process is elucidated by analyzing atomic stress distribution and evolution, and the effects of the chirality and diameter of SWNTs on this phenomenon are examined based on linear elastic fracture mechanics. This work contributes significantly to our understanding of the growth mechanism, defect hierarchies, and mechanical properties of SWNTs.

  11. How structurally stable are global socioeconomic systems?

    Science.gov (United States)

    Saavedra, Serguei; Rohr, Rudolf P; Gilarranz, Luis J; Bascompte, Jordi

    2014-11-06

    The stability analysis of socioeconomic systems has been centred on answering whether small perturbations when a system is in a given quantitative state will push the system permanently to a different quantitative state. However, typically the quantitative state of socioeconomic systems is subject to constant change. Therefore, a key stability question that has been under-investigated is how strongly the conditions of a system itself can change before the system moves to a qualitatively different behaviour, i.e. how structurally stable the systems is. Here, we introduce a framework to investigate the structural stability of socioeconomic systems formed by a network of interactions among agents competing for resources. We measure the structural stability of the system as the range of conditions in the distribution and availability of resources compatible with the qualitative behaviour in which all the constituent agents can be self-sustained across time. To illustrate our framework, we study an empirical representation of the global socioeconomic system formed by countries sharing and competing for multinational companies used as proxy for resources. We demonstrate that the structural stability of the system is inversely associated with the level of competition and the level of heterogeneity in the distribution of resources. Importantly, we show that the qualitative behaviour of the observed global socioeconomic system is highly sensitive to changes in the distribution of resources. We believe that this work provides a methodological basis to develop sustainable strategies for socioeconomic systems subject to constantly changing conditions. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

  12. Helicity content and tokamak applications of helicity

    International Nuclear Information System (INIS)

    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

  13. Bioinspired coupled helical coils for soft tissue engineering of tubular structures - Improved mechanical behavior of tubular collagen type I templates.

    Science.gov (United States)

    Janke, H P; Bohlin, J; Lomme, R M L M; Mihaila, S M; Hilborn, J; Feitz, W F J; Oosterwijk, E

    2017-09-01

    The design of constructs for tubular tissue engineering is challenging. Most biomaterials need to be reinforced with supporting structures such as knittings, meshes or electrospun material to comply with the mechanical demands of native tissues. In this study, coupled helical coils (CHCs) were manufactured to mimic collagen fiber orientation as found in nature. Monofilaments of different commercially available biodegradable polymers were wound and subsequently fused, resulting in right-handed and left-handed polymer helices fused together in joints where the filaments cross. CHCs of different polymer composition were tested to determine the tensile strength, strain recovery, hysteresis, compressive strength and degradation of CHCs of different composition. Subsequently, seamless and stable hybrid constructs consisting of PDSII® USP 2-0 CHCs embedded in porous collagen type I were produced. Compared to collagen alone, this hybrid showed superior strain recovery (93.5±0.9% vs 71.1±12.6% in longitudinal direction; 87.1±6.6% vs 57.2±4.6% in circumferential direction) and hysteresis (18.9±2.7% vs 51.1±12.0% in longitudinal direction; 11.5±4.6% vs 46.3±6.3% in circumferential direction). Furthermore, this hybrid construct showed an improved Young's modulus in both longitudinal (0.5±0.1MPavs 0.2±0.1MPa; 2.5-fold) and circumferential (1.65±0.07MPavs (2.9±0.3)×10 -2 MPa; 57-fold) direction, respectively, compared to templates created from collagen alone. Moreover, hybrid template characteristics could be modified by changing the CHC composition and CHCs were produced showing a mechanical behavior similar to the native ureter. CHC-enforced templates, which are easily tunable to meet different demands may be promising for tubular tissue engineering. Most tubular constructs lack sufficient strength and tunability to comply with the mechanical demands of native tissues. Therefore, we embedded coupled helical coils (CHCs) produced from biodegradable polymers - to

  14. Three-dimensional structure of a schistosome serpin revealing an unusual configuration of the helical subdomain

    Energy Technology Data Exchange (ETDEWEB)

    Granzin, Joachim [Institute of Complex Systems, ICS-6: Structural Biochemistry, Forschungszentrum Jülich, 52425 Jülich (Germany); Huang, Ying; Topbas, Celalettin [Department of Cell Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195 (United States); Huang, Wenying [Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195 (United States); Wu, Zhiping [Department of Cell Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195 (United States); Misra, Saurav [Department of Molecular Cardiology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195 (United States); Hazen, Stanley L. [Department of Cell Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195 (United States); Blanton, Ronald E. [Department of Infectious Diseases, Case Western Reserve University, Cleveland, OH 44190 (United States); Lee, Xavier [Department of Cell Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195 (United States); Weiergräber, Oliver H., E-mail: o.h.weiergraeber@fz-juelich.de [Institute of Complex Systems, ICS-6: Structural Biochemistry, Forschungszentrum Jülich, 52425 Jülich (Germany)

    2012-06-01

    The crystal structure of ShSPI, a serpin from the blood fluke S. haematobium, reveals some peculiar features of the helical subdomain which have not been observed previously in the serpin superfamily. Parasitic organisms are constantly challenged by the defence mechanisms of their respective hosts, which often depend on serine protease activities. Consequently, protease inhibitors such as those belonging to the serpin superfamily have emerged as protective elements that support the survival of the parasites. This report describes the crystal structure of ShSPI, a serpin from the trematode Schistosoma haematobium. The protein is exposed on the surface of invading cercaria as well as of adult worms, suggesting its involvement in the parasite–host interaction. While generally conforming to the well established serpin fold, the structure reveals several distinctive features, mostly concerning the helical subdomain of the protein. It is proposed that these peculiarities are related to the unique biological properties of a small serpin subfamily which is conserved among pathogenic schistosomes.

  15. Polarization Selectivity of Artificial Anisotropic Structures Based on DNA-Like Helices

    International Nuclear Information System (INIS)

    Semchenko, I. V.; Khakhomov, S. A.; Balmakov, A. P.

    2010-01-01

    Currently, 2D and 3D structures of different symmetries can be formed from DNA molecules. The electromagnetic properties of this new natural chiral material can be changed by metalizing DNA. Spatial structures of this type can be used in nanotechnology to prepare metamaterials for the far-UV region. It is shown by the example of an octahedron and a cube composed of DNA-like helices that these structures may exhibit polarization selectivity to electromagnetic radiation. In addition, it is suggested that the effect of the polarization selectivity of DNA-like artificial structures may also occur in the soft X-ray region for all living organisms in nature due to the universal DNA form.

  16. Computer-aided three-dimensional images of the helical structure in the apical tubule of absorbing epithelia

    International Nuclear Information System (INIS)

    Kawai, Yoshinori; Hatae, Tanenori

    1990-01-01

    Computer-aided three-dimensional models of the helical structure within an apical tubule (AT) of several absorbing epithelia (kidney proximal tubule, visceral yolk sac, and ductuli efferentes) were constructed using ray-tracing graphics software to further understand the highly ordered structural configuration. Our previous electron microscopic studies using thin-section technique have first revealed the helical structure within the AT fixed in situ with a mixture of formaldehyde, glutaraldehyde, and osmium tetroxide. In the present study, we construct a computer-aided three-dimensional model of the helical structure in the AT to explain quantitative data obtained by the electron microscopy. The model could well explain several aspects of electron microscopical images and enables us to understand more clearly the three-dimensional configuration of the unique structure associated with the AT. (author)

  17. Electronic structure of helically coiled carbon nanotubes: product Relation between the phason lines and energy band features

    International Nuclear Information System (INIS)

    Akagi, K.; Tamura, R.; Tsukada, M.; Itoh, S.; Ihara, S.

    1996-01-01

    Recently carbon nanotubes with coiled structures (carbon helix) were found and have attracted much attention. The electronic structures of two families of such helices, whose structures are proposed by two of the present authors (Ihara and Itoh), are calculated using a tight-binding method based on development maps. It is shown that the various band structures are classified by parameters characterizing the geometry of helices based on the concept of open-quote open-quote phason line.close-quote close-quote Semimetallic character, which could not be manifested in straight tubes, is found in only one of those families

  18. Free energy determinants of secondary structure formation: I. alpha-Helices.

    Science.gov (United States)

    Yang, A S; Honig, B

    1995-09-22

    The Zimm-Bragg parameters s and sigma are calculated for the helix-coil transition of poly-L-alanine. The theoretical approach involves evaluating gas phase conformational energies for both coil and helical states using the CHARMM potential function and accounting for solvation effects with various continuum solvation models. Conformational free energies are then incorporated into a formalism developed by Go et al. for the calculation of s and sigma. Calculated values for both s and sigma as well as the enthalpy change associated with helix formation are in good agreement with experimental data when the Finite Difference Poisson-Boltzmann (FDPB) method is used to treat solvent effects. The driving force for the helix-coil transition is analyzed in terms of individual free energy components. Hydrogen bond formation is found to contribute little to helix stability because the internal hydrogen bonding energy is largely canceled by the large free energy cost associated with removing polar groups from water. The entropic cost associated with fixing backbone dihedral angles in the helical conformation is found to be approximately 7 e.u./residue (about 2 kcal/mol at room temperature). The major driving force favoring helix formation can be associated with interactions including enhanced van der Waals interactions in the close-packed helix conformation and the hydrophobic effect. These contribute about 2 kcal/mol favoring the helical state. The differences in helical propensities between alanine and glycine are attributed primarily to hydrophobic and packing interactions involving the C beta with a smaller contribution arising from increased conformational freedom for glycine in the coil state. The description of helix formation presented here is consistent with previous conclusions regarding tertiary structure formation which suggest that hydrophobic and close-packed interactions provide stability while hydrogen bond formation constitutes a structural constraint imposed

  19. Syntheses, structures and luminescence properties of lanthanide coordination polymers with helical character

    International Nuclear Information System (INIS)

    Zhou Ruisha; Cui Xiaobing; Song Jiangfeng; Xu Xiaoyu; Xu Jiqing; Wang Tiegang

    2008-01-01

    A series of lanthanide coordination polymers, (Him) n [Ln(ip) 2 (H 2 O)] n [Ln=La(1), Pr(2), Nd(3) and Dy(4), H 2 ip=isophthalic acid, im=imidazole] and [Y 2 (ip) 3 (H 2 O) 2 ] n .nH 2 O (5), have been synthesized and characterized by elemental analyses, infrared (IR), ultraviolet-visible-near infrared (UV-Vis-NIR) and single-crystal X-ray diffraction analyses. The isostructural compounds 1-4 possess 3-D structures with three different kinds of channels. Compound 5 features a 2-D network making of two different kinds of quadruple-helical chains. Compounds 2 and 3 present the characteristic emissions of Pr(III) and Nd(III) ions in NIR region, respectively. Compound 4 shows sensitized luminescence of Dy(III) ions in visible region. - Graphical abstract: A series of lanthanide coodination polymers, (Him) n [Ln(ip) 2 (H 2 O)] n [Ln=La(1), Pr(2), Nd(3) and Dy(4)] and [Y 2 (ip) 3 (H 2 O) 2 ] n .nH 2 O (5), have been reported. The isostructural compounds 1-4 possess 3-D structures with three different kinds of channels. Compound 5 displays a 2-D network making of two kinds of quadruple-helical chains. Display Omitted

  20. Continuous liquid level detection based on two parallel plastic optical fibers in a helical structure

    Science.gov (United States)

    Zhang, Yingzi; Hou, Yulong; Zhang, Yanjun; Hu, Yanjun; Zhang, Liang; Gao, Xiaolong; Zhang, Huixin; Liu, Wenyi

    2018-02-01

    A simple and low-cost continuous liquid-level sensor based on two parallel plastic optical fibers (POFs) in a helical structure is presented. The change in the liquid level is determined by measuring the side-coupling power in the passive fiber. The side-coupling ratio is increased by just filling the gap between the two POFs with ultraviolet-curable optical cement, making the proposed sensor competitive. The experimental results show that the side-coupling power declines as the liquid level rises. The sensitivity and the measurement range are flexible and affected by the geometric parameters of the helical structure. A higher sensitivity of 0.0208 μW/mm is acquired for a smaller curvature radius of 5 mm, and the measurement range can be expanded to 120 mm by enlarging the screw pitch to 40 mm. In addition, the reversibility and temperature dependence are studied. The proposed sensor is a cost-effective solution offering the advantages of a simple fabrication process, good reversibility, and compensable temperature dependence.

  1. DFT computations of the lattice constant, stable atomic structure and ...

    African Journals Online (AJOL)

    This paper presents the most stable atomic structure and lattice constant of Fullerenes (C60). FHI-aims DFT code was used to predict the stable structure and the computational lattice constant of C60. These were compared with known experimental structures and lattice constants of C60. The results obtained showed that ...

  2. An All-Atom Force Field for Tertiary Structure Prediction of Helical Proteins

    Science.gov (United States)

    Herges, T.; Wenzel, W.

    2004-01-01

    We have developed an all-atom free-energy force field (PFF01) for protein tertiary structure prediction. PFF01 is based on physical interactions and was parameterized using experimental structures of a family of proteins believed to span a wide variety of possible folds. It contains empirical, although sequence-independent terms for hydrogen bonding. Its solvent-accessible surface area solvent model was first fit to transfer energies of small peptides. The parameters of the solvent model were then further optimized to stabilize the native structure of a single protein, the autonomously folding villin headpiece, against competing low-energy decoys. Here we validate the force field for five nonhomologous helical proteins with 20–60 amino acids. For each protein, decoys with 2–3 Å backbone root mean-square deviation and correct experimental Cβ–Cβ distance constraints emerge as those with the lowest energy. PMID:15507688

  3. Stable preparations of tyrosine hydroxylase provide the solution structure of the full-length enzyme

    Science.gov (United States)

    Bezem, Maria T.; Baumann, Anne; Skjærven, Lars; Meyer, Romain; Kursula, Petri; Martinez, Aurora; Flydal, Marte I.

    2016-01-01

    Tyrosine hydroxylase (TH) catalyzes the rate-limiting step in the biosynthesis of catecholamine neurotransmitters. TH is a highly complex enzyme at mechanistic, structural, and regulatory levels, and the preparation of kinetically and conformationally stable enzyme for structural characterization has been challenging. Here, we report on improved protocols for purification of recombinant human TH isoform 1 (TH1), which provide large amounts of pure, stable, active TH1 with an intact N-terminus. TH1 purified through fusion with a His-tagged maltose-binding protein on amylose resin was representative of the iron-bound functional enzyme, showing high activity and stabilization by the natural feedback inhibitor dopamine. TH1 purified through fusion with a His-tagged ZZ domain on TALON is remarkably stable, as it was partially inhibited by resin-derived cobalt. This more stable enzyme preparation provided high-quality small-angle X-ray scattering (SAXS) data and reliable structural models of full-length tetrameric TH1. The SAXS-derived model reveals an elongated conformation (Dmax = 20 nm) for TH1, different arrangement of the catalytic domains compared with the crystal structure of truncated forms, and an N-terminal region with an unstructured tail that hosts the phosphorylation sites and a separated Ala-rich helical motif that may have a role in regulation of TH by interacting with binding partners. PMID:27462005

  4. Predicting unfolding thermodynamics and stable intermediates for alanine-rich helical peptides with the aid of coarse-grained molecular simulation.

    Science.gov (United States)

    Calero-Rubio, Cesar; Paik, Bradford; Jia, Xinqiao; Kiick, Kristi L; Roberts, Christopher J

    2016-10-01

    This report focuses on the molecular-level processes and thermodynamics of unfolding of a series of helical peptides using a coarse-grained (CG) molecular model. The CG model was refined to capture thermodynamics and structural changes as a function of temperature for a set of published peptide sequences. Circular dichroism spectroscopy (CD) was used to experimentally monitor the temperature-dependent conformational changes and stability of published peptides and new sequences introduced here. The model predictions were quantitatively or semi-quantitatively accurate in all cases. The simulations and CD results showed that, as expected, in most cases the unfolding of helical peptides is well described by a simply 2-state model, and conformational stability increased with increased length of the helices. A notable exception in a 19-residue helix was when two Ala residues were each replaced with Phe. This stabilized a partly unfolded intermediate state via hydrophobic contacts, and also promoted aggregates at higher peptide concentrations. Copyright © 2016 Elsevier B.V. All rights reserved.

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

    International Nuclear Information System (INIS)

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

    2016-01-01

    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)]·2H 2 O} n (1), {[Zn(bib)(atbip)]·H 2 O} n (2), [Zn(bib)(2,2′-tda)]} n (3) and {[Zn(bib)(5-tbipa)]·EtOH} n (4), (H 2 atibdc=5-amino-2,4,6-triiodoisophthalic acid, H 2 atbip=5-amino-2,4,6-tribromoisophthalic acid, 2,2′-H 2 tad=2,2′-thiodiacetic acid, 5-H 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 1 =209.658 kJ·mol −1 , E 2 =250.037 kJ mol −1 , E 3 =225.300 kJ mol −1 , E 4 =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. ΔH d >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

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

    Science.gov (United States)

    Yu, Edmund; Velikovich, Alexander; Peterson, Kyle

    2014-10-01

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

  7. Effect of Anisotropy Structure on Plume Entropy and Reactive Mixing in Helical Flows

    DEFF Research Database (Denmark)

    Ye, Yu; Chiogna, Gabriele; Lu, Chunhui

    2018-01-01

    Plume dilution and reactive mixing can be considerably enhanced by helical flows occurring in three-dimensional anisotropic porous media. In this study, we perform conservative and reactive transport simulations considering different anisotropy structures of a single inclusion with the objective...... of exploring the effect of the inclusion’s geometry and orientation on the patterns of twisted streamlines and on the overall dilution and reaction of solute plumes. We analyzed 100 different scenarios by varying key parameters such as the angle of the anisotropic structures with respect to the average flow...... velocity, the spacing between alternated heterogeneous zones of coarse and fine materials, the permeability contrast between such matrices, and the magnitude of the seepage velocity. Entropy conservation equations and entropy-based metrics for both conservative and reactive species were adopted to quantify...

  8. Analysis of structure and transition of radial electric field in helical systems

    International Nuclear Information System (INIS)

    Toda, S.; Itoh, K.

    2001-03-01

    A set of transport equations is analyzed, including the bifurcation of the radial electric field in toroidal helical systems. Calculations are made simulating CHS experiments. Both hard and soft transitions are found in the profile of the radial electric field. Whether the electric domain interface exists or not is examined. The electric domain interface is found to exist, depending on the ratio of the electron temperature to the ion temperature. The structure of the electric domain interface is also studied. The steep gradient of the radial electric field is obtained and the width of the electric domain interface is determined by the anomalous diffusivity of the electric field. The region where the electron root and ion root co-exist is obtained when changing the density or the heating power of electrons. The various types of the electrostatic potential structures are found. The condition for the turbulence suppression is examined in the parameter regime studied here. (author)

  9. High-resolution modeling of transmembrane helical protein structures from distant homologues.

    Directory of Open Access Journals (Sweden)

    Kuang-Yui M Chen

    2014-05-01

    Full Text Available Eukaryotic transmembrane helical (TMH proteins perform a wide diversity of critical cellular functions, but remain structurally largely uncharacterized and their high-resolution structure prediction is currently hindered by the lack of close structural homologues. To address this problem, we present a novel and generic method for accurately modeling large TMH protein structures from distant homologues exhibiting distinct loop and TMH conformations. Models of the adenosine A2AR and chemokine CXCR4 receptors were first ranked in GPCR-DOCK blind prediction contests in the receptor structure accuracy category. In a benchmark of 50 TMH protein homolog pairs of diverse topology (from 5 to 12 TMHs, size (from 183 to 420 residues and sequence identity (from 15% to 70%, the method improves most starting templates, and achieves near-atomic accuracy prediction of membrane-embedded regions. Unlike starting templates, the models are of suitable quality for computer-based protein engineering: redesigned models and redesigned X-ray structures exhibit very similar native interactions. The method should prove useful for the atom-level modeling and design of a large fraction of structurally uncharacterized TMH proteins from a wide range of structural homologues.

  10. Bacterial collagen-like proteins that form triple-helical structures

    Science.gov (United States)

    Yu, Zhuoxin; An, Bo; Ramshaw, John A.M.; Brodsky, Barbara

    2014-01-01

    A large number of collagen-like proteins have been identified in bacteria during the past ten years, principally from analysis of genome databases. These bacterial collagens share the distinctive Gly-Xaa-Yaa repeating amino acid sequence of animal collagens which underlies their unique triple-helical structure. A number of the bacterial collagens have been expressed in E. coli, and they all adopt a triple-helix conformation. Unlike animal collagens, these bacterial proteins do not contain the post-translationally modified amino acid, hydroxyproline, which is known to stabilize the triple-helix structure and may promote self-assembly. Despite the absence of collagen hydroxylation, the triple-helix structures of the bacterial collagens studied exhibit a high thermal stability of 35–39 °C, close to that seen for mammalian collagens. These bacterial collagens are readily produced in large quantities by recombinant methods, either in the original amino acid sequence or in genetically manipulated sequences. This new family of recombinant, easy to modify collagens could provide a novel system for investigating structural and functional motifs in animal collagens and could also form the basis of new biomedical materials with designed structural properties and functions. PMID:24434612

  11. Helicity scalings

    Energy Technology Data Exchange (ETDEWEB)

    Plunian, F [ISTerre, CNRS, Universite Joseph Fourier, Grenoble (France); Lessinnes, T; Carati, D [Physique Statistique et Plasmas, Universite Libre de Bruxelles (Belgium); Stepanov, R, E-mail: Franck.Plunian@ujf-grenoble.fr [Institute of Continuous Media Mechanics of the Russian Academy of Science, Perm (Russian Federation)

    2011-12-22

    Using a helical shell model of turbulence, Chen et al. (2003) showed that both helicity and energy dissipate at the Kolmogorov scale, independently from any helicity input. This is in contradiction with a previous paper by Ditlevsen and Giuliani (2001) in which, using a GOY shell model of turbulence, they found that helicity dissipates at a scale larger than the Kolmogorov scale, and does depend on the helicity input. In a recent paper by Lessinnes et al. (2011), we showed that this discrepancy is due to the fact that in the GOY shell model only one helical mode (+ or -) is present at each scale instead of both modes in the helical shell model. Then, using the GOY model, the near cancellation of the helicity flux between the + and - modes cannot occur at small scales, as it should be in true turbulence. We review the main results with a focus on the numerical procedure needed to obtain accurate statistics.

  12. Structure of a Stable G-Hairpin

    Czech Academy of Sciences Publication Activity Database

    Gajarský, M.; Zivkovic, M.L.; Stadlbauer, Petr; Pagano, B.; Fiala, R.; Amato, J.; Tomáška, L´.; Šponer, Jiří; Plavec, J.; Trantírek, L.

    2017-01-01

    Roč. 139, č. 10 (2017), s. 3591-3594 ISSN 0002-7863 R&D Projects: GA ČR GA13-28310S; GA ČR(CZ) GA16-13721S Institutional support: RVO:68081707 Keywords : g-quadruplex structures * human telomeric dna * single-stranded- dna * g-triplex Subject RIV: CE - Biochemistry OBOR OECD: Biochemistry and molecular biology Impact factor: 13.858, year: 2016

  13. Peptide Targeted by Human Antibodies Associated with HIV Vaccine-Associated Protection Assumes a Dynamic α-Helical Structure.

    Science.gov (United States)

    Aiyegbo, Mohammed S; Shmelkov, Evgeny; Dominguez, Lorenzo; Goger, Michael; Battacharya, Shibani; deCamp, Allan C; Gilbert, Peter B; Berman, Phillip W; Cardozo, Timothy

    2017-01-01

    The only evidence of vaccine-induced protection from HIV acquisition in humans was obtained in the RV144 HIV vaccine clinical trial. One immune correlate of risk in RV144 was observed to be higher titers of vaccine-induced antibodies (Abs) reacting with a 23-mer non-glycosylated peptide with the same amino acid sequence as a segment in the second variable (V2) loop of the MN strain of HIV. We used NMR to analyze the dynamic 3D structure of this peptide. Distance restraints between spatially proximate inter-residue protons were calculated from NOE cross peak intensities and used to constrain a thorough search of all possible conformations of the peptide. α-helical folding was strongly preferred by part of the peptide. A high-throughput structure prediction of this segment in all circulating HIV strains demonstrated that α-helical conformations are preferred by this segment almost universally across all subtypes. Notably, α-helical conformations of this segment of the V2 loop cluster cross-subtype-conserved amino acids on one face of the helix and the variable amino acid positions on the other in a semblance of an amphipathic α-helix. Accordingly, some Abs that protected against HIV in RV144 may have targeted a specific, conserved α-helical peptide epitope in the V2 loop of HIV's surface envelope glycoprotein.

  14. High precision and stable structures for particle detectors

    CERN Document Server

    Da Mota Silva, S; Hauviller, Claude

    1999-01-01

    The central detectors used in High Energy Physics Experiments require the use of light and stable structures capable of supporting delicate and precise radiation detection elements. These structures need to be highly stable under environmental conditions where external vibrations, high radiation levels, temperature and humidity gradients should be taken into account. Their main design drivers are high dimension and dynamic stability, high stiffness to mass ratio and large radiation length. For most applications, these constraints lead us to choose Carbon Fiber Reinforced Plastics ( CFRP) as structural element. The construction of light and stable structures with CFRP for these applications can be achieved by careful design engineering and further confirmation at the prototyping phase. However, the experimental environment can influence their characteristics and behavior. In this case, theuse of adaptive structures could become a solution for this problem. We are studying structures in CFRP with bonded piezoel...

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

    Energy Technology Data Exchange (ETDEWEB)

    Li, Lin [School of Environment and Chemical Engineering, Nanchang Hangkong University, Nanchang 330063 (China); Liu, Chong-Bo, E-mail: cbliu@nchu.edu.cn [School of Environment and Chemical Engineering, Nanchang Hangkong University, Nanchang 330063 (China); Yang, Gao-Shan [School of Environment and Chemical Engineering, Nanchang Hangkong University, Nanchang 330063 (China); Xiong, Zhi-Qiang [Center for Analysis and Testing, Nanchang Hangkong University, Nanchang 330063 (China); Liu, Hong [School of Environment and Chemical Engineering, Nanchang Hangkong University, Nanchang 330063 (China); Wen, Hui-Liang [State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047 (China)

    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.

  16. Role of α-Helical Structure in Organic Solvent-Activated Homodimer of Elastase Strain K

    Directory of Open Access Journals (Sweden)

    Chee Fah Wong

    2011-09-01

    Full Text Available Recombinant elastase strain K overexpressed from E. coli KRX/pCon2(3 was purified to homogeneity by a combination of hydrophobic interaction chromatography and ion exchange chromatography, with a final yield of 48% and a 25-fold increase in specific activity. The purified protein had exhibited a first ever reported homodimer size of 65 kDa by SDS-PAGE and MALDI-TOF, a size which is totally distinct from that of typically reported 33 kDa monomer from P. aeruginosa. The organic solvent stability experiment had demonstrated a stability pattern which completely opposed the rules laid out in previous reports in which activity stability and enhancement were observed in hydrophilic organic solvents such as DMSO, methanol, ethanol and 1-propanol. The high stability and enhancement of the enzyme in hydrophilic solvents were explained from the view of alteration in secondary structures. Elastinolytic activation and stability were observed in 25 and 50% of methanol, respectively, despite slight reduction in α-helical structure caused upon the addition of the solvent. Further characterization experiments had postulated great stability and enhancement of elastase strain K in broad range of temperatures, pHs, metal ions, surfactants, denaturing agents and substrate specificity, indicating its potential application in detergent formulation.

  17. Overview of the Structure of All-AT Oligonucleotides: Organization in Helices and Packing Interactions

    Science.gov (United States)

    Campos, Lourdes; Valls, Núria; Urpí, Lourdes; Gouyette, Catherine; Sanmartín, Trinidad; Richter, Michael; Alechaga, Elida; Santaolalla, Alicia; Baldini, Roberto; Creixell, Marc; Ciurans, Ruth; Skokan, Petr; Pous, Joan; Subirana, Juan A.

    2006-01-01

    We present the crystalline organization of 33 all-AT deoxyoligonucleotide duplexes, studied by x-ray diffraction. Most of them have very similar structures, with Watson-Crick basepairs and a standard average twist close to 36°. The molecules are organized as parallel columns of stacked duplexes in a helical arrangement. Such organization of duplexes is very regular and repetitive: all sequences show the same pattern. It is mainly determined by the stacking of the terminal basepairs, so that the twist in the virtual TA base step between neighbor duplexes is always negative, ∼−22°. The distance between the axes of parallel columns is practically identical in all cases, ∼26 Å. Interestingly, it coincides with that found in DNA viruses and fibers in their hexagonal phase. It appears to be a characteristic distance for ordered parallel DNA molecules. This feature is due to the absence of short range intermolecular forces, which are usually due to the presence of CG basepairs at the end of the oligonucleotide sequence. The duplexes apparently interact only through their diffuse ionic atmospheres. The results obtained can thus be considered as intermediate between liquid crystals, fibers, and standard crystal structures. They provide new information on medium range DNA-DNA interactions. PMID:16698788

  18. Exploring the propensities of helices in PrP(C) to form beta sheet using NMR structures and sequence alignments.

    OpenAIRE

    Dima, R I; Thirumalai, D

    2002-01-01

    Neurodegenerative diseases induced by transmissible spongiform encephalopathies are associated with prions. The most spectacular event in the formation of the infectious scrapie form, referred to as PrP(Sc), is the conformational change from the predominantly alpha-helical conformation of PrP(C) to the PrP(Sc) state that is rich in beta-sheet content. Using sequence alignments and structural analysis of the available nuclear magnetic resonance structures of PrP(C), we explore the propensities...

  19. Double-helical - ladder structural transition in the B-DNA is induced by a loss of dispersion energy

    Czech Academy of Sciences Publication Activity Database

    Černý, Jiří; Kabeláč, Martin; Hobza, Pavel

    2008-01-01

    Roč. 130, č. 47 (2008), s. 16055-16059 ISSN 0002-7863 R&D Projects: GA MŠk LC512; GA AV ČR IAA400550808 Institutional research plan: CEZ:AV0Z40550506 Keywords : B-DNA * double-helical structure * ladder-like structure Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 8.091, year: 2008

  20. Amphipathic helices from aromatic amino acid oligomers.

    Science.gov (United States)

    Gillies, Elizabeth R; Dolain, Christel; Léger, Jean-Michel; Huc, Ivan

    2006-10-13

    Synthetic helical foldamers are of significant interest for mimicking the conformations of naturally occurring molecules while at the same time introducing new structures and properties. In particular, oligoamides of aromatic amino acids are attractive targets, as their folding is highly predictable and stable. Here the design and synthesis of new amphipathic helical oligoamides based on quinoline-derived amino acids having either hydrophobic or cationic side chains are described. Their structures were characterized in the solid state by single-crystal X-ray diffraction and in solution by NMR. Results of these studies suggest that an oligomer as short as a pentamer folds into a stable helical conformation in protic solvents, including MeOH and H(2)O. The introduction of polar proteinogenic side chains to these foldamers, as described here for the first time, promises to provide possibilities for the biological applications of these molecules. In particular, amphipathic helices are versatile targets to explore due to their importance in a variety of biological processes, and the unique structure and properties of the quinoline-derived oligoamides may allow new structure-activity relationships to be developed.

  1. Helicity-dependent all-optical switching in hybrid metal-ferromagnet structures for ultrafast magnetic data storage

    Science.gov (United States)

    Cheng, Feng

    The emerging Big Data era demands the rapidly increasing need for speed and capacity of storing and processing information. Standalone magnetic recording devices, such as hard disk drives (HDDs), have always been playing a central role in modern data storage and continuously advancing. Recognizing the growing capacity gap between the demand and production, industry has pushed the bit areal density in HDDs to 900 Giga-bit/square-inch, a remarkable 450-million-fold increase since the invention of the first hard disk drive in 1956. However, the further development of HDD capacity is facing a pressing challenge, the so-called superparamagnetic effect, that leads to the loss of information when a single bit becomes too small to preserve the magnetization. This requires new magnetic recording technologies that can write more stable magnetic bits into hard magnetic materials. Recent research has shown that it is possible to use ultrafast laser pulses to switch the magnetization in certain types of magnetic thin films. Surprisingly, such a process does not require an externally applied magnetic field that always exists in conventional HDDs. Furthermore, the optically induced magnetization switching is extremely fast, up to sub-picosecond (10 -12 s) level, while with traditional recording method the deterministic switching does not take place shorter than 20 ps. It's worth noting that the direction of magnetization is related to the helicity of the incident laser pulses. Namely, the right-handed polarized laser pulses will generate magnetization pointing in one direction while left-handed polarized laser pulses generate magnetization pointing in the other direction. This so-called helicity-dependent all-optical switching (HD-AOS) phenomenon can be potentially used in the next-generation of magnetic storage systems. In this thesis, I explore the HD-AOS phenomenon in hybrid metal-ferromagnet structures, which consist of gold and Co/Pt multilayers. The experiment results show

  2. Dynamics and control of twisting bi-stable structures

    Science.gov (United States)

    Arrieta, Andres F.; van Gemmeren, Valentin; Anderson, Aaron J.; Weaver, Paul M.

    2018-02-01

    Compliance-based morphing structures have the potential to offer large shape adaptation, high stiffness and low weight, while reducing complexity, friction, and scalability problems of mechanism based systems. A promising class of structure that enables these characteristics are multi-stable structures given their ability to exhibit large deflections and rotations without the expensive need for continuous actuation, with the latter only required intermittently. Furthermore, multi-stable structures exhibit inherently fast response due to the snap-through instability governing changes between stable states, enabling rapid configuration switching between the discrete number of programmed shapes of the structure. In this paper, the design and utilisation of the inherent nonlinear dynamics of bi-stable twisting I-beam structures for actuation with low strain piezoelectric materials is presented. The I-beam structure consists of three compliant components assembled into a monolithic single element, free of moving parts, and showing large deflections between two stable states. Finite element analysis is utilised to uncover the distribution of strain across the width of the flange, guiding the choice of positioning for piezoelectric actuators. In addition, the actuation authority is maximised by calculating the generalised coupling coefficient for different positions of the piezoelectric actuators. The results obtained are employed to tailor and test I-beam designs exhibiting desired large deflection between stable states, while still enabling the activation of snap-through with the low strain piezoelectric actuators. To this end, the dynamic response of the I-beams to piezoelectric excitation is investigated, revealing that resonant excitations are insufficient to dynamically trigger snap-through. A novel bang-bang control strategy, which exploits the nonlinear dynamics of the structure successfully triggers both single and constant snap-through between the stable states

  3. Multiplet structure of the defect modes in 1D helical photonic crystals with twist defects

    Energy Technology Data Exchange (ETDEWEB)

    Avendano, C G [Instituto de Fisica, Universidad Nacional Autonoma de Mexico, Apdo. P 20-364 01000, Mexico DF (Mexico); Ponti, S [Dipartimento di Fisica Politecnico di Torino and INFM, Corso Duca degli Abruzzi 24, 10129 Torino (Italy); Reyes, J A [Instituto de Fisica, Universidad Nacional Autonoma de Mexico, Apdo. P 20-364 01000, Mexico DF (Mexico); Oldano, C [Dipartimento di Fisica Politecnico di Torino and INFM, Corso Duca degli Abruzzi 24, 10129 Torino (Italy)

    2005-10-14

    We theoretically analyse the defect modes generated by equispaced twist defects in 1D helical (cholesteric-like) structures within their frequency gap which is such that only the first two of the four eigenwaves 1{sup {+-}}, 2{sup {+-}} are exponentially attenuated. n{sub 0} identical defects generate n{sub 0} different defect modes, each one represented by a linear combination of the four eigenwaves. The components 1{sup +} and 1{sup -} are by far the dominant ones and they are localized near the defect planes. We give exact analytic expressions for the elements of the transfer and scattering matrices of the defect planes, for the functions defining the defect mode when n{sub 0} = 1, and for the defect frequencies when n{sub 0} = 1, 2, 3. In the particular case n{sub 0} = 2 and twist angle {theta} = {pi}/2, the difference between the two defect wavelengths {lambda}{sub d2}, {lambda}{sub d1} depends exponentially on the distance z{sub 1} between the defect planes, going to zero for z{sub 1} {yields} {infinity} and becoming as large as the entire frequency gap for z{sub 1} {yields} 0.

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

    Science.gov (United States)

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

    2015-01-01

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

  5. Crystal structure of tetranectin, a trimeric plasminogen-binding protein with an alpha-helical coiled coil

    DEFF Research Database (Denmark)

    Nielsen, B B; Kastrup, J S; Rasmussen, H

    1997-01-01

    Tetranectin is a plasminogen kringle 4-binding protein. The crystal structure has been determined at 2.8 A resolution using molecular replacement. Human tetranectin is a homotrimer forming a triple alpha-helical coiled coil. Each monomer consists of a carbohydrate recognition domain (CRD) connected...... the third is present only in long-form CRDs. Tetranectin represents the first structure of a long-form CRD with intact calcium-binding sites. In tetranectin, the third disulfide bridge tethers the CRD to the long helix in the coiled coil. The trimerization of tetranectin as well as the fixation of the CRDs...... relative to the helices in the coiled coil indicate a demand for high specificity in the recognition and binding of ligands....

  6. From single helical relaxed states to helical equilibria

    Science.gov (United States)

    Paccagnella, Roberto

    2018-02-01

    This paper analyzes the relationship between the Single Helical relaxed states studied by R. Paccagnella [Phys. Plasmas 23, 092512 (2016)] and the so-called "helical ohmic equilibria," i.e., plasma states that are solutions of the helical Grad Shafranov equation and that satisfy the constraint imposed by the Ohm law. The existence of marginally stable helical equilibria is clearly demonstrated, while the ohmic constraint is not exactly satisfied within the proposed first order perturbation theory. The model predictions are however satisfactorily compared with experimental trends.

  7. Two unique ligand-binding clamps of Rhizopus oryzae starch binding domain for helical structure disruption of amylose.

    Directory of Open Access Journals (Sweden)

    Ting-Ying Jiang

    Full Text Available The N-terminal starch binding domain of Rhizopus oryzae glucoamylase (RoSBD has a high binding affinity for raw starch. RoSBD has two ligand-binding sites, each containing a ligand-binding clamp: a polyN clamp residing near binding site I is unique in that it is expressed in only three members of carbohydrate binding module family 21 (CBM21 members, and a Y32/F58 clamp located at binding site II is conserved in several CBMs. Here we characterized different roles of these sites in the binding of insoluble and soluble starches using an amylose-iodine complex assay, atomic force microscopy, isothermal titration calorimetry, site-directed mutagenesis, and structural bioinformatics. RoSBD induced the release of iodine from the amylose helical cavity and disrupted the helical structure of amylose type III, thereby significantly diminishing the thickness and length of the amylose type III fibrils. A point mutation in the critical ligand-binding residues of sites I and II, however, reduced both the binding affinity and amylose helix disruption. This is the first molecular model for structure disruption of the amylose helix by a non-hydrolytic CBM21 member. RoSBD apparently twists the helical amylose strands apart to expose more ligand surface for further SBD binding. Repeating the process triggers the relaxation and unwinding of amylose helices to generate thinner and shorter amylose fibrils, which are more susceptible to hydrolysis by glucoamylase. This model aids in understanding the natural roles of CBMs in protein-glycan interactions and contributes to potential molecular engineering of CBMs.

  8. Two Unique Ligand-Binding Clamps of Rhizopus oryzae Starch Binding Domain for Helical Structure Disruption of Amylose

    Science.gov (United States)

    Jiang, Ting-Ying; Ci, Yuan-Pei; Chou, Wei-I; Lee, Yuan-Chuan; Sun, Yuh-Ju; Chou, Wei-Yao; Li, Kun-Mou; Chang, Margaret Dah-Tsyr

    2012-01-01

    The N-terminal starch binding domain of Rhizopus oryzae glucoamylase (RoSBD) has a high binding affinity for raw starch. RoSBD has two ligand-binding sites, each containing a ligand-binding clamp: a polyN clamp residing near binding site I is unique in that it is expressed in only three members of carbohydrate binding module family 21 (CBM21) members, and a Y32/F58 clamp located at binding site II is conserved in several CBMs. Here we characterized different roles of these sites in the binding of insoluble and soluble starches using an amylose-iodine complex assay, atomic force microscopy, isothermal titration calorimetry, site-directed mutagenesis, and structural bioinformatics. RoSBD induced the release of iodine from the amylose helical cavity and disrupted the helical structure of amylose type III, thereby significantly diminishing the thickness and length of the amylose type III fibrils. A point mutation in the critical ligand-binding residues of sites I and II, however, reduced both the binding affinity and amylose helix disruption. This is the first molecular model for structure disruption of the amylose helix by a non-hydrolytic CBM21 member. RoSBD apparently twists the helical amylose strands apart to expose more ligand surface for further SBD binding. Repeating the process triggers the relaxation and unwinding of amylose helices to generate thinner and shorter amylose fibrils, which are more susceptible to hydrolysis by glucoamylase. This model aids in understanding the natural roles of CBMs in protein-glycan interactions and contributes to potential molecular engineering of CBMs. PMID:22815939

  9. Interrupted hydrogen/deuterium exchange reveals the stable core of the remarkably helical molten globule of alpha-beta parallel protein flavodoxin.

    NARCIS (Netherlands)

    Nabuurs, S.M.; Mierlo, C.P. van

    2010-01-01

    Kinetic intermediates that appear early during protein folding often resemble the relatively stable molten globule intermediates formed by several proteins under mildly denaturing conditions. Molten globules have a substantial amount of secondary structure but lack virtually all tertiary side-chain

  10. Interrupted hydrogen/deuterium exchange reveals the stable core of the remarkably helical molten globule of a-ß parallel protein flavodoxin

    NARCIS (Netherlands)

    Nabuurs, S.M.; Mierlo, van C.P.M.

    2010-01-01

    Kinetic intermediates that appear early during protein folding often resemble the relatively stable molten globule intermediates formed by several proteins under mildly denaturing conditions. Molten globules have a substantial amount of secondary structure but lack virtually all tertiary side-chain

  11. Molecular structure of r/GCG/d/TATACGC/ - A DNA-RNA hybrid helix joined to double helical DNA

    Science.gov (United States)

    Wang, A. H.-J.; Fujii, S.; Rich, A.; Van Boom, J. H.; Van Der Marel, G. A.; Van Boeckel, S. A. A.

    1982-01-01

    The molecule r(GCG)d(TATACGC) is self-complementary and forms two DNA-RNA hybrid segments surrounding a central region of double helical DNA; its molecular structure has been solved by X-ray analysis. All three parts of the molecule adopt a conformation which is close to that seen in the 11-fold RNA double helix. The conformation of the ribonucleotides is partly determined by water molecules bridging between the ribose O2' hydroxyl group and cytosine O2. The hybrid-DNA duplex junction contains no structural discontinuities. However, the central DNA TATA sequence has some structural irregularities.

  12. The NN final-state interaction in the helicity structure of d->({gamma}->,{pi}-)pp reaction

    Energy Technology Data Exchange (ETDEWEB)

    Darwish, Eed M. [Physics Department, Faculty of Science, South Valley University, Sohag 82524 (Egypt)]. E-mail: eeddarwish@yahoo.com

    2005-02-21

    The influence of final-state NN-rescattering on the helicity structure of the {gamma}->d->->{pi}-pp reaction in the energy range from {pi}-threshold up to 550 MeV has been investigated. The differential polarized cross-section difference for the parallel and antiparallel helicity states is predicted and compared with recent experimental data. It is shown that the effect of NN-rescattering is much less important in the polarized differential cross-section difference than in the previously studied unpolarized differential cross section. Furthermore, the contribution of {gamma}->d->->{pi}-pp to the spin asymmetry of the deuteron is explicitly evaluated over the region of the {delta}(1232)-resonance with inclusion of NN-rescattering. The effect of NN final-state interaction is found to be much larger in the asymmetry than in the total cross section and leads to an appreciable reduction of the spin asymmetry in the {delta}-region.

  13. General architecture of the alpha-helical globule.

    Science.gov (United States)

    Murzin, A G; Finkelstein, A V

    1988-12-05

    A model is presented for the arrangement of alpha-helices in globular proteins. In the model, helices are placed on certain ribs of "quasi-spherical" polyhedra. The polyhedra are chosen so as to allow the close packing of helices around a hydrophobic core and to stress the collective interactions of the individual helices. The model predicts a small set of stable architectures for alpha-helices in globular proteins and describes the geometries of the helix packings. Some of the predicted helix arrangements have already been observed in known protein structures; others are new. An analysis of the three-dimensional structures of all proteins for which co-ordinates are available shows that the model closely approximates the arrangements and packing of helices actually observed. The average deviations of the real helix axes from those in the model polyhedra is +/- 20 degrees in orientation and +/- 2 A in position (1 A = 0.1 nm). We also show that for proteins that are not homologous, but whose helix arrangements are described by the same polyhedron, the root-mean-square difference in the position of the C alpha atoms in the helices is 1.6 to 3.0 A.

  14. Self-Assembling Peptide Surfactants A6K and A6D Adopt a-Helical Structures Useful for Membrane Protein Stabilization

    Directory of Open Access Journals (Sweden)

    Furen Zhuang

    2011-10-01

    Full Text Available Elucidation of membrane protein structures have been greatly hampered by difficulties in producing adequately large quantities of the functional protein and stabilizing them. A6D and A6K are promising solutions to the problem and have recently been used for the rapid production of membrane-bound G protein-coupled receptors (GPCRs. We propose that despite their short lengths, these peptides can adopt α-helical structures through interactions with micelles formed by the peptides themselves. These α-helices are then able to stabilize α-helical motifs which many membrane proteins contain. We also show that A6D and A6K can form β-sheets and appear as weak hydrogels at sufficiently high concentrations. Furthermore, A6D and A6K together in sodium dodecyl sulfate (SDS can form expected β-sheet structures via a surprising α-helical intermediate.

  15. Assessing the Structure and Stability of Transmembrane Oligomeric Intermediates of an α-Helical Toxin.

    Science.gov (United States)

    Desikan, Rajat; Maiti, Prabal K; Ayappa, K Ganapathy

    2017-10-24

    Protein membrane interactions play an important role in our understanding of diverse phenomena ranging from membrane-assisted protein aggregation to oligomerization and folding. Pore-forming toxins (PFTs) are the primary vehicle for infection by several strains of bacteria. These proteins which are expressed in a water-soluble form (monomers) bind to the target membrane and conformationally transform (protomers) and self-assemble to form a multimer transmembrane pore complex through a process of oligomerization. On the basis of the structure of the transmembrane domains, PFTs are broadly classified into β or α toxins. In contrast to β-PFTs, the paucity of available crystal structures coupled with the amphipathic nature of the transmembrane domains has hindered our understanding of α-PFT pore formation. In this article, we use molecular dynamics (MD) simulations to examine the process of pore formation of the bacterial α-PFT, cytolysin A from Escherichia coli (ClyA) in lipid bilayer membranes. Using atomistic MD simulations ranging from 50 to 500 ns, we show that transmembrane oligomeric intermediates or "arcs" form stable proteolipidic complexes consisting of protein arcs with toroidal lipids lining the free edges. By creating initial conditions where the lipids are contained within the arcs, we study the dynamics of spontaneous lipid evacuation and toroidal edge formation. This process occurs on the time scale of tens of nanoseconds, suggesting that once protomers oligomerize, transmembrane arcs are rapidly stabilized to form functional water channels capable of leakage. Using umbrella sampling with a coarse-grained molecular model, we obtain the free energy of insertion of a single protomer into the membrane. A single inserted protomer has a stabilization free energy of -52.9 ± 1.2 kJ/mol and forms a stable transmembrane water channel capable of leakage. Our simulations reveal that arcs are stable and viable intermediates that can occur during the pore

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

    Science.gov (United States)

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

    2003-08-01

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

  17. Highly active and stable oxaloacetate decarboxylase Na⁺ pump complex for structural analysis.

    Science.gov (United States)

    Inoue, Michio; Li, Xiaodan

    2015-11-01

    The oxaloacetate decarboxylase primary Na(+) pump (Oad) produces energy for the surviving of some pathogenic bacteria under anaerobic conditions. Oad composes of three subunits: Oad-α, a biotinylated soluble subunit and catalyzes the decarboxylation of oxaloacetate; Oad-β, a transmembrane subunit and functions as a Na(+) pump; and Oad-γ, a single transmembrane α-helical anchor subunit and assembles Oad-α/β/γ complex. The molecular mechanism of Oad complex coupling the exothermic decarboxylation to generate the Na(+) electrochemical gradient remains unsolved. Our biophysical and biochemical studies suggested that the stoichiometry of Oad complex from Vibrio cholerae composed of α, β, γ in 4:2:2 stoichiometry not that of 4:4:4. The high-resolution structure determination of the Oad complex would reveal the energetic transformation mechanism from the catalytical soluble α subunit to membrane β subunit. Sufficient amount stable, conformational homogenous and active Oad complex with the right stoichiometry is the prerequisite for structural analysis. Here we report an easy and reproducible protocol to obtain high quantity and quality Oad complex protein for structural analysis. Copyright © 2015 Elsevier Inc. All rights reserved.

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

    Science.gov (United States)

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

    2003-01-01

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

  19. Triple helical structure of acid-soluble collagen derived from Nile tilapia skin as affected by extraction temperature.

    Science.gov (United States)

    Thuanthong, Mantaka; Sirinupong, Nualpun; Youravong, Wirote

    2016-08-01

    Fish skin has become a new source of collagen. It is usually extracted at low temperature. Increasing the extraction temperature can increase the collagen yield. However, high temperature might cause degradation of the triple helical structure of collagen, which is related to its functional biomaterial. This work thus aimed to investigate the effect of extraction temperature on the extraction efficiency and characteristics of acid-soluble collagen (ASC), particularly its triple helical structure. ASC was extracted at 5 ± 1, 15 ± 1 and 25 ± 1 °C for 0-24 h with 0.3 or 0.5 mol L(-1) acetic acid. The results showed that extraction with 0.5 mol L(-1) acetic acid gave a higher extraction efficiency than that in 0.3 mol L(-1) acetic acid (P < 0.5). Extraction at 25 ± 1 °C for 5 h with 0.5 mol L(-1) acetic acid gave a higher extraction efficiency (73.73 ± 1.28%), which is higher than that of 5 ± 1 °C by about 1.7-fold. All ASC obtained were identified as type I collagen and showed similar physicochemical properties. The results showed that extraction temperature strongly affected extraction efficiency. Extraction at 25 °C did not affect the triple helical structure, which was confirmed by the results of Fourier transform infrared, circular dichroism spectrum and collagen self-assembly. © 2015 Society of Chemical Industry. © 2015 Society of Chemical Industry.

  20. Recent developments in low cost stable structures for space

    International Nuclear Information System (INIS)

    Thompson, T.C.; Grastataro, C.; Smith, B.G.

    1994-01-01

    The Los Alamos National Laboratory (LANL) in partnership with Composite Optics Incorporated (COI) is advancing the development of low cost, lightweight, composite technology for use in spacecraft and stable structures. The use of advanced composites is well developed, but the application of an all-composite tracker structure has never been achieved. This paper investigates the application of composite technology to the design and fabrication of an all-composite spacecraft bus for small satellites, using technology directly applicable to central tracking in a high luminosity environment. The satellite program Fast On-Orbit Recording of Transient Events (FORTE) is the second in a series of satellites to be launched into orbit for the US Department of Energy (DOE). This paper will discuss recent developments in the area of low cost composites, used for either spacecraft or ultra stable applications in high energy physics (HEP) detectors. The use of advanced composites is a relatively new development in the area of HEP. The Superconducting Super Collider (SSC) spawned a new generation of Trackers which made extensive use of graphite fiber reinforced plastic (GFRP) composite systems. LANL has designed a structure employing new fabrication technology. This concept will lower the cost of composite structures to a point that they may now compete with conventional materials. This paper will discuss the design, analysis and proposed fabrication of a small satellite structure. Central tracking structures using advanced materials capable of operating in an adverse environment typical of that found in a high luminosity collider could use identical concepts

  1. Validation of HFCS-I on Calculation of High-Frequency Parameters of Helical Slow-Wave Structures

    Science.gov (United States)

    Zhu, Xiaofang; Yang, Zhonghai; Li, Bin; Li, Jianqing; Xu, Li

    2010-02-01

    To validate HFCS-I, a newly developed design tool for high frequency circuits of microwave tubes, the high-frequency parameters (including dispersion, interaction impedance and attenuation constant) of a typical helical slow-wave structure (SWS) for millimetre wave travelling-wave tube are calculated by HFCS-I and MAFIA. Both the direct calculation method and the Non-Resonant Perturbation (NRP) technique are adopted to get the interaction impedance. The obtained high-frequency parameters from HFCS-I and MAFIA are compared in detail and the consistency has proved the reliability and validity of HFCS-I.

  2. Exploring biological effects of MoS{sub 2} nanosheets on native structures of α-helical peptides

    Energy Technology Data Exchange (ETDEWEB)

    Gu, Zonglin; Li, Weifeng, E-mail: wfli@suda.edu.cn, E-mail: ruhong@us.ibm.com [School for Radiological and Interdisciplinary Sciences (RAD-X) and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123 (China); Hong, Linbi [Computational Biological Center, IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598 (United States); Zhou, Ruhong, E-mail: wfli@suda.edu.cn, E-mail: ruhong@us.ibm.com [School for Radiological and Interdisciplinary Sciences (RAD-X) and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123 (China); Computational Biological Center, IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598 (United States); Department of Chemistry, Columbia University, New York, New York 10027 (United States)

    2016-05-07

    Recent reports of mono- and few-layer molybdenum disulfide (MoS{sub 2}), a representative transition metal dichacogenide (TMD), as antibacterial and anticancer agents have shed light on their potential in biomedical applications. To better facilitate these promising applications, one needs to understand the biological effects of these TMDs as well, such as their potential adverse effects on protein structure and function. Here, we sought to understand the interaction of MoS{sub 2} nanosheets with peptides using molecular dynamics simulations and a simple model polyalanine with various lengths (PA{sub n}, n = 10, 20, 30, and 40; mainly α − helices). Our results demonstrated that MoS{sub 2} monolayer has an exceptional capability to bind all peptides in a fast and strong manner. The strong attraction from the MoS{sub 2} nanosheet is more than enough to compensate the energy needed to unfold the peptide, regardless of the length, which induces drastic disruptions to the intra-peptide hydrogen bonds and subsequent secondary structures of α − helices. This universal phenomenon may point to the potential nanotoxicity of MoS{sub 2} when used in biological systems. Moreover, these results aligned well with previous findings on the potential cytotoxicity of TMD nanomaterials.

  3. Exploring biological effects of MoS2 nanosheets on native structures of α-helical peptides

    International Nuclear Information System (INIS)

    Gu, Zonglin; Li, Weifeng; Hong, Linbi; Zhou, Ruhong

    2016-01-01

    Recent reports of mono- and few-layer molybdenum disulfide (MoS 2 ), a representative transition metal dichacogenide (TMD), as antibacterial and anticancer agents have shed light on their potential in biomedical applications. To better facilitate these promising applications, one needs to understand the biological effects of these TMDs as well, such as their potential adverse effects on protein structure and function. Here, we sought to understand the interaction of MoS 2 nanosheets with peptides using molecular dynamics simulations and a simple model polyalanine with various lengths (PA n , n = 10, 20, 30, and 40; mainly α − helices). Our results demonstrated that MoS 2 monolayer has an exceptional capability to bind all peptides in a fast and strong manner. The strong attraction from the MoS 2 nanosheet is more than enough to compensate the energy needed to unfold the peptide, regardless of the length, which induces drastic disruptions to the intra-peptide hydrogen bonds and subsequent secondary structures of α − helices. This universal phenomenon may point to the potential nanotoxicity of MoS 2 when used in biological systems. Moreover, these results aligned well with previous findings on the potential cytotoxicity of TMD nanomaterials.

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

    Science.gov (United States)

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

    2017-11-01

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

  5. Temperature-dependent structural changes in intrinsically disordered proteins: formation of alpha-helices or loss of polyproline II?

    DEFF Research Database (Denmark)

    Kjærgaard, Magnus; Nørholm, Ann-Beth; Hendus-Altenburger, Ruth

    2010-01-01

    temperature, which most likely reflects formation of transient alpha-helices or loss of polyproline II (PPII) content. Using three IDPs, ACTR, NHE1, and Spd1, we show that the temperature-induced structural change is common among IDPs and is accompanied by a contraction of the conformational ensemble...... with increasing temperature, and accordingly these were not responsible for the change in the CD spectra. In contrast, the nonhelical regions exhibited a general temperature-dependent structural change that was independent of long-range interactions. The temperature-dependent CD spectroscopic signature of IDPs...... that has been amply documented can be rationalized to represent redistribution of the statistical coil involving a general loss of PPII conformations....

  6. Crystal structure of the N-terminal domain of human SIRT7 reveals a three-helical domain architecture.

    Science.gov (United States)

    Priyanka, Anu; Solanki, Vipul; Parkesh, Raman; Thakur, Krishan Gopal

    2016-10-01

    Human SIRT7 is an NAD(+) dependent deacetylase, which belongs to sirtuin family of proteins. SIRT7, like other sirtuins has conserved catalytic domain and is flanked by N- and C-terminal domains reported to play vital functional roles. Here, we report the crystal structure of the N-terminal domain of human SIRT7 (SIRT7(NTD) ) at 2.3 Å resolution as MBP-SIRT7(NTD) fusion protein. SIRT7(NTD) adopts three-helical domain architecture and comparative structural analyses suggest similarities to some DNA binding motifs and transcription regulators. We also report here the importance of N- and C-terminal domains in soluble expression of SIRT7. Proteins 2016; 84:1558-1563. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  7. Elongated fibrillar structure of a streptococcal adhesin assembled by the high-affinity association of [alpha]- and PPII-helices

    Energy Technology Data Exchange (ETDEWEB)

    Larson, Matthew R.; Rajashankar, Kanagalaghatta R.; Patel, Manisha H.; Robinette, Rebekah A.; Crowley, Paula J.; Michalek, Suzanne; Brady, L. Jeannine; Deivanayagam, Champion (Cornell); (UAB); (Florida)

    2010-08-18

    Streptococcus mutans antigen I/II (AgI/II) is a cell surface-localized protein adhesin that interacts with salivary components within the salivary pellicle. AgI/II contributes to virulence and has been studied as an immunological and structural target, but a fundamental understanding of its underlying architecture has been lacking. Here we report a high-resolution (1.8 {angstrom}) crystal structure of the A{sub 3}VP{sub 1} fragment of S. mutans AgI/II that demonstrates a unique fibrillar form (155 {angstrom}) through the interaction of two noncontiguous regions in the primary sequence. The A{sub 3} repeat of the alanine-rich domain adopts an extended {alpha}-helix that intertwines with the P{sub 1} repeat polyproline type II (PPII) helix to form a highly extended stalk-like structure heretofore unseen in prokaryotic or eukaryotic protein structures. Velocity sedimentation studies indicate that full-length AgI/II that contains three A/P repeats extends over 50 nanometers in length. Isothermal titration calorimetry revealed that the high-affinity association between the A{sub 3} and P{sub 1} helices is enthalpically driven. Two distinct binding sites on AgI/II to the host receptor salivary agglutinin (SAG) were identified by surface plasmon resonance (SPR). The current crystal structure reveals that AgI/II family proteins are extended fibrillar structures with the number of alanine- and proline-rich repeats determining their length.

  8. Lasing thresholds of helical photonic structures with different positions of a single light-amplifying helix turn

    Energy Technology Data Exchange (ETDEWEB)

    Blinov, L M; Palto, S P [A.V. Shubnikov Institute of Crystallography, Russian Academy of Sciences, Moscow, Russian Federaion (Russian Federation)

    2013-09-30

    Numerical simulation is used to assess the lasing threshold of helical structures of cholesteric liquid crystals (CLCs) in which only one turn amplifies light. This turn is located either in the centre of symmetric structures of various sizes or in an arbitrary place in asymmetric structures of preset size. In all cases, we find singularities in light amplification by a one-dimensional CLC structure for the most important band-edge modes (m1, m2 and m3) and plot the threshold gain coefficient k{sub th} against the position of the amplifying turn. For the symmetric structures, the lasing threshold of the m1 mode is shown to vary linearly with the inverse of the square of the cavity length. Moreover, modes with a lower density of photonic states (DOS) in the cavity may have a lower lasing threshold. This can be accounted for by the dependence of the density of photonic states on the position of the amplifying turn and, accordingly, by the nonuniform electromagnetic field intensity distribution along the cavity for different modes. In the asymmetric structures, the same field energy distribution is responsible for a correlation between k{sub th} and DOS curves. (lasers)

  9. Highly stable thin film transistors using multilayer channel structure

    KAUST Repository

    Nayak, Pradipta K.

    2015-03-09

    We report highly stable gate-bias stress performance of thin film transistors (TFTs) using zinc oxide (ZnO)/hafnium oxide (HfO2) multilayer structure as the channel layer. Positive and negative gate-bias stress stability of the TFTs was measured at room temperature and at 60°C. A tremendous improvement in gate-bias stress stability was obtained in case of the TFT with multiple layers of ZnO embedded between HfO2 layers compared to the TFT with a single layer of ZnO as the semiconductor. The ultra-thin HfO2 layers act as passivation layers, which prevent the adsorption of oxygen and water molecules in the ZnO layer and hence significantly improve the gate-bias stress stability of ZnO TFTs.

  10. Structure of stable degeneration of K3 surfaces into pairs of rational elliptic surfaces

    OpenAIRE

    Kimura, Yusuke

    2018-01-01

    F-theory/heterotic duality is formulated in the stable degeneration limit of a K3 fibration on the F-theory side. In this note, we analyze the structure of the stable degeneration limit. We discuss whether stable degeneration exists for pairs of rational elliptic surfaces. We demonstrate that, when two rational elliptic surfaces have an identical complex structure, stable degeneration always exists. We provide an equation that systematically describes the stable degeneration of a K3 surface i...

  11. Structure of the hypothetical protein Ton1535 from Thermococcus onnurineus NA1 reveals unique structural properties by a left-handed helical turn in normal α-solenoid protein.

    Science.gov (United States)

    Jeong, Jae-Hee; Kim, Yi-Seul; Rojvirija, Catleya; Cha, Hyung Jin; Kim, Yeon-Gil; Ha, Sung Chul

    2014-06-01

    The crystal structure of Ton1535, a hypothetical protein from Thermococcus onnurineus NA1, was determined at 2.3 Å resolution. With two antiparallel α-helices in a helix-turn-helix motif as a repeating unit, Ton1535 consists of right-handed coiled N- and C-terminal regions that are stacked together using helix bundles containing a left-handed helical turn. One left-handed helical turn in the right-handed coiled structure produces two unique structural properties. One is the presence of separated concave grooves rather than one continuous concave groove, and the other is the contribution of α-helices on the convex surfaces of the N-terminal region to the extended surface of the concave groove of the C-terminal region and vice versa. © 2013 Wiley Periodicals, Inc.

  12. Self-assembly of organocyanide dianions and metal–organic macrocycles into polymeric architectures including an unprecedented quadruple helical aperiodic structure\

    Czech Academy of Sciences Publication Activity Database

    Zhang, X.; Zhao, H.; Palatinus, Lukáš; Gagnon, K.J.; Bacsa, J.; Dunbar, K.R.

    2016-01-01

    Roč. 16, č. 4 (2016), s. 1805-1811 ISSN 1528-7483 Institutional support: RVO:68378271 Keywords : crystal engineering * self-assembled polymer * modulated structure * helical chain Subject RIV: CC - Organic Chemistry Impact factor: 4.055, year: 2016

  13. Designability landscape reveals sequence features that define axial helix rotation in four-helical homo-oligomeric antiparallel coiled-coil structures.

    Science.gov (United States)

    Szczepaniak, Krzysztof; Lach, Grzegorz; Bujnicki, Janusz M; Dunin-Horkawicz, Stanislaw

    2014-11-01

    Coiled coils are widespread protein domains comprising α-helices wound around each other in a regular fashion. Owing to their regularity, coiled-coil structures can be fully described by parametric equations. This in turn makes them an excellent model for studying sequence-structure relationships in proteins. Here, we used computational design to identify sequence features that determine the degree of helix axial rotation in four-helical homo-oligomeric antiparallel coiled coils. We designed 135,000 artificial sequences for a repertoire of backbone models representing all theoretically possible axial rotation states. Analysis of the designed sequences revealed features that precisely define the rotation of the helices. Based on these features we implemented a bioinformatic tool, which given a coiled-coil sequence, predicts the rotation of the helices in its structure. Moreover, we showed that another structural parameter, helix axial shift, is coupled to helix axial rotation and that dependence between these two parameters narrows the number of possible axial rotation states. Copyright © 2014 Elsevier Inc. All rights reserved.

  14. Stable structural color patterns displayed on transparent insect wings.

    Science.gov (United States)

    Shevtsova, Ekaterina; Hansson, Christer; Janzen, Daniel H; Kjærandsen, Jostein

    2011-01-11

    Color patterns play central roles in the behavior of insects, and are important traits for taxonomic studies. Here we report striking and stable structural color patterns--wing interference patterns (WIPs)--in the transparent wings of small Hymenoptera and Diptera, patterns that have been largely overlooked by biologists. These extremely thin wings reflect vivid color patterns caused by thin film interference. The visibility of these patterns is affected by the way the insects display their wings against various backgrounds with different light properties. The specific color sequence displayed lacks pure red and matches the color vision of most insects, strongly suggesting that the biological significance of WIPs lies in visual signaling. Taxon-specific color patterns are formed by uneven membrane thickness, pigmentation, venation, and hair placement. The optically refracted pattern is also stabilized by microstructures of the wing such as membrane corrugations and spherical cell structures that reinforce the pattern and make it essentially noniridescent over a large range of light incidences. WIPs can be applied to map the micromorphology of wings through direct observation and are useful in several fields of biology. We demonstrate their usefulness as identification patterns to solve cases of cryptic species complexes in tiny parasitic wasps, and indicate their potentials for research on the genetic control of wing development through direct links between the transregulatory wing landscape and interference patterns we observe in Drosophila model species. Some species display sexually dimorphic WIPs, suggesting sexual selection as one of the driving forces for their evolution.

  15. Alpha helical structures in the leader sequence of human GLUD2 glutamate dehydrogenase responsible for mitochondrial import.

    Science.gov (United States)

    Kotzamani, Dimitra; Plaitakis, Andreas

    2012-09-01

    Human glutamate dehydrogenase (hGDH) exists in two highly homologous isoforms with a distinct regulatory and tissue expression profile: a housekeeping hGDH1 isoprotein encoded by the GLUD1 gene and an hGDH2 isoenzyme encoded by the GLUD2 gene. There is evidence that both isoenzymes are synthesized as pro-enzymes containing a 53 amino acid long N-terminal leader peptide that is cleaved upon translocation into the mitochondria. However, this GDH signal peptide is substantially larger than that of most nuclear DNA-encoded mitochondrial proteins, the leader sequence of which typically contains 17-35 amino acids and they often form a single amphipathic α-helix. To decode the structural elements that are essential for the mitochondrial targeting of human GDHs, we performed secondary structure analyses of their leader sequence. These analyses predicted, with 82% accuracy, that both leader peptides are positively charged and that they form two to three α-helices, separated by intermediate loops. The first α-helix of hGDH2 is strongly amphipathic, displaying both a positively charged surface and a hydrophobic plane. We then constructed GLUD2-EGFP deletion mutants and used them to transfect three mammalian cell lines (HEK293, COS 7 and SHSY-5Y). Confocal laser scanning microscopy, following co-transfection with pDsRed2-Mito mitochondrial targeting vector, revealed that deletion of the entire leader sequence prevented the enzyme from entering the mitochondria, resulting in its retention in the cytoplasm. Deletion of the first strongly amphipathic α-helix only was also sufficient to prevent the mitochondrial localization of the truncated protein. Moreover, truncated leader sequences, retaining the second and/or the third putative α-helix, failed to restore the mitochondrial import of hGDH2. As such, the first N-terminal alpha helical structure is crucial for the mitochondrial import of hGDH2 and these findings may have implications in understanding the evolutionary

  16. A new helical crossed-fibre structure of β-keratin in flight feathers and its biomechanical implications.

    Science.gov (United States)

    Lingham-Soliar, Theagarten; Murugan, Nelisha

    2013-01-01

    The feather aerofoil is unequalled in nature. It is comprised of a central rachis, serial paired branches or barbs, from which arise further branches, the barbules. Barbs and barbules arise from the significantly thinner lateral walls (the epicortex) of the rachis and barbs respectively, as opposed to the thicker dorsal and ventral walls (the cortex). We hypothesized a microstructural design of the epicortex that would resist the vertical or shearing stresses. The microstructures of the cortex and epicortex of the rachis and barbs were investigated in several bird species by microbe-assisted selective disassembly and conventional methods via scanning electron microscopy. We report, preeminent of the finds, a novel system of crossed fibres (ranging from ∼100-800 nm in diameter), oppositely oriented in alternate layers of the epicortex in the rachis and barbs. It represents the first cross-fibre microstructure, not only for the feather but in keratin per se. The cortex of the barbs is comprised of syncitial barbule cells, definitive structural units shown in the rachidial cortex in a related study. The structural connection between the cortex of the rachis and barbs appears uninterrupted. A new model on feather microstructure incorporating the findings here and in the related study is presented. The helical fibre system found in the integument of a diverse range of invertebrates and vertebrates has been implicated in profound functional strategies, perhaps none more so potentially than in the aerofoil microstructure of the feather here, which is central to one of the marvels of nature, bird flight.

  17. Insight into the Narrow Structure in η Photoproduction on the Neutron from Helicity-Dependent Cross Sections.

    Science.gov (United States)

    Witthauer, L; Dieterle, M; Abt, S; Achenbach, P; Afzal, F; Ahmed, Z; Annand, J R M; Arends, H J; Bashkanov, M; Beck, R; Biroth, M; Borisov, N S; Braghieri, A; Briscoe, W J; Cividini, F; Costanza, S; Collicott, C; Denig, A; Downie, E J; Drexler, P; Ferretti-Bondy, M I; Gardner, S; Garni, S; Glazier, D I; Glowa, D; Gradl, W; Günther, M; Gurevich, G M; Hamilton, D; Hornidge, D; Huber, G M; Käser, A; Kashevarov, V L; Kay, S; Keshelashvili, I; Kondratiev, R; Korolija, M; Krusche, B; Lazarev, A B; Linturi, J M; Lisin, V; Livingston, K; Lutterer, S; MacGregor, I J D; Mancell, J; Manley, D M; Martel, P P; Metag, V; Meyer, W; Miskimen, R; Mornacchi, E; Mushkarenkov, A; Neganov, A B; Neiser, A; Oberle, M; Ostrick, M; Otte, P B; Paudyal, D; Pedroni, P; Polonski, A; Prakhov, S N; Rajabi, A; Reicherz, G; Ron, G; Rostomyan, T; Sarty, A; Sfienti, C; Sikora, M H; Sokhoyan, V; Spieker, K; Steffen, O; Strakovski, I I; Strub, Th; Supek, I; Thiel, A; Thiel, M; Thomas, A; Unverzagt, M; Usov, Yu A; Wagner, S; Walford, N K; Watts, D P; Werthmüller, D; Wettig, J; Wolfes, M; Zana, L

    2016-09-23

    The double polarization observable E and the helicity dependent cross sections σ_{1/2} and σ_{3/2} were measured for η photoproduction from quasifree protons and neutrons. The circularly polarized tagged photon beam of the A2 experiment at the Mainz MAMI accelerator was used in combination with a longitudinally polarized deuterated butanol target. The almost 4π detector setup of the Crystal Ball and TAPS is ideally suited to detect the recoil nucleons and the decay photons from η→2γ and η→3π^{0}. The results show that the narrow structure previously observed in η photoproduction from the neutron is only apparent in σ_{1/2} and hence, most likely related to a spin-1/2 amplitude. Nucleon resonances that contribute to this partial wave in η production are only N 1/2^{-} (S_{11}) and N 1/2^{+} (P_{11}). Furthermore, the extracted Legendre coefficients of the angular distributions for σ_{1/2} are in good agreement with recent reaction model predictions assuming a narrow resonance in the P_{11} wave as the origin of this structure.

  18. Prediction of atomic structure from sequence for double helical DNA oligomers.

    Science.gov (United States)

    Farwer, Jochen; Packer, Martin J; Hunter, Christopher A

    2006-01-01

    DNA can adopt different conformations depending on the base sequence, solvent, electrolyte composition and concentration, pH, temperature, and interaction with proteins. Here we present a model for calculating the three-dimensional atomic structure of double-stranded DNA oligomers. A theoretical energy function is used for calculating the interactions within the base steps and an empirical backbone function is used to restrict the conformational space accessible to the bases and to account for the conformational coupling of neighboring steps in a sequence. Conformational searching on large structures or a large number of structures is possible, because each base step can be described by just two primary degrees of freedom (slide and shift). A genetic algorithm is used to search for low-energy structures in slide-shift space, and this allows very rapid optimization of DNA oligomers. The other base step parameters have been previously optimized for all possible slide-shift sequence combinations, and a heuristic algorithm is used to add the atomic details of the backbone conformation in the final step of the calculation. The structures obtained by this method are very similar to the corresponding X-ray crystal structures observed experimentally. The average RMSD is 2.24 Angstroms for a set of 20 oligomer structures. For 15 of these sequences, the X-ray crystal structure is the global energy minimum. The other 5 are bistable sequences that have B-form global energy minima but crystallize as A-DNA. Copyright 2005 Wiley Periodicals, Inc.

  19. CHSalign: A Web Server That Builds upon Junction-Explorer and RNAJAG for Pairwise Alignment of RNA Secondary Structures with Coaxial Helical Stacking.

    Directory of Open Access Journals (Sweden)

    Lei Hua

    Full Text Available RNA junctions are important structural elements of RNA molecules. They are formed when three or more helices come together in three-dimensional space. Recent studies have focused on the annotation and prediction of coaxial helical stacking (CHS motifs within junctions. Here we exploit such predictions to develop an efficient alignment tool to handle RNA secondary structures with CHS motifs. Specifically, we build upon our Junction-Explorer software for predicting coaxial stacking and RNAJAG for modelling junction topologies as tree graphs to incorporate constrained tree matching and dynamic programming algorithms into a new method, called CHSalign, for aligning the secondary structures of RNA molecules containing CHS motifs. Thus, CHSalign is intended to be an efficient alignment tool for RNAs containing similar junctions. Experimental results based on thousands of alignments demonstrate that CHSalign can align two RNA secondary structures containing CHS motifs more accurately than other RNA secondary structure alignment tools. CHSalign yields a high score when aligning two RNA secondary structures with similar CHS motifs or helical arrangement patterns, and a low score otherwise. This new method has been implemented in a web server, and the program is also made freely available, at http://bioinformatics.njit.edu/CHSalign/.

  20. Multiple helical modes of vortex breakdown

    DEFF Research Database (Denmark)

    Sørensen, Jens Nørkær; Naumov, I. V.; Okulov, Valery

    2011-01-01

    Experimental observations of vortex breakdown in a rotating lid-driven cavity are presented. The results show that vortex breakdown for cavities with high aspect ratios is associated with the appearance of stable helical vortex multiplets. By using results from stability theory generalizing Kelvin......’s problem on vortex polygon stability, and systematically exploring the cavity flow, we succeeded in identifying two new stable vortex breakdown states consisting of triple and quadruple helical multiplets....

  1. Theoretical study of structure of electric field in helical toroidal plasmas

    International Nuclear Information System (INIS)

    Toda, S.; Itoh, K.

    2001-06-01

    A set of transport equations is analyzed, including the bifurcation of the electric field. The structure of the electric field is studied by use of the theoretical model for the anomalous transport diffusivities. The steep gradient of the electric field is obtained at the electric domain. The suppression of the anomalous transport diffusivity is studied in the presence of the strong shear of the electric field. The hard transition with the multiple ambipolar solutions is examined in the structure of the radial electric field. The details of the structure of the electric domain interface are investigated. (author)

  2. Thermally-Stable High Strain Deployable Structures, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — The proposed innovation is for the development of a thermally-stable composite made of carbon fibers and elastomeric resin. This combination of materials will allow...

  3. Exploiting hydrophobicity for efficient production of transmembrane helices for structure determination by NMR spectroscopy

    DEFF Research Database (Denmark)

    Bugge, Katrine Østergaard; Steinocher, Helena; Brooks, Andrew J.

    2015-01-01

    -labeled protein. In this work, we have exploited the hydrophobic nature of membrane proteins to develop a simple and efficient production scheme for isotope-labeled single-pass transmembrane domains (TMDs) with or without intrinsically disordered regions. We have evaluated the applicability and limitations...... of the strategy using seven membrane protein variants that differ in their overall hydrophobicity and length and show a recovery for suitable variants of >70%. The developed production scheme is cost-efficient and easy to implement and has the potential to facilitate an increase in the number of structures...

  4. A new helical crossed-fibre structure of β-keratin in flight feathers and its biomechanical implications.

    Directory of Open Access Journals (Sweden)

    Theagarten Lingham-Soliar

    Full Text Available The feather aerofoil is unequalled in nature. It is comprised of a central rachis, serial paired branches or barbs, from which arise further branches, the barbules. Barbs and barbules arise from the significantly thinner lateral walls (the epicortex of the rachis and barbs respectively, as opposed to the thicker dorsal and ventral walls (the cortex. We hypothesized a microstructural design of the epicortex that would resist the vertical or shearing stresses. The microstructures of the cortex and epicortex of the rachis and barbs were investigated in several bird species by microbe-assisted selective disassembly and conventional methods via scanning electron microscopy. We report, preeminent of the finds, a novel system of crossed fibres (ranging from ∼100-800 nm in diameter, oppositely oriented in alternate layers of the epicortex in the rachis and barbs. It represents the first cross-fibre microstructure, not only for the feather but in keratin per se. The cortex of the barbs is comprised of syncitial barbule cells, definitive structural units shown in the rachidial cortex in a related study. The structural connection between the cortex of the rachis and barbs appears uninterrupted. A new model on feather microstructure incorporating the findings here and in the related study is presented. The helical fibre system found in the integument of a diverse range of invertebrates and vertebrates has been implicated in profound functional strategies, perhaps none more so potentially than in the aerofoil microstructure of the feather here, which is central to one of the marvels of nature, bird flight.

  5. Splitting of α-Helical Structure as Molecular Basis for Abolishing an Amyloid Formation by Multiple Glycosylation: A Molecular Dynamics Simulation Study

    Energy Technology Data Exchange (ETDEWEB)

    Choi, Youngjin [Hoseo University, Asan (Korea, Republic of); Cho, Eunae; Jung, Seunho [Konkuk University, Seoul (Korea, Republic of)

    2016-07-15

    Molecular details played by glycosylation are complicated by the subtle nature of variations in the glycan structure, and this complexity is one of the research barriers to establish structure-function relationship on the protein modification. This is particularly true for understanding the exact structural consequence of the glycosylation of the biological proteins. The present MD simulation revealed molecular-level mechanism of the glycosylation effect on the peptide to understand the experimentally observed phenomenon for inhibiting amyloid formation in the model peptide. The galactose residue on the Ser17 undermined the helical integrity of main protein region by enhancing sugar–amino acid interaction and perturbing natural interactions between amino acid residues.

  6. Optimization of the Magnetic Field Structure for Sustained Plasma Gun Helicity Injection for Magnetic Turbulence Studies at the Bryn Mawr Plasma Laboratory

    Science.gov (United States)

    Cartagena-Sanchez, C. A.; Schaffner, D. A.; Johnson, H. K.; Fahim, L. E.

    2017-10-01

    A long-pulsed magnetic coaxial plasma gun is being implemented and characterized at the Bryn Mawr Plasma Laboratory (BMPL). A cold cathode discharged between the cylindrical electrodes generates and launches plasma into a 24cm diameter, 2m long chamber. Three separately pulsed magnetic coils are carefully positioned to generate radial magnetic field between the electrodes at the gun edge in order to provide stuffing field. Magnetic helicity is continuously injected into the flux-conserving vacuum chamber in a process akin to sustained slow-formation of spheromaks. The aim of this source, however, is to supply long pulses of turbulent magnetized plasma for measurement rather than for sustained spheromak production. The work shown here details the optimization of the magnetic field structure for this sustained helicity injection.

  7. Tryptophan scanning mutagenesis reveals distortions in the helical structure of the δM4 transmembrane domain of the Torpedo californica nicotinic acetylcholine receptor.

    Science.gov (United States)

    Caballero-Rivera, Daniel; Cruz-Nieves, Omar A; Oyola-Cintrón, Jessica; Torres-Nunez, David A; Otero-Cruz, Jose D; Lasalde-Dominicci, José A

    2012-01-01

    The lipid-protein interface is an important domain of the nicotinic acetylcholine receptor (nAChR) that has recently garnered increased relevance. Several studies have made significant advances toward determining the structure and dynamics of the lipid-exposed domains of the nAChR. However, there is still a need to gain insight into the mechanism by which lipid-protein interactions regulate the function and conformational transitions of the nAChR. In this study, we extended the tryptophan scanning mutagenesis (TrpScanM) approach to dissect secondary structure and monitor the conformational changes experienced by the δM4 transmembrane domain (TMD) of the Torpedo californica nAChR, and to identify which positions on this domain are potentially linked to the regulation of ion channel kinetics. The difference in oscillation patterns between the closed- and open-channel states suggests a substantial conformational change along this domain as a consequence of channel activation. Furthermore, TrpScanM revealed distortions along the helical structure of this TMD that are not present on current models of the nAChR. Our results show that a Thr-Pro motif at positions 462-463 markedly bends the helical structure of the TMD, consistent with the recent crystallographic structure of the GluCl Cys-loop receptor which reveals a highly bent TMD4 in each subunit. This Thr-Pro motif acts as a molecular hinge that delineates two gating blocks in the δM4 TMD. These results suggest a model in which a hinge-bending motion that tilts the helical structure is combined with a spring-like motion during transition between the closed- and open-channel states of the δM4 TMD.

  8. Rational assembly of Pb(II)/Cd(II)/Mn(II) coordination polymers based on flexible V-shaped dicarboxylate ligand: Syntheses, helical structures and properties

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Gao-Shan [School of Environment and Chemical Engineering, Nanchang Hangkong University, Nanchang 330063 (China); Liu, Chong-Bo, E-mail: cbliu@nchu.edu.cn [School of Environment and Chemical Engineering, Nanchang Hangkong University, Nanchang 330063 (China); School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332 (United States); Liu, Hong [School of Environment and Chemical Engineering, Nanchang Hangkong University, Nanchang 330063 (China); Robbins, Julianne; Zhang, Z. John [School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332 (United States); Yin, Hong-Shan [School of Environment and Chemical Engineering, Nanchang Hangkong University, Nanchang 330063 (China); Wen, Hui-Liang [State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047 (China); Wang, Yu-Hua [School of Environment and Chemical Engineering, Nanchang Hangkong University, Nanchang 330063 (China)

    2015-05-15

    Six new coordination polymers, namely, [Pb(L)(H{sub 2}O)] (1), [Pb(L)(phen)] (2), [Pb{sub 2}(L){sub 2}(4,4′-bipy){sub 0.5}] (3), [Cd(L)(phen)] (4), [Cd(L)(4,4′-bipy)]·H{sub 2}O (5) and [Mn(L)(4,4′-bipy)]·H{sub 2}O (6) have been synthesized by the hydrothermal reaction of 2,2′-[hexafluoroisopropylidenebis(p-phenyleneoxy)]diacetic acid (H{sub 2}L) with Pb(II)/Cd(II)/Mn(II) in the presence of ancillary ligands 4,4′-bipyridine (4,4′-bipy) or 1,10-phenanthroline (phen). Complexes 1 and 4–6 exhibit 2-D structures, and complexes 2–3 display 3-D frameworks, of which L{sup 2−} ligands join metal ions to single-stranded helical chains of 1, 3–6 and double-stranded helical chains of 2. Complexes 2 and 3 also contain double-stranded Metal–O helices. Topology analysis reveals that complexes 1 and 4 both represent 4-connected sql net, 2 represents 6-connected pcu net, 3 exhibits a novel (3,12)-connected net, while 5 and 6 display (3,5)-connected gek1 net. The six complexes exhibit two kinds of inorganic–organic connectivities: I{sup 0}O{sup 2} for 1, 4–6, and I{sup 1}O{sup 2} for 2–3. The photoluminescent properties of 4–5 and the magnetic properties of 6 have been investigated. - Graphical abstract: Six new Pb(II)/Cd(II)/Mn(II) coordination polymers with helical structures based on flexible V-shaped dicarboxylate ligand have been synthesized and structurally characterized. Photoluminescent and magnetic properties have been investigated. - Highlights: • Six novel M(II) coordination polymers with 2,2′-[hexafluoroisopropylidenebis(p-phenyleneoxy)]diacetic acid and N-donor ligands. • Complexes 1–6 show diverse intriguing helical characters. • The luminescent properties of complexes 1–5 were investigated. • Complex 6 shows antiferromagnetic coupling.

  9. Hygro-Thermal Transient Analysis for Highly Stable Structures

    CERN Document Server

    Da Mota Silva, S; Hauviller, Claude; Kanoute, P; Ribeiro, R

    1999-01-01

    This paper presents the results obtained with the simulations of a sandwich rectangular plate made of carbon/epoxy composite when subjected to temperature and humidity cycles. Fickian diffusion process, moisture transport along the interfaces and damage caused by slipping and debonding between the components of the microscopic structure are considered. The application of the design methodology to a real structure is shown.

  10. Modeling of high gain helical antenna for improved performance ...

    African Journals Online (AJOL)

    The modeling of High Gain Helical Antenna structure is subdivided into three sections : introduction of helical structures ,Numerical analysis, modeling and simulation based on the parameters of helical antenna. The basic foundation software for the research paper is Matlab technical computing software, the modeling were ...

  11. Amphipathic alpha-helices and putative cholesterol binding domains of the influenza virus matrix M1 protein are crucial for virion structure organisation.

    Science.gov (United States)

    Tsfasman, Tatyana; Kost, Vladimir; Markushin, Stanislav; Lotte, Vera; Koptiaeva, Irina; Bogacheva, Elena; Baratova, Ludmila; Radyukhin, Victor

    2015-12-02

    The influenza virus matrix M1 protein is an amphitropic membrane-associated protein, forming the matrix layer immediately beneath the virus raft membrane, thereby ensuring the proper structure of the influenza virion. The objective of this study was to elucidate M1 fine structural characteristics, which determine amphitropic properties and raft membrane activities of the protein, via 3D in silico modelling with subsequent mutational analysis. Computer simulations suggest the amphipathic nature of the M1 α-helices and the existence of putative cholesterol binding (CRAC) motifs on six amphipathic α-helices. Our finding explains for the first time many features of this protein, particularly the amphitropic properties and raft/cholesterol binding potential. To verify these results, we generated mutants of the A/WSN/33 strain via reverse genetics. The M1 mutations included F32Y in the CRAC of α-helix 2, W45Y and W45F in the CRAC of α-helix 3, Y100S in the CRAC of α-helix 6, M128A and M128S in the CRAC of α-helix 8 and a double L103I/L130I mutation in both a putative cholesterol consensus motif and the nuclear localisation signal. All mutations resulted in viruses with unusual filamentous morphology. Previous experimental data regarding the morphology of M1-gene mutant influenza viruses can now be explained in structural terms and are consistent with the pivotal role of the CRAC-domains and amphipathic α-helices in M1-lipid interactions. Copyright © 2015 Elsevier B.V. All rights reserved.

  12. Active structural control with stable fuzzy PID techniques

    CERN Document Server

    Yu, Wen

    2016-01-01

    This book presents a detailed discussion of intelligent techniques to measure the displacement of buildings when they are subjected to vibration. It shows how these techniques are used to control active devices that can reduce vibration 60–80% more effectively than widely used passive anti-seismic systems. After introducing various structural control devices and building-modeling and active structural control methods, the authors propose offset cancellation and high-pass filtering techniques to solve some common problems of building-displacement measurement using accelerometers. The most popular control algorithms in industrial settings, PD/PID controllers, are then analyzed and then combined with fuzzy compensation. The stability of this combination is proven with standard weight-training algorithms. These conditions provide explicit methods for selecting PD/PID controllers. Finally, fuzzy-logic and sliding-mode control are applied to the control of wind-induced vibration. The methods described are support...

  13. An Energy stable Monolithic Eulerian Fluid-Structure Numerical Scheme *

    OpenAIRE

    Pironneau , Olivier

    2017-01-01

    The conservation laws of continuum mechanic written in an Eulerian frame make no difference between fluids and solids except in the expression of the stress tensors, usually with Newton's hypothesis for the fluids and Helmholtz potentials of energy for hyperelastic solids. By taking the velocities as unknown , monolithic methods for fluid structure interactions (FSI) are built. In this article such a formulation is analyzed when the fluid is compressible and the fluid is incompressible. The i...

  14. Crystalline mesoporous zirconia catalysts having stable tetragonal pore wall structure

    Science.gov (United States)

    Sachtler, Wolfgang M. H.; Huang, Yin-Yan

    1998-01-01

    Methods for the preparation of new sulfated mesoporous zirconia materials/catalysts with crystalline pore walls of predominantly tetragonal crystal structure, characterized by nitrogen physisorption measurement, X-ray diffraction, transmission electron microscopy and catalytic tests using n-butane isomerization to iso-butane and alkylation of 1-naphthol with 4-tert-butylstyrene as probe reactions. Sulfate deposition is preferred for the transformation of a mesoporous precursor with amorphous pore walls into a material with crystalline pore walls maintaining the mesoporous characteristics.

  15. Numerically stable fluid–structure interactions between compressible flow and solid structures

    KAUST Repository

    Grétarsson, Jón Tómas

    2011-04-01

    We propose a novel method to implicitly two-way couple Eulerian compressible flow to volumetric Lagrangian solids. The method works for both deformable and rigid solids and for arbitrary equations of state. The method exploits the formulation of [11] which solves compressible fluid in a semi-implicit manner, solving for the advection part explicitly and then correcting the intermediate state to time tn+1 using an implicit pressure, obtained by solving a modified Poisson system. Similar to previous fluid-structure interaction methods, we apply pressure forces to the solid and enforce a velocity boundary condition on the fluid in order to satisfy a no-slip constraint. Unlike previous methods, however, we apply these coupled interactions implicitly by adding the constraint to the pressure system and combining it with any implicit solid forces in order to obtain a strongly coupled, symmetric indefinite system (similar to [17], which only handles incompressible flow). We also show that, under a few reasonable assumptions, this system can be made symmetric positive-definite by following the methodology of [16]. Because our method handles the fluid-structure interactions implicitly, we avoid introducing any new time step restrictions and obtain stable results even for high density-to-mass ratios, where explicit methods struggle or fail. We exactly conserve momentum and kinetic energy (thermal fluid-structure interactions are not considered) at the fluid-structure interface, and hence naturally handle highly non-linear phenomenon such as shocks, contacts and rarefactions. © 2011 Elsevier Inc.

  16. Spatial variations in food web structures with alternative stable states: evidence from stable isotope analysis in a large eutrophic lake

    Science.gov (United States)

    Li, Yunkai; Zhang, Yuying; Xu, Jun; Zhang, Shuo

    2017-05-01

    Food web structures are well known to vary widely among ecosystems. Moreover, many food web studies of lakes have generally attempted to characterize the overall food web structure and have largely ignored internal spatial and environmental variations. In this study, we hypothesize that there is a high degree of spatial heterogeneity within an ecosystem and such heterogeneity may lead to strong variations in environmental conditions and resource availability, in turn resulting in different trophic pathways. Stable carbon and nitrogen isotopes were employed for the whole food web to describe the structure of the food web in different sub-basins within Taihu Lake. This lake is a large eutrophic freshwater lake that has been intensively managed and highly influenced by human activities for more than 50 years. The results show significant isotopic differences between basins with different environmental characteristics. Such differences likely result from isotopic baseline differences combining with a shift in food web structure. Both are related to local spatial heterogeneity in nutrient loading in waters. Such variation should be explicitly considered in future food web studies and ecosystem-based management in this lake ecosystem.

  17. Helical type vacuum container

    International Nuclear Information System (INIS)

    Owada, Kimio.

    1989-01-01

    Helical type vacuum containers in the prior art lack in considerations for thermal expansion stresses to helical coils, and there is a possibility of coil ruptures. The object of the present invention is to avoid the rupture of helical coils wound around the outer surface of a vacuum container against heat expansion if any. That is, bellows or heat expansion absorbing means are disposed to a cross section of a helical type vacuum container. With such a constitution, thermal expansion of helical coils per se due to temperature elevation of the coils during electric supply can be absorbed by expansion of the bellows or absorption of the heat expansion absorbing means. Further, this can be attained by arranging shear pins in the direction perpendicular to the bellows axis so that the bellows are not distorted when the helical coils are wound around the helical type vacuum container. (I.S.)

  18. Regional Comparisons of Oceanic Food Web Structure Using Stable Isotopes

    Science.gov (United States)

    Choy, A.; Drazen, J.; Popp, B. N.; Robison, B. H.

    2016-02-01

    Food chain length, or the number of trophic steps between primary producers and apex predators within an ecosystem, is a key determinant of ecosystem structure, including overall efficiency, stability, and productivity. Here, we quantitatively estimate food chain length for three pelagic ecosystems characterized by distinct biogeochemical and oceanographic regimes: the Northern California Current (NCC), the North Pacific Subtropical Gyre (NPSG), and the Gulf of California (GoC). From each region, ecologically equivalent organisms were selected from each of four successive trophic steps, including zooplankton (primary consumers), zooplanktivores (secondary consumers), piscivores (tertiary consumers), and higher order predators. Bulk tissue δ15N values of the organisms from all four trophic steps spanned ranges of approximately 9.8‰ (NCC), 1.4‰ (NPSG), and 2.1‰ (GoC). Regional variations in nitrogen biogeochemistry, however, can alter isotopic baselines and food web dynamics, ultimately complicating bulk isotope measurements across regions. Thus, we apply amino acid nitrogen isotope measurements to quantitatively measure and compare food chain length across consumers from the three regions, accounting for biogeochemical disparities in isotopic baseline. Implications for ecosystem production and efficiency are discussed, including the potential for these different ecosystems to withstand environmental change, including shifting oxygen levels and surface productivity.

  19. Dynamics and deformability of α-, 310- and π-helices

    Directory of Open Access Journals (Sweden)

    Narwani Tarun Jairaj

    2018-01-01

    Full Text Available Protein structures are often represented as seen in crystals as (i rigid macromolecules (ii with helices, sheets and coils. However, both definitions are partial because (i proteins are highly dynamic macromolecules and (ii the description of protein structures could be more precise. With regard to these two points, we analyzed and quantified the stability of helices by considering α-helices as well as 310- and π-helices. Molecular dynamic (MD simulations were performed on a large set of 169 representative protein domains. The local protein conformations were followed during each simulation and analyzed. The classical flexibility index (B-factor was confronted with the MD root mean square flexibility (RMSF index. Helical regions were classified according to their level of helicity from high to none. For the first time, a precise quantification showed the percentage of rigid and flexible helices that underlie unexpected behaviors. Only 76.4% of the residues associated with α-helices retain the conformation, while this tendency drops to 40.5% for 310-helices and is never observed for π-helices. α-helix residues that do not remain as an α-helix have a higher tendency to assume β-turn conformations than 310- or π-helices. The 310-helices that switch to the α-helix conformation have a higher B-factor and RMSF values than the average 310-helix but are associated with a lower accessibility. Rare π-helices assume a β-turn, bend and coil conformations, but not α- or 310-helices. The view on π-helices drastically changes with the new DSSP (Dictionary of Secondary Structure of Proteins assignment approach, leading to behavior similar to 310-helices, thus underlining the importance of secondary structure assignment methods.

  20. LHD helical divertor

    International Nuclear Information System (INIS)

    Ohyabu, N.; Watanabe, T.; Ji Hantao

    1993-07-01

    The Large Helical Device (LHD) now under construction is a heliotron/torsatron device with a closed divertor system. The edge LHD magnetic structure has been studied in detail. A peculiar feature of the configuration is existence of edge surface layers, a complicated three dimensional magnetic structure which does not, however, seem to hamper the expected divertor functions. Two divertor operational modes are being considered for the LHD experiment, high density, cold radiative divertor operation as a safe heat removal scheme and high temperature divertor plasma operation. In the latter operation, a divertor plasma with temperature of a few kev, generated by efficient pumping, expects to lead to significant improvement in core plasma confinement. Conceptual designs of the LHD divertor components are under way. (author)

  1. Stable helical solitons in optical media

    Indian Academy of Sciences (India)

    Besides that, these solitons are objects of fundamental interest. To fully examine their stability, it is crucially important to consider collisions between them, and their collisions with fundamental solitons, in (ordinary or hollow) optical fibres. We introduce a system of coupled nonlinear Schrödinger equations for the ...

  2. Stable helical solitons in optical media

    Indian Academy of Sciences (India)

    case is when the centres of the colliding solitons exactly coincide atz =0. In this case, δωl is found by straightforward integration of eq. (14) from z = 0 to z = +∞. The result can be presented in a more natural form, multiplying the net frequency shift by the soliton's temporal width (i.e., normalizing the frequency shift to the ...

  3. ICRF heating on helical devices

    International Nuclear Information System (INIS)

    Rasmussen, D.A.; Lyon, J.F.; Hoffman, D.J.; Murakami, M.; England, A.C.; Wilgen, J.B.

    1995-01-01

    Ion cyclotron range of frequency (ICRF) heating is currently in use on CHS and W7-AS and is a major element of the heating planned for steady state helical devices. In helical devices, the lack of a toroidal current eliminates both disruptions and the need for ICFR current drive, simplifying the design of antenna structures as compared to tokamak applications. However the survivability of plasma facing components and steady state cooling issues are directly applicable to tokamak devices. Results from LHD steady state experiments should be available on a time scale to strongly influence the next generation of steady state tokamak experiments. the helical plasma geometry provides challenges not faced with tokamak ICRF heating, including the potential for enhanced fast ion losses, impurity accumulation, limited access for antenna structures, and open magnetic field lines in the plasma edge. The present results and near term plans provide the basis for steady state ICRF heating of larger helical devices. An approach which includes direct electron, mode conversion, ion minority and ion Bernstein wave heating addresses these issues. 12 refs

  4. Dynamics of helical vortices behind a wind turbine in a stratified atmosphere

    Science.gov (United States)

    Mao, Xuerui; Hussain, Fazle

    2017-11-01

    The wind turbine wake features helical vortices, which are shed from the tips of blades and inflict undesirable fatigue loading on downstream turbines. Prior studies of helical vortices focused on their hydrodynamic instabilities and the following breakup in the neutrally stable, isothermal atmospheres in which the buoyancy force is balanced by gravity. However, the atmosphere is typically mostly unstable during the day and mostly stable at night, but is seldom neutral. The present numerical work addresses the development of helical vortices in a thermally stratified atmosphere and also concentrates on the stable condition which is typical for offshore applications. The Boussinesq approximation is invoked to account for the thermal stratification effect, and an actuator line model is adopted for the turbine blades. In our direct numerical simulations, the helical vortices are found to be increasingly elliptic downstream and subsequently interact with the hub vortex to produce a new mode of breakup into turbulence. Such elliptic structures increase the width of the wake and subsequently the interaction between aligned turbines in large-scale offshore wind farms.

  5. On the Helical Structure of Guanosine 5'-Monophosphate Formed at pH 5: Is It Left- or Right-Handed?

    Science.gov (United States)

    Wu, Gang; Kwan, Irene C M; Yan, Zhimin; Huang, Yining; Ye, Eric

    2017-01-01

    Early X-ray fiber diffraction studies have established that the spontaneous gel formation of guanosine 5'-monophosphate (5'-GMP) under slightly acidic conditions (e.g., pH 5) results from self-assembly of 5'-GMP into a helical structure in which hydrogen-bonded guanine bases form a continuous helix with 15 nucleotides per 4 turns. For more than five decades, the sense of this helix is believed to be left-handed. Using multinuclear solid-state NMR and IR spectroscopic methods, we have finally determined the long-missing structural details of this helix. First, we found that this 5'-GMP helix is right-handed containing exclusive C3'- endo sugar puckers. Second, we showed that the central channel of this helix is free of Na + ions, which is in sharp contrast to the helix formed by 5'-GMP at pH 8 where the central channel is filled with Na + ions.

  6. Disulfide-stabilized Helical Hairpin Structure and Activity of a Novel Antifungal Peptide EcAMP1 from Seeds of Barnyard Grass (Echinochloa crus-galli)*

    Science.gov (United States)

    Nolde, Svetlana B.; Vassilevski, Alexander A.; Rogozhin, Eugene A.; Barinov, Nikolay A.; Balashova, Tamara A.; Samsonova, Olga V.; Baranov, Yuri V.; Feofanov, Alexey V.; Egorov, Tsezi A.; Arseniev, Alexander S.; Grishin, Eugene V.

    2011-01-01

    This study presents purification, activity characterization, and 1H NMR study of the novel antifungal peptide EcAMP1 from kernels of barnyard grass Echinochloa crus-galli. The peptide adopts a disulfide-stabilized α-helical hairpin structure in aqueous solution and thus represents a novel fold among naturally occurring antimicrobial peptides. Micromolar concentrations of EcAMP1 were shown to inhibit growth of several fungal phytopathogens. Confocal microscopy revealed intensive EcAMP1 binding to the surface of fungal conidia followed by internalization and accumulation in the cytoplasm without disturbance of membrane integrity. Close spatial structure similarity between EcAMP1, the trypsin inhibitor VhTI from seeds of Veronica hederifolia, and some scorpion and cone snail toxins suggests natural elaboration of different functions on a common fold. PMID:21561864

  7. Disulfide-stabilized helical hairpin structure and activity of a novel antifungal peptide EcAMP1 from seeds of barnyard grass (Echinochloa crus-galli).

    Science.gov (United States)

    Nolde, Svetlana B; Vassilevski, Alexander A; Rogozhin, Eugene A; Barinov, Nikolay A; Balashova, Tamara A; Samsonova, Olga V; Baranov, Yuri V; Feofanov, Alexey V; Egorov, Tsezi A; Arseniev, Alexander S; Grishin, Eugene V

    2011-07-15

    This study presents purification, activity characterization, and (1)H NMR study of the novel antifungal peptide EcAMP1 from kernels of barnyard grass Echinochloa crus-galli. The peptide adopts a disulfide-stabilized α-helical hairpin structure in aqueous solution and thus represents a novel fold among naturally occurring antimicrobial peptides. Micromolar concentrations of EcAMP1 were shown to inhibit growth of several fungal phytopathogens. Confocal microscopy revealed intensive EcAMP1 binding to the surface of fungal conidia followed by internalization and accumulation in the cytoplasm without disturbance of membrane integrity. Close spatial structure similarity between EcAMP1, the trypsin inhibitor VhTI from seeds of Veronica hederifolia, and some scorpion and cone snail toxins suggests natural elaboration of different functions on a common fold.

  8. Modification of the magnetic field structure of high-beta plasmas with a perturbation field in the Large Helical Device

    International Nuclear Information System (INIS)

    Sakakibara, S; Suzuki, Y; Narushima, Y; Watanabe, K Y; Ohdachi, S; Ida, K; Yoshinuma, M; Narihara, K; Yamada, I; Tanaka, K; Tokuzawa, T; Yamada, H; Takemura, Y

    2013-01-01

    The effect of resonant magnetic perturbation (RMP) on MHD characteristics is investigated in high-beta plasmas of the Large Helical Device. The ramp-up and static m/n = 1/1 RMP field are applied in medium- (∼2%) and high- (∼4%) beta plasmas in order to find beta dependences of mode penetration, MHD activities and confinement. The results show that the threshold of mode penetration linearly increases with the beta value and/or plasma collisionality. The threshold of mode penetration in the RMP ramp-up experiments is roughly consistent with the static RMP case. The beta value gradually decreases with the RMP field strength before mode penetration, which is caused by a reduction in the pressure inside the ι/2π = 1 resonance. The width of the magnetic island after the penetration becomes larger than the given RMP field, and it is further enhanced by the increment of the beta value. (paper)

  9. TGP, an extremely stable, non-aggregating fluorescent protein created by structure-guided surface engineering

    OpenAIRE

    Close, Devin W.; Don Paul, Craig; Langan, Patricia S.; Wilce, Matthew C.J.; Traore, Daouda A.K.; Halfmann, Randal; Rocha, Reginaldo C.; Waldo, Geoffery S.; Payne, Riley J.; Rucker, Joseph B.; Prescott, Mark; Bradbury, Andrew R.M.

    2015-01-01

    In this paper we describe the engineering and X-ray crystal structure of Thermal Green Protein (TGP), an extremely stable, highly soluble, non-aggregating green fluorescent protein. TGP is a soluble variant of the fluorescent protein eCGP123, which despite being highly stable, has proven to be aggregation-prone. The X-ray crystal structure of eCGP123, also determined within the context of this paper, was used to carry out rational surface engineering to improve its solubility, leading to TGP....

  10. Helicity and Filament Channels? The Straight Twist!

    Science.gov (United States)

    Antiochos, Spiro K.

    2010-01-01

    One of the most important and most puzzling features of the coronal magnetic field is that it appears to have smooth magnetic structure with little evidence for non-potentiality except at special locations, photospheric polarity inversions lines where the non-potentiality is observed as a filament channel. This characteristic feature of the closed-field corona is highly unexpected given that photospheric motions continuously tangle its magnetic field. Although reconnection can eliminate some of the injected structure, it cannot destroy the helicity, which should build up to produce observable complexity. We propose that an inverse cascade process transports the injected helicity from the interior of closed flux regions to their boundaries, polarity inversion lines, creating filament channels. We describe how the helicity is injected and transported and calculate the relevant rates. We argue that one process, helicity transport, can explain both the observed lack and presence of structure in the coronal magnetic field.

  11. Structure of stable degeneration of K3 surfaces into pairs of rational elliptic surfaces

    Science.gov (United States)

    Kimura, Yusuke

    2018-03-01

    F-theory/heterotic duality is formulated in the stable degeneration limit of a K3 fibration on the F-theory side. In this note, we analyze the structure of the stable degeneration limit. We discuss whether stable degeneration exists for pairs of rational elliptic surfaces. We demonstrate that, when two rational elliptic surfaces have an identical complex structure, stable degeneration always exists. We provide an equation that systematically describes the stable degeneration of a K3 surface into a pair of isomorphic rational elliptic surfaces. When two rational elliptic surfaces have different complex structures, whether their sum glued along a smooth fiber admits deformation to a K3 surface can be determined by studying the structure of the K3 lattice. We investigate the lattice theoretic condition to determine whether a deformation to a K3 surface exists for pairs of extremal rational elliptic surfaces. In addition, we discuss the configurations of singular fibers under stable degeneration. The sum of two isomorphic rational elliptic surfaces glued together admits a deformation to a K3 surface, the singular fibers of which are twice that of the rational elliptic surface. For special situations, singular fibers of the resulting K3 surface collide and they are enhanced to a fiber of another type. Some K3 surfaces become attractive in these situations. We determine the complex structures and the Weierstrass forms of these attractive K3 surfaces. We also deduce the gauge groups in F-theory compactifications on these attractive K3 surfaces times a K3. E 6, E 7, E 8, SU(5), and SO(10) gauge groups arise in these compactifications.

  12. Novel stable structure of Li3PS4 predicted by evolutionary algorithm under high-pressure

    Directory of Open Access Journals (Sweden)

    S. Iikubo

    2018-01-01

    Full Text Available By combining theoretical predictions and in-situ X-ray diffraction under high pressure, we found a novel stable crystal structure of Li3PS4 under high pressures. At ambient pressure, Li3PS4 shows successive structural transitions from γ-type to β-type and from β-type to α type with increasing temperature, as is well established. In this study, an evolutionary algorithm successfully predicted the γ-type crystal structure at ambient pressure and further predicted a possible stable δ-type crystal structures under high pressure. The stability of the obtained structures is examined in terms of both static and dynamic stability by first-principles calculations. In situ X-ray diffraction using a synchrotron radiation revealed that the high-pressure phase is the predicted δ-Li3PS4 phase.

  13. Structural characterization of an enantiopure hydroxo-bridged binuclear iron(III) complex with empty one-dimensional helical channels.

    Science.gov (United States)

    Alam, Md Akhtarul; Nethaji, Munirathinum; Ray, Manabendra

    2005-03-07

    A H-bond capable chiral tetradentate ligand, Fe3+, and acetate ion assembles into a hydroxo-bridged binuclear complex with the formula [FeIII2(mu-OH)(mu-OAc)(S-L)2] x 4H2O (1) where H2S-L = S-2-(2-hydroxy-benzylamino)-3-(1H-imidazol-4-yl)-propionic acid. The crystal of 1 contains right-handed one-dimensional (1D) helical channels with 7.3-9.8 A diameter. A similar reaction with a ligand having opposite chirality forms the complex with left-handed helical channels (1a). Heating the crystals of 1 at 95 degrees C under reduced pressure selectively removes three waters from the channel forming an enantiopure porous crystal with empty channels (solvent accessible voids 18% v/v). Intermolecular hydrogen bonding between the imidazole N-H and phenolate oxygen in 1-2 forms a C6 symmetric helix with bridging hydroxo groups pointing inside the channels. All the H-bond capable atoms in the ligand along with one water molecule form an extended H-bonded network throughout the crystal. Exposing the empty channels of 2 to iodine vapor indicates partial filling of the channels with iodine. Crystal data for 1 x 4H2O include the following: hexagonal, P61, a = b = 13.164(3) A, c = 36.305 (11) A, alpha = beta = 90 degrees , gamma = 120 degrees , Z = 6, R1 = 0.0387, wR2 = 0.0842. Crystal data for 1a x 2H2O include the following: hexagonal, P6(5), a = b = 13.151(4) A, c = 36.558(2) A, alpha = beta = 90 degrees , gamma = 120 degrees , Z = 6, R1 = 0.0416, wR2 = 0.1190. Crystal data for 2 x H2O include the following: hexagonal, P61, a = b = 13.160(7) A, c = 36.559 (4) A, alpha = beta = 90 degrees , gamma = 120 degrees , Z = 6, R1 = 0.0574, wR2 = 0.1423.

  14. Polymorphic transformation of helical flagella of bacteria

    Science.gov (United States)

    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.

  15. Ratio of ellipticities between 192 and 208 nm (R1 ): An effective electronic circular dichroism parameter for characterization of the helical components of proteins and peptides.

    Science.gov (United States)

    Banerjee, Raja; Sheet, Tridip

    2017-11-01

    Circular dichroism (CD) spectroscopy represents an important tool for characterization of the peptide and protein secondary structures that mainly arise from the conformational disposition of the peptide backbone in solution. In 1991 Manning and Woody proposed that, in addition to the signal intensity, the ratio between [θ]nπ* and [θ]ππ*ǁ ((R 2 ) ≅ [θ] 222 /[θ] 208 ), along with [θ]ππ*⊥ and [θ]ππ*ǁ ((R 1 ) ≅ [θ] 192 /[θ] 208 ), may be utilized towards identifying the peptide/protein conformation (especially 3 10 - and α-helices). However, till date the use of the ratiometric ellipticity component for helical structure analysis of peptides and proteins has not been reported. We studied a series of temperature dependent CD spectra of a thermally stable, model helical peptide and its related analogs in water as a function of added 2,2,2-trifluoroethanol (TFE) in order to explore their landscape of helicity. For the first time, we have experimentally shown here that the R 1 parameter can characterize better the individual helices, while the other parameter R 2 and the signal intensity do not always converge. We emphasize the use of the R 1 ratio of ellipticities for helical characterization because of the common origin of these two bands (exciton splitting of the amide π→ π* transition in a helical polypeptide). This approach may become worthwhile and timely with the increasing accessibility of CD synchrotron sources. © 2017 Wiley Periodicals, Inc.

  16. Helical Antimicrobial Sulfono- {gamma} -AApeptides

    Energy Technology Data Exchange (ETDEWEB)

    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.

  17. Embodied memory: effective and stable perception by combining optic flow and image structure.

    Science.gov (United States)

    Pan, Jing Samantha; Bingham, Ned; Bingham, Geoffrey P

    2013-12-01

    Visual perception studies typically focus either on optic flow structure or image structure, but not on the combination and interaction of these two sources of information. Each offers unique strengths in contrast to the other's weaknesses. Optic flow yields intrinsically powerful information about 3D structure, but is ephemeral. It ceases when motion stops. Image structure is less powerful in specifying 3D structure, but is stable. It remains when motion stops. Optic flow and image structure are intrinsically related in vision because the optic flow carries one image to the next. This relation is especially important in the context of progressive occlusion, in which optic flow provides information about the location of targets hidden in subsequent image structure. In four experiments, we investigated the role of image structure in "embodied memory" in contrast to memory that is only in the head. We found that either optic flow (Experiment 1) or image structure (Experiment 2) alone were relatively ineffective, whereas the combination was effective and, in contrast to conditions requiring reliance on memory-in-the-head, much more stable over extended time (Experiments 2 through 4). Limits well documented for visual short memory (that is, memory-in-the-head) were strongly exceeded by embodied memory. The findings support J. J. Gibson's (1979/1986, The Ecological Approach to Visual Perception, Boston, MA, Houghton Mifflin) insights about progressive occlusion and the embodied nature of perception and memory.

  18. Use of a Novel Two Color PALM Method to Examine Structural Properties of Drp1 Helical Rings during Mammalian Mitochondrial Fission In Situ

    Science.gov (United States)

    Rosenbloom, Alyssa Blair

    In this thesis, we accomplish two goals: 1) we develop a novel two color photoactivatable light microscopy (PALM) method for imaging in mammalian cells and 2) we explore our original biological question and discern the structural properties of the Drp1 helical ring during fission. We established that mitochondrial membranes can be distinguished with the available photoactivatable fluorescent protein mEos2. However, we were not able to use any of the published photoactivatable and photoswitchable green fluorescent proteins, predominantly because of an inability to identify individual fluorescent events due to rapidity of the photoswitiching. Based on published crystal structures, we created novel Dronpa variants with increasing steric hindrance around the chromophore, likely partially inhibiting the isomerization. We replaced Val157 with isoleucine, leucine, or phenyalanine. DronpaV157F showed no fluorescence and was discarded. DronpaV157I and DronpaV157L showed photoswitchable green fluorescence, with individual fluorescent events that were more easily discerned. DronpaV157L in particular had bright fluorescent events that were well separated when imaged in mammalian cells at 20 Hz. We named this new variant rsKame. Using PALM we successfully imaged rsKame expressed and localized to the mammalian mitochondrial inner membrane. With the novel photoswitchable fluorescent protein, rsKame, available, we returned to the development of a novel two color PALM method. We chose PAmCherry1 as the partner for rsKame since PAmCherry1 has distinct and well separated excitation/emission spectra from rsKame and is not activated by low 405 nm laser power density. We first imaged rsKame with 405 nm activation at (0.61 mW/mm2) and 488 nm activation/excitation (5.87 W/mm 2) to completion. We then imaged PAmCherry1 with increasing 405 nm activation (0.6-6.0 W/mm2) and 561 nm excitation (22 W/mm 2). With the novel PALM imaging method, we labeled the inner and outer mitochondrial

  19. Prediction of Stable Ruthenium Silicides from First-Principles Calculations: Stoichiometries, Crystal Structures, and Physical Properties.

    Science.gov (United States)

    Zhang, Chuanzhao; Kuang, Xiaoyu; Jin, Yuanyuan; Lu, Cheng; Zhou, Dawei; Li, Peifang; Bao, Gang; Hermann, Andreas

    2015-12-09

    We present results of an unbiased structure search for stable ruthenium silicide compounds with various stoichiometries, using a recently developed technique that combines particle swarm optimization algorithms with first-principles calculations. Two experimentally observed structures of ruthenium silicides, RuSi (space group P2(1)3) and Ru2Si3 (space group Pbcn), are successfully reproduced under ambient pressure conditions. In addition, a stable RuSi2 compound with β-FeSi2 structure type (space group Cmca) was found. The calculations of the formation enthalpy, elastic constants, and phonon dispersions demonstrate the Cmca-RuSi2 compound is energetically, mechanically, and dynamically stable. The analysis of electronic band structures and densities of state reveals that the Cmca-RuSi2 phase is a semiconductor with a direct band gap of 0.480 eV and is stabilized by strong covalent bonding between Ru and neighboring Si atoms. On the basis of the Mulliken overlap population analysis, the Vickers hardness of the Cmca structure RuSi2 is estimated to be 28.0 GPa, indicating its ultra-incompressible nature.

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

    Science.gov (United States)

    Miyake, Hiroyuki; Tsukube, Hiroshi

    2012-11-07

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

  1. Stimuli-Driven Control of the Helical Axis of Self-Organized Soft Helical Superstructures.

    Science.gov (United States)

    Bisoyi, Hari Krishna; Bunning, Timothy J; Li, Quan

    2018-03-30

    Supramolecular and macromolecular functional helical superstructures are ubiquitous in nature and display an impressive catalog of intriguing and elegant properties and performances. In materials science, self-organized soft helical superstructures, i.e., cholesteric liquid crystals (CLCs), serve as model systems toward the understanding of morphology- and orientation-dependent properties of supramolecular dynamic helical architectures and their potential for technological applications. Moreover, most of the fascinating device applications of CLCs are primarily determined by different orientations of the helical axis. Here, the control of the helical axis orientation of CLCs and its dynamic switching in two and three dimensions using different external stimuli are summarized. Electric-field-, magnetic-field-, and light-irradiation-driven orientation control and reorientation of the helical axis of CLCs are described and highlighted. Different techniques and strategies developed to achieve a uniform lying helix structure are explored. Helical axis control in recently developed heliconical cholesteric systems is examined. The control of the helical axis orientation in spherical geometries such as microdroplets and microshells fabricated from these enticing photonic fluids is also explored. Future challenges and opportunities in this exciting area involving anisotropic chiral liquids are then discussed. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Baryon helicity in B decay

    Energy Technology Data Exchange (ETDEWEB)

    Suzuki, Mahiko [Department of Physics and Lawrence Berkeley National Laboratory, University of California, Berkeley, CA 94720 (United States)

    2005-07-01

    The unexpectedly large transverse polarization measured in the decay B {yields} {phi}K* poses the question whether it is accounted for as a strong interaction effect or possibly points to a hidden nonstandard weak interaction. We extend here the perturbative argument to the helicity structure of the two-body baryonic decay and discuss qualitatively on how the baryonic B decay modes might help us in understanding the issue raised by B {yields} {phi}K*. We find among others that the helicity +1/2 amplitude dominates the leading order in the B(b-barq) decay and that unlike the B {yields} VV decay the dominant amplitude is sensitive to the right-handed b {yields} s current, if any, in the penguin interaction.

  3. Stable isotope applications in biomolecular structure and mechanisms. A meeting to bring together producers and users of stable-isotope-labeled compounds to assess current and future needs

    Energy Technology Data Exchange (ETDEWEB)

    Trewhella, J.; Cross, T.A.; Unkefer, C.J. [eds.

    1994-12-01

    Knowledge of biomolecular structure is a prerequisite for understanding biomolecular function, and stable isotopes play an increasingly important role in structure determination of biological molecules. The first Conference on Stable Isotope Applications in Biomolecular Structure and Mechanisms was held in Santa Fe, New Mexico, March 27--31, 1994. More than 120 participants from 8 countries and 44 institutions reviewed significant developments, discussed the most promising applications for stable isotopes, and addressed future needs and challenges. Participants focused on applications of stable isotopes for studies of the structure and function of proteins, peptides, RNA, and DNA. Recent advances in NMR techniques neutron scattering, EPR, and vibrational spectroscopy were highlighted in addition to the production and synthesis of labeled compounds. This volume includes invited speaker and poster presentations as well as a set of reports from discussion panels that focused on the needs of the scientific community and the potential roles of private industry, the National Stable Isotope Resource, and the National High Magnetic Field Laboratory in serving those needs. This is the leading abstract. Individual papers are processed separately for the database.

  4. Stable isotope applications in biomolecular structure and mechanisms. A meeting to bring together producers and users of stable-isotope-labeled compounds to assess current and future needs

    International Nuclear Information System (INIS)

    Trewhella, J.; Cross, T.A.; Unkefer, C.J.

    1994-12-01

    Knowledge of biomolecular structure is a prerequisite for understanding biomolecular function, and stable isotopes play an increasingly important role in structure determination of biological molecules. The first Conference on Stable Isotope Applications in Biomolecular Structure and Mechanisms was held in Santa Fe, New Mexico, March 27--31, 1994. More than 120 participants from 8 countries and 44 institutions reviewed significant developments, discussed the most promising applications for stable isotopes, and addressed future needs and challenges. Participants focused on applications of stable isotopes for studies of the structure and function of proteins, peptides, RNA, and DNA. Recent advances in NMR techniques neutron scattering, EPR, and vibrational spectroscopy were highlighted in addition to the production and synthesis of labeled compounds. This volume includes invited speaker and poster presentations as well as a set of reports from discussion panels that focused on the needs of the scientific community and the potential roles of private industry, the National Stable Isotope Resource, and the National High Magnetic Field Laboratory in serving those needs. This is the leading abstract. Individual papers are processed separately for the database

  5. Dipolar Quinoidal Acene Analogues as Stable Isoelectronic Structures of Pentacene and Nonacene

    KAUST Repository

    Shi, Xueliang

    2015-10-08

    Quinoidal thia-acene analogues, as the respective isoelectronic structures of pentacene and nonacene, were synthesized and an unusual 1,2-sulfur migration was observed during the Friedel-Crafts alkylation reaction. The analogues display a closed-shell quinoidal structure in the ground state with a distinctive dipolar character. In contrast to their acene isoelectronic structures, both compounds are stable because of the existence of more aromatic sextet rings, a dipolar character, and kinetic blocking. They exhibit unique packing in single crystals resulting from balanced dipole-dipole and [C-H⋯π]/[C-H⋯S] interactions.

  6. Helical magnetized wiggler for synchrotron radiation laser

    CERN Document Server

    Wang Mei; Hirshfield, J L

    1999-01-01

    A helical magnetized iron wiggler has been built for a novel infrared synchrotron radiation laser (SRL) experiment. The wiggler consists of four periods of helical iron structure immersed in a solenoid field. This wiggler is to impart transverse velocity to a prebunched 6 MeV electron beam, and thus to obtain a desired high orbit pitch ratio for the SRL. Field tapering at beam entrance is considered and tested on a similar wiggler. Analytic and simulated characteristics of wigglers of this type are discussed and the performance of the fabricated wigglers is demonstrated experimentally. A 4.7 kG peak field was measured for a 6.4 mm air gap and a 5.4 cm wiggler period at a 20 kG solenoid field. The measured helical fields compare favorably with the analytical solution. This type of helical iron wigglers has the potential to be scaled to small periods with strong field amplitude.

  7. Helical magnetized wiggler for synchrotron radiation laser

    International Nuclear Information System (INIS)

    Wang Mei; Park, S.Y.; Hirshfield, J.L.

    1999-01-01

    A helical magnetized iron wiggler has been built for a novel infrared synchrotron radiation laser (SRL) experiment. The wiggler consists of four periods of helical iron structure immersed in a solenoid field. This wiggler is to impart transverse velocity to a prebunched 6 MeV electron beam, and thus to obtain a desired high orbit pitch ratio for the SRL. Field tapering at beam entrance is considered and tested on a similar wiggler. Analytic and simulated characteristics of wigglers of this type are discussed and the performance of the fabricated wigglers is demonstrated experimentally. A 4.7 kG peak field was measured for a 6.4 mm air gap and a 5.4 cm wiggler period at a 20 kG solenoid field. The measured helical fields compare favorably with the analytical solution. This type of helical iron wigglers has the potential to be scaled to small periods with strong field amplitude

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

    Science.gov (United States)

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

    2016-01-01

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

  9. Stable algorithm for the computation of the electromagnetic field distribution of eigenmodes of periodic diffraction structures.

    Science.gov (United States)

    Bezus, Evgeni A; Doskolovich, Leonid L

    2012-11-01

    In the present work, a stable algorithm for the calculation of the electromagnetic field distributions of the eigenmodes of one-dimensional diffraction gratings is presented. The proposed approach is based on the method for the computation of the propagation constants of Bloch waves of such structures previously presented by Cao et al.[J. Opt. Soc. Am. A 19, 335 (2002)] and uses a modified S-matrix algorithm to ensure numerical stability.

  10. Muon-Substituted Malonaldehyde: Transforming a Transition State into a Stable Structure by Isotope Substitution.

    Science.gov (United States)

    Goli, Mohammad; Shahbazian, Shant

    2016-02-12

    Isotope substitutions are usually conceived to play a marginal role on the structure and bonding pattern of molecules. However, a recent study [Angew. Chem. Int. Ed. 2014, 53, 13706-13709; Angew. Chem. 2014, 126, 13925-13929] further demonstrates that upon replacing a proton with a positively charged muon, as the lightest radioisotope of hydrogen, radical changes in the nature of the structure and bonding of certain species may take place. The present report is a primary attempt to introduce another example of structural transformation on the basis of the malonaldehyde system. Accordingly, upon replacing the proton between the two oxygen atoms of malonaldehyde with the positively charged muon a serious structural transformation is observed. By using the ab initio nuclear-electronic orbital non-Born-Oppenheimer procedure, the nuclear configuration of the muon-substituted species is derived. The resulting nuclear configuration is much more similar to the transition state of the proton transfer in malonaldehyde rather than to the stable configuration of malonaldehyde. The comparison of the "atoms in molecules" (AIM) structure of the muon-substituted malonaldehyde and the AIM structure of the stable and the transition-state configurations of malonaldehyde also unequivocally demonstrates substantial similarities of the muon-substituted malonaldehyde to the transition state. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Biaxial and antiferroelectric structure of the orthogonal smectic phase of a bent-shaped molecule and helical structure in a chiral mixture system

    Science.gov (United States)

    Kang, Sungmin; Nguyen, Ha; Nakajima, Shunpei; Tokita, Masatoshi; Watanabe, Junji

    2013-05-01

    We examined the biaxial and antiferroelectric properties in the Smectic-APA (Sm-APA) phase of bent-shaped DC-S-8. The biaxiality, which results from the existence of a secondary director, was well established from birefringence observations in the homeotropically aligned Sm-APA. By entering into Sm-APA phase, the birefringence (Δn, difference between two refractive indices of short axes) continuously increased from 0 to 0.02 with decreasing temperature. The antiferroelectric switching and second harmonic generation (SHG) activity on the field-on state were also observed in the Sm-APA phase, and the evaluated spontaneous polarization (PS) value strongly depended on temperature. The temperature dependence of Δn and PS resembles each other and follows Haller's approximation, showing that the biaxiality is due to polar packing in which the molecules are preferentially packed with their bent direction arranged in the same direction, and that the phase transition of Sm-APA to Sm-A is second order. The biaxiality was further examined in chiral Sm-APA*. Doping with chiral components induced the helical twisting of the secondary director in the Sm-APA* phase, which was confirmed by observing the reflection of the circular dichroism (CD) bands in the homeotropically aligned cell. The helical pitch of Sm-APA* is tunable in the range of 300-700 nm wavelength with a variation in the chiral content of 5 to 10 weight (wt)%.

  12. Crystal structure of the left-handed archaeal RadA helical filament: identification of a functional motif for controlling quaternary structures and enzymatic functions of RecA family proteins

    Science.gov (United States)

    Chen, Li-Tzu; Ko, Tzu-Ping; Chang, Yuan-Chih; Lin, Kuei-An; Chang, Chia-Seng; Wang, Andrew H.-J.; Wang, Ting-Fang

    2007-01-01

    The RecA family of proteins mediates homologous recombination, an evolutionarily conserved pathway that maintains genomic stability by protecting against DNA double strand breaks. RecA proteins are thought to facilitate DNA strand exchange reactions as closed-rings or as right-handed helical filaments. Here, we report the crystal structure of a left-handed Sulfolobus solfataricus RadA helical filament. Each protomer in this left-handed filament is linked to its neighbour via interactions of a β-strand polymerization motif with the neighbouring ATPase domain. Immediately following the polymerization motif, we identified an evolutionarily conserved hinge region (a subunit rotation motif) in which a 360° clockwise axial rotation accompanies stepwise structural transitions from a closed ring to the AMP–PNP right-handed filament, then to an overwound right-handed filament and finally to the left-handed filament. Additional structural and functional analyses of wild-type and mutant proteins confirmed that the subunit rotation motif is crucial for enzymatic functions of RecA family proteins. These observations support the hypothesis that RecA family protein filaments may function as rotary motors. PMID:17329376

  13. PP3 forms stable tetrameric structures through hydrophobic interactions via the C-terminal amphipathic helix and undergoes reversible thermal dissociation and denaturation.

    Science.gov (United States)

    Pedersen, Lise R L; Nielsen, Søren B; Hansted, Jon G; Petersen, Torben E; Otzen, Daniel E; Sørensen, Esben S

    2012-01-01

    The milk protein proteose peptone component 3 (PP3), also called lactophorin, is a small phosphoglycoprotein that is expressed exclusively in lactating mammary tissue. The C-terminal part of the protein contains an amphipathic helix, which, upon proteolytic liberation, shows antibacterial activity. Previous studies indicate that PP3 forms multimeric structures and inhibits lipolysis in milk. PP3 is the principal component of the proteose peptone fraction of milk. This fraction is obtained by heating and acidifying skimmed milk, and in the dairy industry milk products are also typically exposed to treatments such as pasteurization, which potentially could result in irreversible denaturation and inactivation of bioactive components. We show here, by the use of CD, that PP3 undergoes reversible thermal denaturation and that the α-helical structure of PP3 remains stable even at gastric pH levels. This suggests that the secondary structure survives treatment during the purification and possibly some of the industrial processing of milk. Finally, asymmetric flow field-flow fractionation and multi-angle light scattering reveal that PP3 forms a rather stable tetrameric complex, which dissociates and unfolds in guanidinium chloride. The cooperative unfolding of PP3 was completely removed by the surfactant n-dodecyl-β-d-maltoside and by oleic acid. We interpret this to mean that the PP3 monomers associate through hydrophobic interactions via the hydrophobic surface of the amphipathic helix. These observations suggest that PP3 tetramers act as reservoirs of PP3 molecules, which in the monomeric state may stabilize the milk fat globule. © 2011 The Authors Journal compilation © 2011 FEBS.

  14. Nucleonic helicity distributions revisited with an emphasis on their ...

    Indian Academy of Sciences (India)

    ... on various distribution functions describing nucleonic helicity structure and calculate a complete set of splitting functions relevant for their quantum chromodynamics (QCD) evolutions using light-front Hamiltonian perturbation theory in light front gauge + = 0. Twist-two structures of the helicity distributions are self-evident ...

  15. Structure and Dynamics of Thin Ionomer Films: a Key to A Stable Fuel Cell Membrane.

    Science.gov (United States)

    Perahia, Dvora

    2000-03-01

    The technology for solid polymeric electrolytic membranes for a fuel cells, calls for the thinnest film which is electrochemically stable. At present, none supported polymeric solid state fuel cell membranes, thinner than 50 microns, fail mechanically during fuel cell operation. When approaching the thin film limits, interfacial effects become significant to structure dynamics and consequently, the stability of the membranes. Our work focuses on understanding the interfacial effects on thin per-fluorinated ionomer films, including interfacial effects on the thin films themselves and nanotubes-thin film complexes, mimicking the catalyst-ionomer complexes. In particular we investigated the dynamics and structure in 500 angstrom and less, films made by several perfluorinated ionomers, cast on a solid support. Both the films and their parent solutions were investigated with the goal of resolving the factors that affect the stability in the ultra thin regime. AFM/STM and X-ray and neutron reflectivity were used to investigate the thin films and small angle neutron scattering was utilized to the study of the solutions. Films were both spin-coated and self assembles from solutions on a model oxidized single crystal silicon wafer, treated with HF. When coated from molecular solutions, the films tend to dewet on a time scale of minutes to hours. With increasing concentrations, above the critical micellar concentration of the ionomers in water/alcohol, stable films on the order of 200-500 angstroms were formed. While self-assembled films were found to be stable at temperatures close to Tg of the ionomer, spin-coated ones partially dewet. The surface structure obtained, exhibit periodicity on different length scales, depending on the concentration of the polymer in the solution from which the film was assembled. In the ultra dilute regime, micelles were detected at the solid interface. Films formed from dilute solutions exhibit fractal nature with a fractal dimension varying

  16. Metallofoldamers supramolecular architectures from helicates to biomimetics

    CERN Document Server

    Maayan, Galia

    2013-01-01

    Metallofoldamers are oligomers that fold into three-dimensional structures in a controlled manner upon coordination with metal ions. Molecules in this class have shown an impressive ability to form single-handed helical structures and other three-dimensional architectures. Several metallofoldamers have been applied as sensors due to their selective folding when binding to a specific metal ion, while others show promise for applications as responsive materials on the basis of their ability to fold and unfold upon changes in the oxidation state of the coordinated metal ion, and as novel catalysts. Metallofoldamers: From Helicates to Biomimetic Architectures describes the variety of interactions between oligomers and metal species, with a focus on non-natural synthetic molecules. Topics covered include: the major classes of foldamers and their folding driving force metalloproteins and metalloenzymes helicates: self-assembly, structure and applications abiotic metallo-DNA metallo-PNA and iDNA metallopeptides inte...

  17. Stable Encoding of Task Structure Coexists With Flexible Coding of Task Events in Sensorimotor Striatum

    Science.gov (United States)

    Kubota, Yasuo; Liu, Jun; Hu, Dan; DeCoteau, William E.; Eden, Uri T.; Smith, Anne C.

    2009-01-01

    The sensorimotor striatum, as part of the brain's habit circuitry, has been suggested to store fixed action values as a result of stimulus-response learning and has been contrasted with a more flexible system that conditionally assigns values to behaviors. The stability of neural activity in the sensorimotor striatum is thought to underlie not only normal habits but also addiction and clinical syndromes characterized by behavioral fixity. By recording in the sensorimotor striatum of mice, we asked whether neuronal activity acquired during procedural learning would be stable even if the sensory stimuli triggering the habitual behavior were altered. Contrary to expectation, both fixed and flexible activity patterns appeared. One, representing the global structure of the acquired behavior, was stable across changes in task cuing. The second, a fine-grain representation of task events, adjusted rapidly. Such dual forms of representation may be critical to allow motor and cognitive flexibility despite habitual performance. PMID:19625536

  18. Crystal structures of the FAK kinase in complex with TAE226 and related bis-anilino pyrimidine inhibitors reveal a helical DFG conformation.

    Directory of Open Access Journals (Sweden)

    Daniel Lietha

    Full Text Available Focal Adhesion Kinase (FAK is a non-receptor tyrosine kinase required for cell migration, proliferation and survival. FAK overexpression has been documented in diverse human cancers and is associated with a poor clinical outcome. Recently, a novel bis-anilino pyrimidine inhibitor, TAE226, was reported to efficiently inhibit FAK signaling, arrest tumor growth and invasion and prolong the life of mice with glioma or ovarian tumor implants. Here we describe the crystal structures of the FAK kinase bound to TAE226 and three related bis-anilino pyrimidine compounds. TAE226 induces a conformation of the N-terminal portion of the kinase activation loop that is only observed in FAK, but is distinct from the conformation in both the active and inactive states of the kinase. This conformation appears to require a glycine immediately N-terminal to the "DFG motif", which adopts a helical conformation stabilized by interactions with TAE226. The presence of a glycine residue in this position contributes to the specificity of TAE226 and related compounds for FAK. Our work highlights the fact that kinases can access conformational space that is not necessarily utilized for their native catalytic regulation, and that such conformations can explain and be exploited for inhibitor specificity.

  19. A dynamic C-terminal segment in the Mycobacterium tuberculosis Mn/Fe R2lox protein can adopt a helical structure with possible functional consequences.

    Science.gov (United States)

    Andersson, Charlotta S; Berthold, Catrine L; Högbom, Martin

    2012-09-01

    Mycobacterium tuberculosis R2-like ligand-binding oxidase (MtR2lox) belongs to a recently discovered group of proteins that are homologous to the ribonucleotide reductase R2 proteins. MtR2lox carries a heterodinuclear Mn/Fe cofactor and, unlike R2 proteins, a large ligand-binding cavity. A unique tyrosine-valine cross link is also found in the vicinity of the active site. To date, all known structures of R2 and R2lox proteins show a disordered C-terminal segment. Here, we present two new crystal forms of MtR2lox, revealing an ordered helical C-terminal. The ability of alternating between an ordered and disordered state agrees well with bioinformatic analysis of the protein sequence. Interestingly, ordering of the C-terminal helix shields a large positively charged patch on the protein surface, potentially used for interaction with other cellular components. We hypothesize that the dynamic C-terminal segment may be involved in control of protein function in vivo. Copyright © 2012 Verlag Helvetica Chimica Acta AG, Zürich.

  20. Coaxial triple-layered versus helical Be{sub 6}B{sub 11}{sup -} clusters. Dual structural fluxionality and multifold aromaticity

    Energy Technology Data Exchange (ETDEWEB)

    Guo, Jin-Chang [Institute of Materials Science and Department of Chemistry, Xinzhou Teachers University, Shanxi (China); Nanocluster Laboratory, Institute of Molecular Science, Shanxi University, Taiyuan (China); Feng, Lin-Yan; Wang, Ying-Jin; Zhai, Hua-Jin [Nanocluster Laboratory, Institute of Molecular Science, Shanxi University, Taiyuan (China); Jalife, Said; Vasquez-Espinal, Alejandro; Cabellos, Jose Luis; Pan, Sudip; Merino, Gabriel [Departamento de Fisica Aplicada, Centro de Investigacion y de Estudios Avanzados, Unidad Merida, km 6 Antigua carretera a Progreso, Merida, Yuc. (Mexico)

    2017-08-14

    Two low-lying structures are unveiled for the Be{sub 6}B{sub 11}{sup -} nanocluster system that are virtually isoenergetic. The first, triple-layered cluster has a peripheral B{sub 11} ring as central layer, being sandwiched by two Be{sub 3} rings in a coaxial fashion, albeit with no discernible interlayer Be-Be bonding. The B{sub 11} ring revolves like a flexible chain even at room temperature, gliding freely around the Be{sub 6} prism. At elevated temperatures (1000 K), the Be{sub 6} core itself also rotates; that is, two Be{sub 3} rings undergo relative rotation or twisting with respect to each other. Bonding analyses suggest four-fold (π and σ) aromaticity, offering a dilute and fluxional electron cloud that lubricates the dynamics. The second, helix-type cluster contains a B{sub 11} helical skeleton encompassing a distorted Be{sub 6} prism. It is chiral and is the first nanosystem with a boron helix. Molecular dynamics also shows that at high temperature the helix cluster readily converts into the triple-layered one. (copyright 2017 Wiley-VCH Verlag GmbH and Co. KGaA, Weinheim)

  1. TGP, an extremely stable, non-aggregating fluorescent protein created by structure-guided surface engineering

    Science.gov (United States)

    Close, Devin W.; Don Paul, Craig; Langan, Patricia S.; Wilce, Matthew C.J.; Traore, Daouda A.K.; Halfmann, Randal; Rocha, Reginaldo C.; Waldo, Geoffery S.; Payne, Riley J.; Rucker, Joseph B.; Prescott, Mark; Bradbury, Andrew R.M.

    2014-01-01

    In this paper we describe the engineering and X-ray crystal structure of Thermal Green Protein (TGP), an extremely stable, highly soluble, non-aggregating green fluorescent protein. TGP is a soluble variant of the fluorescent protein eCGP123, which despite being highly stable, has proven to be aggregation-prone. The X-ray crystal structure of eCGP123, also determined within the context of this paper, was used to carry out rational surface engineering to improve its solubility, leading to TGP. The approach involved simultaneously eliminating crystal lattice contacts while increasing the overall negative charge of the protein. Despite intentional disruption of lattice contacts and introduction of high entropy glutamate side chains, TGP crystallized readily in a number of different conditions and the X-ray crystal structure of TGP was determined to 1.9 Å resolution. The structural reasons for the enhanced stability of TGP and eCGP123 are discussed. We demonstrate the utility of using TGP as a fusion partner in various assays and significantly, in amyloid assays in which the standard fluorescent protein, EGFP, is undesirable because of aberrant oligomerization. PMID:25287913

  2. Thermal green protein, an extremely stable, nonaggregating fluorescent protein created by structure-guided surface engineering.

    Science.gov (United States)

    Close, Devin W; Paul, Craig Don; Langan, Patricia S; Wilce, Matthew C J; Traore, Daouda A K; Halfmann, Randal; Rocha, Reginaldo C; Waldo, Geoffery S; Payne, Riley J; Rucker, Joseph B; Prescott, Mark; Bradbury, Andrew R M

    2015-07-01

    In this article, we describe the engineering and X-ray crystal structure of Thermal Green Protein (TGP), an extremely stable, highly soluble, non-aggregating green fluorescent protein. TGP is a soluble variant of the fluorescent protein eCGP123, which despite being highly stable, has proven to be aggregation-prone. The X-ray crystal structure of eCGP123, also determined within the context of this paper, was used to carry out rational surface engineering to improve its solubility, leading to TGP. The approach involved simultaneously eliminating crystal lattice contacts while increasing the overall negative charge of the protein. Despite intentional disruption of lattice contacts and introduction of high entropy glutamate side chains, TGP crystallized readily in a number of different conditions and the X-ray crystal structure of TGP was determined to 1.9 Å resolution. The structural reasons for the enhanced stability of TGP and eCGP123 are discussed. We demonstrate the utility of using TGP as a fusion partner in various assays and significantly, in amyloid assays in which the standard fluorescent protein, EGFP, is undesirable because of aberrant oligomerization. © 2014 Wiley Periodicals, Inc.

  3. The search for the most stable structures of silicon-carbon monolayer compounds.

    Science.gov (United States)

    Li, Pengfei; Zhou, Rulong; Zeng, Xiao Cheng

    2014-10-21

    The most stable structures of two-dimensional (2D) silicon-carbon monolayer compounds with different stoichiometric compositions (i.e., Si : C ratio = 2 : 3, 1 : 3 and 1 : 4) are predicted for the first time based on the particle-swarm optimization (PSO) technique combined with density functional theory optimization. Although the 2D Si-C monolayer compounds considered here are rich in carbon, many of the low-energy metastable and the lowest-energy silicon-carbon structures are not graphene (carbon monolayer) like. Phonon-spectrum calculations and ab initio molecular dynamics simulations were also performed to confirm the dynamical stability of the predicted most stable 2D silicon-carbon structures as well their thermal stability at elevated temperature. The computed electronic band structures show that all three predicted silicon-carbon compounds are semiconductors with direct or indirect bandgaps. Importantly, their bandgaps are predicted to be close to those of bulk silicon or bulk germanium. If confirmed in the laboratory, these 2D silicon-carbon compounds with different stoichiometric compositions may be exploited for future applications in nanoelectronic devices.

  4. Structural insights into methanol-stable variants of lipase T6 from Geobacillus stearothermophilus.

    Science.gov (United States)

    Dror, Adi; Kanteev, Margarita; Kagan, Irit; Gihaz, Shalev; Shahar, Anat; Fishman, Ayelet

    2015-11-01

    Enzymatic production of biodiesel by transesterification of triglycerides and alcohol, catalyzed by lipases, offers an environmentally friendly and efficient alternative to the chemically catalyzed process while using low-grade feedstocks. Methanol is utilized frequently as the alcohol in the reaction due to its reactivity and low cost. However, one of the major drawbacks of the enzymatic system is the presence of high methanol concentrations which leads to methanol-induced unfolding and inactivation of the biocatalyst. Therefore, a methanol-stable lipase is of great interest for the biodiesel industry. In this study, protein engineering was applied to substitute charged surface residues with hydrophobic ones to enhance the stability in methanol of a lipase from Geobacillus stearothermophilus T6. We identified a methanol-stable variant, R374W, and combined it with a variant found previously, H86Y/A269T. The triple mutant, H86Y/A269T/R374W, had a half-life value at 70 % methanol of 324 min which reflects an 87-fold enhanced stability compared to the wild type together with elevated thermostability in buffer and in 50 % methanol. This variant also exhibited an improved biodiesel yield from waste chicken oil compared to commercial Lipolase 100L® and Novozyme® CALB. Crystal structures of the wild type and the methanol-stable variants provided insights regarding structure-stability correlations. The most prominent features were the extensive formation of new hydrogen bonds between surface residues directly or mediated by structural water molecules and the stabilization of Zn and Ca binding sites. Mutation sites were also characterized by lower B-factor values calculated from the X-ray structures indicating improved rigidity.

  5. Analysis of the structural and functional roles of coupling helices in the ATP-binding cassette transporter MsbA through enzyme assays and molecular dynamics simulations.

    Science.gov (United States)

    Furuta, Tadaomi; Yamaguchi, Tomohiro; Kato, Hiroaki; Sakurai, Minoru

    2014-07-08

    ATP-binding cassette (ABC) transporters are constructed from some common structural units: the highly conserved nucleotide-binding domains (NBDs), which work as a nucleotide-dependent engine for driving substrate transport, the diverse transmembrane domains (TMDs), which create the translocation pathway, and the coupling helices (CHs), which are located at the NBD-TMD interface. Although the CHs are believed to be essential for NBD-TMD communication, their roles remain unclear. In this study, we performed enzyme assays and molecular dynamics (MD) simulations of the ABC transporter MsbA and two MsbA mutants in which the amino acid residues of one of the CHs were mutated to alanines: (i) wild type (Wt), (ii) CH1 mutant (Mt1), and (iii) CH2 mutant (Mt2). The experiments show that the CH2 mutation decreases the ATPase activity (kcat) compared with that of the Wt (a decrease of 32%), and a nearly equal degree of decrease in the ATP binding affinity (Km) was observed for both Mt1 and Mt2. The MD simulations successfully accounted for several structural and dynamical origins for these experimental observations. In addition, on the basis of collective motion and morphing analyses, we propose that the reverse-rotational motions and noddinglike motions between the NBDs and TMDs are indispensable for the conformational transition between the inward- and outward-facing conformations. In particular, CH2 is significantly important for the occurrence of the noddinglike motion. These findings provide important insights into the structure-function relationship of ABC transporters.

  6. Electron image reconstruction of helical protein assemblies

    International Nuclear Information System (INIS)

    Cremers, A.F.M.

    1980-01-01

    The analysis of projections of large ordered biological systems obtained by electron microscopy of negatively stained specimens is described. The biological structures amenable to this approach are constructed from a large number of identical protein molecules, which are arranged according to helical symmetry. Electron images of these structures generally contain sufficient information in order to calculate a three-dimensional density map. (Auth.)

  7. Helical plasma thruster

    Energy Technology Data Exchange (ETDEWEB)

    Beklemishev, A. D., E-mail: bekl@bk.ru [Budker Institute of Nuclear Physics SB RAS, Novosibirsk (Russian Federation)

    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.

  8. Observing Changes in the Structure and Oligomerization State of a Helical Protein Dimer Using Solid-State Nanopores.

    Science.gov (United States)

    Niedzwiecki, David J; Lanci, Christopher J; Shemer, Gabriel; Cheng, Phillip S; Saven, Jeffery G; Drndić, Marija

    2015-09-22

    Protein analysis using solid-state nanopores is challenging due to limitations in bandwidth and signal-to-noise ratio. Recent improvements of those two aspects have made feasible the study of small peptides using solid-state nanopores, which have an advantage over biological counterparts in tunability of the pore diameter. Here, we report on the detection and characterization of peptides as small as 33 amino acids. Silicon nitride nanopores with thicknesses less than 10 nm are used to provide signal-to-noise (S/N) levels up to S/N ∼ 10 at 100 kHz. We demonstrate differentiation of monomer and dimer forms of the GCN4-p1 leucine zipper, a coiled-coil structure well studied in molecular biology, and compare with the unstructured 33-residue monomer. GCN4-p1 is sequence segment associated with homodimerization of the transcription factor General Control Nonderepressible 4 (GCN4), which is involved in the control of amino acid synthesis in yeast. The differentiation between two oligomeric forms demonstrates the capabilities of improved solid-state nanopore platforms to extract structural information involving short peptide structures.

  9. Structurally stable gel bead containing entrapped enzyme and method for manufacture thereof

    Science.gov (United States)

    Woodward, J.

    1998-12-08

    This research provides a structurally stable gel bead containing an entrapped enzyme and a method for its manufacture. The enzyme is covalently cross-linked to gelatin in the presence of glutaraldehyde prior to the formation of the gel bead, to prevent leakage of the enzyme. Propylene glycol alginate is then added to the mixture. Once the gel beads are formed, they are then soaked in glutaraldehyde, which imparts structural stability to the gel beads. This method can be used with many types of enzymes, such as proteases, carbohydrases, proteases, ligases, isomerases, oxidoreductases, and specialty enzymes. These and other enzymes can be immobilized in the gel beads and utilized in a number of enzymatic processes. Exogenously added ions are not required to maintain the structural stability of these gel beads. 7 figs.

  10. Phases in holographic helical superconductor

    Science.gov (United States)

    Mukhopadhyay, Subir; Paul, Chandrima

    2017-05-01

    We study SU(2)×U(1) gauge theory with Chern-Simons term, coupled to scalar field in adjoint, in a probe approximation by ignoring back reaction on metric. Considering a simple ansatz for non-Abelian gauge field with helical structure, we find it admits s-wave and p-wave phases along with their coexistence. We study free energies for different phases along with those for p-wave phases for different values of pitch and frequency dependence of optical conductivities below critical temperature.

  11. Helical-D pinch

    International Nuclear Information System (INIS)

    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-Dclose 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 dynamoclose 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

  12. Helical thermoelectrics and refrigeration.

    Science.gov (United States)

    Mani, Arjun; Benjamin, Colin

    2018-02-01

    The thermoelectric properties of a three-terminal quantum spin Hall (QSH) sample are examined. The inherent helicity of the QSH sample helps to generate a large charge power efficiently. Along with charge the system can be designed to work as a highly efficient spin heat engine too. The advantage of a helical over a chiral sample is that, while a multiterminal quantum Hall sample can only work as a quantum heat engine due to broken time reversal (TR) symmetry, a multiterminal QSH system can work effectively as both a charge or spin heat engine and as a charge or spin refrigerator as the TR symmetry is preserved.

  13. Helical thermoelectrics and refrigeration

    Science.gov (United States)

    Mani, Arjun; Benjamin, Colin

    2018-02-01

    The thermoelectric properties of a three-terminal quantum spin Hall (QSH) sample are examined. The inherent helicity of the QSH sample helps to generate a large charge power efficiently. Along with charge the system can be designed to work as a highly efficient spin heat engine too. The advantage of a helical over a chiral sample is that, while a multiterminal quantum Hall sample can only work as a quantum heat engine due to broken time reversal (TR) symmetry, a multiterminal QSH system can work effectively as both a charge or spin heat engine and as a charge or spin refrigerator as the TR symmetry is preserved.

  14. Rich stoichiometries of stable Ca-Bi system: Structure prediction and superconductivity

    Science.gov (United States)

    Dong, Xu; Fan, Changzeng

    2015-03-01

    Using a variable-composition ab initio evolutionary algorithm implemented in the USPEX code, we have performed a systematic search for stable compounds in the Ca-Bi system at different pressures. In addition to the well-known tI12-Ca2Bi and oS12-CaBi2, a few more structures were found by our calculations, among which phase transitions were also predicted in Ca2Bi (tI12 --> oI12 --> hP6), Ca3Bi2 (hP5 --> mC20 --> aP5) and CaBi (tI2 --> tI8), as well as a new phase (Ca3Bi) with a cF4 structure. All the newly predicted structures can be both dynamically and thermodynamically stable with increasing pressure. The superconductive properties of cF4-CaBi3, tI2-CaBi and cF4-Ca3Bi were studied and the superconducting critical temperature Tc can be as high as 5.16, 2.27 and 5.25 K, respectively. Different superconductivity behaviors with pressure increasing have been observed by further investigations.

  15. Entropy stable high order discontinuous Galerkin methods for ideal compressible MHD on structured meshes

    Science.gov (United States)

    Liu, Yong; Shu, Chi-Wang; Zhang, Mengping

    2018-02-01

    We present a discontinuous Galerkin (DG) scheme with suitable quadrature rules [15] for ideal compressible magnetohydrodynamic (MHD) equations on structural meshes. The semi-discrete scheme is analyzed to be entropy stable by using the symmetrizable version of the equations as introduced by Godunov [32], the entropy stable DG framework with suitable quadrature rules [15], the entropy conservative flux in [14] inside each cell and the entropy dissipative approximate Godunov type numerical flux at cell interfaces to make the scheme entropy stable. The main difficulty in the generalization of the results in [15] is the appearance of the non-conservative "source terms" added in the modified MHD model introduced by Godunov [32], which do not exist in the general hyperbolic system studied in [15]. Special care must be taken to discretize these "source terms" adequately so that the resulting DG scheme satisfies entropy stability. Total variation diminishing / bounded (TVD/TVB) limiters and bound-preserving limiters are applied to control spurious oscillations. We demonstrate the accuracy and robustness of this new scheme on standard MHD examples.

  16. Use of systematics in the interpretation of nuclear structure far from the beta-stable region

    International Nuclear Information System (INIS)

    Wood, J.L.

    1979-01-01

    The use of systematics in the interpretation of nuclear structure far from the beta-stable region is discussed. In particular, a set of rules for the use of systematics is presented together with some experimental criteria that need to be fulfilled for radioactive decay scheme studies in order that all states up to a given spin-parity and energy are located. Illustrative examples are taken from the region 180 < A < 210, with particular emphasis on the odd-mass Au and Hg nuclei. 6 figures

  17. Stable isotopes provide insight into population structure and segregation in eastern North Atlantic sperm whales

    DEFF Research Database (Denmark)

    Borrell, Asunción; Velásquez Vacca, Adriana; Pinela, Ana M.

    2013-01-01

    highly mobile, shows indication of structuring in the eastern North Atlantic, an ocean basin in which a single population is believed to occur. To do so, we examined stable isotope values in sequential growth layer groups of teeth from individuals sampled in Denmark and NW Spain. In each layer we...... measured oxygen-isotope ratios (delta O-18) in the inorganic component (hydroxyapatite), and nitrogen and carbon isotope ratios (delta N-15: delta C-13) in the organic component (primarily collagenous). We found significant differences between Denmark and NW Spain in delta N-15 and delta O-18 values...

  18. Structural flexibility of the G alpha s alpha-helical domain in the beta2-adrenoceptor Gs complex

    DEFF Research Database (Denmark)

    Westfield, Gerwin H; Rasmussen, Søren Gøgsig Faarup; Su, Min

    2011-01-01

    The active-state complex between an agonist-bound receptor and a guanine nucleotide-free G protein represents the fundamental signaling assembly for the majority of hormone and neurotransmitter signaling. We applied single-particle electron microscopy (EM) analysis to examine the architecture...... of agonist-occupied β(2)-adrenoceptor (β(2)AR) in complex with the heterotrimeric G protein Gs (Gαsβγ). EM 2D averages and 3D reconstructions of the detergent-solubilized complex reveal an overall architecture that is in very good agreement with the crystal structure of the active-state ternary complex...

  19. Structure-Guided Redesign Increases the Propensity of HIV Env To Generate Highly Stable Soluble Trimers.

    Science.gov (United States)

    Guenaga, Javier; Dubrovskaya, Viktoriya; de Val, Natalia; Sharma, Shailendra K; Carrette, Barbara; Ward, Andrew B; Wyatt, Richard T

    2015-12-30

    Due to high viral diversity, an effective HIV-1 vaccine will likely require Envs derived from multiple subtypes to generate broadly neutralizing antibodies (bNAbs). Soluble Env mimics, like the native flexibly linked (NFL) and SOSIP trimers, derived from the subtype A BG505 Env, form homogeneous, stable native-like trimers. However, other Env sequences, such as JRFL and 16055 from subtypes B and C, do so to a lesser degree. The high-resolution BG505 SOSIP crystal structures permit the identification and redesign of Env elements involved in trimer stability. Here, we identified structure trimer-derived (TD) residues that increased the propensity of the subtype B JRFL and subtype C 16055 Env sequences to form well-ordered, homogenous, and highly stable soluble trimers. The generation of these spike mimics no longer required antibody-based selection, positive or negative. Using the redesigned subtype B and C trimer representatives as respective foundations, we further stabilized the NFL TD trimers by engineering an intraprotomer disulfide linkage in the prebridging sheet, I201C-A433C (CC), that locks the gp120 in the receptor nontriggered state. We demonstrated that this disulfide pair prevented CD4 induced-conformational rearrangements in NFL trimers derived from the prototypic subtype A, B, and C representatives. Coupling the TD-based design with the engineered disulfide linkage, CC, increased the propensity of Env to form soluble highly stable spike mimics that are resistant to CD4-induced changes. These advances will allow testing of the hypothesis that such stabilized immunogens will more efficiently elicit neutralizing antibodies in small-animal models and primates. HIV-1 displays unprecedented global diversity circulating in the human population. Since the envelope glycoprotein (Env) is the target of neutralizing antibodies, Env-based vaccine candidates that address such diversity are needed. Soluble well-ordered Env mimics, typified by NFL and SOSIP trimers

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

    OpenAIRE

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

    2017-01-01

    α-Helical transmembrane proteins are a ubiquitous and important class of proteins, but present difficulties for crystallographic structure solution. Here, the effectiveness of the AMPLE molecular replacement pipeline in solving α-helical transmembrane-protein structures is assessed using a small library of eight ideal helices, as well as search models derived from ab initio models generated both with and without evolutionary contact information. The ideal helices prove to be surprisingly effe...

  1. Solution NMR structure of CD1104B from pathogenic Clostridium difficile reveals a distinct α-helical architecture and provides first structural representative of protein domain family PF14203.

    Science.gov (United States)

    Pulavarti, Surya V S R K; Eletsky, Alexander; Lee, Hsiau-Wei; Acton, Thomas B; Xiao, Rong; Everett, John K; Prestegard, James H; Montelione, Gaetano T; Szyperski, Thomas

    2013-12-01

    A high-quality structure of the 68-residue protein CD1104B from Clostridium difficile strain 630 exhibits a distinct all α-helical fold. The structure presented here is the first representative of bacterial protein domain family PF14203 (currently 180 members) of unknown function (DUF4319) and reveals that the side-chains of the only two strictly conserved residues (Glu 8 and Lys 48) form a salt bridge. Moreover, these two residues are located in the vicinity of the largest surface cleft which is predicted to contribute to a surface area involved in protein-protein interactions. This, along with its coding in transposon CTn4, suggests that CD1104B (and very likely all members of Pfam 14203) functions by interacting with other proteins required for the transfer of transposons between different bacterial species.

  2. Two new twisted helical nickel (II) and cobalt (III) octahedral ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Chemical Sciences; Volume 126; Issue 6. Two new twisted helical nickel(II) and cobalt(III) octahedral monomer complexes: Synthesis and structural characterization. Malay Dolai ... Keywords. Coordination chemistry; nickel(II); cobalt(III); Schiff base; twisted helicity; supramolecular interactions.

  3. Review of the helicity formalism

    International Nuclear Information System (INIS)

    Barreiro, F.; Cerrada, M.; Fernandez, E.

    1972-01-01

    Our purpose in these notes has been to present a brief and general review of the helicity formalism. We begin by discussing Lorentz invariance, spin and helicity ideas, in section 1 . In section 2 we deal with the construction of relativistic states and scattering amplitudes in the helicity basis and we study their transformation properties under discrete symmetries. Finally we present some more sophisticated topics like kinematical singularities of helicity amplitudes, kinematical constraints and crossing relations 3, 4, 5 respectively. (Author) 8 refs

  4. Helicity of the Neutrino

    Indian Academy of Sciences (India)

    IAS Admin

    Measurement of the helicity of the neutrino was crucial in identifying the nature of weak interac- tion. The measurement is an example of great ingenuity in choosing, (i) the right nucleus with a specific type of decay, (ii) the technique of res- onant fluorescence scattering for determining di- rection of neutrino and (iii) ...

  5. Toroidal helical fields

    International Nuclear Information System (INIS)

    Kucinski, M.Y.; Caldas, I.L.

    1986-08-01

    Using the conventional toroidal coordinate system Laplace's equation for the magnetic scalar potential due to toroidal helical currents is solved. The potential is written as a sum of an infinite series of functions. Each partial sum represents the potential within some accuracy. The effect of the winding law is analysed in the case of small curvature. (Author) [pt

  6. Helicity of the Neutrino

    Indian Academy of Sciences (India)

    IAS Admin

    attention as soon as we focus our gaze on it. The ex- periment on the determination of helicity of the neutrino falls in a similar category among experiments in the field of modern physics. The experiments on the discovery of parity violation in 1957 [1] had established that the vi- olation parity was maximal in beta decay and ...

  7. A flagellar A-kinase anchoring protein with two amphipathic helices forms a structural scaffold in the radial spoke complex.

    Science.gov (United States)

    Sivadas, Priyanka; Dienes, Jennifer M; St Maurice, Martin; Meek, William D; Yang, Pinfen

    2012-11-12

    A-kinase anchoring proteins (AKAPs) contain an amphipathic helix (AH) that binds the dimerization and docking (D/D) domain, RIIa, in cAMP-dependent protein kinase A (PKA). Many AKAPs were discovered solely based on the AH-RIIa interaction in vitro. An RIIa or a similar Dpy-30 domain is also present in numerous diverged molecules that are implicated in critical processes as diverse as flagellar beating, membrane trafficking, histone methylation, and stem cell differentiation, yet these molecules remain poorly characterized. Here we demonstrate that an AKAP, RSP3, forms a dimeric structural scaffold in the flagellar radial spoke complex, anchoring through two distinct AHs, the RIIa and Dpy-30 domains, in four non-PKA spoke proteins involved in the assembly and modulation of the complex. Interestingly, one AH can bind both RIIa and Dpy-30 domains in vitro. Thus, AHs and D/D domains constitute a versatile yet potentially promiscuous system for localizing various effector mechanisms. These results greatly expand the current concept about anchoring mechanisms and AKAPs.

  8. Trophic structure in a seabird host-parasite food web: insights from stable isotope analyses.

    Directory of Open Access Journals (Sweden)

    Elena Gómez-Díaz

    2010-05-01

    Full Text Available Ecological studies on food webs rarely include parasites, partly due to the complexity and dimensionality of host-parasite interaction networks. Multiple co-occurring parasites can show different feeding strategies and thus lead to complex and cryptic trophic relationships, which are often difficult to disentangle by traditional methods. We analyzed stable isotope ratios of C ((13C/(12C, delta(13C and N ((15N/(14N, delta(15N of host and ectoparasite tissues to investigate trophic structure in 4 co-occurring ectoparasites: three lice and one flea species, on two closely related and spatially segregated seabird hosts (Calonectris shearwaters. delta(13C isotopic signatures confirmed feathers as the main food resource for the three lice species and blood for the flea species. All ectoparasite species showed a significant enrichment in delta(15N relatively to the host tissue consumed (discrimination factors ranged from 2 to 5 per thousand depending on the species. Isotopic differences were consistent across multiple host-ectoparasite locations, despite of some geographic variability in baseline isotopic levels. Our findings illustrate the influence of both ectoparasite and host trophic ecology in the isotopic structuring of the Calonectris ectoparasite community. This study highlights the potential of stable isotope analyses in disentangling the nature and complexity of trophic relationships in symbiotic systems.

  9. Ultra-Stable Zero-CTE HoneySiC and H2CMN Mirror Support Structures, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — NASA MSFC, GSFC and JPL are interested in Ultra-Stable Mirror Support Structures for Exoplanet Missions. Telescopes with Apertures of 4-meters or larger and using an...

  10. Ultra-Stable Zero-CTE HoneySiC and H2CMN Mirror Support Structures, Phase II

    Data.gov (United States)

    National Aeronautics and Space Administration — NASA MSFC, GSFC and JPL are interested in Ultra-Stable Mirror Support Structures for Exoplanet Missions. Telescopes with Apertures of 4-meters or larger and using an...

  11. Folding thermodynamics of c-Myb DNA-binding domain in correlation with its α-helical contents.

    Science.gov (United States)

    Inaba, Satomi; Fukada, Harumi; Oda, Masayuki

    2016-01-01

    The conformational and thermal stabilities of the minimum functional unit for c-Myb DNA-binding domain, tandem repeat 2 and 3 (R2R3), were analyzed under different pH conditions, ranging from 4.0 to 7.5, using circular dichroism and differential scanning calorimetry. Secondary structure analysis showed that the solution pH largely affects the conformational stability of the protein domain. Of all conditions analyzed, the α-helical content was maximal at pH 6.5, and the thermal stability was highest at pH 5.0. Thermodynamic parameters for thermal unfolding of R2R3 were determined using differential scanning calorimetry, and the origin of folding thermodynamics at the different pHs and its correlation with the α-helical content were further analyzed. It should be noted that the α-helical content correlates well with the enthalpy change in the pH range from 4.5 to 7.5, suggesting that the strength of hydrogen bonds and salt bridges needed for maintenance of helical structure is related to enthalpy in the native state. Under physiological pH conditions, c-Myb R2R3 exists in the enthalpically unstable but entropically stable state. Due to loss of rigid structure and high stability, the protein can now obtain structural flexibility, befitting its function. Copyright © 2015 Elsevier B.V. All rights reserved.

  12. Sarkosyl-Induced Helical Structure of an Antimicrobial Peptide GW-Q6 Plays an Essential Role in the Binding of Surface Receptor OprI in Pseudomonas aeruginosa.

    Directory of Open Access Journals (Sweden)

    Tien-Sheng Tseng

    Full Text Available The emergence of antibiotic-resistant microbial strains has become a public health issue and there is an urgent need to develop new anti-infective molecules. Although natural antimicrobial peptides (AMPs can exert bactericidal activities, they have not shown clinical efficacy. The limitations of native peptides may be overcome with rational design and synthesis. Here, we provide evidence that the bactericidal activity of a synthetic peptide, GW-Q6, against Pseudomonas aeruginosa is mediated through outer membrane protein OprI. Hyperpolarization/depolarization of membrane potential and increase of membrane permeability were observed after GW-Q6 treatment. Helical structure as well as hydrophobicity was induced by an amphipathic surfactant, sarkosyl, for binding to OprI and possible to membrane. NMR studies demonstrated GW-Q6 is an amphipathic α-helical structure in DPC micelles. The paramagnetic relaxation enhancement (PRE approach revealed that GW-Q6 orients its α-helix segment (K7-K17 into DPC micelles. Additionally, this α-helix segment is critical for membrane permeabilization and antimicrobial activity. Moreover, residues K3, K7, and K14 could be critical for helical formation and membrane binding while residues Y19 and W20 for directing the C-terminus of the peptide to the surface of micelle. Taken together, our study provides mechanistic insights into the mode of action of the GW-Q6 peptide and suggests its applicability in modifying and developing potent AMPs as therapeutic agents.

  13. Morphology, molecular structure, and stable carbon isotopic composition of black carbon (BC) in urban topsoils.

    Science.gov (United States)

    Zong, Yutong; Xiao, Qing; Lu, Shenggao

    2018-02-01

    Urban soils contain significant amounts of black carbon (BC) from biomass and fossil fuel combustion and regard to be a pool of BC. BC in urban soils has multiple effects on environmental processes in urban system, such as global climate change, air quality, and public health. Urban topsoil samples (0-10 cm) were collected from Anshan, Liaoning Province, northeast China, which is one of the most important old steel industrial bases in China. The BC in urban topsoils was extracted using the density method. Their chemical composition, morphology, molecular structure, and stable carbon isotopic composition were examined using elemental analysis, scanning electron microscopy with energy-dispersive X-ray spectroscopy (SEM-EDS), Fourier transform infrared spectroscopy (FTIR), thermogravimetric analysis (TGA), X-ray diffraction (XRD), and stable carbon isotope (δ 13 C). Elemental analysis shows that carbon content in the BC of studied soils ranged from 64.5 to 78.4%, with the average more than 70%. The O/C atomic ratio of BC is on average 0.18. The BC particle displays different morphology, including porous spherical, irregular porous fragmentary, and blocky shapes. The porous spherical BC particles has atomic molar O/C ratio determined by SEM-EDS ranging from 0.04 to 0.37. XRD indicates that BC exists in mainly combining with mineral phases hematite (Fe 2 O 3 ), kaolinite (Al 2 Si 2 O 5 (OH) 4 ), quartz (SiO 2 ), and calcite (CaCO 3 ). The FTIR spectra of BC particles show major bands at approximately 3400 cm -1 (O-H), 2920 cm -1 (C = H), 1600 cm -1 (C = C), 1230 cm -1 (C = O), and 1070 cm -1 (C = O). The stable carbon isotope (δ 13 C) of BC ranges from -24.48 to -23.18‰ with the average of -23.79 ± 0.39‰. The concentration of BC in the industrial area is significantly (p fuel combustion. Results indicated that a combination of atomic O/C ratio, porous structure, and stable carbon isotopic (δ 13 C) of BC could reflect effectively the origin of BC

  14. Nondispersive optical activity of meshed helical metamaterials.

    Science.gov (United States)

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

    2014-11-17

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

  15. Stimuli-Directed Helical Chirality Inversion and Bio-Applications

    Directory of Open Access Journals (Sweden)

    Ziyu Lv

    2016-08-01

    Full Text Available Helical structure is a sophisticated ubiquitous motif found in nature, in artificial polymers, and in supramolecular assemblies from microscopic to macroscopic points of view. Significant progress has been made in the synthesis and structural elucidation of helical polymers, nevertheless, a new direction for helical polymeric materials, is how to design smart systems with controllable helical chirality, and further use them to develop chiral functional materials and promote their applications in biology, biochemistry, medicine, and nanotechnology fields. This review summarizes the recent progress in the development of high-performance systems with tunable helical chirality on receiving external stimuli and discusses advances in their applications as drug delivery vesicles, sensors, molecular switches, and liquid crystals. Challenges and opportunities in this emerging area are also presented in the conclusion.

  16. Topological characteristics of helical repeat proteins

    NARCIS (Netherlands)

    Groves, M R; Barford, D

    The recent elucidation of protein structures based upon repeating amino acid motifs, including the armadillo motif, the HEAT motif and tetratricopeptide repeats, reveals that they belong to the class of helical repeat proteins. These proteins share the common property of being assembled from tandem

  17. Effect of surface texture and structure on the development of stable fluvial armors

    Science.gov (United States)

    Bertin, Stephane; Friedrich, Heide

    2018-04-01

    Stable fluvial armors are found in river systems under conditions of partial sediment transport and limited sediment supply, a common occurrence in nature. Stable armoring is also readily recreated in experimental flumes. Initially, this bed stabilizing phenomenon was examined for different flow discharges and solely related to surface coarsening and bedload transport reduction. The models developed suggest a specific armor composition (i.e., texture) dependent on the parent bed material and formative discharge. Following developments in topographic remote sensing, recent research suggests that armor structure is an important control on bed stability and roughness. In this paper, replicated flume runs during which digital elevation models (DEMs) were collected from both exposed and flooded gravel beds are used to interpret armoring manifestations and to assess their replicability. A range of methodologies was used for the analysis, providing information on (i) surface grain size and orientation, (ii) bed-elevation distributions, (iii) the spatial coherence of the elevations at the grain-scale, (iv) surface slope and aspect, (v) grain imbrication and (vi) the spatial variability in DEM properties. The bed-surface topography was found to be more responsive than bed-material size to changes in flow strength. Our experimental results also provide convincing evidence that gravel-beds' response to water-work during parallel degradation is unique (i.e., replicable) given the formative parameters. Based on this finding, relationships between the armors' properties and formative parameters are proposed, and are supported by adding extensive data from previous research.

  18. Determination of Trophic Structure in Selected Freshwater Ecosystems by using Stable Isotope Analysis.

    Science.gov (United States)

    Zainordin, 'Amila Faqhira; Ab Hamid, Suhaila

    2017-07-01

    Stable isotope analysis has been used extensively to establish trophic relationships in many ecosystems. Present study utilised stable isotope signatures of carbon and nitrogen to identify trophic structure of aquatic food web in river and rice field ecosystems in Perak, northern peninsular Malaysia. The mean δ 13 C values of all producers ranged from -35.29 ± 0.21 to -26.00 ± 0.050‰. The greatest δ 15 N values noted was in zenarchopterid fish with 9.68 ± 0.020‰. The δ 15 N values of aquatic insects ranged between 2.59 ± 0.107 in Elmidae (Coleoptera) and 8.11 ± 0.022‰ in Nepidae (Hemiptera). Correspondingly, with all the δ 13 C and δ 15 N values recorded, it can be deduced that there are four trophic levels existed in the freshwater ecosystems which started with the producer (plants), followed by primary consumer (aquatic insects and non-predatory fish), secondary consumer (invertebrate predators) and lastly tertiary consumer (vertebrate predators).

  19. Towards control of the size and helicity of skyrmions in helimagnetic alloys by spin-orbit coupling

    Science.gov (United States)

    Shibata, K.; Yu, X. Z.; Hara, T.; Morikawa, D.; Kanazawa, N.; Kimoto, K.; Ishiwata, S.; Matsui, Y.; Tokura, Y.

    2013-10-01

    Chirality--that is, left- or right-handedness--is an important concept in a broad range of scientific areas. In condensed matter, chirality is found not only in molecular or crystal forms, but also in magnetic structures. A magnetic skyrmion is a topologically stable spin vortex structure, as observed in chiral-lattice helimagnets, and is one example of such a structure. The spin swirling direction (skyrmion helicity) should be closely related to the underlying lattice chirality via the relativistic spin-orbit coupling. Here, we report on the correlation between skyrmion helicity and crystal chirality in alloys of helimagnets Mn1-xFexGe with varying compositions by Lorentz transmission electron microscopy and convergent-beam electron diffraction over a broad range of compositions (x = 0.3-1.0). The skyrmion lattice constant shows non-monotonous variation with composition x, with a divergent behaviour around x = 0.8, where the correlation between magnetic helicity and crystal chirality changes sign. This originates from continuous variation of the spin-orbit coupling strength and its sign reversal in the metallic alloys as a function of x. Controllable spin-orbit coupling may offer a promising way to tune skyrmion size and helicity.

  20. Crystal structure of a one-dimensional helical-type silver(I coordination polymer: catena-poly[[silver(I-μ-N-(pyridin-4-ylmethylpyridine-3-amine-κ2N:N′] nitrate dimethyl sulfoxide disolvate

    Directory of Open Access Journals (Sweden)

    Bokhee Moon

    2014-12-01

    Full Text Available The asymmetric unit of the title compound, {[Ag(C11H11N3]NO3·2(CH32SO}n, comprises one AgI atom, one N-(pyridine-4-ylmethylpyridine-3-amine ligand, one nitrate anion and two dimethyl sulfoxide molecules. The AgI atoms are bridged by two pyridine N atoms from two symmetry-related ligands, forming a helical chain and adopting a slightly distorted linear coordination geometry [N—Ag—N = 175.37 (8°]. The helical chain, with a pitch length of 16.7871 (8 Å, propagates along the b-axis direction. In the crystal, symmetry-related right- and left-handed helical chains are alternately arranged via Ag...Ag interactions [3.4145 (4 Å] and π–π stacking interactions [centroid–centroid distance = 3.650 (2 Å], resulting in the formation of a two-dimensional supramolecular network extending parallel to (100. Weak Ag...O [2.775 (2, 3.169 (4 and 2.690 (2 Å] interactions, as well as several N—H...O and C—H...O hydrogen-bonding interactions, contribute to the stabilization of the crystal structure. Parts of the dimethyl sulfoxide solvent molecule are disordered over two sets of sites in a 0.937 (3:0.063 (3 ratio.

  1. Stable anilinyl radicals coordinated to nickel: X-ray crystal structure and characterization.

    Science.gov (United States)

    Kochem, Amélie; Gellon, Gisèle; Leconte, Nicolas; Baptiste, Benoit; Philouze, Christian; Jarjayes, Olivier; Orio, Maylis; Thomas, Fabrice

    2013-12-02

    Two anilinosalen and a mixed phenol-anilinosalen ligands involving sterically hindered anilines moieties were synthesized. Their nickel(II) complexes 1, 2, and 3 were prepared and characterized. They could be readily one-electron oxidized (E(1/2)=-0.30, -0.26 and 0.10 V vs. Fc(+)/Fc, respectively) into anilinyl radicals species [1](+), [2](+), and [3](+), respectively. The radical complexes are extremely stable and were isolated as single crystals. X-ray crystallographic structures reveal that the changes in bond length resulting from oxidation do not exceed 0.02 Å within the ligand framework in the symmetrical [1](+) and [2](+). No quinoid bond pattern was present. In contrast, larger structural rearrangements were evidenced for the unsymmetrical [3](+), with shortening of one C(ortho)-C(meta) bond. Radical species [1](+) and [2](+) exhibit a strong absorption band at around 6000 cm(-1) (class III mixed valence compounds). This band is significantly less intense than [3](+), consistent with a rather localized anilinyl radical character, and thus a classification of this species as class II mixed-valence compound. Magnetic and electronic properties, as well as structural parameters, have been computed by DFT methods. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Helical vortices: linear stability analysis and nonlinear dynamics

    Science.gov (United States)

    Selçuk, C.; Delbende, I.; Rossi, M.

    2018-02-01

    We numerically investigate, within the context of helical symmetry, the dynamics of a regular array of two or three helical vortices with or without a straight central hub vortex. The Navier–Stokes equations are linearised to study the instabilities of such basic states. For vortices with low pitches, an unstable mode is extracted which corresponds to a displacement mode and growth rates are found to compare well with results valid for an infinite row of point vortices or an infinite alley of vortex rings. For larger pitches, the system is stable with respect to helically symmetric perturbations. In the nonlinear regime, we follow the time-evolution of the above basic states when initially perturbed by the dominant instability mode. For two vortices, sequences of overtaking events, leapfrogging and eventually merging are observed. The transition between such behaviours occurs at a critical ratio involving the core size and the vortex-separation distance. Cases with three helical vortices are also presented.

  3. Probing the role of nascent helicity in p27 function as a cell cycle regulator.

    Directory of Open Access Journals (Sweden)

    Steve Otieno

    Full Text Available p27 regulates the activity of Cdk complexes which are the principal governors of phase transitions during cell division. Members of the p27 family of proteins, which also includes p21 and p57, are called the Cip/Kip cyclin-dependent kinase regulators (CKRs. Interestingly, the Cip/Kip CKRs play critical roles in cell cycle regulation by being intrinsically unstructured, a characteristic contrary to the classical structure-function paradigm. They exhibit nascent helicity which has been localized to a segment referred to as sub-domain LH. The nascent helicity of this sub-domain is conserved and we hypothesize that it is an important determinant of their functional properties. To test this hypothesis, we successfully designed and prepared p27 variants in which domain LH was either more or less helical with respect to the wild-type protein. Thermal denaturation experiments showed that the ternary complexes of the p27 variants bound to Cdk2/Cyclin A were less stable compared to the wild-type complex. Isothermal titration calorimetry experiments showed a decrease in the enthalpy of binding for all the mutants with respect to p27. The free energies of binding varied within a much narrower range. In vitro Cdk2 inhibition assays showed that the p27 variants exhibited disparate inhibitory potencies. Furthermore, when over-expressed in NIH 3T3 mouse fibroblast cells, the less helical p27 variants were less effective in causing cell cycle arrest relative to the wild-type p27. Our results indicate that the nascent helicity of sub-domain LH plays a key role mediating the biological function of p27.

  4. Aedes aegypti has spatially structured and seasonally stable populations in Yogyakarta, Indonesia.

    Science.gov (United States)

    Rašić, Gordana; Endersby-Harshman, Nancy; Tantowijoyo, Warsito; Goundar, Anjali; White, Vanessa; Yang, Qiong; Filipović, Igor; Johnson, Petrina; Hoffmann, Ary A; Arguni, Eggi

    2015-12-01

    Dengue fever, the most prevalent global arboviral disease, represents an important public health problem in Indonesia. Control of dengue relies on the control of its main vector, the mosquito Aedes aegypti, yet nothing is known about the population history and genetic structure of this insect in Indonesia. Our aim was to assess the spatio-temporal population genetic structure of Ae. aegypti in Yogyakarta, a densely populated region on Java with common dengue outbreaks. We used multiple marker systems (microsatellites, nuclear and mitochondrial genome-wide single nucleotide polymorphisms generated via Restriction-site Associated DNA sequencing) to analyze 979 Ae. aegypti individuals collected from the Yogyakarta city and the surrounding hamlets during the wet season in 2011 and the following dry season in 2012. We employed individual- and group-based approaches for inferring genetic structure. We found that Ae. aegypti in Yogyakarta has spatially structured and seasonally stable populations. The spatial structuring was significant for the nuclear and mitochondrial markers, while the temporal structuring was non-significant. Nuclear markers identified three main genetic clusters, showing that hamlets have greater genetic isolation from each other and from the inner city sites. However, one hamlet experienced unrestricted mosquito interbreeding with the inner city, forming a single genetic cluster. Genetic distance was poorly correlated with the spatial distance among mosquito samples, suggesting stronger influence of human-assisted gene flow than active mosquito movement on spatial genetic structure. A star-shaped mitochondrial haplotype network and a significant R(2) test statistic (R(2) = 0.0187, P = 0.001) support the hypothesis that Ae. aegypti in Yogyakarta originated from a small or homogeneous source and has undergone a relatively recent demographic expansion. We report the first insights into the spatio-temporal genetic structure and the underlying

  5. A Fundamental Approach to Developing Aluminium based Bulk Amorphous Alloys based on Stable Liquid Metal Structures and Electronic Equilibrium - 154041

    Science.gov (United States)

    2017-03-28

    AFRL-AFOSR-JP-TR-2017-0027 A Fundamental Approach to Developing Aluminium -based Bulk Amorphous Alloys based on Stable Liquid-Metal Structures and...to 16 Dec 2016 4.  TITLE AND SUBTITLE A Fundamental Approach to Developing Aluminium -based Bulk Amorphous Alloys based on Stable Liquid-Metal...Air Force Research Laboratory for accurately predicting compositions of new amorphous alloys specifically based on aluminium with properties superior

  6. A structural framework for a near-minimal form of life: mass and compositional analysis of the helical mollicute Spiroplasma melliferum BC3.

    Directory of Open Access Journals (Sweden)

    Shlomo Trachtenberg

    Full Text Available Spiroplasma melliferum is a wall-less bacterium with dynamic helical geometry. This organism is geometrically well defined and internally well ordered, and has an exceedingly small genome. Individual cells are chemotactic, polar, and swim actively. Their dynamic helicity can be traced at the molecular level to a highly ordered linear motor (composed essentially of the proteins fib and MreB that is positioned on a defined helical line along the internal face of the cell's membrane. Using an array of complementary, informationally overlapping approaches, we have taken advantage of this uniquely simple, near-minimal life-form and its helical geometry to analyze the copy numbers of Spiroplasma's essential parts, as well as to elucidate how these components are spatially organized to subserve the whole living cell. Scanning transmission electron microscopy (STEM was used to measure the mass-per-length and mass-per-area of whole cells, membrane fractions, intact cytoskeletons and cytoskeletal components. These local data were fit into whole-cell geometric parameters determined by a variety of light microscopy modalities. Hydrodynamic data obtained by analytical ultracentrifugation allowed computation of the hydration state of whole living cells, for which the relative amounts of protein, lipid, carbohydrate, DNA, and RNA were also estimated analytically. Finally, ribosome and RNA content, genome size and gene expression were also estimated (using stereology, spectroscopy and 2D-gel analysis, respectively. Taken together, the results provide a general framework for a minimal inventory and arrangement of the major cellular components needed to support life.

  7. Helical CT for lumbosacral spinal

    Energy Technology Data Exchange (ETDEWEB)

    Tatsuno, Satoshi; Fukuda, Kunihiko [Jikei Univ., Tokyo (Japan). School of Medicine

    1996-10-01

    The aim of this study was to investigate the efficacy of helical CT for lumbosacral pathology. We performed helical CT with multiplanar reconstruction, including the formation of oblique transaxial and coronal images, in 62 patients with various lumboscral disorders, including 32 non-enhanced CT and 36 CT after myelography. We correlated the appearance of the stenotic spinal canal and neoplastic disease with the findings on MRI obtained at nearly the same time. We obtained helical CT images in all cases in about 30 seconds. The diagnostic ability of helical CT was roughly equal to that of MRI in patients with spondylosis deformans, spondylolisthesis and herniated nucleus pulposus. There was no significant difference in diagnostic value for degenerative lumbosacral disease with canal and foraminal stenosis between non-enhanced and post-myelography helical CT. However, non-enhanced helical CT could not clearly demonstrate neoplastic disease because of the poor contrast resolution. Helical CT was useful in evaluating degenerative disorder and its diagnostic value was nearly equal to that of MRI. We considered that helical CT may be suitable for the assessment of patients with severe lumbago owing to the markedly shortened examination time. However, if helical CT is used as a screening method for lumbosacral disease, one must be careful of its limitations, for example, poor detectability of neoplastic disease, vascular anomalies and so on. (author)

  8. Extension of operation regimes and investigation of three-dimensional current-less plasmas in the Large Helical Device

    International Nuclear Information System (INIS)

    Kaneko, O.

    2012-11-01

    The Large Helical Device (LHD) has shown the advantages of heliotron plasma for fusion reactor from operational point of view not only such as disruption free and steady state operation, but also as high density and stable high beta operation. Since the last Fusion Energy Conference in Daejon in 2010 (Yamada, 2011 Nucl. Fusion 51 094021), physical understanding as well as parameter improvement of net-current free helical plasmas has progressed successively. The current efforts are focused on optimization of plasma edge condition to extend the operation regime towards higher ion temperature and more stable high density. In LHD a part of open helical divertors are being modified to the baffle-structured closed ones to aim at active control of the edge plasma. It has been demonstrated that the neutral pressure in the closed helical divertor was more than 10 times higher than that in the open helical divertor. The central ion temperature has exceeded 7 keV. This high-T i plasma was obtained by a carbon pellet injection and the kinetic-energy confinement was improved by a factor of 1.5. Transport analysis of the high-T i plasmas has shown that the ion-thermal conductivity and the viscosity reduced after the pellet injection. Study of physics in 3-D geometry is highlighted in the topics of the response to Resonant Magnetic Perturbation such as ELM mitigation and divertor detachment. Novel approaches of non-local and non-diffusive transport have also been advanced. In this paper, highlighted results in these two years are overviewed. (author)

  9. On statistical equilibrium in helical fluid flows

    Directory of Open Access Journals (Sweden)

    M. V. Kurgansky

    2006-01-01

    Full Text Available 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.

  10. Structure of stable binary neutron star merger remnants: Role of initial spin

    Science.gov (United States)

    Kastaun, W.; Ciolfi, R.; Endrizzi, A.; Giacomazzo, B.

    2017-08-01

    We present general relativistic numerical simulations of binary neutron star (BNS) mergers with different initial spin configurations. We focus on models with stars of mass 1.4 M⊙ each, which employ the equation of state (EOS) by Shen, Horowitz, and Teige, and which result in stable NSs as merger remnants. For comparison, we consider two irrotational equal mass (M =1.35 M⊙) and unequal mass (M =1.29 , 1.42 M⊙ ) BNS models using the APR4 EOS, which result in a supramassive merger remnant. We present visualizations of the fluid flow and temperature distribution and find a strong impact of the spin on vortex structure and nonaxisymmetric deformation. We compute the radial mass distribution and the rotation profile in the equatorial plane using recently developed measures independent of spatial gauge, revealing slowly rotating cores that can be well approximated by the cores of spherical stars. We also study the influence of the spin on the inspiral phase and the gravitational wave (GW) signal. Using a newly developed analysis method, we further show that gravitational waveforms from BNS mergers can exhibit one or more phase jumps after merger, which occur together with minima of the strain amplitude. We provide a natural explanation in terms of the remnant's quadrupole moment, and show that cancellation effects due to phase jumps can have a strong impact on the GW power spectrum. Finally, we discuss the impact of the spin on the amount of ejected matter.

  11. Exploration of stable compounds, crystal structures, and superconductivity in the Be-H system

    Directory of Open Access Journals (Sweden)

    Shuyin Yu

    2014-10-01

    Full Text Available Using first-principles variable-composition evolutionary methodology, we explored the high-pressure structures of beryllium hydrides between 0 and 400 GPa. We found that BeH2 remains the only stable compound in this pressure range. The pressure-induced transformations are predicted as I b a m → P 3 ̄ m 1 → R 3 ̄ m → C m c m → P 4 / n m m , which occur at 24, 139, 204 and 349 GPa, respectively. P 3 ̄ m 1 and R 3 ̄ m structures are layered polytypes based on close packings of H atoms with Be atoms filling all octahedral voids in alternating layers. Cmcm and P4/nmm contain two-dimensional triangular networks with each layer forming a kinked slab in the ab-plane. P 3 ̄ m 1 and R 3 ̄ m are semiconductors while Cmcm and P4/nmm are metallic. We have explored superconductivity of both metal phases, and found large electron-phonon coupling parameters of λ = 0.63 for Cmcm with a Tc of 32.1-44.1 K at 250 GPa and λ = 0.65 for P4/nmm with a Tc of 46.1-62.4 K at 400 GPa. The dependence of Tc on pressure indicates that Tc initially increases to a maximum of 45.1 K for Cmcm at 275 GPa and 97.0 K for P4/nmm at 365 GPa, and then decreases with increasing pressure for both phases.

  12. Structure of stable binary neutron star merger remnants: A case study

    Science.gov (United States)

    Kastaun, W.; Ciolfi, R.; Giacomazzo, B.

    2016-08-01

    In this work, we study the merger of two neutron stars with a gravitational mass of 1.4 M⊙ each, employing the Shen-Horowitz-Teige equation of state. This equation of state is a corner case, allowing the formation of a stable neutron star with the given total baryonic mass of 3.03 M⊙. We investigate in unprecedented detail the structure of the remnant, in particular the mass distribution, the thermal structure, and the rotation profile. We also compute fluid trajectories both inside the remnant and those relevant for the formation of the disk. We find a peanut-shaped fluid flow inside the remnant following a strong m =2 perturbation. Moreover, the flow is locally compressive, causing the appearance of dynamic hot spots. Further, we introduce new diagnostic measures that are easy to implement in numeric simulations and that allow one to quantify mass and compactness of merger remnants in a well-defined way. As in previous studies of supra- and hypermassive stars, we find a remnant with a slowly rotating core and an outer envelope rotating at nearly Keplerian velocity. We compute a Tolman-Oppenheimer-Volkoff star model which agrees well with that of the remnant in the core, while the latter possesses extensive outer layers rotating close to Kepler velocity. Finally, we extract the gravitational wave signal and discuss the detectability with modern observatories. This study has implications for the interpretation of gravitational wave detections from the postmerger phase and is relevant for short gamma-ray burst models.

  13. Helical polymer carrying helical grafts from peptide-based acetylene macromonomers: synthesis.

    Science.gov (United States)

    Sanda, Fumio; Gao, Guangzheng; Masuda, Toshio

    2004-06-25

    N-Propargylamide-terminated peptide-based macromonomers with a degree of polymerization ranging from 4 to 40 were synthesized by the polymerization of gamma-benzyl and gamma-stearyl-L-glutamate-N-carboxy anhydrides initiated with propargylamine. The macromonomers took an alpha-helical structure, which was confirmed by signals at 208 and 220 nm in CD spectra. The macromonomers were subjected to polymerization and copolymerization with an alanine-derived N-propargylamide [N-(tert-butoxycarbonyl)-L-alanine-N'-propargylamide] catalyzed with (2,5-norbornadiene)Rh+[eta6-C6H5B- (C6H5)3]. It was confirmed through a CD spectroscopic study that the copolymer obtained from the copolymerization of the gamma-stearyl-L-glutamate-based macromonomer with the alanine-derived N-propargylamide had a helical polyacetylene main chain and helical polypeptide side chains.

  14. Employing Helicity Amplitudes for Resummation

    NARCIS (Netherlands)

    Moult, I.; Stewart, I.W.; Tackmann, F.J.; Waalewijn, W.J.

    2015-01-01

    Many state-of-the-art QCD calculations for multileg processes use helicity amplitudes as their fundamental ingredients. We construct a simple and easy-to-use helicity operator basis in soft-collinear effective theory (SCET), for which the hard Wilson coefficients from matching QCD onto SCET are

  15. Effects of duct configuration on flow and temperature structure in sodium-cooled 19-rod simulated LMFBR fuel bundles with helical wire-wrap spacers

    International Nuclear Information System (INIS)

    Wantland, J.L.; Fontana, M.H.; Gnadt, P.A.; Hanus, N.; MacPherson, R.E.; Smith, C.M.

    1976-01-01

    Thermal-hydrodynamic testing of sodium-cooled 19-rod simulated LMFBR fuel bundles is being conducted at the O ak Ridge National Laboratory in the Fuel Failure Mockup (FFM), an engineering-scale high-temperature sodium facility which provides prototypic flows, temperatures and power densities. Electrically heated bundles have been tested with two scalloped and two hexagonal duct configurations. Peripheral helical flows, attributed to the spacers, have been observed with strengths dependent upon the evenness and relative sizes of the peripheral flow areas. Diametral sodium temperature profiles are more uniform with smaller peripheral flow areas

  16. Magnetic design constraints of helical solenoids

    Energy Technology Data Exchange (ETDEWEB)

    Lopes, M. L. [Fermi National Accelerator Lab. (FNAL), Batavia, IL (United States); Krave, S. T. [Fermi National Accelerator Lab. (FNAL), Batavia, IL (United States); Tompkins, J. C. [Fermi National Accelerator Lab. (FNAL), Batavia, IL (United States); Yonehara, K. [Fermi National Accelerator Lab. (FNAL), Batavia, IL (United States); Flanagan, G. [Muons Inc., Batavia, IL (United States); Kahn, S. A. [Muons Inc., Batavia, IL (United States); Melconian, K. [Texas A & M Univ., College Station, TX (United States)

    2015-01-30

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

  17. Geometry Dynamics of α-Helices in Different Class I Major Histocompatibility Complexes

    Directory of Open Access Journals (Sweden)

    Reiner Ribarics

    2015-01-01

    Full Text Available MHC α-helices form the antigen-binding cleft and are of particular interest for immunological reactions. To monitor these helices in molecular dynamics simulations, we applied a parsimonious fragment-fitting method to trace the axes of the α-helices. Each resulting axis was fitted by polynomials in a least-squares sense and the curvature integral was computed. To find the appropriate polynomial degree, the method was tested on two artificially modelled helices, one performing a bending movement and another a hinge movement. We found that second-order polynomials retrieve predefined parameters of helical motion with minimal relative error. From MD simulations we selected those parts of α-helices that were stable and also close to the TCR/MHC interface. We monitored the curvature integral, generated a ruled surface between the two MHC α-helices, and computed interhelical area and surface torsion, as they changed over time. We found that MHC α-helices undergo rapid but small changes in conformation. The curvature integral of helices proved to be a sensitive measure, which was closely related to changes in shape over time as confirmed by RMSD analysis. We speculate that small changes in the conformation of individual MHC α-helices are part of the intrinsic dynamics induced by engagement with the TCR.

  18. Observation of persistent α-helical content and discrete types of backbone disorder during a molten globule to ordered peptide transition via deep-UV resonance Raman spectroscopy.

    Science.gov (United States)

    Brown, Mia C; Mutter, Andrew; Koder, Ronald L; JiJi, Renee D; Cooley, Jason W

    2013-07-01

    The molten globule state can aide in the folding of a protein to a functional structure and is loosely defined as an increase in structural disorder with conservation of the ensemble secondary structure content. Simultaneous observation of persistent secondary structure content with increased disorder has remained experimentally problematic. As a consequence, modeling how the molten globule state remains stable and how it facilitates proper folding remains difficult due to a lack of amenable spectroscopic techniques to characterize this class of partially unfolded proteins. Previously, deep-UV resonance Raman (dUVRR) spectroscopy has proven useful in the resolution of global and local structural fluctuations in the secondary structure of proteins. In this work, dUVRR was employed to study the molten globule to ordered transition of a model four-helix bundle protein, HP7. Both the average ensemble secondary structure and types of local disorder were monitored, without perturbation of the solvent, pH, or temperature. The molten globule to ordered transition is induced by stepwise coordination of two heme molecules. Persistent dUVRR spectral features in the amide III region at 1295-1301 and 1335-1338 cm -1 confirm previous observations that HP7 remains predominantly helical in the molten globule versus the fully ordered state. Additionally, these spectra represent the first demonstration of conserved helical content in a molten globule protein. With successive heme binding significant losses are observed in the spectral intensity of the amide III 3 and S regions (1230-1260 and 1390 cm -1 , respectively), which are known to be sensitive to local disorder. These observations indicate that there is a decrease in the structural populations able to explore various extended conformations, with successive heme binding events. DUVRR spectra indicate that the first heme coordination between two helical segments diminishes exploration of more elongated backbone structural

  19. Macroscopic ordering of helical pores for arraying guest molecules noncentrosymmetrically

    Science.gov (United States)

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

    2015-09-01

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

  20. Molecular Dynamics with Helical Periodic Boundary Conditions

    Czech Academy of Sciences Publication Activity Database

    Kessler, Jiří; Bouř, Petr

    2014-01-01

    Roč. 35, č. 21 (2014), s. 1552-1559 ISSN 0192-8651 R&D Projects: GA ČR GAP208/11/0105; GA MŠk(CZ) LH11033 Grant - others:GA AV ČR(CZ) M200551205; GA MŠk(CZ) LM2010005 Institutional support: RVO:61388963 Keywords : periodic boundary conditions * helical symmetry * molecular dynamics * protein structure * amyloid fibrils Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.589, year: 2014

  1. Epicyclic Helical Channels for Parametric Resonance Ionization Cooling

    Energy Technology Data Exchange (ETDEWEB)

    Andrei Afanaciev, Alex Bogacz, Yaroslav Derbenev, Kevin Beard, Valentin Ivanov, Rolland Johnson, Guimei Wang, Katsuya Yonehara

    2009-05-01

    In order to achieve cooling of muons in addition to 6D helical cooling channel (HCC) [1], we develop a technique based on a parametric resonance. The use of parametric resonances requires alternating dispersion, minimized at locations of thin absorbers, but maximized in between in order to compensate for chromatic aberrations [2]. These solutions can be combined in an Epicyclic Helical Cooling Channel (EHCC) that meets requirements of alternating dispersion of beam periodic orbit with best conditions for maintenance of stable beam transport in a continuous solenoid-type field [3]. We discuss here basic features and new simulation results for EHCC.

  2. High-n helicity-induced shear Alfven eigenmodes

    International Nuclear Information System (INIS)

    Nakajima, N.; Cheng, C.Z.; Okamoto, M.

    1992-05-01

    The high-n Helicity-induced shear Alfven Eigenmodes (HAE) are considered both analytically and numerically for the straight helical magnetic system, where n is the toroidal mode number. The eigenmode equation for the high-n HAE modes is derived along the field line and with the aid of the averaging method is shown to reduce to the Mathieu equation asymptotically. The discrete HAE modes are shown to exist inside the continuum spectrum gaps. The continuous spectrum gaps appear around ω 2 = ω A 2 [N(lι-m)/2] 2 for N = 1,2,.., where ω A is the toroidal Alfven transit frequency, and l, m, and ι are the polarity of helical coils, the toroidal pitch number of helical coils, and the rotational transform, respectively. For the same ω A and ι, the frequency of the helical continuum gap is larger than that of the continuum gap in tokamak plasmas by |l-ι -1 m|. The polarity of helical coils l plays a crucial role in determining the spectrum gaps and the properties of the high-n HAE modes. The spectrum gaps near the magnetic axis are created by the helical ripple with circular flux surfaces for l = 1, and ≥ 3 helicals. For l = 2 helical systems, the spectrum gaps are created by the ellipticity of the flux surfaces. These analytical results for the continuum gaps and the existence of the high-n HAE modes in the continuum gaps are confirmed numerically for the l = 2 case, and we find that the HAE modes exist for mode structures with the even and the odd parities. (author)

  3. The C-terminal portion of the fibrinogen-binding protein of Streptococcus equi subsp. equi contains extensive alpha-helical coiled-coil structure and contributes to thermal stability.

    Science.gov (United States)

    Meehan, Mary; Kelly, Sharon M; Price, Nicholas C; Owen, Peter

    2002-01-02

    The major cell wall-associated protein of the equine pathogen Streptococcus equi subsp. equi is a fibrinogen-binding protein (FgBP) which binds horse fibrinogen and equine IgG-Fc avidly through residues located in the N-terminal half and central regions of the molecule, respectively. The molecule is a major virulence factor for the organism and displays protective potential. In the present study, we use circular dichroism spectroscopy to investigate the secondary structure of the protein and show through the analysis of a panel of recombinant FgBP truncates that the C-terminal portion of FgBP contains an extensive alpha-helical coiled-coil structure that contributes to the thermal stability of the molecule.

  4. Helicity evolution at small x

    International Nuclear Information System (INIS)

    Kovchegov, Yuri V.; Pitonyak, Daniel; Sievert, Matthew D.

    2016-01-01

    We construct small-x evolution equations which can be used to calculate quark and anti-quark helicity TMDs and PDFs, along with the g 1 structure function. These evolution equations resum powers of α s ln 2  (1/x) in the polarization-dependent evolution along with the powers of α s 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-N c and large-N c   N f limits. As a cross-check, in the ladder approximation, our equations map onto the same ladder limit of the infrared evolution equations for the g 1 structure function derived previously by Bartels, Ermolaev and Ryskin http://dx.doi.org/10.1007/s002880050285.

  5. Godbillon Vey Helicity and Magnetic Helicity in Magnetohydrodynamics

    Science.gov (United States)

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

    2017-12-01

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

  6. Energy and helicity of magnetic torus knots and braids

    Science.gov (United States)

    Oberti, Chiara; Ricca, Renzo L.

    2018-02-01

    By considering steady magnetic fields in the shape of torus knots and unknots in ideal magnetohydrodynamics, we compute some fundamental geometric and physical properties to provide estimates for magnetic energy and helicity. By making use of an appropriate parametrization, we show that knots with dominant toroidal coils that are a good model for solar coronal loops have negligible total torsion contribution to magnetic helicity while writhing number provides a good proxy. Hence, by the algebraic definition of writhe based on crossing numbers, we show that the estimated values of writhe based on image analysis provide reliable information for the exact values of helicity. We also show that magnetic energy is linearly related to helicity, and the effect of the confinement of magnetic field can be expressed in terms of geometric information. These results can find useful application in solar and plasma physics, where braided structures are often present.

  7. Helicity multiplexed broadband metasurface holograms

    Science.gov (United States)

    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

    2015-09-01

    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.

  8. DNA-based stable isotope probing: a link between community structure and function

    Czech Academy of Sciences Publication Activity Database

    Uhlík, Ondřej; Ječná, K.; Leigh, M. B.; Macková, Martina; Macek, Tomáš

    2009-01-01

    Roč. 407, č. 12 (2009), s. 3611-3619 ISSN 0048-9697 Grant - others:GA MŠk(CZ) 2B08031 Program:2B Institutional research plan: CEZ:AV0Z40550506 Keywords : DNA-based stable isotope probing * microbial diversity * bioremediation Subject RIV: EI - Biotechnology ; Bionics Impact factor: 2.905, year: 2009

  9. Employing helicity amplitudes for resummation

    International Nuclear Information System (INIS)

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

    2015-08-01

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

  10. A chemically stable electrolyte with a novel sandwiched structure for proton-conducting solid oxide fuel cells (SOFCs)

    KAUST Repository

    Bi, Lei

    2013-11-01

    A chemically stable electrolyte structure was developed for proton-conducting SOFCs by using two layers of stable BaZr0.7Pr 0.1Y0.2O3 -δ to sandwich a highly-conductive but unstable BaCe0.8Y0.2O 3 -δ electrolyte layer. The sandwiched electrolyte structure showed good chemical stability in both CO2 and H2O atmosphere, indicating that the BZPY layers effectively protect the inner BCY electrolyte, while the BCY electrolyte alone decomposed completely under the same conditions. Fuel cell prototypes fabricated with the sandwiched electrolyte achieved a relatively high performance of 185 mW cm- 2 at 700 C, with a high electrolyte film conductivity of 4 × 10- 3 S cm- 1 at 600 C. © 2013 Elsevier B.V.

  11. What makes single-helical metamaterials generate "pure" circularly polarized light?

    Science.gov (United States)

    Wu, Lin; Yang, ZhenYu; Zhao, Ming; Zhang, Peng; Lu, ZeQing; Yu, Yang; Li, ShengXi; Yuan, XiuHua

    2012-01-16

    Circular polarizers with left-handed helical metamaterials can transmit right-handed circularly polarized (RCP) light with few losses. But a certain amount of left-handed circularly polarized (LCP) light will occur in the transmitted light, which is the noise of the circular polarizer. Therefore, we defined the ratio of the RCP light intensity to the LCP light intensity as the signal-to-noise (S/N) ratio. In our previous work, it's found that circular polarizers with multi-helical metamaterials have two orders higher S/N ratios than that of single-helical metamaterials. However, it has been a great challenge to fabricate such multi-helical structures with micron or sub-micron feature sizes. Is it possible for the single-helical metamaterials to obtain equally high S/N ratios as the multi-helical ones? To answer this question, we systematically investigated the influences of structure parameters of single-helical metamaterials on the S/N ratios using the finite-different time-domain (FDTD) method. It was found that the single-helical metamaterials can also reach about 30dB S/N ratios, which are equal to the multi-helical ones. Furthermore, we explained the phenomenon by the antenna theory and optimized the performances of the single-helical circular polarizers.

  12. Closed Pore Structured NiCo2O4-Coated Nickel Foams for Stable and Effective Oil/Water Separation.

    Science.gov (United States)

    Li, Yan; Zheng, Xi; Yan, Zhanheng; Tian, Dongliang; Ma, Jianmin; Zhang, Xiaofang; Jiang, Lei

    2017-08-30

    To solve the serious problem caused by oily wastewater pollution, unique interface designs, for example, membranes with superwetting properties such as superhydrophobicity/superoleophilicity and superhydrophilicity/underwater superoleophobicity, provide a good way to achieve oil/water separation. Here, inspired by the liquid storage property of the honeycomb structure, we propose a strategy to fabricate NiCo 2 O 4 -coated nickel foams for stable and efficient oil/water separation. NiCo 2 O 4 with a closed-pore structure was formed by assembling nanoflakes with a micro/nanoscale hierarchical structure. Compared with nickel foam coated by NiCo 2 O 4 with an open-pore structure (NiCo 2 O 4 nanowires), the enclosed nanostructure of NiCo 2 O 4 nanoflakes can firmly hold water for a more stable superhydrophilic/underwater superoleophobic interface. As a consequence, the NiCo 2 O 4 -nanoflake-coated nickel foam has a larger oil breakthrough pressure than the NiCo 2 O 4 -nanowire-coated nickel foam because of a slightly larger oil advancing angle and a lower underwater oil adhesion force, which makes it more stable and efficient for oil/water separation. Moreover, the NiCo 2 O 4 -coated nickel foams have excellent chemical and mechanical stability, and they are reusable for oil-water separation. This work will be beneficial for the design and development of stable underwater superoleophobic self-cleaning materials and related device applications, such as oil/water separation.

  13. Nanosized helical magnetic domains in strongly frustrated Fe3PO4O3

    Science.gov (United States)

    Ross, K. A.; Bordelon, M. M.; Terho, G.; Neilson, J. R.

    2015-10-01

    Fe3PO4O3 forms a noncentrosymmetric lattice structure (space group R 3 m ) comprising triangular motifs of Fe3 + coupled by strong antiferromagnetic interactions (| ΘC W|>900 K). Neutron diffraction from polycrystalline samples shows that strong frustration eventually gives way to an ordered helical incommensurate structure below TN = 163 K, with the helical axis in the hexagonal a b plane and a modulation length to ˜86 Å. The magnetic structure consists of an unusual needlelike correlation volume that extends past 900 Å along the hexagonal c axis but is limited to ˜70 Å in the a b plane, despite the three-dimensional nature of the magnetic sublattice topology. The small in-plane correlation length, which persists to at least T =TN/40 , indicates a robust blocking of long-range order of the helical magnetic structure, and therefore stable domain walls, or other defect spin textures, must be abundant in Fe3PO4O3 . Temperature-dependent neutron powder diffraction reveals small negative thermal expansion below TN. No change in lattice symmetry is observed on cooling through TN, as revealed by high-resolution synchrotron x-ray diffraction. The previously reported reduced moment of the Fe3 + ions (S =5 /2 ), μ ˜4.2 μB , is confirmed here through magnetization studies of a magnetically diluted solid solution series of compounds, Fe(3 -x )GaxPO4O3 , and is consistent with the refined magnetic moment from neutron diffraction 4.14(2) μB. We attribute the reduced moment to a modified spin density distribution arising from ligand charge transfer in this insulating oxide.

  14. Molecular architecture with carbohydrate functionalized β-peptides adopting 314-helical conformation

    Directory of Open Access Journals (Sweden)

    Nitin J. Pawar

    2014-04-01

    Full Text Available Carbohydrate recognition is essential in cellular interactions and biological processes. It is characterized by structural diversity, multivalency and cooperative effects. To evaluate carbohydrate interaction and recognition, the structurally defined attachment of sugar units to a rigid template is highly desired. β-Peptide helices offer conformationally stable templates for the linear presentation of sugar units in defined distances. The synthesis and β-peptide incorporation of sugar-β-amino acids are described providing the saccharide units as amino acid side chain. The respective sugar-β-amino acids are accessible by Michael addition of ammonia to sugar units derivatized as α,β-unsaturated esters. Three sugar units were incorporated in β-peptide oligomers varying the sugar (glucose, galactose, xylose and sugar protecting groups. The influence of sugar units and the configuration of sugar-β-amino acids on β-peptide secondary structure were investigated by CD spectroscopy.

  15. Finding the Stable Structures of WxN1-x with an ab-initio High-Throughput Approach

    Science.gov (United States)

    2014-03-13

    properties must be energetically stable against decomposition into other compounds. This stability can only be found after the determination of the...polarized. However, in every structure the self-consistent magnetic moment was negligible, and the final calculations were all done assuming no moment. The...of NaCl) we looked at all 255 combinations. We found 34 unique structures, including NbO itself, CsCl, S3U4, ReO3,[59] cubic perovskite (with formula

  16. Dynamics of three-dimensional radiative structures during RMP assisted detached plasmas on the large helical device and its comparison with EMC3-EIRENE modeling

    Science.gov (United States)

    Pandya, Shwetang N.; Peterson, Byron J.; Kobayashi, Masahiro; Ida, Katsumi; Mukai, Kiyofumi; Sano, Ryuichi; Miyazawa, Junichi; Tanaka, Hirohiko; Masuzaki, Suguru; Akiyama, Tsuyoshi; Motojima, Gen; Ohno, Noriyasu; LHD Experiment Group

    2016-04-01

    The resonant magnetic perturbation (RMP) island introduced in the stochastic edge of the large helical device (LHD) plasma plays an important role in the stabilization of the plasma detachment (Kobayashi et al 2013 Nucl. Fusion 53 093032). The plasma enters in the sustained detachment phase in the presence of an RMP once the line averaged density exceeds a critical value with a given input power. During detachment the enhanced radiation from the stochastic edge of the LHD undergoes several spatiotemporal changes which are studied quantitatively by an infrared imaging video bolometer (IRVB) diagnostic. The experimental results are compared qualitatively and quantitatively with the radiation predicted by the 3D transport simulation with fluid model, EMC3-EIRENE. A fair amount of qualitative agreement, before and after the detachment, is reported. The issue of overestimated radiation from the model is addressed by changing the free parameters in the EMC3-EIRENE code till the total radiation and the radiation profiles match closely, within a factor of two with the experimental observations. A better quantitative match between the model and the experiment is achieved at higher cross-field impurity diffusion coefficient and lower sputtering coefficient after the detachment. In this article a comparison, the first of its kind, is established between the quantified radiation from the experiments and the synthetic image obtained from the simulation code. This exercise is aimed towards validating the model assumptions against the experimentally measured radiation.

  17. Magnetic helicity of a flux rope in the magnetotail: THEMIS results

    Directory of Open Access Journals (Sweden)

    Y. C. Zhang

    2010-09-01

    Full Text Available The magnetic field in many regions of magnetosphere has a complex topological structure. As a parameter to measure the topological complexity, the concept of magnetic helicity is a useful tool in magnetospheric physics. Here we present a case study of magnetic helicity in the flux rope (FR in the near-Earth plasma sheet (PS based on the in-situ observation from THEMIS for the first time. With the help of the Grad-Shafranov reconstruction technique, we determine the spatial distribution of magnetic field and evaluate the magnetic helicity in the flux rope. The conservation of magnetic helicity during multiple X-line reconnections and the transport of magnetic helicity between different magnetic field configurations are also discussed. The further application of helicity in magnetosphere will provide us more knowledge about the topologic property of the magnetic fields there and more attention should be paid to that.

  18. Stable feature selection for clinical prediction: exploiting ICD tree structure using Tree-Lasso.

    Science.gov (United States)

    Kamkar, Iman; Gupta, Sunil Kumar; Phung, Dinh; Venkatesh, Svetha

    2015-02-01

    Modern healthcare is getting reshaped by growing Electronic Medical Records (EMR). Recently, these records have been shown of great value towards building clinical prediction models. In EMR data, patients' diseases and hospital interventions are captured through a set of diagnoses and procedures codes. These codes are usually represented in a tree form (e.g. ICD-10 tree) and the codes within a tree branch may be highly correlated. These codes can be used as features to build a prediction model and an appropriate feature selection can inform a clinician about important risk factors for a disease. Traditional feature selection methods (e.g. Information Gain, T-test, etc.) consider each variable independently and usually end up having a long feature list. Recently, Lasso and related l1-penalty based feature selection methods have become popular due to their joint feature selection property. However, Lasso is known to have problems of selecting one feature of many correlated features randomly. This hinders the clinicians to arrive at a stable feature set, which is crucial for clinical decision making process. In this paper, we solve this problem by using a recently proposed Tree-Lasso model. Since, the stability behavior of Tree-Lasso is not well understood, we study the stability behavior of Tree-Lasso and compare it with other feature selection methods. Using a synthetic and two real-world datasets (Cancer and Acute Myocardial Infarction), we show that Tree-Lasso based feature selection is significantly more stable than Lasso and comparable to other methods e.g. Information Gain, ReliefF and T-test. We further show that, using different types of classifiers such as logistic regression, naive Bayes, support vector machines, decision trees and Random Forest, the classification performance of Tree-Lasso is comparable to Lasso and better than other methods. Our result has implications in identifying stable risk factors for many healthcare problems and therefore can

  19. Toroidal helical quartz forming machine

    International Nuclear Information System (INIS)

    Hanks, K.W.; Cole, T.R.

    1977-01-01

    The Scyllac fusion experimental machine used 10 cm diameter smooth bore discharge tubes formed into a simple toroidal shape prior to 1974. At about that time, it was discovered that a discharge tube was required to follow the convoluted shape of the load coil. A machine was designed and built to form a fused quartz tube with a toroidal shape. The machine will accommodate quartz tubes from 5 cm to 20 cm diameter forming it into a 4 m toroidal radius with a 1 to 5 cm helical displacement. The machine will also generate a helical shape on a linear tube. Two sets of tubes with different helical radii and wavelengths have been successfully fabricated. The problems encountered with the design and fabrication of this machine are discussed

  20. Generalized helicity and Beltrami fields

    International Nuclear Information System (INIS)

    Buniy, Roman V.; Kephart, Thomas W.

    2014-01-01

    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 ∫ Ω trF μν F μν d 4 x subject to the local constraint ε μναβ trF μν F 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. Generalized helicity and Beltrami fields

    Energy Technology Data Exchange (ETDEWEB)

    Buniy, Roman V., E-mail: roman.buniy@gmail.com [Schmid College of Science, Chapman University, Orange, CA 92866 (United States); Isaac Newton Institute, University of Cambridge, Cambridge, CB3 0EH (United Kingdom); Kephart, Thomas W., E-mail: tom.kephart@gmail.com [Department of Physics and Astronomy, Vanderbilt University, Nashville, TN 37235 (United States); Isaac Newton Institute, University of Cambridge, Cambridge, CB3 0EH (United Kingdom)

    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.

  2. New Classes of Quasi-helically Symmetric Stellarators

    International Nuclear Information System (INIS)

    Ku, L.P.; Boozer, A.H.

    2010-01-01

    New classes of quasi-helically symmetric stellarators with aspect ratios (le) 10 have been found which are stable to the perturbation of magnetohydrodynamic modes at plasma pressures of practical interest. These configurations have large rotational transform and good quality of flux surfaces. Characteristics of some selected examples are discussed in detail. The feasibility of using modular coils for these stellarators has been investigated. It is shown that practical designs for modular coils can be achieved.

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

    Science.gov (United States)

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

    2017-12-01

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

  4. Single-Helical-Axis States in Reversed-Field-Pinch Plasmas

    International Nuclear Information System (INIS)

    Lorenzini, R.; Terranova, D.; Alfier, A.; Innocente, P.; Martines, E.; Pasqualotto, R.; Zanca, P.

    2008-01-01

    The transition to a new magnetic topology, characterized by a quasi-single-helicity state with a single helical magnetic axis has been experimentally observed for the first time in a reversed-field-pinch plasma. The occurrence of the new state, which has been dubbed a single-helical-axis state, was found to provide magnetic chaos healing and enhanced thermal content of the plasma. The helical structure extends on both sides of the vessel geometric axis, and is related to exceeding a threshold in the ratio between the amplitude of the dominant MHD mode and the amplitude of the secondary ones

  5. Sonochemical synthesis, structure and magnetic properties of air-stable Fe3O4/Au nanoparticles

    International Nuclear Information System (INIS)

    Wu Wei; He Quanguo; Chen Hong; Tang Jianxin; Nie Libo

    2007-01-01

    Air-stable nanoparticles of Fe 3 O 4 /Au were prepared via sonolysis of a solution mixture of hydrogen tetrachloroaureate(III) trihydrate (HAuCl 4 ) and (3-aminopropyl)triethoxysilane (APTES)-coated Fe 3 O 4 nanoparticles with further drop-addition of sodium citrate. The Fe 3 O 4 /Au nanoparticles were characterized by x-ray powder diffraction (XRD), ultraviolet-visible spectroscopy (UV-vis), scanning electron microscopy (SEM) with energy dispersive spectroscopy (EDS), transmission electron microscopy (TEM), x-ray photoelectron spectroscopy (XPS) and superconducting quantum interference device (SQUID) magnetometry. Nanoparticles of Fe 3 O 4 /Au obtained under appropriate conditions possess a very high saturation magnetization of about 63 emu g -1 and their average diameter is about 30 nm

  6. Formation of classical crystals of dipolar particles in a helical geometry

    DEFF Research Database (Denmark)

    K. Pedersen, J.; V. Fedorov, D.; S. Jensen, A.

    2014-01-01

    We consider crystal formation of particles with dipole-dipole interactions that are confined to move in a one-dimensional helical geometry with their dipole moments oriented along the symmetry axis of the confining helix. The stable classical lowest energy configurations are found to be chain...... structures for a large range of pitch-to-radius ratios for relatively low density of dipoles and a moderate total number of particles. The classical normal mode spectra support the chain interpretation both through structure and the distinct degeneracies depending discretely on the number of dipoles per...... dipoles per revolution, this implies a breaking of the initial periodicity to form a cluster of two chains close together and a third chain removed from the cluster. This is driven by the competition between in-chain and out-of-chain interactions, or alternatively the side-by-side repulsion and the head...

  7. Resonant helical fields in tokamaks

    International Nuclear Information System (INIS)

    Okano, V.

    1990-01-01

    Poincare maps of magnetic field lines of a toroidal helical system were made. The magnetic field is a linear superposition of the magnetic fields produced by a toroidal plasma in equilibrium and by external helical currents. Analytical expression for the Poincare maps was no obtained since the magnetic field do not have symmetry. In order to obtain the maps, the equation minus derivative of l vector times B vector = 0 was numerically integrated. In the Poincare maps, the principal and the secondary magnetic island were observed. (author)

  8. Signs of helicity in solar prominences and related features

    Science.gov (United States)

    Martin, S.

    This review illustrates several ways to identify the chirality (handedness) of solar prominences (filaments) from their structure and the structure of their surrounding magnetic fields in the chromosphere and corona. For prominences, these structural elements include the axial magnetic field direction, orientation of barbs, and direction of the prominence fine structure. The surrounding structures include the pattern of fibrils beneath the prominences and the pattern of coronal loops above the prominences. These ways of identifying chirality are then interpreted in terms of the formal definitions of helicity to yield a consistent set of one-to-one helicity relationships for all features. The helicity of some prominences can also be independently determined during their eruption by their fine structure, apparent crossings in the line-of-sight of different parts of the same prominence, and by large- scale twist of the prominence structure. Unlike observations of prominences (filaments) observed prior to eruption, in some cases evidence of both signs of helicity are found within the same erupting prominence. This indicates the continued application of forces on the prominences during the eruption process or the possible introduction of force(s) not present during earlier stages of their evolution.

  9. Benthic Food Web Structure across the Canadian Arctic Ocean: Insights from stable isotopes and the IP25 biomarker

    Science.gov (United States)

    Friscourt, N.; Archambault, P.; Masse, G.; Nozais, C.

    2016-02-01

    In recent decades, the Arctic Ocean has undergone unprecedented changes, such as an increase in the surface temperature and a reduction of sea ice cover. These changes may cause variations in the intensity and spatial distribution of primary production and the nature of pelagic-benthic coupling. This could affect the amount and quality of organic matter that settles onto the seafloor, and the benthic communities that feed upon it. The objectives of this study were i) to describe the trophic structure and resilience of regional benthic food webs using stable carbon and nitrogen isotope analyses and ii) to evaluate the significance of ice algae in the diet of benthic communities using the sea ice proxy IP25. The study area extends from the North Water Polynya to the Chukchi Sea across five geographic regions (North Water Polynya, Canadian Archipelago, Amundsen Gulf, Beaufort Sea and Chukchi Sea) based on environmental factors. To reach these objectives, we collected particulate organic matter (POM), sediments and zoobenthic samples from July to October 2014 aboard the CCGS Amundsen. Stable isotope and IP25 data, the trophic structure within regions and comparison between regions will be presented. Potential impacts of climate change and human activities on benthic ecosystems in the Arctic are still difficult to assess because of the lack of baseline data. The baseline data once provided will enable us to make further predictions on how these changes may affect benthic food web structure.

  10. Soil structure stability and distribution of carbon in water-stable aggregates in different tilled and fertilized Haplic Luvisol

    Directory of Open Access Journals (Sweden)

    Vladimír Šimanský

    2012-01-01

    Full Text Available The influence of tillage and fertilization on soil structure stability and the distribution of carbon in water-stable aggregates of loamy Haplic Luvisol were studied. Soil samples from the locality of Dolná Malanta (experimental station of SUA Nitra were collected (in 2007–2009 from a depth of 0–0.2 m in two tillage variants: (1. conventional tillage, 2. minimal tillage and three treatments of fertilization: (1. without fertilization, 2. crop residues and NPK fertilizers, 3. NPK fertilizers. The minimal tillage system has a positive effect on both the aggregation processes and sequestration of carbon in size fractions of water-stable aggregates, as well as ploughing of crop residues together with NPK fertilizers. On the other hand, application of only NPK fertilizers had a negative effect on SOM content. Under the minimal tillage system and in treatment with crop residues together with NPK fertilizers, what has been observed is a statistically significant increase in the total organic carbon contents by increasing size fractions of water-stable aggregates. Organic carbon did not influence the aggregation processes with dependence on tillage systems. Under conventional tillage as well as in treatment with ploughing crop residues with NPK fertilizers, a very important effect on aggregation had bivalent cations Ca2+ and Mg2+.

  11. Fabrication of a magnetic helical mesostructured silica rod

    Science.gov (United States)

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

    2008-10-01

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

  12. Antiviral activity of α-helical stapled peptides designed from the HIV-1 capsid dimerization domain

    Directory of Open Access Journals (Sweden)

    Cowburn David

    2011-05-01

    Full Text Available Abstract Background The C-terminal domain (CTD of HIV-1 capsid (CA, like full-length CA, forms dimers in solution and CTD dimerization is a major driving force in Gag assembly and maturation. Mutations of the residues at the CTD dimer interface impair virus assembly and render the virus non-infectious. Therefore, the CTD represents a potential target for designing anti-HIV-1 drugs. Results Due to the pivotal role of the dimer interface, we reasoned that peptides from the α-helical region of the dimer interface might be effective as decoys to prevent CTD dimer formation. However, these small peptides do not have any structure in solution and they do not penetrate cells. Therefore, we used the hydrocarbon stapling technique to stabilize the α-helical structure and confirmed by confocal microscopy that this modification also made these peptides cell-penetrating. We also confirmed by using isothermal titration calorimetry (ITC, sedimentation equilibrium and NMR that these peptides indeed disrupt dimer formation. In in vitro assembly assays, the peptides inhibited mature-like virus particle formation and specifically inhibited HIV-1 production in cell-based assays. These peptides also showed potent antiviral activity against a large panel of laboratory-adapted and primary isolates, including viral strains resistant to inhibitors of reverse transcriptase and protease. Conclusions These preliminary data serve as the foundation for designing small, stable, α-helical peptides and small-molecule inhibitors targeted against the CTD dimer interface. The observation that relatively weak CA binders, such as NYAD-201 and NYAD-202, showed specificity and are able to disrupt the CTD dimer is encouraging for further exploration of a much broader class of antiviral compounds targeting CA. We cannot exclude the possibility that the CA-based peptides described here could elicit additional effects on virus replication not directly linked to their ability to bind

  13. Solid-state nuclear magnetic resonance measurements of HIV fusion peptide 13CO to lipid 31P proximities support similar partially inserted membrane locations of the α helical and β sheet peptide structures.

    Science.gov (United States)

    Gabrys, Charles M; Qiang, Wei; Sun, Yan; Xie, Li; Schmick, Scott D; Weliky, David P

    2013-10-03

    Fusion of the human immunodeficiency virus (HIV) membrane and the host cell membrane is an initial step of infection of the host cell. Fusion is catalyzed by gp41, which is an integral membrane protein of HIV. The fusion peptide (FP) is the ∼25 N-terminal residues of gp41 and is a domain of gp41 that plays a key role in fusion catalysis likely through interaction with the host cell membrane. Much of our understanding of the FP domain has been accomplished with studies of "HFP", i.e., a ∼25-residue peptide composed of the FP sequence but lacking the rest of gp41. HFP catalyzes fusion between membrane vesicles and serves as a model system to understand fusion catalysis. HFP binds to membranes and the membrane location of HFP is likely a significant determinant of fusion catalysis perhaps because the consequent membrane perturbation reduces the fusion activation energy. In the present study, many HFPs were synthesized and differed in the residue position that was (13)CO backbone labeled. Samples were then prepared that each contained a singly (13)CO labeled HFP incorporated into membranes that lacked cholesterol. HFP had distinct molecular populations with either α helical or oligomeric β sheet structure. Proximity between the HFP (13)CO nuclei and (31)P nuclei in the membrane headgroups was probed by solid-state NMR (SSNMR) rotational-echo double-resonance (REDOR) measurements. For many samples, there were distinct (13)CO shifts for the α helical and β sheet structures so that the proximities to (31)P nuclei could be determined for each structure. Data from several differently labeled HFPs were then incorporated into a membrane location model for the particular structure. In addition to the (13)CO labeled residue position, the HFPs also differed in sequence and/or chemical structure. "HFPmn" was a linear peptide that contained the 23 N-terminal residues of gp41. "HFPmn_V2E" contained the V2E mutation that for HIV leads to greatly reduced extent of fusion and

  14. Solid-State Nuclear Magnetic Resonance Measurements of HIV Fusion Peptide 13CO to Lipid 31P Proximities Support Similar Partially Inserted Membrane Locations of the α Helical and β Sheet Peptide Structures

    Science.gov (United States)

    Gabrys, Charles M.; Qiang, Wei; Sun, Yan; Xie, Li; Schmick, Scott D.; Weliky, David P.

    2013-10-01

    Fusion of the human immunodeficiency virus (HIV) membrane and the host cell membrane is an initial step of infection of the host cell. Fusion is catalyzed by gp41, which is an integral membrane protein of HIV. The fusion peptide (FP) is the -25 N-terminal residues of gp41 and is a domain of gp41 that plays a key role in fusion catalysis likely through interaction with the host cell membrane. Much of our understanding of the FP domain has been accomplished with studies of -HFP-, i.e., a -25-residue peptide composed of the FP sequence but lacking the rest of gp41. HFP catalyzes fusion between membrane vesicles and serves as a model system to understand fusion catalysis. HFP binds to membranes and the membrane location of HFP is likely a significant determinant of fusion catalysis perhaps because the consequent membrane perturbation reduces the fusion activation energy. In the present study, many HFPs were synthesized and differed in the residue position that was 13CO backbone labeled. Samples were then prepared that each contained a singly 13CO labeled HFP incorporated into membranes that lacked cholesterol. HFP had distinct molecular populations with either α helical or oligomeric - sheet structure. Proximity between the HFP 13CO nuclei and 31P nuclei in the membrane headgroups was probed by solid-state NMR (SSNMR) rotational-echo double-resonance (REDOR) measurements. For many samples, there were distinct 13CO shifts for the α helical and - sheet structures so that the proximities to 31P nuclei could be determined for each structure. Data from several differently labeled HFPs were then incorporated into a membrane location model for the particular structure. In addition to the 13CO labeled residue position, the HFPs also differed in sequence and/or chemical structure. -HFPmn- was a linear peptide that contained the 23 N-terminal residues of gp41. -HFPmn_V2E- contained the V2E mutation that for HIV leads to greatly reduced extent of fusion and infection. The

  15. DNA-based stable isotope probing: a link between community structure and function

    International Nuclear Information System (INIS)

    Uhlik, Ondrej; Jecna, Katerina; Leigh, Mary Beth; Mackova, Martina; Macek, Tomas

    2009-01-01

    DNA-based molecular techniques permit the comprehensive determination of microbial diversity but generally do not reveal the relationship between the identity and the function of microorganisms. The first direct molecular technique to enable the linkage of phylogeny with function is DNA-based stable isotope probing (DNA-SIP). Applying this method first helped describe the utilization of simple compounds, such as methane, methanol or glucose and has since been used to detect microbial communities active in the utilization of a wide variety of compounds, including various xenobiotics. The principle of the method lies in providing 13C-labeled substrate to a microbial community and subsequent analyses of the 13C-DNA isolated from the community. Isopycnic centrifugation permits separating 13C-labeled DNA of organisms that utilized the substrate from 12C-DNA of the inactive majority. As the whole metagenome of active populations is isolated, its follow-up analysis provides successful taxonomic identification as well as the potential for functional gene analyses. Because of its power, DNA-SIP has become one of the leading techniques of microbial ecology research. But from other point of view, it is a labor-intensive method that requires careful attention to detail during each experimental step in order to avoid misinterpretation of results.

  16. Conjugated organic framework with three-dimensionally ordered stable structure and delocalized π clouds

    Science.gov (United States)

    Guo, Jia; Xu, Yanhong; Jin, Shangbin; Chen, Long; Kaji, Toshihiko; Honsho, Yoshihito; Addicoat, Matthew A.; Kim, Jangbae; Saeki, Akinori; Ihee, Hyotcherl; Seki, Shu; Irle, Stephan; Hiramoto, Masahiro; Gao, Jia; Jiang, Donglin

    2013-01-01

    Covalent organic frameworks are a class of crystalline organic porous materials that can utilize π–π-stacking interactions as a driving force for the crystallization of polygonal sheets to form layered frameworks and ordered pores. However, typical examples are chemically unstable and lack intrasheet π-conjugation, thereby significantly limiting their applications. Here we report a chemically stable, electronically conjugated organic framework with topologically designed wire frameworks and open nanochannels, in which the π conjugation-spans the two-dimensional sheets. Our framework permits inborn periodic ordering of conjugated chains in all three dimensions and exhibits a striking combination of properties: chemical stability, extended π-delocalization, ability to host guest molecules and hole mobility. We show that the π-conjugated organic framework is useful for high on-off ratio photoswitches and photovoltaic cells. Therefore, this strategy may constitute a step towards realizing ordered semiconducting porous materials for innovations based on two-dimensionally extended π systems. PMID:24220603

  17. Plasmodium vivax antigen discovery based on alpha-helical coiled coil protein motif

    DEFF Research Database (Denmark)

    Céspedes, Nora; Habel, Catherine; Lopez-Perez, Mary

    2014-01-01

    Protein α-helical coiled coil structures that elicit antibody responses, which block critical functions of medically important microorganisms, represent a means for vaccine development. By using bioinformatics algorithms, a total of 50 antigens with α-helical coiled coil motifs orthologous to Pla...

  18. Magnetic Helicity and Large Scale Magnetic Fields: A Primer

    Science.gov (United States)

    Blackman, Eric G.

    2015-05-01

    Magnetic fields of laboratory, planetary, stellar, and galactic plasmas commonly exhibit significant order on large temporal or spatial scales compared to the otherwise random motions within the hosting system. Such ordered fields can be measured in the case of planets, stars, and galaxies, or inferred indirectly by the action of their dynamical influence, such as jets. Whether large scale fields are amplified in situ or a remnant from previous stages of an object's history is often debated for objects without a definitive magnetic activity cycle. Magnetic helicity, a measure of twist and linkage of magnetic field lines, is a unifying tool for understanding large scale field evolution for both mechanisms of origin. Its importance stems from its two basic properties: (1) magnetic helicity is typically better conserved than magnetic energy; and (2) the magnetic energy associated with a fixed amount of magnetic helicity is minimized when the system relaxes this helical structure to the largest scale available. Here I discuss how magnetic helicity has come to help us understand the saturation of and sustenance of large scale dynamos, the need for either local or global helicity fluxes to avoid dynamo quenching, and the associated observational consequences. I also discuss how magnetic helicity acts as a hindrance to turbulent diffusion of large scale fields, and thus a helper for fossil remnant large scale field origin models in some contexts. I briefly discuss the connection between large scale fields and accretion disk theory as well. The goal here is to provide a conceptual primer to help the reader efficiently penetrate the literature.

  19. Applications of 2D helical vortex dynamics

    DEFF Research Database (Denmark)

    Okulov, Valery; Sørensen, Jens Nørkær

    2010-01-01

    In the paper, we show how the assumption of helical symmetry in the context of 2D helical vortices can be exploited to analyse and to model various cases of rotating flows. From theory, examples of three basic applications of 2D dynamics of helical vortices embedded in flows with helical symmetry...... of the vorticity field are addressed. These included some of the problems related to vortex breakdown, instability of far wakes behind rotors and vortex theory of ideal rotors....

  20. Parameterization and measurements of helical magnetic fields

    International Nuclear Information System (INIS)

    Fischer, W.; Okamura, M.

    1997-01-01

    Magnetic fields with helical symmetry can be parameterized using multipole coefficients (a n , b n ). We present a parameterization that gives the familiar multipole coefficients (a n , b n ) for straight magnets when the helical wavelength tends to infinity. To measure helical fields all methods used for straight magnets can be employed. We show how to convert the results of those measurements to obtain the desired helical multipole coefficients (a n , b n )

  1. Optimized multi-step NMR-crystallography approach for structural characterization of a stable quercetin solvate.

    Science.gov (United States)

    Filip, Xenia; Miclaus, Maria; Martin, Flavia; Filip, Claudiu; Grosu, Ioana Georgeta

    2017-05-10

    Herein we report the preparation and solid state structural investigation of the 1,4-dioxane-quercetin solvate. NMR crystallography methods were employed for crystal structure determination of the solvate from microcrystalline powder. The stability of the compound relative to other reported quercetin solvates is discussed and found to be in perfect agreement with the hydrogen bonding networks/supra-molecular architectures formed in each case. It is also clearly shown that NMR crystallography represents an ideal analytical tool in such cases when hydrogen-bonding networks are required to be constrained at a high accuracy level. Copyright © 2017 Elsevier B.V. All rights reserved.

  2. A hypoplastic constitutive model for clays with meta-stable structure

    Czech Academy of Sciences Publication Activity Database

    Mašín, David

    2007-01-01

    Roč. 44, č. 3 (2007), s. 363-375 ISSN 0008-3674 R&D Projects: GA AV ČR(CZ) IAA200710605 Institutional research plan: CEZ:AV0Z20710524 Keywords : constitutive relations * hypoplasticity * clays * structure of soils Subject RIV: JM - Building Engineering Impact factor: 0.542, year: 2007

  3. Structurally stable design of output regulation for a class of nonlinear systems

    Czech Academy of Sciences Publication Activity Database

    Villanueva-Novelo, C.; Čelikovský, Sergej; Castillo-Toledo, B.

    2001-01-01

    Roč. 37, č. 5 (2001), s. 517-561 ISSN 0023-5954 R&D Projects: GA ČR GA102/99/1368 Institutional research plan: AV0Z1075907 Keywords : nonlinear systems * structural stability * output regulation Subject RIV: BC - Control Systems Theory Impact factor: 0.316, year: 2001

  4. Atomic-scale structure and properties of highly stable antiphase boundary defects in Fe3O4.

    Science.gov (United States)

    McKenna, Keith P; Hofer, Florian; Gilks, Daniel; Lazarov, Vlado K; Chen, Chunlin; Wang, Zhongchang; Ikuhara, Yuichi

    2014-12-10

    The complex and intriguing properties of the ferrimagnetic half metal magnetite (Fe 3 O 4 ) are of continuing fundamental interest as well as being important for practical applications in spintronics, magnetism, catalysis and medicine. There is considerable speculation concerning the role of the ubiquitous antiphase boundary (APB) defects in magnetite, however, direct information on their structure and properties has remained challenging to obtain. Here we combine predictive first principles modelling with high-resolution transmission electron microscopy to unambiguously determine the three-dimensional structure of APBs in magnetite. We demonstrate that APB defects on the {110} planes are unusually stable and induce antiferromagnetic coupling between adjacent domains providing an explanation for the magnetoresistance and reduced spin polarization often observed. We also demonstrate how the high stability of the {110} APB defects is connected to the existence of a metastable bulk phase of Fe 3 O 4 , which could be stabilized by strain in films or nanostructures.

  5. Helicity Within and Among Macromolecules

    Science.gov (United States)

    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.

  6. Identification of Complex Carbon Nanotube Structures

    Science.gov (United States)

    Han, Jie; Saini, Subhash (Technical Monitor)

    1998-01-01

    A variety of complex carbon nanotube (CNT) structures have been observed experimentally. These include sharp bends, branches, tori, and helices. They are believed to be formed by using topological defects such as pentagons and heptagons to connect different CNT. The effects of type, number, and arrangement (separation and orientation) of defects on atomic structures and energetics of complex CNT are investigated using topology, quantum mechanics and molecular mechanics calculations. Energetically stable models are derived for identification of observed complex CNT structures.

  7. Three-dimensional structural analysis of the group B polysaccharide of Neisseria meningitidis 6275 by two-dimensional NMR: The polysaccharide is suggested to exist in helical conformations in solution

    Energy Technology Data Exchange (ETDEWEB)

    Yamasaki, Ryohei; Bacon, B. (Univ. of California, San Francisco (USA) Veterans Administration Medical Center, San Francisco, CA (USA))

    1991-01-22

    The solution conformations of the group B polysaccharide of Neisseria meningitidis were analyzed by DQF-COSY and pure absorption 2D NOE NMR with three mixing times. The pyranose ring of the sialic acid residue was found to be in the {sup 2}C{sub 5} conformation. The DQF-COSY analysis indicated that the orientations of H6 and H7 and of H7 and H8 are both gauche. In order to overcome the difficulties in analyzing the NOE data due to the two sets of proton overlaps, molecular modeling of {alpha}-2,8-linked sialic acid oligomers was carried out to investigate possible conformers, and theoretical NOE calculations were performed by using CORMA (complete relaxation matrix analysis). The analysis suggests that the polysaccharide adopts helical structures for which the {phi} (defined by O6-C2-O8-C8) and {psi} (C2-O8-C8-C7) angles are in the following ranges: {phi}-60 to 0{degree}, {psi} 115-175{degree} or {phi} 90-120{degree}, {psi}55-175{degree}. The weak affinity of anti-B antibodies for smaller {alpha}-2,8-linked oligosaccharides may be due to the fact that such oligomers are more flexible and may not form an ordered structure as the poly(sialic acid) does.

  8. Structural changes, market concentration and vertical integration: would they lead to more stable markets

    International Nuclear Information System (INIS)

    Tahmassebi, H.

    1991-01-01

    This communication is concerned with three major developments that are likely to have significant impact on the future structure of world oil markets: oil company mergers and acquisitions, shift of exploration and production activity from the United States to overseas, and joint venture agreements between producing countries and oil companies aimed at further downstream integration by OPEC. The last two developments are likely to contribute substantially to price and market stability in the future

  9. l=1 helical axis heliotron device in Kyoto university

    International Nuclear Information System (INIS)

    Nagasaki, K.; Sano, F.; Mizuuchi, T.; Hanatani, K.; Okada, H.; Obiki, T.

    1999-01-01

    Helical systems are an attractive candidate for magnetic fusion reactor. Recently, there has been great progress in theoretical research of three dimensional magnetic field structures, resulting in several kinds of confinement optimization being proposed for toroidal magnetic confinement system. For example, some sophisticated ideas have appeared on stage such as quasi-helical symmetry and quasi-isodynamic system. To find experimentally which way is the best Optimisation, a new helical axis heliotron device, so called 'Heliotron J', is under construction in the Institute of Advanced Energy, Kyoto University, Japan. In this conference, the basic concept and the present status will be presented. In the conventional plane axis helical system, it was difficult to have both good particle confinement and good MHD stability simultaneously. The goal of Heliotron J project is to clarify their compatibility in the spatial axis toroidal device. The best way for Optimising the helical magnetic field configuration will be explored by investigating the plasma response to the change in the field components. The main subjects for plasma experiment are: demonstration of the existence of good magnetic flux surfaces, reduction of neoclassical transport in collisionless regime, MHD Stabilisation in high β plasma, controllability of bootstrap current, good confinement of high energy particles

  10. Microscopic Processes in Global Relativistic Jets Containing Helical Magnetic Fields

    Directory of Open Access Journals (Sweden)

    Ken-Ichi Nishikawa

    2016-09-01

    Full Text Available In the study of relativistic jets one of the key open questions is their interaction with the environment on the microscopic level. Here, we study the initial evolution of both electron–proton ( e − – p + and electron–positron ( e ± relativistic jets containing helical magnetic fields, focusing on their interaction with an ambient plasma. We have performed simulations of “global” jets containing helical magnetic fields in order to examine how helical magnetic fields affect kinetic instabilities such as the Weibel instability, the kinetic Kelvin-Helmholtz instability (kKHI and the Mushroom instability (MI. In our initial simulation study these kinetic instabilities are suppressed and new types of instabilities can grow. In the e − – p + jet simulation a recollimation-like instability occurs and jet electrons are strongly perturbed. In the e ± jet simulation a recollimation-like instability occurs at early times followed by a kinetic instability and the general structure is similar to a simulation without helical magnetic field. Simulations using much larger systems are required in order to thoroughly follow the evolution of global jets containing helical magnetic fields.

  11. Helicity Selection Rules and Non-Interference for BSM Amplitudes

    CERN Document Server

    Azatov, Aleksandr; Machado, Camila S.; Riva, Francesco

    2017-01-01

    Precision studies of scattering processes at colliders provide powerful indirect constraints on new physics. We study the helicity structure of scattering amplitudes in the SM and in the context of an effective Lagrangian description of BSM dynamics. Our analysis reveals a novel set of helicity selection rules according to which, in the majority of 2 to 2 scattering processes at high energy, the SM and the leading BSM effects do not interfere. In such situations, the naive expectation that dimension-6 operators represent the leading BSM contribution is compromised, as corrections from dimension-8 operators can become equally (if not more) important well within the validity of the effective field theory approach.

  12. Synthesis, model and stability of helically coiled carbon nanotubes

    DEFF Research Database (Denmark)

    Fejes, Dora; Raffai, Manuella; Hernadi, Klara

    2013-01-01

    Structural model of helically coiled carbon nanotubes is proposed. It is constructed by means of topological coordinate method. Relaxation and cohesive energy calculation are performed by molecular mechanics, using second-generation bond order potential for hydrocarbons introduced by D. W. Brenner....... Our experiments focused on the production and development of catalysts for the synthesis of helically coiled CNTs (carbon nanotubes). The catalysts were tested in the decomposition of acetylene by CCVD (Catalytic Chemical Vapor Deposition) method. The carbon deposit was imaged by TEM (Transmission...

  13. Stable isotope evidence of long-term changes in North Sea food web structure

    DEFF Research Database (Denmark)

    Richardson, Katherine; Christensen, Jens Tang

    2008-01-01

    coast. Porpoises collected after ~1960 had significantly lower d15N than porpoises collected earlier. This change in d15N implies that fundamental changes in food web structure in, or nutrient availability to, the North Sea have taken place over the last ~150 yr and that most of the change occurred over...... reported here may be a reflection of a change in the isotope signature of nitrogen entering the food web. Regardless of its underlying cause, the recorded change in isotopic signature in harbour porpoises is noteworthy as it represents the first fisheries-independent documentation of a long-term temporal...

  14. Cooperative polymerization of α-helices induced by macromolecular architecture

    Science.gov (United States)

    Baumgartner, Ryan; Fu, Hailin; Song, Ziyuan; Lin, Yao; Cheng, Jianjun

    2017-07-01

    Catalysis observed in enzymatic processes and protein polymerizations often relies on the use of supramolecular interactions and the organization of functional elements in order to gain control over the spatial and temporal elements of fundamental cellular processes. Harnessing these cooperative interactions to catalyse reactions in synthetic systems, however, remains challenging due to the difficulty in creating structurally controlled macromolecules. Here, we report a polypeptide-based macromolecule with spatially organized α-helices that can catalyse its own formation. The system consists of a linear polymeric scaffold containing a high density of initiating groups from which polypeptides are grown, forming a brush polymer. The folding of polypeptide side chains into α-helices dramatically enhances the polymerization rate due to cooperative interactions of macrodipoles between neighbouring α-helices. The parameters that affect the rate are elucidated by a two-stage kinetic model using principles from nucleation-controlled protein polymerizations; the key difference being the irreversible nature of this polymerization.

  15. Experimental measurement of fluid force coefficients for helical tube arrays in air cross flow

    International Nuclear Information System (INIS)

    Shen Shifang; Liu Reilan

    1993-01-01

    A helical coil steam generator is extensively used in the High Temperature Gas Cooled Reactor (HTGCR) and Sodium Cooled Reactor (SCR) nuclear power stations because of its compact structure, good heat-exchange, and small volume. The experimental model is established by the structure parameter of 200MW HTGCR. The fluid elastic instability of helical tube arrays in air cross flow is studied in this experiment, and the fluid force coefficients of helical tube arrays having the same notational direction of two adjacent layers in air cross flow are obtained. As compared to the fluid force coefficients of cylinder tube arrays, the fluid force coefficients of helical tube arrays are smaller in the low velocity area, and greater in the high velocity area. The experimental results help the study of the dynamic characteristics of helical tube arrays in air cross flow

  16. Helicity and other conservation laws in perfect fluid motion

    Science.gov (United States)

    Serre, Denis

    2018-03-01

    In this review paper, we discuss helicity from a geometrical point of view and see how it applies to the motion of a perfect fluid. We discuss its relation with the Hamiltonian structure, and then its extension to arbitrary space dimensions. We also comment about the existence of additional conservation laws for the Euler equation, and its unlikely integrability in Liouville's sense.

  17. Is gadolinium a helical antiferromagnet or a collinear ferromagnet?

    Indian Academy of Sciences (India)

    they rule out the possibility of a helical spin structure in Gd and clearly bring out the role of long- range dipolar interactions in stabilising collinear ferromagnetic ... Symposium on Advances in Superconductivity and Mag- netism: Materials, Mechanisms and Devices, ASMM2D-2001, 25–28 September 2001, Mangalore,. India ...

  18. Helquats: A facile, modular, scalable route to novel helical dications

    Czech Academy of Sciences Publication Activity Database

    Adriaenssens, Louis; Severa, Lukáš; Šálová, Tereza; Císařová, I.; Pohl, Radek; Šaman, David; Rocha, S. V.; Finney, N. S.; Pospíšil, Lubomír; Slavíček, P.; Teplý, Filip

    2009-01-01

    Roč. 15, č. 5 (2009), s. 1072-1076 ISSN 0947-6539 Grant - others:GA MŠk(CZ) OC 140 Program:OC Institutional research plan: CEZ:AV0Z40550506 Keywords : air-tolerant cycloisomerization * diquat * elektrochemistry * helical structures Subject RIV: CC - Organic Chemistry Impact factor: 5.382, year: 2009

  19. Is gadolinium a helical antiferromagnet or a collinear ferromagnet?

    Indian Academy of Sciences (India)

    as low as 15 Oe suffice to transform the helical antiferromagnetism into collinear ferro- magnetism. This picture of the spin structure in Gd had to be discarded after subsequent. £Article presented at the International Symposium on Advances in Superconductivity and Mag- netism: Materials, Mechanisms and Devices, ...

  20. Bacterioplankton communities of Crater Lake, OR: Dynamic changes with euphotic zone food web structure and stable deep water populations

    Science.gov (United States)

    Urbach, E.; Vergin, K.L.; Larson, G.L.; Giovannoni, S.J.

    2007-01-01

    The distribution of bacterial and archaeal species in Crater Lake plankton varies dramatically over depth and with time, as assessed by hybridization of group-specific oligonucleotides to RNA extracted from lakewater. Nonmetric, multidimensional scaling (MDS) analysis of relative bacterial phylotype densities revealed complex relationships among assemblages sampled from depth profiles in July, August and September of 1997 through 1999. CL500-11 green nonsulfur bacteria (Phylum Chloroflexi) and marine Group I crenarchaeota are consistently dominant groups in the oxygenated deep waters at 300 and 500 m. Other phylotypes found in the deep waters are similar to surface and mid-depth populations and vary with time. Euphotic zone assemblages are dominated either by ??-proteobacteria or CL120-10 verrucomicrobia, and ACK4 actinomycetes. MDS analyses of euphotic zone populations in relation to environmental variables and phytoplankton and zooplankton population structures reveal apparent links between Daphnia pulicaria zooplankton population densities and microbial community structure. These patterns may reflect food web interactions that link kokanee salmon population densities to community structure of the bacterioplankton, via fish predation on Daphnia with cascading consequences to Daphnia bacterivory and predation on bacterivorous protists. These results demonstrate a stable bottom-water microbial community. They also extend previous observations of food web-driven changes in euphotic zone bacterioplankton community structure to an oligotrophic setting. ?? 2007 Springer Science+Business Media B.V.

  1. Conformal avoidance helical tomotherapy for dogs with nasopharyngeal tumors

    International Nuclear Information System (INIS)

    Welsh, J.S.; Turek, M.; Mackie, T.R.; Miller, P.; Mehta, M.P.; Forrest, L.J.

    2003-01-01

    Helical tomotherapy provides a unique means of delivering intensity-modulated radiation therapy (IMRT) using a novel treatment unit, which merges features of a linear accelerator with a helical CT scanner. Thanks to the CT imaging capacity, targeted regions can be visualized prior to, during, or immediately after each treatment. Such image-guidance through megavoltage CT will allow the realization and refinement of the concept of adaptive radiotherapy - the reconstruction of the actually delivered daily dose (as opposed to planned dose) accompanied by prescription adjustments when appropriate. In addition to this unique feature, helical tomotherapy promises further improvements in the specific avoidance of critical normal structures, i.e. conformal avoidance, the counterpart of conformal therapy. The first definitive treatment protocol using helical tomotherapy is presently underway for dogs with nasopharyngeal tumors. In general, such tumors can be treated with conventional external beam radiation therapy but at the cost of severe ocular toxicity due to the anatomy of the canine head. These are readily measurable toxicities and are almost universal in incidence; therefore, the canine nasopharyngeal tumor presents an ideal model to assess the ability to conformally avoid critical structures. It is hoped that conformal avoidance helical tomotherapy will improve tumor control via dose-escalation while reducing ocular toxicity in these veterinary patients. A total of 10 fractions are scheduled for these patients; the first 3 dogs have all received at least 7 fractions delivered via helical tomotherapy. Although preliminary, the first 3 dogs treated have not shown any evidence of ocular toxicity in this ongoing study

  2. Generalized helicity and its time derivative

    International Nuclear Information System (INIS)

    Jarboe, T.R.; Marklin, G.J.

    1985-01-01

    Spheromaks can be sustained against resistive decay by helicity injection because they tend to obey the minimum energy principle. This principle states that a plasma-laden magnetic configuration will relax to a state of minimum energy subject to the constraint that the magnetic helicity is conserved. Use of helicity as a constraint on the minimization of energy was first proposed by Woltjer in connection with astrophysical phenomena. Helicity does decay on the resistive diffusion time. However, if helicity is created and made to flow continuoiusly into a confinement geometry, these additional linked fluxes can relax and sustain the configuration indefinitely against the resistive decay. In this paper we will present an extension of the definition of helicity to include systems where B vector can penetrate the boundary and the penetration can be varying in time. We then discuss the sustainment of RFPs and spheromaks in terms of helicity injection

  3. Pyridine and phosphonate containing ligands for stable lanthanide complexation. An experimental and theoretical study to assess the solution structure.

    Science.gov (United States)

    Mato-Iglesias, Marta; Balogh, Edina; Platas-Iglesias, Carlos; Tóth, Eva; de Blas, Andrés; Rodríguez Blas, Teresa

    2006-12-07

    We report an experimental and theoretical study of the stability and solution structure of lanthanide complexes with two novel ligands containing pyridine units and phosphonate pendant arms on either ethane-1,2-diamine (L2) or cyclohexane-1,2-diamine (L3) backbones. Potentiometric studies have been carried out to determine the protonation constants of the ligands and the stability constants of the complexes with Gd(III) and the endogenous metal ions Zn(II) and Cu(II). While the stability constant of the GdL2 complex is too high to be determined by direct pH-potentiometric titrations, the cyclohexyl derivative GdL3 has a lower and assessable stability (log K(GdL3)=17.62). Due to the presence of the phosphonate groups, various protonated species can be detected up to pH approximately 8 for both ligands and all metal ions studied. The molecular clusters [Ln(L)(H2O)](3-).19H2O (Ln=La, Nd, Ho or Lu; L=L2 or L3) were characterized by theoretical calculations at the HF level. Our calculations provide two minimum energy geometries where the ligand adopts different conformations: twist-wrap (tw), in which the ligand wraps around the metal ion by twisting the pyridyl units relative to each other, and twist-fold (tf), where the slight twisting of the pyridyl units is accompanied by an overall folding of the two pyridine units towards one of the phosphonate groups. The relative free energies of the tw and tf conformations of [Ln(L)(H2O)]3- (L=L2, L3) complexes calculated in aqueous solution (C-PCM) by using the B3LYP model indicate that the tw form is the most stable one along the whole lanthanide series for the complexes of L3, while for those of L2 only the Gd(III) complex is more stable in the tf conformation by ca. 0.5 kcal mol-1. 1H NMR studies of the Eu(III) complex of L3 show the initial formation of the tf complex in aqueous solution, which slowly converts to the thermodynamically stable tw form. The structures calculated for the Nd(III) complexes are in reasonably

  4. Induction of helical structure in a heptapeptide with a metal cross-link: modification of the Lifson-Roig helix-coil theory to account for covalent cross-links.

    Science.gov (United States)

    Kise, Kenneth J; Bowler, Bruce E

    2002-12-31

    A short peptide, acetyl-AHAAAHA-carboxamide, has been synthesized and the histidines cross-linked with a cis-tetraammineruthenium(III) moiety. In the absence of the Ru(III) cross-link, the heptapeptide is essentially structureless, as judged by circular dichroism, NMR chemical shift, and NMR-monitored hydrogen deuterium exchange data. The presence of the cis-Ru(III) cross-link is confirmed by mass spectral data and the characteristic pH dependence of the UV-vis spectrum of the cis-(bis-(imidazole))ruthenium(III) unit. Circular dichroism data indicate that the Ru(III) cross-linked heptapeptide is approximately 37% helical at 0 degrees C. The NMR spectrum of the cross-linked peptide has been fully assigned using TOCSY and ROESY experiments. ROE interactions and J-coupling data provide evidence for helical structure. NMR-monitored hydrogen-deuterium exchange data for the Ru(III)-cross-linked peptide, resolved at the level of the individual amides, give larger protection factors at the ends than in the center of the helix. Steric and polarization effects of the Ru(III) cross-link are proposed to cause this unusual apparent protection pattern. A modification to the Lifson-Roig helix-coil model to account for the effect of the i,i+4 Ru(III) cross-link on the helix-coil transition of a peptide is presented. The model provides an excellent fit to the temperature dependence of the circular dichroism spectrum of the Ru(III)-cross-linked peptide. The modified model indicates that the effect of the cross-link on the nucleation parameter, v(2), is modest (about 7-fold) for residues bounded by the cross-link. Significant increases in the propagation parameter, w, occur for residues within the cross-link. The modification to the Lifson-Roig model accounts for the effect of a Ru(III) cross-link on the circular dichroism spectrum of a previously reported 17 residue peptide.

  5. Global population structure of the stable fly (Stomoxys calcitrans) inferred by mitochondrial and nuclear sequence data.

    Science.gov (United States)

    Dsouli-Aymes, N; Michaux, J; De Stordeur, E; Couloux, A; Veuille, M; Duvallet, G

    2011-03-01

    Stomoxys calcitrans (Diptera: Muscidae: Stomoxyini), a synanthropic fly with a worldwide distribution, is recognized to have an important medical and veterinary impact. We conducted a phylogeographic analysis based on several populations from five major zoogeographic regions of the world in order to analyse population genetic structure of S. calcitrans and to trace its global dispersion. Results from mitochondrial (COI, Cyt-b and ND1-16S) and nuclear (ITS2) DNA show a substantial differentiation of Oriental populations (first lineage) from the Afrotropical, Palearctic, Nearctic, Neotropical and Oceanian populations (second lineage). The divergence time analyses suggest the separation between the two lineages approximately in mid-Pleistocene. Oriental populations are isolated and would not have participated in the colonization of other regions, unlike the Afrotropical one which seems to be the source of S. calcitrans dispersion towards other regions. Demographic analyses indicate that Oriental, Afrotropical and Palearctic regions have undergone a population expansion during late Pleistocene-early Holocene. The expansion time of this cosmopolitan species could have been influenced by continental human expansions and by animal domestication. Copyright © 2010 Elsevier B.V. All rights reserved.

  6. Peculiarities of the fundamental mode structure in stable-resonator lasers upon spatially inhomogeneous amplification

    International Nuclear Information System (INIS)

    Gorbunkov, Mikhail V; Kostryukov, P V; Telegin, L S; Tunkin, V G; Yakovlev, D V

    2007-01-01

    The structure of the fundamental mode of a laser is calculated by the iteration Fox-Li method in the case of inhomogeneous unsaturated amplification produced by axially symmetric longitudinal pumping. The calculation is performed for different parameters g 1 and g 2 of the resonator within the entire stability region. It is shown that in the case of inhomogeneous amplification, the fundamental mode considerably deviates from the Gaussian mode of an empty resonator only in the so-called critical configurations of the resonator, when the quantity [arccos(g 1 g 2 ) 1/2 ]/π is zero or takes a number of values expressed by irreducible fractions m/n. For the Fresnel number N F = 9, configurations with m/n = 1/2, 2/5, 3/8, 1/3, 3/10, 1/4, 1/5, 1/6, 1/8, and 1/10 are pronounced. As N F increases, the number of critical configurations increases. The expansion in a system of Laguerre-Gaussian beams shows that the fundamental mode in critical configurations is formed by a set of beams with certain radial indices p phased in the active medium. (resonators. modes)

  7. A helical scintillating fiber hodoscope

    CERN Document Server

    Altmeier, M; Bisplinghoff, J; Bissel, T; Bollmann, R; Busch, M; Büsser, K; Colberg, T; Demiroers, L; Diehl, O; Dohrmann, F; Engelhardt, H P; Eversheim, P D; Felden, O; Gebel, R; Glende, M; Greiff, J; Gross, A; Gross-Hardt, R; Hinterberger, F; Jahn, R; Jeske, M; Jonas, E; Krause, H; Lahr, U; Langkau, R; Lindemann, T; Lindlein, J; Maier, R; Maschuw, R; Mayer-Kuckuck, T; Meinerzhagen, A; Naehle, O; Pfuff, M; Prasuhn, D; Rohdjess, H; Rosendaal, D; Von Rossen, P; Sanz, B; Schirm, N; Schulz-Rojahn, M; Schwarz, V; Scobel, W; Thomas, S; Trelle, H J; Weise, E; Wellinghausen, A; Wiedmann, W; Woller, K; Ziegler, R

    1999-01-01

    A novel scintillating fiber hodoscope in helically cylindric geometry has been developed for detection of low multiplicity events of fast protons and other light charged particles in the internal target experiment EDDA at the Cooler Synchrotron COSY. The hodoscope consists of 640 scintillating fibers (2.5 mm diameter), arranged in four layers surrounding the COSY beam pipe. The fibers are helically wound in opposing directions and read out individually using 16-channel photomultipliers connected to a modified commercial encoding system. The detector covers an angular range of 9 deg. <= THETA<=72 deg. and 0 deg. <=phi (cursive,open) Greek<=360 deg. in the lab frame. The detector length is 590 mm, the inner diameter 161 mm. Geometry and granularity of the hodoscope afford a position resolution of about 1.3 mm. The detector design took into consideration a maximum of reliability and a minimum of maintenance. An LED array may be used for monitoring purposes. (author)

  8. Helical screw expander evaluation project

    Science.gov (United States)

    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.

  9. An experimental superconducting helical undulator

    Energy Technology Data Exchange (ETDEWEB)

    Caspi, S.; Taylor, C. [Lawrence Berkeley Lab., CA (United States)

    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.

  10. The structure of mAG, a monomeric mutant of the green fluorescent protein Azami-Green, reveals the structural basis of its stable green emission

    International Nuclear Information System (INIS)

    Ebisawa, Tatsuki; Yamamura, Akihiro; Kameda, Yasuhiro; Hayakawa, Kou; Nagata, Koji; Tanokura, Masaru

    2010-01-01

    The crystal structure of a monomeric mutant of Azami-Green (mAG) from G. fascicularis was determined at 2.2 Å resolution. Monomeric Azami-Green (mAG) from the stony coral Galaxea fascicularis is the first known monomeric green-emitting fluorescent protein that is not a variant of Aequorea victoria green fluorescent protein (avGFP). These two green fluorescent proteins are only 27% identical in their amino-acid sequences. mAG is more similar in its amino-acid sequence to four fluorescent proteins: Dendra2 (a green-to-red irreversibly photoconverting fluorescent protein), Dronpa (a bright-and-dark reversibly photoswitchable fluorescent protein), KikG (a tetrameric green-emitting fluorescent protein) and Kaede (another green-to-red irreversibly photoconverting fluorescent protein). To reveal the structural basis of stable green emission by mAG, the 2.2 Å crystal structure of mAG has been determined and compared with the crystal structures of avGFP, Dronpa, Dendra2, Kaede and KikG. The structural comparison revealed that the chromophore formed by Gln62-Tyr63-Gly64 (QYG) and the fixing of the conformation of the imidazole ring of His193 by hydrogen bonds and van der Waals contacts involving His193, Arg66 and Thr69 are likely to be required for the stable green emission of mAG. The crystal structure of mAG will contribute to the design and development of new monomeric fluorescent proteins with faster maturation, brighter fluorescence, improved photostability, new colours and other preferable properties as alternatives to avGFP and its variants

  11. Synthesis, structure and topological analysis of glycine templated highly stable cadmium sulfate framework: A New Lewis Acid catalyst

    Science.gov (United States)

    Paul, Avijit Kumar

    2018-04-01

    One new open-framework two-dimensional layer, [Cd(NH3CH2COO)(SO4)], I, has been synthesized using amino acid as templating agent. Single crystal structural analysis shows that the compound crystallizes in monoclinic cell with non-centrosymmetric space group P21, a = 4.9513(1) Å, b = 7.9763(2) Å, c = 8.0967(2) Å, β = 105.917(1)° and V = 307.504(12) Å3. The compound has connectivity between the Cd-centers and the sulfate units forming a two-dimensional layer structure. Sulfate unit is coordinated to metal center with η3, μ4 mode possessing a coordination free oxygen atom. The zwitterionic form of glycine molecule is present in the structure bridging with two metal centers through μ2-mode by carboxylate oxygens. The topological analysis reveals that the two-dimensional network is formed with a novel 4- and 6-connected binodal net of (32,42,52)(34,44,54,63) topology. Although one end of the glycine molecule is free from coordination, the structure is highly stable up to 350 °C. Strong N-H⋯ O hydrogen bonding interactions play an important role in the stabilization and formation of three-dimensional supramolecular structure. The cyanosilylation of imines using the present compounds as heterogeneous catalyst indicates good catalytic behavior. The present study illustrates the usefulness of the amino acid for the structure building in less studied sulfate based framework materials as well as designing of new heterogeneous catalysts for the broad application. The compound has also been characterized through elemental analysis, PXRD, IR, SEM and TG-DT studies.

  12. Crystal structure of JHP933 from Helicobacter pylori J99 shows two-domain architecture with a DUF1814 family nucleotidyltransferase domain and a helical bundle domain.

    Science.gov (United States)

    Yoon, Ji Young; Lee, Sang Jae; Kim, Do Jin; Lee, Bong-Jin; Yang, Jin Kuk; Suh, Se Won

    2014-09-01

    The jhp0933 gene in the plasticity region of Helicobacter pylori J99 encodes a hypothetical protein (JHP933), which may play some roles in pathogenesis. Here, we have determined the crystal structure of JHP933 at 2.17 Å. It represents the first crystal structure of the DUF1814 protein family. JHP933 consists of two domains: an N-terminal domain of the nucleotidyltransferase (NTase) fold and a C-terminal helix bundle domain. A highly positively charged surface patch exists adjacent to the putative NTP binding site. Structural similarity of JHP933 to known NTases is very remote, suggesting that it may function as a novel NTase. © 2014 Wiley Periodicals, Inc.

  13. Helical type thermonuclear device and control method

    International Nuclear Information System (INIS)

    Ishigaki, Yukio.

    1990-01-01

    In a conventional helical type thermonuclear device, electric current flows in the toroidal direction under magnetic fields of helical coils and vertical magnetic coils, by which a circulating electric field is caused. Therefore, there is a problem that electrons as a seed are generated by cosmic rays, etc., the electrons are confined in a magnetic field boundary, are accelerated by the circulating electric field, to reach a high energy level, collide against structures in a vacuum vessel and emit a great amount of X-rays. Then, compensation coils for offsetting the magnetic fields generated upon energization and deenergization of the vertical magnetic coils and the power source therefor are disposed at the positions opposing to each other on both sides of the vertical magnetic coils for controlling the variation coefficient rate of electric current upon energization and deenergization of the vertical magnetic coils. Since the compensation coils also offset the magnetic field generated upon energization and deenergization of the vertical magnetic field coils by this control, the circulating magnetic field is not caused in the vacuum vessel to reduce the X-ray radiation by electrons at high energy level. (N.H.)

  14. The effect of temperature on generic stable periodic structures in the parameter space of dissipative relativistic standard map

    Science.gov (United States)

    Horstmann, Ana C. C.; Albuquerque, Holokx A.; Manchein, Cesar

    2017-05-01

    In this work, we have characterized changes in the dynamics of a two-dimensional relativistic standard map in the presence of dissipation and specially when it is submitted to thermal effects modeled by a Gaussian noise reservoir. By the addition of thermal noise in the dissipative relativistic standard map (DRSM) it is possible to suppress typical stable periodic structures (SPSs) embedded in the chaotic domains of parameter space for large enough temperature strengths. Smaller SPSs are first affected by thermal effects, starting from their borders, as a function of temperature. To estimate the necessary temperature strength capable to destroy those SPSs we use the largest Lyapunov exponent to obtain the critical temperature (TC) diagrams. For critical temperatures the chaotic behavior takes place with the suppression of periodic motion, although the temperature strengths considered in this work are not so large to convert the deterministic features of the underlying system into a stochastic ones.

  15. Stable isotopes indicate population structuring in the southwest Atlantic population of right whales (Eubalaena australis.

    Directory of Open Access Journals (Sweden)

    Morgana Vighi

    Full Text Available From the early 17th century to the 1970s southern right whales, Eubalaena australis, were subject to intense exploitation along the Atlantic coast of South America. Catches along this coast recorded by whalers originally formed a continuum from Brazil to Tierra del Fuego. Nevertheless, the recovery of the population has apparently occurred fragmentarily, and with two main areas of concentration, one off southern Brazil (Santa Catarina and another off central Argentina (Peninsula Valdés. This pattern suggests some level of heterogeneity amongst the population, which is apparently contradicted by records that traced individuals moving throughout the whole geographical extension covered by the species in the Southwest Atlantic. To test the hypothesis of the potential occurrence of discrete subpopulations exploiting specific habitats, we investigated N, C and O isotopic values in 125 bone samples obtained from whaling factories operating in the early 1970s in southern Brazil (n=72 and from contemporary and more recent strandings occurring in central Argentina (n=53. Results indicated significant differences between the two sampling areas, being δ13C and δ18O values significantly higher in samples from southern Brazil than in those from central Argentina. This variation was consistent with isotopic baselines from the two areas, indicating the occurrence of some level of structure in the Southwest Atlantic right whale population and equally that whales more likely feed in areas commonly thought to exclusively serve as nursing grounds. Results aim at reconsidering of the units currently used in the management of the southern right whale in the Southwest Atlantic Ocean. In the context of the current die-off affecting the species in Peninsula Valdés, these results also highlight the necessity to better understand movements of individuals and precisely identify their feeding areas.

  16. Stable isotopes indicate population structuring in the southwest Atlantic population of right whales (Eubalaena australis).

    Science.gov (United States)

    Vighi, Morgana; Borrell, Asunción; Crespo, Enrique A; Oliveira, Larissa R; Simões-Lopes, Paulo C; Flores, Paulo A C; García, Néstor A; Aguilar, Alex; Aguilar, Alejandro

    2014-01-01

    From the early 17th century to the 1970s southern right whales, Eubalaena australis, were subject to intense exploitation along the Atlantic coast of South America. Catches along this coast recorded by whalers originally formed a continuum from Brazil to Tierra del Fuego. Nevertheless, the recovery of the population has apparently occurred fragmentarily, and with two main areas of concentration, one off southern Brazil (Santa Catarina) and another off central Argentina (Peninsula Valdés). This pattern suggests some level of heterogeneity amongst the population, which is apparently contradicted by records that traced individuals moving throughout the whole geographical extension covered by the species in the Southwest Atlantic. To test the hypothesis of the potential occurrence of discrete subpopulations exploiting specific habitats, we investigated N, C and O isotopic values in 125 bone samples obtained from whaling factories operating in the early 1970s in southern Brazil (n=72) and from contemporary and more recent strandings occurring in central Argentina (n=53). Results indicated significant differences between the two sampling areas, being δ13C and δ18O values significantly higher in samples from southern Brazil than in those from central Argentina. This variation was consistent with isotopic baselines from the two areas, indicating the occurrence of some level of structure in the Southwest Atlantic right whale population and equally that whales more likely feed in areas commonly thought to exclusively serve as nursing grounds. Results aim at reconsidering of the units currently used in the management of the southern right whale in the Southwest Atlantic Ocean. In the context of the current die-off affecting the species in Peninsula Valdés, these results also highlight the necessity to better understand movements of individuals and precisely identify their feeding areas.

  17. Truncated Glucagon-like Peptide-1 and Exendin-4 α-Conotoxin pl14a Peptide Chimeras Maintain Potency and α-Helicity and Reveal Interactions Vital for cAMP Signaling in Vitro*

    Science.gov (United States)

    Swedberg, Joakim E.; Schroeder, Christina I.; Mitchell, Justin M.; Fairlie, David P.; Edmonds, David J.; Griffith, David A.; Ruggeri, Roger B.; Derksen, David R.; Loria, Paula M.; Price, David A.; Liras, Spiros; Craik, David J.

    2016-01-01

    Glucagon-like peptide-1 (GLP-1) signaling through the glucagon-like peptide 1 receptor (GLP-1R) is a key regulator of normal glucose metabolism, and exogenous GLP-1R agonist therapy is a promising avenue for the treatment of type 2 diabetes mellitus. To date, the development of therapeutic GLP-1R agonists has focused on producing drugs with an extended serum half-life. This has been achieved by engineering synthetic analogs of GLP-1 or the more stable exogenous GLP-1R agonist exendin-4 (Ex-4). These synthetic peptide hormones share the overall structure of GLP-1 and Ex-4, with a C-terminal helical segment and a flexible N-terminal tail. Although numerous studies have investigated the molecular determinants underpinning GLP-1 and Ex-4 binding and signaling through the GLP-1R, these have primarily focused on the length and composition of the N-terminal tail or on how to modulate the helicity of the full-length peptides. Here, we investigate the effect of C-terminal truncation in GLP-1 and Ex-4 on the cAMP pathway. To ensure helical C-terminal regions in the truncated peptides, we produced a series of chimeric peptides combining the N-terminal portion of GLP-1 or Ex-4 and the C-terminal segment of the helix-promoting peptide α-conotoxin pl14a. The helicity and structures of the chimeric peptides were confirmed using circular dichroism and NMR, respectively. We found no direct correlation between the fractional helicity and potency in signaling via the cAMP pathway. Rather, the most important feature for efficient receptor binding and signaling was the C-terminal helical segment (residues 22–27) directing the binding of Phe22 into a hydrophobic pocket on the GLP-1R. PMID:27226591

  18. Magnetic helicity and active filament configuration

    Science.gov (United States)

    Romano, P.; Zuccarello, F.; Poedts, S.; Soenen, A.; Zuccarello, F. P.

    2009-11-01

    Context: The role of magnetic helicity in active filament formation and destabilization is still under debate. Aims: Although active filaments usually show a sigmoid shape and a twisted configuration before and during their eruption, it is unclear which mechanism leads to these topologies. In order to provide an observational contribution to clarify these issues, we describe a filament evolution whose characteristics seem to be directly linked to the magnetic helicity transport in corona. Methods: We applied different methods to determine the helicity sign and the chirality of the filament magnetic field. We also computed the magnetic helicity transport rate at the filament footpoints. Results: All the observational signatures provided information on the positive helicity and sinistral chirality of the flux rope containing the filament material: its forward S shape, the orientation of its barbs, the bright and dark threads at 195 Å. Moreover, the magnetic helicity transport rate at the filament footpoints showed a clear accumulation of positive helicity. Conclusions: The study of this event showed a correspondence between several signatures of the sinistral chirality of the filament and several evidences of the positive magnetic helicity of the filament magnetic field. We also found that the magnetic helicity transported along the filament footpoints showed an increase just before the change of the filament shape observed in Hα images. We argued that the photospheric regions where the filament was rooted might be the preferential ways where the magnetic helicity was injected along the filament itself and where the conditions to trigger the eruption were yielded.

  19. Diazole-based powdered cocrystal featuring a helical hydrogen-bonded network: structure determination from PXRD, solid-state NMR and computer modeling.

    Science.gov (United States)

    Sardo, Mariana; Santos, Sérgio M; Babaryk, Artem A; López, Concepción; Alkorta, Ibon; Elguero, José; Claramunt, Rosa M; Mafra, Luís

    2015-02-01

    We present the structure of a new equimolar 1:1 cocrystal formed by 3,5-dimethyl-1H-pyrazole (dmpz) and 4,5-dimethyl-1H-imidazole (dmim), determined by means of powder X-ray diffraction data combined with solid-state NMR that provided insight into topological details of hydrogen bonding connectivities and weak interactions such as CH···π contacts. The use of various 1D/2D (13)C, (15)N and (1)H high-resolution solid-state NMR techniques provided structural insight on local length scales revealing internuclear proximities and relative orientations between the dmim and dmpz molecular building blocks of the studied cocrystal. Molecular modeling and DFT calculations were also employed to generate meaningful structures. DFT refinement was able to decrease the figure of merit R(F(2)) from ~11% (PXRD only) to 5.4%. An attempt was made to rationalize the role of NH···N and CH···π contacts in stabilizing the reported cocrystal. For this purpose four imidazole derivatives with distinct placement of methyl substituents were reacted with dmpz to understand the effect of methylation in blocking or enabling certain intermolecular contacts. Only one imidazole derivative (dmim) was able to incorporate into the dmpz trimeric motif thus resulting in a cocrystal, which contains both hydrophobic (methyl groups) and hydrophilic components that self-assemble to form an atypical 1D network of helicoidal hydrogen bonded pattern, featuring structural similarities with alpha-helix arrangements in proteins. The 1:1 dmpz···dmim compound I is the first example of a cocrystal formed by two different azoles. Copyright © 2014 Elsevier Inc. All rights reserved.

  20. Crystal structures of MW1337R and lin2004: Representatives of a novel protein family that adopt a four-helical bundle fold

    Energy Technology Data Exchange (ETDEWEB)

    Kozbial, Piotr; Xu, Qingping; Chiu, Hsiu-Ju; McMullan, Daniel; Krishna, S. Sri; Miller, Mitchell D.; Abdubek, Polat; Acosta, Claire; Astakhova, Tamara; Axelrod, Herbert L.; Carlton, Dennis; Clayton, Thomas; Deller, Marc; Duan, Lian; Elias, Ylva; Elsliger, Marc-André; Feuerhelm, Julie; Grzechnik, Slawomir K.; Hale, Joanna; Han, Gye Won; Jaroszewski, Lukasz; Jin, Kevin K.; Klock, Heath E.; Knuth, Mark W.; Koesema, Eric; Kumar, Abhinav; Marciano, David; Morse, Andrew T.; Murphy, Kevin D.; Nigoghossian, Edward; Okach, Linda; Oommachen, Silvya; Reyes, Ron; Rife, Christopher L.; Spraggon, Glen; Trout, Christina V.; ban den Bedem, Henry; Weekes, Dana; White, Aprilfawn; Wolf, Guenter; Zubieta, Chloe; Hodgson, Keith O.; Wooley, John; Deacon, Ashley M.; Godzik, Adam; Lesley, Scott A.; Wilson, Ian A. (Scripps); (SSRL); (JCSG); (UCSD); (Burnham)

    2009-08-28

    To extend the structural coverage of proteins with unknown functions, we targeted a novel protein family (Pfam accession number PF08807, DUF1798) for which we proposed and determined the structures of two representative members. The MW1337R gene of Staphylococcus aureus subsp. aureus Rosenbach (Wood 46) encodes a protein with a molecular weight of 13.8 kDa (residues 1-116) and a calculated isoelectric point of 5.15. The lin2004 gene of the nonspore-forming bacterium Listeria innocua Clip11262 encodes a protein with a molecular weight of 14.6 kDa (residues 1-121) and a calculated isoelectric point of 5.45. MW1337R and lin2004, as well as their homologs, which, so far, have been found only in Bacillus, Staphylococcus, Listeria, and related genera (Geobacillus, Exiguobacterium, and Oceanobacillus), have unknown functions and are annotated as hypothetical proteins. The genomic contexts of MW1337R and lin2004 are similar and conserved in related species. In prokaryotic genomes, most often, functionally interacting proteins are coded by genes, which are colocated in conserved operons. Proteins from the same operon as MW1337R and lin2004 either have unknown functions (i.e., belong to DUF1273, Pfam accession number PF06908) or are similar to ypsB from Bacillus subtilis. The function of ypsB is unclear, although it has a strong similarity to the N-terminal region of DivIVA, which was characterized as a bifunctional protein with distinct roles during vegetative growth and sporulation. In addition, members of the DUF1273 family display distant sequence similarity with the DprA/Smf protein, which acts downstream of the DNA uptake machinery, possibly in conjunction with RecA. The RecA activities in Bacillus subtilis are modulated by RecU Holliday-junction resolvase. In all analyzed cases, the gene coding for RecU is in the vicinity of MW1337R, lin2004, or their orthologs, but on a different operon located in the complementary DNA strand. Here, we report the crystal structures

  1. Hexagonally Ordered Arrays of α-Helical Bundles Formed from Peptide-Dendron Hybrids

    Energy Technology Data Exchange (ETDEWEB)

    Barkley, Deborah A. [Department; Rokhlenko, Yekaterina [Department; Marine, Jeannette E. [Department; David, Rachelle [Department; Sahoo, Dipankar [Department; Watson, Matthew D. [Department; Koga, Tadanori [Department; Department; Osuji, Chinedum O. [Department; Rudick, Jonathan G. [Department

    2017-10-24

    Combining monodisperse building blocks that have distinct folding properties serves as a modular strategy for controlling structural complexity in hierarchically organized materials. We combine an α-helical bundle-forming peptide with self-assembling dendrons to better control the arrangement of functional groups within cylindrical nanostructures. Site-specific grafting of dendrons to amino acid residues on the exterior of the α-helical bundle yields monodisperse macromolecules with programmable folding and self-assembly properties. The resulting hybrid biomaterials form thermotropic columnar hexagonal mesophases in which the peptides adopt an α-helical conformation. Bundling of the α-helical peptides accompanies self-assembly of the peptide-dendron hybrids into cylindrical nanostructures. The bundle stoichiometry in the mesophase agrees well with the size found in solution for α-helical bundles of peptides with a similar amino acid sequence.

  2. Diagnostic utility of helical CT for laryngeal cancer. A study on surgical specimens

    Energy Technology Data Exchange (ETDEWEB)

    Uemura, Hirokazu; Fujii, Takashi; Yoshino, Kunitoshi; Sato, Takeo [Osaka Medical Center for Cancer and Cardiovascular Diseases (Japan); Miyahara, Hiroshi; Fukuda, Takehiko

    2000-11-01

    Helical CT, in which X-ray source rotation and patient transition occur simultaneously during data acquisition, has the feature that a volume data set is obtained in a short period of time. The data can be viewed as conventional transaxial images or with MPR (multiplanar reconstruction) and 3-D (three-dimensional) methods. With the latest helical CT and software, anatomical structures and lesions are easily evaluated in detail. In this study, we compared surgical specimens of laryngeal cancer to images with MPR and 3-D methods to determine the advantage and limitation of helical CT. Thinking of helical-CT-scanning for diagnosis of tumor extension, images with 3-D methods have limitations of motion-artifact, phantom images, and difficulty in showing details of small lesions. It is accordingly necessary to give patients an understandable explanation before helical-CT-scanning, and to use 3-D images in careful consideration of MPR images. (author)

  3. New formulae for magnetic relative helicity and field line helicity

    Science.gov (United States)

    Aly, Jean-Jacques

    2018-01-01

    We consider a magnetic field {B} occupying the simply connected domain D and having all its field lines tied to the boundary S of D. We assume here that {B} has a simple topology, i.e., the mapping {M} from positive to negative polarity areas of S associating to each other the two footpoints of any magnetic line, is continuous. We first present new formulae for the helicity H of {B} relative to a reference field {{B}}r having the same normal component {B}n on S, and for its field line helicity h relative to a reference vector potential {{C}}r of {{B}}r. These formulae make immediately apparent the well known invariance of these quantities under all the ideal MHD deformations that preserve the positions of the footpoints on S. They express indeed h and H either in terms of {M} and {B}n, or in terms of the values on S of a pair of Euler potentials of {B}. We next show that, for a specific choice of {{C}}r, the field line helicity h of {B} fully characterizes the magnetic mapping {M} and then the topology of the lines. Finally, we give a formula that describes the rate of change of h in a situation where the plasma moves on the perfectly conducting boundary S without changing {B}n and/or non-ideal processes, described by an unspecified term {N} in Ohm’s law, are at work in some parts of D.

  4. Evolutionary Optimization of a Quadrifilar Helical Antenna

    Science.gov (United States)

    Lohn, Jason D.; Kraus, William F.; Linden, Derek S.; Clancy, Daniel (Technical Monitor)

    2002-01-01

    Automated antenna synthesis via evolutionary design has recently garnered much attention in the research literature. Evolutionary algorithms show promise because, among search algorithms, they are able to effectively search large, unknown design spaces. NASA's Mars Odyssey spacecraft is due to reach final Martian orbit insertion in January, 2002. Onboard the spacecraft is a quadrifilar helical antenna that provides telecommunications in the UHF band with landed assets, such as robotic rovers. Each helix is driven by the same signal which is phase-delayed in 90 deg increments. A small ground plane is provided at the base. It is designed to operate in the frequency band of 400-438 MHz. Based on encouraging previous results in automated antenna design using evolutionary search, we wanted to see whether such techniques could improve upon Mars Odyssey antenna design. Specifically, a co-evolutionary genetic algorithm is applied to optimize the gain and size of the quadrifilar helical antenna. The optimization was performed in-situ in the presence of a neighboring spacecraft structure. On the spacecraft, a large aluminum fuel tank is adjacent to the antenna. Since this fuel tank can dramatically affect the antenna's performance, we leave it to the evolutionary process to see if it can exploit the fuel tank's properties advantageously. Optimizing in the presence of surrounding structures would be quite difficult for human antenna designers, and thus the actual antenna was designed for free space (with a small ground plane). In fact, when flying on the spacecraft, surrounding structures that are moveable (e.g., solar panels) may be moved during the mission in order to improve the antenna's performance.

  5. Computer simulations and modeling-assisted ToxR screening in deciphering 3D structures of transmembrane α-helical dimers: ephrin receptor A1

    International Nuclear Information System (INIS)

    Volynsky, P E; Mineeva, E A; Goncharuk, M V; Ermolyuk, Ya S; Arseniev, A S; Efremov, R G

    2010-01-01

    Membrane-spanning segments of numerous proteins (e.g. receptor tyrosine kinases) represent a novel class of pharmacologically important targets, whose activity can be modulated by specially designed artificial peptides, the so-called interceptors. Rational construction of such peptides requires understanding of the main factors driving peptide–peptide association in lipid membranes. Here we present a new method for rapid prediction of the spatial structure of transmembrane (TM) helix–helix complexes. It is based on computer simulations in membrane-like media and subsequent refinement/validation of the results using experimental studies of TM helix dimerization in a bacterial membrane by means of the ToxR system. The approach was applied to TM fragments of the ephrin receptor A1 (EphA1). A set of spatial structures of the dimer was proposed based on Monte Carlo simulations in an implicit membrane followed by molecular dynamics relaxation in an explicit lipid bilayer. The resulting models were employed for rational design of wild-type and mutant genetic constructions for ToxR assays. The computational and the experimental data are self-consistent and provide an unambiguous spatial model of the TM dimer of EphA1. The results of this work can be further used to develop new biologically active 'peptide interceptors' specifically targeting membrane domains of proteins

  6. Stable phase CdS nanoparticles for optoelectronics: a study on surface morphology, structural and optical characterization

    Directory of Open Access Journals (Sweden)

    Kumar Suresh

    2016-06-01

    Full Text Available This work presents a study on the surface morphology, structure and optical behavior of stable phase cadmium sulphide (CdS nanoparticles synthesized via co-precipitation technique. Scanning electron microscopy (SEM analysis has been employed to study a cluster formation in the aggregated nanoparticles. An image analysis approach using ImageJ has been used to measure the size of nanoparticles from the SEM micrographs. Fourier transform infrared spectroscopic (FT-IR analysis identified absorption peaks of Cd–S stretching along with moisture content. X-ray diffraction (XRD analysis showed that CdS nanoparticles crystallized in wurtzite structure with a preferential orientation along (0 0 2 plane. The particle size, microstrain and lattice constants have been evaluated using XRD data. The lattice parameters of these nanoparticles were found to be shorter than the bulk value which led to lattice contraction. The optical absorption study showed a blue shift in the fundamental absorption edge indicating a quantum size effect.

  7. Impact of forest harvesting on trophic structure of eastern Canadian Boreal Shield lakes: insights from stable isotope analyses.

    Directory of Open Access Journals (Sweden)

    Patricia Glaz

    Full Text Available Perturbations on ecosystems can have profound immediate effects and can, accordingly, greatly alter the natural community. Land-use such as forestry activities in the Canadian Boreal region have increased in the last decades, raising concerns about their potential impact on aquatic ecosystems. The objective of this study was to evaluate the impact of forest harvesting on trophic structure in eastern Canadian Boreal Shield lakes. We measured carbon and nitrogen stable isotopes values for aquatic primary producers, terrestrial detritus, benthic macroinvertebrates, zooplankton and brook trout (Salvelinus fontinalis over a three-year period in eight eastern Boreal Shield lakes. Four lakes were studied before, one and two years after forest harvesting (perturbed lakes and compared with four undisturbed reference lakes (unperturbed lakes sampled at the same time. Stable isotope mixing models showed leaf-litter to be the main food source for benthic primary consumers in both perturbed and unperturbed lakes, suggesting no logging impact on allochthonous subsidies to the littoral food web. Brook trout derived their food mainly from benthic predatory macroinvertebrates in unperturbed lakes. However, in perturbed lakes one year after harvesting, zooplankton appeared to be the main contributor to brook trout diet. This change in brook trout diet was mitigated two years after harvesting. Size-related diet shift were also observed for brook trout, indicating a diet shift related to size. Our study suggests that carbon from terrestrial habitat may be a significant contribution to the food web of oligotrophic Canadian Boreal Shield lakes. Forest harvesting did not have an impact on the diet of benthic primary consumers. On the other hand, brook trout diet composition was affected by logging with greater zooplankton contribution in perturbed lakes, possibly induced by darker-colored environment in these lakes one year after logging.

  8. Impact of forest harvesting on trophic structure of eastern Canadian Boreal Shield lakes: insights from stable isotope analyses.

    Science.gov (United States)

    Glaz, Patricia; Sirois, Pascal; Archambault, Philippe; Nozais, Christian

    2014-01-01

    Perturbations on ecosystems can have profound immediate effects and can, accordingly, greatly alter the natural community. Land-use such as forestry activities in the Canadian Boreal region have increased in the last decades, raising concerns about their potential impact on aquatic ecosystems. The objective of this study was to evaluate the impact of forest harvesting on trophic structure in eastern Canadian Boreal Shield lakes. We measured carbon and nitrogen stable isotopes values for aquatic primary producers, terrestrial detritus, benthic macroinvertebrates, zooplankton and brook trout (Salvelinus fontinalis) over a three-year period in eight eastern Boreal Shield lakes. Four lakes were studied before, one and two years after forest harvesting (perturbed lakes) and compared with four undisturbed reference lakes (unperturbed lakes) sampled at the same time. Stable isotope mixing models showed leaf-litter to be the main food source for benthic primary consumers in both perturbed and unperturbed lakes, suggesting no logging impact on allochthonous subsidies to the littoral food web. Brook trout derived their food mainly from benthic predatory macroinvertebrates in unperturbed lakes. However, in perturbed lakes one year after harvesting, zooplankton appeared to be the main contributor to brook trout diet. This change in brook trout diet was mitigated two years after harvesting. Size-related diet shift were also observed for brook trout, indicating a diet shift related to size. Our study suggests that carbon from terrestrial habitat may be a significant contribution to the food web of oligotrophic Canadian Boreal Shield lakes. Forest harvesting did not have an impact on the diet of benthic primary consumers. On the other hand, brook trout diet composition was affected by logging with greater zooplankton contribution in perturbed lakes, possibly induced by darker-colored environment in these lakes one year after logging.

  9. Population-Level Metrics of Trophic Structure Based on Stable Isotopes and Their Application to Invasion Ecology

    Science.gov (United States)

    Jackson, Michelle C.; Donohue, Ian; Jackson, Andrew L.; Britton, J. Robert; Harper, David M.; Grey, Jonathan

    2012-01-01

    Biological invasions are a significant driver of human-induced global change and many ecosystems sustain sympatric invaders. Interactions occurring among these invaders have important implications for ecosystem structure and functioning, yet they are poorly understood. Here we apply newly developed metrics derived from stable isotope data to provide quantitative measures of trophic diversity within populations or species. We then use these to test the hypothesis that sympatric invaders belonging to the same functional feeding group occupy a smaller isotopic niche than their allopatric counterparts. Two introduced, globally important, benthic omnivores, Louisiana swamp crayfish (Procambarus clarkii) and carp (Cyprinus carpio), are sympatric in Lake Naivasha, Kenya. We applied our metrics to an 8-year data set encompassing the establishment of carp in the lake. We found a strong asymmetric interaction between the two invasive populations, as indicated by inverse correlations between carp abundance and measures of crayfish trophic diversity. Lack of isotopic niche overlap between carp and crayfish in the majority of years indicated a predominantly indirect interaction. We suggest that carp-induced habitat alteration reduced the diversity of crayfish prey, resulting in a reduction in the dietary niche of crayfish. Stable isotopes provide an integrated signal of diet over space and time, offering an appropriate scale for the study of population niches, but few isotope studies have retained the often insightful information revealed by variability among individuals in isotope values. Our population metrics incorporate such variation, are robust to the vagaries of sample size and are a useful additional tool to reveal subtle dietary interactions among species. Although we have demonstrated their applicability specifically using a detailed temporal dataset of species invasion in a lake, they have a wide array of potential ecological applications. PMID:22363724

  10. Helical magnetic structure and hyperfine interactions in FeP studied by {sup 57}Fe Mössbauer spectroscopy and {sup 31}P NMR

    Energy Technology Data Exchange (ETDEWEB)

    Sobolev, Alexey V., E-mail: alex@radio.chem.msu.ru [Department of Chemistry, Lomonosov Moscow State University, 119991, Moscow (Russian Federation); Presniakov, Igor A. [Department of Chemistry, Lomonosov Moscow State University, 119991, Moscow (Russian Federation); Gippius, Andrey A. [Department of Physics, Lomonosov Moscow State University, 119991, Moscow (Russian Federation); Experimental Physics V, University of Augsburg, 86159, Augsburg (Germany); Chernyavskii, Ivan V. [Department of Chemistry, Lomonosov Moscow State University, 119991, Moscow (Russian Federation); Schaedler, Martina; Buettgen, Norbert [Experimental Physics V, University of Augsburg, 86159, Augsburg (Germany); Ibragimov, Sergey A.; Morozov, Igor V.; Shevelkov, Andrei V. [Department of Chemistry, Lomonosov Moscow State University, 119991, Moscow (Russian Federation)

    2016-08-05

    We report results of {sup 57}Fe Mössbauer and {sup 31}P NMR studies of a phosphide FeP powder sample performed in a wide temperature range including the point (T{sub N} ≈ 120 K) of magnetic phase transitions. The {sup 57}Fe Mössbauer spectra at low temperatures T < T{sub N} present a very complex Zeeman pattern with line broadenings and sizeable spectral asymmetry. It was shown that the change of the observed spectral shape is consistent with the transition into a space-modulated helicoidal magnetic structure. Analysis of the experimental spectra was carried out assuming an anisotropy of the magnetic hyperfine field H{sub hf} at the {sup 57}Fe nuclei when the Fe{sup 3+} magnetic moment rotates with respect to the principal axis of the electric field gradient (EFG) tensor. The obtained large temperature independent anharmonicity parameter m ≈ 0.96 of the helicoidal spin structure results from easy-axis anisotropy in the plane of the iron spin rotation. It was assumed that a very low maximal value of H{sub hf}(11 K) ≈ 36 kOe and its high anisotropy ΔH{sub anis}(11 K) ≈ 30 kOe can be attributed to the stabilization of iron cations in the low-spin state (S{sub Fe} = 1/2). The {sup 31}P NMR measurements demonstrate an extremely broad linewidth reflecting the spatial distribution of the transferred internal magnetic fields of the Fe{sup 3+} ions onto P sites in the magnetically ordered state. - Highlights: • The {sup 57}Fe Mössbauer and {sup 31}P NMR studies of FeP in a wide temperature range. • Anharmonicity of helicoidal magnetic structure results from easy-axis anisotropy. • The spatial distribution of the transferred magnetic fields of the Fe{sup 3+} ions onto P sites. • Mechanisms of the anisotropy of the magnetic hyperfine field H{sub hf} at the {sup 57}Fe nuclei.

  11. Beyond textbook illustrations: Hand-held models of ordered DNA and protein structures as 3D supplements to enhance student learning of helical biopolymers.

    Science.gov (United States)

    Jittivadhna, Karnyupha; Ruenwongsa, Pintip; Panijpan, Bhinyo

    2010-11-01

    Textbook illustrations of 3D biopolymers on printed paper, regardless of how detailed and colorful, suffer from its two-dimensionality. For beginners, computer screen display of skeletal models of biopolymers and their animation usually does not provide the at-a-glance 3D perception and details, which can be done by good hand-held models. Here, we report a study on how our students learned more from using our ordered DNA and protein models assembled from colored computer-printouts on transparency film sheets that have useful structural details. Our models (reported in BAMBED 2009), having certain distinguished features, helped our students to grasp various aspects of these biopolymers that they usually find difficult. Quantitative and qualitative learning data from this study are reported. Copyright © 2010 International Union of Biochemistry and Molecular Biology, Inc.

  12. Examining the Conservation of Kinks in Alpha Helices.

    Directory of Open Access Journals (Sweden)

    Eleanor C Law

    Full Text Available Kinks are a structural feature of alpha-helices and many are known to have functional roles. Kinks have previously tended to be defined in a binary fashion. In this paper we have deliberately moved towards defining them on a continuum, which given the unimodal distribution of kink angles is a better description. From this perspective, we examine the conservation of kinks in proteins. We find that kink angles are not generally a conserved property of homologs, pointing either to their not being functionally critical or to their function being related to conformational flexibility. In the latter case, the different structures of homologs are providing snapshots of different conformations. Sequence identity between homologous helices is informative in terms of kink conservation, but almost equally so is the sequence identity of residues in spatial proximity to the kink. In the specific case of proline, which is known to be prevalent in kinked helices, loss of a proline from a kinked helix often also results in the loss of a kink or reduction in its kink angle. We carried out a study of the seven transmembrane helices in the GPCR family and found that changes in kinks could be related both to subfamilies of GPCRs and also, in a particular subfamily, to the binding of agonists or antagonists. These results suggest conformational change upon receptor activation within the GPCR family. We also found correlation between kink angles in different helices, and the possibility of concerted motion could be investigated further by applying our method to molecular dynamics simulations. These observations reinforce the belief that helix kinks are key, functional, flexible points in structures.

  13. Employing helicity amplitudes for resummation in SCET

    International Nuclear Information System (INIS)

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

    2016-05-01

    Helicity amplitudes are the fundamental ingredients of many QCD calculations for multi-leg processes. We describe how these can seamlessly be combined with resummation in Soft-Collinear Effective Theory (SCET), by constructing a helicity operator basis for which the Wilson coefficients are directly given in terms of color-ordered helicity amplitudes. This basis is crossing symmetric and has simple transformation properties under discrete symmetries.

  14. MHD stability analysis of helical system plasmas

    International Nuclear Information System (INIS)

    Nakamura, Yuji

    2000-01-01

    Several topics of the MHD stability studies in helical system plasmas are reviewed with respect to the linear and ideal modes mainly. Difference of the method of the MHD stability analysis in helical system plasmas from that in tokamak plasmas is emphasized. Lack of the cyclic (symmetric) coordinate makes an analysis more difficult. Recent topic about TAE modes in a helical system is also described briefly. (author)

  15. Winding light beams along elliptical helical trajectories

    Science.gov (United States)

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

    2016-07-01

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

  16. Field-theoretic calculation of kinetic helicity flux

    Indian Academy of Sciences (India)

    In the inertial range the kinetic helicity flux is found to be constant and forward. The universal constant KH appearing in the spectrum of kinetic helicity was found to be. 2.47. Keywords. Kinetic helicity; helical turbulence. PACS Nos 47.27.Ak; 47.27.Gs. Kinetic helicity plays an important role in the dynamics of turbulence.

  17. Trophic structure of mesopelagic fishes in the Gulf of Mexico revealed by gut content and stable isotope analyses

    Science.gov (United States)

    McClain-Counts, Jennifer P.; Demopoulos, Amanda W.J.; Ross, Steve W.

    2017-01-01

    Mesopelagic fishes represent an important component of the marine food web due to their global distributions, high abundances and ability to transport organic material throughout a large part of the water column. This study combined stable isotope (SIAs) and gut content analyses (GCAs) to characterize the trophic structure of mesopelagic fishes in the North-Central Gulf of Mexico. Additionally, this study examined whether mesopelagic fishes utilized chemosynthetic energy from cold seeps. Specimens were collected (9–25 August 2007) over three deep (>1,000 m) cold seeps at discrete depths (surface to 1,503 m) over the diurnal cycle. GCA classified 31 species (five families) of mesopelagic fishes into five feeding guilds: piscivores, large crustacean consumers, copepod consumers, generalists and mixed zooplanktivores. However, these guilds were less clearly defined based on stable isotope mixing model (MixSIAR) results, suggesting diets may be more mixed over longer time periods (weeks–months) and across co-occurring species. Copepods were likely important for the majority of mesopelagic fishes, consistent with GCA (this study) and previous literature. MixSIAR results also identified non-crustacean prey items, including salps and pteropods, as potentially important prey items for mesopelagic fishes, including those fishes not analysed in GCA (Sternoptyx spp. and Melamphaidae). Salps and other soft-bodied species are often missed in GCAs. Mesopelagic fishes had δ13C results consistent with particulate organic matter serving as the baseline organic carbon source, fueling up to three trophic levels. Fishes that undergo diel vertical migration were depleted in 15N relative to weak migrators, consistent with depth-specific isotope trends in sources and consumers, and assimilation of 15N-depleted organic matter in surface waters. Linear correlations between fish size and δ15N values suggested ontogenetic changes in fish diets for several species. While there was

  18. Étude expérimentale de structures stables en turbulence bidimensionnelle, comparaison avec une théorie de mécanique statistique

    OpenAIRE

    DENOIX , Marie-Alice

    1992-01-01

    We create two-dimensional flows within a thin layer of mercury, horizontal and subjected to a vertical uniform magnetic field. The fluid is set in motion by injecting electrical currents. We are interested in the inertial organization into stable structures of two-dimensional turbulence. With the experimental conditions in two areas of initial vorticity, we get axisymmetric structures, elliptical, or eccentric. We study these structures using visualizations and also measurements by potential ...

  19. Helical Phase Inflation and Monodromy in Supergravity Theory

    Directory of Open Access Journals (Sweden)

    Tianjun Li

    2015-01-01

    Full Text Available We study helical phase inflation which realizes “monodromy inflation” in supergravity theory. In the model, inflation is driven by the phase component of a complex field whose potential possesses helicoid structure. We construct phase monodromy based on explicitly breaking global U(1 symmetry in the superpotential. By integrating out heavy fields, the phase monodromy from single complex scalar field is realized and the model fulfills natural inflation. The phase-axion alignment is achieved from explicitly symmetry breaking and gives super-Planckian phase decay constant. The F-term scalar potential provides strong field stabilization for all the scalars except inflaton, which is protected by the approximate global U(1 symmetry. Besides, we show that helical phase inflation can be naturally realized in no-scale supergravity with SU(2,1/SU(2×U(1 symmetry since the supergravity setup needed for phase monodromy is automatically provided in the no-scale Kähler potential. We also demonstrate that helical phase inflation can be reduced to another well-known supergravity inflation model with shift symmetry. Helical phase inflation is free from the UV-sensitivity problem although there is super-Planckian field excursion, and it suggests that inflation can be effectively studied based on supersymmetric field theory while a UV-completed framework is not prerequisite.

  20. Structurally Deformed MoS2 for Electrochemically Stable, Thermally Resistant, and Highly Efficient Hydrogen Evolution Reaction.

    Science.gov (United States)

    Chen, Yen-Chang; Lu, Ang-Yu; Lu, Ping; Yang, Xiulin; Jiang, Chang-Ming; Mariano, Marina; Kaehr, Bryan; Lin, Oliver; Taylor, André; Sharp, Ian D; Li, Lain-Jong; Chou, Stanley S; Tung, Vincent

    2017-11-01

    The emerging molybdenum disulfide (MoS 2 ) offers intriguing possibilities for realizing a transformative new catalyst for driving the hydrogen evolution reaction (HER). However, the trade-off between catalytic activity and long-term stability represents a formidable challenge and has not been extensively addressed. This study reports that metastable and temperature-sensitive chemically exfoliated MoS 2 (ce-MoS 2 ) can be made into electrochemically stable (5000 cycles), and thermally robust (300 °C) while maintaining synthetic scalability and excellent catalytic activity through physical-transformation into 3D structurally deformed nanostructures. The dimensional transition enabled by a high throughput electrohydrodynamic process provides highly accessible, and electrochemically active surface area and facilitates efficient transport across various interfaces. Meanwhile, the hierarchically strained morphology is found to improve electronic coupling between active sites and current collecting substrates without the need for selective engineering the electronically heterogeneous interfaces. Specifically, the synergistic combination of high strain load stemmed from capillarity-induced-self-crumpling and sulfur (S) vacancies intrinsic to chemical exfoliation enables simultaneous modulation of active site density and intrinsic HER activity regardless of continuous operation or elevated temperature. These results provide new insights into how catalytic activity, electrochemical-, and thermal stability can be concurrently enhanced through the physical transformation that is reminiscent of nature, in which properties of biological materials emerge from evolved dimensional transitions. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. Structural, physiological, and stable carbon isotopic evidence that the enigmatic Paleozoic fossil Prototaxites formed from rolled liverwort mats.

    Science.gov (United States)

    Graham, Linda E; Cook, Martha E; Hanson, David T; Pigg, Kathleen B; Graham, James M

    2010-02-01

    New structural, nutritional, and stable carbon isotope data may resolve a long-standing mystery-the biological affinities of the fossil Prototaxites, the largest organism on land during the Late Silurian to Late Devonian (420-370 Ma). The tree trunk-shaped specimens, of varying dimensions but consistent tubular anatomy, first formed prior to vascular plant dominance. Hence, Prototaxites has been proposed to represent giant algae, fungi, or lichens, despite incompatible biochemical and anatomical observations. Our comparative analyses instead indicate that Prototaxites formed from partially degraded, wind-, gravity-, or water-rolled mats of mixotrophic liverworts having fungal and cyanobacterial associates, much like the modern liverwort genus Marchantia. We propose that the fossil body is largely derived from abundant, highly degradation-resistant, tubular rhizoids of marchantioid liverworts, intermixed with tubular microbial elements. Our concept explains previously puzzling fossil features and is consistent with evidence for liverworts and microbial associates in Ordovician-Devonian deposits, extensive ancient and modern marchantioid mats, and modern associations of liverworts with cyanobacteria and diverse types of fungi. Our interpretation indicates that liverworts were important components of Devonian ecosystems, that some macrofossils and microfossils previously attributed to "nematophytes" actually represent remains of ancient liverworts, and that mixotrophy and microbial associations were features of early land plants.

  2. Structurally Deformed MoS2 for Electrochemically Stable, Thermally Resistant, and Highly Efficient Hydrogen Evolution Reaction

    KAUST Repository

    Chen, Yen-Chang

    2017-10-12

    The emerging molybdenum disulfide (MoS2) offers intriguing possibilities for realizing a transformative new catalyst for driving the hydrogen evolution reaction (HER). However, the trade-off between catalytic activity and long-term stability represents a formidable challenge and has not been extensively addressed. This study reports that metastable and temperature-sensitive chemically exfoliated MoS2 (ce-MoS2) can be made into electrochemically stable (5000 cycles), and thermally robust (300 °C) while maintaining synthetic scalability and excellent catalytic activity through physical-transformation into 3D structurally deformed nanostructures. The dimensional transition enabled by a high throughput electrohydrodynamic process provides highly accessible, and electrochemically active surface area and facilitates efficient transport across various interfaces. Meanwhile, the hierarchically strained morphology is found to improve electronic coupling between active sites and current collecting substrates without the need for selective engineering the electronically heterogeneous interfaces. Specifically, the synergistic combination of high strain load stemmed from capillarity-induced-self-crumpling and sulfur (S) vacancies intrinsic to chemical exfoliation enables simultaneous modulation of active site density and intrinsic HER activity regardless of continuous operation or elevated temperature. These results provide new insights into how catalytic activity, electrochemical-, and thermal stability can be concurrently enhanced through the physical transformation that is reminiscent of nature, in which properties of biological materials emerge from evolved dimensional transitions.

  3. Highly transparent, stable, and superhydrophobic coatings based on gradient structure design and fast regeneration from physical damage

    Science.gov (United States)

    Chen, Zao; Liu, Xiaojiang; Wang, Yan; Li, Jun; Guan, Zisheng

    2015-12-01

    Optical transparency, mechanical flexibility, and fast regeneration are important factors to expand the application of superhydrophobic surfaces. Herein, we fabricated highly transparent, stable, and superhydrophobic coatings through a novel gradient structure design by versatile dip-coating of silica colloid particles (SCPs) and diethoxydimethysiliane cross-linked silica nanoparticles (DDS-SNPs) on polyethylene terephthalate (PET) film and glass, followed by the modification of octadecyltrichlorosiliane (OTCS). When the DDS concentration reached 5 wt%, the modified SCPs/DDS-SNPs coating exhibited a water contact angle (WCA) of 153° and a sliding angle (SA) superhydrophobic coating on PET film and glass was increased by 2.7% and 1% in the visible wavelength, respectively. This superhydrophobic coating also showed good robustness and stability against water dropping impact, ultrasonic damage, and acid solution. Moreover, the superhydrophobic PET film after physical damage can quickly regain the superhydrophobicity by one-step spray regenerative solution of dodecyltrichlorosilane (DTCS) modified silica nanoparticles at room temperature. The demonstrated method for the preparation and regeneration of superhydrophobic coating is available for different substrates and large-scale production at room temperature.

  4. Microbial communities of the Lemon Creek Glacier show subtle structural variation yet stable phylogenetic composition over space and time

    Directory of Open Access Journals (Sweden)

    Cody Springer Sheik

    2015-05-01

    Full Text Available Glaciers are geologically important yet transient ecosystems that support diverse, biogeochemically significant microbial communities. During the melt season glaciers undergo dramatic physical, geochemical and biological changes that exert great influence on downstream biogeochemical cycles. Thus, we sought to understand the temporal melt-season dynamics of microbial communities and associated geochemistry at the terminus of Lemon Creek Glacier (LCG in coastal southern Alaska. Due to late season snowfall, sampling of LCG occurred in three interconnected areas: proglacial Lake Thomas, the lower glacial outflow stream and the glacier’s terminus. LCG associated microbial communities were phylogenetically diverse and varied by sampling location. However, Betaproteobacteria, Alphaproteobacteria and Bacteroidetes dominated communities at all sampling locations. Strict anaerobic groups such as methanogens, SR1, and OP11 were also recovered from glacier outflows, indicating anoxic conditions in at least some portions of the LCG subglacial environment. Microbial community structure was significantly correlated with sampling location and sodium concentrations. Microbial communities sampled from terminus outflow waters exhibited day-to-day fluctuation in taxonomy and phylogenetic similarity. However, these communities were not significantly different from randomly constructed communities from all three sites. These results indicate that glacial outflows share a large proportion of phylogenetic overlap with downstream environments and that the observed significant shifts in community structure are driven by changes in relative abundance of different taxa, and not complete restructuring of communities. We conclude that LCG glacial discharge hosts a diverse and relatively stable microbiome that shifts at fine taxonomic scales in response to geochemistry and likely water residence time.

  5. A Study of Future Measurements of W Boson Helicity in t -> Wb at CDF

    Energy Technology Data Exchange (ETDEWEB)

    Tweedie, Brock; /Rochester U.

    2002-02-01

    The interactions of the top quark will soon be coming under greater scrutiny at CDF with Run II of the Fermilab Tevatron collider. This investigation gauges CDF's improved ability to measure the helicity of W bosons produced in top quark decays. Such measurements will provide a direct indication of the spin structure of the weak interaction responsible for the top decay process. Simulated CDF Run II data is used to study the W helicity sensitivity of the muon momentum in {mu} + jets events, as limited by both statistical and systematic uncertainties. Optimization of helicity measurements via appropriate choices of event variables and data criteria is also addressed.

  6. Trefoil knot timescales for reconnection and helicity

    Science.gov (United States)

    Kerr, Robert M.

    2018-02-01

    Three-dimensional images of evolving numerical trefoil vortex knots are used to study the growth and decay of the enstrophy and helicity. Negative helicity density (hhydrofoil models is used to correct the published experimental circulations Γ that use only the flat-plate approximation.

  7. Generalized helicity and its time derivative

    International Nuclear Information System (INIS)

    Jarboe, T.R.; Marklin, G.J.

    1986-01-01

    Spheromaks can be sustained against resistive decay by helicity injection because they tend to obey the minimum energy principle. This principle states that a plasma-laden magnetic configuration will relax to a state of minimum energy subject to the constraint that the magnetic helicity is conserved. Use of helicity as a constraint on the minimization of energy was first proposed by Woltjer in connection with astrophysical phenomena. Use of the helicity constraint was first applied to the spheromak by Wells and Norwood. The principle was later applied to the reversed-field pinch (RFP) by Taylor, who was most responsible for the eventual acceptance and recognition of the principle as being important for RFP-type confinement devices. Of course, helicity does decay on the resistive diffusion time. However, if helicity is created and made to flow continuously into a confinement geometry, these additional linked fluxes can relax and sustain the configuration indefinitely against the resistive decay. In this paper an extension of the definition of helicity to include systems where B can penetrate the boundary and the penetration can be varying in time is presented. The sustainment of RFPs and spheromaks in terms of helicity injection is discussed

  8. Passive base isolation with superelastic nitinol SMA helical springs

    International Nuclear Information System (INIS)

    Huang, Bin; Zhang, Haiyang; Wang, Han; Song, Gangbing

    2014-01-01

    Seismic isolation of structures such as multi-story buildings, nuclear reactors, bridges, and liquid storage tanks should be designed to preserve structural integrity. By implementing seismic isolation technology, the deformation of superstructures can be dramatically reduced, consequently helping to protect their safety as well. In this paper, an innovative type of passive base isolation system, which is mainly composed of superelastic nitinol SMA helical springs, is developed. In order to verify the effectiveness of the proposed system, a two-story experimental steel frame model is constructed, and two superelastic SMA helical springs are thermo-mechanically built in the laboratory. To describe the nonlinear mechanical properties of the superelastic SMA helical springs under reciprocating load, a phenomenological model is presented in terms of a series of tensile tests. Afterwards, a numerical model of the two-story frame with the suggested isolation system is set up to simulate the response of the isolated frame subjected to an earthquake. Both the experimental and the numerical simulation results indicate that the proposed base isolation system can remarkably suppress structural vibrations and has improved isolation effects when compared with a steel spring isolation system. Due to the capabilities of energy dissipation as well as fully re-centering, it is very applicable to utilize the suggested isolation system in base isolated structures to resist earthquakes. (paper)

  9. Predicting helical topologies in RNA junctions as tree graphs.

    Directory of Open Access Journals (Sweden)

    Christian Laing

    Full Text Available RNA molecules are important cellular components involved in many fundamental biological processes. Understanding the mechanisms behind their functions requires knowledge of their tertiary structures. Though computational RNA folding approaches exist, they often require manual manipulation and expert intuition; predicting global long-range tertiary contacts remains challenging. Here we develop a computational approach and associated program module (RNAJAG to predict helical arrangements/topologies in RNA junctions. Our method has two components: junction topology prediction and graph modeling. First, junction topologies are determined by a data mining approach from a given secondary structure of the target RNAs; second, the predicted topology is used to construct a tree graph consistent with geometric preferences analyzed from solved RNAs. The predicted graphs, which model the helical arrangements of RNA junctions for a large set of 200 junctions using a cross validation procedure, yield fairly good representations compared to the helical configurations in native RNAs, and can be further used to develop all-atom models as we show for two examples. Because junctions are among the most complex structural elements in RNA, this work advances folding structure prediction methods of large RNAs. The RNAJAG module is available to academic users upon request.

  10. Predicting helical topologies in RNA junctions as tree graphs.

    Science.gov (United States)

    Laing, Christian; Jung, Segun; Kim, Namhee; Elmetwaly, Shereef; Zahran, Mai; Schlick, Tamar

    2013-01-01

    RNA molecules are important cellular components involved in many fundamental biological processes. Understanding the mechanisms behind their functions requires knowledge of their tertiary structures. Though computational RNA folding approaches exist, they often require manual manipulation and expert intuition; predicting global long-range tertiary contacts remains challenging. Here we develop a computational approach and associated program module (RNAJAG) to predict helical arrangements/topologies in RNA junctions. Our method has two components: junction topology prediction and graph modeling. First, junction topologies are determined by a data mining approach from a given secondary structure of the target RNAs; second, the predicted topology is used to construct a tree graph consistent with geometric preferences analyzed from solved RNAs. The predicted graphs, which model the helical arrangements of RNA junctions for a large set of 200 junctions using a cross validation procedure, yield fairly good representations compared to the helical configurations in native RNAs, and can be further used to develop all-atom models as we show for two examples. Because junctions are among the most complex structural elements in RNA, this work advances folding structure prediction methods of large RNAs. The RNAJAG module is available to academic users upon request.

  11. Predicting Helical Topologies in RNA Junctions as Tree Graphs

    Science.gov (United States)

    Kim, Namhee; Elmetwaly, Shereef; Zahran, Mai; Schlick, Tamar

    2013-01-01

    RNA molecules are important cellular components involved in many fundamental biological processes. Understanding the mechanisms behind their functions requires knowledge of their tertiary structures. Though computational RNA folding approaches exist, they often require manual manipulation and expert intuition; predicting global long-range tertiary contacts remains challenging. Here we develop a computational approach and associated program module (RNAJAG) to predict helical arrangements/topologies in RNA junctions. Our method has two components: junction topology prediction and graph modeling. First, junction topologies are determined by a data mining approach from a given secondary structure of the target RNAs; second, the predicted topology is used to construct a tree graph consistent with geometric preferences analyzed from solved RNAs. The predicted graphs, which model the helical arrangements of RNA junctions for a large set of 200 junctions using a cross validation procedure, yield fairly good representations compared to the helical configurations in native RNAs, and can be further used to develop all-atom models as we show for two examples. Because junctions are among the most complex structural elements in RNA, this work advances folding structure prediction methods of large RNAs. The RNAJAG module is available to academic users upon request. PMID:23991010

  12. Stable isotopes

    International Nuclear Information System (INIS)

    Evans, D.K.

    1986-01-01

    Seventy-five percent of the world's stable isotope supply comes from one producer, Oak Ridge Nuclear Laboratory (ORNL) in the US. Canadian concern is that foreign needs will be met only after domestic needs, thus creating a shortage of stable isotopes in Canada. This article describes the present situation in Canada (availability and cost) of stable isotopes, the isotope enrichment techniques, and related research programs at Chalk River Nuclear Laboratories (CRNL)

  13. Study on reinforced concrete beams with helical transverse reinforcement

    Science.gov (United States)

    Kaarthik Krishna, N.; Sandeep, S.; Mini, K. M.

    2018-02-01

    In a Reinforced Concrete (R.C) structure, major reinforcement is used for taking up tensile stresses acting on the structure due to applied loading. The present paper reports the behavior of reinforced concrete beams with helical reinforcement (transverse reinforcement) subjected to monotonous loading by 3-point flexure test. The results were compared with identically similar reinforced concrete beams with rectangular stirrups. During the test crack evolution, load carrying capacity and deflection of the beams were monitored, analyzed and compared. Test results indicate that the use of helical reinforcement provides enhanced load carrying capacity and a lower deflection proving to be more ductile, clearly indicating the advantage in carrying horizontal loads. An analysis was also carried out using ANSYS software in order to compare the test results of both the beams.

  14. Asymptotic Helicity Conservation in SUSY

    CERN Document Server

    Gounaris, G J; Renard, F M

    2010-01-01

    We summarize the extensive work started in ref.1, according to which total helicity is conserved for any two-to-two process, at sqrt{s} larger than M_{SUSY} and fixed angles, in any SUSY extension of SM. Asymptotically the theorem is exact. But it may also have important implications at lower energies sqrt{s} close to M_{SUSY}. Up to now, these have been investigated to 1loop electroweak (EW) order for the processes ug to d W+, sd_L chi+; as well as the 17 gg to HH', and the 9 gg to VH processes, where H,H' denote Higgs or Goldstone bosons, and V=Z, W.

  15. Topology of helical fluid flow

    DEFF Research Database (Denmark)

    Andersen, Morten; Brøns, Morten

    2014-01-01

    Phys. Fluids 25, 1949–1952) contains an infinite sum of modified Bessel functions. Using the approach by Okulov (Okulov, V. L. 1995 Russ. J. Eng. Thermophys. 5, 63–75) we obtain a closed-form approximation which is considerably easier to analyse. Critical points of the stream function can be found from...... function for the topology of the streamline pattern in incompressible flows. On this basis, we perform a comprehensive study of the topology of the flow field generated by a helical vortex filament in an ideal fluid. The classical expression for the stream function obtained by Hardin (Hardin, J. C. 1982...... the zeroes of a single real function of one variable, and we show that three different flow topologies can occur, depending on a single dimensionless parameter. By including the self-induced velocity on the vortex filament by a localised induction approximation, the stream function is slightly modified...

  16. Electric Control of Spin Helicity in a Magnetic Ferroelectric

    International Nuclear Information System (INIS)

    Yamasaki, Y.; Goto, T.; Sagayama, H.; Matsuura, M.; Hirota, K.; Arima, T.; Tokura, Y.

    2007-01-01

    Magnetic ferroelectrics or multiferroics, which are currently extensively explored, may provide a good arena to realize a novel magnetoelectric function. Here we demonstrate the genuine electric control of the spiral magnetic structure in one such magnetic ferroelectric, TbMnO 3 . A spin-polarized neutron scattering experiment clearly shows that the spin helicity, clockwise or counterclockwise, is controlled by the direction of spontaneous polarization and hence by the polarity of the small electric field applied on cooling

  17. Swimming Characteristics of Bioinspired Helical Microswimmers Based on Soft Lotus-Root Fibers

    Directory of Open Access Journals (Sweden)

    Jia Liu

    2017-11-01

    Full Text Available Various kinds of helical swimmers inspired by E. coli bacteria have been developed continually in many types of researches, but most of them are proposed by the rigid bodies. For the targeted drug delivery, the rigid body may hurt soft tissues of the working region with organs. Due to this problem, the biomedical applications of helical swimmers may be restricted. However, the helical microswimmers with the soft and deformable body are appropriate and highly adaptive in a confined environment. Thus, this paper presents a lotus-root-based helical microswimmer, which is fabricated by the fibers of lotus-root coated with magnetic nanoparticles to active under the magnetic fields. The helical microstructures are derived from the intrinsic biological structures of the fibers of the lotus-root. This paper aims to study the swimming characteristic of lotus-root-based microswimmers with deformable helical bodies. In the initial step under the uniform magnetic actuation, the helical microswimmers are bent lightly due to the heterogeneous distribution of the internal stress, and then they undergo a swimming motion which is a spindle-like rotation locomotion. Our experiments report that the microswimmers with soft bodies can locomote faster than those with rigid bodies. Moreover, we also find that the curvature of the shape decreases as a function of actuating field frequency which is related to the deformability of lotus-root fibers.

  18. Magnetic Helicity Estimations in Models and Observations of the Solar Magnetic Field. III. Twist Number Method

    Energy Technology Data Exchange (ETDEWEB)

    Guo, Y. [School of Astronomy and Space Science and Key Laboratory of Modern Astronomy and Astrophysics in Ministry of Education, Nanjing University, Nanjing 210023 (China); Pariat, E.; Moraitis, K. [LESIA, Observatoire de Paris, PSL Research University, CNRS, Sorbonne Université, UPMC Univ. Paris 06, Univ. Paris Diderot, Sorbonne Paris Cité, F-92190 Meudon (France); Valori, G. [University College London, Mullard Space Science Laboratory, Holmbury St. Mary, Dorking, Surrey, RH5 6NT (United Kingdom); Anfinogentov, S. [Institute of Solar-Terrestrial Physics SB RAS 664033, Irkutsk, P.O. box 291, Lermontov Street, 126a (Russian Federation); Chen, F. [Max-Plank-Institut für Sonnensystemforschung, D-37077 Göttingen (Germany); Georgoulis, M. K. [Research Center for Astronomy and Applied Mathematics of the Academy of Athens, 4 Soranou Efesiou Street, 11527 Athens (Greece); Liu, Y. [W. W. Hansen Experimental Physics Laboratory, Stanford University, Stanford, CA 94305 (United States); Thalmann, J. K. [Institute of Physics, Univeristy of Graz, Universitätsplatz 5/II, A-8010 Graz (Austria); Yang, S., E-mail: guoyang@nju.edu.cn [Key Laboratory of Solar Activity, National Astronomical Observatories, Chinese Academy of Sciences, Beijing 100012 (China)

    2017-05-01

    We study the writhe, twist, and magnetic helicity of different magnetic flux ropes, based on models of the solar coronal magnetic field structure. These include an analytical force-free Titov–Démoulin equilibrium solution, non-force-free magnetohydrodynamic simulations, and nonlinear force-free magnetic field models. The geometrical boundary of the magnetic flux rope is determined by the quasi-separatrix layer and the bottom surface, and the axis curve of the flux rope is determined by its overall orientation. The twist is computed by the Berger–Prior formula, which is suitable for arbitrary geometry and both force-free and non-force-free models. The magnetic helicity is estimated by the twist multiplied by the square of the axial magnetic flux. We compare the obtained values with those derived by a finite volume helicity estimation method. We find that the magnetic helicity obtained with the twist method agrees with the helicity carried by the purely current-carrying part of the field within uncertainties for most test cases. It is also found that the current-carrying part of the model field is relatively significant at the very location of the magnetic flux rope. This qualitatively explains the agreement between the magnetic helicity computed by the twist method and the helicity contributed purely by the current-carrying magnetic field.

  19. Scattering bottleneck for spin dynamics in metallic helical antiferromagnetic dysprosium

    Science.gov (United States)

    Langner, M. C.; Roy, S.; Kemper, A. F.; Chuang, Y.-D.; Mishra, S. K.; Versteeg, R. B.; Zhu, Y.; Hertlein, M. P.; Glover, T. E.; Dumesnil, K.; Schoenlein, R. W.

    2015-11-01

    Ultrafast studies of magnetization dynamics have revealed fundamental processes that govern spin dynamics, and the emergence of time-resolved x-ray techniques has extended these studies to long-range spin structures that result from interactions with competing symmetries. By combining time-resolved resonant x-ray scattering and ultrafast magneto-optical Kerr studies, we show that the dynamics of the core spins in the helical magnetic structure occur on much longer time scales than the excitation of conduction electrons in the lanthanide metal Dy. The observed spin behavior differs markedly from that observed in the ferromagnetic phase of other lanthanide metals or transition metals and is strongly dependent on temperature and excitation fluence. This unique behavior results from coupling of the real-space helical spin structure to the shape of the conduction electron Fermi surface in momentum space, which creates a bottleneck in spin scattering events that transfer the valence excitation to the core spins. The dependence of the dynamics on the intersite interactions renders the helical ordering much more robust to perturbations than simple ferromagnetic or antiferromagnetic ordering, where dynamics are driven primarily by on-site interactions.

  20. Seismic analysis of a helical coil type heat exchanger

    International Nuclear Information System (INIS)

    Nishiguchi, I.; Baba, O.; Yatabe, H.

    1984-01-01

    The intermediate heat exchanger (IHX) which forms the reactor coolant pressure boundary is one of the most important components of the Multi-purpose Experimental Very High Temperature Gas-cooled Reactor (ex. VHTR) under development at Japan Atomic Energy Research Institute. This paper presents the results of the finite element modeling, eigenvalue analysis and dynamic response analysis of the IHX. For the modeling, the structure of the IHX was separated into a helical tube bundle, inner and outer vessels, and a center pipe. The eigenvalue analysis was made for each structure with a detailed three-dimensional finite element model. Then the simplified model of the whole structure of the IHX was constructed using the result of the eigenvalue analysis. A dynamic response analysis was made for the simplified model with and without stoppers of the helical tube bundle supports and the center pipe. The effect of stoppers on the behavior of the center pipe, the helical tube, and the connecting tube is discussed. (author)

  1. Optimization of the AGS superconducting helical partial snake strength

    International Nuclear Information System (INIS)

    Lin, F.; Huang, H.; Luccio, A.U.; Roser, T.

    2008-01-01

    Two helical partial snakes, one super-conducting (a.k.a cold snake) and one normal conducting (a.k.a warm snake), have preserved the polarization of proton beam up to 65% in the Brookhaven Alternating Gradient Synchrotron (AGS) at the extraction energy from 85% at injection. In order to overcome spin resonances, stronger partial snakes would be required. However, the stronger the partial snake, the more the stable spin direction tilted producing a stronger horizontal intrinsic resonance. The balance between increasing the spin tune gap generated by the snakes and reducing the tilted stable spin direction has to be considered to maintain the polarization. Because the magnetic field of the warm snake has to be a constant, only the cold snake with a maximum 3T magnetic field can be varied to find out the optimum snake strength. This paper presents simulation results by spin tracking with different cold snake magnetic fields. Some experimental data are also analyzed

  2. Evidence for Mixed Helicity in Erupting Filaments

    Science.gov (United States)

    Muglach, K.; Wang, Y.-M.; Kliem, B.

    2009-09-01

    Erupting filaments are sometimes observed to undergo a rotation about the vertical direction as they rise. This rotation of the filament axis is generally interpreted as a conversion of twist into writhe in a kink-unstable magnetic flux rope. Consistent with this interpretation, the rotation is usually found to be clockwise (as viewed from above) if the post-eruption arcade has right-handed helicity, but counterclockwise if it has left-handed helicity. Here, we describe two non-active-region filament events recorded with the Extreme-Ultraviolet Imaging Telescope on the Solar and Heliospheric Observatory in which the sense of rotation appears to be opposite to that expected from the helicity of the post-event arcade. Based on these observations, we suggest that the rotation of the filament axis is, in general, determined by the net helicity of the erupting system, and that the axially aligned core of the filament can have the opposite helicity sign to the surrounding field. In most cases, the surrounding field provides the main contribution to the net helicity. In the events reported here, however, the helicity associated with the filament "barbs" is opposite in sign to and dominates that of the overlying arcade.

  3. Stable and High OSNR Compound Linear-Cavity Single-Longitudinal-Mode Erbium-Doped Silica Fiber Laser Based on an Asymmetric Four-Cavity Structure

    International Nuclear Information System (INIS)

    Feng Ting; Yan Feng-Ping; Li Qi; Peng Wan-Jing; Feng Su-Chun; Wen Xiao-Dong; Tan Si-Yu; Liu Peng

    2012-01-01

    We propose a stable and high optical signal-to-noise ratio (OSNR) compound linear-cavity single-longitudinal-mode (SLM) erbium-doped silica fiber laser. It consists of three uniform fiber Bragg gratings (FBGs) and two fiber couplers to form a simple asymmetric four-cavity structure to select the longitudinal mode. The stable SLM operation at the wavelength of 1544.053 nm with a 3 dB bandwidth of 0.014 nm and an OSNR of ∼60 dB was verified experimentally. Under laboratory conditions, a power fluctuation performance of less than 0.05 dB for 5 h and wavelength variation of less than 0.01 nm for about 150 min is demonstrated. Finally, the characteristic of laser output power as a function of pump power is investigated. The proposed system provides a simple and cost-effective approach to realize a stable SLM fiber laser

  4. Fluid motion and mixing in helical static mixers

    Science.gov (United States)

    Jones, S. Casey; Sotiropoulos, Fotis

    2001-11-01

    Helical static mixers are used for mixing in a variety of industrial settings under a wide range of flow conditions. To obtain a more fundamental understanding of how these mixers operate, a detailed computational fluid dynamics model study of the helical static mixer was performed using a second-order accurate method for solving the incompressible Navier-Stokes equations on fine computational grids. We investigate the fluid structure in the mixers as a function the Reynolds number and the number of mixer elements. The Reynolds number was varied from 100 to 500, and the number of elements was varied from two to six. Mixing was investigated by applying dynamical systems techniques to the trajectories of a large number of particles released from the inlet of the mixer. We also consider closely two numerical issues: the length of the inlet and outlet sections attached to the mixer and the periodicity of the flow field within the mixer sections.

  5. Organocatalyzed Asymmetric Synthesis of Axially, Planar, and Helical Chiral Compounds.

    Science.gov (United States)

    Shirakawa, Seiji; Liu, Shiyao; Kaneko, Shiho

    2016-02-04

    Axially, planar, and helical chiral compounds are indispensable building blocks in modern organic synthesis. A wide variety of chiral ligands and catalysts were designed based on these chiral scaffolds, and these chiral ligands and catalysts were used for various catalytic asymmetric transformations to produce important chiral compounds in an optically enriched form. Furthermore, these chiral skeletons are found in the structure of biologically active natural products. Thus, the development of efficient enantioselective methods for the synthesis of these chiral compounds is an important task in the field of organic chemistry. In the last few years, organocatalyzed approaches, which are one of the most reliable catalytic asymmetric methods, became a hot topic. This Focus Review summarizes asymmetric organocatalytic methods for the synthesis of axially, planar, and helical chiral compounds as useful chiral building blocks. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. Small-x Asymptotics of the Quark Helicity Distribution.

    Science.gov (United States)

    Kovchegov, Yuri V; Pitonyak, Daniel; Sievert, Matthew D

    2017-02-03

    We construct a numerical solution of the small-x evolution equations derived in our recent work [J. High Energy Phys. 01 (2016) 072.JHEPFG1029-847910.1007/JHEP01(2016)072] for the (anti)quark transverse momentum dependent helicity TMDs and parton distribution functions (PDFs) as well as the g_{1} structure function. We focus on the case of large N_{c}, where one finds a closed set of equations. Employing the extracted intercept, we are able to predict directly from theory the behavior of the quark helicity PDFs at small x, which should have important phenomenological consequences. We also give an estimate of how much of the proton's spin carried by the quarks may be at small x and what impact this has on the spin puzzle.

  7. MemBrain: improving the accuracy of predicting transmembrane helices.

    Directory of Open Access Journals (Sweden)

    Hongbin Shen

    Full Text Available Prediction of transmembrane helices (TMH in alpha helical membrane proteins provides valuable information about the protein topology when the high resolution structures are not available. Many predictors have been developed based on either amino acid hydrophobicity scale or pure statistical approaches. While these predictors perform reasonably well in identifying the number of TMHs in a protein, they are generally inaccurate in predicting the ends of TMHs, or TMHs of unusual length. To improve the accuracy of TMH detection, we developed a machine-learning based predictor, MemBrain, which integrates a number of modern bioinformatics approaches including sequence representation by multiple sequence alignment matrix, the optimized evidence-theoretic K-nearest neighbor prediction algorithm, fusion of multiple prediction window sizes, and classification by dynamic threshold. MemBrain demonstrates an overall improvement of about 20% in prediction accuracy, particularly, in predicting the ends of TMHs and TMHs that are shorter than 15 residues. It also has the capability to detect N-terminal signal peptides. The MemBrain predictor is a useful sequence-based analysis tool for functional and structural characterization of helical membrane proteins; it is freely available at http://chou.med.harvard.edu/bioinf/MemBrain/.

  8. Spin versus helicity in processes involving transversity

    CERN Document Server

    Mekhfi, Mustapha

    2011-01-01

    We construct the spin formalism in order to deal in a direct and natural way with processes involving transversity which are now of increasing popularity. The helicity formalism which is more appropriate for collision processes of definite helicity has been so far used also to manage processes with transversity, but at the price of computing numerous helicity amplitudes generally involving unnecessary kinematical variables.In a second step we work out the correspondence between both formalisms and retrieve in another way all results of the helicity formalism but in simpler forms.We then compute certain processes for comparison.A special process:the quark dipole magnetic moment is shown to be exclusively treated within the spin formalism as it is directly related to the transverse spin of the quark inside the baryon.

  9. 2,6,10-Tris(dialkylamino)-trioxatriangulenium Ions. Synthesis, Structure, and Properties of Exceptionally Stable Carbenium Ions

    DEFF Research Database (Denmark)

    Laursen, Bo W.; Krebs, Frederik C; Nielsen, Merete F.

    1998-01-01

    is expressed as the pK(R+) value, which is determined in strongly basic nonaqueous solution on-the basis of a new acidity function C-. The pK(R+) value of 5a is measured to be 19.7, which is 10 orders of magnitude higher than the values found for the most stable carbenium ions previously reported...

  10. Neutronics investigation of advanced self-cooled liquid blanket systems in helical reactor

    International Nuclear Information System (INIS)

    Tanaka, T.; Sagara, A.; Muroga, T.; Youssef, M.Z.

    2006-10-01

    Neutronics performances of advanced self-cooled liquid blanket systems have been investigated in design activity of the helical-type reactor FFHR2. In the present study, a new three-dimensional (3-D) neutronics calculation system has been developed for the helical-type reactor to enhance quick feedback between neutronics evaluation and design modification. Using this new calculation system, advanced Flibe-cooled and Li-cooled liquid blanket systems proposed for FFHR2 have been evaluated to make clear design issues to enhance neutronics performance. Based on calculated results, modification of the blanket dimensions and configuration have been attempted to achieve the adequate tritium breeding ability and neutron shielding performance in the helical reactor. The total tritium breeding ratios (TBRs) obtained after modifying the blanket dimensions indicated that all the advanced blanket systems proposed for FFHR2 would achieve adequate tritium self-sufficiency by dimension adjustment and optimization of structures in the breeder layers. Issues in neutron shielding performance have been investigated quantitatively using 3-D geometry of the helical blanket system, support structures, poloidal coils etc. Shielding performance of the helical coils against direct neutrons from core plasma would achieve design target by further optimization of shielding materials. However, suppression of the neutron streaming and reflection through the divertor pumping areas in the original design is important issue to protect the poloidal coils and helical coils, respectively. Investigation of the neutron wall loading indicated that the peaking factor of the neutron wall load distribution would be moderated by the toroidal and helical effect of the plasma distribution in the helical reactor. (author)

  11. Dynamics of helicity transport and Taylor relaxation

    International Nuclear Information System (INIS)

    Diamond, P.H.; Malkov, M.

    2003-01-01

    A simple model of the dynamics of Taylor relaxation is derived using symmetry principles alone. No statistical closure approximations are invoked or detailed plasma model properties assumed. Notably, the model predicts several classes of nondiffusive helicity transport phenomena, including traveling nonlinear waves and superdiffusive turbulent pulses. A universal expression for the scaling of the effective magnetic Reynolds number of a system undergoing Taylor relaxation is derived. Some basic properties of intermittency in helicity transport are examined

  12. Lumineszierende zweikernig dreisträngige Helicate

    OpenAIRE

    Schmid, Sören

    2005-01-01

    Luminescent triple-stranded dinuclear helicates The building of systems showing a special function or a property that makes them suitable for the preparation of functional materials will become more and more important in the next years. Based on the "bottom-up approach" supramolecular chemistry can play an important part on this field. This work deals with the building and examination of triple-stranded dinuclear helicates. By using special ligand systems and metals, it its possible to give t...

  13. Intrahepatic arterioportal shunt: helical CT findings

    Energy Technology Data Exchange (ETDEWEB)

    Quiroga, S.; Sebastia, M.C.; Moreiras, M.; Pallisa, E.; Rius, J.M.; Alvarez-Castells, A. [I. D. I. Hospital General i Universitari Vall d`Hebron, Barcelona (Spain). Servei de Radiodiagnostic

    1999-08-01

    The purpose of this study was to characterize the appearance of intrahepatic arterioportal shunts (APS) on two-phase helical CT, with emphasis on the importance of the hepatic arterial-dominant phase (HAP) to demonstrate perfusion disorders. We review eight cases of APS diagnosed by helical CT in our institution from January 1996 to March 1997 and describe the CT findings that established diagnosis. Five of them were confirmed by angiography. In seven (87.5 %) cases of APS we found early enhancement of the peripheral portal branches during the HAP of helical CT, whereas the superior mesenteric and splenic veins remained unenhanced. In five (62.5 %) cases of APS, transient, peripheral, triangular parenchymal enhancement was depicted during the HAP of helical CT; in four of these cases there was associated early enhancement of the portal branches. Helical CT can show perfusion alterations that might remain undiagnosed with conventional CT. An understanding of the hemodynamic changes that occur in APS can help in the interpretation of focal transient hepatic parenchymal enhancement and to differentiate APS from hypervascular tumors. We believe that the helical CT findings described herein are characteristic enough to suggest the diagnosis of APS. (orig.) With 3 figs., 1 tab., 16 refs.

  14. Towards online patient imaging during helical radiotherapy

    International Nuclear Information System (INIS)

    Yu, L.; Lancaster, C.M.; Sylvander, S.R.; Poole, C.M.

    2015-01-01

    Exit-detector data from helical radiation therapy have been studied extensively for delivery verification and dose reconstruction. Since the same radiation source is used for both imaging and treatment, this work investigates the possibility of utilising exit-detector raw data for imaging purposes. This gives rise to potential clinical applications such as retrospective daily setup verification and inter-fractional setup error detection. The exit-detector raw data were acquired and independently analysed using Python programming language. The raw data were extracted from the treatment machine’s onboard computer, and converted into 2D array files. The contours of objects (phantom or patient) were acquired by applying a logarithmic function to the ratio of two sinograms, one with the object in the beam and one without. The setup variation between any two treatment deliveries can be detected by applying the same function to their corresponding exit-detector sinograms. The contour of the object was well defined by the secondary radiation from the treatment beam and validated with the imaging beam, although no internal structures were discernible due to the interference from the primary radiation. The sensitivity of the setup variation detection was down to 2 mm, which was mainly limited by the resolution of the exit-detector itself. The exit-detector data from treatment procedures contain valuable photon exit fluence maps which can be utilised for contour definition and verification of patient alignment without reconstruction.

  15. Flexibility of LHD configuration with multi-layer helical coils

    Energy Technology Data Exchange (ETDEWEB)

    Ichiguchi, Katsuji; Motojima, Osamu; Yamazaki, Kozo; Nakajima, Noriyoshi; Okamoto, Masao

    1995-11-01

    The Large Helical Device (LHD) is a heliotron device with two helical coils, each of which has a structure of three current layers. It is designed so that the current in each layer should be controlled independently. By changing the combination of the coil current in the layers, it is possible to vary the effective minor radius of the helical coils, which enlarges the flexibility of the configuration. The properties of the plasmas for several combinations of the layers are investigated numerically. In the vacuum configuration, it is obtained that the combination of the layers corresponding to a large effective coil radius has a large outermost surface. In this case, the rotational transform decreases and the magnetic hill is reduced compared with the configuration with all three layers. The large Shafranov shift which is due to the small rotational transform enhances the magnetic well and the magnetic shear to stabilize the Mercier mode, however, it degrades the equilibrium beta limit. In the case of the combination for a small effective coil radius, the Mercier mode is destabilized, because the magnetic hill is enhanced. The effect on the bootstrap current is also studied. (author).

  16. Acousto-optical and SAW propagation characteristics of temperature stable multilayered structures based on LiNbO3 and diamond

    International Nuclear Information System (INIS)

    Shandilya, Swati; Sreenivas, K; Gupta, Vinay

    2008-01-01

    Theoretical studies on the surface acoustic wave (SAW) properties of c-axis oriented LiNbO 3 /IDT/diamond and diamond/IDT/128 0 rotated Y-X cut LiNbO 3 multilayered structures have been considered. Both layered structures exhibit a positive temperature coefficient of delay (TCD) characteristic, and a zero TCD device is obtained after integrating with an over-layer of either tellurium dioxide (TeO 2 ) or silicon dioxide (SiO 2 ). The presence of a TeO 2 over-layer enhanced the electromechanical coupling coefficients of both multilayered structures, which acts as a better temperature compensation layer than SiO 2 . The temperature stable TeO 2 /LiNbO 3 /IDT/diamond layered structure exhibits good electromechanical coefficient and higher phase velocity for SAW device applications. On the other hand, a high acousto-optical (AO) figure of merit (30-37) x 10 -15 s 3 kg -1 has been obtained for the temperature stable SiO 2 /diamond/IDT/LiNbO 3 layered structure indicating a promising device structure for AO applications

  17. Stable structures of Al510–800 clusters and lowest energy sequence of truncated octahedral Al clusters up to 10,000 atoms

    International Nuclear Information System (INIS)

    Wu, Xia; He, Chengdong

    2012-01-01

    Highlights: ► The stable structures of Al 510–800 clusters are obtained with the NP-B potential. ► Al 510–800 clusters adopt truncated octahedral (TO) growth pattern based on complete TOs at Al 405 , Al 586 , and Al 711 . ► The lowest energy sequence of complete TOs up to the size 10,000 is proposed. -- Abstract: The stable structures of Al 510–800 clusters are obtained using dynamic lattice searching with constructed cores (DLSc) method by the NP-B potential. According to the structural growth rule, octahedra and truncated octahedra (TO) configurations are adopted as the inner cores in DLSc method. The results show that in the optimized structures two complete TO structures are found at Al 586 and Al 711 . Furthermore, Al 510–800 clusters adopt TO growth pattern on complete TOs at Al 405 , Al 586 , and Al 711 , and the configurations of the surface atoms are investigated. On the other hand, Al clusters with complete TO motifs are studied up to the size 10,000 by the geometrical construction method. The structural characteristics of complete TOs are denoted by the term “family”, and the growth sequence of Al clusters is investigated. The lowest energy sequence of complete TOs is proposed.

  18. Revisiting the Helical Cooperativity of Synthetic Polypeptides in Solution.

    Science.gov (United States)

    Ren, Yuan; Baumgartner, Ryan; Fu, Hailin; van der Schoot, Paul; Cheng, Jianjun; Lin, Yao

    2017-08-14

    Using synthetic polypeptides as a model system, the theories of helix-coil transition were developed into one of the most beautiful and fruitful subjects in macromolecular science. The classic models proposed by Schellman and Zimm-Bragg more than 50 years ago, differ in the assumption on whether the configuration of multiple helical sequences separated by random coil sections is allowed in a longer polypeptide chain. Zimm also calculated the critical chain lengths that facilitate such interrupted helices in different solvent conditions. The experimental validation of Zimm's prediction, however, was not carefully examined at that time. Herein, we synthesize a series of homopolypeptide samples with different lengths, to systematically examine their helix-coil transition and folding cooperativity in solution. We find that for longer chains, polypeptides do exist as interrupted helices with scattered coil sections even in helicogenic solvent conditions, as predicted in the Zimm-Bragg model. The critical chain lengths that facilitate such interrupted helices, however, are substantially smaller than Zimm's original estimation. The inaccuracy is in part due to an approximation that Zimm made in simplifying the calculation. But more importantly, we find there exist intramolecular interactions between different structural segments in the longer polypeptides, which are not considered in the classic helix-coil theories. As such, even the Zimm-Bragg model in its exact form cannot fully describe the transition behavior and folding cooperativity of longer polypeptides. The results suggest that long "all-helix" chains may be much less prevalent in solution than previously imagined, and a revised theory is required to accurately account for the helix-coil transition of the longer chains with potential "non-local" intramolecular interactions.

  19. Stable isotope studies

    International Nuclear Information System (INIS)

    Ishida, T.

    1992-01-01

    The research has been in four general areas: (1) correlation of isotope effects with molecular forces and molecular structures, (2) correlation of zero-point energy and its isotope effects with molecular structure and molecular forces, (3) vapor pressure isotope effects, and (4) fractionation of stable isotopes. 73 refs, 38 figs, 29 tabs

  20. Use of reconstructed 3D equilibria to determine onset conditions of helical cores in tokamaks for extrapolation to ITER

    Science.gov (United States)

    Wingen, A.; Wilcox, R. S.; Seal, S. K.; Unterberg, E. A.; Cianciosa, M. R.; Delgado-Aparicio, L. F.; Hirshman, S. P.; Lao, L. L.

    2018-03-01

    Large, spontaneous m/n  =  1/1 helical cores are shown to be expected in tokamaks such as ITER with extended regions of low- or reversed- magnetic shear profiles and q near 1 in the core. The threshold for this spontaneous symmetry breaking is determined using VMEC scans, beginning with reconstructed 3D equilibria from DIII-D and Alcator C-Mod based on observed internal 3D deformations. The helical core is a saturated internal kink mode (Wesson 1986 Plasma Phys. Control. Fusion 28 243); its onset threshold is shown to be proportional to (dp/dρ)/B_t2 around q  =  1. Below the threshold, applied 3D fields can drive a helical core to finite size, as in DIII-D. The helical core size thereby depends on the magnitude of the applied perturbation. Above it, a small, random 3D kick causes a bifurcation from axisymmetry and excites a spontaneous helical core, which is independent of the kick size. Systematic scans of the q-profile show that the onset threshold is very sensitive to the q-shear in the core. Helical cores occur frequently in Alcator C-Mod during ramp-up when slow current penetration results in a reversed shear q-profile, which is favorable for helical core formation. Finally, a comparison of the helical core onset threshold for discharges from DIII-D, Alcator C-Mod and ITER confirms that while DIII-D is marginally stable, Alcator C-Mod and especially ITER are highly susceptible to helical core formation without being driven by an externally applied 3D magnetic field.

  1. Microbunch preserving in-line system for an APPLE II helical radiator at the LCLS baseline

    International Nuclear Information System (INIS)

    Geloni, Gianluca; Kocharyan, Vitali; Saldin, Evgeni

    2011-05-01

    In a previous work we proposed a scheme for polarization control at the LCLS baseline, which exploited the microbunching from the planar undulator. After the baseline undulator, the electron beam is transported through a drift by a FODO focusing system, and through a short helical radiator. The microbunching structure can be preserved, and intense coherent radiation is emitted in the helical undulator at fundamental harmonic. The driving idea of this proposal is that the background linearly-polarized radiation from the baseline undulator is suppressed by spatial filtering. Filtering is achieved by letting radiation and electron beam through Be slits upstream of the helical radiator, where the radiation spot size is about ten times larger than the electron beam transverse size. Several changes considered in the present paper were made to improve the previous design. Slits are now placed immediately behind the helical radiator. The advantage is that the electron beam can be spoiled by the slits, and narrower slits width can be used for spatial filtering. Due to this fundamental reason, the present setup is shorter than the previous one. The helical radiator is now placed immediately behind the SHAB undulator. It is thus sufficient to use the existing FODO focusing system of the SHAB undulator for transporting themodulated electron beam. This paper presents complete GENESIS code calculations for the new design, starting from the baseline undulator entrance up to the helical radiator exit including the modulated electron beam transport by the SHAB FODO focusing system. (orig.)

  2. Hydrogen recycling and transport in the helical divertor of TEXTOR

    Energy Technology Data Exchange (ETDEWEB)

    Clever, Meike

    2010-07-01

    The aim of this thesis was to investigate the hydrogen recycling at the target plates of the helical divertor in TEXTOR and by this the capability of this divertor configuration to access such favourable operational regimes. In order to study the different divertor density regimes in TEXTOR, discharges were performed in which the total plasma density was increased continuously up to the density limit. The recycling was investigated in a fixed helical divertor structure where four helical strike points with a poloidal width of about 8-10 cm are created at the divertor target plates. The experimental investigation of the hydrogen recycling was carried out using mainly spectroscopic methods supplemented by Langmuir probe, interferometric and atomic beam measurements. In the framework of this thesis a spectroscopic multi camera system has been built that facilitates the simultaneous observation of four different spectral lines, recording images of the divertor target plates and the plasma volume close to the target. The system facilitates the simultaneous measurement of the poloidal and toroidal pattern of the recycling flux at the divertor target without the need for sweeping the plasma structure. The simultaneous observation of different spectral lines reduces the uncertainty in the analysis based on several lines, as the contribution from uncertainties in the reproducibility of plasma parameters in different discharges are eliminated and only the uncertainty of the measurement method limits the accuracy. The spatial resolution of the system in poloidal and toroidal direction (0.8 mm{+-}0.01 mm) is small compared to the separation of the helical strike points, the capability of the measurement method to resolve these structures is therefore limited by the line-of-sight integration and the penetration depth of the light emitting species. The measurements showed that the recycling flux increases linearly with increasing plasma density, a high recycling regime is not

  3. Hydrogen recycling and transport in the helical divertor of TEXTOR

    International Nuclear Information System (INIS)

    Clever, Meike

    2010-01-01

    The aim of this thesis was to investigate the hydrogen recycling at the target plates of the helical divertor in TEXTOR and by this the capability of this divertor configuration to access such favourable operational regimes. In order to study the different divertor density regimes in TEXTOR, discharges were performed in which the total plasma density was increased continuously up to the density limit. The recycling was investigated in a fixed helical divertor structure where four helical strike points with a poloidal width of about 8-10 cm are created at the divertor target plates. The experimental investigation of the hydrogen recycling was carried out using mainly spectroscopic methods supplemented by Langmuir probe, interferometric and atomic beam measurements. In the framework of this thesis a spectroscopic multi camera system has been built that facilitates the simultaneous observation of four different spectral lines, recording images of the divertor target plates and the plasma volume close to the target. The system facilitates the simultaneous measurement of the poloidal and toroidal pattern of the recycling flux at the divertor target without the need for sweeping the plasma structure. The simultaneous observation of different spectral lines reduces the uncertainty in the analysis based on several lines, as the contribution from uncertainties in the reproducibility of plasma parameters in different discharges are eliminated and only the uncertainty of the measurement method limits the accuracy. The spatial resolution of the system in poloidal and toroidal direction (0.8 mm±0.01 mm) is small compared to the separation of the helical strike points, the capability of the measurement method to resolve these structures is therefore limited by the line-of-sight integration and the penetration depth of the light emitting species. The measurements showed that the recycling flux increases linearly with increasing plasma density, a high recycling regime is not

  4. Helicity Transformation under the Collision and Merging of Magnetic Flux Ropes

    Science.gov (United States)

    Dehaas, Timothy

    2016-10-01

    A magnetic flux rope is a tube-like, current carrying plasma embedded in an external magnetic field. The magnetic field lines resemble threads in a rope, which vary in pitch according to radius. Flux ropes are ubiquitous in astrophysical plasmas, and bundles of these structures play an important role in the dynamics of the space environment. They are observed in the solar atmosphere and near-earth environment where they are seen to twist, merge, tear, and writhe. In this MHD context, their global dynamics are bound by rules of magnetic helicity conservation, unless, under a non-ideal process, helicity is transformed through magnetic reconnection, turbulence, or localized instabilities. These processes are tested under experimental conditions in the Large Plasma Device (LAPD). The device is a twenty-meter long, one-meter diameter, cylindrical vacuum vessel designed to generate a highly reproducible, magnetized plasma. Reliable shot-to-shot repetition of plasma parameters and over four hundred diagnostic ports enable the collection of volumetric datasets (measurements of ne, Te, Vp, B, J, E, uflow) as two kink-unstable flux ropes form, move, collide, and merge. Similar experiments on the LAPD have utilized these volumetric datasets, visualizing magnetic reconnection through a topological quasi-separatrix layer, or QSL. This QSL is shown to be spatially coincident with the reconnection rate, ∫ E . dl , and oscillates (although out of phase) with global helicity. Magnetic helicity is observed to have a negative sign and its counterpart, cross helicity, a positive one. These quantities oscillate 8% peak-to-peak, and the changes in helicity are visualized as 1) the transport of helicity (ϕB + E × A) and 2) the dissipation of the helicity - 2 E . B . This work is supported by LANL-UC research Grant and done at the Basic Plasma Science Facility, which is funded by DOE and NSF.

  5. SU-E-T-197: Helical Cranial-Spinal Treatments with a Linear Accelerator

    Energy Technology Data Exchange (ETDEWEB)

    Anderson, J; Bernard, D; Liao, Y; Templeton, A; Turian, J; Chu, J [Rush University Medical Center, Chicago, IL (United States)

    2014-06-01

    Purpose: Craniospinal irradiation (CSI) of systemic disease requires a high level of beam intensity modulation to reduce dose to bone marrow and other critical structures. Current helical delivery machines can take 30 minutes or more of beam-on time to complete these treatments. This pilot study aims to test the feasibility of performing helical treatments with a conventional linear accelerator using longitudinal couch travel during multiple gantry revolutions. Methods: The VMAT optimization package of the Eclipse 10.0 treatment planning system was used to optimize pseudo-helical CSI plans of 5 clinical patient scans. Each gantry revolution was divided into three 120° arcs with each isocenter shifted longitudinally. Treatments requiring more than the maximum 10 arcs used multiple plans with each plan after the first being optimized including the dose of the others (Figure 1). The beam pitch was varied between 0.2 and 0.9 (couch speed 5- 20cm/revolution and field width of 22cm) and dose-volume histograms of critical organs were compared to tomotherapy plans. Results: Viable pseudo-helical plans were achieved using Eclipse. Decreasing the pitch from 0.9 to 0.2 lowered the maximum lens dose by 40%, the mean bone marrow dose by 2.1% and the maximum esophagus dose by 17.5%. (Figure 2). Linac-based helical plans showed dose results comparable to tomotherapy delivery for both target coverage and critical organ sparing, with the D50 of bone marrow and esophagus respectively 12% and 31% lower in the helical linear accelerator plan (Figure 3). Total mean beam-on time for the linear accelerator plan was 8.3 minutes, 54% faster than the tomotherapy average for the same plans. Conclusions: This pilot study has demonstrated the feasibility of planning pseudo-helical treatments for CSI targets using a conventional linac and dynamic couch movement, and supports the ongoing development of true helical optimization and delivery.

  6. Application of Nitrogen and Carbon Stable Isotopes (δ15N and δ13C) to Quantify Food Chain Length and Trophic Structure

    OpenAIRE

    Perkins, Matthew J.; McDonald, Robbie A.; van Veen, F. J. Frank; Kelly, Simon D.; Rees, Gareth; Bearhop, Stuart

    2014-01-01

    Increasingly, stable isotope ratios of nitrogen (δ(15)N) and carbon (δ(13)C) are used to quantify trophic structure, though relatively few studies have tested accuracy of isotopic structural measures. For laboratory-raised and wild-collected plant-invertebrate food chains spanning four trophic levels we estimated nitrogen range (NR) using δ(15)N, and carbon range (CR) using δ(13)C, which are used to quantify food chain length and breadth of trophic resources respectively. Across a range of kn...

  7. Piecewise Phototuning of Self-Organized Helical Superstructures.

    Science.gov (United States)

    Qin, Lang; Gu, Wei; Wei, Jia; Yu, Yanlei

    2018-02-01

    Cholesteric liquid crystals (CLCs) exhibit selective reflection that can be tuned owing to the dynamic control of inherent self-organized helical superstructures. Although phototunable reflection is reported, these systems hitherto suffer from a limitation in that the tuning range is restricted to one narrow period and the optically addressed images have to sacrifice one color in the visible spectrum to serve as the background, resulting from the insufficient variation in helical twisting power of existing photoresponsive chiral switches that are all bistable. Here, delicate patterns of three primary red, green, and blue (RGB) colors with a black background are presented, which is realized based on piecewise reflection tuning of the CLC induced by a newly designed photoresponsive tristable chiral switch. Three stable configurations of the chiral switch endow the CLC with two continuous and adjacent tuning periods of the reflection, covering not only entire visible spectrum, but also one more wide period within near-infrared region. Therefore, the concept of piecewise tuning in CLC system demonstrates a new strategy for phototunable RGB and black reflective display. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. Sulfono-g-AApeptides as a New Class of Nonnatural Helical Foldamer

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Haifan; Qiao, Qiao; Hu, Yaogang; Teng, Peng; Gao, Wenyang; Zuo, Xiaobing; Wojtas, Lukasz; Larsen, Randy W.; Ma, Shengqian; Cai, Jianfeng

    2015-02-02

    Foldamers offer an attractive opportunity for the design of novel molecules that mimic the structures and functions of proteins and enzymes including biocatalysis and biomolecular recognition. Herein we report a new class of nonnatural helical sulfono-g-AApeptide foldamers of varying lengths. The crystal structure of the sulfono-g-AApeptide monomer S6 illustrates the intrinsic folding propensity of sulfono-g-AApeptides, which likely originates from the bulkiness of tertiary sulfonamide moiety. The two-dimensional solution NMR spectroscopy data for the longest sequence S1 demonstrates a 10/16 right-handed helical structure. Optical analysis using circular dichroism further supports welldefined helical conformation of sulfono-g-AApeptides in solution containing as few as five building blocks. Future development of sulfono-g-AApeptides may lead to new foldamers with discrete functions, enabling expanded application in chemical biology and biomedical sciences.

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

    Science.gov (United States)

    Yamchi, Mahdi Zaeifi; Bowles, Richard K.

    2015-07-01

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

  10. Fabrication and experimentation of FRP helical spring

    Science.gov (United States)

    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.

  11. Synthesis and characterization of highly efficient and stable Pr6O11/Ag3PO4/Pt ternary hybrid structure

    International Nuclear Information System (INIS)

    Deng, Jiatao; Liu, Lin; Niu, Tongjun; Sun, Xiaosong

    2017-01-01

    Highlights: • Visible-light-driven Pr 6 O 11 /Ag 3 PO 4 /Pt photocatalysts were prepared. • Pr 6 O 11 /Ag 3 PO 4 /Pt showed highly efficient and stable photocatalystic activity. • The photocatalytic mechanism of Pr 6 O 11 /Ag 3 PO 4 /Pt composite was given. - Abstract: Ag 3 PO 4 is an excellent photocatalyst with high efficiency and quantum yield, but suffers from the fast recombination of photogenerated electron-hole pairs and photo-corrosion. Hereby, the highly efficient and stable visible-light-driven Pr 6 O 11 /Ag 3 PO 4 /Pt photocatalyst were prepared via a three-step wet chemical approach. The as-prepared Pr 6 O 11 /Ag 3 PO 4 /Pt composite was characterized by X-ray diffraction, US-vis diffuse reflectance spectroscopy, scanning electron microscopy, transmission electron microscopy, X-ray photoelectron spectroscopy, photoluminescence spectra and transient photocurrent as well. Comparing with single Pr 6 O 11 or Ag 3 PO 4 , the prepared Pr 6 O 11 /Ag 3 PO 4 /Pt composite exhibited much higher photocatalytic activity and stability for the degradation of Rhodamine B under visible light irradiation (>420 nm). The enhanced photocatalytic performance of Pr 6 O 11 /Ag 3 PO 4 /Pt composite has been attributed to the efficient separation of photo-generated electron-hole pairs through a scheme system composed of Pr 6 O 11, Ag 3 PO 4 and Pt.

  12. Highly stable new organic-inorganic perovskite (CH₃NH₃)₂PdBr₄: synthesis, structure and physical properties.

    Science.gov (United States)

    Liu, Xixia; Huang, Tang Jiao; Zhang, Liuyang; Tang, Baoshan; Zhang, Nengduo; Shi, Diwen; Gong, Hao

    2018-01-11

    Lead halide perovskite has attracted striking attention recently due to their appealing properties. However, toxicity and stability are two main factors restricting its application. In this work, we experimentally synthesized less toxic and highly stable Pd-based hybrid perovskite after exploring different experimental conditions. This new hybrid organic-inorganic perovskite (CH₃NH₃)₂PdBr₄ was found to be an orthorhombic crystal (Cmce, Z=4) with lattice parameters a=8.00 Å, b=7.99 Å, c= 18.89 Å. The Cmce symmetry and lattices parameters were confirmed using Pawley refinement. The atoms positions were testified based on DFT calculation. This perovskite compound was determined to be a p-type semiconductor, with a resistivity of 102.9 kΩ*cm, a carrier concentration of 3.4 ×1012 /cm³ and a mobility of 23.4 cm² /(V*S). Interestingly, XRD and UV-vis measurements indicated that the phase of this new perovskite was maintained with an optical gap of 1.91 eV after leaving in air with a high humidity of 60% for 4 days, and unchanged for months in N₂ ambiance, much more stable than most existing organic-inorganic perovskites. The synthesis and various characterizations of this work further the understanding of this (CH₃NH₃)₂PdBr₄ organic-inorganic hybrid perovskite material. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. Stable particles

    International Nuclear Information System (INIS)

    Samios, N.P.

    1994-01-01

    I have been asked to review the subject of stable particles, essentially the particles that eventually comprised the meson and baryon octets, with a few more additions - with an emphasis on the contributions made by experiments utilizing the bubble chamber technique. In this activity, much work had been done by the photographic emulsion technique and cloud chambers - exposed to cosmic rays as well as accelerator based beams. In fact, many if not most of the stable particles were found by these latter two techniques, however, the foree of the bubble chamber (coupled with the newer and more powerful accelerators) was to verify, and reinforce with large statistics, the existence of these states, to find some of the more difficult ones, mainly neutrals and further to elucidate their properties, i.e., spin, parity, lifetimes, decay parameters, etc. (orig.)

  14. Stable particles

    International Nuclear Information System (INIS)

    Samios, N.P.

    1993-01-01

    I have been asked to review the subject of stable particles, essentially the particles that eventually comprised the meson and baryon octets. with a few more additions -- with an emphasis on the contributions made by experiments utilizing the bubble chamber technique. In this activity, much work had been done by the photographic emulsion technique and cloud chambers-exposed to cosmic rays as well as accelerator based beams. In fact, many if not most of the stable particles were found by these latter two techniques, however, the forte of the bubble chamber (coupled with the newer and more powerful accelerators) was to verify, and reinforce with large statistics, the existence of these states, to find some of the more difficult ones, mainly neutrals and further to elucidate their properties, i.e., spin, parity, lifetimes, decay parameters, etc

  15. Conformational Changes in Two Inter-Helical Loops of Mhp1 Membrane Transporter.

    Directory of Open Access Journals (Sweden)

    Hyun Deok Song

    Full Text Available Mhp1 is a bacterial secondary transporter with high-resolution crystal structures available for both the outward- and inward-facing conformations. Through molecular dynamics simulations of the ligand-free Mhp1 as well as analysis of its crystal structures, here we show that two inter-helical loops, respectively located at the extra- and intracellular ends of the "hash motif" in the protein, play important roles in the conformational transition. In the outward- and inward-facing states of the protein, the loops adopt different secondary structures, either wrapped to the end of an alpha-helix, or unwrapped to extended conformations. In equilibrium simulations of 100 ns with Mhp1 in explicit lipids and water, the loop conformations remain largely stable. In targeted molecular dynamics simulations with the protein structure driven from one state to the other, the loops exhibit resistance and only undergo abrupt changes when other parts of the protein already approach the target conformation. Free energy calculations on the isolated loops further confirm that the wrapping/unwrapping transitions are associated with substantial energetic barriers, and consist of multiple sequential steps involving the rotation of certain backbone torsion angles. Furthermore, in simulations with the loops driven from one state to the other, a large part of the protein follows the loops to the target conformation. Taken together, our simulations suggest that changes of the loop secondary structures would be among the slow degrees of freedom in the conformational transition of the entire protein. Incorporation of detailed loop structures into the reaction coordinate, therefore, should improve the convergence and relevance of the resulting conformational free energy.

  16. Experiments on helical modes in magnetized thin foil-plasmas

    Science.gov (United States)

    Yager-Elorriaga, David

    2017-10-01

    This paper gives an in-depth experimental study of helical features on magnetized, ultrathin foil-plasmas driven by the 1-MA linear transformer driver at University of Michigan. Three types of cylindrical liner loads were designed to produce: (a) pure magneto-hydrodynamic (MHD) modes (defined as being void of the acceleration-driven magneto-Rayleigh-Taylor instability, MRT) using a non-imploding geometry, (b) pure kink modes using a non-imploding, kink-seeded geometry, and (c) MRT-MHD coupled modes in an unseeded, imploding geometry. For each configuration, we applied relatively small axial magnetic fields of Bz = 0.2-2.0 T (compared to peak azimuthal fields of 30-40 T). The resulting liner-plasmas and instabilities were imaged using 12-frame laser shadowgraphy and visible self-emission on a fast framing camera. The azimuthal mode number was carefully identified with a tracking algorithm of self-emission minima. Our experiments show that the helical structures are a manifestation of discrete eigenmodes. The pitch angle of the helix is simply m / kR , from implosion to explosion, where m, k, and R are the azimuthal mode number, axial wavenumber, and radius of the helical instability. Thus, the pitch angle increases (decreases) during implosion (explosion) as R becomes smaller (larger). We found that there are one, or at most two, discrete helical modes that arise for magnetized liners, with no apparent threshold on the applied Bz for the appearance of helical modes; increasing the axial magnetic field from zero to 0.5 T changes the relative weight between the m = 0 and m = 1 modes. Further increasing the applied axial magnetic fields yield higher m modes. Finally, the seeded kink instability overwhelms the intrinsic instability modes of the plasma. These results are corroborated with our analytic theory on the effects of radial acceleration on the classical sausage, kink, and higher m modes. Work supported by US DOE award DE-SC0012328, Sandia National Laboratories

  17. Helicity antenna showers for hadron colliders

    Energy Technology Data Exchange (ETDEWEB)

    Fischer, Nadine; Skands, Peter [Monash University, School of Physics and Astronomy, Clayton, VIC (Australia); Lifson, Andrew [Monash University, School of Physics and Astronomy, Clayton, VIC (Australia); ETH Zuerich, Zurich (Switzerland)

    2017-10-15

    We present a complete set of helicity-dependent 2 → 3 antenna functions for QCD initial- and final-state radiation. The functions are implemented in the Vincia shower Monte Carlo framework and are used to generate showers for hadron-collider processes in which helicities are explicitly sampled (and conserved) at each step of the evolution. Although not capturing the full effects of spin correlations, the explicit helicity sampling does permit a significantly faster evaluation of fixed-order matrix-element corrections. A further speed increase is achieved via the implementation of a new fast library of analytical MHV amplitudes, while matrix elements from Madgraph are used for non-MHV configurations. A few examples of applications to QCD 2 → 2 processes are given, comparing the newly released Vincia 2.200 to Pythia 8.226. (orig.)

  18. Helicity antenna showers for hadron colliders

    Science.gov (United States)

    Fischer, Nadine; Lifson, Andrew; Skands, Peter

    2017-10-01

    We present a complete set of helicity-dependent 2→ 3 antenna functions for QCD initial- and final-state radiation. The functions are implemented in the Vincia shower Monte Carlo framework and are used to generate showers for hadron-collider processes in which helicities are explicitly sampled (and conserved) at each step of the evolution. Although not capturing the full effects of spin correlations, the explicit helicity sampling does permit a significantly faster evaluation of fixed-order matrix-element corrections. A further speed increase is achieved via the implementation of a new fast library of analytical MHV amplitudes, while matrix elements from Madgraph are used for non-MHV configurations. A few examples of applications to QCD 2→ 2 processes are given, comparing the newly released Vincia 2.200 to Pythia 8.226.

  19. Clinical application of helical CT colonography

    International Nuclear Information System (INIS)

    Zeng Huiliang; Zhu Xinjin; Liang Rujian; Liang Jianhao; Ou Weiqian; Wen Haomao

    2009-01-01

    Objective: To investigate the clinical value of 16-slice helical CT colonography in the diagnosis of colon tumor and polypus. Methods: 16-slice helical CT volumetric scanning was performed in 18 patients with colonic disease, including colonic tumor (n=16) and colonic polypus (n=2). 3D images, virtual endoscopy and multiplanar reformation were obtained in the AW4.1 workstation. CT appearances were compared with operation and fiberoptic colonoscopy. Results: Satisfied results were achieved from 18 patients, no difference found in results between CT colonography and operation in 16 patients with colonic tumor. Conclusion: 16-slice helical CT colonography is of great value in preoperative staging of colonic tumor and have a high value in clinical application. (authors)

  20. Single-superfield helical-phase inflation

    Energy Technology Data Exchange (ETDEWEB)

    Ketov, Sergei V., E-mail: ketov@tmu.ac.jp [Department of Physics, Tokyo Metropolitan University, Minami-ohsawa 1-1, Hachioji-shi, Tokyo 192-0397 (Japan); Kavli Institute for the Physics and Mathematics of the Universe (IPMU), The University of Tokyo, Chiba 277-8568 (Japan); Institute of Physics and Technology, Tomsk Polytechnic University, 30 Lenin Ave., Tomsk 634050 (Russian Federation); Terada, Takahiro, E-mail: takahiro@hep-th.phys.s.u-tokyo.ac.jp [Department of Physics, The University of Tokyo, Tokyo 113-0033 (Japan); Deutsches Elektronen-Synchrotron (DESY), 22607 Hamburg (Germany)

    2016-01-10

    Large-field inflation in supergravity requires the approximate global symmetry needed to protect flatness of the scalar potential. In helical-phase inflation, the U(1) symmetry of the Kähler potential is assumed, the phase part of the complex scalar of a chiral superfield plays the role of inflaton, and the radial part is strongly stabilized. The original model of helical phase inflation, proposed by Li, Li and Nanopoulos (LLN), employs an extra (stabilizer) superfield. We propose a more economical new class of the helical phase inflationary models without a stabilizer superfield. As the specific examples, the quadratic, the natural, and the Starobinsky-type inflationary models are studied in our approach.

  1. Neutrino's helicity in a gravitational field

    International Nuclear Information System (INIS)

    Pansart, J.P.

    1996-01-01

    By using approximated solutions of Dirac's equation, we show that there is no helicity reversal for light neutrinos in the Schwarzschild metric nor in an expanding universe. The actual coupling between a particle spin and the angular momentum of a heavy rotating body induces a possible helicity reversal but with an unobservable probability proportional to m 2 p / E 2 , where m p is the particle mass and E its energy. In these calculations, the helicity is defined through the spin orientation with respect to the current and not with respect to the linear momentum. This definition gives simple expressions and is equal to the usual definition in the case of a flat space. (N.T.)

  2. Paranemic Crossover DNA: A Generalized Holliday Structure with Applications in Nanotechnology

    Science.gov (United States)

    Shen, Zhiyong; Yan, Hao; Wang, Tong; Seeman, Nadrian C.

    2013-01-01

    Paranemic crossover (PX) DNA is a four-stranded coaxial DNA structure containing a central dyad axis that relates two flanking parallel double helices. The strands are held together exclusively by Watson-Crick base pairing. The key feature of the structure is that the two adjacent parallel DNA double helices form crossovers at every point possible. Hence, reciprocal crossover points flank the central dyad axis at every major or minor groove separation. This motif has been modeled and characterized in an oligonucleotide system; a minor groove separation of 5 nucleotide pairs and major groove separations of 6, 7, or 8 nucleotide pairs produce stable PX DNA molecules; a major groove separation of 9 nucleotide pairs is possible at low concentrations. Every strand undergoes a crossover every helical repeat (11, 12, 13 or 14 nucleotides), but the structural period of each strand corresponds to two helical repeats (22, 24, 26 or 28 nucleotides). Non-denaturing gel electrophoresis shows that the molecules are stable, forming well-behaved complexes. PX DNA can be produced from closed dumbbells, demonstrating that the molecule is paranemic. Ferguson analysis indicates that the molecules are similar in shape to DNA double crossover molecules. Circular dichroism spectra are consistent with B-form DNA. Thermal transition profiles suggest a premelting transition in each of the molecules. Hydroxyl radical autofootprinting analysis confirms that there is a crossover point at each of the positions expected in the secondary structure. These molecules are generalized Holliday junctions that have applications in nanotechnology. PMID:14871096

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

    Science.gov (United States)

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

    2014-08-01

    Three-dimensional (3D) printing is a fabrication method that enables creation of structures from digital models. Among the different structures fabricated by 3D printing methods, helical microstructures attracted the attention of the researchers due to their potential in different fields such as MEMS, lab-on-a-chip systems, microelectronics and telecommunications. Here we review different types of 3D printing methods capable of fabricating 3D freeform helical microstructures. The techniques including two more common microfabrication methods (i.e., focused ion beam chemical vapour deposition and microstereolithography) and also five methods based on computer-controlled robotic direct deposition of ink filament (i.e., fused deposition modeling, meniscus-confined electrodeposition, conformal printing on a rotating mandrel, UV-assisted and solvent-cast 3D printings) and their advantages and disadvantages regarding their utilization for the fabrication of helical microstructures are discussed. Focused ion beam chemical vapour deposition and microstereolithography techniques enable the fabrication of very precise shapes with a resolution down to ~100 nm. However, these techniques may have material constraints (e.g., low viscosity) and/or may need special process conditions (e.g., vacuum chamber) and expensive equipment. The five other techniques based on robotic extrusion of materials through a nozzle are relatively cost-effective, however show lower resolution and less precise features. The popular fused deposition modeling method offers a wide variety of printable materials but the helical microstructures manufactured featured a less precise geometry compared to the other printing methods discussed in this review. The UV-assisted and the solvent-cast 3D printing methods both demonstrated high performance for the printing of 3D freeform structures such as the helix shape. However, the compatible materials used in these methods were limited to UV-curable polymers and

  4. The peroxisomal receptor Pex19p forms a helical mPTS recognition domain

    OpenAIRE

    Schueller, Nicole; Holton, Simon J; Fodor, Krisztian; Milewski, Morlin; Konarev, Petr; Stanley, Will A; Wolf, Janina; Erdmann, Ralf; Schliebs, Wolfgang; Song, Young-Hwa; Wilmanns, Matthias

    2010-01-01

    The protein Pex19p functions as a receptor and chaperone of peroxisomal membrane proteins (PMPs). The crystal structure of the folded C-terminal part of the receptor reveals a globular domain that displays a bundle of three long helices in an antiparallel arrangement. Complementary functional experiments, using a range of truncated Pex19p constructs, show that the structured α-helical domain binds PMP-targeting signal (mPTS) sequences with about 10 μM affinity. Removal of a conserved N-termin...

  5. Mechanics of patterned helical Si springs on Si substrate.

    Science.gov (United States)

    Liu, D L; Ye, D X; Khan, F; Tang, F; Lim, B K; Picu, R C; Wang, G C; Lu, T M

    2003-12-01

    The elastic response, including the spring constant, of individual Si helical-shape submicron springs, was measured using a tip-cantilever assembly attached to a conventional atomic force microscope. The isolated, four-turn Si springs were fabricated using oblique angle deposition with substrate rotation, also known as the glancing angle deposition, on a templated Si substrate. The response of the structures was modeled using finite elements, and it was shown that the conventional formulae for the spring constant required modifications before they could be used for the loading scheme used in the present experiment.

  6. Analytic all-plus-helicity gluon amplitudes in QCD

    Science.gov (United States)

    Dunbar, David C.; Godwin, John H.; Jehu, Guy R.; Perkins, Warren B.

    2017-12-01

    We detail the calculation of two-loop all-plus-helicity amplitudes for pure Yang-Mills theory. The four-dimensional unitarity methods and augmented recursion techniques we have developed, together with a knowledge of the singular structure of the amplitudes, allow us to compute these in compact analytic forms. Specifically we present the computation and analytic results for the six- and seven-gluon leading color two-loop amplitudes, these being the first QCD two-loop amplitudes beyond five points.

  7. Helical post stellarator. Part 1: Vacuum configuration

    International Nuclear Information System (INIS)

    Moroz, P.E.

    1997-08-01

    Results on a novel type of stellarator configuration, the Helical Post Stellarator (HPS), are presented. This configuration is different significantly from all previously known stellarators due to its unique geometrical characteristics and unique physical properties. Among those are: the magnetic field has only one toroidal period (M = 1), the plasma has an extremely low aspect ratio, A ∼ 1, and the variation of the magnetic field, B, along field lines features a helical ripple on the inside of the torus. Among the main advantages of a HPS for a fusion program are extremely compact, modular, and simple design compatible with significant rotational transform, large plasma volume, and improved particle transport characteristics

  8. Helicity and nuclear β decay correlations

    Science.gov (United States)

    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.

  9. Helicity injection experiment in the SINP tokamak

    International Nuclear Information System (INIS)

    Bhattacharyya, Krishnendu; Ray, Nihar Ranjan

    2000-01-01

    The current drive or sustainment in magnetized toroidal resistive plasmas can be though of as a 'balance' between helicity injection and dissipation. In the present work, the mechanisms of the 'balance' in the fluctuating magnetized resistive plasmas of the SINP tokamak, have been studied experimentally. The result shows that the oscillatory vertical magnetic field and oscillatory plasmas' velocity in a definite phase relationship causes the balancing effect between helicity injection and dissipation and thus sustainment of plasma current for a longer period of time has been observed in the resistive plasmas of the SINP tokamak. (author)

  10. Buckling control of morphing composite airfoil structure using multi-stable laminate by piezoelectric sensors/actuators

    Science.gov (United States)

    Zareie, Shahin; Zabihollah, Abolghassem; Azizi, Aydin

    2011-04-01

    In the present work, an unsymmetric laminated plate with surface bonded piezoelectric sensors, and actuators has been considered. Piezoelectric sensor were used to monitor the load and deformation bifurcation occurs. Monitoring the shape and load of a morphing structure is essential to ascertain that the structure is properly deployed and it is not loaded excessively ,thus, preventing structural to failure. A piezoceramic actuator is used to provide activation load and to force the structure to change its stability state from one to another. A non-linear finite element model based on the layerwise displacement theory considering the electro-mechanical coupling effects of piezoelectric elements has been developed for simulation purposes. A control mechanism is also employed to actively control the shape of the structure. It is observed that, utilizing multistable composite to design a morphing structure may significantly reduce the energy required for changing the shape. Further controlling the buckling phenomena using piezoelectric sensor and actuator along with an ON/OFF controller can effectively and efficiency enhance the performance of the morphing structure during manoeuver.

  11. Nucleic acid helices: I. Structure of M1 RNA from E. coli as determined bypsoralen crosslinking. II. Thermodynamics of the helix-coil transition of DNA oligonucleotides in solutions containing 3.0 M tetramethylammonium chloride

    International Nuclear Information System (INIS)

    Lipson, S.E.

    1987-01-01

    This work includes two different investigations examining nucleic acid helices. The first study discusses secondary and tertiary interactions in the RNA moiety of ribonuclease P from Escherichia coli. The second study discusses the thermodynamics of the helix-coil transition of DNA oligonucleotides in solutions containing tetramethylammonium chloride. The RNA moiety of ribonuclease P from Escherichia coli (M1 RNA) has been photoreacted with 4'-hydroxymethyl-4,5'8-trimethylpsoralen and long wave UV light (320-380 nm) in a buffer in which the M1 RNA alone acts as a true catalyst of tRNA processing. Limited specific digestion followed by two dimensional gel electrophoresis yields fragments crosslinked by HMT. The positions of the crosslinks have been determined to within ±15 nucleotides by photoreversal of the isolated crosslinked fragments and enzymatic sequencing of the resulting RNA. Further assignments of the exact locations of the crosslinks have been made on the known photoreactivity of the psoralen with different bases

  12. Helicity of Convective Flows from Localized Heat Source in a Rotating Layer

    Directory of Open Access Journals (Sweden)

    Sukhanovskii A.

    2017-06-01

    Full Text Available Experimental and numerical study of the steady-state cyclonic vortex from isolated heat source in a rotating fluid layer is described. The structure of laboratory cyclonic vortex is similar to the typical structure of tropical cyclones from observational data and numerical modelling including secondary flows in the boundary layer. Differential characteristics of the flow were studied by numerical simulation using CFD software FlowVision. Helicity distribution in rotating fluid layer with localized heat source was analysed. Two mechanisms which play role in helicity generation are found. The first one is the strong correlation of cyclonic vortex and intensive upward motion in the central part of the vessel. The second one is due to large gradients of velocity on the periphery. The integral helicity in the considered case is substantial and its relative level is high.

  13. Characteristics of magnetized plasma flow for helicity injection into reversed-field pinch

    Science.gov (United States)

    Suzuki, Shotaro; Asai, Tomohiko; Nagata, Masayoshi; Koguchi, Haruhisa; Hirano, Yoichi; Sakakita, Hajime; Kiyama, Satoru

    2007-11-01

    The magnetized plasma flow injection experiment has been performed on the large sized reversed-field pinch (RFP) device of TPE-RX. The magnetized plasma flow injection has been demonstrated to support RFP formation fueling and helicity injection. In the start-up experiment with the plasma flow injection, reduced density pump-out, loop voltage and Da emission have been observed clearly. Also the effect of plasma flow on the RFP with improved confinement by PPCD technique has been evaluated. To determine the efficiency of fueling and helicity injection, density, temperature and magnetic structure have been measured by using Langmuir and magnetic probe arrays.The series of experiments will show the magnetic structure and actual helicity and energy contents of injected magnetized plasma flow.

  14. Self-assembly of α-helical polypeptides driven by complex coacervation.

    Science.gov (United States)

    Priftis, Dimitrios; Leon, Lorraine; Song, Ziyuan; Perry, Sarah L; Margossian, Khatcher O; Tropnikova, Anna; Cheng, Jianjun; Tirrell, Matthew

    2015-09-14

    Reported is the ability of α-helical polypeptides to self-assemble with oppositely-charged polypeptides to form liquid complexes while maintaining their α-helical secondary structure. Coupling the α-helical polypeptide to a neutral, hydrophilic polymer and subsequent complexation enables the formation of nanoscale coacervate-core micelles. While previous reports on polypeptide complexation demonstrated a critical dependence of the nature of the complex (liquid versus solid) on chirality, the α-helical structure of the positively charged polypeptide prevents the formation of β-sheets, which would otherwise drive the assembly into a solid state, thereby, enabling coacervate formation between two chiral components. The higher charge density of the assembly, a result of the folding of the α-helical polypeptide, provides enhanced resistance to salts known to inhibit polypeptide complexation. The unique combination of properties of these materials can enhance the known potential of fluid polypeptide complexes for delivery of biologically relevant molecules. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. An α-Helical Core Encodes the Dual Functions of the Chlamydial Protein IncA*

    Science.gov (United States)

    Ronzone, Erik; Wesolowski, Jordan; Bauler, Laura D.; Bhardwaj, Anshul; Hackstadt, Ted; Paumet, Fabienne

    2014-01-01

    Chlamydia is an intracellular bacterium that establishes residence within parasitophorous compartments (inclusions) inside host cells. Chlamydial inclusions are uncoupled from the endolysosomal pathway and undergo fusion with cellular organelles and with each other. To do so, Chlamydia expresses proteins on the surface of the inclusion using a Type III secretion system. These proteins, termed Incs, are located at the interface between host and pathogen and carry out the functions necessary for Chlamydia survival. Among these Incs, IncA plays a critical role in both protecting the inclusion from lysosomal fusion and inducing the homotypic fusion of inclusions. Within IncA are two regions homologous to eukaryotic SNARE (soluble N-ethylmaleimide-sensitive factor attachment receptor) domains referred to as SNARE-like domain 1 (SLD1) and SNARE-like domain 2 (SLD2). Using a multidisciplinary approach, we have discovered the functional core of IncA that retains the ability to both inhibit SNARE-mediated fusion and promote the homotypic fusion of Chlamydia inclusions. Circular dichroism and analytical ultracentrifugation experiments show that this core region is composed almost entirely of α-helices and assembles into stable homodimers in solution. Altogether, we propose that both IncA functions are encoded in a structured core domain that encompasses SLD1 and part of SLD2. PMID:25324548

  16. An α-helical core encodes the dual functions of the chlamydial protein IncA.

    Science.gov (United States)

    Ronzone, Erik; Wesolowski, Jordan; Bauler, Laura D; Bhardwaj, Anshul; Hackstadt, Ted; Paumet, Fabienne

    2014-11-28

    Chlamydia is an intracellular bacterium that establishes residence within parasitophorous compartments (inclusions) inside host cells. Chlamydial inclusions are uncoupled from the endolysosomal pathway and undergo fusion with cellular organelles and with each other. To do so, Chlamydia expresses proteins on the surface of the inclusion using a Type III secretion system. These proteins, termed Incs, are located at the interface between host and pathogen and carry out the functions necessary for Chlamydia survival. Among these Incs, IncA plays a critical role in both protecting the inclusion from lysosomal fusion and inducing the homotypic fusion of inclusions. Within IncA are two regions homologous to eukaryotic SNARE (soluble N-ethylmaleimide-sensitive factor attachment receptor) domains referred to as SNARE-like domain 1 (SLD1) and SNARE-like domain 2 (SLD2). Using a multidisciplinary approach, we have discovered the functional core of IncA that retains the ability to both inhibit SNARE-mediated fusion and promote the homotypic fusion of Chlamydia inclusions. Circular dichroism and analytical ultracentrifugation experiments show that this core region is composed almost entirely of α-helices and assembles into stable homodimers in solution. Altogether, we propose that both IncA functions are encoded in a structured core domain that encompasses SLD1 and part of SLD2. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

  17. Stable beams

    CERN Multimedia

    2015-01-01

    Stable beams: two simple words that carry so much meaning at CERN. When LHC page one switched from "squeeze" to "stable beams" at 10.40 a.m. on Wednesday, 3 June, it triggered scenes of jubilation in control rooms around the CERN sites, as the LHC experiments started to record physics data for the first time in 27 months. This is what CERN is here for, and it’s great to be back in business after such a long period of preparation for the next stage in the LHC adventure.   I’ve said it before, but I’ll say it again. This was a great achievement, and testimony to the hard and dedicated work of so many people in the global CERN community. I could start to list the teams that have contributed, but that would be a mistake. Instead, I’d simply like to say that an achievement as impressive as running the LHC – a machine of superlatives in every respect – takes the combined effort and enthusiasm of everyone ...

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

    Energy Technology Data Exchange (ETDEWEB)

    Teng, Peng; Ma, Ning; Cerrato, Darrell Cole; She, Fengyu; Odom, Timothy; Wang, Xiang; Ming, Li-June; van der Vaart, Arjan; Wojtas, Lukasz; Xu, Hai; Cai, Jianfeng

    2017-05-16

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

  19. Thermally Stable and Electrically Conductive, Vertically Aligned Carbon Nanotube/Silicon Infiltrated Composite Structures for High-Temperature Electrodes.

    Science.gov (United States)

    Zou, Qi Ming; Deng, Lei Min; Li, Da Wei; Zhou, Yun Shen; Golgir, Hossein Rabiee; Keramatnejad, Kamran; Fan, Li Sha; Jiang, Lan; Silvain, Jean-Francois; Lu, Yong Feng

    2017-10-25

    Traditional ceramic-based, high-temperature electrode materials (e.g., lanthanum chromate) are severely limited due to their conditional electrical conductivity and poor stability under harsh circumstances. Advanced composite structures based on vertically aligned carbon nanotubes (VACNTs) and high-temperature ceramics are expected to address this grand challenge, in which ceramic serves as a shielding layer protecting the VACNTs from the oxidation and erosive environment, while the VACNTs work as a conductor. However, it is still a great challenge to fabricate VACNT/ceramic composite structures due to the limited diffusion of ceramics inside the VACNT arrays. In this work, we report on the controllable fabrication of infiltrated (and noninfiltrated) VACNT/silicon composite structures via thermal chemical vapor deposition (CVD) [and laser-assisted CVD]. In laser-assisted CVD, low-crystalline silicon (Si) was quickly deposited at the VACNT subsurfaces/surfaces followed by the formation of high-crystalline Si layers, thus resulting in noninfiltrated composite structures. Unlike laser-assisted CVD, thermal CVD activated the precursors inside and outside the VACNTs simultaneously, which realized uniform infiltrated VACNT/Si composite structures. The growth mechanisms for infiltrated and noninfiltrated VACNT/ceramic composites, which we attributed to the different temperature distributions and gas diffusion mechanism in VACNTs, were investigated. More importantly, the as-farbicated composite structures exhibited excellent multifunctional properties, such as excellent antioxidative ability (up to 1100 °C), high thermal stability (up to 1400 °C), good high velocity hot gas erosion resistance, and good electrical conductivity (∼8.95 Sm -1 at 823 K). The work presented here brings a simple, new approach to the fabrication of advanced composite structures for hot electrode applications.

  20. 2,6,10-Tris(dialkylamino)trioxatriangulenium ions. Synthesis, structure, and properties of exceptionally stable carbenium ions

    DEFF Research Database (Denmark)

    Laursen, B.W.; Krebs, Frederik C; Nielsen, M.F.

    1998-01-01

    A general synthetic route to a novel type of triamino-substituted planar carbenium ions (5) is reported. The synthetic method is based on a facile and selective nucleophilic aromatic substitution on the 4,6-trimethoxyphenyl)carbenium ion (1) with amines and gives access to a wide variety of more...... complex amino-substituted carbenium ions. X-ray crystallography shows that the cis(N-pyrrolidinyl)-4,8,12-trioxatriangulenium ion (5b) is planar and forms segregated stacks of cations and PF6 anions in the solid phase. The stability of the 2,6, 0-tris(diethylamino)- 4,8,12-trioxatriangulenium ion 5a...... is expressed as the pK(R+) value, which is determined in strongly basic nonaqueous solution on-the basis of a new acidity function C-. The pK(R+) value of 5a is measured to be 19.7, which is 10 orders of magnitude higher than the values found for the most stable carbenium ions previously reported...

  1. More Stable Ties or Better Structure? An Examination of the Impact of Co-author Network on Team Knowledge Creation

    Directory of Open Access Journals (Sweden)

    Mingze Li

    2017-09-01

    Full Text Available This study aims to explore the influence of co-author network on team knowledge creation. Integrating the two traditional perspectives of network relationship and network structure, we examine the direct and interactive effects of tie stability and structural holes on team knowledge creation. Tracking scientific articles published by 111 scholars in the research field of human resource management from the top 8 American universities, we analyze scholars’ scientific co-author networks. The result indicates that tie stability changes the teams’ information processing modes and, when graphed, results in an inverted U-shape relationship between tie stability and team knowledge creation. Moreover, structural holes in co-author network are proved to be harmful to team knowledge sharing and diffusion, thereby impeding team knowledge creation. Also, tie stability and structural hole interactively influence team knowledge creation. When the number of structural hole is low in the co-author network, the graphical representation of the relationship between tie stability and team knowledge creation tends to be a more distinct U-shape.

  2. The use of protein structure/activity relationships in the rational design of stable particulate delivery systems

    Directory of Open Access Journals (Sweden)

    M.H.B. Costa

    2002-06-01

    Full Text Available The recombinant heat shock protein (18 kDa-hsp from Mycobacterium leprae was studied as a T-epitope model for vaccine development. We present a structural analysis of the stability of recombinant 18 kDa-hsp during different processing steps. Circular dichroism and ELISA were used to monitor protein structure after thermal stress, lyophilization and chemical modification. We observed that the 18 kDa-hsp is extremely resistant to a wide range of temperatures (60% of activity is retained at 80ºC for 20 min. N-Acylation increased its ordered structure by 4% and decreased its ß-T1 structure by 2%. ELISA demonstrated that the native conformation of the 18 kDa-hsp was preserved after hydrophobic modification by acylation. The recombinant 18 kDa-hsp resists to a wide range of temperatures and chemical modifications without loss of its main characteristic, which is to be a source of T epitopes. This resistance is probably directly related to its lack of organization at the level of tertiary and secondary structures.

  3. Review of the helicity formalism; Revision del formalismo de helicidad

    Energy Technology Data Exchange (ETDEWEB)

    Barreiro, F.; Cerrada, M.; Fernandez, E.

    1972-07-01

    Our purpose in these notes has been to present a brief and general review of the helicity formalism. We begin by discussing Lorentz invariance, spin and helicity ideas, in section 1 . In section 2 we deal with the construction of relativistic states and scattering amplitudes in the helicity basis and we study their transformation properties under discrete symmetries. Finally we present some more sophisticated topics like kinematical singularities of helicity amplitudes, kinematical constraints and crossing relations 3, 4, 5 respectively. (Author) 8 refs.

  4. A Prospective Evaluation of Helical Tomotherapy

    International Nuclear Information System (INIS)

    Bauman, Glenn; Yartsev, Slav; Rodrigues, George; Lewis, Craig; Venkatesan, Varagur M.; Yu, Edward; Hammond, Alex; Perera, Francisco; Ash, Robert; Dar, A. Rashid; Lock, Michael; Baily, Laura; Coad, Terry C; Trenka, Kris C.; Warr, Barbara; Kron, Tomas; Battista, Jerry; Van Dyk, Jake

    2007-01-01

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

  5. Helical chirality induction of expanded porphyrin analogues

    Indian Academy of Sciences (India)

    2,2 -Bipyridine was readily obtained from 6,6 - dibromo-2,2 -bipyridine and then used for synthesizing cyclotetrapyrroletetrapyridine O3.18. 3. Helical chirality induction. 3.1 Chirality sensing of carboxylic acids by O1. Facile methods for the determination of molecular chi- rality are of increasing interest in view of the role of.

  6. Helical CT without contrast in choledocholithiasis diagnosis

    International Nuclear Information System (INIS)

    Jimenez Cuenca, I.; Perez Homs, M.; Olmo Martinez, L. del

    2001-01-01

    The goal of this study was to determine the diagnostic value of the helical CT without contrast in suspected cases of choledocholithiasis, comparing this test with endoscopic retrograde cholangiopancreatography (ERCP). Forty patients with possible choledocholithiasis were studied prospectively. There were 23 women and 17 men, ranging in age from 24 to 91 years. Helical CT was performed immediately before ERCP (time interval between the two procedures was less than 1 h). A biliary area previously selected was studied with a technique of pitch 1 and slice thickness of 3.2 mm. Average time was 30 s. Reconstruction with different increments and windows were made. Stone presence was evaluated in bile duct and Vater's ampulla. Biliary dilation was evaluated too. Endoscopic retrograde cholangiopancreatography found stones in 19 patients and absence of stones in 20. One case was failed, but stones in bile duct were demonstrated during intraoperative cholangiography. Helical CT demonstrated stones in 15 of the 19 patients with positive ERCP. There were no false positives with CT. Patients without stones in ERCP were also negative in CT. The patient having the failed ERCP was considered positive in CT. The CT sensitivity was 80 % and specificity was 100 %, with an accuracy of 90 %. Helical CT without contrast has sensitivity and specificity good enough to be used as a screening technique in patients with suspected choledocholithiasis. (orig.)

  7. Helical CT without contrast in choledocholithiasis diagnosis

    Energy Technology Data Exchange (ETDEWEB)

    Jimenez Cuenca, I.; Perez Homs, M. [Radiodiagnostic Service, Hospital Universitario, Valladolid (Spain); Olmo Martinez, L. del [Digestive Service, Hospital Universitario, Valladolid (Spain)

    2001-02-01

    The goal of this study was to determine the diagnostic value of the helical CT without contrast in suspected cases of choledocholithiasis, comparing this test with endoscopic retrograde cholangiopancreatography (ERCP). Forty patients with possible choledocholithiasis were studied prospectively. There were 23 women and 17 men, ranging in age from 24 to 91 years. Helical CT was performed immediately before ERCP (time interval between the two procedures was less than 1 h). A biliary area previously selected was studied with a technique of pitch 1 and slice thickness of 3.2 mm. Average time was 30 s. Reconstruction with different increments and windows were made. Stone presence was evaluated in bile duct and Vater's ampulla. Biliary dilation was evaluated too. Endoscopic retrograde cholangiopancreatography found stones in 19 patients and absence of stones in 20. One case was failed, but stones in bile duct were demonstrated during intraoperative cholangiography. Helical CT demonstrated stones in 15 of the 19 patients with positive ERCP. There were no false positives with CT. Patients without stones in ERCP were also negative in CT. The patient having the failed ERCP was considered positive in CT. The CT sensitivity was 80 % and specificity was 100 %, with an accuracy of 90 %. Helical CT without contrast has sensitivity and specificity good enough to be used as a screening technique in patients with suspected choledocholithiasis. (orig.)

  8. Stable loop in the crystal structure of the intercalated four-stranded cytosine-rich metazoan telomere

    Science.gov (United States)

    Kang, C.; Berger, I.; Lockshin, C.; Ratliff, R.; Moyzis, R.; Rich, A.

    1995-01-01

    In most metazoans, the telomeric cytosine-rich strand repeating sequence is d(TAACCC). The crystal structure of this sequence was solved to 1.9-A resolution. Four strands associate via the cytosine-containing parts to form a four-stranded intercalated structure held together by C.C+ hydrogen bonds. The base-paired strands are parallel to each other, and the two duplexes are intercalated into each other in opposite orientations. One TAA end forms a highly stabilized loop with the 5' thymine Hoogsteen-base-paired to the third adenine. The 5' end of this loop is in close proximity to the 3' end of one of the other intercalated cytosine strands. Instead of being entirely in a DNA duplex, this structure suggests the possibility of an alternative conformation for the cytosine-rich telomere strands.

  9. Electrotransfection of Polyamine Folded DNA Origami Structures.

    Science.gov (United States)

    Chopra, Aradhana; Krishnan, Swati; Simmel, Friedrich C

    2016-10-12

    DNA origami structures are artificial molecular nanostructures in which DNA double helices are forced into a closely packed configuration by a multitude of DNA strand crossovers. We show that three different types of origami structures (a flat sheet, a hollow tube, and a compact origami block) can be formed in magnesium-free buffer solutions containing low (origami folding is proportional to the DNA concentration. At excessive amounts, the structures aggregate and precipitate. In contrast to origami structures formed in conventional buffers, the resulting structures are stable in the presence of high electric field pulses, such as those commonly used for electrotransfection experiments. We demonstrate that spermidine-stabilized structures are stable in cell lysate and can be delivered into mammalian cells via electroporation.

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

    International Nuclear Information System (INIS)

    Zou Yu; Pan Xiaochuan; Xia Dan; Wang Ge

    2005-01-01

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

  11. Field-theoretic calculation of kinetic helicity flux

    Indian Academy of Sciences (India)

    In this paper we apply perturbative field-theoretic technique to helical turbulence. In the inertial range the kinetic helicity flux is found to be constant and forward. The universal constant H appearing in the spectrum of kinetic helicity was found to be 2.47.

  12. Facile synthesis of stable structured MoS{sub 2}-Mo-CNFs heteroarchitecture with enhanced hydrogen evolution

    Energy Technology Data Exchange (ETDEWEB)

    Mo, Qionghua [Research Institute for New Materials Technology, Chongqing University of Arts and Sciences, Chongqing 402160 (China); Faculty of Material and Energy, South West University, Chongqing 400700 (China); Yao, Yucen [Research Institute for New Materials Technology, Chongqing University of Arts and Sciences, Chongqing 402160 (China); Liu, Bitao, E-mail: liubitao007@163.com [Research Institute for New Materials Technology, Chongqing University of Arts and Sciences, Chongqing 402160 (China); Peng, Lingling; Yan, Hengqing; Hou, Zhupei; Wang, Jun [Research Institute for New Materials Technology, Chongqing University of Arts and Sciences, Chongqing 402160 (China); Lin, Yue, E-mail: linyue@ustc.edu.cn [Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Anhui 230026 (China)

    2017-06-01

    3D structured MoS{sub 2} are grown in-situ on Mo particles embedded carbon nanofibers (CNFs) via a hydrothermal method. Due to this special structure, the bonding and effective electron delivery between CNFs and MoS{sub 2} are both enhanced, and which will exhibits a better hydrogen evolution activity. The onset potential of this MoS{sub 2}-Mo-CNFs catalyst will decreased to 60 mV compared to the 90 mV for the MoS{sub 2}-CNFs. And its current density nearly no change with 5000 cycles which is better than the 32.3% decrease of MoS{sub 2}-CNFs at η = 300 mV (V vs RHE). - Highlights: • Newly structured MoS{sub 2}-Mo-CNFs with effectively connection between MoS{sub 2} and CNFs successfully synthesized. • This structure can enhance the charge transfer and significantly increase electrocatalytic efficiency. • Nearly no HER activity loss after 5000 CV cycles.

  13. Microbial food web mapping: linking carbon cycling and community structure in soils through pyrosequencing enabled stable isotope probing

    Energy Technology Data Exchange (ETDEWEB)

    Buckley, Daniel H. [Cornell Univ., Ithaca, NY (United States)

    2015-03-15

    Soil represents a massive reservoir of active carbon and climate models vary dramatically in predicting how this carbon will respond to climate change over the coming century. A major cause of uncertainty is that we still have a very limited understand the microorganisms that dominate the soil carbon cycle. The vast majority of soil microbes cannot be cultivated in the laboratory and the diversity of organisms and enzymes that participate in the carbon cycle is staggeringly complex. We have developed a new toolbox for exploring the carbon cycle and the metabolic and ecological characteristics of uncultivated microorganisms. The high-resolution nucleic acid stable isotope probing approach that we have developed makes it possible to characterize microbial carbon cycling dynamics in soil. The approach allows us to track multiple 13C-labeled substrates into thousands of microbial taxa over time. Using this approach we have discovered several major lineages of uncultivated microorganisms that participate in cellulose metabolism and are found widely in soils (including Verrucomicrobia and Chloroflexi, which have not previously been implicated as major players in the soil carbon cycle). Furthermore, isotopic labelling of nucleic acids enables community genomics and permits genome fragment binning for a majority of these cellulolytic microorganisms allowing us to explore the metabolic underpinnings of cellulose degradation. This approach has allowed us to describe unexpected dynamics of carbon metabolism with different microbial taxa exhibiting characteristic patterns of carbon substrate incorporation, indicative of distinct ecological strategies. The data we describe allows us to characterize the activity of novel microorganisms as they occur in the environment and these data provide a basis for understanding how the physiological traits of discrete microorganisms sum to govern the complex responses of the soil carbon cycle.

  14. Modeling food web structure and selenium biomagnification in Lake Macquarie, New South Wales, Australia, using stable carbon and nitrogen isotopes.

    Science.gov (United States)

    Schneider, Larissa; Maher, William A; Potts, Jaimie; Taylor, Anne M; Batley, Graeme E; Krikowa, Frank; Chariton, Anthony A; Gruber, Bernd

    2015-03-01

    As a consequence of coal-fired power station operations, elevated selenium concentrations have been reported in the sediments and biota of Lake Macquarie (New South Wales, Australia). In the present study, an ecosystem-scale model has been applied to determine how selenium in a seagrass food web is processed from sediments and water through diet to predators, using stable isotopes (δ(13) C and δ(15) N) to establish the trophic position of organisms. Trophic position, habitat, and feeding zone were examined as possible factors influencing selenium bioaccumulation. Selenium concentrations ranged from 0.2 μg/g dry weight in macroalgae species to 12.9 μg/g in the carnivorous fish Gerres subfasciatus. A mean magnification factor of 1.39 per trophic level showed that selenium is biomagnifying in the seagrass food web. Habitat and feeding zone influenced selenium concentrations in invertebrates, whereas feeding zone was the only significant factor influencing selenium concentrations in fish. The sediment-water partitioning coefficient (Kd ) of 4180 showed that partitioning of selenium entering the lake to particulate organic material (POM) is occurring, and consequently availability to food webs from POM is high. Trophic transfer factors (invertebrate = 1.9; fish = 1.2) were similar to those reported for other water bodies, showing that input source is not the main determinant of the magnitude of selenium bioaccumulation in a food web, but rather the initial partitioning of selenium into bioavailable POM. Environ Toxicol Chem 2015;34:608-617. © 2014 SETAC. © 2014 SETAC.

  15. Dynamic reorganization of chromatin structure and selective DNA demethylation prior to stable enhancer complex formation during differentiation of primary hematopoietic cells in vitro.

    Science.gov (United States)

    Tagoh, Hiromi; Melnik, Svitlana; Lefevre, Pascal; Chong, Suyinn; Riggs, Arthur D; Bonifer, Constanze

    2004-04-15

    In order to gain insights in the true molecular mechanisms involved in cell fate decisions, it is important to study the molecular details of gene activation where such decisions occur, which is at the level of the chromatin structure of individual genes. In the study presented here we addressed this issue and examined the dynamic development of an active chromatin structure at the chicken lysozyme locus during the differentiation of primary myeloid cells from transgenic mouse bone marrow. Using in vivo footprinting we found that stable enhancer complex assembly and high-level gene expression are late events in cell differentiation. However, even before the onset of gene expression and stable transcription factor binding, specific chromatin alterations are observed. This includes changes in DNA topology and the selective demethylation of CpG dinucleotides located in the cores of critical transcription factor binding sites, but not in flanking DNA. These results firmly support the idea that epigenetic programs guiding blood cell differentiation are engraved into the chromatin of lineage-specific genes and that such chromatin changes are implemented before cell lineage specification.

  16. Membrane-bound state of the colicin E1 channel domain as an extended two-dimensional helical array.

    Science.gov (United States)

    Zakharov, S D; Lindeberg, M; Griko, Y; Salamon, Z; Tollin, G; Prendergast, F G; Cramer, W A

    1998-04-14

    Atomic level structures have been determined for the soluble forms of several colicins and toxins, but the structural changes that occur after membrane binding have not been well characterized. Changes occurring in the transition from the soluble to membrane-bound state of the C-terminal 190-residue channel polypeptide of colicin E1 (P190) bound to anionic membranes are described. In the membrane-bound state, the alpha-helical content increases from 60-64% to 80-90%, with a concomitant increase in the average length of the helical segments from 12 to 16 or 17 residues, close to the length required to span the membrane bilayer in the open channel state. The average distance between helical segments is increased and interhelix interactions are weakened, as shown by a major loss of tertiary structure interactions, decreased efficiency of fluorescence resonance energy transfer from an energy donor on helix V of P190 to an acceptor on helix IX, and decreased resonance energy transfer at higher temperatures, not observed in soluble P190, implying freedom of motion of helical segments. Weaker interactions are also shown by a calorimetric thermal transition of low cooperativity, and the extended nature of the helical array is shown by a 3- to 4-fold increase in the average area subtended per molecule to 4,200 A2 on the membrane surface. The latter, with analysis of the heat capacity changes, implies the absence of a developed hydrophobic core in the membrane-bound P190. The membrane interfacial layer thus serves to promote formation of a highly helical extended two-dimensional flexible net. The properties of the membrane-bound state of the colicin channel domain (i.e., hydrophobic anchor, lengthened and loosely coupled alpha-helices, and close association with the membrane interfacial layer) are plausible structural features for the state that is a prerequisite for voltage gating, formation of transmembrane helices, and channel opening.

  17. Pyrolysis of Helical Coordination Polymers for Metal-Sulfide-Based Helices with Broadband Chiroptical Activity.

    Science.gov (United States)

    Hirai, Kenji; Yeom, Bongjun; Sada, Kazuki

    2017-06-27

    Fabrication of chiroptical materials with broadband response in the visible light region is vital to fully realize their potential applications. One way to achieve broadband chiroptical activity is to fabricate chiral nanostructures from materials that exhibit broadband absorption in the visible light region. However, the compounds used for chiroptical materials have predominantly been limited to materials with narrowband spectral response. Here, we synthesize Ag 2 S-based nanohelices derived from helical coordination polymers. The right- and left-handed coordination helices used as precursors are prepared from l- and d-glutathione with Ag + and a small amount of Cu 2+ . The pyrolysis of the coordination helices yields right- and left-handed helices of Cu 0.12 Ag 1.94 S/C, which exhibit chiroptical activity spanning the entire visible light region. Finite element method simulations substantiate that the broadband chiroptical activity is attributed to synergistic broadband light absorption and light scattering. Furthermore, another series of Cu 0.10 Ag 1.90 S/C nanohelices are synthesized by choosing the l- or d-Glu-Cys as starting materials. The pitch length of nanohelicies is controlled by changing the peptides, which alters their chiroptical properties. The pyrolysis of coordination helices enables one to fabricate helical Ag 2 S-based materials that enable broadband chiroptical activity but have not been explored owing to the lack of synthetic routes.

  18. Bearing capacity of helical pile foundation in peat soil from different, diameter and spacing of helical plates

    Science.gov (United States)

    Fatnanta, F.; Satibi, S.; Muhardi

    2018-03-01

    In an area dominated by thick peat soil layers, driven piles foundation is often used. These piles are generally skin friction piles where the pile tips do not reach hard stratum. Since the bearing capacity of the piles rely on the resistance of their smooth skin, the bearing capacity of the piles are generally low. One way to increase the bearing capacity of the piles is by installing helical plates around the pile tips. Many research has been performed on helical pile foundation. However, literature on the use of helical pile foundation on peat soil is still hardly found. This research focus on the study of axial bearing capacity of helical pile foundation in peat soil, especially in Riau Province. These full-scale tests on helical pile foundation were performed in a rectangular box partially embedded into the ground. The box is filled with peat soil, which was taken from Rimbo Panjang area in the district of Kampar, Riau Province. Several helical piles with different number, diameter and spacing of the helical plates have been tested and analysed. The tests result show that helical pile with three helical plates of uniform diameter has better bearing capacity compared to other helical piles with varying diameter and different number of helical plates. The bearing capacity of helical pile foundation is affected by the spacing between helical plates. It is found that the effective helical plates spacing for helical pile foundation with diameter of 15cm to 35cm is between 20cm to 30cm. This behaviour may be considered to apply to other type of helical pile foundations in peat soil.

  19. Collective helicity switching of a DNA-coat assembly

    Science.gov (United States)

    Kim, Yongju; Li, Huichang; He, Ying; Chen, Xi; Ma, Xiaoteng; Lee, Myongsoo

    2017-07-01

    Hierarchical assemblies of biomolecular subunits can carry out versatile tasks at the cellular level with remarkable spatial and temporal precision. As an example, the collective motion and mutual cooperation between complex protein machines mediate essential functions for life, such as replication, synthesis, degradation, repair and transport. Nucleic acid molecules are far less dynamic than proteins and need to bind to specific proteins to form hierarchical structures. The simplest example of these nucleic acid-based structures is provided by a rod-shaped tobacco mosaic virus, which consists of genetic material surrounded by coat proteins. Inspired by the complexity and hierarchical assembly of viruses, a great deal of effort has been devoted to design similarly constructed artificial viruses. However, such a wrapping approach makes nucleic acid dynamics insensitive to environmental changes. This limitation generally restricts, for example, the amplification of the conformational dynamics between the right-handed B form to the left-handed Z form of double-stranded deoxyribonucleic acid (DNA). Here we report a virus-like hierarchical assembly in which the native DNA and a synthetic coat undergo repeated collective helicity switching triggered by pH change under physiological conditions. We also show that this collective helicity inversion occurs during translocation of the DNA-coat assembly into intracellular compartments. Translating DNA conformational dynamics into a higher level of hierarchical dynamics may provide an approach to create DNA-based nanomachines.

  20. Numerical simulation of helical-vortex effects in Rayleigh-Bénard convection

    Directory of Open Access Journals (Sweden)

    G. V. Levina

    2006-01-01

    Full Text Available A numerical approach is substantiated for searching for the large-scale alpha-like instability in thermoconvective turbulence. The main idea of the search strategy is the application of a forcing function which can have a physical interpretation. The forcing simulates the influence of small-scale helical turbulence generated in a rotating fluid with internal heat sources and is applied to naturally induced fully developed convective flows. The strategy is tested using the Rayleigh-Bénard convection in an extended horizontal layer of incompressible fluid heated from below. The most important finding is an enlargement of the typical horizontal scale of the forming helical convective structures accompanied by a cells merging, an essential increase in the kinetic energy of flows and intensification of heat transfer. The results of modeling allow explaining how the helical feedback can work providing the non-zero mean helicity generation and the mutual intensification of horizontal and vertical circulation, and demonstrate how the energy of the additional helical source can be effectively converted into the energy of intensive large-scale vortex flow.

  1. Asymmetric fan beams (AFB) for improvement of the craniocaudal dose distribution in helical tomotherapy delivery

    International Nuclear Information System (INIS)

    Gladwish, Adam; Kron, Tomas; McNiven, Andrea; Bauman, Glenn; Van Dyk, Jake

    2004-01-01

    Helical tomotherapy (HT) is a novel radiotherapy technique that utilizes intensity modulated fan beams that deliver highly conformal dose distributions in a helical beam trajectory. The most significant limitation in dose delivery with a constant fan beam thickness (FBT) is the penumbra width of the dose distribution in the craniocaudal direction, which is equivalent to the FBT. We propose to employ a half-blocked fan beam at start and stop location to reduce the penumbra width by half. By opening the jaw slowly during the helical delivery until the desired FBT is achieved it is possible to create a sharper edge in the superior and inferior direction from the target. The technique was studied using a tomotherapy beam model implemented on a commercial treatment planning system (Theraplan Plus V3.0). It was demonstrated that the dose distribution delivered using a 25 mm fan beam can be improved significantly, to reduce the dose to normal structures located superiorly and inferiorly of the target. Dosimetry for this technique is straightforward down to a FBT of 15 mm and implementation should be simple as no changes in couch movement are required compared to a standard HT delivery. We conclude that the use of asymmetric collimated fan beams for the start and stop of the helical tomotherapeutic dose delivery has the potential of significantly improving the dose distribution in helical tomotherapy

  2. Helical magnetic ground states in the vicinity of the superconducting state of MnP

    Science.gov (United States)

    Dissanayake, Sachith; Matsuda, M.; Ye, F.; Chi, S.; Cheng, J.-G.; Ma, J.; Zhou, H. D.; Yan, J.-Q.; Matsubayashi, K.; Okada, T.; Gouchi, J.; Uwatoko, Y.

    MnP, the first Mn-based superconductor under pressure, exhibits superconductivity near the critical pressure of 7.5 GPa. It shows a ferromagnetic order followed by a helical order (helical-c) with the spins lying in the ab plane and the helical rotation propagating along c axis at ambient pressure. We performed high pressure single crystal neutron diffraction study up to 7 GPa, which is in the vicinity of the superconducting phase. Our results indicate that the magnetic phase in the vicinity of the superconducting phase has a helical-b structure with the spins lying in the ac plane and the magnetic propagation vector along b axis. Polarized single crystal neutron diffraction measurements at 1.8 GPa confirmed the helicity in the ac plane. With increasing pressure, incommensurability δ increases and the magnetic moment decreases. Furthermore, small lattice anomalies were observed at different magnetic transitions, indicating that magnetoelastic coupling works to stabilize the magnetic order. This research at ORNL's HFIR and SNS was sponsored by the Scientific User Facilities Division, Office of Basic Energy Sciences, U.S. Department of Energy.

  3. Evolution and breakdown of helical vortex wakes behind a wind turbine

    International Nuclear Information System (INIS)

    Nemes, A; Jacono, D Lo; Sheridan, J; Blackburn, H M; Sherry, M

    2014-01-01

    The wake behind a three-bladed Glauert model rotor in a water channel was investigated. Planar particle image velocimetry was used to measure the velocity fields on the wake centre-line, with snapshots phase-locked to blade position of the rotor. Phase- locked averages of the velocity and vorticity fields are shown, with tip vortex interaction and entanglement of the helical filaments elucidated. Proper orthogonal decomposition and topology-based vortex identification are used to filter the PIV images for coherent structures and locate vortex cores. Application of these methods to the instantaneous data reveals unsteady behaviour of the helical filaments that is statistically quantifiable

  4. MBAR-enhanced lattice Monte Carlo simulation of the effect of helices on membrane protein aggregation

    Science.gov (United States)

    Xu, Yuanwei; Rodger, P. Mark

    2017-03-01

    We study the effect of helical structure on the aggregation of proteins using a simplified lattice protein model with an implicit membrane environment. A recently proposed Monte Carlo approach, which exploits the proven statistical optimality of the MBAR estimator in order to improve simulation efficiency, was used. The results show that with both two and four proteins present, the tendency to aggregate is strongly expedited by the presence of amphipathic helix (APH), whereas a transmembrane helix (TMH) slightly disfavours aggregation. When four protein molecules are present, partially aggregated states (dimers and trimers) were more common when the APH was present, compared with the cases where no helices or only the TMH is present.

  5. Fundamental understanding of oxygen reduction and reaction behavior and developing high performance and stable hetero-structured cathodes

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Xingbo [West Virginia Univ., Morgantown, WV (United States)

    2016-11-14

    New unique hetero-structured cathode has been developed in this project. La2NiO4+δ (LNO) as a surface catalyst with interstitial oxygen defects was introduced onto the state-of-the-art (La0.6Sr0.4)0.95Co0.2Fe0.8O3-δ (LSCF) cathode to enhance the surface-limited ORR kinetics on SOFC cathode. Furthermore, the hetero-structured cathode surface maintains high activity under electrode polarization with much less negative effects from surface cation segregation of Sr, which is known to cause degradation issues for conventional LSCF and LSC cathodes, thus improving the cathode long-term stability. The interface chemistry distribution and oxygen transport properties have been studied to prove the enhancement of power out and stability of LNO-infiltrated LSCF cathode. The further investigation demonstrates that CeO2 & La2-xNiO4+δ (x=0-0.2) co-infiltration is a simple and cost-effective method to improve both performance and stability of LSCF cathode by limiting nano-particles growth/delamination and further improve the surface stability. For the first time, a physical model is proposed to illustrate how unique interstitial species on hetero-structured cathode surface work to regulate the exchange rate of the incorporation reaction. Meanwhile, fundamental investigation of the surface oxygen exchange and bulk oxygen transport properties under over-potential conditions across cathode materials have been carried out in this project, which were discussed and compared to the Nernst equation that is generally applied to treat any oxide electrodes under equilibrium.

  6. Atomic structure of a stable high-index Ge surface: G2(103)-(4x1)

    DEFF Research Database (Denmark)

    Seehofer, L.; Bunk, O.; Falkenberg, G.

    1997-01-01

    Based on scanning tunneling microscopy and surface X-ray diffraction, we propose a complex structural model for the Ge(103)-(4 x 1) reconstruction. Each unit cell contains two (103) double steps, which gives rise to the formation of stripes of Ge atoms oriented in the [] direction....... The stripes and the spaces between them are covered with threefold-coordinated Ge adatoms. Charge is transferred from the bulk-like edge atoms of the double steps to the adatoms. The formation of the reconstruction can be explained in terms of stress relief, charge transfer, and minimization of the dangling...

  7. Synthesis of Helquats Based on Phenanthridinium Units: Four-Step Procedure to Novel Extended Helical Dications

    Czech Academy of Sciences Publication Activity Database

    Sonawane, Manoj R.; Vávra, Jan; Šaman, David; Císařová, I.; Teplý, Filip

    2015-01-01

    Roč. 47, č. 22 (2015), s. 3479-3488 ISSN 0039-7881 Grant - others:GA AV ČR(CZ) M200551208 Institutional support: RVO:61388963 Keywords : helical structures * rhodium * catalysis * cycloadditions * heterocycles * Sonogashira coupling Subject RIV: CC - Organic Chemistry Impact factor: 2.652, year: 2015

  8. Synthesis and magnetic properties of a 1-D helical chain derived ...

    Indian Academy of Sciences (India)

    Moreover the helical structure in 1 is maintained predominantly through covalent bond rather than supramolecular interactions. Direct current magnetic susceptibility measurement suggests that complex 1 obeys the Curie law. The fitting of magnetic data using the PHI software package yields parameters of = 1, = 2.26 ...

  9. Preparation of porous SnO2 helical nanotubes and SnO2 sheets

    International Nuclear Information System (INIS)

    Fei, Ling; Xu, Yun; Chen, Zheng; Yuan, Bin; Wu, Xiaofei; Hill, Joshua; Lin, Qianglu; Deng, Shuguang; Andersen, Paul; Lu, Yunfeng; Luo, Hongmei

    2013-01-01

    We report a surfactant-free chemical solution route for synthesizing one-dimensional porous SnO 2 helical nanotubes templated by helical carbon nanotubes and two-dimensional SnO 2 sheets templated by graphite sheets. Transmission electron microscopy, X-ray diffraction, cyclic voltammetry, and galvanostatic discharge–charge analysis are used to characterize the SnO 2 samples. The unique nanostructure and morphology make them promising anode materials for lithium-ion batteries. Both the SnO 2 with the tubular structure and the sheet structure shows small initial irreversible capacity loss of 3.2% and 2.2%, respectively. The SnO 2 helical nanotubes show a specific discharge capacity of above 800 mAh g −1 after 10 charge and discharge cycles, exceeding the theoretical capacity of 781 mAh g −1 for SnO 2 . The nanotubes remain a specific discharge capacity of 439 mAh g −1 after 30 cycles, which is better than that of SnO 2 sheets (323 mAh g −1 ). - Highlights: • Synthesized porous SnO 2 helical nanotubes with diameters of 100–120 nm. • Synthesized porous SnO 2 sheets template by graphite sheets. • The tubular and sheet SnO 2 have small initial irreversible capacity loss of 3.2 and 2.2%. • The tubular structure shows better discharge capacity than the sheet structure

  10. Nucleic acid helices: I. Structure of M1 RNA from E. coli as determined bypsoralen crosslinking. II. Thermodynamics of the helix-coil transition of DNA oligonucleotides in solutions containing 3. 0 M tetramethylammonium chloride

    Energy Technology Data Exchange (ETDEWEB)

    Lipson, S.E.

    1987-01-01

    This work includes two different investigations examining nucleic acid helices. The first study discusses secondary and tertiary interactions in the RNA moiety of ribonuclease P from Escherichia coli. The second study discusses the thermodynamics of the helix-coil transition of DNA oligonucleotides in solutions containing tetramethylammonium chloride. The RNA moiety of ribonuclease P from Escherichia coli (M1 RNA) has been photoreacted with 4{prime}-hydroxymethyl-4,5{prime}8-trimethylpsoralen and long wave UV light (320-380 nm) in a buffer in which the M1 RNA alone acts as a true catalyst of tRNA processing. Limited specific digestion followed by two dimensional gel electrophoresis yields fragments crosslinked by HMT. The positions of the crosslinks have been determined to within {plus minus}15 nucleotides by photoreversal of the isolated crosslinked fragments and enzymatic sequencing of the resulting RNA. Further assignments of the exact locations of the crosslinks have been made on the known photoreactivity of the psoralen with different bases.

  11. Crystal structure of a helical silver(I coordination polymer based on an unsymmetrical dipyridyl ligand: catena-poly[[silver(I-μ-N-(pyridin-4-ylmethylpyridine-3-amine-κ2N:N′] tetrafluoridoborate methanol hemisolvate

    Directory of Open Access Journals (Sweden)

    Suk-Hee Moon

    2015-11-01

    Full Text Available The asymmetric unit of the title compound, {[AgL]·BF4·0.5CH3OH}n, L = N-(pyridin-4-ylmethylpyridine-3-amine, C11H11N3, contains one AgI ion, one ligand L, one tetrafluoridoborate anion disordered over two orientations in a 0.669 (13:0.331 (13 ratio and one half of a methanol solvent molecule situated on an inversion center. Each AgI ion is coordinated by two N atoms from two L ligands in a distorted linear geometry [N—Ag—N = 174.70 (19°]. Each L ligand bridges two AgI ions, thus forming polymeric helical chains propagating in [010]. In the crystal, Ag...Ag [3.3369 (10 Å] and π–π interactions between the aromatic rings [centroid-to-centroid distance = 3.676 (4 Å] link these chains into layers parallel to (10-1. Ag...F and weak N(C—H...F interactions further consolidate the crystal packing.

  12. Stable structures and potential energy surface of the metallic clusters: Ni, Cu, Ag, Au, Pd, and Pt

    Science.gov (United States)

    Wu, Xia; Sun, Yan

    2017-06-01

    Metallic clusters have been widely studied due to their special electrical, optical, and catalytic properties. The many-body Gupta potential is applied to describe the interatomic interaction of Ni, Cu, Ag, Au, Pd, and Pt clusters, and their global minimal structures within 100 atoms are optimized using dynamic lattice searching (DLS) method. The configurational distribution of global minima is analyzed, and the geometrical difference among these clusters is demonstrated. Results show that the dominant motif of Ni and Cu clusters is the icosahedron, and in Ag and Au clusters the number of decahedra is slightly larger than that of the icosahedra. However, more face-centered cubic (fcc), stacking fault fcc, and amorphous structures are formed in Au clusters than in Ag clusters. Furthermore, the main motif of Pd and Pt clusters is the decahedron. In particular, Ni98 adopts a Leary tetrahedral motif, and Pt54 is a central vacant icosahedron. The difference related to the potential parameters of these metallic clusters is further investigated by energy analysis. Moreover, the potential energy surfaces (PES) of 38-atom metallic clusters is characterized in terms of conformational analysis. It was found that the sequence of the number of local minima on the PES from large to low is Ni, Cu, Ag, Pt, Pd, and Au.

  13. Structural and photoluminescence behavior of thermally stable Eu3+activated CaWO4 nanophosphors via Li+ incorporation

    Science.gov (United States)

    Ramakrishna, P. V.; Lakshmana Rao, T.; Singh, Arvind; Benarji, B.; Dash, S.

    2017-12-01

    We have studied the structural and photo physical analogue of Eu3+ activated CaWO4 nanophosphors via Lithium (Li+ = 2, 5 7 and 10 at.%) ion incorporation. As-prepared (APS) samples were annealed at 900 °C to eliminate unwanted organic moieties present in the sample and to improve crystallinity. The samples are characterized employing X-ray diffraction (XRD), Fourier transform IR spectroscopy (FTIR), UV-VIS spectroscopy, photoluminescence studies and lifetime decay studies. FTIR features an absorption band at ∼832 cm-1, which correspond to its antisymmetric vibrations into Osbnd Wsbnd O band in the WO42- tetrahedron. CaWO4 having the scheelite type structure with C4h point group and I41/a space group. The surface morphology of the samples are studied with Scanning Electron Microscopy (SEM). Lithium Co-doped CaWO4:Eu3+ nanoparticles show red luminescence because of strong host contribution and different energy transfer rates from host to Eu3+ ions under 266 nm excitations. Lithium ion enhances the crystallinity and radiative transition rate thus results in higher emissive property. Calculated CIE co-ordinates of these Li+ doped 900 °C annealed samples under 266 nm excitation is x = 0.65 & y = 0.34, which are closer to the standard of NTSC (x = 0.67 & y = 0.33). This material may be potential candidates for white light emitting diodes.

  14. The high Andes, gene flow and a stable hybrid zone shape the genetic structure of a wide-ranging South American parrot

    Directory of Open Access Journals (Sweden)

    Schaefer H Martin

    2011-06-01

    Full Text Available Abstract Background While the gene flow in some organisms is strongly affected by physical barriers and geographical distance, other highly mobile species are able to overcome such constraints. In southern South America, the Andes (here up to 6,900 m may constitute a formidable barrier to dispersal. In addition, this region was affected by cycles of intercalating arid/moist periods during the Upper/Late Pleistocene and Holocene. These factors may have been crucial in driving the phylogeographic structure of the vertebrate fauna of the region. Here we test these hypotheses in the burrowing parrot Cyanoliseus patagonus (Aves, Psittaciformes across its wide distributional range in Chile and Argentina. Results Our data show a Chilean origin for this species, with a single migration event across the Andes during the Upper/Late Pleistocene, which gave rise to all extant Argentinean mitochondrial lineages. Analyses suggest a complex population structure for burrowing parrots in Argentina, which includes a hybrid zone that has remained stable for several thousand years. Within this zone, introgression by expanding haplotypes has resulted in the evolution of an intermediate phenotype. Multivariate regressions show that present day climatic variables have a strong influence on the distribution of genetic heterogeneity, accounting for almost half of the variation in the data. Conclusions Here we show how huge barriers like the Andes and the regional environmental conditions imposed constraints on the ability of a parrot species to colonise new habitats, affecting the way in which populations diverged and thus, genetic structure. When contact between divergent populations was re-established, a stable hybrid zone was formed, functioning as a channel for genetic exchange between populations.

  15. Numerical simulation of an excited round jet under helical disturbances by three-dimensional discrete vortex method; Helical kakuran ni yoru reiki enkei funryu no uzuho simulation

    Energy Technology Data Exchange (ETDEWEB)

    Izawa, S.; Kiya, M.; Mochizuki, O. [Hokkaido University, Sapporo (Japan)

    1998-09-25

    The evolution of vortical structure in an impulsively started round jet has been studied numerically by means of a three-dimensional vortex blob method. The viscous diffusion of vorticity is approximated by a core spreading model originally proposed by Leonard (1980). The jet is forced by axisymmetric, helical and multiple disturbances. The multiple disturbances are combinations of two helical disturbances of the same mode rotating in the opposite directions. The multiple disturbances are found to enhance both the generation of small-scale structures and the growth rate of the jet. The small-scale structures have highly organized spatial distributions. The core spreading method is effective in aquiring the core overlapping in regions of high extensional rate of strain. 21 refs., 12 figs.

  16. SUPERCONDUCTING HELICAL SNAKE MAGNETS: CONSTRUCTION AND MEASUREMENTS

    International Nuclear Information System (INIS)

    Mackay, W.W.; Anerella, M.; Courant, E.

    1999-01-01

    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 o in a length of 2.4 m. The design and construction of the magnets is described in this paper

  17. Statistical mechanics of helical wormlike chain model

    Science.gov (United States)

    Liu, Ya; Pérez, Toni; Li, Wei; Gunton, J. D.; Green, Amanda

    2011-02-01

    We investigate the statistical mechanics of polymers with bending and torsional elasticity described by the helical wormlike model. Noticing that the energy function is factorizable, we provide a numerical method to solve the model using a transfer matrix formulation. The tangent-tangent and binormal-binormal correlation functions have been calculated and displayed rich profiles which are sensitive to the combination of the temperature and the equilibrium torsion. Their behaviors indicate that there is no finite temperature Lifshitz point between the disordered and helical phases. The asymptotic behavior at low temperature has been investigated theoretically and the predictions fit the numerical results very well. Our analysis could be used to understand the statics of dsDNA and other chiral polymers.

  18. Helical CT of congenital ossicular anomalies

    International Nuclear Information System (INIS)

    Osada, Hisato; Machida, Kikuo; Honda, Norinari

    2001-01-01

    Since January 1996 to December 2000, 26 cases of congenital ossicular anomaly could be diagnosed with helical CT. All cases were unilateral. In 8 patients with malformation of the external ear, CT showed malleoincudal fixation (n=5), malleoincudal fixation and deformed incuts long process (n=1), deformed incus long process (n=1), and partial fusion of malleus neck and incus long process (n=1). In 18 patients with normal external ear, CT showed defect of the incus long process (n=5), defect of both the incus long process and stapes superstructure (n=8, 2 patients with congenital cholesteatoma, 1 with hypoplastic oval window), defect of the stapes superstructure (n=2, 1 patient with oval window absence), defect of the malleus manubrium (n=1), ossification of the stampede's tendon (n=1), and monopod stapes (n=1). Helical CT can evaluate the auditory ossicular chain in detail and is useful for diagnosing congenital ossicular anomaly. (author)

  19. Vacuum systems for the ILC helical undulator

    CERN Document Server

    Malyshev, O B; Clarke, J A; Bailey, I R; Dainton, J B; Malysheva, L I; Barber, D P; Cooke, P; Baynham, E; Bradshaw, T; Brummitt, A; Carr, S; Ivanyushenkov, Y; Rochford, J; Moortgat-Pick, G A

    2007-01-01

    The International Linear Collider (ILC) positron source uses a helical undulator to generate polarized photons of ∼10MeV∼10MeV at the first harmonic. Unlike many undulators used in synchrotron radiation sources, the ILC helical undulator vacuum chamber will be bombarded by photons, generated by the undulator, with energies mostly below that of the first harmonic. Achieving the vacuum specification of ∼100nTorr∼100nTorr in a narrow chamber of 4–6mm4–6mm inner diameter, with a long length of 100–200m100–200m, makes the design of the vacuum system challenging. This article describes the vacuum specifications and calculations of the flux and energy of photons irradiating the undulator vacuum chamber and considers possible vacuum system design solutions for two cases: cryogenic and room temperature.

  20. Recent progress in Large Helical Device experiments

    Energy Technology Data Exchange (ETDEWEB)

    Komori, A.; Morisaki, T.; Mutoh, T.; Sakakibara, S.; Takeiri, Y.; Kumazawa, R.; Kubo, S.; Ida, K.; Morita, S.; Narihara, K.; Shimozuma, T.; Tanaka, K.; Watanabe, K. Y.; Yamada, H.; Yoshinuma, M.; Akiyama, T.; Ashikawa, N.; Beidler, C. D.; Emoto, M.; Fujita, T.

    2005-07-01

    In order to realize the thermonuclear fusion reactor some critical issues to be solved are underlying in our path. The steady state operation with high confinement performance is known to be essential for the purpose. From the view point of economic feasibility, the high beta operation is favorable for the reduction of the construction cost. However compatibility between good confinement and high beta plasma is an important issue for the helical devices. When the plasma shifts outward with an increasing in beta, confinement degradation takes place because orbit of helically trapped particles drifts from the magnetic flux surfaces [1,2]. The restrict of the plasma shift is possible and valid for high-beta plasma production, to be sure, while it is important to investigate the beta-limit determined by the magnetohydrodynamics (MHD) equilibrium and stability, which is an essential subject to repress the confinement degradation due to other causes. (Author)

  1. Ultra-stable Molecule-Surface Architectures at Metal Oxides: Structure, Bonding, and Electron-transfer Processes

    Energy Technology Data Exchange (ETDEWEB)

    Hamers, Robert John

    2013-12-07

    Research funded by this project focused on the development of improved strategies for functionalization of metal oxides to enhance charge-transfer processes relevant to solar energy conversion. Initial studies included Fe2O3, WO3, TiO2, SnO2, and ZnO as model oxide systems; these systems were chosen due to differences in metal oxidation state and chemical bonding types in these oxides. Later studies focused largely on SnO2 and ZnO, as these materials show particularly promising surface chemistry, have high electron mobility, and can be readily grown in both spherical nanoparticles and as elongated nanorods. New molecules were synthesized that allowed the direct chemical assembly of novel nanoparticle ?dyadic? structures in which two different oxide materials are chemically joined, leading to an interface that enhances the separation of of charge upon illumination. We demonstrated that such junctions enhance photocatalytic efficiency using model organic compounds. A separate effort focused on novel approaches to linking dye molecules to SnO2 and ZnO as a way to enhance solar conversion efficiency. A novel type of surface binding through

  2. Helicity non-conserving form factor of the proton

    Energy Technology Data Exchange (ETDEWEB)

    Voutier, E.; Furget, C.; Knox, S. [Universite Joseph Fourier, Grenoble (France)] [and others

    1994-04-01

    The study of the hadron structure in the high Q{sup 2} range contributes to the understanding of the mechanisms responsible for the confinement of quarks and gluons. Among the numerous experimental candidates sensitive to these mechanisms, the helicity non-conserving form factor of the proton is a privileged observable since it is controlled by non-perturbative effects. The authors investigate here the feasibility of high Q{sup 2} measurements of this form factor by means of the recoil polarization method in the context of the CEBAF 8 GeV facility. For that purpose, they discuss the development of a high energy proton polarimeter, based on the H({rvec p},pp) elastic scattering, to be placed at the focal plane of a new hadron spectrometer. It is shown that this experimental method significantly improves the knowledge of the helicity non-conserving form factor of the proton up to 10 GeV{sup 2}/c{sup 2}.

  3. Frequency-domain synthetic aperture focusing for helical ultrasonic imaging

    Science.gov (United States)

    Jin, H.; Chen, J.; Wu, E.; Yang, K.

    2017-04-01

    The synthetic aperture focusing technique (SAFT) is widely used to provide significant improvement in the lateral resolution of ultrasonic images. Frequency-domain SAFT has shown higher accuracy and greater efficiency than time-domain SAFT. However, frequency-domain SAFT should be helix-based for ultrasonic scanning of cylindrical structures such as pipes and axletrees. In this study, a frequency-domain SAFT is proposed for 3D helical ultrasonic imaging applications. This technique adjusts the phase spectra of the images to complete the synthetic aperture focusing process. The focused image is precise because the proposed algorithm is established on the basis of the wave equation in a helical coordinate system. In addition, the algorithm can efficiently separate out point scatterers and present volume scatterers. The experimental results show that the proposed algorithm yields lower side lobes and enhances the angular resolution of the ultrasonic image to approximately 1°- 1.5°, which is much better than the performance of time-domain SAFT. The maximum deviations are only 0.6 mm, 0.5°, and 0.4 mm along the r-axes, θ-axes, and z-axes, respectively, which are appropriate for normal ultrasonic nondestructive testing.

  4. Winding light beams along elliptical helical trajectories

    OpenAIRE

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

    2016-01-01

    Conventional caustic methods in real or Fourier space produced accelerating optical beams only with convex trajectories. We develop a superposition caustic method capable of winding light beams along non-convex trajectories. We ascertain this method by constructing a one-dimensional (1D) accelerating beam moving along a sinusoidal trajectory, and subsequently extending to two-dimensional (2D) accelerating beams along arbitrarily elliptical helical trajectories. We experimentally implement the...

  5. Relational dynamics in the multi-helices knowledge production system

    DEFF Research Database (Denmark)

    Thai, Thi Minh; Hjortsø, Carsten Nico Portefée

    in an emerging economy. Findings highlight the emergence of a fifth-helices knowledge production system includes the state, science and education, industry, international actors, and society. The system comprises two major segments, one associated with the traditional command economy and characterized......-level dynamics are characterized by political ambidexterity that enables the state to maintain control by privileging traditional science and education constituencies, and at the same time support the transition of the knowledge production system towards international methodology and quality standards through......Drawing on the triple helix framework and organizational institutionalism, this article applies a qualitative research approach to analyze structures, institutional logics, power relations that shape inter-organizational relations and the structuration of a knowledge production system...

  6. Experimental investigation of density regimes in the helical divertor at TEXTOR

    International Nuclear Information System (INIS)

    Clever, M.; Brezinsek, S.; Frerichs, H.; Lehnen, M.; Pospieszczyk, A.; Reiter, D.; Samm, U.; Schmitz, O.; Schweer, B.

    2012-01-01

    Using the capabilities of the dynamic ergodic divertor in the limiter tokamak TEXTOR, we have experimentally investigated the hydrogen recycling in a complex, three-dimensional, helical divertor structure similar to divertor structures found in stellarators. The observations were then compared with results from modelling with the three-dimensional transport code EMC3-EIRENE. The measurements showed that the recycling flux at the divertor target increases linearly with increasing plasma density, a high recycling regime is not observed. At highest plasma densities before the density limit disruption, the formation of a poloidally structured and helically inclined radiating belt, a helical divertor MARFE, is observed. The radial penetration depth of the neutral hydrogen particles (λ n ≈ 3 cm) estimated from spectroscopic measurements was found to be often larger than the varying radial extent of the scrape-off layer of the helical divertor (few mm up to 6 cm) which points to convective heat transport reducing parallel temperature gradients and inhibiting flux amplification. The detailed comparison of the experimental observations and the modelling results showed agreement in this high density behaviour confirming the absence of a high recycling regime. Also agreement in the absolute values of the calculated and measured target particle fluxes was observed. Simulations using different cross-field transport coefficients showed, that this agreement is only found above a certain level of cross-field transport (D ⊥ = 1 m 2 s −1 ). (paper)

  7. Functional Aspects of the Solution Structure and Dynamics of PAF, a Highly Stable Antifungal Protein from Penicillium chrysogenum

    Science.gov (United States)

    Batta, Gyula; Barna, Teréz; Gáspári, Zoltán; Sándor, Szabolcs; Kövér, Katalin E.; Binder, Ulrike; Sarg, Bettina; Kaiserer, Lydia; Chhillar, Anil Kumar; Eigentler, Andrea; Leiter, Éva; Hegedüs, Nikoletta; Pócsi, István; Lindner, Herbert; Marx, Florentine

    2015-01-01

    Summary PAF is a promising antimycotic without toxic effects on mammalian cells and therefore may be a drug candidate against the often lethal Aspergillus infections in human. The pathogenesis of PAF on sensitive fungi involves G-protein coupled signaling followed by apoptosis. Here, the solution structure of this small, cationic, antifungal protein from Penicillium chrysogenum is determined by solution NMR. We proved that PAF belongs to the SCOP fold class of its closest homologue AFP from Aspergillus giganteus. PAF comprises five β—strands forming two orthogonally packed β—sheets sharing a common interface. The ambiguity in the assignment of two disulfide bonds of three was investigated by NMR dynamics combined with restrained molecular dynamics calculations. The clue could not be resolved: two ensembles with different disulfide patterns and the one with no S-S bond exhibit essentially the same fold. 15N relaxation dispersion and interference experiments did not reveal disulfide bond rearrangements via slow exchange. The measured order parameters and the 3.0 ns correlation time is appropriate for a compact monomeric protein of this size. We demonstrated by site-directed mutagenesis that the highly conserved and positively charged lysine-rich domain region on the surface enhances the toxicity of PAF. However, the efficacy of the OB fold is reduced in PAF compared to AFP, due to less solvent exposed aromatic regions explaining the absence of chitobiose binding. The present work lends further support to the understanding of the documented substantial differences between the mode of action of two highly homologous antifungal proteins. PMID:19459942

  8. Superconducting Helical Snake Magnet for the AGS

    CERN Document Server

    Willen, Erich; Escallier, John; Ganetis, George; Ghosh, Arup; Gupta, Ramesh C; Harrison, Michael; Jain, Animesh K; Luccio, Alfredo U; MacKay, William W; Marone, Andrew; Muratore, Joseph F; Okamura, Masahiro; Plate, Stephen R; Roser, Thomas; Tsoupas, Nicholaos; Wanderer, Peter

    2005-01-01

    A superconducting helical magnet has been built for polarized proton acceleration in the Brookhaven AGS. This "partial Snake" magnet will help to reduce the loss of polarization of the beam due to machine resonances. It is a 3 T magnet some 1940 mm in magnetic length in which the dipole field rotates with a pitch of 0.2053 degrees/mm for 1154 mm in the center and a pitch of 0.3920 degrees/mm for 393 mm in each end. The coil cross-section is made of two slotted cylinders containing superconductor. In order to minimize residual offsets and deflections of the beam on its orbit through the Snake, a careful balancing of the coil parameters was necessary. In addition to the main helical coils, a solenoid winding was built on the cold bore tube inside the main coils to compensate for the axial component of the field that is experienced by the beam when it is off-axis in this helical magnet. Also, two dipole corrector magnets were placed on the same tube with the solenoid. A low heat leak cryostat was built so that t...

  9. THE EFFECTS OF SPATIAL SMOOTHING ON SOLAR MAGNETIC HELICITY PARAMETERS AND THE HEMISPHERIC HELICITY SIGN RULE

    Energy Technology Data Exchange (ETDEWEB)

    Ocker, Stella Koch [Department of Physics, Oberlin College, Oberlin, OH 44074 (United States); Petrie, Gordon, E-mail: socker@oberlin.edu, E-mail: gpetrie@nso.edu [National Solar Observatory, Boulder, CO 80303 (United States)

    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.

  10. Hydrodynamic studies of CNT nanofluids in helical coil heat exchanger

    Science.gov (United States)

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

    2017-12-01

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

  11. Locomotion of helical bodies in viscoelastic fluids: enhanced swimming at large helical amplitudes.

    Science.gov (United States)

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

    2013-08-09

    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.

  12. Helical muon beam cooling channel engineering design

    Energy Technology Data Exchange (ETDEWEB)

    Johnson, Rolland [Muons, Inc., Batavia, IL (United States)

    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

  13. Helical muon beam cooling channel engineering design

    International Nuclear Information System (INIS)

    Johnson, Rolland

    2015-01-01

    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. 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 Nb 3 Sn-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 Nb 3 Sn 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 Nb 3 Sn solenoid as originally planned. Instead, a complementary project was approved by the

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

    Science.gov (United States)

    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

  15. Application of nitrogen and carbon stable isotopes (δ(15N and δ(13C to quantify food chain length and trophic structure.

    Directory of Open Access Journals (Sweden)

    Matthew J Perkins

    Full Text Available Increasingly, stable isotope ratios of nitrogen (δ(15N and carbon (δ(13C are used to quantify trophic structure, though relatively few studies have tested accuracy of isotopic structural measures. For laboratory-raised and wild-collected plant-invertebrate food chains spanning four trophic levels we estimated nitrogen range (NR using δ(15N, and carbon range (CR using δ(13C, which are used to quantify food chain length and breadth of trophic resources respectively. Across a range of known food chain lengths we examined how NR and CR changed within and between food chains. Our isotopic estimates of structure are robust because they were calculated using resampling procedures that propagate variance in sample means through to quantified uncertainty in final estimates. To identify origins of uncertainty in estimates of NR and CR, we additionally examined variation in discrimination (which is change in δ(15N or δ(13C from source to consumer between trophic levels and among food chains. δ(15N discrimination showed significant enrichment, while variation in enrichment was species and system specific, ranged broadly (1.4‰ to 3.3‰, and importantly, propagated variation to subsequent estimates of NR. However, NR proved robust to such variation and distinguished food chain length well, though some overlap between longer food chains infers a need for awareness of such limitations. δ(13C discrimination was inconsistent; generally no change or small significant enrichment was observed. Consequently, estimates of CR changed little with increasing food chain length, showing the potential utility of δ(13C as a tracer of energy pathways. This study serves as a robust test of isotopic quantification of food chain structure, and given global estimates of aquatic food chains approximate four trophic levels while many food chains include invertebrates, our use of four trophic level plant-invertebrate food chains makes our findings relevant for a majority

  16. Application of Nitrogen and Carbon Stable Isotopes (δ15N and δ13C) to Quantify Food Chain Length and Trophic Structure

    Science.gov (United States)

    Perkins, Matthew J.; McDonald, Robbie A.; van Veen, F. J. Frank; Kelly, Simon D.; Rees, Gareth; Bearhop, Stuart

    2014-01-01

    Increasingly, stable isotope ratios of nitrogen (δ15N) and carbon (δ13C) are used to quantify trophic structure, though relatively few studies have tested accuracy of isotopic structural measures. For laboratory-raised and wild-collected plant-invertebrate food chains spanning four trophic levels we estimated nitrogen range (NR) using δ15N, and carbon range (CR) using δ13C, which are used to quantify food chain length and breadth of trophic resources respectively. Across a range of known food chain lengths we examined how NR and CR changed within and between food chains. Our isotopic estimates of structure are robust because they were calculated using resampling procedures that propagate variance in sample means through to quantified uncertainty in final estimates. To identify origins of uncertainty in estimates of NR and CR, we additionally examined variation in discrimination (which is change in δ15N or δ13C from source to consumer) between trophic levels and among food chains. δ15N discrimination showed significant enrichment, while variation in enrichment was species and system specific, ranged broadly (1.4‰ to 3.3‰), and importantly, propagated variation to subsequent estimates of NR. However, NR proved robust to such variation and distinguished food chain length well, though some overlap between longer food chains infers a need for awareness of such limitations. δ13C discrimination was inconsistent; generally no change or small significant enrichment was observed. Consequently, estimates of CR changed little with increasing food chain length, showing the potential utility of δ13C as a tracer of energy pathways. This study serves as a robust test of isotopic quantification of food chain structure, and given global estimates of aquatic food chains approximate four trophic levels while many food chains include invertebrates, our use of four trophic level plant-invertebrate food chains makes our findings relevant for a majority of ecological systems

  17. Application of nitrogen and carbon stable isotopes (δ(15)N and δ(13)C) to quantify food chain length and trophic structure.

    Science.gov (United States)

    Perkins, Matthew J; McDonald, Robbie A; van Veen, F J Frank; Kelly, Simon D; Rees, Gareth; Bearhop, Stuart

    2014-01-01

    Increasingly, stable isotope ratios of nitrogen (δ(15)N) and carbon (δ(13)C) are used to quantify trophic structure, though relatively few studies have tested accuracy of isotopic structural measures. For laboratory-raised and wild-collected plant-invertebrate food chains spanning four trophic levels we estimated nitrogen range (NR) using δ(15)N, and carbon range (CR) using δ(13)C, which are used to quantify food chain length and breadth of trophic resources respectively. Across a range of known food chain lengths we examined how NR and CR changed within and between food chains. Our isotopic estimates of structure are robust because they were calculated using resampling procedures that propagate variance in sample means through to quantified uncertainty in final estimates. To identify origins of uncertainty in estimates of NR and CR, we additionally examined variation in discrimination (which is change in δ(15)N or δ(13)C from source to consumer) between trophic levels and among food chains. δ(15)N discrimination showed significant enrichment, while variation in enrichment was species and system specific, ranged broadly (1.4‰ to 3.3‰), and importantly, propagated variation to subsequent estimates of NR. However, NR proved robust to such variation and distinguished food chain length well, though some overlap between longer food chains infers a need for awareness of such limitations. δ(13)C discrimination was inconsistent; generally no change or small significant enrichment was observed. Consequently, estimates of CR changed little with increasing food chain length, showing the potential utility of δ(13)C as a tracer of energy pathways. This study serves as a robust test of isotopic quantification of food chain structure, and given global estimates of aquatic food chains approximate four trophic levels while many food chains include invertebrates, our use of four trophic level plant-invertebrate food chains makes our findings relevant for a majority of

  18. Starch Catabolism by a Prominent Human Gut Symbiont Is Directed by the Recognition of Amylose Helices

    Energy Technology Data Exchange (ETDEWEB)

    Koropatkin, Nicole M.; Martens, Eric C.; Gordon, Jeffrey I.; Smith, Thomas J. (WU); (Danforth)

    2009-01-12

    The human gut microbiota performs functions that are not encoded in our Homo sapiens genome, including the processing of otherwise undigestible dietary polysaccharides. Defining the structures of proteins involved in the import and degradation of specific glycans by saccharolytic bacteria complements genomic analysis of the nutrient-processing capabilities of gut communities. Here, we describe the atomic structure of one such protein, SusD, required for starch binding and utilization by Bacteroides thetaiotaomicron, a prominent adaptive forager of glycans in the distal human gut microbiota. The binding pocket of this unique {alpha}-helical protein contains an arc of aromatic residues that complements the natural helical structure of starch and imposes this conformation on bound maltoheptaose. Furthermore, SusD binds cyclic oligosaccharides with higher affinity than linear forms. The structures of several SusD/oligosaccharide complexes reveal an inherent ligand recognition plasticity dominated by the three-dimensional conformation of the oligosaccharides rather than specific interactions with the composite sugars.

  19. System assessment of helical reactors in comparison with tokamaks

    International Nuclear Information System (INIS)

    Yamazaki, K.; Imagawa, S.; Muroga, T.; Sagara, A.; Okamura, S.

    2002-01-01

    A comparative assessment of tokamak and helical reactors has been performed using equivalent physics/engineering model and common costing model. Higher-temperature plasma operation is required in tokamak reactors to increase bootstrap current fraction and to reduce current-drive (CD) power. In helical systems, lower-temperature operation is feasible and desirable to reduce helical ripple transport. The capital cost of helical reactor is rather high, however, the cost of electricity (COE) is almost same as that of tokamak reactor because of smaller re-circulation power (no CD power) and less-frequent blanket replacement (lower neutron wall loading). The standard LHD-type helical reactor with 5% beta value is economically equivalent to the standard tokamak with 3% beta. The COE of lower-aspect ratio helical reactor is on the same level of high-β N tokamak reactors. (author)

  20. Towards tricking a pathogen's protease into fighting infection: the 3D structure of a stable circularly permuted onconase variant cleavedby HIV-1 protease.

    Directory of Open Access Journals (Sweden)

    Mariona Callís

    Full Text Available Onconase® is a highly cytotoxic amphibian homolog of Ribonuclease A. Here, we describe the construction of circularly permuted Onconase® variants by connecting the N- and C-termini of this enzyme with amino acid residues that are recognized and cleaved by the human immunodeficiency virus protease. Uncleaved circularly permuted Onconase® variants are unusually stable, non-cytotoxic and can internalize in human T-lymphocyte Jurkat cells. The structure, stability and dynamics of an intact and a cleaved circularly permuted Onconase® variant were determined by Nuclear Magnetic Resonance spectroscopy and provide valuable insight into the changes in catalytic efficiency caused by the cleavage. The understanding of the structural environment and the dynamics of the activation process represents a first step toward the development of more effective drugs for the treatment of diseases related to pathogens expressing a specific protease. By taking advantage of the protease's activity to initiate a cytotoxic cascade, this approach is thought to be less susceptible to known resistance mechanisms.

  1. Plasmodium vivax antigen discovery based on alpha-helical coiled coil protein motif.

    Directory of Open Access Journals (Sweden)

    Nora Céspedes

    Full Text Available Protein α-helical coiled coil structures that elicit antibody responses, which block critical functions of medically important microorganisms, represent a means for vaccine development. By using bioinformatics algorithms, a total of 50 antigens with α-helical coiled coil motifs orthologous to Plasmodium falciparum were identified in the P. vivax genome. The peptides identified in silico were chemically synthesized; circular dichroism studies indicated partial or high α-helical content. Antigenicity was evaluated using human sera samples from malaria-endemic areas of Colombia and Papua New Guinea. Eight of these fragments were selected and used to assess immunogenicity in BALB/c mice. ELISA assays indicated strong reactivity of serum samples from individuals residing in malaria-endemic regions and sera of immunized mice, with the α-helical coiled coil structures. In addition, ex vivo production of IFN-γ by murine mononuclear cells confirmed the immunogenicity of these structures and the presence of T-cell epitopes in the peptide sequences. Moreover, sera of mice immunized with four of the eight antigens recognized native proteins on blood-stage P. vivax parasites, and antigenic cross-reactivity with three of the peptides was observed when reacted with both the P. falciparum orthologous fragments and whole parasites. Results here point to the α-helical coiled coil peptides as possible P. vivax malaria vaccine candidates as were observed for P. falciparum. Fragments selected here warrant further study in humans and non-human primate models to assess their protective efficacy as single components or assembled as hybrid linear epitopes.

  2. Design Studies of Magnet Systems for Muon Helical Cooling Channels

    Energy Technology Data Exchange (ETDEWEB)

    Kashikhin, V.; Kashikhin, V.S.; Lamm, M.J.; Lopes, M.L.; Zlobin, A.V.; /Fermilab; Alsharo' a, M.; Johnson, R.P.; Kahn, Stephen A.; /MUONS Inc., Batavia

    2008-06-25

    Helical cooling channels with superimposed solenoid and helical dipole and quadrupole coils, and a pressurized gas absorber in the aperture offer high efficiency of 6D muon beam cooling. In this paper, we continue design studies and comparison of two basic concepts of magnet system proposed for a helical cooling channel focusing on the high field sections. The results of magnetic analysis and Lorentz force calculations as well as the superconductor choice are presented and discussed.

  3. Performance studies of oil lubricated helical groove journal bearing

    OpenAIRE

    Khan, Muhammad Zubair

    1992-01-01

    This thesis was submitted for the degree of Doctor of Philosophy and awarded by Brunel University. The provision of helical grooves on the surface of a plain journal bearing can improve the stability of a rotor-bearing system. However, the improvement depends on the arrangement of the grooves along the axial length of the bearing. In order to verify this improved stability three types of helical groove bearing and a reference plain journal bearing were investigated. The helical groove jour...

  4. Helical Polyisocyanopeptides as Lyotropic Liquid Crystals for Measuring Residual Dipolar Couplings.

    Science.gov (United States)

    Li, Gao-Wei; Cao, Jiang-Ming; Zong, Wen; Hu, Li; Hu, Mao-Lin; Lei, Xinxiang; Sun, Han; Tan, Ren Xiang

    2017-06-07

    Residual dipolar couplings (RDC) emerged to be an important structural parameter for organic and biomolecules. Herein, a new helical polyisocyanopeptide (l,l-PIAF-OBn) that forms lyotropic liquid crystals (LLC) in CDCl 3 is proposed as a novel weakly orienting medium for acquiring residual dipolar couplings (RDCs) of organic molecules. We demonstrate its application for the structural elucidation of strychnine and triptolide. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. How curved membranes recruit amphipathic helices and protein anchoring motifs.

    Science.gov (United States)

    Hatzakis, Nikos S; Bhatia, Vikram K; Larsen, Jannik; Madsen, Kenneth L; Bolinger, Pierre-Yves; Kunding, Andreas H; Castillo, John; Gether, Ulrik; Hedegård, Per; Stamou, Dimitrios

    2009-11-01

    Lipids and several specialized proteins are thought to be able to sense the curvature of membranes (MC). Here we used quantitative fluorescence microscopy to measure curvature-selective binding of amphipathic motifs on single liposomes 50-700 nm in diameter. Our results revealed that sensing is predominantly mediated by a higher density of binding sites on curved membranes instead of higher affinity. We proposed a model based on curvature-induced defects in lipid packing that related these findings to lipid sorting and accurately predicted the existence of a new ubiquitous class of curvature sensors: membrane-anchored proteins. The fact that unrelated structural motifs such as alpha-helices and alkyl chains sense MC led us to propose that MC sensing is a generic property of curved membranes rather than a property of the anchoring molecules. We therefore anticipate that MC will promote the redistribution of proteins that are anchored in membranes through other types of hydrophobic moieties.

  6. Static and dynamic behaviours of helical spring in MR fluid

    International Nuclear Information System (INIS)

    Kaewunruen, S; Akintoye, O; Papaelias, M

    2016-01-01

    MR fluid has been used in automobile industry for vibration suppression device. However its dynamic interaction between structural spring and electro-magnetised MR fluid has not been thoroughly investigated. As a result, this paper highlights static and dynamic behaviours of helical spring interacting with MR fluid magnetised at various levels. Static hysteresis behaviours have been evaluated altogether with the dynamic modal properties of the system. Modal impact hammer testing technique was used to investigate the modal parameters. It is found that MR fluid improves the hysteresis capacity and dynamic properties of the systems when it is electro-magnetised. The outcome of this study will lead to a new development of new spring-dashpot system using MR fluid for better control in adaptive tuneable vibration damping and stiffness suppressing real-time dynamic motions such as the train body, passenger seats, train door, etc. (paper)

  7. Modelling of helical current filaments induced by LHW on EAST

    Energy Technology Data Exchange (ETDEWEB)

    Rack, Michael; Denner, Peter; Liang, Yunfeng [Institute of Energy and Climate Research - Plasma Physics, Forschungszentrum Juelich GmbH, Association EURATOM-FZJ, Partner in the Trilateral Euregio Cluster, D-52425 Juelich (Germany); Zeng, Long [Institute of Energy and Climate Research - Plasma Physics, Forschungszentrum Juelich GmbH, Association EURATOM-FZJ, Partner in the Trilateral Euregio Cluster, D-52425 Juelich (Germany); Institute of Plasma Physics, Chinese Academy of Sciences, Hefei 230031 (China); Gong, Xianzu; Gan, Kaifu; Wang, Liang; Liu, Fukun; Qian, Jinping; Shen, Biao; Li, Jiangang [Institute of Plasma Physics, Chinese Academy of Sciences, Hefei 230031 (China); Gauthier, Eric [Association EURATOM-CEA, IRFM, F-13108 Saint-Paul-lez-Durance (France); Collaboration: the EAST Team

    2013-07-01

    Helical radiation belts have been observed in the scrape-off layer (SOL) of the plasma during the application of lower hybrid wave (LHW) heating at the superconducting tokamak EAST. Modelled SOL field lines, starting in-front of the LHW antennas, show agreement in position and pitch angle to the experimental observed radiation belts. A splitting of the strike-line can be observed on the outer divertor plates during the application of LHW heating. Agreement in the comparison of the Mirnov coil signals and a modelled electric current flow along these SOL field lines was found. A lower hybrid current drive can induce such an electric current flow near the plasma edge. This electric current flow causes a change of the plasma topology which could result in the splitting of the strike-line as known from the application of resonant magnetic perturbation fields. Comparisons of modelled footprint structures and experimental observed heat load patterns in the divertor region are discussed.

  8. Nonlinear MHD simulations of spherical tokamak and helical plasmas

    Energy Technology Data Exchange (ETDEWEB)

    Hayashi, T.; Mizuguchi, N.; Miura, H.; Kanno, R.; Nakajima, N.; Okamoto, M. [National Inst. for Fusion Science, Toki, Gifu (Japan)

    2002-11-01

    Nonlinear magnetohydrodynamic (MHD) simulations on relaxation phenomena in a spherical tokamak and a helical plasma, including three-dimensional (3D) equilibrium computations, are executed in full toroidal geometries. For a spherical tokamak, two-step evolution of the medium-n ballooning instabilities and a successive excitation of an internal n=1 crash has been observed. A similar process has been observed in an actual tokamak experiment of TFTR. The process is compared with a previous simulation for another MHD activity that is called the internal reconnection event (IRE). Three dimensional equilibrium code HINT is modified to extend functions, by which an n=1 island structure used for the local island diverter (LID) experiment in the LHD device is analyzed in finite pressure equilibria. Nonlinear simulations are executed for LHD plasma and pressure deformation due to evolution of m=2/n=1 pressure driven mode is observed, which has larger growth rate and saturation level than medium-n ballooning modes. (author)

  9. Alteration of helical vortex core without change in flow topology

    DEFF Research Database (Denmark)

    Velte, Clara Marika; Okulov, Valery; Hansen, Martin Otto Laver

    2011-01-01

    The abrupt expansion of the slender vortex core with changes in flow topology is commonly known as vortex breakdown. We present new experimental observations of an alteration of the helical vortex core in wall bounded turbulent flow with abrupt growth in core size, but without change in flow...... topology. The helical symmetry as such is preserved, although the characteristic parameters of helical symmetry of the vortex core transfer from a smooth linear variation to a different trend under the influence of a non-uniform pressure gradient, causing an increase in helical pitch without changing its...

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

    Science.gov (United States)

    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.

  11. Rotation influence on the plasma helical instability

    International Nuclear Information System (INIS)

    Gutkin, T.I.; Tsypin, V.S.; Boleslavskaya, G.I.

    1980-01-01

    The influence of the rotation on helical instability of a plasma with the fixed boundaries (HIFB) is investigated taking into account the compressibility. A case of infinitely long cylinder with distributed current is considered. Cases when a rotating plasma is confined by current magnetic field are analytically considered. It is shown that in the case of the fixed boundary taking into account the compressibility in the HIFB increment increases and the picture of the rotation influence on HIFB considerably changes. Besides, it is shown that in the case of high plasma pressures HIFB can stabilize as a result of the rotation

  12. Holographic Metals and Insulators with Helical Symmetry

    CERN Document Server

    Donos, Aristomenis; Kiritsis, Elias

    2014-01-01

    Homogeneous, zero temperature scaling solutions with Bianchi VII spatial geometry are constructed in Einstein-Maxwell-Dilaton theory. They correspond to quantum critical saddle points with helical symmetry at finite density. Assuming $AdS_{5}$ UV asymptotics, the small frequency/(temperature) dependence of the AC/(DC) electric conductivity along the director of the helix are computed. A large class of insulating and conducting anisotropic phases is found, as well as isotropic, metallic phases. Conduction can be dominated by dissipation due to weak breaking of translation symmetry or by a quantum critical current.

  13. Insertion of helical Siberian snakes in RHIC

    International Nuclear Information System (INIS)

    Luccio, A.; Pilat, F.

    1995-01-01

    Spin rotators and Siberian snakes for RHIC can be built using 4 helical magnets obtained, by twisting, from the cosine dipoles. The authors found that the fringe fields are important. In the calculations they have used a plausible model for the fringe. However, only magnetic measurements on the prototypes presently being built will allow a final optimization. The linear coupling at injection, ΔQ min -2 , is well within the range of the RHIC decoupling system. At storage, the coupling introduced by the devices (ΔQ min -4 ) is negligible

  14. Preliminary examination of food web structure of Nicola Lake (Taim Hydrological System, south Brazil using dual C and N stable isotope analyses

    Directory of Open Access Journals (Sweden)

    Alexandre M. Garcia

    Full Text Available Taim Ecological Reserve is located within the Taim Hydrological System and was created to protect a heterogeneous and productive landscape harboring exceptional biological diversity in southern Brazil. Using stable isotope ratio analyses of carbon (delta13C and nitrogen (delta15N, we provide a preliminary description of the food web structure, including estimates of production sources supporting fish populations and vertical trophic structure, within a representative lake of this system. A total of 21 organisms (5 macrophytes, 3 mollusks and 13 adult fishes representing 16 species were collected for isotope analysis. Fishes had delta13C values ranging from -24.30º/oo to -28.31º/oo , showing concordance with the range of values observed for macrophytes (-25.49 to -27.10º/oo, and suggesting that these plants could be a major carbon source supporting these fishes. delta13C signatures of Corbicula (-30.81º/oo and Pomacea (-24.26º/oo indirectly suggest that phytoplankton and benthic algae could be alternative carbon sources for some consumers. Nitrogen isotope ratios indicated approximately three consumer trophic levels. The pearl cichlid Geophagus brasiliensis was a primary consumer. Two catfishes (Trachelyopterus lucenai and Loricariichthys anus were secondary consumers. Two congeneric pike cichclids (Crenicichla lepidota and C. punctata, a catfish (Pimelodus maculatus and the characids Astyanax fasciatus and Oligosarcus robustus were tertiary consumers. Further studies including additional primary producers and consumers and greater sample numbers should be conducted to provide a more complete and detailed description of food web structure and dynamics within the reserve.

  15. Stretchable Helical Architecture Inorganic-Organic Hetero Thermoelectric Generator

    KAUST Repository

    Rojas, Jhonathan Prieto

    2016-10-26

    To achieve higher power output from a thermoelectric generator (TEG), one needs to maintain a larger temperature difference between hot and cold end. In that regard, a stretchable TEG can be interesting to adaptively control the temperature difference. Here we show, the development of simple yet versatile and highly stretchable thermoelectric generators (TEGs), by combining well-known inorganic thermoelectric materials Bismuth Telluride and Antimony Telluride (Bi2Te3 and Sb2Te3) with organic substrates (Off-Stoichiometry Thiol-Enes polymer platform – OSTE, polyimide or paper) and novel helical architecture (double-arm spirals) to achieve over 100% stretchability. First, an OSTE-based TEG design demonstrates higher open circuit voltage generation at 100% strain than at rest, although it exhibits high internal resistance and a relatively complex fabrication process. The second, simpler TEG design, achieves a significant resistance reduction and two different structural substrates (PI and paper) are compared. The paper-based TEG generates 17 nW (ΔT = 75 °C) at 60% strain, which represents more than twice the power generation while at rest (zero strain). On the other hand, polyimide produces more conductive TE films and higher power (~35 nW at ΔT = 75 °C) but due to its higher thermal conductivity, power does not increase at stretch. In conclusion, highly stretchable TEGs can lead to higher temperature gradients (thus higher power generation), given that thermal conductivity of the structural material is low enough. Furthermore, either horizontal or vertical displacement can be achieved with double-arm helical architecture, hence allowing to extend the device to any nearby and mobile heat sink for continuous, effectively higher power generation.

  16. What Helicity Can Tell Us about Solar Magnetic Fields Alexei A ...

    Indian Academy of Sciences (India)

    damental properties as hemispheric helicity rule, and role of helicity in magnetic reconnection and ... however, might not be always practical especially if one has no physical access to an object. Alternatively, one .... magnetic helicity), it has the same sign as Hm. Two different helicity proxies based on current helicity were ...

  17. Electronic transport in single-helical protein molecules: Effects of multiple charge conduction pathways and helical symmetry

    Energy Technology Data Exchange (ETDEWEB)

    Kundu, Sourav, E-mail: sourav.kunduphy@gmail.com; Karmakar, S.N.

    2016-07-15

    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.

  18. The geometrical origin of the strain-twist coupling in double helices

    Directory of Open Access Journals (Sweden)

    Kasper Olsen

    2011-03-01

    Full Text Available A simple geometrical explanation for the counterintuitive phenomenon when twist leads to extension in double helices is presented. The coupling between strain and twist is investigated using a tubular description. It is shown that the relation between strain and rotation is universal and depends only on the pitch angle. For pitch angles below 39.4° strain leads to further winding, while for larger pitch angles strain leads to unwinding. The zero-twist structure, with a pitch angle of 39.4°, is at the unique point between winding and unwinding and independent of the mechanical properties of the double helix. The existence of zero-twist structures, i.e. structures that display neither winding, nor unwinding under strain is discussed. Close-packed double helices are shown to extend rather than shorten when twisted. Numerical estimates of this elongation upon winding are given for DNA, chromatin, and RNA.

  19. Highlights from the assembly of the helical field coils for the Advanced Toroidal Facility

    International Nuclear Information System (INIS)

    Benson, R.D.

    1985-01-01

    The helical field (HF) coils in the Advanced Toroidal Facility (ATF) device consist of a set of 24 identical segments connected to form a continuous pair of helical coils wrapped around a toroidal vacuum vessel. Each segment weighs approximately 1364 kg (3000 lb) and is composed of 14 water-cooled copper plate conductors bolted to a cast stainless steel structural support member with a T-shape cross section (known as the structural tee). The segment components are electrically insulated with Kapton adhesive tape, G-10, Tefzel, and rubber to withstand 2.5 kV. As a final insulator and structural support, the entire segment is vacuum impregnated with epoxy. This paper offers a brief overview of the processes used to assemble the component parts into a completed segment, including identification of items that required special attention. 4 figs

  20. Conceptual design of the superconducting magnet system for the helical fusion reactor

    International Nuclear Information System (INIS)

    Yanagi, Nagato; Hamaguchi, Shinji; Takahata, Kazuya; Natsume, Kyohei

    2013-01-01

    Current status of conceptual design of superconducting magnet system and low temperature system for the helical fusion reactor are introduced. There are three kinds of candidates of superconducting magnets such as Cable-in-conduit (CIC), Low-Temperature Superconductor (LTS) and High-Temperature Superconductor (HTS). Their characteristic properties, coil designs and cooling systems are stated. The freezer and low temperature distribution system, bus line and current lead, and excitation power source for superconducting coil are reported. The various elements of superconducting magnet system of FFHR-d1, partial cross section of FFHR helical coil using CIC, conceptual diagram of helical coil winding method of FFHR using CIC, relation among mass flow of supercritical helium supplied into CIC conductor and temperature increasing and pressure loss, cross section structure of LTS indirect-cooling conductor at 100 kA, cross section of 100-kA HTS conductor, connection method of helical coil segment and YBCO conductor are illustrated. (S.Y.)