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Sample records for helical pulseline structures

  1. Helical Pulseline Structures for Ion Acceleration

    CERN Document Server

    Briggs, R J; Waldron, William

    2005-01-01

    The basic concept of the "Pulseline Ion Accelerator" involves launching a ramped high voltage pulse on a broad band traveling wave (slow-wave) structure. An applied voltage pulse at the input end with a segment rising linearly in time becomes a linear voltage ramp in space that propagates down the line, corresponding to a (moving) region of constant axial accelerating electric field. The ions can "surf" on this traveling wave, experiencing a total energy gain that can greatly exceed the peak of the applied voltage. The applied voltage waveform can also be shaped to longitudinally confine the beam against its own space charge forces, and (in the final stage) to impart an inward compression to the beam for neutralized drift compression in heavy ion HEDP applications. In the first stages of a heavy ion accelerator, the pulseline velocity needs to be the order of 1% of the speed of light and the line must be sufficiently non-dispersive for the broad band voltage pulse propagating down the line to have minimal dis...

  2. 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...

  3. Helical surface structures

    CERN Document Server

    Brandenburg, A; Brandenburg, Axel; Blackman, Eric G.

    2002-01-01

    Over the past few years there has been growing interest in helical magnetic field structures seen at the solar surface, in coronal mass ejections, as well as in the solar wind. Although there is a great deal of randomness in the data, on average the extended structures are mostly left-handed on the northern hemisphere and right-handed on the southern. Surface field structures are also classified as dextral (= right bearing) and sinistral (= left bearing) occurring preferentially in the northern and southern hemispheres respectively. Of particular interest here is a quantitative measurement of the associated emergence rates of helical structures, which translate to magnetic helicity fluxes. In this review, we give a brief survey of what has been found so far and what is expected based on models. Particular emphasis is put on the scale dependence of the associated fields and an attempt is made to estimate the helicity flux of the mean field vs. fluctuating field.

  4. The helical structure of DNA facilitates binding

    Science.gov (United States)

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

    2016-09-01

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

  5. Electronic structure calculations on helical conducting polymers.

    Science.gov (United States)

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

    2010-10-21

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

  6. Cryo-EM Structure Determination Using Segmented Helical Image Reconstruction.

    Science.gov (United States)

    Fromm, S A; Sachse, C

    2016-01-01

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

  7. Synthesis and structure of neutral double helicate

    Institute of Scientific and Technical Information of China (English)

    SU, Xun-Cheng; ZHOU, Zhi-Fen; ZHU, Shou-Rong; CHEN, Yun-Ti; LENG, Xue-Bing; WENG, Lin-Hong; LIN, Hua-Kuan

    2000-01-01

    A new approach to geaerating supramolecular architectures, based on easy-to-prepare sehiff base ligands, is described to gether with its application to the self-assembly of supramolecu lar neutral double helicates.

  8. A survey of left-handed helices in protein structures.

    Science.gov (United States)

    Novotny, Marian; Kleywegt, Gerard J

    2005-03-25

    All naturally occurring amino acids with the exception of glycine contain one or more chiral carbon atoms and can therefore occur in two different configurations, L (levo, left-handed) and D (dextro, right-handed). Proteins are almost exclusively built from L-amino acids. The stereochemical bias of nature is further reflected at the secondary structure level where right-handed helices are strongly preferred over left-handed helices. The handedness of helices has not received much attention in the past and is often overlooked during the analysis, description and deposition of experimentally solved protein structures. Therefore, an extensive survey of left-handed helices in the Protein Data Bank (PDB) was undertaken to analyse their frequency of occurrence, length, amino acid composition, conservation and possible structural or functional role. All left-handed helices (of four or more residues) in a non-redundant subset of the PDB, were identified using hydrogen-bonding analysis, comparison of related structures, and experimental electron density assessment to filter out likely spurious and artefactual hits. This analysis yielded 31 verified left-handed helices in a set of 7284 proteins. The phi angles of the residues in the left-handed helices lie between 30 degrees and 130 degrees and the psi angles lie between -50 degrees and 100 degrees . Most of the helices are short (four residues) and for 87% of them, it was possible to determine that they are important for the stability of the protein, for ligand binding, or as part of the active site. This suggests that, even though left-handed helices are rare, when they do occur, they are structurally or functionally significant. Four secondary structure assignment programs were tested for their ability to identify the handedness of the helices. Of these programs, only DSSP correctly assigns the handedness.

  9. First Helical Structure in the Nano-world

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    @@ Although a commonplace structure in nature, the helix remains a mystery to scientific researchers. In biology,the structure is important as DNA is helical and so does the substructure of many proteins. Since its discovery more than 50 years ago, the double helix has offered an important approach to interpret and make use of bio-organic structures. Yet, it is seldom to see a helical structure formed by inorganic crystalstate materials.

  10. The Writhe of Helical Structures in the Solar Corona

    Science.gov (United States)

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

    2010-01-01

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

  11. Supramolecular helices: chirality transfer from conjugated molecules to structures.

    Science.gov (United States)

    Yang, Yang; Zhang, Yajie; Wei, Zhixiang

    2013-11-13

    Different scales of chirality endow a material with many excellent properties and potential applications. In this review, using π-conjugated molecules as functional building blocks, recent progress on supramolecular helices inspired by biological helicity is summarized. First, induced chirality on conjugated polymers and small molecules is introduced. Molecular chirality can be amplified to nanostructures, superstructures, and even macroscopic structures by a self-assembly process. Then, the principles for tuning the helicity of supramolecular chirality, as well as formation of helical heterojunctions, are summarized. Finally, the potential applications of chiral structures in chiral sensing and organic electronic devices are critically reviewed. Due to recent progress in chiral structures, an interdisciplinary area called "chiral electronics" is expected to gain wide popularity in the near future.

  12. The Role of Magnetic Helicity in Structuring the Solar Corona

    Science.gov (United States)

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

    2017-01-01

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

  13. Variation in the Helical Structure of Native Collagen

    Science.gov (United States)

    2014-02-24

    Hongo C, Noguchi K (2006) Helical twists of collagen model peptides. Biopolymers 84: 421–432. 39. Kramer R, Bella J, Mayville P, Brodsky B, Berman H...Iguchi M, Noguchi K (2006) Revision of collagen molecular structure. Biopolymers 84: 181–191. 43. Shoulders MD, Raines RT (2009) Collagen structure

  14. The Role of Magnetic Helicity in Structuring the Solar Corona

    Science.gov (United States)

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

    2017-01-01

    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.

  15. 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.

  16. Conservation of helical bundle structure between the exocyst subunits.

    Directory of Open Access Journals (Sweden)

    Nicole J Croteau

    Full Text Available BACKGROUND: The exocyst is a large hetero-octomeric protein complex required for regulating the targeting and fusion of secretory vesicles to the plasma membrane in eukaryotic cells. Although the sequence identity between the eight different exocyst subunits is less than 10%, structures of domains of four of the subunits revealed a similar helical bundle topology. Characterization of several of these subunits has been hindered by lack of soluble protein for biochemical and structural studies. METHODOLOGY/PRINCIPAL FINDINGS: Using advanced hidden Markov models combined with secondary structure predictions, we detect significant sequence similarity between each of the exocyst subunits, indicating that they all contain helical bundle structures. We corroborate these remote homology predictions by identifying and purifying a predicted domain of yeast Sec10p, a previously insoluble exocyst subunit. This domain is soluble and folded with approximately 60% alpha-helicity, in agreement with our predictions, and capable of interacting with several known Sec10p binding partners. CONCLUSIONS/SIGNIFICANCE: Although all eight of the exocyst subunits had been suggested to be composed of similar helical bundles, this has now been validated by our hidden Markov model structure predictions. In addition, these predictions identified protein domains within the exocyst subunits, resulting in creation and characterization of a soluble, folded domain of Sec10p.

  17. Structural mechanics and helical geometry of thin elastic composites.

    Science.gov (United States)

    Wada, Hirofumi

    2016-09-21

    Helices are ubiquitous in nature, and helical shape transition is often observed in residually stressed bodies, such as composites, wherein materials with different mechanical properties are glued firmly together to form a whole body. Inspired by a variety of biological examples, the basic physical mechanism responsible for the emergence of twisting and bending in such thin composite structures has been extensively studied. Here, we propose a simplified analytical model wherein a slender membrane tube undergoes a helical transition driven by the contraction of an elastic ribbon bound to the membrane surface. We analytically predict the curvature and twist of an emergent helix as functions of differential strains and elastic moduli, which are confirmed by our numerical simulations. Our results may help understand shapes observed in different biological systems, such as spiral bacteria, and could be applied to novel designs of soft machines and robots.

  18. Stabilization of helical magnetic structures in thin multilayers

    OpenAIRE

    Dzemiantsova, L. V.; Meier, G.; R. Röhlsberger

    2014-01-01

    Based on micromagnetic simulations, we report on a novel helical magnetic structure in a soft magnetic film that is sandwiched between and exchange-coupled to two hard magnetic layers. Confined between antiparallel hard magnetic moments, a helix with a turn of 180$^{\\circ}$ is stable without the presence of an external magnetic field. The magnetic stability is determined by the energy minimization and is a result of an internal field created by exchange interaction and anisotropy. Since the i...

  19. 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.

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

    DEFF Research Database (Denmark)

    Olsen, Kasper; Bohr, Jakob

    2010-01-01

    The formation of helices is an ubiquitous phenomenon for molecular structures whether they are biological, organic, or inorganic, in nature. Helical structures have geometrical constraints analogous to close packing of three-dimensional crystal structures. For helical packing the geometrical cons....... For double helices comparisons are made to the A,B, and Z forms of DNA. The helical geometry of the A form is nearly close-packed. The packing density for the B and Z form are found to be approximately equal to each other....

  1. Domain and wall structures in films with helical magnetization profile

    Energy Technology Data Exchange (ETDEWEB)

    Dubuget, Vincent [Laboratoire d' Electrodynamique des Materiaux Avances, Universite Francois Rabelais, CNRS UMR 6157, Parc de Grandmont, F-37200 Tours (France); CEA, DAM, Le Ripault, F-37260 Monts (France); Thiaville, Andre [Laboratoire de Physique des Solides, Universite Paris-Sud, CNRS UMR 8502, Bat. 510, F-91405 Orsay (France); Adenot-Engelvin, Anne-Lise, E-mail: anne-lise.adenot-engelvin@cea.f [CEA, DAM, Le Ripault, F-37260 Monts (France); Duverger, Francois; Dubourg, Sebastien [CEA, DAM, Le Ripault, F-37260 Monts (France)

    2011-06-15

    We study soft magnetic bilayers having orthogonal, in-plane easy axes. The layers are thicker than the Bloch wall width linked to the anisotropy, so that a helical magnetization with a large angle exists across the sample thickness. The magnetic domains structure has been investigated at both sample surfaces, using magneto-optical microscopy. The domain structure is found to be similar to that of double films with biquadratic coupling. Two kinds of domain walls are identified, namely with a 90{sup o} and 180{sup o} rotation of the average magnetization. The detailed structure and energy of these walls are studied by micromagnetic calculations. - Research highlights: This paper is devoted to the peculiar domain structure resulting from an anisotropy distribution in the thickness of the sample, realized through specific elaboration conditions. The helical magnetization profile obtained leads to a complex dynamic behaviour described and modelled in Phys.Rev. B 80, 134412 (published in October 2009) which has been already cited three times. This paper sheds light on of the demagnetized state of such samples: a variety of domains structure has been observed by Kerr microscopy, under various saturation fields. The most striking conclusion is driven by the analysis of the magnetization process which implies the co-existence of two types of domain walls in the sample, with four possible directions for the mean magnetization. The magnetization profile of the two walls has been confirmed by numerical simulation.

  2. The effect of surface adsorption on tertiary structure formation in helical polymers

    Science.gov (United States)

    Williams, Matthew J.; Bachmann, Michael

    2017-07-01

    The formation of tertiary structures made up of helical polymer segments is influenced by the introduction of an attractive substrate onto which the polymer can adsorb. We perform replica-exchange Monte Carlo simulations to study the formation of helical structures in the vicinity of an attractive generic substrate by means of a coarse-grained hybrid model and compare the structural phase space for both adsorbed and free helical polymers. We introduce suitable structural order parameters to understand the features of distinct structural phases. Hyperphase diagrams, parameterized by the torsional energy scale and temperature, enable the investigation of structural properties of entire classes of helical polymers.

  3. Downstream Evolution of Longitudinal Embedded Vortices with Helical Structure

    DEFF Research Database (Denmark)

    Velte, Clara Marika; Okulov, Valery; Hansen, Martin Otto Laver

    2009-01-01

    In the present work the downstream development of device induced vortices with helical symmetry embedded in wall bounded flow on a bump is studied with the aid of Stereoscopic Particle Image Velocimetry (SPIV). The downstream evolution of characteristic parameters of helical vortices is studied...

  4. 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 electr

  5. Technical Characteristics of a Novel Helical-Groove Traveling-Wave Tube Structure

    Science.gov (United States)

    Wallett, Thomas M.; Vaden, Karl R.; Freeman, Jon; Qureshi, A. Haq

    1998-01-01

    Experimental measurements of the dispersion characteristics of a C-band helix structure were carried out and compared to the dispersion characteristics found from a helix model using the three-dimensional electromagnetic computer code MAFIA. A conceptually novel design comprising a helical thread of the same pitch and inner diameter in a cylindrical waveguide also were calculated using the MAFIA code. The helical-groove structure exhibits a smaller bandwidth but at a much higher frequency range than the traditional helical structure for similar physical dimensions. It is physically more robust in construction. The interaction impedance also compares favorably with those of the conventional structure.

  6. Crystal Structure of Borophosphate with 61 Screw Axis Helices

    Institute of Scientific and Technical Information of China (English)

    石恒真; 单永奎; 戴立益; 刘煜炎; 翁林红

    2003-01-01

    A brilliant purple octahedral single crystal is hydrothermally synthesized by the reaction of CoCl2·6H2O, H3BO3 and H3PO4 in NaOH aqueous solution of CH3(CH2)15N(CH3)3Br, and its crystal structure has been characterized by single-crystal X-ray diffraction. The compound, NaCo(H2O)2BP2O8·H2O (Mr = 336.72), belongs to hexagonal, space group P6122 with a = 9.447(5), c = 15.83(1) (A。), V = 1223(1) (A。)3, Dc = 2.742 g/cm3, Z = 6, F(000) = 1002 and β= 2.606 mm-1. The three-dimensional framework in the compound is built up from the linkage tetrahedral ribbons, in which the BO4 and PO4 tetrahedra alternate with CoO6 octahedra. The sodium ions and water molecules are located within the free thread of the helical ribbons.

  7. 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.

  8. The Role of Magnetic Helicity in Structuring the Solar Corona

    CERN Document Server

    Knizhnik, Kalman J; DeVore, C Richard

    2016-01-01

    Two of the most widely observed and yet most puzzling features of the Sun's magnetic field are coronal loops that are smooth and laminar and prominences/filaments that are strongly sheared. These two features would seem to be quite unrelated in that the loops are near their minimum-energy current-free state, whereas filaments are regions of high magnetic stress and intense electric currents. We argue that, in fact, these two features are inextricably linked in that both are due to 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 \\citet{Parker72} 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 \\citet{Antiochos13}, the inverse cascade of helicity by magnetic reconnection results in the formation of prom...

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

    Energy Technology Data Exchange (ETDEWEB)

    Pagel, M.D. [Univ. of California, Berkeley, CA (United States). Dept. of Chemistry]|[Lawrence Berkeley Lab., CA (United States)

    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 {alpha}-helix, a {open_quotes}scaffold{close_quotes} 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 Ca{sup 2+}-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 {lambda} Cro with the apamin disulfide scaffold. However, Apa-Cro did not bind the consensus DNA operator half-site of {lambda} 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 {alpha}-helix constrained at the C-terminal end by two disulfide bridges and a two-stranded {beta}sheet 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 {sup 15}N NMR relaxation properties.

  10. 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.

  11. Similar structures, different characteristics: circular dichroism of metallic helix arrays with single-, double-, and triple-helical structures.

    Science.gov (United States)

    Zhang, Peng; Yang, Zhenyu; Zhao, Ming; Wu, Lin; Lu, Zeqin; Cheng, Yongzhi; Gong, Rongzhou; Zheng, Yu; Duan, Jian

    2013-04-01

    We fabricated three-dimensional metallic helix arrays with single-, double-, and triple-helical structures. The transmission performances with the normal incident angle were measured in the microwave frequency of 12-18 GHz. For the single- and double-helical structures, giant circular dichroism with fairly wide bands is observed in the transmission spectra. However, the triple-helical structure does not exhibit circular dichroism. Based on the phenomenon of circular dichroism, the single- and double-helical structures can be used as broadband circular polarizers in the microwave region, but triple-helical ones cannot. The experiments have a good agreement with our simulation results, which were studied by the finite-difference time domain method.

  12. Validation of the magnetic energy vs. helicity scaling in solar magnetic structures

    CERN Document Server

    Tziotziou, K; Georgoulis, M K; Archontis, V

    2014-01-01

    We assess the validity of the free magnetic energy - relative magnetic helicity diagram for solar magnetic structures. We used two different methods of calculating the free magnetic energy and the relative magnetic helicity budgets: a classical, volume-calculation nonlinear force-free (NLFF) method applied to finite coronal magnetic structures and a surface-calculation NLFF derivation that relies on a single photospheric or chromospheric vector magnetogram. Both methods were applied to two different data sets, namely synthetic active-region cases obtained by three-dimensional magneto-hydrodynamic (MHD) simulations and observed active-region cases, which include both eruptive and noneruptive magnetic structures. The derived energy--helicity diagram shows a consistent monotonic scaling between relative helicity and free energy with a scaling index 0.84$\\pm$0.05 for both data sets and calculation methods. It also confirms the segregation between noneruptive and eruptive active regions and the existence of thresh...

  13. On the peculiar structure of a helical wake vortex behind an inclined prolate spheroid

    DEFF Research Database (Denmark)

    Jiang, Fengjian; Andersson, Helge I.; Gallardo, José P.;

    2016-01-01

    The self-similarity law for axisymmetric wakes has for the first time been examined and verified in a complex helical vortex in the far part of an asymmetric wake by means of direct numerical simulation (DNS). The helical vortex is the main coherent flow structure in the transitional non......-axisymmetric wake behind an inclined 6:1 prolate spheroid at Reynolds number 3000 based on the minor axis. The gradual development of the complex helical vortex structure has been described in detail all the way from its inception at the spheroid and into the far wake. We observed a complex vortex composition...... in the generation stage, a rare jet-like wake pattern in the near wake and an abrupt change of helical symmetry in the vortex core without an accompanying change in flow topology, i.e. with no recirculation bubble....

  14. Orientation determination of protein helical secondary structures using linear and nonlinear vibrational spectroscopy.

    Science.gov (United States)

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

    2009-09-10

    In this paper, we systematically presented the orientation determination of protein helical secondary structures using vibrational spectroscopic methods, particularly, nonlinear sum frequency generation (SFG) vibrational spectroscopy, along with linear vibrational spectroscopic techniques such as infrared spectroscopy and Raman scattering. SFG amide I signals can be collected using different polarization combinations of the input laser beams and output signal beam to measure the second-order nonlinear optical susceptibility components of the helical amide I modes, which are related to their molecular hyperpolarizability elements through the orientation distribution of these helices. The molecular hyperpolarizability elements of amide I modes of a helix can be calculated based on the infrared transition dipole moment and Raman polarizability tensor of the helix; these quantities are determined by using the bond additivity model to sum over the individual infrared transition dipole moments and Raman polarizability tensors, respectively, of the peptide units (or the amino acid residues). The computed overall infrared transition dipole moment and Raman polarizability tensor of a helix can be validated by experimental data using polarized infrared and polarized Raman spectroscopy on samples with well-aligned helical structures. From the deduced SFG hyperpolarizability elements and measured SFG second-order nonlinear susceptibility components, orientation information regarding helical structures can be determined. Even though such orientation information can also be measured using polarized infrared or polarized Raman amide I signals, SFG has a much lower detection limit, which can be used to study the orientation of a helix when its surface coverage is much lower than a monolayer. In addition, the combination of different vibrational spectroscopic techniques, for example, SFG and attenuated total reflectance Fourier transform infrared spectroscopy, provides more

  15. Structural investigation of amylose complexes with small ligands: helical conformation, crystalline structure and thermostability.

    Science.gov (United States)

    Le Bail, P; Rondeau, C; Buléon, A

    2005-03-01

    Crystalline amylose complexes were prepared with decanal, 1-butanol, menthone and alpha-naphtol. Their crystalline structure and the related helical conformation, determined by wide angle X-ray diffraction (WAXD) and 13C CPMAS solid state NMR, were assigned to V6I, V6II, V6III and V8 types, respectively. It was possible to propose some hypotheses on the possible nature of interactions and especially intra-/inter-helical inclusion. Some shifts in the NMR C1 carbon signals were attributed to the presence of ligand in specific sites inside the structure for a same type of V6 helical conformation. Moreover, the crystallinity and polymorphic changes induced by desorption/rehydration were studied. A general increase of the carbon resonances sharpness upon rehydration has been observed, but also a V6II-V6I transition when decreasing the water content. Differential scanning calorimetry (DSC) experiments were also performed to approach the thermostability of the four types of complex and also the way they form again after melting/cooling sequences.

  16. Computational Investigation of Experimental Interaction Impedance Obtained by Perturbation for Helical Traveling Wave Tube Structures

    Science.gov (United States)

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

    1998-01-01

    Conventional methods used to measure the cold- test interaction impedance of helical slow-wave structures involve perturbing a helical circuit with a cylindrical dielectric rod placed on the central axis of the circuit It has been shown that the difference in resonant frequency or axial phase shift between the perturbed and unperturbed circuits can be related to the interaction impedance. However, because of the complex configuration of the helical circuit, deriving this relationship involves several approximations. With the advent of accurate three-dimensional (3-D) helical circuit models, these standard approximations can be fully Investigated. This paper addresses the most prominent approximations made in the analysis for measured interaction impedance by Lagerstrom and investigates their accuracy using the 3-D simulation code MAFIA. It is shown that a more accurate value of interaction impedance can be obtained by using 3-D computational methods rather than performing costly and time consuming experimental cold-test measurements.

  17. Computational Investigation of Experimental Interaction Impedance Obtained by Perturbation for Helical Traveling-Wave Tube Structures

    Science.gov (United States)

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

    1998-01-01

    Conventional methods used to measure the cold-test interaction impedance of helical slow-wave structures involve perturbing a helical circuit with a cylindrical dielectric rod placed on the central axis of the circuit. It has been shown that the difference in resonant frequency or axial phase shift between the perturbed and unperturbed circuits can be related to the interaction impedance. However, because of the complex configuration of the helical circuit, deriving this relationship involves several approximations. With the advent of accurate three-dimensional (3-D) helical circuit models, these standard approximations can be fully investigated. This paper addresses the most prominent approximations made in the analysis for measured interaction impedance by Lagerstrom and investigates their accuracy using the 3-D simulation code MAFIA. It is shown that a more accurate value of interaction impedance can be obtained by using 3-D computational methods rather than performing costly and time consuming experimental cold-test measurements.

  18. Direct visualization of protease action on collagen triple helical structure.

    Directory of Open Access Journals (Sweden)

    Gabriel Rosenblum

    Full Text Available Enzymatic processing of extracellular matrix (ECM macromolecules by matrix metalloproteases (MMPs is crucial in mediating physiological and pathological cell processes. However, the molecular mechanisms leading to effective physiological enzyme-ECM interactions remain elusive. Only scant information is available on the mode by which matrix proteases degrade ECM substrates. An example is the enzymatic degradation of triple helical collagen II fragments, generated by the collagenase MMP-8 cleavage, during the course of acute inflammatory conditions by gelatinase B/MMP-9. As is the case for many other matrix proteases, it is not clear how MMP-9 recognizes, binds and digests collagen in this important physiological process. We used single molecule imaging to directly visualize this protease during its interaction with collagen fragments. We show that the initial binding is mediated by the diffusion of the protease along the ordered helix on the collagen (3/4 fragment, with preferential binding of the collagen tail. As the reaction progressed and prior to collagen degradation, gelatin-like morphologies resulting from the denaturation of the triple helical collagen were observed. Remarkably, this activity was independent of enzyme proteolysis and was accompanied by significant conformational changes of the working protease. Here we provide the first direct visualization of highly complex mechanisms of macromolecular interactions governing the enzymatic processing of ECM substrates by physiological protease.

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

    Science.gov (United States)

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

    2016-03-01

    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.

  20. 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…

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

    Science.gov (United States)

    Karimi, Afshin

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

  2. Helicity in proton-proton elastic scattering and the spin structure of the pomeron

    Science.gov (United States)

    Ewerz, Carlo; Lebiedowicz, Piotr; Nachtmann, Otto; Szczurek, Antoni

    2016-12-01

    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.

  3. 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.

  4. Helicity in Proton-Proton Elastic Scattering and the Spin Structure of the Pomeron

    CERN Document Server

    Ewerz, Carlo; Nachtmann, Otto; Szczurek, Antoni

    2016-01-01

    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 r_5 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.

  5. 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.

  6. New helical-shape magnetic pole design for Magnetic Lead Screw enabling structure simplification

    DEFF Research Database (Denmark)

    Lu, Kaiyuan; Xia, Yongming; Wu, Weimin

    2015-01-01

    Magnetic lead screw (MLS) is a new type of high performance linear actuator that is attractive for many potential applications. The main difficulty of the MLS technology lies in the manufacturing of its complicated helical-shape magnetic poles. Structure simplification is, therefore, quite essent...

  7. 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 ...

  8. Structural insights for designed alanine-rich helices: Comparing NMR helicity measures and conformational ensembles from molecular dynamics simulation

    Science.gov (United States)

    Song, Kun; Stewart, James M.; Fesinmeyer, R. Matthew

    2013-01-01

    The temperature dependence of helical propensities for the peptides Ac-ZGG-(KAAAA)3X-NH2 (Z = Y or G, X = A, K, and d-Arg) were studied both experimentally and by molecular dynamics simulations. Good agreement is observed in both the absolute helical propensities as well as relative helical content along the sequence; the global minimum on the calculated free energy landscape corresponds to a single α-helical conformation running from K4 – A18 with some terminal fraying, particularly at the C-terminus. Energy component analysis shows that the single helix state has favorable intramolecular electrostatic energy due to hydrogen bonds, and that less-favorable two-helix globular states have favorable solvation energy. The central lysine residues do not appear to increase helicity; however, both experimental and simulation studies show increasing helicity in the series X = Ala → Lys → d-Arg. This C-capping preference was also experimentally confirmed in Ac-(KAAAA)3X-GY-NH2 and (KAAAA)3X-GY-NH2 sequences. The roles of the C-capping groups, and of lysines throughout the sequence, in the MD-derived ensembles are analyzed in detail. PMID:18428207

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

    Science.gov (United States)

    Sankararamakrishnan, R; Samsom, M S

    1994-12-01

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

  10. 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......Structural characterization of intrinsically disordered proteins (IDPs) is mandatory for deciphering their potential unique physical and biological properties. A large number of circular dichroism (CD) studies have demonstrated that a structural change takes place in IDPs with increasing....... This phenomenon was explored at residue resolution by multidimensional NMR spectroscopy. Intrinsic chemical shift referencing allowed us to identify regions of transiently formed helices and their temperature-dependent changes in helicity. All helical regions were found to lose rather than gain helical structures...

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

    Science.gov (United States)

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

    2016-10-01

    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.

  12. Electromagnetic Simulations of Helical-Based Ion Acceleration Structures

    CERN Document Server

    Nelson, Scott D; Caporaso, George; Friedman, Alex; Poole, Brian R; Waldron, William

    2005-01-01

    Helix structures have been proposed* for accelerating low energy ion beams using MV/m fields in order to increase the coupling effeciency of the pulsed power system and to tailor the electromagnetic wave propagation speed with the particle beam speed as the beam gains energy. Calculations presented here show the electromagnetic field as it propagates along the helix structure, field stresses around the helix structure (for voltage breakdown determination), optimizations to the helix and driving pulsed power waveform, and simulations showing test particles interacting with the simulated time varying fields.

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

    Science.gov (United States)

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

    2014-02-01

    NMR spectroscopy of helical membrane proteins has been very challenging on multiple fronts. The expression and purification of these proteins while maintaining functionality has consumed countless graduate student hours. Sample preparations have depended on whether solution or solid-state NMR spectroscopy was to be performed - neither have been easy. In recent years it has become increasingly apparent that membrane mimic environments influence the structural result. Indeed, in these recent years we have rediscovered that Nobel laureate, Christian Anfinsen, did not say that protein structure was exclusively dictated by the amino acid sequence, but rather by the sequence in a given environment (Anfinsen, 1973) [106]. The environment matters, molecular interactions with the membrane environment are significant and many examples of distorted, non-native membrane protein structures have recently been documented in the literature. However, solid-state NMR structures of helical membrane proteins in proteoliposomes and bilayers are proving to be native structures that permit a high resolution characterization of their functional states. Indeed, solid-state NMR is uniquely able to characterize helical membrane protein structures in lipid environments without detergents. Recent progress in expression, purification, reconstitution, sample preparation and in the solid-state NMR spectroscopy of both oriented samples and magic angle spinning samples has demonstrated that helical membrane protein structures can be achieved in a timely fashion. Indeed, this is a spectacular opportunity for the NMR community to have a major impact on biomedical research through the solid-state NMR spectroscopy of these proteins. Copyright © 2013 Elsevier Inc. All rights reserved.

  14. 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.

  15. Dielectric relaxation process of a partially unwound helical structure in ferroelectric liquid crystals.

    Science.gov (United States)

    Choudhary, Amit; Bawa, Ambika; Rajesh; Singh, Surinder P; Biradar, Ashok M

    2017-06-01

    The fluctuations of unwound helical structure have been observed in deformed helix ferroelectric liquid crystal (DHFLC) and conventional FLC sample cells. The helix is partially unwound by strong anchoring on the substrates. In such sample cells, the helical decarlization lines are not observed in the texture under crossed polarized microscope. The dielectric spectroscopy is employed to observe the behavior of dielectric relaxation processes in these sample cells. A dielectric relaxation process is observed at a lower frequency than the Goldstone mode processes in DHFLC and FLC, which we call partially unwound helical mode (p-UHM). However, the p-UHM process is not observed in the sample cell in which the helical lines appear. The application of various amplitudes of probing ac voltages on this mode has shown the higher frequency shift, i.e., the larger the amplitude of ac voltage, the higher is the relaxation frequency of p-UHM. At sufficient amplitude of applied probing ac voltage, the p-UHM merges with the Goldstone mode process and is difficult to detect. However, the Goldstone mode relaxation frequency is almost independent of the cell geometry and sample configuration. The electro-optical behavior of the p-UHM has also been confirmed by electro-optical technique. The dielectric relaxation of UHM at a frequency lower than the Goldstone mode is interpreted as the fluctuation of partially unwound helix.

  16. Potential Magnetic Field around a Helical Flux-rope Current Structure in the Solar Corona

    CERN Document Server

    Petrie, G J D

    2007-01-01

    We consider the potential magnetic field associated with a helical electric line current flow, idealizing the near-potential coronal field within which a highly localized twisted current structure is embedded. It is found that this field has a significant axial component off the helical magnetic axis where there is no current flow, such that the flux winds around the axis. The helical line current field, in including the effects of flux rope writhe, is therefore more topologically complex than straight line and ring current fields sometimes used in solar flux rope models. The axial flux in magnetic fields around confined current structures may be affected by the writhe of these current structures such that the field twists preferentially with the same handedness as the writhe. This property of fields around confined current structures with writhe may be relevant to classes of coronal magnetic flux rope, including structures observed to have sigmoidal forms in soft X-rays and prominence magnetic fields. For ex...

  17. Ionic liquid-induced formation of the α-helical structure of β-lactoglobulin.

    Science.gov (United States)

    Takekiyo, Takahiro; Koyama, Yoshihiro; Yamazaki, Kumiko; Abe, Hiroshi; Yoshimura, Yukihiro

    2013-09-01

    Structural modification of bovine milk β-lactoglobulin (β-LG) in aqueous 1-butyl-3-methylimidazolium nitrate ([bmim][NO3]) and ethylammonium nitrate ([EAN][NO3]) solutions has been investigated by Fourier transform infrared and circular dichroism spectroscopy. Remarkably, high ionic liquid (IL) concentrations (>15 mol %IL) caused formation of a non-native α-helical structure of β-LG and disruption of its tertiary structure. Furthermore, while [bmim][NO3] promoted protein aggregation, [EAN][NO3] inhibited it probably owing to differences in the unique solution structure (nanoheterogeneity) of the ILs by the different cationic species. The IL-induced α-helical formation of β-LG shows a behavior similar to the alcohol denaturation, but a disordered structure-rich state was observed in the β-α transition process by adding IL, in contrast to the case of an aqueous alcohol solution of protein. We propose that the molten salt-like property of aqueous IL solutions strongly support α-helical formation of proteins.

  18. Exitation of Whistler Waves by a Helical Wave Structure

    DEFF Research Database (Denmark)

    Balmashnov, A. A.; Lynov, Jens-Peter; Michelsen, Poul

    1981-01-01

    The excitation of whistler waves in a radial inhomogeneous plasma is investigated experimentally, using a slow-wave structure consisting of a helix of variable length surrounding the plasma column. The excited waves were observed to have a wave-vector parallel to the external magnetic field....... The possibility of exciting the waves in different radial regions is demonstrated....

  19. Antimicrobial peptides: the role of hydrophobicity in the alpha helical structure

    Directory of Open Access Journals (Sweden)

    Pandurangan Perumal

    2013-12-01

    Full Text Available The antimicrobial peptides (AMPs are a class of molecule obtained from plants, insects, animals, and humans. These peptides have been classified into five categories: 1. Anionic peptide, 2. Linear alpha helical cationic peptide, 3. Cationic peptide, 4. Anionic and cationic peptides with disulphide bonds, and 5. Anionic and cationic peptide fragments of larger proteins. Factors affecting AMPs are sequence, size, charge, hydrophobicity, amphipathicity, structure and conformation. Synthesis of these peptides is convenient by using solid phase peptide synthesis by using FMOC chemistry protocol. The secondary structures of three synthetic peptides were determined by circular dichroism. Also, it was compared the stability of the α-helical structure and confirmed the percentage of helix of these peptides by using circular dichroism. Some of these AMPs show therapeutic properties like antimicrobial, antiviral, contraceptive, and anticancer. The formulations of some peptides have been entered into the phase I, II, or III of clinical trials. This article to review briefly the sources, classification, factors affecting AMPs activity, synthesis, characterization, mechanism of action and therapeutic concern of AMPs and mainly focussed on percentage of α-helical structure in various medium.

  20. Phase diagram of structure of radial electric field in helical plasmas

    Energy Technology Data Exchange (ETDEWEB)

    Toda, S.; Itoh, K.

    2002-01-01

    A set of transport equations in toroidal helical plasmas is analyzed, including the bifurcation of the radial electric field. Multiple solutions of E{sub r} for the ambipolar condition induces domains of different electric polarities. A structure of the domain interface is analyzed and a phase diagram is obtained in the space of the external control parameters. The region of the reduction of the anomalous transport is identified. (author)

  1. Numerical investigation of leaky modes in helical structural waveguides embedded into a solid medium.

    Science.gov (United States)

    Nguyen, K L; Treyssède, F

    2015-03-01

    Helical multi-wire cables are widely used in bridges (suspended or prestressed) and anchored retaining wall constructions. Such structures can be damaged or degraded due to corrosion and fatigue. Non destructive evaluation techniques are required to reveal defects inside cable structures. Among these numerous techniques, elastic guided waves are of potential interest owing to their ability to propagate over long distances. However in civil engineering, cables are often buried or grouted in large solid media that can be considered as unbounded. Waves can strongly attenuate along the guide axis due to the energy leakage into the surrounding medium, which reduces the propagating distance. This energy leakage can be enhanced in helical structures, which further complicates their inspection. Searching modes with low attenuation becomes necessary. The goal of this work is to propose a numerical approach to compute modes in embedded helical structures, combining the so-called semi analytical finite element method and a radial perfectly matched layer technique. Two types of radial perfectly matched layer, centered and off-centered, are considered. Both are implemented in a twisting coordinate system which preserves translational invariance. The centered configuration is validated thanks to the twisted cylinder test case. The effect of twist on the eigenspectrum is briefly discussed. Then, an embedded helical wire of circular cross-section is considered. The off-centered configuration is shown to give the same results as the centered one. The effect of twist on modal attenuation is investigated. Finally, computations are performed for a seven-wire strand embedded into concrete, widely used in civil engineering cables. Copyright © 2014 Elsevier B.V. All rights reserved.

  2. Analysis on sliding helices and strands in protein structural comparisons: A case study with protein kinases

    Indian Academy of Sciences (India)

    V S Gowri; K Anamika; S Gore; N Srinivasan

    2007-08-01

    Protein structural alignments are generally considered as ‘golden standard’ for the alignment at the level of amino acid residues. In this study we have compared the quality of pairwise and multiple structural alignments of about 5900 homologous proteins from 718 families of known 3-D structures. We observe shifts in the alignment of regular secondary structural elements (helices and strands) between pairwise and multiple structural alignments. The differences between pairwise and multiple structural alignments within helical and -strand regions often correspond to 4 and 2 residue positions respectively. Such shifts correspond approximately to “one turn” of these regular secondary structures. We have performed manual analysis explicitly on the family of protein kinases. We note shifts of one or two turns in helix-helix alignments obtained using pairwise and multiple structural alignments. Investigations on the quality of the equivalent helix-helix, strand-strand pairs in terms of their residue side-chain accessibilities have been made. Our results indicate that the quality of the pairwise alignments is comparable to that of the multiple structural alignments and, in fact, is often better. We propose that pairwise alignment of protein structures should also be used in formulation of methods for structure prediction and evolutionary analysis.

  3. Structural fragment clustering reveals novel structural and functional motifs in α-helical transmembrane proteins

    Directory of Open Access Journals (Sweden)

    Vassilev Boris

    2010-04-01

    Full Text Available Abstract Background A large proportion of an organism's genome encodes for membrane proteins. Membrane proteins are important for many cellular processes, and several diseases can be linked to mutations in them. With the tremendous growth of sequence data, there is an increasing need to reliably identify membrane proteins from sequence, to functionally annotate them, and to correctly predict their topology. Results We introduce a technique called structural fragment clustering, which learns sequential motifs from 3D structural fragments. From over 500,000 fragments, we obtain 213 statistically significant, non-redundant, and novel motifs that are highly specific to α-helical transmembrane proteins. From these 213 motifs, 58 of them were assigned to function and checked in the scientific literature for a biological assessment. Seventy percent of the motifs are found in co-factor, ligand, and ion binding sites, 30% at protein interaction interfaces, and 12% bind specific lipids such as glycerol or cardiolipins. The vast majority of motifs (94% appear across evolutionarily unrelated families, highlighting the modularity of functional design in membrane proteins. We describe three novel motifs in detail: (1 a dimer interface motif found in voltage-gated chloride channels, (2 a proton transfer motif found in heme-copper oxidases, and (3 a convergently evolved interface helix motif found in an aspartate symporter, a serine protease, and cytochrome b. Conclusions Our findings suggest that functional modules exist in membrane proteins, and that they occur in completely different evolutionary contexts and cover different binding sites. Structural fragment clustering allows us to link sequence motifs to function through clusters of structural fragments. The sequence motifs can be applied to identify and characterize membrane proteins in novel genomes.

  4. Measuring the translational and rotational velocity of particles in helical motion using structured light

    CERN Document Server

    Rosales-Guzmán, Carmelo; Belmonte, Aniceto; Torres, Juan P

    2014-01-01

    We measure the rotational and translational velocity components of particles moving in helical motion using the frequency shift they induced to the structured light beam illuminating them. Under Laguerre-Gaussian mode illumination, a particle with a helical motion reflects light that acquires an additional frequency shift proportional to the angular velocity of rotation in the transverse plane, on top of the usual frequency shift due to the longitudinal motion. We determined both the translational and rotational velocities of the particles by switching between two modes: by illuminating with a Gaussian beam, we can isolate the longitudinal frequency shift; and by using a Laguerre-Gaussian mode, the frequency shift due to the rotation can be determined. Our technique can be used to characterize the motility of microorganisms with a full three-dimensional movement.

  5. 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.

  6. Self-association of collagen triple helic peptides into higher order structures.

    Science.gov (United States)

    Kar, Karunakar; Amin, Priyal; Bryan, Michael A; Persikov, Anton V; Mohs, Angela; Wang, Yuh-Hwa; Brodsky, Barbara

    2006-11-03

    Interest in self-association of peptides and proteins is motivated by an interest in the mechanism of physiologically higher order assembly of proteins such as collagen as well as the mechanism of pathological aggregation such as beta-amyloid formation. The triple helical form of (Pro-Hyp-Gly)(10), a peptide that has proved a useful model for molecular features of collagen, was found to self-associate, and its association properties are reported here. Turbidity experiments indicate that the triple helical peptide self-assembles at neutral pH via a nucleation-growth mechanism, with a critical concentration near 1 mM. The associated form is more stable than individual molecules by about 25 degrees C, and the association is reversible. The rate of self-association increases with temperature, supporting an entropically favored process. After self-association, (Pro-Hyp-Gly)(10) forms branched filamentous structures, in contrast with the highly ordered axially periodic structure of collagen fibrils. Yet a number of characteristics of triple helix assembly for the peptide resemble those of collagen fibril formation. These include promotion of fibril formation by neutral pH and increasing temperature; inhibition by sugars; and a requirement for hydroxyproline. It is suggested that these similar features for peptide and collagen self-association are based on common lateral underlying interactions between triple helical molecules mediated by hydrogen-bonded hydration networks involving hydroxyproline.

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

    Science.gov (United States)

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

    2016-07-01

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

  8. Helical filaments

    Energy Technology Data Exchange (ETDEWEB)

    Barbieri, Nicholas; Lim, Khan; Durand, Magali; Baudelet, Matthieu; Richardson, Martin [Townes Laser Institute, CREOL—The College of Optics and Photonics, University of Central Florida, Orlando, Florida 32816 (United States); Hosseinimakarem, Zahra; Johnson, Eric [Micro-Photonics Laboratory – Center for Optical Material Science, Clemson, Anderson, South Carolina 29634 (United States)

    2014-06-30

    The shaping of laser-induced filamenting plasma channels into helical structures by guiding the process with a non-diffracting beam is demonstrated. This was achieved using a Bessel beam superposition to control the phase of an ultrafast laser beam possessing intensities sufficient to induce Kerr effect driven non-linear self-focusing. Several experimental methods were used to characterize the resulting beams and confirm the observed structures are laser air filaments.

  9. Aromatic Interactions Promote Self-association of Collagen Triple-helical Peptides to Higher Order Structures

    Science.gov (United States)

    Kar, Karunakar; Ibrar, Sajjad; Nanda, Vikas; Getz, Todd M.; Kunapuli, Satya P.; Brodsky, Barbara

    2009-01-01

    Aromatic residues are relatively rare within the collagen triple-helix, but they appear to play a specialized role in higher order structure and function. The role of aromatic amino acids in the self-assembly of triple-helical peptides was investigated in terms of the kinetics of self-association, the nature of aggregated species formed, and the ability of these species to activate platelet aggregation. The presence of aromatic residues on both ends of a type IV collagen model peptide is observed to greatly accelerate the kinetics of self-association, decreasing the lag time and leading to insoluble, well defined linear fibrils as well as small soluble aggregates. Both macroscopic visible aggregates and small multi-molecular complexes in solution are capable of inducing platelet aggregation through the glycoprotein VI receptor on platelets. Proline-aromatic CH⋯π interactions are often observed within globular proteins and in protein complexes, and examination of molecular packing in the crystal structure of the integrin binding collagen peptide shows Phe interacts with Pro/Hyp in a neighboring triple-helical molecule. An intermolecular interaction between aromatic amino acids and imino acids within the triple-helix is also supported by the observed inhibitory effect of isolated Phe amino acids on the self-association of (Pro-Hyp-Gly)10. Given the high fraction of Pro and Hyp residues on the surface of collagen molecules, it is likely that imino acid-aromatic CH⋯π interactions are important in formation of higher order structure. It is suggested that the catalysis of type I collagen fibrillogenesis by non-helical telopeptides is due to specific intermolecular CH⋯π interactions between aromatic residues in the telopeptides and Pro/Hyp residues within the triple-helix. PMID:19610672

  10. Aromatic Interactions Promote Self-association of Collagen Triple-helical Peptides to Higher Order Structures

    OpenAIRE

    Kar, Karunakar; Ibrar, Sajjad; Nanda, Vikas; Getz, Todd M.; Kunapuli, Satya P.; Brodsky, Barbara

    2009-01-01

    Aromatic residues are relatively rare within the collagen triple-helix, but they appear to play a specialized role in higher order structure and function. The role of aromatic amino acids in the self-assembly of triple-helical peptides was investigated in terms of the kinetics of self-association, the nature of aggregated species formed, and the ability of these species to activate platelet aggregation. The presence of aromatic residues on both ends of a type IV collagen model peptide is obse...

  11. 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.

  12. Syntheses and structures of dinuclear double-stranded helicates of divalent manganese, iron, cobalt, and zinc.

    Science.gov (United States)

    Reid, Stuart D; Blake, Alexander J; Wilson, Claire; Love, Jason B

    2006-01-23

    The syntheses and solid-state and solution structures of a series of unusually volatile, charge neutral, [4 + 4] double-stranded helical complexes of divalent manganese, iron, cobalt, and zinc are described. Deprotonation of the N4-donor iminopyrrole ligand H2L by KH cleanly generates the salt K2(THF)2L, which displays both sigma and pi interactions between K and iminopyrrolyl fragments in the X-ray crystal structure. Transamination, salt elimination, and protonolysis reactions were found to be versatile and, in general, high-yielding routes to the dinuclear double helicates [M2(L)2] (M = Mn, Fe, Co, and Zn). These compounds are isomorphous in the solid state by X-ray crystallography and adopt dinuclear cleft motifs as a result of pi stacking between opposing iminopyrrolyl fragments. This motif was also observed in the solution structures of [Fe2(L)2] and [Zn2(L)2] below 230 and 200 K, respectively (DeltaG++ = approximately 46 and 39.0 kJ mol(-1), respectively).

  13. High regression rate hybrid rocket fuel grains with helical port structures

    Science.gov (United States)

    Walker, Sean D.

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

  14. Hydrogen bonded helices: Synthesis, crystal structure and self-assembled microtubes

    Science.gov (United States)

    Mosae Selvakumar, P.; Suresh, E.; Subramanian, P. S.

    2009-02-01

    Dicarboxylic bola-shaped compounds 1- 3, possessing phthalyl head groups and diol spacers are synthesized and characterized. Keeping phthalyl head group common for all three diester-dicarboxylic acids, the spacer moiety is systematically altered by two and four carbon atoms in 1 and 2, 3, respectively. The flexible spacer moiety ethane-1,2-diol in compound 1 is replaced by cis-but-2-ene-1,4-diol and 1,4-butane diol in 2 and 3, respectively, to study the effect on the morphology of the microcrystal grown on them. Thus compound 2 and 3 though posses four carbon atoms in their respective spacer moiety, they differ by their rigidity. The single crystal X-ray structure obtained for 1, 2 and 3 indicates the formation of self-assembled single stranded helical structure mediated through O-H…O interaction of the end carboxylic acids. Interestingly compound 1 self-assembled into microtubes in ethanol:water solvent mixture. The solvent and the O-H…O; C-H…O interaction combinedly play crucial role in molecular self-assembly process and defines the morphology for 1 into "microtube" whereas 2 and 3 forming "bar" fails to produce such tubular texture though their respective crystal structure shows single stranded helices. The role of weak C-H...O interaction, incorporation of rigid spacer and various other factors such as polarity of the solvents are discussed in detail to explore the difference in the morphology.

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

    Science.gov (United States)

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

    2002-11-27

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

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

    Science.gov (United States)

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

    2016-05-20

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

  17. Twisted X-rays: incoming waveforms yielding discrete diffraction patterns for helical structures

    CERN Document Server

    Friesecke, Gero; Jüstel, Dominik

    2015-01-01

    Conventional X-ray methods use incoming plane waves and result in discrete diffraction patterns when scattered at crystals. Here we find, by a systematic method, incoming waveforms which exhibit discrete diffraction patterns when scattered at helical structures. As examples we present simulated diffraction patterns of carbon nanotubes and tobacco mosaic virus. The new incoming waveforms, which we call twisted waves due to their geometric shape, are found theoretically as closed-form solutions to Maxwell's equations. The theory of the ensuing diffraction patterns is developed in detail. A twisted analogue of the Von Laue condition is seen to hold, with the peak locations encoding the symmetry and the helix parameters, and the peak intensities indicating the electronic structure in the unit cell. If suitable twisted X-ray sources can in the future be realized experimentally, it appears from our mathematical results that they will provide a powerful tool for directly determining the detailed atomic structure of ...

  18. 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

  19. Magneto-acoustic waves driven by self-generated magnetic field: relevance to helical structures in MagLIF experiments

    Science.gov (United States)

    Davies, Jonathan; Barnak, Daniel; Betti, Riccardo; Carreon, Adam; Chang, Po-Yu; Fiksel, Gennady

    2014-10-01

    The observation of coherent helical structures in liner implosions on Z when an axial magnetic field more than 100 times smaller than the azimuthal field is added has yet to be adequately explained. The results have been reproduced in a 3D MHD code by initializing helices on the outer surface, but this produces helices independently of the axial magnetic field. We present the hypothesis that helices are seeded by self-generated magnetic field, which adds a driving term to the dispersion relation for magneto-acoustic waves when there is a temperature gradient perpendicular to the fluid motion. The key feature of this instability is that it is stable when magnetic pressure exceeds a fraction of the thermal pressure, therefore, instability driven by the helical field resulting from the combination of the initial axial field and the growing azimuthal field will stabilize before the net field has a small pitch angle and before the implosion starts, seeding helices on the surface. This work was supported by the Department of Energy National Nuclear Security Administration, Award Number DE-NA0001944, and the Fusion Science Center supported by the Office of Fusion Energy Sciences, Number DE-FG02-04ER54786.

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

    Energy Technology Data Exchange (ETDEWEB)

    He, Tian [Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi’an 710069 (China); Yue, Ke-Fen, E-mail: ykflyy@nwu.edu.cn [Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi’an 710069 (China); Zhao, Yi-xing; Chen, San-Ping [Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi’an 710069 (China); Zhou, Chun-sheng, E-mail: slzhoucs@126.com.cn [Shaanxi Key Laboratory of Comprehensive Utilization of Tailings Resources, College of Chemical Engineering and Modern Materials, Shangluo University, Shangluo 726000 (China); Yan, Ni [Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi’an 710069 (China)

    2016-07-15

    Solvothermal reactions of Zn(II) acetates and four V-shaped carboxylates ligands in the presence of 1,4-Bis(2-methyl-imidazol-1-yl)butane afforded four interesting Zn(II) coordination polymers with helical chains, namely, {[Zn(bib)(atibdc)]·2H_2O}{sub n} (1), {[Zn(bib)(atbip)]·H_2O}{sub n} (2), {[Zn(bib)(2,2′-tda)]}{sub n} (3) and {[Zn(bib)(5-tbipa)]·EtOH}{sub n} (4), (H{sub 2}atibdc=5-amino-2,4,6-triiodoisophthalic acid, H{sub 2}atbip=5-amino-2,4,6-tribromoisophthalic acid, 2,2′-H{sub 2}tad=2,2′-thiodiacetic acid, 5-H{sub 2}tbipa=5-tert-butyl-isophthalic acid). 1 reveals a 3D chiral framework with three kinds of helical chains along a, b and c axis. 2 shows a 2D step-type chiral framework with right-handed helical chains. 3 displays a wavelike 2D layer network possessing alternate left- and right-handed helical chains. 4 presents a four-connected 3D framework with zigzag and meso-helical chains. The different spacers and substituent group of carboxylic acid ligands may lead to the diverse network structures of 1–4. The fluorescent properties of complexes 1−4 were studied. In addition, the thermal decompositions properties of 1–4 were investigated by simultaneous TG/DTG–DSC technique. The apparent activation energy E and the pre-exponential factor (A) of skeleton collapse for the complexes 1–4 are calculated by the integral Kissinger's method and Ozawa–Doyle's method. The activation energy E (E{sub 1}=209.658 kJ·mol{sup −1}, E{sub 2}=250.037 kJ mol{sup −1}, E{sub 3}=225.300 kJ mol{sup −1}, E{sub 4}=186.529 kJ·mol{sup −1}) demonstrates that the reaction rate of the melting decomposition is slow. The thermodynamic parameters (ΔH{sup ‡}, ΔG{sup ‡} and ΔS{sup ‡}) at the peak temperatures of the DTG curves were also calculated. ΔG{sup ‡}>0 indicates that the skeleton collapse is not spontaneous. ΔH{sub d}>0 suggests that the skeleton collapse is endothermic, corresponding to the intense endothermic peak of the DSC

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

    Science.gov (United States)

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

    2012-11-01

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

  2. 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.

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

    Science.gov (United States)

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

    2015-01-12

    Molecular hydrocarbons are well-known to polymerize under pressure to form covalently bonded frameworks. Here we predict by ab initio calculations two distinct three-dimensional hydrocarbon crystalline structures composed of 3-fold and 4-fold helical CH chains in rhombohedral (R3) and tetragonal (I4₁/a) symmetry, respectively. Both structures with 1:1 stoichiometry are found to be energetically more favorable than solid acetylene and cubane, and even more stable than benzene II solid at high pressure. The calculations on vibrational, electronic, and optical properties reveal that the new chiral hydrocarbons are dynamically stable with large bulk moduli around 200 GPa, and exhibit a transparent insulating behavior with indirect band gaps of 5.9 ~ 6.7 eV and anisotropic adsorption spectra. Such forms of hydrocarbon, once synthesized, would have wide applications in mechanical, optoelectronic, and biological materials.

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

    Energy Technology Data Exchange (ETDEWEB)

    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)

  5. Influence of 63Ser phosphorylation and dephosphorylation on the structure of the stathmin helical nucleation sequence: a molecular dynamics study.

    Science.gov (United States)

    Missimer, John H; Steinmetz, Michel O; van Gunsteren, Wilfred F; Dolenc, Jožica

    2012-10-23

    Phosphorylation is an important mechanism regulating protein-protein interactions involving intrinsically disordered protein regions. Stathmin, an archetypical example of an intrinsically disordered protein, is a key regulator of microtubule dynamics in which phosphorylation of 63Ser within the helical nucleation sequence strongly down-regulates the tubulin binding and microtubule destabilizing activities of the protein. Experimental studies on a peptide encompassing the 19-residue helical nucleation sequence of stathmin (residues 55-73) indicate that phosphorylation of 63Ser destabilizes the peptide's secondary structure by disrupting the salt bridges supporting its helical conformation. In order to investigate this hypothesis at atomic resolution, we performed molecular dynamics simulations of nonphosphorylated and phosphorylated stathmin-[55-73] at room temperature and pressure, neutral pH, and explicit solvation using the recently released GROMOS force field 54A7. In the simulations of nonphosphorylated stathmin-[55-73] emerged salt bridges associated with helical configurations. In the simulations of 63Ser phosphorylated stathmin-[55-73] these configurations dispersed and were replaced by a proliferation of salt bridges yielding disordered configurations. The transformation of the salt bridges was accompanied by emergence of numerous interactions between main and side chains, involving notably the oxygen atoms of the phosphorylated 63Ser. The loss of helical structure induced by phosphorylation is reversible, however, as a final simulation showed. The results extend the hypothesis of salt bridge derangement suggested by experimental observations of the stathmin nucleation sequence, providing new insights into regulation of intrinsically disordered protein systems mediated by phosphorylation.

  6. Structures of the compact helical core domains of feline calicivirus and murine norovirus VPg proteins.

    Science.gov (United States)

    Leen, Eoin N; Kwok, K Y Rex; Birtley, James R; Simpson, Peter J; Subba-Reddy, Chennareddy V; Chaudhry, Yasmin; Sosnovtsev, Stanislav V; Green, Kim Y; Prater, Sean N; Tong, Michael; Young, Joanna C; Chung, Liliane M W; Marchant, Jan; Roberts, Lisa O; Kao, C Cheng; Matthews, Stephen; Goodfellow, Ian G; Curry, Stephen

    2013-05-01

    We report the solution structures of the VPg proteins from feline calicivirus (FCV) and murine norovirus (MNV), which have been determined by nuclear magnetic resonance spectroscopy. In both cases, the core of the protein adopts a compact helical structure flanked by flexible N and C termini. Remarkably, while the core of FCV VPg contains a well-defined three-helix bundle, the MNV VPg core has just the first two of these secondary structure elements. In both cases, the VPg cores are stabilized by networks of hydrophobic and salt bridge interactions. The Tyr residue in VPg that is nucleotidylated by the viral NS7 polymerase (Y24 in FCV, Y26 in MNV) occurs in a conserved position within the first helix of the core. Intriguingly, given its structure, VPg would appear to be unable to bind to the viral polymerase so as to place this Tyr in the active site without a major conformation change to VPg or the polymerase. However, mutations that destabilized the VPg core either had no effect on or reduced both the ability of the protein to be nucleotidylated and virus infectivity and did not reveal a clear structure-activity relationship. The precise role of the calicivirus VPg core in virus replication remains to be determined, but knowledge of its structure will facilitate future investigations.

  7. Helical waves and non-linear dynamics of fluid/structure interactions in a tube row

    Energy Technology Data Exchange (ETDEWEB)

    Moon, F.C.; Thothadri, M. [Cornell Univ., Ithaca, NY (United States)

    1997-12-31

    The goal of this study has been to investigate low-dimensional models for fluid-structure dynamics of flow across a row of cylindrical tubes. Four principle results of this experimental-theoretical study are discussed. (i) Experimental evidence has shown that the dynamic instability of the tube row is a subcritical Hopf bifurcation. (ii) The critical flow velocity decreases as the number of flexible cylinders increases. (iii) The linear model exhibits coupled helical wave solutions in the tube dynamics. (iv) A nonlinear model of the tube motions shows a complex subcritical Hopf bifurcation with a secondary bifurcation to a torus or quasi-periodic oscillation. In this analysis the tools of center manifolds, normal forms and numerical simulation are used.

  8. Structural and magnetic properties of a variety of transition metal incorporated DNA double helices.

    Science.gov (United States)

    Samanta, Pralok K; Pati, Swapan K

    2014-02-03

    By using density functional theory calculations, the structural, energetic, magnetic, and optical properties for a variety of transition metal (M = Mn, Fe, Co, Ni and Cu) ions incorporated modified-DNA (M-DNA) double helices has been investigated. The DNA is modified with either hydroxypyridone (H) or bis(salicylaldehyde)ethylenediamine (S-en) metalated bases. We find the formation of extended M-O network leading to the ferromagnetic interactions for the case of H-DNA for all the metal ions. More ordered stacking arrangement was found for S-en-DNA. We calculate the exchange coupling constant (J) considering Heisenberg Hamiltonian for quantitative description of magnetic interactions. The ferromagnetic and antiferromagnetic interactions are obtained by varying different transition metal ions. The extent of the magnetic interaction depends on the number of transition metal ions. Optical profiles show peaks below 2 eV, a clear signature of spin-spin coupling.

  9. Effect of aqueous ethanol on the triple helical structure of collagen.

    Science.gov (United States)

    Gopinath, Arun; Reddy, Samala Murali Mohan; Madhan, Balaraman; Shanmguam, Ganesh; Rao, Jonnalagadda Raghava

    2014-12-01

    Collagen, the most abundant protein in mammals, is widely used for making biomaterials. Recently, organic solvents have been used to fabricate collagen-based biomaterials for biological applications. It is therefore necessary to understand the behavior of collagen in the presence of organic solvents at low (≤50%, v/v) and high (≥90%, v/v) concentrations. This study was conducted to examine how collagen reacts when exposed to low and high concentrations of ethanol, one of the solvents used to make collagen-based biomaterials. Solubility testing indicated that collagen remains in solution at low concentrations (≤50%, v/v) of ethanol but precipitates (gel-like) thereafter, irrespective of the method of addition of ethanol (single shot or gradual addition); this behavior is different from that observed recently with acetonitrile. Collagen retains its triple helix in the presence of ethanol but becomes thermodynamically unstable, with substantially reduced melting temperature, with increasing concentration of ethanol. It was also found that the CD ellipticity at 222 nm, characteristic of the triple-helical structure, does not correlate with the thermal stability of collagen. Time-dependent experiments reveal that the collagen triple helix is kinetically stable in the presence of 0-40% (v/v) ethanol at low temperature (5 °C) but highly unstable in the presence of ethanol at elevated temperature (~34 °C). These results indicate that when ethanol is used to process collagen-based biomaterials, such factors as temperature and duration should be done taking into account, to prevent extensive damage to the triple-helical structure of collagen.

  10. Modeling the Effect of Helical Fiber Structure on Wood Fiber Composite Elastic Properties

    Science.gov (United States)

    Marklund, Erik; Varna, Janis

    2009-08-01

    The effect of the helical wood fiber structure on in-plane composite properties has been analyzed. The used analytical concentric cylinder model is valid for an arbitrary number of phases with monoclinic material properties in a global coordinate system. The wood fiber was modeled as a three concentric cylinder assembly with lumen in the middle followed by the S3, S2 and S1 layers. Due to its helical structure the fiber tends to rotate upon loading in axial direction. In most studies on the mechanical behavior of wood fiber composites this extension-twist coupling is overlooked since it is assumed that the fiber will be restricted from rotation within the composite. Therefore, two extreme cases, first modeling fiber then modeling composite were examined: (i) free rotation and (ii) no rotation of the cylinder assembly. It was found that longitudinal fiber modulus depending on the microfibril angle in S2 layer is very sensitive with respect to restrictions for fiber rotation. In-plane Poisson’s ratio was also shown to be greatly influenced. The results were compared to a model representing the fiber by its cell wall and using classical laminate theory to model the fiber. It was found that longitudinal fiber modulus correlates quite well with results obtained with the concentric cylinder model, whereas Poisson’s ratio gave unsatisfactory matching. Finally using typical thermoset resin properties the longitudinal modulus and Poisson’s ratio of an aligned softwood fiber composite with varying fiber content were calculated for various microfibril angles in the S2 layer.

  11. Efficiency of paramagnetism-based constraints to determine the spatial arrangement of {alpha}-helical secondary structure elements

    Energy Technology Data Exchange (ETDEWEB)

    Bertini, Ivano [University of Florence, CERM and Department of Chemistry (Italy)], E-mail: bertini@cerm.unifi.it; Longinetti, Marco [Dipartimento di Ingegneria Agraria e Forestale (Italy); Luchinat, Claudio; Parigi, Giacomo [University of Florence, CERM and Department of Agricultural Biotechnology (Italy); Sgheri, Luca [Istituto di Analisi Globale ed Applicazioni (CNR) (Italy)

    2002-02-15

    A computational approach has been developed to assess the power of paramagnetism-based backbone constraints with respect to the determination of the tertiary structure, once the secondary structure elements are known. This is part of the general assessment of paramagnetism-based constraints which are known to be relevant when used in conjunction with all classical constraints. The paramagnetism-based constraints here investigated are the pseudocontact shifts, the residual dipolar couplings due to self-orientation of the metalloprotein in high magnetic fields, and the cross correlation between dipolar relaxation and Curie relaxation. The relative constraints are generated by back-calculation from a known structure. The elements of secondary structure are supposed to be obtained from chemical shift index. The problem of the reciprocal orientation of the helices is addressed. It is shown that the correct fold can be obtained depending on the length of the {alpha}-helical stretches with respect to the length of the non helical segments connecting the {alpha}-helices. For example, the correct fold is straightforwardly obtained for the four-helix bundle protein cytochrome b{sub 562}, while the double EF-hand motif of calbindin D{sub 9k} is hardly obtained without ambiguity. In cases like calbindin D{sub 9k}, the availability of datasets from different metal ions is helpful, whereas less important is the location of the metal ion with respect to the secondary structure elements.

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

    Science.gov (United States)

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

    2014-06-01

    A large number of collagen-like proteins have been identified in bacteria during the past 10years, 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 Escherichia 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.

  13. Characteristics of Arbitrarily-Shaped Helical Groove Slow-Wave Structure Loaded with a Concentric Dielectric-Rod

    Science.gov (United States)

    Gong, Yu-Bin; Wei, Yan-Yu; Liu, Hong-Tao

    2010-12-01

    The dielectric-rod is loaded on the central axis of the arbitrarily-shaped helical groove slow-wave structure. Meanwhile, the profile of the groove is replaced by a series of continuous rectangular steps. The unified dispersion equation of the arbitrarily-shaped helical groove waveguide loaded with a concentric dielectric-rod is obtained by means of a combination of filed-matching method and admittance-matching technique. Then, the effect of the change of groove shape and the dielectric-rod parameters on the dispersion and coupling impedance is approached by theory calculation. The results show that: loaded with dielectric-rod, the bandwidth of the helical groove traveling wave tube (TWT) is effectively broadened, but the coupling impedance is reduced. Among the five different groove shapes, the triangle-type groove has the widest bandwidth but the smallest coupling impedance, and the swallow-tailed-type groove has the narrowest bandwidth but the largest coupling impedance.

  14. Helical Shell Structures of Ni-Al Alloy Nanowires and Their Electronic Transport Properties

    Institute of Scientific and Technical Information of China (English)

    ZHANG Xue-Qing; LI Hui; LIEW Kim-Meow; LI Yun-Fang; SUN Feng-Wei

    2007-01-01

    Six kinds of Ni-Al alloy nanowires are optimized by means of simulated annealing. The optimized structures show that the Ni-Al alloy nanowires are helical shell structures that are wound by three atomic strands, which is very similar to the case with pure metallic nanowires. The densities of states (DOS), transmission function T(E), current-voltage (Ⅰ-Ⅴ) curves, and the conductance spectra of these alloy nanowires are also investigated. Our results indicate that the conductance spectra depend on the geometric structure properties and the ingredients of the alloy nanowires. We observe and study the nonlinear contribution to the Ⅰ-Ⅴ characteristics that are due to the quantum size effect and the impurity effect. The addition of Ni atoms decreases the conductance of the Ni-Al alloy nanowire because the doping atom Ni change the electronic band structures and the charge density distribution. The interesting statistical results shed light on the physics of quantum transport at the nano-scale.

  15. Rational Design, Structural and Thermodynamic Characterization of a Hyperstable Variant of the Villin Headpiece Helical Subdomain

    Energy Technology Data Exchange (ETDEWEB)

    Bi,Y.; Cho, J.; Kim, E.; Shan, B.; Schindelin, H.; Raleigh, D.

    2007-01-01

    A hyperstable variant of the small independently folded helical subdomain (HP36) derived from the F-actin binding villin headpiece was designed by targeting surface electrostatic interactions and helical propensity. A double mutant N68A, K70M was significantly more stable than wild type. The T{sub m} of wild type in aqueous buffer is 73.0 {sup o}C, whereas the double mutant did not display a complete unfolding transition. The double mutant could not be completely unfolded even by 10 M urea. In 3 M urea, the T{sub m} of wild type is 54.8 {sup o}C while that of the N68AK70M double mutant is 73.9 {sup o}C. Amide H/{sup 2}H exchange studies show that the pattern of exchange is very similar for wild type and the double mutant. The structures of a K70M single mutant and the double mutant were determined by X-ray crystallography and are identical to that of the wild type. Analytical ultracentrifugation demonstrates that the proteins are monomeric. The hyperstable mutant described here is expected to be useful for folding studies of HP36 because studies of the wild type domain have sometimes been limited by its marginal stability. The results provide direct evidence that naturally occurring miniature protein domains have not been evolutionarily optimized for global stability. The stabilizing effect of this double mutant could not be predicted by sequence analysis because K70 is conserved in the larger intact headpiece for functional reasons.

  16. The Role of Magnetic Helicity in the Structure and Heating of the Sun's Corona

    CERN Document Server

    Knizhnik, Kalman J

    2016-01-01

    Two of the most important features of the solar atmosphere are its hot, smooth coronal loops and the concentrations of magnetic shear, known as filament channels, that reside above photospheric polarity inversion lines (PILs). The shear observed in filament channels represents magnetic helicity, while the smoothness of the coronal loops indicates an apparent lack of magnetic helicity in the rest of the corona. At the same time, models that attempt to explain the high temperatures observed in these coronal loops require magnetic energy, in the form of twist, to be injected at the photosphere. In addition to magnetic energy, this twist also represents magnetic helicity. Unlike magnetic energy, magnetic helicity is conserved under reconnection, and is consequently expected to accumulate and be observed in the corona. However, filament channels, rather than the coronal loops, are the locations in the corona where magnetic helicity is observed, and it manifests itself in the form of shear, rather than twist. This ...

  17. Comprehensive analysis of the numbers, lengths and amino acid compositions of transmembrane helices in prokaryotic, eukaryotic and viral integral membrane proteins of high-resolution structure.

    Science.gov (United States)

    Saidijam, Massoud; Azizpour, Sonia; Patching, Simon G

    2017-02-15

    We report a comprehensive analysis of the numbers, lengths and amino acid compositions of transmembrane helices in 235 high-resolution structures of integral membrane proteins. The properties of 1551 transmembrane helices in the structures were compared with those obtained by analysis of the same amino acid sequences using topology prediction tools. Explanations for the 81 (5.2%) missing or additional transmembrane helices in the prediction results were identified. Main reasons for missing transmembrane helices were mis-identification of N-terminal signal peptides, breaks in α-helix conformation or charged residues in the middle of transmembrane helices and transmembrane helices with unusual amino acid composition. The main reason for additional transmembrane helices was mis-identification of amphipathic helices, extramembrane helices or hairpin re-entrant loops. Transmembrane helix length had an overall median of 24 residues and an average of 24.9 ± 7.0 residues and the most common length was 23 residues. The overall content of residues in transmembrane helices as a percentage of the full proteins had a median of 56.8% and an average of 55.7 ± 16.0%. Amino acid composition was analysed for the full proteins, transmembrane helices and extramembrane regions. Individual proteins or types of proteins with transmembrane helices containing extremes in contents of individual amino acids or combinations of amino acids with similar physicochemical properties were identified and linked to structure and/or function. In addition to overall median and average values, all results were analysed for proteins originating from different types of organism (prokaryotic, eukaryotic, viral) and for subgroups of receptors, channels, transporters and others.

  18. 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.

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

    Science.gov (United States)

    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. PMID:28107435

  20. 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

  1. 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.

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

    Science.gov (United States)

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

    2013-05-01

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

  3. Helical motions of fine-structure prominence threads observed by Hinode and IRIS

    CERN Document Server

    Okamoto, Takenori J; Tsuneta, Saku

    2016-01-01

    Fine-structure dynamics in solar prominences holds critical clues to understanding their physical nature of significant space-weather implications. We report evidence of rotational motions of horizontal helical threads in two active-region prominences observed by the \\emph{Hinode} and/or \\emph{IRIS} satellites at high resolution. In the first event, we found transverse motions of brightening threads at speeds up to 55~km~s$^{-1}$ seen in the plane of the sky. Such motions appeared as sinusoidal space--time trajectories with a typical period of $\\sim$390~s, which is consistent with plane-of-sky projections of rotational motions. Phase delays at different locations suggest propagation of twists along the threads at phase speeds of 90--270~km~s$^{-1}$. At least 15 episodes of such motions occurred in two days, none associated with any eruption. For these episodes, the plane-of-sky speed is linearly correlated with the vertical travel distance, suggestive of a constant angular speed. In the second event, we found...

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

    Directory of Open Access Journals (Sweden)

    Daniel J Kuster

    Full Text Available 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

  5. 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

  6. Observation of glycine zipper and unanticipated occurrence of ambidextrous helices in the crystal structure of a chiral undecapeptide

    Directory of Open Access Journals (Sweden)

    Ramagopal Udupi A

    2007-08-01

    Full Text Available Abstract Background The de novo design of peptides and proteins has recently surfaced as an approach for investigating protein structure and function. This approach vitally tests our knowledge of protein folding and function, while also laying the groundwork for the fabrication of proteins with properties not precedented in nature. The success of these studies relies heavily on the ability to design relatively short peptides that can espouse stable secondary structures. To this end, substitution with α, β-dehydroamino acids, especially α, β-dehydrophenylalanine (ΔPhe comes in use for spawning well-defined structural motifs. Introduction of ΔPhe induces β-bends in small and 310-helices in longer peptide sequences. Results The present report is an investigation of the effect of incorporating two glycines in the middle of a ΔPhe containing undecapeptide. A de novo designed undecapeptide, Ac-Gly1-Ala2-ΔPhe3-Leu4-Gly5-ΔPhe6-Leu7-Gly8-ΔPhe9-Ala10-Gly11-NH2, was synthesized and characterized using X-ray diffraction and Circular Dichroism spectroscopic methods. Crystallographic studies suggest that, despite the presence of L-amino acid (L-Ala and L-Leu residues in the middle of the sequence, the peptide adopts a 310-helical conformation of ambidextrous screw sense, one of them a left-handed (A and the other a right-handed (B 310-helix with A and B being antiparallel to each other. However, CD studies reveal that the undecapeptide exclusively adopts a right-handed 310-helical conformation. In the crystal packing, three different interhelical interfaces, Leu-Leu, Gly-Gly and ΔPhe-ΔPhe are observed between the helices A and B. A network of C-H...O hydrogen bonds are observed at ΔPhe-ΔPhe and Gly-Gly interhelical interfaces. An important feature observed is the occurrence of glycine zipper motif at Gly-Gly interface. At this interface, the geometric pattern of interhelical interactions seems to resemble those observed between helices in

  7. 1.5 octave wideband traveling-wave tube with heavily-loaded helical slow-wave structure

    CERN Document Server

    Jung, S S; Han, S T; Jeon, S; Soukhov, A V; Park, G S

    2001-01-01

    Summary form only given. A 1.5 octave wideband traveling wave tube (TWT) with a helical structure loaded by the thick dielectric support rods has been designed and fabricated for the frequency range of 6-18 GHz. Helical slow-wave structure (SWS) was modeled using three- dimensional HFSS code. The nonresonant perturbation measurement using a thin copper wire with 20 mm diameter was performed to verify the phase velocity and interaction impedance of the helical structure. The performance of TWT was predicted using one-dimensional (1-D) nonlinear theory involving a macro particle beam model. The harmonic effect was considered in this calculation. The measured performance of TWT using a beam voltage 4 kV and a beam current of 120 mA was shown. These results were compared with a 1-D nonlinear theory. The comparison showed that the measured power and gain were less than the predicted one but had a similar trend over the operating frequency range. The 2nd harmonic levels at the low frequency range of 6-8 GHz were ne...

  8. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Kroncke, Brett M.; Horanyi, Peter S.; Columbus, Linda (UV)

    2010-12-07

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

  10. Helical structure of longitudinal vortices embedded in turbulent wall-bounded flow

    DEFF Research Database (Denmark)

    Velte, Clara Marika; Hansen, Martin Otto Laver; Okulov, Valery

    2009-01-01

    Embedded vortices in turbulent wall-bounded flow over a flat plate, generated by a passive rectangular vane-type vortex generator with variable angle \\beta to the incoming flow in a low-Reynolds number flow (Re = 2600 based on the inlet grid mesh size L = 0:039 m and free stream velocity U......_{\\infty} = 1.0 ms^{-1}) have been studied with respect to helical symmetry. The studies were carried out in a low-speed closed-circuit wind tunnel utilizing Stereoscopic Particle Image Velocimetry (SPIV). The vortices have been shown to possess helical symmetry, allowing the flow to be described in a simple...

  11. Are Spine--Sheath Polarization Structures in the Jets of Active Galactic Nuclei Associated with Helical Magnetic Fields?

    CERN Document Server

    Gabuzda, Denise C; O'Neill, Eamonn L

    2014-01-01

    One possible origin for polarization structures across jets of Active Galactic Nuclei (AGNs) with a central "spine" of orthogonal magnetic field and a "sheath" of longitudinal magnetic field along one or both edges of the jet is the presence of a helical jet magnetic field. Simultaneous Very Long Baseline Array (VLBA) polarization observations of AGN displaying partial or full spine--sheath polarization structures were obtained at 4.6, 5.0, 7.9, 8.9, 12.9 and 15.4 GHz, in order to search for additional evidence for helical jet magnetic fields, such as transverse Faraday rotation gradients (due to the systematic change in the line-of-sight magnetic-field component across the jet). Results for eight sources displaying monotonic transverse Faraday rotation gradients with significances $\\geq 3\\sigma$ are presented here. Reversals in the directions of the transverse RM gradients with distance from the core or with time are detected in three of these AGNs. These can be interpreted as evidence for a nested helical m...

  12. Three new structures of left-handed RADA helical filaments: structural flexibility of N-terminal domain is critical for recombinase activity.

    Science.gov (United States)

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

    2009-01-01

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

  13. 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.

  14. Atomic structure of the vimentin central α-helical domain and its implications for intermediate filament assembly.

    Science.gov (United States)

    Chernyatina, Anastasia A; Nicolet, Stefan; Aebi, Ueli; Herrmann, Harald; Strelkov, Sergei V

    2012-08-21

    Together with actin filaments and microtubules, intermediate filaments (IFs) are the basic cytoskeletal components of metazoan cells. Over 80 human diseases have been linked to mutations in various IF proteins to date. However, the filament structure is far from being resolved at the atomic level, which hampers rational understanding of IF pathologies. The elementary building block of all IF proteins is a dimer consisting of an α-helical coiled-coil (CC) "rod" domain flanked by the flexible head and tail domains. Here we present three crystal structures of overlapping human vimentin fragments that comprise the first half of its rod domain. Given the previously solved fragments, a nearly complete atomic structure of the vimentin rod has become available. It consists of three α-helical segments (coils 1A, 1B, and 2) interconnected by linkers (L1 and L12). Most of the CC structure has a left-handed twist with heptad repeats, but both coil 1B and coil 2 also exhibit untwisted, parallel stretches with hendecad repeats. In the crystal structure, linker L1 was found to be α-helical without being involved in the CC formation. The available data allow us to construct an atomic model of the antiparallel tetramer representing the second level of vimentin assembly. Although the presence of the nonhelical head domains is essential for proper tetramer stabilization, the precise alignment of the dimers forming the tetramer appears to depend on the complementarity of their surface charge distribution patterns, while the structural plasticity of linker L1 and coil 1A plays a role in the subsequent IF assembly process.

  15. 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...... to a long alpha-helix. Tetranectin has been classified in a distinct group of the C-type lectin superfamily but has structural similarity to the proteins in the group of collectins. Tetranectin has three intramolecular disulfide bridges. Two of these are conserved in the C-type lectin superfamily, whereas...

  16. Solution structure of the porcine sapovirus VPg core reveals a stable three-helical bundle with a conserved surface patch.

    Science.gov (United States)

    Hwang, Hyo-Jeong; Min, Hye Jung; Yun, Hyosuk; Pelton, Jeffery G; Wemmer, David E; Cho, Kyoung-Oh; Kim, Jeong-Sun; Lee, Chul Won

    2015-04-17

    Viral protein genome-linked (VPg) proteins play a critical role in the life cycle of vertebrate and plant positive-sense RNA viruses by acting as a protein primer for genome replication and as a protein cap for translation initiation. Here we report the solution structure of the porcine sapovirus VPg core (VPg(C)) determined by multi-dimensional NMR spectroscopy. The structure of VPg(C) is composed of three α-helices stabilized by several conserved hydrophobic residues that form a helical bundle core similar to that of feline calicivirus VPg. The putative nucleotide acceptor Tyr956 within the first helix of the core is completely exposed to solvent accessible surface to facilitate nucleotidylation by viral RNA polymerase. Comparison of VPg structures suggests that the surface for nucleotidylation site is highly conserved among the Caliciviridae family, whereas the backbone core structures are different. These structural features suggest that caliciviruses share common mechanisms of VPg-dependent viral replication and translation. Copyright © 2015 Elsevier Inc. All rights reserved.

  17. Analysis of π-mode Stopband in an Asymmetric Millimeter-Wave Helical Slow-Wave Structure

    Science.gov (United States)

    Datta, S. K.; Kumar, Lalit; Basu, B. N.

    2008-11-01

    A simple closed form formula for the estimation of π-mode stopband in an azimuthally asymmetric helical slow-wave structure (SWS) was developed following coupled-mode analysis of multiple reflections of the degenerate space-harmonic modes from the support rod discontinuities. The method incorporates the effects of circuit loss, and accrues the accuracy of 3D electromagnetic analysis by allowing the use of dispersion characteristics obtainable from any standard electromagnetic modeling. The formula is simple and amenable to easy computation, even using a scientific calculator, and without resorting to exhaustive and time-intensive numerical computation, and at the same time, without sacrificing the accuracy in results. The analysis was benchmarked against published results and excellent agreement observed. The analysis was further used for demonstrating the stopband phenomenon for a typical millimeter-wave helical slow-wave structure. Compared to low frequency structures, the stopband phenomenon for a millimeter-wave structure was found to be more pronounced, and an interesting inference was drawn as to how asymmetry induced stopband might be made to advantage in combating π-mode instabilities in a millimeter-wave traveling-wave tube.

  18. 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.

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

    Science.gov (United States)

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

    2016-11-01

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

  20. Solution structure of the spectrin repeat: a left-handed antiparallel triple-helical coiled-coil.

    Science.gov (United States)

    Pascual, J; Pfuhl, M; Walther, D; Saraste, M; Nilges, M

    1997-10-31

    Cytoskeletal proteins belonging to the spectrin family have an elongated structure composed of repetitive units. The three-dimensional solution structure of the 16th repeat from chicken brain alpha-spectrin (R16) has been determined by NMR spectroscopy and distance geometry-simulated annealing calculations. We used a total of 1035 distance restraints, which included 719 NOE-based values obtained by applying the ambiguous restraints for iterative assignment (ARIA) method. In addition, we performed a direct refinement against 1H-chemical shifts. The final ensemble of 20 structures shows an average RMSD of 1.52 A from the mean for the backbone atoms, excluding loops and N and C termini. R16 is made up of three antiparallel alpha-helices separated by two loops, and folds into a left-handed coiled-coil. The basic unit of spectrin is an antiparallel heterodimer composed of two homologous chains, beta and alpha. These assemble a tetramer via a mechanism that relies on the completion of a single repeat by association of the partial repeats located at the C terminus of the beta-chain (two helices) and at the N terminus of the alpha-chain (one helix). This tetramer is the assemblage able to cross-link actin filaments. Model building by homology of the "tetramerization" repeat from human erythrocyte spectrin illuminates the possible role of point mutations which cause hemolytic anemias.

  1. New Structure of Optical Fiber Protection Cable Using Helical Composite Spring

    Science.gov (United States)

    Chung, Seunghwan; Yoon, Youngki; Lee, Woo‑Il; Lee, Byoungho

    2006-07-01

    A new type of cable is introduced for protecting optical fiber from mechanical bending or abrupt temperature changes. It shows superior ability to protect fiber from severe bending and lowers the thermal sensitivity compared with conventional optical fiber cable. It can be used as a protection sleeve or cable in special regions. The proposed device consists of a helical composite spring, a thermal insulator (i.e., polyurethane foam) and a heat-shrinkable tube which coats the outside of the spring. These components can be acquired for a moderate price and manufactured by simple processes.

  2. Highly sensitive strain sensor based on helical structure combined with Mach-Zehnder interferometer in multicore fiber.

    Science.gov (United States)

    Zhang, Hailiang; Wu, Zhifang; Shum, Perry Ping; Dinh, Xuan Quyen; Low, Chun Wah; Xu, Zhilin; Wang, Ruoxu; Shao, Xuguang; Fu, Songnian; Tong, Weijun; Tang, Ming

    2017-04-18

    Optical fiber sensors for strain measurement have been playing important roles in structural health monitoring for buildings, tunnels, pipelines, aircrafts, and so on. A highly sensitive strain sensor based on helical structures (HSs) assisted Mach-Zehnder interference in an all-solid heterogeneous multicore fiber (MCF) is proposed and experimentally demonstrated. Due to the HSs, a maximum strain sensitivity as high as -61.8 pm/με was experimentally achieved. This is the highest sensitivity among interferometer-based strain sensors reported so far, to the best of our knowledge. Moreover, the proposed sensor has the ability to discriminate axial strain and temperature, and offers several advantages such as repeatability of fabrication, robust structure and compact size, which further benefits its practical sensing applications.

  3. RosettaTMH: a method for membrane protein structure elucidation combining EPR distance restraints with assembly of transmembrane helices

    Directory of Open Access Journals (Sweden)

    Andrew Leaver-Fay

    2015-12-01

    Full Text Available Membrane proteins make up approximately one third of all proteins, and they play key roles in a plethora of physiological processes. However, membrane proteins make up less than 2% of experimentally determined structures, despite significant advances in structure determination methods, such as X-ray crystallography, nuclear magnetic resonance spectroscopy, and cryo-electron microscopy. One potential alternative means of structure elucidation is to combine computational methods with experimental EPR data. In 2011, Hirst and others introduced RosettaEPR and demonstrated that this approach could be successfully applied to fold soluble proteins. Furthermore, few computational methods for de novo folding of integral membrane proteins have been presented. In this work, we present RosettaTMH, a novel algorithm for structure prediction of helical membrane proteins. A benchmark set of 34 proteins, in which the proteins ranged in size from 91 to 565 residues, was used to compare RosettaTMH to Rosetta’s two existing membrane protein folding protocols: the published RosettaMembrane folding protocol (“MembraneAbinitio” and folding from an extended chain (“ExtendedChain”. When EPR distance restraints are used, RosettaTMH+EPR outperforms ExtendedChain+EPR for 11 proteins, including the largest six proteins tested. RosettaTMH+EPR is capable of achieving native-like folds for 30 of 34 proteins tested, including receptors and transporters. For example, the average RMSD100SSE relative to the crystal structure for rhodopsin was 6.1 ± 0.4 Å and 6.5 ± 0.6 Å for the 449-residue nitric oxide reductase subunit B, where the standard deviation reflects variance in RMSD100SSE values across ten different EPR distance restraint sets. The addition of RosettaTMH and RosettaTMH+EPR to the Rosetta family of de novo folding methods broadens the scope of helical membrane proteins that can be accurately modeled with this software suite.

  4. The NN final-state interaction in the helicity structure of $\\vec d(\\vec\\gamma,\\pi^-)pp$ reaction

    CERN Document Server

    Darwish, E M

    2005-01-01

    The influence of final-state $NN$-rescattering on the helicity structure of the $\\vec\\gamma\\vec d\\to\\pi^-pp$ 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 $\\vec\\gamma\\vec d\\to\\pi^-pp$ 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.

  5. Transport timescale calculations of sawteeth and helical structures in non-circular tokamak plasmas

    Science.gov (United States)

    Jardin, Stephen; Ferraro, Nate; Breslau, Josh; Chen, Jin

    2012-10-01

    We present results of using the implicit 3D MHD code M3D-C^1 [1,2] to perform 3D nonlinear magnetohydrodynamics calculations of the internal dynamics of a shaped cross-section tokamak plasma that span the timescales associated with ideal and resistive stability as well as parallel and perpendicular transport. We specify the transport coefficients and apply a ``current controller'' that adjusts the boundary loop-voltage to keep the total plasma current fixed. The 3D 2-fluid plasma model advances the magnetic field, velocities, electron and ion temperatures, and plasma density. We find that the plasma either reaches a stationary quasi-helical state in which the central safety factor is approximately unity, or it periodically undergoes either simple or compound sawtooth oscillations [3] with a period that approaches a constant value. By comparing a dee-shaped cross section with an elliptical shaped cross section, it is shown that the plasma shape has a large effect on determining the sawtooth behavior and the associated mode activity. Application to ITER shaped tokamak plasmas predict the magnitude of the 3D boundary deformation as a result of a stationary quasi-helical state forming in the interior. [4pt] [1] J. Breslau, N. Ferraro, S.C. Jardin, Physics of Plasmas 16 092503 (2009) [0pt] [2] S. C. Jardin, N. Ferraro, J. Breslau, J. Chen, Computational Science and Discovery 5 014002 (2012) [0pt] [3] X. von Goeler, W. Stodiek, and N. Sauthoff, Phys. Rev. Lett. 33, 1201 (1974)

  6. Aromatic interactions promote self-association of collagen triple-helical peptides to higher-order structures.

    Science.gov (United States)

    Kar, Karunakar; Ibrar, Sajjad; Nanda, Vikas; Getz, Todd M; Kunapuli, Satya P; Brodsky, Barbara

    2009-08-25

    Aromatic residues are relatively rare within the collagen triple helix, but they appear to play a specialized role in higher-order structure and function. The role of aromatic amino acids in the self-assembly of triple-helical peptides was investigated in terms of the kinetics of self-association, the nature of aggregated species formed, and the ability of these species to activate platelet aggregation. The presence of aromatic residues on both ends of a type IV collagen model peptide is observed to greatly accelerate the kinetics of self-association, decreasing the lag time and leading to insoluble, well-defined linear fibrils as well as small soluble aggregates. Both macroscopic visible aggregates and small multimolecular complexes in solution are capable of inducing platelet aggregation through the glycoprotein VI receptor on platelets. Proline-aromatic CH...pi interactions are often observed within globular proteins and in protein complexes, and examination of molecular packing in the crystal structure of the integrin binding collagen peptide shows Phe interacts with Pro/Hyp in a neighboring triple-helical molecule. An intermolecular interaction between aromatic amino acids and imino acids within the triple helix is also supported by the observed inhibitory effect of isolated Phe amino acids on the self-association of (Pro-Hyp-Gly)(10). Given the high fraction of Pro and Hyp residues on the surface of collagen molecules, it is likely that imino acid-aromatic CH...pi interactions are important in formation of higher-order structure. We suggest that the catalysis of type I collagen fibrillogenesis by nonhelical telopeptides is due to specific intermolecular CH...pi interactions between aromatic residues in the telopeptides and Pro/Hyp residues within the triple helix.

  7. The Structure and Organization within the Membrane of the Helices Composing the Pore-Forming Domain of Bacillus thuringiensis δ -Endotoxin are Consistent with an ``Umbrella-Like'' Structure of the Pore

    Science.gov (United States)

    Gazit, Ehud; La Rocca, Paolo; Sansom, Mark S. P.; Shai, Yechiel

    1998-10-01

    The aim of this study was to elucidate the mechanism of membrane insertion and the structural organization of pores formed by Bacillus thuringiensis δ -endotoxin. We determined the relative affinities for membranes of peptides corresponding to the seven helices that compose the toxin pore-forming domain, their modes of membrane interaction, their structures within membranes, and their orientations relative to the membrane normal. In addition, we used resonance energy transfer measurements of all possible combinatorial pairs of membrane-bound helices to map the network of interactions between helices in their membrane-bound state. The interaction of the helices with the bilayer membrane was also probed by a Monte Carlo simulation protocol to determine lowest-energy orientations. Our results are consistent with a situation in which helices α 4 and α 5 insert into the membrane as a helical hairpin in an antiparallel manner, while the other helices lie on the membrane surface like the ribs of an umbrella (the ``umbrella model''). Our results also support the suggestion that α 7 may serve as a binding sensor to initiate the structural rearrangement of the pore-forming domain.

  8. 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

  9. 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.

  10. Structure and membrane remodeling activity of ESCRT-III helical polymers

    Science.gov (United States)

    McCullough, John; Clippinger, Amy K.; Talledge, Nathaniel; Skowyra, Michael L.; Saunders, Marissa G.; Naismith, Teresa V.; Colf, Leremy A.; Afonine, Pavel; Arthur, Christopher; Sundquist, Wesley I.; Hanson, Phyllis I.; Frost, Adam

    2015-01-01

    The Endosomal Sorting Complexes Required for Transport (ESCRT) proteins mediate fundamental membrane remodeling events that require stabilizing negative membrane curvature. These include endosomal intralumenal vesicle formation, HIV budding, nuclear envelope closure and cytokinetic abscission. ESCRT-III subunits perform key roles in these processes by changing conformation and polymerizing into membrane-remodeling filaments. Here, we report the 4 Å resolution cryo-EM reconstruction of a one-start, double-stranded helical copolymer composed of two different human ESCRT-III subunits, CHMP1B and IST1. The inner strand comprises “open” CHMP1B subunits that interlock in an elaborate domain-swapped architecture, and is encircled by an outer strand of “closed” IST1 subunits. Unlike other ESCRT-III proteins, CHMP1B and IST1 polymers form external coats on positively-curved membranes in vitro and in vivo. Our analysis suggests how common ESCRT-III filament architectures could stabilize different degrees and directions of membrane curvature. PMID:26634441

  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.

  12. Influence of Magnetic Helicity in MHD

    CERN Document Server

    Candelaresi, Simon; Brandenburg, Axel

    2010-01-01

    Observations have shown that the Sun's magnetic field has helical structures. The helicity content in magnetic field configurations is a crucial constraint on the dynamical evolution of the system. Since helicity is connected with the number of links we investigate configurations with interlocked magnetic flux rings and one with unlinked rings. It turns out that it is not the linking of the tubes which affects the magnetic field decay, but the content of magnetic helicity.

  13. Secondary structure of Ac-Ala$_n$-LysH$^+$ polyalanine peptides ($n$=5,10,15) in vacuo: Helical or not?

    CERN Document Server

    Rossi, M; Kupser, P; von Helden, G; Bierau, F; Pagel, K; Meijer, G; Scheffler, M

    2010-01-01

    The polyalanine-based peptide series Ac-Ala_n-LysH+ (n=5-20) is a prime example that a secondary structure motif which is well-known from the solution phase (here: helices) can be formed in vacuo. We here revisit this conclusion for n=5,10,15, using density-functional theory (van der Waals corrected generalized gradient approximation), and gas-phase infrared vibrational spectroscopy. For the longer molecules (n=10,15) \\alpha-helical models provide good qualitative agreement (theory vs. experiment) already in the harmonic approximation. For n=5, the lowest energy conformer is not a simple helix, but competes closely with \\alpha-helical motifs at 300K. Close agreement between infrared spectra from experiment and ab initio molecular dynamics (including anharmonic effects) supports our findings.

  14. Nano-structure and optical properties (plasmonic) of graded helical square tower-like (terraced) Mn sculptured thin films

    Science.gov (United States)

    Savaloni, Hadi; Fakharpour, Mahsa; Siabi-Garjan, Araz; Placido, Frank; Babaei, Ferydon

    2017-01-01

    Graded helical square tower-like terraced sculptured Mn thin films (GHSTTS) are produced in three stages with different number of arms using oblique angle deposition together with rotation of substrate holder about its surface normal, plus a shadowing block fixed at the centre of the substrate holder. The structural characterization of the produced samples was obtained using field emission scanning electron microscope (FESEM) and atomic force microscope (AFM). Results showed a structural gradient with distance from the edge of the shadowing block, which in turn is responsible for the decrease in the volume of void fraction and increase of grain size. Plasmon absorption peaks observed in the optical analysis of these nano-structures showed that their wavelength region and intensity depend on the polarization and the incident angle of light, as well as the distance from the edge of the shadowing block. According to our model and discrete dipole approximation (DDA) calculations, when the number of parallel nano-rods of different lengths and radii are increased the peak in the spectrum shifts to shorter wavelengths (blue shift). Also when the diameters of the nano-rods increases (a situation that occurs with increasing film thickness) the results is again a blue shift in the spectrum. The presence of defects in these sculptured structures caused by the shadowing effect is predicted by the theoretical DDA investigation of their optical spectra. Good agreement is obtained between our theoretical results and the experimental observations in this work.

  15. Multiple structural states exist throughout the helical nucleation sequence of the intrinsically disordered protein stathmin, as reported by electron paramagnetic resonance spectroscopy.

    Science.gov (United States)

    Chui, Ashley J; López, Carlos J; Brooks, Evan K; Chua, Katherina C; Doupey, Tonia G; Foltz, Gretchen N; Kamel, Joseph G; Larrosa, Estefania; Sadiki, Amissi; Bridges, Michael D

    2015-03-10

    The intrinsically disordered protein (IDP) stathmin plays an important regulatory role in cytoskeletal maintenance through its helical binding to tubulin and microtubules. However, it lacks a stable fold in the absence of its binding partner. Although stathmin has been a focus of research over the past two decades, the solution-phase conformational dynamics of this IDP are poorly understood. It has been reported that stathmin is purely monomeric in solution and that it bears a short helical region of persistent foldedness, which may act to nucleate helical folding in the C-terminal direction. Here we report a comprehensive study of the structural equilibria local to this region in stathmin that contradicts these two claims. Using the technique of electron paramagnetic resonance (EPR) spectroscopy on spin-labeled stathmin mutants in the solution-phase and when immobilized on Sepharose solid support, we show that all sites in the helical nucleation region of stathmin exhibit multiple spectral components that correspond to dynamic states of differing mobilities and stabilities. Importantly, a state with relatively low mobility dominates each spectrum with an average population greater than 50%, which we suggest corresponds to an oligomerized state of the protein. This is in contrast to a less populated, more mobile state, which likely represents a helically folded monomeric state of stathmin, and a highly mobile state, which we propose is the random coil conformer of the protein. Our interpretation of the EPR data is confirmed by further characterization of the protein using the techniques of native and SDS PAGE, gel filtration chromatography, and multiangle and dynamic light scattering, all of which show the presence of oligomeric stathmin in solution. Collectively, these data suggest that stathmin exists in a diverse equilibrium of states throughout the purported helical nucleation region and that this IDP exhibits a propensity toward oligomerization.

  16. Mycobacterium tuberculosis Chaperonin 10 Is Secreted in the Macrophage Phagosome: Is Secretion Due to Dissociation and Adoption of a Partially Helical Structure at the Membrane?

    Science.gov (United States)

    Fossati, Gianluca; Izzo, Gaetano; Rizzi, Emanuele; Gancia, Emanuela; Modena, Daniela; Moras, Maria Luisa; Niccolai, Neri; Giannozzi, Elena; Spiga, Ottavia; Bono, Letizia; Marone, Piero; Leone, Eugenio; Mangili, Francesca; Harding, Stephen; Errington, Neil; Walters, Christopher; Henderson, Brian; Roberts, Michael M.; Coates, Anthony R. M.; Casetta, Bruno; Mascagni, Paolo

    2003-01-01

    To confirm that Mycobacterium tuberculosis chaperonin 10 (Cpn10) is secreted outside the live bacillus, infected macrophages were examined by electron microscopy. This revealed that the mycobacterial protein accumulates both in the wall of the bacterium and in the matrix of the phagosomes in which ingested mycobacteria survive within infected macrophages. To understand the structural implications underlying this secretion, a structural study of M. tuberculosis Cpn10 was performed under conditions that are generally believed to mimic the membrane environment. It was found that in buffer-organic solvent mixtures, the mycobacterial protein forms two main species, namely, a partially helical monomer that prevails in dilute solutions at room temperature and a dimer that folds into a β-sheet-dominated structure and prevails in either concentrated protein solutions at room temperature or in dilute solutions at low temperature. A partially helical monomer was also found and was completely associated with negatively charged detergents in a micelle-bound state. Remarkably, zwitterionic lipids had no effect on the protein structure. By using N- and C-truncated forms of the protein, the C- and N-terminal sequences were identified as possessing an amphiphilic helical character and as selectively associating with acidic detergent micelles. When the study was extended to other chaperonins, it was found that human Cpn10 is also monomeric and partially helical in dilute organic solvent-buffer mixtures. In contrast, Escherichia coli Cpn10 is mostly dimeric and predominately β-sheet in both dilute and concentrated solutions. Interestingly, human Cpn10 also crosses biological membranes, whereas the E. coli homologue is strictly cytosolic. These results suggest that dissociation to partially helical monomers and interaction with acidic lipids may be two important steps in the mechanism of secretion of M. tuberculosis Cpn10 to the external environment. PMID:12837802

  17. 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

  18. Plasmodium vivax tryptophan-rich antigen PvTRAg33.5 contains alpha helical structure and multidomain architecture.

    Directory of Open Access Journals (Sweden)

    Hema Bora

    Full Text Available Tryptophan-rich proteins from several malarial parasites have been identified where they play an important role in host-parasite interaction. Structural characterization of these proteins is needed to develop them as therapeutic targets. Here, we describe a novel Plasmodium vivax tryptophan-rich protein named PvTRAg33.5. It is expressed by blood stage(s of the parasite and its gene contains two exons. The exon 1 encodes for a 23 amino acids long putative signal peptide which is likely to be cleaved off whereas the exon 2 encodes for the mature protein of 252 amino acids. The mature protein contains B-cell epitopes which were recognized by the human immune system during P.vivax infection. The PvTRAg33.5 contains 24 (9.5% tryptophan residues and six motifs whose patterns were similar among tryptophan-rich proteins. The modeled structure of the PvTRAg33.5 consists of a multidomain architecture which is stabilized by the presence of large number of tryptophan residues. The recombinant PvTRAg33.5 showed predominantly α helical structure and alpha helix to beta sheet transition at pH below 4.5. Protein acquires an irreversible non-native state at temperature more than 50°C at neutral pH. Its secondary and tertiary structures remain stable in the presence of 35% alcohol but these structures are destabilized at higher alcohol concentrations due to the disturbance of hydrophobic interactions between tryptophanyl residues. These structural changes in the protein might occur during its translocation to interact with other proteins at its final destination for biological function such as erythrocyte invasion.

  19. 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.

  20. 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.; A2 Collaboration at MAMI

    2016-09-01

    The double polarization observable E and the helicity dependent cross sections σ1 /2 and σ3 /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 4 π detector setup of the Crystal Ball and TAPS is ideally suited to detect the recoil nucleons and the decay photons from η →2 γ and η →3 π0. The results show that the narrow structure previously observed in η photoproduction from the neutron is only apparent in σ1 /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- (S11) and N 1 /2+ (P11). Furthermore, the extracted Legendre coefficients of the angular distributions for σ1 /2 are in good agreement with recent reaction model predictions assuming a narrow resonance in the P11 wave as the origin of this structure.

  1. 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/.

  2. 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

    Despite the biological and pharmaceutical significance of membrane proteins, their tertiary structures constitute less than 3% of known structures. One of the major obstacles for initiating structural studies of membrane proteins by NMR spectroscopy is the generation of high amounts of isotope......-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...

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

    Energy Technology Data Exchange (ETDEWEB)

    Cnudde, Sara E.; Prorok, Mary; Jia, Xaofei; Castellino, Francis J.; Geiger, James H. (MSU); (Notre)

    2012-02-15

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

  4. Validation and Benchmarking of a Practical Free Magnetic Energy and Relative Magnetic Helicity Budget Calculation in Solar Magnetic Structures

    CERN Document Server

    Moraitis, K; Georgoulis, M K; Archontis, V

    2014-01-01

    In earlier works we introduced and tested a nonlinear force-free (NLFF) method designed to self-consistently calculate the free magnetic energy and the relative magnetic helicity budgets of the corona of observed solar magnetic structures. The method requires, in principle, only a single, photospheric or low-chromospheric, vector magnetogram of a quiet-Sun patch or an active region and performs calculations in the absence of three-dimensional magnetic and velocity-field information. In this work we strictly validate this method using three-dimensional coronal magnetic fields. Benchmarking employs both synthetic, three-dimensional magnetohydrodynamic simulations and nonlinear force-free field extrapolations of the active-region solar corona. We find that our time-efficient NLFF method provides budgets that differ from those of more demanding semi-analytical methods by a factor of ~3, at most. This difference is expected from the physical concept and the construction of the method. Temporal correlations show mo...

  5. Helical secondary structure of polyalanine peptides in vacuo: Ac-Alan-LysH^+ (n=5,10,15), experiment and theory

    Science.gov (United States)

    Rossi, Mariana; Blum, Volker; Kupser, Peter; von Helden, Gert; Bierau, Frauke; Meijer, Gerard; Scheffler, Matthias

    2009-03-01

    The presence of a solvent is often viewed as indispensable to explain the structure of peptides and proteins. However, well defined secondary structure motifs (helices, sheets, ...) also exist in vacuo, offering a unique ``clean room'' condition to quantify the stabilizing interactions. We here unravel the structure of LysineH^+ capped polyalanine peptides Ac-Alan-LysH^+ (n-5,10,15), by combining experimental multi-photon IR spectra obtained using the FELIX free-electron laser at room-temperature with van der Waals-corrected all-electron density-functional theory (DFT) in the generalized gradient approximation in the FHI-aims code [1]. Earlier ion mobility studies of these molecules indicate helical structure [2], which we here demonstrate quantitatively. For n=5, we find a close energetic competition of different helix motifs (α, 310), with similar and good agreement between measured and calculated vibrational spectra. We show how the LysH^+ termination acts to induce helices also for longer peptides, and how vibrational modes develop with helix length (n=10,15), yielding, e.g., a softening of collective modes towards the infinite helix limit. [1] V. Blum et al, Comp. Phys. Comm. (2008), accepted. [2] M. Kohtani et al., JACS 120, 12975 (1998).

  6. A series of chiral coordination polymers containing helicals assembled from a new chiral (R)-2-(4'-(4''-carboxybenzyloxy)phenoxy)propanoic acid: syntheses, structures and photoluminescent properties.

    Science.gov (United States)

    He, Wei-Wei; Yang, Jin; Yang, Yan; Liu, Ying-Ying; Ma, Jian-Fang

    2012-08-28

    Ten new chiral coordination polymers, namely, [Ni(L)(H(2)O)(2)] (1), [Co(L)(H(2)O)(2)] (2), [Cd(L)(H(2)O)] (3), [Cd(L)(phen)] (4), [Mn(2)(L)(2) (phen)(2)]·H(2)O (5), [Cd(2)(L)(2)(biim-4)(2)] (6), [Zn(2)(L)(2)(biim-4)(2)] (7), [Cd(L)(pbib)] (8), [Cd(L)(bbtz)] (9) and [Cd(L)(biim-6)] (10), where phen = 1,10-phenathroline, biim-4 = 1,1'-(1,4-butanediyl)bis(imidazole), pbib = 1,4-bis(imidazole-1-ylmethyl)benzene, bbtz = 1,4-bis(1,2,4-triazol-1-ylmethyl)benzene, biim-6 = 1,1'-(1,6-hexanedidyl)bis(imidazole), and H(2)L = (R)-2-(4'-(4''-carboxybenzyloxy)phenoxy)propanoic acid, have been synthesized under hydrothermal conditions. Their structures have been determined by single-crystal X-ray diffraction analyses and further characterized by infrared spectra (IR), powder X-ray diffraction (PXRD), elemental analyses and thermogravimetric (TG) analyses. Compounds 1 and 2 exhibit similar 1D left-handed helical chains, which are further extended into 3D supramolecular structures through O-H···O hydrogen-bonding interactions, respectively. Compound 3 shows a 2D double-layer architecture containing helical chains. Compound 4 features two types of 2D undulated sheets with helical chains, which are stacked in an ABAB fashion along the c direction. Compound 5 possesses a 1D double chain ribbon structure containing unusual meso-helical chains, which is linked by π-π interactions into a 2D supramolecular layer. These layers are further extended by hydrogen-bonding interactions to form a 3D supramolecular assembly. Compounds 6 and 7 are isostructural and exhibit 2D (4(4))-sql networks with helical chains. Neighboring sheets are further linked by C-H···O hydrogen-bonding interactions to generate 3D supramolecular architectures. Compounds 8-10 are isostructural and display 3D 3-fold interpenetrating diamond frameworks with helical chains. The effects of coordination modes of L anions, metal ions and N-donor ligands on the structures of the coordination polymers have been

  7. Assemblies of a new flexible multicarboxylate ligand and d10 metal centers toward the construction of homochiral helical coordination polymers: structures, luminescence, and NLO-active properties.

    Science.gov (United States)

    Zang, Shuangquan; Su, Yang; Li, Yizhi; Ni, Zhaoping; Meng, Qingjin

    2006-01-01

    Hydro(solvo)thermal reactions between a new flexible multicarboxylate ligand of 2,2',3,3'-oxydiphthalic acid (2,2',3,3'-H(4)ODPA) and M(NO(3))(2).xH(2)O (M = Zn, x = 6; M = Cd, x = 4) in the presence of 4,4'-bipyridine (bpy) afford two novel homochiral helical coordination polymers [[Zn(2)(2,2',3,3'-ODPA)(bpy)(H(2)O)(3)].(H(2)O)(2) for 1 and [Cd(2)(2,2',3,3'-ODPA)(bpy)(H(2)O)(3)].(H(2)O)(2) for 2]. Though having almost the same chemical formula, they have different space groups (P2(1)2(1)2(1) for 1 and P2(1) for 2) and different bridging modes of the 2,2',3,3'-ODPA ligand. Two kinds of homochiral helices (right-handed) are found in both 1 and 2, each of which discriminates only one kind of crystallographical nonequivalent metal atom. 1 has a 2D metal-organic framework and can be seen as the unity of two parallel homochiral Zn1 and Zn2 helices, in which the nodes are etheric oxygen atoms. In contrast, 2 has a 3D metal-organic framework and consists of two partially overlapped homochiral Cd1 and Cd2 helices in the two dimensions. Moreover, metal-ODPA helices give a 2D chiral herringbone structural motif in both 1 and 2 in the two dimensions, which are further strengthened by the second ligand of bpy. Bulk materials for 1 and 2 all have good second-harmonic generation activity, approximately 1 and 0.8 times that of urea.

  8. The triple helical structure and stability of collagen model peptide with 4(S)-hydroxyprolyl-Pro-Gly units.

    Science.gov (United States)

    Motooka, Daisuke; Kawahara, Kazuki; Nakamura, Shota; Doi, Masamitsu; Nishi, Yoshinori; Nishiuchi, Yuji; Kang, Young Kee; Nakazawa, Takashi; Uchiyama, Susumu; Yoshida, Takuya; Ohkubo, Tadayasu; Kobayashi, Yuji

    2012-01-01

    Extensive studies on the structure of collagen have revealed that the hydroxylation of Pro residues in a variety of model peptides with the typical (X-Y-Gly)(n) repeats (X and Y: Pro and its analogues) represents one of the major factors influencing the stability of triple helices. While(2S,4R)-hydroxyproline (Hyp) at the position Y stabilizes the triple helix, (2S,4S)-hydroxyproline (hyp) at the X-position destabilizes the helix as demonstrated that the triple helix of (hyp-Pro-Gly)(15) is less stable than that of (Pro-Pro-Gly)(15) and that a shorter peptide (hyp-Pro-Gly)(10) does not form the helix. To clarify the role of the hydroxyl group of Pro residues to play in the stabilization mechanism of the collagen triple helix, we synthesized and crystallized a model peptide (Pro-Hyp-Gly)(4) -(hyp-Pro-Gly)(2) -(Pro-Hyp-Gly)(4) and analyzed its structure by X-ray crystallography and CD spectroscopy. In the crystal, the main-chain of this peptide forms a typical collagen like triple helix. The majority of hyp residues take down pucker with exceptionally shallow angles probably to relieve steric hindrance, but the remainders protrude the hydroxyl group toward solvent with the less favorable up pucker to fit in a triple helix. There is no indication of the existence of an intra-molecular hydrogen bond between the hydroxyl moiety and the carbonyl oxygen of hyp supposed to destabilize the triple helix. We also compared the conformational energies of up and down packers of the pyrrolidine ring in Ac-hyp-NMe(2) by quantum mechanical calculations.

  9. Decay of helical and non-helical magnetic knots

    CERN Document Server

    Candelaresi, Simon

    2011-01-01

    We present calculations of the relaxation of magnetic field structures that have the shape of particular knots and links. A set of helical magnetic flux configurations is considered, which we call $n$-foil knots of which the trefoil knot is the most primitive member. We also consider two non-helical knots, namely the Borromean rings as well as a single interlocked flux rope that also serves as the logo of the Inter-University Centre for Astronomy and Astrophysics in Pune, India. The field decay characteristics of both configurations is investigated and compared with previous calculations of helical and non-helical triple ring configurations. For the $n$-foil knots the decay is described by power laws that range form $t^{-2/3}$ to $t^{-1/3}$, which can be as slow as the $t^{-1/3}$ behavior for helical triple-ring structures that was seen in earlier work. The two non-helical configurations decay like $t^{-1}$, which is somewhat slower than the previously obtained $t^{-3/2}$ behavior in the decay of interlocked ...

  10. 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

  11. The structure of the SBP-Tag–streptavidin complex reveals a novel helical scaffold bridging binding pockets on separate subunits

    Energy Technology Data Exchange (ETDEWEB)

    Barrette-Ng, Isabelle H.; Wu, Sau-Ching; Tjia, Wai-Mui; Wong, Sui-Lam; Ng, Kenneth K. S., E-mail: ngk@ucalgary.ca [University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4 (Canada)

    2013-05-01

    The structure of the SBP-Tag–streptavidin complex reveals a novel mode of peptide recognition in which a single peptide binds simultaneously to biotin-binding pockets from adjacent subunits of streptavidin. The molecular details of peptide recognition suggest how the SBP-Tag can be further modified to become an even more useful tag for a wider range of biotechnological applications. The 38-residue SBP-Tag binds to streptavidin more tightly (K{sub d} ≃ 2.5–4.9 nM) than most if not all other known peptide sequences. Crystallographic analysis at 1.75 Å resolution shows that the SBP-Tag binds to streptavidin in an unprecedented manner by simultaneously interacting with biotin-binding pockets from two separate subunits. An N-terminal HVV peptide sequence (residues 12–14) and a C-terminal HPQ sequence (residues 31–33) form the bulk of the direct interactions between the SBP-Tag and the two biotin-binding pockets. Surprisingly, most of the peptide spanning these two sites (residues 17–28) adopts a regular α-helical structure that projects three leucine side chains into a groove formed at the interface between two streptavidin protomers. The crystal structure shows that residues 1–10 and 35–38 of the original SBP-Tag identified through in vitro selection and deletion analysis do not appear to contact streptavidin and thus may not be important for binding. A 25-residue peptide comprising residues 11–34 (SBP-Tag2) was synthesized and shown using surface plasmon resonance to bind streptavidin with very similar affinity and kinetics when compared with the SBP-Tag. The SBP-Tag2 was also added to the C-terminus of β-lactamase and was shown to be just as effective as the full-length SBP-Tag in affinity purification. These results validate the molecular structure of the SBP-Tag–streptavidin complex and establish a minimal bivalent streptavidin-binding tag from which further rational design and optimization can proceed.

  12. Critical structure sparing in stereotactic ablative radiotherapy for central lung lesions: helical tomotherapy vs. volumetric modulated arc therapy.

    Directory of Open Access Journals (Sweden)

    Alexander Chi

    Full Text Available BACKGROUND: Helical tomotherapy (HT and volumetric modulated arc therapy (VMAT are both advanced techniques of delivering intensity-modulated radiotherapy (IMRT. Here, we conduct a study to compare HT and partial-arc VMAT in their ability to spare organs at risk (OARs when stereotactic ablative radiotherapy (SABR is delivered to treat centrally located early stage non-small-cell lung cancer or lung metastases. METHODS: 12 patients with centrally located lung lesions were randomly chosen. HT, 2 & 8 arc (Smart Arc, Pinnacle v9.0 plans were generated to deliver 70 Gy in 10 fractions to the planning target volume (PTV. Target and OAR dose parameters were compared. Each technique's ability to meet dose constraints was further investigated. RESULTS: HT and VMAT plans generated essentially equivalent PTV coverage and dose conformality indices, while a trend for improved dose homogeneity by increasing from 2 to 8 arcs was observed with VMAT. Increasing the number of arcs with VMAT also led to some improvement in OAR sparing. After normalizing to OAR dose constraints, HT was found to be superior to 2 or 8-arc VMAT for optimal OAR sparing (meeting all the dose constraints (p = 0.0004. All dose constraints were met in HT plans. Increasing from 2 to 8 arcs could not help achieve optimal OAR sparing for 4 patients. 2/4 of them had 3 immediately adjacent structures. CONCLUSION: HT appears to be superior to VMAT in OAR sparing mainly in cases which require conformal dose avoidance of multiple immediately adjacent OARs. For such cases, increasing the number of arcs in VMAT cannot significantly improve OAR sparing.

  13. Long-period helical structures and twist-grain boundary phases induced by chemical substitution in the Mn1 -x(Co,Rh ) xGe chiral magnet

    Science.gov (United States)

    Martin, N.; Deutsch, M.; Chaboussant, G.; Damay, F.; Bonville, P.; Fomicheva, L. N.; Tsvyashchenko, A. V.; Rössler, U. K.; Mirebeau, I.

    2017-07-01

    We study the evolution of helical magnetism in MnGe chiral magnet upon partial substitution of Mn for 3 d -Co and 4 d -Rh ions. At high doping levels, we observe spin helices with very long periods—more than ten times larger than in the pure compound—and sizable ordered moments. This behavior calls for a change in the energy balance of interactions leading to the stabilization of the observed magnetic structures. Strikingly, neutron scattering unambiguously shows a double periodicity in the observed spectra at x =0.5 and >0.2 for Co- and Rh-doping, respectively. In analogy with observations made in smectic liquid crystals, we suggest that it may reveal the presence of magnetic "twist grain boundary" phases, involving a dense short-range correlated network of magnetic screw dislocations. The dislocation cores are here tentatively described as smooth textures, made of nonradial double-core skyrmions.

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

    Energy Technology Data Exchange (ETDEWEB)

    Zhou, Shi [Key Laboratory of Polyoxometalates Science of Ministry of Education, College of Chemistry, Northeast Normal University, Changchun 130024 (China); College of Chemistry, Jilin Normal University, Siping 136000 (China); Liu, Bo [College of Chemistry, Jilin Normal University, Siping 136000 (China); Li, Xiao-Min; Shi, Tian [Key Laboratory of Polyoxometalates Science of Ministry of Education, College of Chemistry, Northeast Normal University, Changchun 130024 (China); Chen, Ya-Guang, E-mail: chenyg146@nenu.edu.cn [Key Laboratory of Polyoxometalates Science of Ministry of Education, College of Chemistry, Northeast Normal University, Changchun 130024 (China)

    2014-11-15

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

  15. 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.

  16. Robust trans-amide helical structure of oligomers of bicyclic mimics of β-proline: impact of positional switching of bridgehead substituent on amide cis-trans equilibrium.

    Science.gov (United States)

    Wang, Siyuan; Otani, Yuko; Liu, Xin; Kawahata, Masatoshi; Yamaguchi, Kentaro; Ohwada, Tomohiko

    2014-06-06

    Because homooligomers of 7-azabicyclo[2.2.1]heptane-2-endo-carboxylic acid, a bridged β-proline analogue with a substituent installed at the remote C4-bridgehead position, completely biased the amide cis-trans equilibrium to the cis-amide structure, we expected that introduction of a substituent at the C1-bridgehead position adjacent to the carboxylic acid moiety, rather than the remote C4-bridgehead position, would tip the cis-trans amide equilibrium toward trans-amide structure without the aid of hydrogen bonding. Thus, in this work we established an efficient synthetic route to an optically active bicyclic analogue of 1,1-disubstituted β-proline, bearing a substituent at the C1-bridgehead position. Crystallographic, spectroscopic, and computational studies showed that indeed oligomers of this analogue take a consistent helical structure involving all-trans-amide linkages, independently of the number of residues, from the dimer up to the octamer. Oligomers composed of (R)-β-amino acid units form an extended left-handed helix with about 2.7 residues per turn and an approximately 4.0 Å rise per residue, characterized by complete lack of main-chain hydrogen bonding. This unique helical structure shows some similarity in shape to the trans-amide-based polyproline II (PPII) helix. The present helix was stable in various kinds of solvents such as alcohols. The present work provided a fundamental structural basis for future applications.

  17. Effect of hydration on the stability of the collagen-like triple-helical structure of [4(R)-hydroxyprolyl-4(R)-hydroxyprolylglycine]10.

    Science.gov (United States)

    Kawahara, Kazuki; Nishi, Yoshinori; Nakamura, Shota; Uchiyama, Susumu; Nishiuchi, Yuji; Nakazawa, Takashi; Ohkubo, Tadayasu; Kobayashi, Yuji

    2005-12-06

    X-ray analysis has been carried out on a crystal of the collagen model peptide (Hyp(R)-Hyp(R)-Gly)10 [where Hyp(R) is 4(R)-hydroxyproline] with 1.5 A resolution. The triple-helical structure of (Hyp(R)-Hyp(R)-Gly)10 has the same helical parameters and Rich and Crick II hydrogen bond patterns as those of other collagen model peptides. However, our full-length crystal structure revealed that almost all consecutive Hyp(R) residues take the up-up pucker in contrast to putative down-up puckering propensities of other collagen model peptides. The unique feature of thermodynamic parameters associated with the conformational transition of this peptide from triple helix to single coil is that both enthalpy and entropy changes of the transition are much smaller than those of other model peptides such as (Pro-Pro-Gly)10 and (Pro-Hyp(R)-Gly)10. To corroborate the precise structural information including main- and side-chain dihedral angles and intra- and interwater bridge networks, we estimated the degrees of hydration by comparing molecular volumes observed experimentally in solution to those calculated ones from the crystal structure. The results showed that the degree of hydration of (Hyp(R)-Hyp(R)-Gly)10 is comparable to that of (Pro-Hyp(R)-Gly)10 in the triple-helical state, but the former was more highly hydrated than (Pro-Hyp(R)-Gly)10 in the single-coil state. Because hydration reduces the enthalpy due to the formation of a hydrogen bond with a water molecule and diminishes the entropy due to the restriction of water molecules surrounding a peptide molecule, we concluded that the high thermal stability of (Hyp(R)-Hyp(R)-Gly)10 is able to be described by its high hydration in the single-coil state.

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

    Science.gov (United States)

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

    2014-11-01

    Two isostructural polyoxometalate-based inorganic-organic hybrids with 1D helical chain, [CuH3L2(GeMo12O40)]·2H2O (1) and [CuH3L2(SiMo12O40)]·2H2O (2), where L=2,4,5-tri(4-pyridyl)-imidazole have been synthesized under hydrothermal conditions. It is the first time to use the L ligand to synthesis the Keggin-type polyoxometalate-based inorganic-organic hybrids. The two compounds possess the left- and right-handed helical chains and the POMs as pendants attach in the helical chains through Cu-O bonds. The two compounds have been characterized by elemental analyses, infrared (IR) spectroscopy, powder X-ray diffraction (PXRD), X-ray photoelectron spectra (XPS), thermogravimetric analysis (TGA) and photoluminescent spectroscopy. Moreover, nitrogen adsorption-desorption measurement, electrochemical and photocatalysis properties for degradation of methylene blue (MB) upon a UV irradiation of compound 1 have been examined.

  19. 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.

  20. Currents for Arbitrary Helicity

    CERN Document Server

    Dragon, Norbert

    2016-01-01

    Using Mackey's classification of unitary representations of the Poincar\\'e group on massles states of arbitrary helicity we disprove the claim that states with helicity |h|>=1 cannot couple to a conserved current by constructing such a current.

  1. Two new twisted helical nickel(II) and cobalt(III) octahedral monomer complexes: Synthesis and structural characterization

    Indian Academy of Sciences (India)

    Malay Dolai; Mahammad Ali

    2014-11-01

    Two mononuclear complexes namely [NiII(L)] (1) and [CoIII(L)](NO3) (2) of a hexacoordinating N4O2 donor Schiff base ligand were synthesized and characterized by single crystal X-ray studies. In compound 2 the central cobalt is in +3 oxidation state while `in' compound 2, the nickel ion is in +2 oxidation state. The two complexes are isostructural with octahedral coordination environment exhibiting helical twist topology. They also display strong H-bonding as well as CH- interactions to generate 1D chain.

  2. Helicity dependent parton distributions

    CERN Document Server

    Scopetta, Sergio; 10.4249/scholarpedia.10226

    2011-01-01

    The helicity dependent parton distributions describe the number density of partons with given longitudinal momentum x and given polarization in a hadron polarized longitudinally with respect to its motion. After the discovery, more than 70 years ago, that the proton is not elementary, the observation of Bjorken scaling in the late 1960s lead to the idea of hadrons containing almost pointlike constituents, the partons. Since then, Deep Inelastic Scattering (DIS) has played a crucial role in our understanding of hadron structure. Through DIS experiments it has been possible to link the partons to the quarks, and to unveil the presence of other pointlike constituents, the gluons, which lead into a dynamical theory of quarks and gluons - quantum chromodynamics (QCD). Polarized DIS, i.e. the collision of a longitudinally polarized lepton beam on a polarized target (either longitudinally or transversely polarized), provides a complementary information regarding the structure of the nucleon. Whereas ordinary DIS pro...

  3. Stabilization of helical macromolecular phases by confined bending

    CERN Document Server

    Williams, Matthew J

    2015-01-01

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

  4. Solubilization and fractionation of paired helical filaments.

    Science.gov (United States)

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

    1992-09-01

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

  5. Shearing Wind Helicity and Thermal Wind Helicity

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    Helicity is defined as H=V.ω, where V and ω are the velocity and vorticity vectors, respectively.Many works have pointed out that the larger the helicity is, the longer the life cycle of the weather system is. However, the direct relationship of the helicity to the evolution of the weather system is not quite clear. In this paper, the concept of helicity is generalized as shearing wind helicity (SWH). Dynamically,it is found that the average SWH is directly related to the increase of the average cyclonic rotation of the weather system. Physically, it is also pointed out that the SWH, as a matter of fact, is the sum of the torsion terms and the divergence term in the vorticity equation. Thermal wind helicity (TWH), as a derivative of SWH, is also discussed here because it links the temperature field and the vertical wind field. These two quantities may be effective for diagnosing a weather system. This paper applies these two quantities in cylindrical coordinates to study the development of Hurricane Andrew to validate their practical use. Through analyzing the hurricane, it is found that TWH can well describe the characteristics of the hurricane such as the strong convection and release of latent heat. SWH is not only a good quantity for diagnosing the weather system, but also an effective one for diagnosing the development of the hurricane.

  6. Segregation of helicity in inertial wave packets

    Science.gov (United States)

    Ranjan, A.

    2017-03-01

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

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

    Science.gov (United States)

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

    2016-11-22

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

  8. Syntheses, Structures and Fluorescent Properties of Copper(II) and Manganese(II) Helical Complexes Bridged by 4,4'-Dipyridylsulfide

    Institute of Scientific and Technical Information of China (English)

    LI Jun-Xia; DU Zhong-Xiang

    2012-01-01

    Two isostructural helical coordination polymers, {[Cu(dps)2(Hssa)-(H2O)2]'3H2O}n (1) and {[Mn(dps)2(Hssa)(H2O)2]'2H2O}n (2), have been synthesized by the solvothermal reaction of dps and Hsssa with CuCI2 or Mn(CH3COO)2 (dps = 4,4'-dipyridylsulfide, H3ssa -- 5- sulfosalicylic acid). Both compounds crystallize in monoclinic, space group P21/n. In either complex, the central metal ion (Cu11 for compound 1 and MnIt for compound 2) is surrounded by one Hssa2- ligand, two coordinated aquas and three dps molecules with a N303 donor set in a distorted octahedral coordination geometry. Half of the dps is monodentate and another half acts as μ2-bridging ligands. It is through the bridging function of dps that the neighbouring metal centers are connected and a one-dimensional helical structure of compound 1 or 2 forms. Fluorescence studies indicate that compounds 1 and 2 have blue emission bands centered at 403 and 405 nm, respectively.

  9. Mechanical resonances of helically coiled carbon nanowires

    National Research Council Canada - National Science Library

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

    2014-01-01

    ...) mainly due to their geometrical complexity. The advent of helically coiled micro/nanoscale structures in nano-robotics, nano-inductors, and impact protection coatings has necessitated the development of new methodologies for determining...

  10. Design of aromatic helical polymers for STM visualization: imaging of single and double helices with a pattern of π-π stacking.

    Science.gov (United States)

    Zhu, Junyan; Dong, Zeyuan; Lei, Shengbin; Cao, Lili; Yang, Bing; Li, Wenfang; Zhang, Yuanchao; Liu, Junqiu; Shen, Jiacong

    2015-03-02

    From scanning tunneling microscopy (STM) images of rationally designed helical polymers with a pattern of π-π stacking, we successfully identified the single- and double-helical superstructures. The STM images of the helical structures revealed the smallest helical architecture (diameter ca. 1.3 nm) that has been seen so far. Furthermore, the interconversion of single and double helices was further underpinned by experimental analyses. Significantly, the formation of double helices induced different supramolecular chirality to that observed for the single helices.

  11. 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.

  12. Web-based toolkits for topology prediction of transmembrane helical proteins, fold recognition, structure and binding scoring, folding-kinetics analysis and comparative analysis of domain combinations.

    Science.gov (United States)

    Zhou, Hongyi; Zhang, Chi; Liu, Song; Zhou, Yaoqi

    2005-07-01

    We have developed the following web servers for protein structural modeling and analysis at http://theory.med.buffalo.edu: THUMBUP, UMDHMM(TMHP) and TUPS, predictors of transmembrane helical protein topology based on a mean-burial-propensity scale of amino acid residues (THUMBUP), hidden Markov model (UMDHMM(TMHP)) and their combinations (TUPS); SPARKS 2.0 and SP3, two profile-profile alignment methods, that match input query sequence(s) to structural templates by integrating sequence profile with knowledge-based structural score (SPARKS 2.0) and structure-derived profile (SP3); DFIRE, a knowledge-based potential for scoring free energy of monomers (DMONOMER), loop conformations (DLOOP), mutant stability (DMUTANT) and binding affinity of protein-protein/peptide/DNA complexes (DCOMPLEX & DDNA); TCD, a program for protein-folding rate and transition-state analysis of small globular proteins; and DOGMA, a web-server that allows comparative analysis of domain combinations between plant and other 55 organisms. These servers provide tools for prediction and/or analysis of proteins on the secondary structure, tertiary structure and interaction levels, respectively.

  13. Triple-stranded ferric helices: a π-π interaction-driven structural hierarchy of Fe5, Fe7, and Fe17 clusters.

    Science.gov (United States)

    Shiga, Takuya; Noguchi, Mao; Sato, Hiroki; Matsumoto, Takuto; Newton, Graham N; Oshio, Hiroki

    2013-12-07

    Three polypyridine ligand-supported multinuclear iron complexes, [Fe5], [Fe7] and [Fe17], were synthesized and their physical properties were investigated. The complexes had triple-stranded helical structures with pseudo threefold symmetry, and were stabilized by varying degrees of intramolecular π-π stacking. The pentanuclear iron complex consisted of two Fe(II) and three Fe(III) ions, supported by three ligands, while the heptanuclear complex comprised four Fe(II) centres, three Fe(III) ions, and six ligands, and the heptadecanuclear complex contained seventeen Fe(III) ions and nine ligands. Electrochemical studies revealed that the pentanuclear and heptanuclear iron complexes showed pseudo-reversible three- and five-step redox behaviours, respectively. Magnetic measurements conducted on the pentanuclear and heptanuclear complexes revealed that antiferromagnetic interactions were operative between neighbouring iron ions through the oxo- and pyrazole-bridges.

  14. Molecular Dynamics Investigations of the Local Structural Characteristics of DNA Oligonucleotides: Studies of Helical Axis Deformations, Conformational Sequence Dependence and Modified Nucleoside Perturbations.

    Science.gov (United States)

    Louise-May, Shirley

    The present DNA studies investigate the local structure of DNA oligonucleotides in order to characterize helical axis deformations, sequence dependent fine structure and modified nucleoside perturbations of selected oligonucleotide sequences. The molecular dynamics method is used to generate an ensemble of energetically feasible DNA conformations which can then be analyzed for dynamical conformational properties, some of which can be compared to experimentally derived values. A theory and graphical presentation for the analysis of helical deformations of DNA based on the configurational statistics of polymers, called "Persistence Analysis", was designed. The results of the analysis on prototype forms, static crystal structures and two solvated MD simulations of the sequence d(CGCGAATTCGCG) indicate that all of the expected features of bending can be sensitively and systematically identified by this approach. Comparison of the relative performance of three molecular dynamics potential functions commonly used for dynamical modeling of biological macromolecules; CHARMm, AMBER and GROMOS was investigated via in vacuo MD simulations on the dodecamer sequence d(CGCGAATTCGCG)_2 with respect to the conformational properties of each dynamical model and their ability to support A and B families of DNA. Vacuum molecular dynamics simulations using the CHARMm force field carried out on simple homo- and heteropolymers of DNA led to the conclusion that sequence dependent fine structure appears to be well defined for adenine-thymine rich sequences both at the base pair and base step level whereas much of the the fine structure found in cytosine -guanine rich sequences appears to be context dependent. The local conformational properties of the homopolymer poly (dA) -poly (dT) revealed one dynamical model which was found in general agreement with fiber models currently available. Investigation of the relative structural static and dynamical effect of the misincorporation of

  15. A c subunit with four transmembrane helices and one ion (Na+)-binding site in an archaeal ATP synthase: implications for c ring function and structure.

    Science.gov (United States)

    Mayer, Florian; Leone, Vanessa; Langer, Julian D; Faraldo-Gómez, José D; Müller, Volker

    2012-11-16

    The ion-driven membrane rotors of ATP synthases consist of multiple copies of subunit c, forming a closed ring. Subunit c typically comprises two transmembrane helices, and the c ring features an ion-binding site in between each pair of adjacent subunits. Here, we use experimental and computational methods to study the structure and specificity of an archaeal c subunit more akin to those of V-type ATPases, namely that from Pyrococcus furiosus. The c subunit was purified by chloroform/methanol extraction and determined to be 15.8 kDa with four predicted transmembrane helices. However, labeling with DCCD as well as Na(+)-DCCD competition experiments revealed only one binding site for DCCD and Na(+), indicating that the mature c subunit of this A(1)A(O) ATP synthase is indeed of the V-type. A structural model generated computationally revealed one Na(+)-binding site within each of the c subunits, mediated by a conserved glutamate side chain alongside other coordinating groups. An intriguing second glutamate located in-between adjacent c subunits was ruled out as a functional Na(+)-binding site. Molecular dynamics simulations indicate that the c ring of P. furiosus is highly Na(+)-specific under in vivo conditions, comparable with the Na(+)-dependent V(1)V(O) ATPase from Enterococcus hirae. Interestingly, the same holds true for the c ring from the methanogenic archaeon Methanobrevibacter ruminantium, whose c subunits also feature a V-type architecture but carry two Na(+)-binding sites instead. These findings are discussed in light of their physiological relevance and with respect to the mode of ion coupling in A(1)A(O) ATP synthases.

  16. Time-Mean Helicity Distribution in Turbulent Swirling Jets

    Directory of Open Access Journals (Sweden)

    V. Tesař

    2005-01-01

    Full Text Available Helicity offers an alternative approach to investigations of the structure of turbulent flows. Knowledge of the spatial distribution of the time-mean component of helicity is the starting point. Yet very little is known even about basic cases in which Helicity plays important role, such as the case of a swirling jet. This is the subject of the present investigations, based mainly on numerical flowfield computations. The region of significantly large time-mean helicity density is found only in a rather small region reaching to several nozzle diameters downstream from the exit. The most important result is the similarity of the helicity density profiles. 

  17. Single Band Helical Antenna in Axial Mode

    Directory of Open Access Journals (Sweden)

    Parminder Singh

    2012-11-01

    Full Text Available Helical antennas have been widely used in a various useful applications, due to their low weight and low profile conformability, easy and cheap realization.Radiation properties of this antenna are examined both theoretically and experimentally. In this paper, an attempt has been made to investigate new helical antenna structure for Applications. CST MWS Software is used for the simulation and design calculations of the helical antennas. The axial ratio, return loss, VSWR, Directivity, gain, radiation pattern is evaluated. Using CST MWS simulation software proposed antenna is designed/simulated and optimized. The antenna exhibits a single band from 0 GHz to 3 GHz for GPS and several satellite applications

  18. Analysis on two novel spherical helical antennas

    Institute of Scientific and Technical Information of China (English)

    Hou ZHANG; Yingzeng YIN; Dongyu XIA

    2009-01-01

    Two novel spherical helical antennas are designed by projecting the planar equiangular spiral antenna onto hemisphere and partial sphere surfaces.Their radiation properties are analyzed by the moment method with curved basis and test function,and the curves of the voltage standing wave ratio (VSWR),gain,polarization and pattern that change with frequency are also given,respectively.It can be seen that the circular polarization band of the novel hemispherical helical antenna is broader.The gain curve of the partial spherical helical antenna is flatter and the structure is simpler.

  19. Iterative assembly of helical proteins by optimal hydrophobic packing.

    Science.gov (United States)

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

    2008-08-06

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

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

    Science.gov (United States)

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

    2016-10-01

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

  1. 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.

  2. 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

  3. Autonomously folded α-helical lockers promote RNAi*

    Science.gov (United States)

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

    2016-01-01

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

  4. Autonomously folded α-helical lockers promote RNAi.

    Science.gov (United States)

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

    2016-10-10

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

  5. Autonomously folded α-helical lockers promote RNAi*

    Science.gov (United States)

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

    2016-10-01

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

  6. Helicity dynamics in stratified turbulence in the absence of forcing

    CERN Document Server

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

    2012-01-01

    A numerical study of decaying stably-stratified flows is performed. Relatively high stratification and moderate Reynolds numbers are considered, and a particular emphasis is placed on the role of helicity (velocity-vorticity correlations). The problem is tackled by integrating the Boussinesq equations in a periodic cubical domain using different initial conditions: a non-helical Taylor-Green (TG) flow, a fully helical Beltrami (ABC) flow, and random flows with a tunable helicity. We show that for stratified ABC flows helicity undergoes a substantially slower decay than for unstratified ABC flows. This fact is likely associated to the combined effect of stratification and large scale coherent structures. Indeed, when the latter are missing, as in random flows, helicity is rapidly destroyed by the onset of gravitational waves. A type of large-scale dissipative "cyclostrophic" balance can be invoked to explain this behavior. When helicity survives in the system it strongly affects the temporal energy decay and t...

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

    Science.gov (United States)

    Miyake, Hiroyuki; Tsukube, Hiroshi

    2012-11-01

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

  8. Microfluidic Lithography of Bioinspired Helical Micromotors.

    Science.gov (United States)

    Yu, Yunru; Shang, Luoran; Gao, Wei; Zhao, Ze; Wang, Huan; Zhao, Yuanjin

    2017-07-29

    Considerable efforts have been devoted to developing artificial micro/nanomotors that can convert energy into movement. A flow lithography integrated microfluidic spinning and spiraling system is developed for the continuous generation of bioinspired helical micromotors. Because the generation processes could be precisely tuned by adjusting the flow rates and the illuminating frequency, the length, diameter, and pitch of the helical micromotors were highly controllable. Benefiting from the fast online gelation and polymerization, the resultant helical micromotors could be imparted with Janus, triplex, and core-shell cross-sectional structures that have never been achieved by other methods. Owing to the spatially controlled encapsulation of functional nanoparticles in the microstructures, the helical micromotors can perform locomotion not only by magnetically actuated rotation or corkscrew motion but also through chemically powered catalytic reaction. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. 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.

  10. Helical superconducting black holes.

    Science.gov (United States)

    Donos, Aristomenis; Gauntlett, Jerome P

    2012-05-25

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

  11. Unraveling the molecular structure of the catalytic domain of matrix metalloproteinase-2 in complex with a triple-helical peptide by means of molecular dynamics simulations.

    Science.gov (United States)

    Díaz, Natalia; Suárez, Dimas; Valdés, Haydeé

    2013-11-26

    Herein, we present the results of a computational study that employed various simulation methodologies to build and validate a series of molecular models of a synthetic triple-helical peptide (fTHP-5) both in its native state and in a prereactive complex with the catalytic domain of the MMP-2 enzyme. First, the structure and dynamical properties of the fTHP-5 substrate are investigated by means of molecular dynamics (MD) simulations. Then, the propensity of each of the three peptide chains in fTHP-5 to be distorted around the scissile peptide bond is assessed by carrying out potential of mean force calculations. Subsequently, the distorted geometries of fTHP-5 are docked within the MMP-2 active site following a semirigid protocol, and the most stable docked structures are fully relaxed and characterized by extensive MD simulations in explicit solvent. Following a similar approach, we also investigate a hypothetical ternary complex formed between two MMP-2 catalytic units and a single fTHP-5 molecule. Overall, our models for the MMP-2/fTHP-5 complexes unveil the extent to which the triple helix is distorted to allow the accommodation of an individual peptide chain within the MMP active site.

  12. Significance of bending restraints for the stability of helical polymer conformations

    Science.gov (United States)

    Williams, Matthew J.; Bachmann, Michael

    2016-06-01

    We performed parallel-tempering Monte Carlo simulations to investigate the formation and stability of helical tertiary structures for flexible and semiflexible polymers, employing a generic coarse-grained model. Structural conformations exhibit helical order with tertiary ordering into single helices, multiple helical segments organized into bundles, and disorganized helical arrangements. For both bending-restrained semiflexible and bending-unrestrained flexible helical polymers, the stability of the structural phases is discussed systematically by means of hyperphase diagrams parametrized by suitable order parameters, temperature, and torsion strength. This exploration lends insight into the restricted flexibility of biological polymers such as double-stranded DNA and proteins.

  13. Significance of bending restraints for the stability of helical polymer conformations.

    Science.gov (United States)

    Williams, Matthew J; Bachmann, Michael

    2016-06-01

    We performed parallel-tempering Monte Carlo simulations to investigate the formation and stability of helical tertiary structures for flexible and semiflexible polymers, employing a generic coarse-grained model. Structural conformations exhibit helical order with tertiary ordering into single helices, multiple helical segments organized into bundles, and disorganized helical arrangements. For both bending-restrained semiflexible and bending-unrestrained flexible helical polymers, the stability of the structural phases is discussed systematically by means of hyperphase diagrams parametrized by suitable order parameters, temperature, and torsion strength. This exploration lends insight into the restricted flexibility of biological polymers such as double-stranded DNA and proteins.

  14. The solution structure of double helical arabino nucleic acids (ANA and 2'F-ANA): effect of arabinoses in duplex-hairpin interconversion.

    Science.gov (United States)

    Martín-Pintado, Nerea; Yahyaee-Anzahaee, Maryam; Campos-Olivas, Ramón; Noronha, Anne M; Wilds, Christopher J; Damha, Masad J; González, Carlos

    2012-10-01

    We report here the first structure of double helical arabino nucleic acid (ANA), the C2'-stereoisomer of RNA, and the 2'-fluoro-ANA analogue (2'F-ANA). A chimeric dodecamer based on the Dickerson sequence, containing a contiguous central segment of arabino nucleotides, flanked by two 2'-deoxy-2'F-ANA wings was studied. Our data show that this chimeric oligonucleotide can adopt two different structures of comparable thermal stabilities. One structure is a monomeric hairpin in which the stem is formed by base paired 2'F-ANA nucleotides and the loop by unpaired ANA nucleotides. The second structure is a bimolecular duplex, with all the nucleotides (2'F-ANA and ANA) forming Watson-Crick base pairs. The duplex structure is canonical B-form, with all arabinoses adopting a pure C2'-endo conformation. In the ANA:ANA segment, steric interactions involving the 2'-OH substituent provoke slight changes in the glycosidic angles and, therefore, in the ANA:ANA base pair geometry. These distortions are not present in the 2'F-ANA:2'F-ANA regions of the duplex, where the -OH substituent is replaced by a smaller fluorine atom. 2'F-ANA nucleotides adopt the C2'-endo sugar pucker and fit very well into the geometry of B-form duplex, allowing for favourable 2'F···H8 interactions. This interaction shares many features of pseudo-hydrogen bonds previously observed in 2'F-ANA:RNA hybrids and in single 2'F-ANA nucleotides.

  15. Pentagonal helices in a periodic metal-organic framework. Crystals as computers for discovering structures of minimal transitivity.

    Science.gov (United States)

    Li, Mian; Li, Dan; O'Keeffe, Michael; Su, Zhong-Min

    2015-08-07

    The structure of a recently-published metal-organic framework is deconstructed into its underlying net which is found to be of exceptional complexity. It is shown that this is because of local pentagonal symmetry and the structure is in fact the simplest possible (minimal transitivity) given that local symmetry.

  16. A Helical Polymer with a Cooperative Response to Chiral Information

    Science.gov (United States)

    Green, Mark M.; Peterson, Norman C.; Sato, Takahiro; Teramoto, Akio; Cook, Robert; Lifson, Shneior

    1995-06-01

    Polyisocyanates, long studied as theoretical models for wormlike chains in dilute solution and liquid crystals, differ from their biological helical analogs in the absence of a predetermined helical sense. These polymers have an unusual sensitivity to chiral effects that arises from a structure in which alternating right- and left-handed long helical blocks are separated by infrequent and mobile helical reversals. Statistical thermodynamic methods yield an exact description of the polymer and the cooperative nature of its chiral properties. Minute energies that favor one of the helical senses drive easily measurable conformational changes, even though such energies may be extremely difficult to calculate from structural theory. In addition, the chiral nature of the polymer can be used to test theoretical ideas concerned with cholesteric liquid crystals, one of which solves the problem of assigning the helical sense.

  17. Left- and right-handed alpha-helical turns in homo- and hetero-chiral helical scaffolds.

    Science.gov (United States)

    Shepherd, Nicholas E; Hoang, Huy N; Abbenante, Giovanni; Fairlie, David P

    2009-11-04

    Proteins typically consist of right-handed alpha helices, whereas left-handed alpha helices are rare in nature. Peptides of 20 amino acids or less corresponding to protein helices do not form thermodynamically stable alpha helices in water away from protein environments. The smallest known water-stable right- (alpha(R)) and left- (alpha(L)) handed alpha helices are reported, each stabilized in cyclic pentapeptide units containing all L- or all D-amino acids. Homochiral decapeptides comprising two identical cyclic pentapeptides (alpha(R)alpha(R) or alpha(L)alpha(L)) are continuous alpha-helical structures that are extremely stable to denaturants, degradative proteases, serum, and additives like TFE, acid, and base. Heterochiral decapeptides comprising two different cyclic pentapeptides (alpha(L)alpha(R) or alpha(R)alpha(L)) maintain the respective helical handedness of each monocyclic helical turn component but adopt extended or bent helical structures depending on the solvent environment. Adding TFE to their aqueous solutions caused a change to bent helical structures with slightly distorted N-terminal alpha(R) or alpha(L)-helical turns terminated by a Schellman-like motif adjacent to the C-terminal alpha(L) or alpha(R)-turn. This hinge-like switching between structures in response to an external cue suggests possible uses in larger structures to generate smart materials. The library of left- and right-handed 1-3 turn alpha-helical compounds reported herein project their amino acid side chains into very different regions of 3D space, constituting a unique and potentially valuable class of novel scaffolds.

  18. Water-stable helical structure of tertiary amides of bicyclic β-amino acid bearing 7-azabicyclo[2.2.1]heptane. Full control of amide cis-trans equilibrium by bridgehead substitution.

    Science.gov (United States)

    Hosoya, Masahiro; Otani, Yuko; Kawahata, Masatoshi; Yamaguchi, Kentaro; Ohwada, Tomohiko

    2010-10-27

    Helical structures of oligomers of non-natural β-amino acids are significantly stabilized by intramolecular hydrogen bonding between main-chain amide moieties in many cases, but the structures are generally susceptible to the environment; that is, helices may unfold in protic solvents such as water. For the generation of non-hydrogen-bonded ordered structures of amides (tertiary amides in most cases), control of cis-trans isomerization is crucial, even though there is only a small sterical difference with respect to cis and trans orientations. We have established methods for synthesis of conformationally constrained β-proline mimics, that is, bridgehead-substituted 7-azabicyclo[2.2.1]heptane-2-endo-carboxylic acids. Our crystallographic, 1D- and 2D-NMR, and CD spectroscopic studies in solution revealed that a bridgehead methoxymethyl substituent completely biased the cis-trans equilibrium to the cis-amide structure along the main chain, and helical structures based on the cis-amide linkage were generated independently of the number of residues, from the minimalist dimer through the tetramer, hexamer, and up to the octamer, and irrespective of the solvent (e.g., water, alcohol, halogenated solvents, and cyclohexane). Generality of the control of the amide equilibrium by bridgehead substitution was also examined.

  19. Synthesis of poly(Pro-Hyp-Gly)(n) by direct poly-condensation of (Pro-Hyp-Gly)(n), where n=1, 5, and 10, and stability of the triple-helical structure.

    Science.gov (United States)

    Kishimoto, Takahiro; Morihara, Yasushi; Osanai, Michinori; Ogata, Shin-Ichi; Kamitakahara, Masanobu; Ohtsuki, Chikara; Tanihara, Masao

    2005-10-15

    Pro-Hyp-Gly is a characteristic amino acid sequence found in fibrous collagens, and (Pro-Hyp-Gly)(10), which has been widely used as a collagen-model peptide, forms a stable triple-helical structure. Here, we synthesized polypeptides consisting of the Pro-Hyp-Gly sequence by direct poly-condensation of (Pro-Hyp-Gly)(n), where n=1, 5, and 10, using 1-hydroxybenzotriazole and 1-ethyl-3-(3-dimethyl-aminopropyl)-carbodiimide hydrochloride in both phosphate buffer (pH=7.4) and dimethylsulfoxide (DMSO) solutions for 48 h at 20 degrees C. The reaction of (Pro-Hyp-Gly)(5) and (Pro-Hyp-Gly)(10) in DMSO successfully gave polypeptides with molecular weights over 10,000, whereas low molecular weight products were obtained by reaction in phosphate buffer (pH=7.4). In contrast, Pro-Hyp-Gly at a concentration of 50 mg/mL in phosphate buffer (pH=7.4) gave polypeptides with molecular weights over 10,000. The Fourier transform infrared (FTIR) and (1)H nuclear magnetic resonance (NMR) spectra of poly(Pro-Hyp-Gly)(10) revealed that the polymerization of (Pro-Hyp-Gly)(10) described in this report had no side reactions. Each polypeptide obtained shows a collagen-like triple-helical structure, and the triple-helical structures of poly(Pro-Hyp-Gly) and poly(Pro-Hyp-Gly)(10) were stable up to T=80 degrees C, which suggests that the high molecular weight promotes stability of the triple-helical structure, in addition to the high Hyp content. Furthermore, transmission electron microscopy (TEM) observations show that poly(Pro-Hyp-Gly)(10) aggregates to form nanofiber-like structures about 10 nm in width, which suggests that a Pro-Hyp-Gly repeating sequence contains enough information for triple-helix formation, and for subsequent nanofiber-like structure formation.

  20. The GCN4 basic region leucine zipper binds DNA as a dimer of uninterrupted alpha helices: crystal structure of the protein-DNA complex.

    Science.gov (United States)

    Ellenberger, T E; Brandl, C J; Struhl, K; Harrison, S C

    1992-12-24

    The yeast transcriptional activator GCN4 is 1 of over 30 identified eukaryotic proteins containing the basic region leucine zipper (bZIP) DNA-binding motif. We have determined the crystal structure of the GCN4 bZIP element complexed with DNA at 2.9 A resolution. The bZIP dimer is a pair of continuous alpha helices that form a parallel coiled coil over their carboxy-terminal 30 residues and gradually diverge toward their amino termini to pass through the major groove of the DNA-binding site. The coiled-coil dimerization interface is oriented almost perpendicular to the DNA axis, giving the complex the appearance of the letter T. There are no kinks or sharp bends in either bZIP monomer. Numerous contacts to DNA bases and phosphate oxygens are made by basic region residues that are conserved in the bZIP protein family. The details of the bZIP dimer interaction with DNA can explain recognition of the AP-1 site by the GCN4 protein.

  1. Structural acid-base chemistry in the metallic state: how μ3-neutralization drives interfaces and helices in Ti21Mn25.

    Science.gov (United States)

    Stacey, Timothy E; Fredrickson, Daniel C

    2013-08-05

    Intermetallic phases remain a large class of compounds whose vast structural diversity is unaccounted for by chemical theory. A recent resurgence of interest in intermetallics, due to their potential in such applications as catalysis and thermoelectricity, has intensified the need for models connecting their compositions to their structures and stability. In this Article, we illustrate how the μ3-acidity model, an extension of the acid/base concept based on the Method of Moments, offers intuitive explanations for puzzling structural progressions occurring in intermetallics formed between transition metals. Simple CsCl-type structures are frequently observed for phases with near 1:1 ratios of transition metals. However, in two compounds, TiCu and Ti21Mn25, structures are adopted which deviate from this norm. μ3-Acidity analysis shows that the formation of CsCl-type phases in these exceptional systems would yield an imbalance in the acid/base strength pairing, resulting in overneutralization of the weaker partner and thus instability. Intriguing geometrical features emerge in response, which serve to improve the neutralization of the constituent elements. In both TiCu and Ti21Mn25, part of the structure shields weaker acids or bases from their stronger partners by enhancing homoatomic bonding in the sublattice of the weaker acid or base. In TiCu, this protection is accomplished by developing doubled layers of Ti atoms to reduce their heteroatomic contacts. In Ti21Mn25 the structural response is more extreme: Ti-poor TiMn2 domains are formed to guard Mn from the Ti atoms, while the remaining Ti segregates to regions between the TiMn2 domains. The geometrical details of this arrangement fine-tune the acid/base interactions for an even greater level of stability. The most striking of these occurs in the Ti-rich region, where a paucity of Mn neighbors leads to difficulty in achieving strong neutralization. The Ti atoms arrange themselves in helical tubes, maximizing

  2. Conversion from mutual helicity to self-helicity observed with IRIS

    Science.gov (United States)

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

    2014-10-01

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

  3. PAGAL - Properties and corresponding graphics of alpha helical structures in proteins [v3; ref status: indexed, http://f1000r.es/524

    Directory of Open Access Journals (Sweden)

    Sandeep Chakraborty

    2015-02-01

    Full Text Available Alpha helices (AH are peptide fragments characterized by regular patterns of hydrogen bonding between the carbonyl oxygen and amino nitrogen of residues regularly spaced in sequence, resulting in spiral conformations. Their preponderance in protein structures underlines their importance. Interestingly, AHs are present in most anti-microbial peptides, although they might remain in random-coil conformations depending on the solvent dielectric. For example, the cecropin component of the chimeric anti-microbial protein designed previously by our group comprises of two AHs linked by a short stretch of random coil. These anti-microbial peptides are often amphipathic (quantified by a hydrophobic moment, aligning hydrophobic residues on one surface and charged residues on the others. In the current work, we reproduce previously described computational methods to compute the hydrophobic moment of AHs - and provide open access to the source code (PAGAL. We simultaneously generated input files for TikZ (a package for creating high resolution graphics programmatically to obtain the Edmundson wheel and showing the direction and magnitude of the hydrophobic moment, and Pymol scripts to generate color coded protein surfaces. Additionally, we have observed an empirical structural property of AHs: the distance between the Cα atoms of the ith and (i+4th residue is equal to the distance between the carbonyl oxygens of the ith and (i+4th residue. We validated this using 100 non-homologous high resolution structures from the PISCES database. The source code and manual is available at http://github.com/sanchak/pagal and on http://dx.doi.org/10.5281/zenodo.11136.

  4. PAGAL - Properties and corresponding graphics of alpha helical structures in proteins [v2; ref status: indexed, http://f1000r.es/4e7

    Directory of Open Access Journals (Sweden)

    Sandeep Chakraborty

    2014-09-01

    Full Text Available Alpha helices (AH are peptide fragments characterized by regular patterns of hydrogen bonding between the carbonyl oxygen and amino nitrogen of residues regularly spaced in sequence, resulting in spiral conformations. Their preponderance in protein structures underlines their importance. Interestingly, AHs are present in most anti-microbial peptides, although they might remain in random-coil conformations depending on the solvent dielectric. For example, the cecropin component of the chimeric anti-microbial protein designed previously by our group comprises of two AHs linked by a short stretch of random coil. These anti-microbial peptides are often amphipathic (quantified by a hydrophobic moment, aligning hydrophobic residues on one surface and charged residues on the others. In the current work, we reproduce previously described computational methods to compute the hydrophobic moment of AHs - and provide open access to the source code (PAGAL. We simultaneously generated input files for TikZ (a package for creating high resolution graphics programmatically to obtain the Edmundson wheel and showing the direction and magnitude of the hydrophobic moment, and Pymol scripts to generate color coded protein surfaces. Additionally, we have observed an empirical structural property of AHs: the distance between the Cα atoms of the ith and (i+4th residue is equal to the distance between the carbonyl oxygens of the ith and (i+4th residue. We validated this using 100 non-homologous high resolution structures from the PISCES database. The source code and manual is available at http://github.com/sanchak/pagal and on http://dx.doi.org/10.5281/zenodo.11136.

  5. 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...

  6. Helicity, Reconnection, and Dynamo Effects

    Energy Technology Data Exchange (ETDEWEB)

    Ji, Hantao

    1998-11-01

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

  7. Mathisson's helical motions demystified

    CERN Document Server

    Costa, L Filipe O; Zilhão, Miguel

    2012-01-01

    The motion of spinning test particles in general relativity is described by Mathisson-Papapetrou-Dixon equations, which are undetermined up to a spin supplementary condition, the latter being today still an open question. The Mathisson-Pirani (MP) condition is known to lead to rather mysterious helical motions which have been deemed unphysical, and for this reason discarded. We show that these assessments are unfounded and originate from a subtle (but crucial) misconception. We discuss the kinematical explanation of the helical motions, and dynamically interpret them through the concept of hidden momentum, which has an electromagnetic analogue. We also show that, contrary to previous claims, the frequency of the helical motions coincides exactly with the zitterbewegung frequency of the Dirac equation for the electron.

  8. 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.

  9. Statistical mechanics of double-helical polymers.

    Science.gov (United States)

    De Col, Alvise; Liverpool, Tanniemola B

    2004-06-01

    We introduce a simple geometric model for a double-stranded and double-helical polymer. We study the statistical mechanics of such polymers using both analytical techniques and simulations. Our model has a single energy scale which determines both the bending and twisting rigidity of the polymer. The helix melts at a particular temperature T(c) below which the chain has a helical structure and above which this structure is disordered. Under extension we find that for small forces, the behavior is very similar to wormlike chain behavior but becomes very different at higher forces.

  10. Helicity conservation under quantum reconnection of vortex rings

    CERN Document Server

    Zuccher, Simone

    2016-01-01

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

  11. General aspects of peptide selectivity towards lipid bilayers and cell membranes studied by variation of the structural parameters of amphipathic helical model peptides.

    Science.gov (United States)

    Dathe, Margitta; Meyer, Jana; Beyermann, Michael; Maul, Björn; Hoischen, Christian; Bienert, Michael

    2002-02-01

    Model compounds of modified hydrophobicity (Eta), hydrophobic moment (mu) and angle subtended by charged residues (Phi) were synthesized to define the general roles of structural motifs of cationic helical peptides for membrane activity and selectivity. The peptide sets were based on a highly hydrophobic, non-selective KLA model peptide with high antimicrobial and hemolytic activity. Variation of the investigated parameters was found to be a suitable method for modifying peptide selectivity towards either neutral or highly negatively charged lipid bilayers. Eta and mu influenced selectivity preferentially via modification of activity on 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine (POPC) bilayers, while the size of the polar/hydrophobic angle affected the activity against 1-palmitoyl-2-oleoylphosphatidyl-DL-glycerol (POPG). The influence of the parameters on the activity determining step was modest in both lipid systems and the activity profiles were the result of the parameters' influence on the second less pronounced permeabilization step. Thus, the activity towards POPC vesicles was determined by the high permeabilizing efficiency, however, changes in the structural parameters preferentially influenced the relatively moderate affinity. In contrast, intensive peptide accumulation via electrostatic interactions was sufficient for the destabilization of highly negatively charged POPG lipid membranes, but changes in the activity profile, as revealed by the modification of Phi, seem to be preferentially caused by variation of the low permeabilizing efficiency. The parameters proved very effective also in modifying antimicrobial and hemolytic activity. However, their influence on cell selectivity was limited. A threshold value of hydrophobicity seems to exist which restricted the activity modifying potential of mu and Phi on both lipid bilayers and cell membranes.

  12. Novel 1D Copper(ll) Helical Chain Formed by Weak Coordination-driven Self-assembly: Synthesis, Structure, and Magnetic Property

    Institute of Scientific and Technical Information of China (English)

    黄婉云; 陈自卢; 邹华红; 刘冬成; 梁福沛

    2012-01-01

    A novel 1D copper(II) helical chain is constructed through the connection of tetranuclear copper(ll) units [Cu4(L)(Py)4] (H8L=N,N'-(BINOL-3,3'-dicarboxyl)-disalicylhydrazide, where BINOL is 1,l'-binaphthalenyl-2,2'- diol, py=pyridine) by weak coordination-driven self-assembly, and characterized by IR, single crystal X-ray dif- fraction, thermogravimetric analysis, and X-ray power diffraction analysis. Interestingly, the helical chains are packed in an alternating left-(M) and right-handed (P) chirality, the orientation of the helices was determined by the axial chirality of the ligand. The complex shows antiferromagnetic interactions between the copper centers.

  13. Triple-meso helices as alcohol reservoirs and discriminators: structural properties and thermal behaviors of silver(I) coordination molecular braids containing diethylbis(4-pyridyl)silanes.

    Science.gov (United States)

    Moon, So Yun; Kim, Euni; Noh, Tae Hwan; Lee, Young-A; Jung, Ok-Sang

    2013-10-14

    Self-assembly of silver triflate with L in alcohol solvent produces characteristic triple-meso helices [Ag3(L)3(ROH)](CF3SO3)3 (L = diethylbis(4-pyridyl)silane; R = Me, Et, n-Pr, and n-Bu) with six units in each turn. Their unit cell volumes are sensitive to the size of the coordinated alcohol molecules. An unusual "alcohol molecules at triple-meso helices" system is a characteristic reversible alcohol container and discriminator via appropriate association/dissociation. The meso helical solids are favored in the order MeOH > EtOH > n-PrOH > n-BuOH via an interaction between the silver(I) ion and the alcohol molecule. The crystals evaporate the coordinated alcohol molecules at low temperatures, and finally calcination at 600 °C produces micro-sized chaotic surface materials consisting of silver(0) without silicon(IV) oxide.

  14. Synthesis of stabilized alpha-helical peptides.

    Science.gov (United States)

    Bernal, Federico; Katz, Samuel G

    2014-01-01

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

  15. Regio-selective detection of dynamic structure of transmembrane alpha-helices as revealed from (13)C NMR spectra of [3-13C]Ala-labeled bacteriorhodopsin in the presence of Mn2+ ion.

    Science.gov (United States)

    Tuzi, S; Hasegawa, J; Kawaminami, R; Naito, A; Saitô, H

    2001-07-01

    13C Nuclear magnetic resonance (NMR) spectra of [3-(13)C]Ala-labeled bacteriorhodopsin (bR) were edited to give rise to regio-selective signals from hydrophobic transmembrane alpha-helices by using NMR relaxation reagent, Mn(2+) ion. As a result of selective suppression of (13)C NMR signals from the surfaces in the presence of Mn(2+) ions, several (13)C NMR signals of Ala residues in the transmembrane alpha-helices were identified on the basis of site-directed mutagenesis without overlaps from (13)C NMR signals of residues located near the bilayer surfaces. The upper bound of the interatomic distances between (13)C nucleus in bR and Mn(2+) ions bound to the hydrophilic surface to cause suppressed peaks by the presence of Mn(2+) ion was estimated as 8.7 A to result in the signal broadening to 100 Hz and consistent with the data based on experimental finding. The Ala C(beta) (13)C NMR peaks corresponding to Ala-51, Ala-53, Ala-81, Ala-84, and Ala-215 located around the extracellular half of the proton channel and Ala-184 located at the kink in the helix F were successfully identified on the basis of (13)C NMR spectra of bR in the presence of Mn(2+) ion and site-directed replacement of Ala by Gly or Val. Utilizing these peaks as probes to observe local structure in the transmembrane alpha-helices, dynamic conformation of the extracellular half of bR at ambient temperature was examined, and the local structures of Ala-215 and 184 were compared with those elucidated at low temperature. Conformational changes in the transmembrane alpha-helices induced in D85N and E204Q and its long-range transmission from the proton release site to the site around the Schiff base in E204Q were also examined.

  16. Helicity separation in Heavy-Ion Collisions

    CERN Document Server

    Baznat, Mircea; Sorin, Alexander; Teryaev, Oleg

    2013-01-01

    We study the P-odd effects related to the vorticity of the medium formed in noncentral heavy ion collisions. Using the kinetic Quark-Gluon Strings Model we perform the numerical simulations of the vorticity and hydrodynamical helicity for the various atomic numbers, energies and centralities. We observed the vortical structures typically occupying the relatively small fraction of the fireball volume. In the course of numerical simulations the noticeable hydrodanamical helicity was observed manifesting the specific mirror behaviour with respect to the reaction plane. The effect is maximal at the NICA and FAIR energy range.

  17. Unusually Stable Helical Coil Allotrope of Phosphorus.

    Science.gov (United States)

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

    2016-12-14

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

  18. Manipulation of wavefront using helical metamaterials.

    Science.gov (United States)

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

    2016-08-01

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

  19. 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.

  20. 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.

  1. Broadband circularly polarizing dichroism with high efficient plasmonic helical surface.

    Science.gov (United States)

    Hu, Jingpei; Zhao, Xiaonan; Li, Ruibin; Zhu, Aijiao; Chen, Linghua; Lin, Yu; Cao, Bing; Zhu, Xiaojun; Wang, Chinhua

    2016-05-16

    We propose and experimentally demonstrate a broadband and high efficient circularly polarizing dichroism using a simple single-cycle and single-helical plasmonic surface array arranged in square lattice. Two types of helical surface structures (partially or completely covered with a gold film) are investigated. It is shown that the circular polarization dichroism in the mid-IR range (3µm - 5µm) can reach 80% (when the surface is partially covered with gold) or 65% (when the surface is completely covered with gold) with a single-cycle and single-helical surface. Experimental fabrications of the proposed helical plasmonic surface are implemented with direct 3D laser writing followed by electron beam evaporation deposition of gold. The experimental evaluations of the circular polarization dichroism are in excellent agreement with the simulation. The proposed helical surface structure is of advantages of easy-fabrication, high-dichroism and scalable to other frequencies as a high efficient broadband circular polarizer.

  2. Measurements of Magnetic Helicity within Two Interacting Flux Ropes

    Science.gov (United States)

    Dehaas, Timothy; Gekelman, Walter

    2016-10-01

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

  3. Inhomogeneous helicity effect in the solar angular-momentum transport

    Science.gov (United States)

    Yokoi, Nobumitsu

    2017-04-01

    Coupled with mean absolute vorticity Ω∗ (rotation and mean relative vorticity), inhomogeneous turbulent helicity is expected to contribute to the generation of global flow structure against the linear and angular momentum mixing due to turbulent or eddy viscosity. This inhomogeneous helicity effect was originally derived in Yokoi & Yoshizawa (1993) [1], and recently has been validated by direct numerical simulations (DNSs) of rotating helical turbulence [2]. Turbulence effect enters the mean-vorticity equation through the turbulent vortexmotive force ⟨u'×ω'⟩ [u': velocity fluctuation, ω'(= ∇× u'): vorticity fluctuation], which is the vorticity counterpart of the electromotive force ⟨u'× b'⟩ (b': magnetic fluctuation) in the mean magnetic-field induction. The mean velocity induction δU is proportional to the vortexmotive force. According to the theoretical result [1,2], it is expressed as δU = -νT∇×Ω∗-ηT(∇2H)Ω∗, where ηT is the transport coefficient, H = ⟨u'ṡω'⟩ the turbulent helicity, and Ω∗ the mean absolute vorticity. The first term corresponds to the enhanced diffusion due to turbulent viscosity νT. The second term expresses the large-scale flow generation due to inhomogeneous helicity. Since helicity is self-generated in rotating stratified turbulence [3], an inhomogeneous helicity distribution is expected to exist in the solar convection zone. A rising flow with expansion near the surface of the Sun generates a strongly negative helicity there [4]. This spatial distribution of helicity would lead to a positive Laplacian of turbulent helicity (∇2H > 0) in the subsurface layer of the Sun. In the combination with the large-scale vorticity associated with the meridional circulation, the inhomogeneous helicity effect works for accelerating the mean velocity in the azimuthal direction. The relevance of this inhomogeneous helicity effect in the solar convection zone is discussed further. References [1] Yokoi, N. and

  4. Flat Helical Nanosieves

    CERN Document Server

    Mei, Shengtao; Hussain, Sajid; Huang, Kun; Ling, Xiaohui; Siew, Shawn Yohanes; Liu, Hong; Teng, Jinghua; Danner, Aaron; Qiu, Cheng-Wei

    2016-01-01

    Compact and miniaturized devices with flexible functionalities are always highly demanded in optical integrated systems. Plasmonic nanosieve has been successfully harnessed as an ultrathin flat platform for complex manipulation of light, including holography, vortex generation and non-linear processes. Compared with most of reported single-functional devices, multi-functional nanosieves might find more complex and novel applications across nano-photonics, optics and nanotechnology. Here, we experimentally demonstrate a promising roadmap for nanosieve-based helical devices, which achieves full manipulations of optical vortices, including its generation, hybridization, spatial multiplexing, focusing and non-diffraction propagation etc., by controlling the geometric phase of spin light via over 121 thousands of spatially-rotated nano-sieves. Thanks to such spin-conversion nanosieve helical elements, it is no longer necessary to employ the conventional two-beam interferometric measurement to characterize optical ...

  5. Helices and vector bundles

    CERN Document Server

    Rudakov, A N

    1990-01-01

    This volume is devoted to the use of helices as a method for studying exceptional vector bundles, an important and natural concept in algebraic geometry. The work arises out of a series of seminars organised in Moscow by A. N. Rudakov. The first article sets up the general machinery, and later ones explore its use in various contexts. As to be expected, the approach is concrete; the theory is considered for quadrics, ruled surfaces, K3 surfaces and P3(C).

  6. Nonlinear helical MHD instability

    Energy Technology Data Exchange (ETDEWEB)

    Zueva, N.M.; Solov' ev, L.S.

    1977-07-01

    An examination is made of the boundary problem on the development of MHD instability in a toroidal plasma. Two types of local helical instability are noted - Alfven and thermal, and the corresponding criteria of instability are cited. An evaluation is made of the maximum attainable kinetic energy, limited by the degree to which the law of conservation is fulfilled. An examination is made of a precise solution to a kinematic problem on the helical evolution of a cylindrical magnetic configuration at a given velocity distribution in a plasma. A numerical computation of the development of MHD instability in a plasma cylinder by a computerized solution of MHD equations is made where the process's helical symmetry is conserved. The development of instability is of a resonance nature. The instability involves the entire cross section of the plasma and leads to an inside-out reversal of the magnetic surfaces when there is a maximum unstable equilibrium configuration in the nonlinear stage. The examined instability in the tore is apparently stabilized by a magnetic hole when certain limitations are placed on the distribution of flows in the plasma. 29 references, 8 figures.

  7. Synthesis and structural characterization of silver(I), copper(I) coordination polymers and a helicate palladium(II) complex of dipyrrolylmethane-based dipyrazole ligands: the effect of meso substituents on structural formation.

    Science.gov (United States)

    Guchhait, Tapas; Barua, Bhagyasree; Biswas, Aritra; Basak, Biswanath; Mani, Ganesan

    2015-05-21

    A new class of multidentate dipyrrolylmethane based ditopic tecton, 1,9-bis(3,5-dimethylpyrazolylmethyl)dipyrrolylmethane, containing diethyl (L1) or cyclohexylidene (L2) substituents at the meso carbon atom were readily synthesized in 28-45% yields in two different ways starting from dipyrrolylmethanes. A one dimensional coordination polymer structure ([(L2)Ag][BF4])n was obtained when L2 was treated with AgBF4, whereas the analogous reaction between L1 and AgBF4 afforded the dicationic binuclear metallacycle complex [(L1)2Ag2][BF4]2. In addition, yet another coordination polymeric structure [(L1)CuI]n was obtained from the reaction between L1 and CuI. The analogous reaction of L1 with [Pd(PhCN)2Cl2] afforded the binuclear palladium complex [(L1)2Pd2Cl4] having a double-stranded helicate structure. The observed structural differences are attributed to the effects of the substituents present at the meso carbon atom of the ligand, in addition to the nature of the metal centre, coordination number and the preferred geometry.

  8. Hierarchical Helical Order in the Twisted Growth of Plant Organs

    Science.gov (United States)

    Wada, Hirofumi

    2012-09-01

    The molecular and cellular basis of left-right asymmetry in plant morphogenesis is a fundamental issue in biology. A rapidly elongating root or hypocotyl of twisting mutants of Arabidopsis thaliana exhibits a helical growth with a handedness opposite to that of the underlying cortical microtubule arrays in epidermal cells. However, how such a hierarchical helical order emerges is currently unknown. We propose a model for investigating macroscopic chiral asymmetry in Arabidopsis mutants. Our elastic model suggests that the helical pattern observed is a direct consequence of the simultaneous presence of anisotropic growth and tilting of cortical microtubule arrays. We predict that the root helical pitch angle is a function of the microtubule helical angle and elastic moduli of the tissues. The proposed model is versatile and is potentially important for other biological systems ranging from protein fibrous structures to tree trunks.

  9. Chiral Exact Relations for Helicities in Hall Magnetohydrodynamic Turbulence

    CERN Document Server

    Banerjee, Supratik

    2016-01-01

    Besides total energy, three-dimensional incompressible Hall magnetohydrodynamics (MHD) possesses two inviscid invariants which are the magnetic helicity and the generalized helicity. New exact relations are derived for homogeneous (non-isotropic) stationary Hall MHD turbulence (and also for its inertialess electron MHD limit) with non-zero helicities and in the asymptotic limit of large Reynolds numbers. The universal laws are written only in terms of mixed second-order structure functions, i.e. the scalar product of two different increments. It provides, therefore, a direct measurement of the dissipation rates for the corresponding invariant flux. This study shows that the generalized helicity cascade is strongly linked to the left polarized fluctuations while the magnetic helicity cascade is linked to the right polarized fluctuations.

  10. Chiral exact relations for helicities in Hall magnetohydrodynamic turbulence.

    Science.gov (United States)

    Banerjee, Supratik; Galtier, Sébastien

    2016-03-01

    Besides total energy, three-dimensional incompressible Hall magnetohydrodynamics (MHD) possesses two inviscid invariants, which are the magnetic helicity and the generalized helicity. Exact relations are derived for homogeneous (nonisotropic) stationary Hall MHD turbulence (and also for its inertialess electron MHD limit) with nonzero helicities and in the asymptotic limit of large Reynolds numbers. The universal laws are written only in terms of mixed second-order structure functions, i.e., the scalar product of two different increments. It provides, therefore, a direct measurement of the dissipation rates for the corresponding invariant flux. This study shows that the generalized helicity cascade is strongly linked to the left polarized fluctuations, while the magnetic helicity cascade is linked to the right polarized fluctuations.

  11. Magnetic stripes and skyrmions with helicity reversals.

    Science.gov (United States)

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

    2012-06-05

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

  12. Cationic Nitrogen Doped Helical Nanographenes.

    Science.gov (United States)

    Xu, Kun; Feng, Xinliang; Berger, Reinhard; Popov, Alexey A; Weigand, Jan J; Vincon, Ilka; Machata, Peter; Hennersdorf, Felix; Zhou, Youjia; Fu, Yubin

    2017-09-13

    Herein, we report on the synthesis of a series of novel cationic nitrogen doped nanographenes (CNDN) by rhodium catalyzed annulation reactions. This powerful method allows for the synthesis of cationic nanographenes with non-planar, axial chiral geometries. Single-crystal X-ray analysis reveals helical and cove-edged structures. Compared to their all-carbon analogues, the CNDN exhibit energetically lower lying frontier orbitals with a reduced optical energy gap and an electron accepting behavior. All derivatives show quasi reversible reductions in cyclic voltammetry. Depending on the number of nitrogen dopant, in situ spectroelectrochemistry proves the formation of neutral radicals (one nitrogen dopant) or radical cations (two nitrogen dopants) upon reduction. The developed synthetic protocol paves the way for the design and synthesis of expanded nanographenes or even graphene nanoribbons containing cationic nitrogen doping. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. Formation of helical ion chains

    CERN Document Server

    Nigmatullin, Ramil; De Chiara, Gabriele; Morigi, Giovanna; Plenio, Martin B; Retzker, Alex

    2011-01-01

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

  14. Best packing of identical helices

    Science.gov (United States)

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

    2016-10-01

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

  15. 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)

  16. Helicity Transfer in Turbulent Models

    CERN Document Server

    Biferale, L; Toschi, F

    1998-01-01

    Helicity transfer in a shell model of turbulence is investigated. We show that a Reynolds-independent helicity flux is present in the model when the large scale forcing breaks inversion symmetry. The equivalent in Shell Models of the ``2/15 law'', obtained from helicity conservation in Navier-Stokes eqs., is derived and tested. The odd part of helicity flux statistic is found to be dominated by a few very intense events. In a particular model, we calculate analytically leading and sub-leading contribution to the scaling of triple velocity correlation.

  17. 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.

  18. Helical Ordering in Chiral Block Copolymers

    Science.gov (United States)

    Zhao, Wei; Hong, Sung Woo; Chen, Dian; Grason, Gregory; Russell, Thomas

    2012-02-01

    Introducing molecular chirality into the segments of block copolymers can influence the nature of the resultant morphology. Such an effect was found for poly(styrene-b-L-lactide) (PS-b-PLLA) diblock copolymers where hexagonally packed PLLA helical microdomains (H* phase) form in a PS matrix. However, molecular ordering of PLLA within the helical microdomains and the transfer of chirality from the segmental level to the mesoscale is still not well understood. We developed a field theoretic model to describe the interactions between segments of chiral blocks, which have the tendency to form a ``cholesteric'' texture. Based on the model, we calculated the bulk morphologies of chiral AB diblock copolymers using self-consistent field theory (SCFT). Experiments show that the H* phase only forms when microphase separation between PS and PLLA block happens first and crystallization of PLLA block is suppressed or happens within confined microdomain. Hence, crystalline ordering is not necessary for H* phase formation. The SCFT offers the chance to explore the range of thermodynamic stability of helical structures in the phase diagram of chiral block copolymer melts, by tuning parameters not only like the block segregation strength and composition, but also new parameters such as the ratio between preferred helical pitch to the radius of gyration and the Frank elastic constant for inter-segment distortions.

  19. 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 dire

  20. Quark Helicity and Transversity Distributions

    CERN Document Server

    Hwang, Dae Sung

    2016-01-01

    The quark transversity distribution inside nucleon is less understood than the quark unpolarized and helicity distributions inside nucleon. In particular, it is important to know clearly why the quark helicity and transversity distributions are different. We investigate the origin of their discrepancy.

  1. 新型螺旋状一维超分子链配合物的晶体结构%The Crystal Structure of A Novel Helical Supramolecular One-Dimensional Chain Complex

    Institute of Scientific and Technical Information of China (English)

    建方方; 侯玉霞; 肖海连

    2004-01-01

    The crystal structure of quasi-one-dimensional compound Ni[S2CPyrd]2 (Pyrd=pyrrolidine) has been determined by X-ray diffraction technique. It crystallizes in the monoclinic system, space group P21/c, with lattice parameters a=0.631 6(1) nm, b=0.746 5(2) nm, c=1.576 5(4) nm, β=106.08(3)°, and Z=2. The nickel atom had a square-planar geometry. The most prominent feature in the crystal structure is that the bis(pyrrolidinedithiocarbamato) nickel(Ⅱ) forms a well-separated stacking column along the a-axis through supramolecular interaction, and they are uniformly spaced to give a helical one-dimensional chain structure. CCDC: 220648.

  2. Broadband optical isolator based on helical metamaterials.

    Science.gov (United States)

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

    2015-05-01

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

  3. 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.

  4. Design study of a normal conducting helical snake for AGS

    CERN Document Server

    Takano, Junpei; Okamura, Masahiro; Roser, Thomas; MacKay, William W; Luccio, Alfredo U; Takano, Koji

    2004-01-01

    A new normal conducting snake magnet is being fabricated for the Alternate Gradient Synchrotron (AGS) at Brookhaven National Laboratory (BNL). In the Relativistic Heavy Ion Collider (RHIC) project, a superconducting type helical dipole magnets had been developed and it performed successfully in high-energy polarized proton acceleration. The new AGS helical snake has the same basic magnetic structure but is more complicated. To achieve no beam shift and no beam deflection in one magnetic device, helical pitches and rotating angles were carefully calculated. Compared to a superconducting magnet, a normal warm magnet must have a large cross- sectional area of conductors which make it difficult to design a magnet with large helical pitch. We developed a modified window frame structure to accommodate the large number of conductors. Its three dimensional magnetic field was simulated by using OPERA3D/TOSCA. 3 Refs.

  5. The Advanced Helical Generator

    Energy Technology Data Exchange (ETDEWEB)

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

    2009-10-26

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

  6. A designed protein with packing between left-handed and right-handed helices.

    Science.gov (United States)

    Sia, S K; Kim, P S

    2001-07-31

    A common motif in protein structures is the assembly of alpha-helices. Natural alpha-helical assemblies, such as helical bundles and coiled coils, consist of multiple right-handed alpha-helices. Here we design a protein complex containing both left-handed and right-handed helices, with peptides of D- and L-amino acids, respectively. The two peptides, D-Acid and L-Base, feature hydrophobic heptad repeats and are designed to pack against each other in a "knobs-into-holes" manner. In solution, the peptides form a stable, helical heterotetramer with tight packing in the most solvent-protected core. This motif may be useful for designing protease-resistant, helical D-peptide ligands against biological protein targets.

  7. Synthesis and Crystal Structure of a New One-dimensional Double Helical-chain Polymer, {Zn(O2CC12H8CO2)(H2O)}n

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    A new zinc polymer, {Zn(O2CC12H8CO2)(H2O)}n or {Zn(DPHA)(H2O)}n (O2CC12-H8CO2, DPHA = 1,1 ′-biphenyl-2,2′-dicarboxylate dianion) has been synthesized under hydrothermal conditions. The crystal is of monoclinic, space group P21/c with a = 12.8418(5), b = 5.9505(2),c = 17.2989(5) (A), β = 104.020(2)°, V= 1282.52(8)(A)3, C14H10O5Zn, Mr= 323.61, Z = 4, Dc = 1.676g/cm3,μ = 1.930 mm- 1, F(000) = 656, R = 0.0766 and wR = 0.1871 for 1775 observed reflections (I > 2σ(I)). It consists of Zn2(DPHA)2(H2O)2 units, which are further extended into a one-dimensional double helical-chain polymer via Zn-O bonding. The hydrogen bonding interactions extend the helical chains into a two-dimensional layer structure.

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

    Science.gov (United States)

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

    2016-06-01

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

  9. A Novel Method for Sampling Alpha-Helical Protein Backbones

    Science.gov (United States)

    Fain, Boris; Levitt, Michael

    2001-01-01

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

  10. Tokamak magnetohydrodynamic equilibrium states with axisymmetric boundary and a 3D helical core.

    Science.gov (United States)

    Cooper, W A; Graves, J P; Pochelon, A; Sauter, O; Villard, L

    2010-07-16

    Magnetohydrodynamic (MHD) equilibrium states with imposed axisymmetric boundary are computed in which a spontaneous bifurcation develops to produce an internal three-dimensional (3D) configuration with a helical structure in addition to the standard axisymmetric system. Equilibrium states with similar MHD energy levels are shown to develop very different geometric structures. The helical equilibrium states resemble saturated internal kink mode structures.

  11. Turbulent Dynamos and Magnetic Helicity

    Energy Technology Data Exchange (ETDEWEB)

    Ji, Hantao

    1999-04-01

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

  12. SPring-8 twin helical undulator.

    Science.gov (United States)

    Hara, T; Tanaka, T; Tanabe, T; Maréchal, X M; Kumagai, K; Kitamura, H

    1998-05-01

    There are several ways of producing circularly polarized light, such as using asymmetric devices, crossed undulators etc. The SPring-8 helical undulator introduces a simple way of producing both horizontal and vertical fields in one undulator. All the magnet arrays are arranged above and below the plane of the electron orbit, so there is no limitation of access from the sides of the undulator. For the SPring-8 BL25SU, two helical undulators will be installed in tandem, and the helicity of the polarization can be switched at up to 10 Hz using five kicker magnets.

  13. Mechanical Resonances of Helically Coiled Carbon Nanowires

    Science.gov (United States)

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

    2014-07-01

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

  14. Buckling transition in long α-helices

    Energy Technology Data Exchange (ETDEWEB)

    Palenčár, Peter; Bleha, Tomáš, E-mail: bleha@savba.sk [Polymer Institute, Slovak Academy of Sciences, 845 41 Bratislava (Slovakia)

    2014-11-07

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

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

    CERN Document Server

    Blackman, Eric G

    2014-01-01

    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. H...

  16. Direct numerical simulations of helical dynamo action: MHD and beyond

    Directory of Open Access Journals (Sweden)

    D. O. Gómez

    2004-01-01

    Full Text Available Magnetohydrodynamic dynamo action is often invoked to explain the existence of magnetic fields in several astronomical objects. In this work, we present direct numerical simulations of MHD helical dynamos, to study the exponential growth and saturation of magnetic fields. Simulations are made within the framework of incompressible flows and using periodic boundary conditions. The statistical properties of the flow are studied, and it is found that its helicity displays strong spatial fluctuations. Regions with large kinetic helicity are also strongly concentrated in space, forming elongated structures. In dynamo simulations using these flows, we found that the growth rate and the saturation level of magnetic energy and magnetic helicity reach an asymptotic value as the Reynolds number is increased. Finally, extensions of the MHD theory to include kinetic effects relevant in astrophysical environments are discussed.

  17. Helical dipole partial Siberian snake for the AGS

    Energy Technology Data Exchange (ETDEWEB)

    Takano, J [RIKEN, Saitama, (Japan); Ahrens, L A [Brookhaven National Laboratory, Upton, NY 11973 (United States); Alforque, R [Brookhaven National Laboratory, Upton, NY 11973 (United States); Bai, M [Brookhaven National Laboratory, Upton, NY 11973 (United States); Brown, K [Brookhaven National Laboratory, Upton, NY 11973 (United States); Courant, E D [Brookhaven National Laboratory, Upton, NY 11973 (United States); Ganetis, G [Brookhaven National Laboratory, Upton, NY 11973 (United States); Gardner, C J [Brookhaven National Laboratory, Upton, NY 11973 (United States); Glenn, J W [Brookhaven National Laboratory, Upton, NY 11973 (United States); Hattori, T [Tokyo Institute of Technology, Tokyo, (Japan); Huang, H [Brookhaven National Laboratory, Upton, NY 11973 (United States); Jain, A [Brookhaven National Laboratory, Upton, NY 11973 (United States); Luccio, A U [Brookhaven National Laboratory, Upton, NY 11973 (United States); MacKay, W W [Brookhaven National Laboratory, Upton, NY 11973 (United States); Okamura, M [Brookhaven National Laboratory, Upton, NY 11973 (United States); Roser, T [Brookhaven National Laboratory, Upton, NY 11973 (United States); Tsoupas, N [Brookhaven National Laboratory, Upton, NY 11973 (United States); Tepikian, S [Brookhaven National Laboratory, Upton, NY 11973 (United States); Tuozzolo, J [Brookhaven National Laboratory, Upton, NY 11973 (United States); Wood, J [Brookhaven National Laboratory, Upton, NY 11973 (United States); Zelenski, A [Brookhaven National Laboratory, Upton, NY 11973 (United States); Zeno, K [Brookhaven National Laboratory, Upton, NY 11973 (United States)

    2006-11-15

    Overcoming depolarization resonances in medium class synchrotrons (3 to 50 GeV) is one of the key issues in accelerating a highly polarized proton beam up to very high energies. Since such synchrotrons, including the Alternating Gradient Synchrotron (AGS) and the J-PARC Main Ring, generally do not have sufficiently long straight sections to accommodate full Siberian snakes with reasonable beam excursions, the practical solution is to use partial Siberian snakes that rotate the particle spin about a horizontal axis by a fraction of 180 degrees. For the AGS, we designed and installed a new partial Siberian snake consisting of a helical dipole magnet with a double pitch structure. The helical structure reduced the amount of transverse coupling as compared to that achieved by the previous solenoidal partial snake. This coupling led to partial depolarization at certain energies from horizontal betatron oscillations. The helical magnetic field in the snake magnet was calculated using a 3D magnetic field code TOSCA, and was optimized by segmenting the helical pitch and varying the lengths of the segments. Fabrication errors were checked and verified to be within required tolerances. Finally, the transverse field was measured by rotating harmonic coils. After installation, we achieved a 37.5% improvement in polarization - from 40% with the old solenoid to 55% with the new helical snake, thereby demonstrating that the helical partial snake is an effective device to suppress depolarization resonances in medium-sized synchrotrons.

  18. Helical dipole partial Siberian snake for the AGS

    Science.gov (United States)

    Takano, J.; Ahrens, L. A.; Alforque, R.; Bai, M.; Brown, K.; Courant, E. D.; Ganetis, G.; Gardner, C. J.; Glenn, J. W.; Hattori, T.; Huang, H.; Jain, A.; Luccio, A. U.; MacKay, W. W.; Okamura, M.; Roser, T.; Tsoupas, N.; Tepikian, S.; Tuozzolo, J.; Wood, J.; Zelenski, A.; Zeno, K.

    2006-11-01

    Overcoming depolarization resonances in medium class synchrotrons (3 to 50 GeV) is one of the key issues in accelerating a highly polarized proton beam up to very high energies. Since such synchrotrons, including the Alternating Gradient Synchrotron (AGS) and the J-PARC Main Ring, generally do not have sufficiently long straight sections to accommodate full Siberian snakes with reasonable beam excursions, the practical solution is to use partial Siberian snakes that rotate the particle spin about a horizontal axis by a fraction of 180 degrees. For the AGS, we designed and installed a new partial Siberian snake consisting of a helical dipole magnet with a double pitch structure. The helical structure reduced the amount of transverse coupling as compared to that achieved by the previous solenoidal partial snake. This coupling led to partial depolarization at certain energies from horizontal betatron oscillations. The helical magnetic field in the snake magnet was calculated using a 3D magnetic field code TOSCA, and was optimized by segmenting the helical pitch and varying the lengths of the segments. Fabrication errors were checked and verified to be within required tolerances. Finally, the transverse field was measured by rotating harmonic coils. After installation, we achieved a 37.5% improvement in polarization - from 40% with the old solenoid to 55% with the new helical snake, thereby demonstrating that the helical partial snake is an effective device to suppress depolarization resonances in medium-sized synchrotrons.

  19. Biomimetic Hierarchical Assembly of Helical Supraparticles from Chiral Nanoparticles.

    Science.gov (United States)

    Zhou, Yunlong; Marson, Ryan L; van Anders, Greg; Zhu, Jian; Ma, Guanxiang; Ercius, Peter; Sun, Kai; Yeom, Bongjun; Glotzer, Sharon C; Kotov, Nicholas A

    2016-03-22

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

  20. Magnetic Helicity and Planetary Dynamos

    Science.gov (United States)

    Shebalin, John V.

    2012-01-01

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

  1. Asymmetric catalysis with helical polymers

    NARCIS (Netherlands)

    Megens, Rik P.; Roelfes, Gerard

    Inspired by nature, the use of helical biopolymer catalysts has emerged over the last years as a new approach to asymmetric catalysis. In this Concept article the various approaches and designs and their application in asymmetric catalysis will be discussed.

  2. Asymmetric catalysis with helical polymers

    NARCIS (Netherlands)

    Megens, Rik P.; Roelfes, Gerard

    2011-01-01

    Inspired by nature, the use of helical biopolymer catalysts has emerged over the last years as a new approach to asymmetric catalysis. In this Concept article the various approaches and designs and their application in asymmetric catalysis will be discussed.

  3. Modeling helicity dissipation-rate equation

    CERN Document Server

    Yokoi, Nobumitsu

    2016-01-01

    Transport equation of the dissipation rate of turbulent helicity is derived with the aid of a statistical analytical closure theory of inhomogeneous turbulence. It is shown that an assumption on the helicity scaling with an algebraic relationship between the helicity and its dissipation rate leads to the transport equation of the turbulent helicity dissipation rate without resorting to a heuristic modeling.

  4. The next large helical devices

    Science.gov (United States)

    Iiyoshi, Atsuo; Yamazaki, Kozo

    1995-06-01

    Helical systems have the strong advantage of inherent steady-state operation for fusion reactors. Two large helical devices with fully superconducting coil systems are presently under design and construction. One is the LHD (Large Helical Device) [Fusion Technol. 17, 169 (1990)] with major radius=3.9 m and magnetic field=3-4 T, that is under construction during 1990-1997 at NIFS (National Institute for Fusion Science), Nagoya/Toki, Japan; it features continuous helical coils and a clean helical divertor focusing on edge configuration optimization. The other one in the W7-X (Wendelstein 7-X) [in Plasma Physics and Controlled Fusion Nuclear Research, 1990, (International Atomic Energy Agency, Vienna, 1991), Vol. 3, p. 525] with major radius=5.5 m and magnetic field=3 T, that is under review at IPP (Max-Planck Institute for Plasma Physics), Garching, Germany; it has adopted a modular coil system after elaborate optimization studies. These two programs are complementary in promoting world helical fusion research and in extending the understanding of toroidal plasmas through comparisons with large tokamaks.

  5. omega-Helices in proteins.

    Science.gov (United States)

    Enkhbayar, Purevjav; Boldgiv, Bazartseren; Matsushima, Norio

    2010-05-01

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

  6. Employing Helicity Amplitudes for Resummation

    CERN Document Server

    Moult, Ian; Tackmann, Frank J; Waalewijn, Wouter 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 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 m...

  7. 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.

  8. Single-particle based helical reconstruction—how to make the most of real and Fourier space

    Directory of Open Access Journals (Sweden)

    Carsten Sachse

    2015-06-01

    Full Text Available The helical assembly is a fundamental organization principle of biomacromolecules. To determine the structures of helical filaments or tubes has been helped by the fact that many different views of the helical unit are present to reconstruct a three-dimensional image from a single helix. In this review, I present the current state of helical image reconstruction from electron cryo-micrographs by introducing Fourier-based processing alongside real-space approaches. Based on this foundation, I describe how they can be applied to determine the symmetry and high-resolution structure of helical assemblies. In the past, the main structure determination approach of helical assemblies from electron micrographs was the Fourier-Bessel method, which is based on a comprehensive theory and has generated many successful applications in the last 40 years. The emergence of the single-particle technique allowed segmented helical specimens to be treated as single particles, thus rendering new specimens amenable to 3D helical reconstruction and facilitating high-resolution structure analysis. However, helical symmetry determination remains the crucial step for a successful 3D reconstruction. Depending on the helical specimen, Fourier and real-space approaches or a combination of both provide important clues to establish the correct helical symmetry. I discuss recent developments in combining traditional Fourier-Bessel procedures with single-particle algorithms to provide a versatile and comprehensive approach to structure determination of helical specimens. Upon introduction of direct electron detectors, a series of near-atomic resolution structures from helical assemblies have become available. As helical organization is fundamental to many structural assemblies of the cell, these approaches to structure elucidation open up promising capabilities to study the underlying structures at atomistic resolution.

  9. Passive scalars: mixing, diffusion and intermittency in helical and non-helical rotating turbulence

    CERN Document Server

    Imazio, P Rodriguez

    2015-01-01

    We use direct numerical simulations to compute structure functions, scaling exponents, probability density functions and turbulent transport coefficients of passive scalars in turbulent rotating helical and non-helical flows. We show that helicity affects the inertial range scaling of the velocity and of the passive scalar when rotation is present, with a spectral law consistent with $\\sim k_{\\perp}^{-1.4}$ for the passive scalar variance spectrum. This scaling law is consistent with the phenomenological argument presented in \\cite{imazio2011} for rotating non-helical flows, wich states that if energy follows a $E(k)\\sim k^{-n}$ law, then the passive scalar variance follows a law $V(k) \\sim k^{-n_{\\theta}}$ with $n_{\\theta}=(5-n)/2$. With the second order scaling exponent obtained from this law, and using the Kraichnan model, we obtain anomalous scaling exponents for the passive scalar that are in good agreement with the numerical results. Intermittency of the passive scalar is found to be stronger than in th...

  10. Differential geometry of proteins. Helical approximations.

    Science.gov (United States)

    Louie, A H; Somorjai, R L

    1983-07-25

    We regard a protein molecule as a geometric object, and in a first approximation represent it as a regular parametrized space curve passing through its alpha-carbon atoms (the backbone). In an earlier paper we argued that the regular patterns of secondary structures of proteins (morphons) correspond to geodesics on minimal surfaces. In this paper we discuss methods of recognizing these morphons on space curves that represent the protein backbone conformation. The mathematical tool we employ is the differential geometry of curves and surfaces. We introduce a natural approximation of backbone space curves in terms of helical approximating elements and present a computer algorithm to implement the approximation. Simple recognition criteria are given for the various morphons of proteins. These are incorporated into our helical approximation algorithm, together with more non-local criteria for the recognition of beta-sheet topologies. The method and the algorithm are illustrated with several examples of representative proteins. Generalizations of the helical approximation method are considered and their possible implications for protein energetics are sketched.

  11. 双核三螺旋铁配合物的合成和结构%Synthesis and Crystal Structure of Triple-Helical Di-iron (Ⅲ) Complex

    Institute of Scientific and Technical Information of China (English)

    郭栋; 李继辉; 谢婧婧; 段春迎; 孟庆金

    2002-01-01

    The self-assembly and structural characterization of the new iron (Ⅲ) molecular helix Fe2L3 was achieved from an inexpensive and easy-to-prepare bis-bidentate Schiff base ligand, H2L, [ (HO) (C10H6) CH = N-N = CH (C10H6)(OH) ]. The triple helical Fe2L3 molecule contains two iron (Ⅲ) atoms and three ligands. Each metal center is bound to three bidentate NO units to attain a pseudo-octahedral co-ordination geometry. The ligand wraps in a helical arrangement around the two metal ions. It is suggested that the intramolecular and intermolecular π-π stacking interactions play important roles in the metal-assisted self-assembling process. Crystal structure of the free ligand was also reported for comparison. CCDC: 197370, 197371.%本文选择了2-羟基-1-萘醛与水合肼形成的席夫碱,[(HO)(C10H6)CH=N-N=CH(C10H6)(OH)],作为配体,设计组装了双核三螺旋的三价铁配合物.配合物中每一个铁离子以准八面体的配位方式分别与三个NO双齿单元配位,三个配体分别桥联两个金属形成特定的三螺旋构型.分子内和分子间的π-π堆积作用对螺旋体的形成和堆积方式起着十分重要的作用.作为对照,本文还报道了配体的晶体结构.

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

    Science.gov (United States)

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

    2016-09-01

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

  13. Magnetic structure and Dzyaloshinskii-Moriya interaction in the S =1/2 helical-honeycomb antiferromagnet α -Cu2V2O7

    Science.gov (United States)

    Gitgeatpong, G.; Zhao, Y.; Avdeev, M.; Piltz, R. O.; Sato, T. J.; Matan, K.

    2015-07-01

    Magnetic properties of the S =1/2 antiferromagnet α -Cu2V2O7 have been studied using magnetization, quantum Monte Carlo (QMC) simulations, and neutron diffraction. Magnetic susceptibility shows a broad peak at ˜50 K followed by an abrupt increase indicative of a phase transition to a magnetically ordered state at TN=33.4 (1 ) K. Above TN, a fit to the Curie-Weiss law gives a Curie-Weiss temperature of Θ =-73 (1 ) K suggesting the dominant antiferromagnetic coupling. The result of the QMC calculations on the helical-honeycomb spin network with two antiferromagnetic exchange interactions J1 and J2 provides a better fit to the susceptibility than the previously proposed spin-chain model. Two sets of the coupling parameters J1:J2=1 :0.45 with J1=5.79 (1 ) meV and 0.65 :1 with J2=6.31 (1 ) meV yield equally good fits down to ˜TN . Below TN, weak ferromagnetism due to spin canting is observed. The canting is caused by the Dzyaloshinskii-Moriya interaction with an estimated b c -plane component |Dp|≃0.14 J1 . Neutron diffraction reveals that the S =1/2 Cu2 + spins antiferromagnetically align in the F d'd'2 magnetic space group. The ordered moment of 0.93(9) μB is predominantly along the crystallographic a axis.

  14. 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.

  15. 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.

  16. Helical Growth of Ultrathin Gold-Copper Nanowires.

    Science.gov (United States)

    Mendoza-Cruz, Rubén; Bazán-Díaz, Lourdes; Velázquez-Salazar, J Jesús; Plascencia-Villa, Germán; Bahena-Uribe, Daniel; Reyes-Gasga, José; Romeu, David; Guisbiers, Grégory; Herrera-Becerra, Raúl; José-Yacamán, Miguel

    2016-03-09

    In this work, we report the synthesis and detailed structural characterization of novel helical gold-copper nanowires. The nanowires possess the Boerdijk-Coxeter-Bernal structure, based on the pile up of octahedral, icosahedral, and/or decahedral seeds. They are self-assembled into a coiled manner as individual wires or into a parallel-ordering way as groups of wires. The helical nanowires are ultrathin with a diameter of less than 10 nm and variable length of several micrometers, presenting a high density of twin boundaries and stacking faults. To the best of our knowledge, such gold-copper nanowires have never been reported previously.

  17. Preferential sampling of helicity by isotropic helicoids

    CERN Document Server

    Gustavsson, Kristian

    2016-01-01

    We present a theoretical and numerical study on the motion of isotropic helicoids in complex flows. These are particles whose motion is invariant under rotations but not under mirror reflections of the particle. This is the simplest, yet unexplored, extension of the much studied case of small spherical particles. We show that heavy isotropic helicoids, due to the coupling between translational and rotational degrees of freedom, preferentially sample different helical regions in laminar or chaotic advecting flows. This opens the way to control and engineer particles able to track complex flow structures with potential applications to microfluidics and turbulence.

  18. Electric field domain interface in helical systems

    Energy Technology Data Exchange (ETDEWEB)

    Itoh, Kimitaka; Sanuki, Heiji; Toda, Shinichiro; Yokoyama, Masayuki [National Inst. for Fusion Science, Toki, Gifu (Japan); Itoh, Sanae-I.; Yagi, Masatoshi [Kyushu Univ., Research Institute for Applied Mechanics, Kasuga, Fukuoka (Japan); Fukuyama, Atsushi [Kyoto Univ., Department of Nuclear Engineering, Kyoto (Japan)

    2001-07-01

    The electric field bifurcation in helical plasmas under the condition of continuous fluxes is investigated. The stationary solution of the transport equation, together with charge neutrality condition, is investigated. It is shown that the anomalous flux plays an important role in determining multiple electric field solutions. The transition to the branch with a strong positive electric field occurs when the heat flux exceeds a critical value. Condition for the presence of transition is obtained. The radial structure of the electric field domain interface is obtained. The condition that the suppression of turbulence is expected to occur is discussed. Comparison with experimental observation is briefly mentioned. (author)

  19. Exchange-striction associated with the elliptical proper helical magnetic structure in the ferroelectric phase of CuFe{sub 1-y}Ga{sub y}O{sub 2}

    Energy Technology Data Exchange (ETDEWEB)

    Terada, N; Kitazawa, H [National Institute for Materials Science (NIMS), Tsukuba, Ibaraki, 305-0047 (Japan); Nakajima, T; Mitsuda, S [Department of Physics, Tokyo University of Science, Tokyo 162-8601 (Japan); Matsuda, M; Kakurai, K [Japan Atomic Energy Agency, Tokai, Ibaraki, 319-1195 (Japan); Tanaka, Y, E-mail: terada.noriki@nims.go.j [RIKEN SPring-8 Center, Harima Institute, Sayo, Hyogo 679-5148 (Japan)

    2010-02-01

    Recently, the detail magnetic structure in the ferroelectric phase of CuFe{sub 1-y}Ga{sub y}O{sub 2} has been determined to be the proper helical structure with the ellipticity of {approx} 0.9 by the comprehensive neutron diffraction study.[Nakajima et al. Phys. Rev. B 79 214423 (2009)] In the present study, we have investigated the lattice modulation associated with the elliptical magnetic structure, using the resonant X-ray diffraction measurements on CuFe{sub 0.965}Ga{sub 0.035}O{sub 2}. We observed the superlattice reflection indexed as (0 1 + 2q{sub m} 0), where q{sub m} is the wave number of the magnetic modulation. The energy spectrum near the Fe-K absorption edge for the (0 1 + 2q{sub m} 0) intensity conforms with that for the fundamental (0 2 0) intensity within experimental accuracy, suggesting that the superlattice modulation is at least associated with displacements of the Fe ions. We discuss the origin of the superlattice modulation with the exchange striction model.

  20. 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

  1. Brownian motion of helical flagella.

    Science.gov (United States)

    Hoshikawa, H; Saito, N

    1979-07-01

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

  2. Optical and Infrared Helical Metamaterials

    Directory of Open Access Journals (Sweden)

    Kaschke Johannes

    2016-09-01

    Full Text Available By tailoring metamaterials with chiral unit cells, giant optical activity and strong circular dichroism have been achieved successfully over the past decade. Metamaterials based on arrays of metal helices have revolutionized the field of chiral metamaterials, because of their capability of exhibiting these pronounced chiro-optical effects over previously unmatched bandwidths. More recently, a large number of new metamaterial designs based on metal helices have been introduced with either optimized optical performance or other chiro-optical properties for novel applications.

  3. A hypothesis on neutrino helicity

    CERN Document Server

    Sahin, I

    2016-01-01

    It is firmly established by experimental results that neutrinos are almost 100\\% longitudinally polarized and left-handed. It is also confirmed by neutrino oscillation experiments that neutrinos have tiny but non-zero masses. Since the helicity is not a Lorentz invariant quantity for massive particles, neutrinos can not be strictly left-handed. On the other hand, it is generally assumed that ultrarelativistic massive fermions can be described well enough by the Weyl equations. We discuss the validity of this assumption and propose a new hypothesis according to which neutrinos can be described by pure helicity states although they are not massless.

  4. Magnetic Helicity Injection in Solar Active Regions

    Institute of Scientific and Technical Information of China (English)

    Hong-Qi Zhang

    2006-01-01

    We present the evolution of magnetic field and its relationship with magnetic (current) helicity in solar active regions from a series of photospheric vector magnetograms obtained by Huairou Solar Observing Station, longitudinal magnetograms by MDI of SOHO and white light images of TRACE. The photospheric current helicity density is a quantity reflecting the local twisted magnetic field and is related to the remaining magnetic helicity in the photosphere, even if the mean current helicity density brings the general chiral property in a layer of solar active regions. As new magnetic flux emerges in active regions, changes of photospheric current helicity density with the injection of magnetic helicity into the corona from the subatmosphere can be detected, including changes in sign caused by the injection of magnetic helicity of opposite sign. Because the injection rate of magnetic helicity and photospheric current helicity density have different means in the solar atmosphere,the injected magnetic helicity is probably not proportional to the current helicity density remaining in the photosphere. The evidence is that rotation of sunspots does not synchronize exactly with the twist of photospheric transverse magnetic field in some active regions (such as, delta active regions). They represent different aspects of magnetic chirality. A combined analysis of the observational magnetic helicity parameters actually provides a relative complete picture of magnetic helicity and its transfer in the solar atmosphere.

  5. 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.

  6. Helical crystallization on lipid nanotubes: streptavidin as a model protein.

    Science.gov (United States)

    Dang, Thanh X; Farah, Sammy J; Gast, Alice; Robertson, Channing; Carragher, Bridget; Egelman, Edward; Wilson-Kubalek, Elizabeth M

    2005-04-01

    In this study, we use streptavidin (SA) as a model system to study helical protein array formation on lipid nanotubes, an alternative to 2D studies on lipid monolayers. We demonstrate that wild-type and a mutant form of SA form helical arrays on biotinylated lipid nanotubes. 3D maps from helical arrays of wild-type and mutant SA were reconstructed using two different approaches: Fourier-Bessel methods and an iterative single particle algorithm. The maps show that wild-type and mutant streptavidin molecules order differently. The molecular packing arrangements of SA on the surface of the lipid nanotubes differ from previously reported lattice packing of SA on biotinylated monolayers. Helical crystallization on lipid nanotubes presents an alternative platform to explore fundamentals of protein ordering, intermolecular protein interaction and phase behavior. We demonstrate that lipid nanotubes offer a robust and reproducible substrate for forming helical protein arrays which present a means for studying protein structure and structure-function relationships.

  7. The Transport of Relative Canonical Helicity

    CERN Document Server

    You, Setthivoine

    2012-01-01

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

  8. 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...

  9. 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....

  10. On the triple correlations in helical turbulence

    CERN Document Server

    Chkhetiani, O

    1997-01-01

    The evolution of correlation characteristics in homogeneous helical turbulence is considered. Additional K'arm'an-Howarth type equations, describing the evolution of the mixed correlation tensor of the velocity and vorticity are obtained. In the helical scaling region, the solution of obtained equation gives the exact relation between antisymmetric component of a rank-three tensor and the average dissipation of helicity. This relation is a helical analogue of Kolmogorov's known 4/5 law.

  11. Hybrid helical snakes and rotators for RHIC

    Energy Technology Data Exchange (ETDEWEB)

    Courant, E.D.

    1995-06-13

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

  12. Enantiomeric differentiation by synthetic helical polymers.

    Science.gov (United States)

    Yashima, Eiji; Iida, Hiroki; Okamoto, Yoshio

    2013-01-01

    Recent advances in the synthesis of helical polymers and their applications as chiral materials, in particular chiral stationary phases (CSPs), for high-performance liquid chromatography (HPLC) are reviewed with an emphasis on the key role of the helical conformations with one-handedness for the prominent chiral recognition of enantiomers. The historical background of artificial optically active helical polymers is also briefly described.

  13. Quantification of a Helical Origami Fold

    Science.gov (United States)

    Dai, Eric; Han, Xiaomin; Chen, Zi

    2015-03-01

    Origami, the Japanese art of paper folding, is traditionally viewed as an amusing pastime and medium of artistic expression. However, in recent years, origami has served as a source of inspiration for innovations in science and engineering. Here, we present the geometric and mechanical properties of a twisting origami fold. The origami structure created by the fold exhibits several interesting properties, including rigid foldibility, local bistability and finely tunable helical coiling, with control over pitch, radius and handedness of the helix. In addition, the pattern generated by the fold closely mimics the twist buckling patterns shown by thin materials, for example, a mobius strip. We use six parameters of the twisting origami pattern to generate a fully tunable graphical model of the fold. Finally, we present a mathematical model of the local bistability of the twisting origami fold. Our study elucidates the mechanisms behind the helical coiling and local bistability of the twisting origami fold, with potential applications in robotics and deployable structures. Acknowledgment to Branco Weiss Fellowship for funding.

  14. IR investigation on dehydrophenylalanine containing model peptides in helical conformation deposited on a crystal surface

    Science.gov (United States)

    Gupta; Mehrotra; Tewari; Jain; Chauhan

    1999-11-01

    Fourier transform ir spectra have been recorded for three 3(10)-helical and one alpha-helical pentapeptides containing dehydrophenylalanine, in a thin solid film, in order to find marker bands for various secondary structures encountered in peptides containing dehydroaminoacids. The peptide solutions were deposited and dried as thin film on zinc selenide crystal surface. This convenient sampling method has provided reliable estimates of peptide secondary structure in solid state. Detailed vibrational assignments in the spectral region between 1200-1700 cm(-1) are reported. In this region, peptide amide I, II, and III vibrations occur. Spectra-structure correlation has been presented based on the amide modes. Comparison of the ir spectra with available crystal structure data provides qualitative support for assignments of ir bands to 3(10)-helical structure and alpha-helical structure in dehydrophenylalanine containing pentapeptides. Band frequency assignments for 3(10)-helical conformation are consistent for all three peptides. All the assignments agree closely with the theoretical predictions. The spectral differences between 3(10)-helical peptides and the alpha-helical peptide have been highlighted. These findings demonstrate that a method based on ir spectroscopy can be developed for a useful approximation of three-dimensional structure of dehydropeptides in solid state. Copyright 1999 John Wiley & Sons, Inc.

  15. 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.

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

    CERN Document Server

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

    2016-01-01

    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.

  17. Small-$x$ asymptotics of the quark helicity distribution

    CERN Document Server

    Kovchegov, Yuri V; Sievert, Matthew D

    2016-01-01

    We construct a numerical solution of the small-$x$ evolution equations recently derived in \\cite{Kovchegov:2015pbl} for the (anti)quark helicity TMDs and 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 helicity PDFs at small $x$, which should have important phenomenological consequences. We also give an estimate of how much of the proton's spin may be at small $x$ and what impact this has on the so-called "spin crisis."

  18. 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...

  19. Helicity statistics in homogeneous and isotropic turbulence and turbulence models

    CERN Document Server

    Sahoo, Ganapati; Biferale, Luca

    2016-01-01

    We study the statistical properties of helicity in direct numerical simulations of fully developed homogeneous and isotropic turbulence and in a class of turbulence shell models. We consider correlation functions based on combinations of vorticity and velocity increments that are not invariant under mirror symmetry. We also study the scaling properties of high-order structure functions based on the moments of the velocity increments projected on a subset of modes with either positive or negative helicity (chirality). We show that mirror symmetry is recovered at small-scales, i.e. chiral terms are always subleading and they are well captured by a dimensional argument plus a small anomalous correction. We confirm these findings with numerical study of helical shell models at high Reynolds numbers.

  20. Helicity statistics in homogeneous and isotropic turbulence and turbulence models

    Science.gov (United States)

    Sahoo, Ganapati; De Pietro, Massimo; Biferale, Luca

    2017-02-01

    We study the statistical properties of helicity in direct numerical simulations of fully developed homogeneous and isotropic turbulence and in a class of turbulence shell models. We consider correlation functions based on combinations of vorticity and velocity increments that are not invariant under mirror symmetry. We also study the scaling properties of high-order structure functions based on the moments of the velocity increments projected on a subset of modes with either positive or negative helicity (chirality). We show that mirror symmetry is recovered at small scales, i.e., chiral terms are subleading and they are well captured by a dimensional argument plus anomalous corrections. These findings are also supported by a high Reynolds numbers study of helical shell models with the same chiral symmetry of Navier-Stokes equations.

  1. 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.

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

    CERN Document Server

    Nishikawa, Ken-Ichi; Niemiec, Jacek; Kobzar, Oleh; Pohl, Martin; Gomez, Jose L; Dutan, Ioana; Pe'er, Asaf; Frederiksen, Jacob Trier; Nordlund, AAke; Meli, Athina; Sol, Helene; Hardee, Philip E; Hartmann, Dieter H

    2016-01-01

    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 ($e^{\\pm}$) 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 $e^{\\pm}$ jet simulation a recollimation-like instability occurs at early times followed by a kinetic instability and the general structure is similar to ...

  3. Performance tests on helical Savonius rotors

    Energy Technology Data Exchange (ETDEWEB)

    Kamoji, M.A.; Kedare, S.B. [Department of Energy Science and Engineering, Indian Institute of Technology, Bombay (India); Prabhu, S.V. [Department of Mechanical Engineering, Indian Institute of Technology, Bombay (India)

    2009-03-15

    Conventional Savonius rotors have high coefficient of static torque at certain rotor angles and a negative coefficient of static torque from 135 to 165 and from 315 to 345 in one cycle of 360 . In order to decrease this variation in static torque from 0 to 360 , a helical Savonius rotor with a twist of 90 is proposed. In this study, tests on helical Savonius rotors are conducted in an open jet wind tunnel. Coefficient of static torque, coefficient of torque and coefficient of power for each helical Savonius rotor are measured. The performance of helical rotor with shaft between the end plates and helical rotor without shaft between the end plates at different overlap ratios namely 0.0, 0.1 and 0.16 is compared. Helical Savonius rotor without shaft is also compared with the performance of the conventional Savonius rotor. The results indicate that all the helical Savonius rotors have positive coefficient of static torque at all the rotor angles. The helical rotors with shaft have lower coefficient of power than the helical rotors without shaft. Helical rotor without shaft at an overlap ratio of 0.0 and an aspect ratio of 0.88 is found to have almost the same coefficient of power when compared with the conventional Savonius rotor. Correlation for coefficient of torque and power is developed for helical Savonius rotor for a range of Reynolds numbers studied. (author)

  4. Differential Geometric Analysis of Alterations in MH α-Helices

    Science.gov (United States)

    Hischenhuber, Birgit; Havlicek, Hans; Todoric, Jelena; Höllrigl-Binder, Sonja; Schreiner, Wolfgang; Knapp, Bernhard

    2013-01-01

    Antigen presenting cells present processed peptides via their major histocompatibility (MH) complex to the T cell receptors (TRs) of T cells. If a peptide is immunogenic, a signaling cascade can be triggered within the T cell. However, the binding of different peptides and/or different TRs to MH is also known to influence the spatial arrangement of the MH α-helices which could itself be an additional level of T cell regulation. In this study, we introduce a new methodology based on differential geometric parameters to describe MH deformations in a detailed and comparable way. For this purpose, we represent MH α-helices by curves. On the basis of these curves, we calculate in a first step the curvature and torsion to describe each α-helix independently. In a second step, we calculate the distribution parameter and the conical curvature of the ruled surface to describe the relative orientation of the two α-helices. On the basis of four different test sets, we show how these differential geometric parameters can be used to describe changes in the spatial arrangement of the MH α-helices for different biological challenges. In the first test set, we illustrate on the basis of all available crystal structures for (TR)/pMH complexes how the binding of TRs influences the MH helices. In the second test set, we show a cross evaluation of different MH alleles with the same peptide and the same MH allele with different peptides. In the third test set, we present the spatial effects of different TRs on the same peptide/MH complex. In the fourth test set, we illustrate how a severe conformational change in an α-helix can be described quantitatively. Taken together, we provide a novel structural methodology to numerically describe subtle and severe alterations in MH α-helices for a broad range of applications. © 2013 Wiley Periodicals, Inc. PMID:23703160

  5. Predictive supracolloidal helices from patchy particles

    Science.gov (United States)

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

    2014-11-01

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

  6. 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)

  7. A helical scintillating fiber hodoscope

    Energy Technology Data Exchange (ETDEWEB)

    Altmeier, M.; Bauer, F.; Bisplinghoff, J.; Bissel, T.; Bollmann, R.; Busch, M.; Buesser, 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.; Rossen, P. von; 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

    1999-07-21

    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. Adjustable phase planar helical undulator

    Science.gov (United States)

    Carr, Roger G.; Lidia, Steve

    1993-11-01

    We present here the design description of a new type of planar helical undulator, which we are constructing for the SPEAR storage ring at the Stanford Synchrotron Radiation Laboratory. It comprises four rows of pure permanent magnet blocks, one row in each quadrant about the axis defined by the electron beam. Rows may be translated longitudinally with respect to each other to change the helicity of the magnetic field they create at the position of the beam. They may also be translated longitudinally to vary the energy of the x-rays emitted, unlike designs where this function is performed by varying the gap between the rows. This work includes numerical calculations of the fields, electron trajectories, and x-ray spectra, including off-axis effects.

  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. Microwave Studies of Perfluoropentane and its Helicity

    Science.gov (United States)

    Fournier, Joseph A.; Bohn, Robert K.; Montgomery, John A.; , Jr.

    2009-06-01

    Unlike hydrocarbons, fluorocarbons are helical in their all-trans most stable conformations. A definitive experimental determination of the helical angle has not been accomplished because single crystal X-ray studies are not available due to the lack of suitable crystallization solvents, but a value of 17^° from exactly trans is generally accepted from X-ray fiber studies. Using a pulsed-jet Fourier Transform microwave spectrometer, we have observed and assigned the rotational spectra of the lowest energy all-anti C_2 symmetry form of perfluoro-n-pentane and all three of its ^{13}C isotopomers. A, B, and C values of the parent species are 990.6394(4) MHz, 314.00020(14) MHz, and 304.37034(14) MHz, respectively. A range of effective r_0 structures incorporating various model constraints are consistent with about 16^° torsion and a Kraitchman analysis of the parent and ^{13}C species gives 13.3^°. Ab initio calculations are consistent with the experimental results.

  11. Cool and hot flux ropes, their helicity

    Science.gov (United States)

    Nindos, Alexander

    2016-07-01

    We will review recent indirect and direct evidence for the existence of magnetic flux ropes in the solar atmosphere. Magnetic flux ropes may appear as S-shaped or reverse S-shaped (sigmoidal) structures in regions that are likely to erupt, and may also show in nonlinear force-free field extrapolations that use data from photospheric vector magnetograms as boundary condition. The availability of high sensitivity data recorded with unprecedented spatial and temporal resolution in hot EUV wavelengths by the Atmospheric Imaging Assembly (AIA) onboard the Solar Dynamics Observatory (SDO) has revealed the existence of coherent structures identified as hot flux ropes. In this presentation, we will review the properties of both cool and hot flux ropes with an emphasis on the frequency of their occurrence in large flares and on their magnetic helicity content.

  12. Helical metallic micro- and nanostructures: fabrication and application

    Science.gov (United States)

    Liu, Lichun; Zhang, Liqiu; Kim, Sang Min; Park, Sungho

    2014-07-01

    Metal elements occupy more than 70% of the positions in the periodic table, and their use has accelerated human civilization due to their invaluable chemical and physical characteristics. With the rapid development of metals, various structures of microscopic metal particles have been fabricated and investigated as functional materials in scientific research and practical applications. The phrase `structure determines properties' has been widely acknowledged as a golden rule in chemistry and materials science, especially when the size of small particles is in the micro- or nanoscale dimension. Helical metallic micro- and nanostructures with complex shapes have recently emerged and may be used for various useful applications such as photonics, sensors, actuators, micro-/nanorobotics, and micro-/nanoelectronics, based on their unique mechanical, electrical, and electromagnetic properties. This review paper specifically focuses on the fabrication and application of helical metallic structures with a size ranging from the micro- to nanoscale. The unusual spatial distribution of active atoms in helical metallic micro- and nanostructures and their helical morphology could offer new opportunities for applications beyond those of other conventional metallic and nonmetallic micro- and nanostructures.

  13. Mechanics of tunable helices and geometric frustration in biomimetic seashells

    Science.gov (United States)

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

    2014-03-01

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

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

    Science.gov (United States)

    Zhao, Biao; Deng, Jinrui; Deng, Jianping

    2016-04-01

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

  15. Helically twisted photonic crystal fibres.

    Science.gov (United States)

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

    2017-02-28

    Recent theoretical and experimental work on helically twisted photonic crystal fibres (PCFs) is reviewed. Helical Bloch theory is introduced, including a new formalism based on the tight-binding approximation. It is used to explore and explain a variety of unusual effects that appear in a range of different twisted PCFs, including fibres with a single core and fibres with N cores arranged in a ring around the fibre axis. We discuss a new kind of birefringence that causes the propagation constants of left- and right-spinning optical vortices to be non-degenerate for the same order of orbital angular momentum (OAM). Topological effects, arising from the twisted periodic 'space', cause light to spiral around the fibre axis, with fascinating consequences, including the appearance of dips in the transmission spectrum and low loss guidance in coreless PCF. Discussing twisted fibres with a single off-axis core, we report that optical activity in a PCF is opposite in sign to that seen in a step-index fibre. Fabrication techniques are briefly described and emerging applications reviewed. The analytical results of helical Bloch theory are verified by an extensive series of 'numerical experiments' based on finite-element solutions of Maxwell's equations in a helicoidal frame.This article is part of the themed issue 'Optical orbital angular momentum'. © 2017 The Authors.

  16. Helically twisted photonic crystal fibres

    Science.gov (United States)

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

    2017-02-01

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

  17. Helically twisted photonic crystal fibres

    Science.gov (United States)

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

    2017-01-01

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

  18. Crystal Structure of Jun a 1, the Major Cedar Pollen Allergen from Juniperus ashei, Reveals a Parallel β-Helical Core*

    Science.gov (United States)

    Czerwinski, Edmund W.; Midoro-Horiuti, Terumi; White, Mark A.; Brooks, Edward G.; Goldblum, Randall M.

    2008-01-01

    Pollen from cedar and cypress trees is a major cause of seasonal hypersensitivity in humans in several regions of the Northern Hemisphere. We report the first crystal structure of a cedar allergen, Jun a 1, from the pollen of the mountain cedar Juniperus ashei (Cupressaceae). The core of the structure consists primarily of a parallel β-helix, which is nearly identical to that found in the pectin/pectate lyases from several plant pathogenic microorganisms. Four IgE epitopes mapped to the surface of the protein are accessible to the solvent. The conserved vWiDH sequence is covered by the first 30 residues of the N terminus. The potential reactive arginine, analogous to the pectin/pectate lyase reaction site, is accessible to the solvent, but the substrate binding groove is blocked by a histidine-aspartate salt bridge, a glutamine, and an α-helix, all of which are unique to Jun a 1. These observations suggest that steric hindrance in Jun a 1 precludes enzyme activity. The overall results suggest that it is the structure of Jun a 1 that makes it a potent allergen. PMID:15539389

  19. Structural basis for broad neutralization of HIV-1 through the molecular recognition of 10E8 helical epitope at the membrane interface

    Science.gov (United States)

    Rujas, Edurne; Caaveiro, Jose M. M.; Partida-Hanon, Angélica; Gulzar, Naveed; Morante, Koldo; Apellániz, Beatriz; García-Porras, Miguel; Bruix, Marta; Tsumoto, Kouhei; Scott, Jamie K.; Jiménez, M. Ángeles; Nieva, José L.

    2016-01-01

    The mechanism by which the HIV-1 MPER epitope is recognized by the potent neutralizing antibody 10E8 at membrane interfaces remains poorly understood. To solve this problem, we have optimized a 10E8 peptide epitope and analyzed the structure and binding activities of the antibody in membrane and membrane-like environments. The X-ray crystal structure of the Fab-peptide complex in detergents revealed for the first time that the epitope of 10E8 comprises a continuous helix spanning the gp41 MPER/transmembrane domain junction (MPER-N-TMD; Env residues 671–687). The MPER-N-TMD helix projects beyond the tip of the heavy-chain complementarity determining region 3 loop, indicating that the antibody sits parallel to the plane of the membrane in binding the native epitope. Biophysical, biochemical and mutational analyses demonstrated that strengthening the affinity of 10E8 for the TMD helix in a membrane environment, correlated with its neutralizing potency. Our research clarifies the molecular mechanisms underlying broad neutralization of HIV-1 by 10E8, and the structure of its natural epitope. The conclusions of our research will guide future vaccine-design strategies targeting MPER. PMID:27905530

  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. Evolution of Magnetic Helicity and Energy Spectra of Solar Active Regions

    CERN Document Server

    Zhang, Hongqi; Sokoloff, D D

    2015-01-01

    We adopt an isotropic representation of the Fourier-transformed two-point correlation tensor of the magnetic field for estimating magnetic energy and helicity spectra as well as current helicity spectra of individual active regions and the change of their spectral indices with the solar cycle. The departure of the spectral index of current helicity from 5/3 is analyzed, and it is found that it is lower than that of magnetic energy. There is no obvious relationship between the change of the normalized magnetic helicity and the integral scale of the magnetic field for individual active regions. The evolution of the spectral index reflects the development and distribution of various scales of magnetic structures in active regions. It is found that around solar maximum the magnetic energy and helicity spectra are steeper.

  2. Optimal dynamical systems of Navier-Stokes equations based on generalized helical-wave bases and the fundamental elements of turbulence

    Science.gov (United States)

    Peng, NaiFu; Guan, Hui; Wu, ChuiJie

    2016-11-01

    In this paper, we present the theory of constructing optimal generalized helical-wave coupling dynamical systems. Applying the helical-wave decomposition method to Navier-Stokes equations, we derive a pair of coupling dynamical systems based on optimal generalized helical-wave bases. Then with the method of multi-scale global optimization based on coarse graining analysis, a set of global optimal generalized helical-wave bases is obtained. Optimal generalized helical-wave bases retain the good properties of classical helical-wave bases. Moreover, they are optimal for the dynamical systems of Navier-Stokes equations, and suitable for complex physical and geometric boundary conditions. Then we find that the optimal generalized helical-wave vortexes fitted by a finite number of optimal generalized helical-wave bases can be used as the fundamental elements of turbulence, and have important significance for studying physical properties of complex flows and turbulent vortex structures in a deeper level.

  3. Nucleonic helicity distributions revisited with an emphasis on their evolutions and twists

    Indian Academy of Sciences (India)

    Rajen Kundu

    2014-12-01

    In this work, we uphold and extend the formalism advocated by us more than a decade ago in order to extract information 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 in our calculation. Sum rules associated with these helicity distributions are also verified in a frame-independent way.

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

    DEFF Research Database (Denmark)

    Laursen, Jonas Striegler; Harris, Pernille; Fristrup, Peter;

    2015-01-01

    β-Peptoids are peptidomimetics based on N-alkylated β-aminopropionic acid residues (or N-alkyl-β-alanines). This type of peptide mimic has previously been incorporated in biologically active ligands and has been hypothesized to be able to exhibit foldamer properties. Here we show, for the first...... time, that β-peptoids can be tuned to fold into stable helical structures. We provide high-resolution X-ray crystal structures of homomeric β-peptoid hexamers, which reveal right-handed helical conformations with exactly three residues per turn and a helical pitch of 9.6-9.8 Å between turns...

  5. Enhancement of spin polarization in transport through protein-like single-helical molecules

    Science.gov (United States)

    Wu, Hai-Na; Wang, Xiao; Zhang, Ya-Jing; Yi, Guang-Yu; Gong, Wei-Jiang

    2016-06-01

    We investigate the spin-polarized electron transport through the single-helical molecules connected with two normal metallic leads. On the basis of an effective model Hamiltonian, influences of the structural parameters on the conductance and the spin polarization are calculated by using the Landauer-Büttiker formula. The optimal structural parameters for the maximal spin polarization are analyzed. Our results show that the dephasing term is an important factor to enhance the spin polarization, in addition to the intrinsic parameters of the single-helical molecule. This work can be helpful in optimizing the spin polarization in the protein-like single-helical molecules.

  6. Structure of the cytoplasmic loop between putative helices II and III of the mannitol permease of Escherichia coli: a tryptophan and 5-fluorotryptophan spectroscopy study.

    Science.gov (United States)

    Vos, Erwin P P; Bokhove, Marcel; Hesp, Ben H; Broos, Jaap

    2009-06-16

    In this work, four single tryptophan (Trp) mutants of the dimeric mannitol transporter of Escherichia coli, EII(mtl), are characterized using Trp and 5-fluoroTrp (5-FTrp) fluorescence spectroscopy. The four positions, 97, 114, 126, and 133, are located in a region shown by recent studies to be involved in the mannitol translocation process. To spectroscopically distinguish between the Trp positions in each subunit of dimeric EII(mtl), 5-FTrp was biosynthetically incorporated because of its much simpler photophysics compared to those of Trp. The steady-state and time-resolved fluorescence methodologies used point out that all four positions are in structured environments, both in the absence and in the presence of a saturating concentration of mannitol. The fluorescence decay of all 5-FTrp-containing mutants was highly homogeneous, suggesting similar microenvironments for both probes per dimer. However, Stern-Volmer quenching experiments using potassium iodide indicate different solvent accessibilities for the two probes at positions 97 and 133. A 5 A two-dimensional (2D) projection map of the membrane-embedded IIC(mtl) dimer showing 2-fold symmetry is available. The results of this work are in better agreement with a 7 A projection map from a single 2D crystal on which no symmetry was imposed.

  7. Helical graphene oxide fibers as a stretchable sensor and an electrocapillary sucker

    Science.gov (United States)

    Hua, Chunfei; Shang, Yuanyuan; Li, Xiying; Hu, Xiaoyang; Wang, Ying; Wang, Xinchang; Zhang, Yingjiu; Li, Xinjian; Duan, Huiling; Cao, Anyuan

    2016-05-01

    Fibers made from carbon nanotubes or graphene are strong and conductive; encoding helical structures into these fibers may render useful properties such as high stretchability. Here, we directly spin freestanding graphene oxide (GO) films into helical fibers consisting of uniformly arranged loops with tunable diameters, under controlled environmental humidity. Reduced GO fibers with a helical shape are stretched elastically with a reversible electrical resistance change for many strain cycles. Stretchable temperature sensors built on helical fibers work at large strains (up to 50%) and high temperature (up to 300 °C), with a reliable deformation-independent response. The GO fibers also contain through-channels inside with suitable pore size, which can take up an aqueous electrolyte quickly under a low bias, resulting in a fiber-shaped, on-off switchable electrocapillary sucker. Our multifunctional helical and hollow GO fibers have potential applications in stretchable fiber-shaped sensors, actuators and nano-fluid systems.Fibers made from carbon nanotubes or graphene are strong and conductive; encoding helical structures into these fibers may render useful properties such as high stretchability. Here, we directly spin freestanding graphene oxide (GO) films into helical fibers consisting of uniformly arranged loops with tunable diameters, under controlled environmental humidity. Reduced GO fibers with a helical shape are stretched elastically with a reversible electrical resistance change for many strain cycles. Stretchable temperature sensors built on helical fibers work at large strains (up to 50%) and high temperature (up to 300 °C), with a reliable deformation-independent response. The GO fibers also contain through-channels inside with suitable pore size, which can take up an aqueous electrolyte quickly under a low bias, resulting in a fiber-shaped, on-off switchable electrocapillary sucker. Our multifunctional helical and hollow GO fibers have potential

  8. TO DEDUCTION OF MASS FLOW RATE FOR HELICAL HEAT EXCHANGER AT MULTIPLE CROSS-SECTIONS USING CFD

    OpenAIRE

    Surendra Kumar Vishwakarma*, Sanjay Kumbhare, K.K. Thakur

    2016-01-01

    Enhancing the heat transfer by the use of helical coils has been studied and researched by many researchers, because the fluid dynamics inside the pipes of a helical coil heat exchanger offer certain advantages over the straight tubes, shell and tube type heat exchanger, in terms of better heat transfer and mass transfer coefficients. Various configurations of coil structure are possible, and the configuration in which there is a series of vertically stacked helically coiled tubes is the most...

  9. Winding light beams along elliptical helical trajectories

    CERN Document Server

    Wen, Yuanhui; 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 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 non-convex trajectories, thereby opening up a new route of manipulating light beams for fundamental research and practical ap...

  10. Helical Aharonov-Casher edge states

    OpenAIRE

    Heremans, J. J.; Xu, L. L.

    2010-01-01

    It is shown that an Aharonov-Casher vector potential in a two-dimensional geometry can lead to helical edge states. The Aharonov-Casher vector potential is the electromagnetic dual of the magnetic vector potential, and leads to traveling states at the sample edge in analogy to the integer quantum Hall effect. The helical edge states are predicted to appear in a narrow channel geometry with parabolic or sufficiently symmetric confinement potential. The implications of the helical Aharonov-Cash...

  11. Employing Helicity Amplitudes for Resummation in SCET

    CERN Document Server

    Moult, Ian; Tackmann, Frank J; Waalewijn, Wouter J

    2016-01-01

    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.

  12. Dynamic control of chirality and self-assembly of double-stranded helicates with light.

    Science.gov (United States)

    Zhao, Depeng; van Leeuwen, Thomas; Cheng, Jinling; Feringa, Ben L

    2017-03-01

    Helicity switching in biological and artificial systems is a fundamental process that allows for the dynamic control of structures and their functions. In contrast to chemical approaches to responsive behaviour in helicates, the use of light as an external stimulus offers unique opportunities to invert the chirality of helical structures in a non-invasive manner with high spatiotemporal precision. Here, we report that unidirectional rotary motors with connecting oligobipyridyl ligands, which can dynamically change their chirality upon irradiation, assemble into metal helicates that are responsive to light. The motor function controls the self-assembly process as well as the helical chirality, allowing switching between oligomers and double-stranded helicates with distinct handedness. The unidirectionality of the light-induced motion governs the sequence of programmable steps, enabling the highly regulated self-assembly of fully responsive helical structures. This discovery paves the way for the future development of new chirality-dependent photoresponsive systems including smart materials, enantioselective catalysts and light-driven molecular machines.

  13. Dynamic control of chirality and self-assembly of double-stranded helicates with light

    Science.gov (United States)

    Zhao, Depeng; van Leeuwen, Thomas; Cheng, Jinling; Feringa, Ben L.

    2016-11-01

    Helicity switching in biological and artificial systems is a fundamental process that allows for the dynamic control of structures and their functions. In contrast to chemical approaches to responsive behaviour in helicates, the use of light as an external stimulus offers unique opportunities to invert the chirality of helical structures in a non-invasive manner with high spatiotemporal precision. Here, we report that unidirectional rotary motors with connecting oligobipyridyl ligands, which can dynamically change their chirality upon irradiation, assemble into metal helicates that are responsive to light. The motor function controls the self-assembly process as well as the helical chirality, allowing switching between oligomers and double-stranded helicates with distinct handedness. The unidirectionality of the light-induced motion governs the sequence of programmable steps, enabling the highly regulated self-assembly of fully responsive helical structures. This discovery paves the way for the future development of new chirality-dependent photoresponsive systems including smart materials, enantioselective catalysts and light-driven molecular machines.

  14. Revisiting fermion helicity flip in Podolsky's Electromagnetism

    CERN Document Server

    Sales, Jorge Henrique; Thibes, Ronaldo

    2016-01-01

    The spin projection of a massive particle onto its direction of motion is called helicity (or "handedness"). It can therefore be positive or negative. When a particle's helicity changes from positive to negative (or vice-versa) due to its interaction with other particles or fields, we say there is a helicity flip. In this work we show that such helicity flip can be seen for an electron of $20 MeV$ of energy interacting with a charged scalar meson through the exchange of a virtual photon. This photon {\\it does not} necessarily need to be Podolsky's proposed photon; in fact, it is independent of it.

  15. Higher helicity invariants and solar dynamo

    Science.gov (United States)

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

    2017-01-01

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

  16. Helicity and internal twist within the vortex filament model

    CERN Document Server

    Hietala, N; Salman, H

    2016-01-01

    For ideal fluids, besides energy, kinetic helicity is the only other known quadratic invariant of the Euler equations besides energy and is understood to be inherently linked to the degree of knotting of vortex lines within the fluid. For vortices arising in superfluid $^4$He, the vorticity is concentrated along vortex filaments. In this setting, helicity would be expected to acquire its simplest form. However, the lack of a core structure for vortex filaments appears to result in a helicity that does not retain its key attribute as a quadratic invariant. By defining the spanwise vector to coincide with the Seifert framing, we are able to introduce twist and henceforth recover the key properties of helicity. Through a detailed analysis of the velocity field induced in the vicinity of the superfluid vortices we are able to express our choice of the spanwise vector in terms of the tangential component of velocity along the filament. Since adding an arbitrary tangential velocity does not alter the configuration ...

  17. 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.

  18. Chiral Charge Erasure via Thermal Fluctuations of Magnetic Helicity

    CERN Document Server

    Long, Andrew J

    2016-01-01

    We consider a relativistic plasma of fermions coupled to an Abelian gauge field and carrying a chiral charge asymmetry, which might arise in the early Universe through baryogenesis. It is known that on large length scales, $\\lambda \\gtrsim 1/(\\alpha \\mu_5)$, the chiral anomaly opens an instability toward the erasure of chiral charge and growth of magnetic helicity. Here the chemical potential $\\mu_{5}$ parametrizes the chiral asymmetry and $\\alpha$ is the fine-structure constant. We study the process of chiral charge erasure through the thermal fluctuations of magnetic helicity and contrast with the well-studied phenomenon of Chern-Simons number diffusion. Through the fluctuation-dissipation theorem we estimate the amplitude and time scale of helicity fluctuations on the length scale $\\lambda$, finding $\\delta \\mathcal{H} \\sim \\lambda T$ and $\\tau \\sim \\alpha \\lambda^3 T^2$ for a relativistic plasma at temperature $T$. We argue that the presence of a chiral asymmetry allows the helicity to grow diffusively fo...

  19. Impact of vibrational entropy on the stability of unsolvated peptide helices with increasing length

    CERN Document Server

    Rossi, Mariana; Scheffler, Matthias

    2012-01-01

    Helices are a key folding motif in protein structure. The question which factors determine helix stability for a given polypeptide or protein is an ongoing challenge. Here we use van der Waals corrected density-functional theory to address a part of this question in a bottom-up approach. We show how intrinsic helical structure is stabilized with length and temperature for a series of experimentally well studied unsolvated alanine based polypeptides, Ac-Alan-LysH+. By exploring extensively the conformational space of these molecules, we find that helices emerge as the preferred structure in the length range n=4-8 not just due to enthalpic factors (hydrogen bonds and their cooperativity, van der Waals dispersion interactions, electrostatics), but importantly also by a vibrational entropic stabilization over competing conformers at room temperature. The stabilization is shown to be due to softer low-frequency vibrational modes in helical conformers than in more compact ones. This observation is corroborated by i...

  20. Helical coil thermal hydraulic model

    Science.gov (United States)

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

    2014-11-01

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

  1. The interplay between helicity and rotation in turbulence: implications for scaling laws and small-scale dynamics

    CERN Document Server

    Pouquet, A

    2009-01-01

    Invariance properties of physical systems govern their behavior: energy conservation in turbulence drives a wide distribution of energy among modes, observed in geophysical or astrophysical flows. In ideal hydrodynamics, the role of helicity conservation (correlation between velocity and its curl, measuring departures from mirror symmetry) remains unclear since it does not alter the energy spectrum. However, with solid body rotation, significant differences emerge between helical and non-helical flows. We first outline several results, like the energy and helicity spectral distribution and the breaking of strict universality for the individual spectra. Using massive numerical simulations, we then show that small-scale structures and their intermittency properties differ according to whether helicity is present or not, in particular with respect to the emergence of Beltrami-core vortices (BCV) that are laminar helical vertical updrafts. These results point to the discovery of a small parameter besides the Ross...

  2. Fabrication of Ni-decorated helical ribbon composite microstructure from self-assembled lipid tubule by electroless metallization

    Institute of Scientific and Technical Information of China (English)

    FU Yubin; ZHANG Lide; ZHENG Jiyong

    2006-01-01

    Lipid molecules can self-assemble into a tubular structure, which is formed by tightly wound helical ribbons. Lipid tubules are utilized as a precursor to fabricate a novel Ni-decorated helical ribbon composite microstructure in a high yield by electroless deposition. The microstructure carries Ni nanoparticles on the flat face and wires at the edge of helical ribbon, in which the average size of nanoparticles is about 40-60 nm, and the wires are of a layered structure strongly correlated with a multi-bilayer structure in the lipid membrane. Compared with the tubular precursor, the Ni-decorated composite microstructure becomes short and irregular shapes due to the breakage in the deposition, and its formation is largely bound up with the tubular helical structure and the different catalytic process. Finally, the helical composite microstructure would have a potential application in the development of electric active materials.

  3. Magnetic Helicity and the Solar Dynamo

    Science.gov (United States)

    Canfield, Richard C.

    1997-01-01

    The objective of this investigation is to open a new window into the solar dynamo, convection, and magnetic reconnection through measurement of the helicity density of magnetic fields in the photosphere and tracing of large-scale patterns of magnetic helicity in the corona.

  4. The AGS synchrotron with four helical magnets

    Energy Technology Data Exchange (ETDEWEB)

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

    2012-05-20

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

  5. Helical Magnetic Fields in AGN Jets

    Indian Academy of Sciences (India)

    Y. J. Chen; G.-Y. Zhao; Z.-Q. Shen

    2014-09-01

    We establish a simple model to describe the helical magnetic fields in AGN jets projected on the sky plane and the line-of-sight. This kind of profile has been detected in the polarimetric VLBI observation of many blazar objects, suggesting the existence of helical magnetic fields in these sources.

  6. Silica biomineralization via the self-assembly of helical biomolecules.

    Science.gov (United States)

    Liu, Ben; Cao, Yuanyuan; Huang, Zhehao; Duan, Yingying; Che, Shunai

    2015-01-21

    The biomimetic synthesis of relevant silica materials using biological macromolecules as templates via silica biomineralization processes attract rapidly rising attention toward natural and artificial materials. Biomimetic synthesis studies are useful for improving the understanding of the formation mechanism of the hierarchical structures found in living organisms (such as diatoms and sponges) and for promoting significant developments in the biotechnology, nanotechnology and materials chemistry fields. Chirality is a ubiquitous phenomenon in nature and is an inherent feature of biomolecular components in organisms. Helical biomolecules, one of the most important types of chiral macromolecules, can self-assemble into multiple liquid-crystal structures and be used as biotemplates for silica biomineralization, which renders them particularly useful for fabricating complex silica materials under ambient conditions. Over the past two decades, many new silica materials with hierarchical structures and complex morphologies have been created using helical biomolecules. In this review, the developments in this field are described and the recent progress in silica biomineralization templating using several classes of helical biomolecules, including DNA, polypeptides, cellulose and rod-like viruses is summarized. Particular focus is placed on the formation mechanism of biomolecule-silica materials (BSMs) with hierarchical structures. Finally, current research challenges and future developments are discussed in the conclusion.

  7. Passive base isolation with superelastic nitinol SMA helical springs

    Science.gov (United States)

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

    2014-06-01

    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.

  8. Helical chirality induction of expanded porphyrin analogues

    Indian Academy of Sciences (India)

    Jun-Ichiro Setsune

    2012-11-01

    Expanded porphyrin analogues with unique figure-eight conformation were prepared by way of useful pyrrole intermediates such as bis(azafulvene)s and 2-borylpyrrole. Supramolecular chirogenesis of cyclooctapyrrole O1 with 32-cycloconjugation was successfully applied to determine absolute configuration of chiral carboxylic acids. Dinuclear CuII complex of cyclooctapyrrole O2 with interrupted -conjugation was resolved by HPLC into enantiomers and their helical handedness was determined by theoretical simulation of their CD spectral pattern. Enantioselective induction of helicity in the metal helicate formation in the presence of a chiral promoter was demonstrated by using ()-(+)-1-(1-phenyl)ethylamine that favoured , helicity. Dinuclear CoII complexes of cyclotetrapyrroletetrapyridine O3 were found to be substitution labile and pick up amino acid anions in water. Those amino acid complexes of O3Co2 were rendered to adopt a particular unidirectional helical conformation preferentially depending on the ligated amino acid anion.

  9. Collagenolytic Matrix Metalloproteinase Activities toward Peptomeric Triple-Helical Substrates.

    Science.gov (United States)

    Stawikowski, Maciej J; Stawikowska, Roma; Fields, Gregg B

    2015-05-19

    Although collagenolytic matrix metalloproteinases (MMPs) possess common domain organizations, there are subtle differences in their processing of collagenous triple-helical substrates. In this study, we have incorporated peptoid residues into collagen model triple-helical peptides and examined MMP activities toward these peptomeric chimeras. Several different peptoid residues were incorporated into triple-helical substrates at subsites P3, P1, P1', and P10' individually or in combination, and the effects of the peptoid residues were evaluated on the activities of full-length MMP-1, MMP-8, MMP-13, and MMP-14/MT1-MMP. Most peptomers showed little discrimination between MMPs. However, a peptomer containing N-methyl Gly (sarcosine) in the P1' subsite and N-isobutyl Gly (NLeu) in the P10' subsite was hydrolyzed efficiently only by MMP-13 [nomenclature relative to the α1(I)772-786 sequence]. Cleavage site analysis showed hydrolysis at the Gly-Gln bond, indicating a shifted binding of the triple helix compared to the parent sequence. Favorable hydrolysis by MMP-13 was not due to sequence specificity or instability of the substrate triple helix but rather was based on the specific interactions of the P7' peptoid residue with the MMP-13 hemopexin-like domain. A fluorescence resonance energy transfer triple-helical peptomer was constructed and found to be readily processed by MMP-13, not cleaved by MMP-1 and MMP-8, and weakly hydrolyzed by MT1-MMP. The influence of the triple-helical structure containing peptoid residues on the interaction between MMP subsites and individual substrate residues may provide additional information about the mechanism of collagenolysis, the understanding of collagen specificity, and the design of selective MMP probes.

  10. All Next-to-Maximally-Helicity-Violating One-Loop Gluon Amplitudes in N=4 Super-Yang-Mills Theory

    CERN Document Server

    Bern, Z; Kosower, D A; Bern, Zvi; Dixon, Lance J.; Kosower, David A.

    2004-01-01

    We compute the next-to-MHV one-loop n-gluon amplitudes in N=4 super-Yang-Mills theory. These amplitudes contain three negative-helicity gluons and an arbitrary number of positive-helicity gluons, and are the first infinite series of amplitudes beyond the simplest, MHV, amplitudes. We also discuss some aspects of their twistor-space structure.

  11. Dielectric effect on the rf characteristics of a helical groove travelling wave tube

    Institute of Scientific and Technical Information of China (English)

    Wei Yan-Yu(魏彦玉); Wang Wen-Xiang(王文祥); Sun Jia-Hong(孙嘉鸿); Liu Sheng-Gang(刘盛纲); Baofu Jia; Gun-Sik Park

    2002-01-01

    A new type of partial-dielectric-loaded helical groove slow-wave structure (SWS) for millimetre wave travellingwave tube (TWT) is presented in this paper. The radio-frequency characteristics including the dispersion properties,the longitudinal electric field distribution and the beam-wave coupling impedance of this structure are analysed. Theresults show that the dispersion of the helical groove circuit is weakened, the phase velocity is reduced and the positionof the maximum Ez is moved from the mouth to the inside of the groove after partially filling the dielectric materialsin the helical groove SWS. Therefore, the dielectric-loaded helical groove SWS is suitable for a multi-beam TWT withbroad band and high gain.

  12. Dielectric effect on the rf characteristics of a helical groove travelling wave tube

    Science.gov (United States)

    Wei, Yan-Yu; Wang, Wen-Xiang; Sun, Jia-Hong; Liu, Sheng-Gang; Baofu, Jia; Gun-Sik, Park

    2002-03-01

    A new type of partial-dielectric-loaded helical groove slow-wave structure (SWS) for millimetre wave travelling wave tube (TWT) is presented in this paper. The radio-frequency characteristics including the dispersion properties, the longitudinal electric field distribution and the beam-wave coupling impedance of this structure are analysed. The results show that the dispersion of the helical groove circuit is weakened, the phase velocity is reduced and the position of the maximum Ez is moved from the mouth to the inside of the groove after partially filling the dielectric materials in the helical groove SWS. Therefore, the dielectric-loaded helical groove SWS is suitable for a multi-beam TWT with broad band and high gain.

  13. Stabilization of collagen-model, triple-helical peptides for in vitro and in vivo applications.

    Science.gov (United States)

    Bhowmick, Manishabrata; Fields, Gregg B

    2013-01-01

    The triple-helical structure of collagen has been accurately reproduced in numerous chemical and recombinant model systems. Triple-helical peptides and proteins have found application for dissecting collagen-stabilizing forces, isolating receptor- and protein-binding sites in collagen, mechanistic examination of collagenolytic proteases, and development of novel biomaterials. Introduction of native-like sequences into triple-helical constructs can reduce the thermal stability of the triple-helix to below that of the physiological environment. In turn, incorporation of nonnative amino acids and/or templates can enhance triple-helix stability. We presently describe approaches by which triple-helical structure can be modulated for use under physiological or near-physiological conditions.

  14. Chiral effects on helicity studied via the energy landscape of short (D, L)-alanine peptides.

    Science.gov (United States)

    Neelamraju, Sridhar; Oakley, Mark T; Johnston, Roy L

    2015-10-28

    The homochirality of natural amino acids facilitates the formation of regular secondary structures such as α-helices and β-sheets. Here, we study the relationship between chirality and backbone structure for the example of hexa-alanine. The most stable stereoisomers are identified through global optimisation. Further, the energy landscape, a database of connected low-energy local minima and transition points, is constructed for various neutral and zwitterionic stereoisomers of hexa-alanine. Three order parameters for partial helicity are applied and metric disconnectivity graphs are presented with partial helicity as a metric. We also apply the Zimm-Bragg model to derive average partial helicities for Ace-(L-Ala)6-NHMe, Ace-(D-Ala-L-Ala)3-NHMe, and Ace-(L-Ala)3-(D-Ala)3-NHMe from the database of local minima and compare with previous studies.

  15. Inherent helicity in an extended tris-bipyridyl molecular cage

    Energy Technology Data Exchange (ETDEWEB)

    Perkins, D.; Lindoy, L.; Meehan, G.; Turner, P. (University of Sydney)

    2010-11-16

    A new molecular cage incorporating three bipyridyl units has been synthesised by a conventional multi-step procedure as well as, much more efficiently, by a Ni(II) template procedure; an X-ray structure of the nickel complex shows that it adopts an exo configuration of each of the bridgehead nitrogen lone pairs, the central metal ion acts to promote a triple helical twist that extends {approx}22 {angstrom} along the axial length of the molecule.

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

    Indian Academy of Sciences (India)

    S N Kaul

    2003-03-01

    Controversial issues concerning the nature of magnetic ordering in gadolinium are briefly reviewed. The recent experimental results are shown to resolve most of such issues in that 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 order for temperatures between the spin-reorientation temperature and the Curie point.

  17. Weak Boson Production Amplitude Zeros; Equalities of the Helicity Amplitudes

    CERN Document Server

    Mamedov, F

    2002-01-01

    We investigate the radiation amplitude zeros exhibited by many Standard Model amplitudes for triple weak gauge boson production processes. We show that $WZ\\gamma$ production amplitudes have especially rich structure in terms of zeros, these amplitudes have zeros originating from several different sources. It is also shown that TYPE I current null zone is the special case of the equality of the specific helicity amplitudes.

  18. EVOLUTION OF MAGNETIC HELICITY AND ENERGY SPECTRA OF SOLAR ACTIVE REGIONS

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Hongqi [Key Laboratory of Solar Activity, National Astronomical Observatories, Chinese Academy of Sciences, Beijing 100012 (China); Brandenburg, Axel [Nordita, KTH Royal Institute of Technology and Stockholm University, Roslagstullsbacken 23, SE-10691 Stockholm (Sweden); Sokoloff, D. D., E-mail: hzhang@bao.ac.cn [Department of Physics, Moscow University, 119992 Moscow (Russian Federation)

    2016-03-10

    We adopt an isotropic representation of the Fourier-transformed two-point correlation tensor of the magnetic field to estimate the magnetic energy and helicity spectra as well as current helicity spectra of two individual active regions (NOAA 11158 and NOAA 11515) and the change of the spectral indices during their development as well as during the solar cycle. The departure of the spectral indices of magnetic energy and current helicity from 5/3 are analyzed, and it is found that it is lower than the spectral index of the magnetic energy spectrum. Furthermore, the fractional magnetic helicity tends to increase when the scale of the energy-carrying magnetic structures increases. The magnetic helicity of NOAA 11515 violates the expected hemispheric sign rule, which is interpreted as an effect of enhanced field strengths at scales larger than 30–60 Mm with opposite signs of helicity. This is consistent with the general cycle dependence, which shows that around the solar maximum the magnetic energy and helicity spectra are steeper, emphasizing the large-scale field.

  19. α-Helical to β-Helical Conformation Change in the C-Terminal of the Mammalian Prion Protein

    Science.gov (United States)

    Singh, Jesse; Whitford, Paul; Hayre, Natha; Cox, Daniel; Onuchic, José.

    2011-03-01

    We employ all-atom structure-based models with mixed basis contact maps to explore whether there are any significant geometric or energetic constraints limiting conjectured conformational transitions between the alpha-helical (α H) and the left handed beta helical (LHBH) conformations for the C-terminal (residues 166-226) of the mammalian prion protein. The LHBH structure has been proposed to describe infectious oligomers and one class of in vitro grown fibrils, as well as possibly self- templating the conversion of normal cellular prion protein to the infectious form. Our results confirm that the kinetics of the conformation change are not strongely limited by large scale geometry modification and there exists an overall preference for the LHBH conformation.

  20. Diffraction by DNA, carbon nanotubes and other helical nanostructures

    Science.gov (United States)

    Lucas, Amand A.; Lambin, Philippe

    2005-05-01

    This review discusses the diffraction patterns of x-rays or electrons scattered by fibres of helical biological molecules and by carbon nanotubes (CNTs) from the unified point of view of the Fourier-Bessel transform of an atomic helix. This paper is intended for scientists who are not professional crystallographers. X-ray fibre diffraction patterns of Pauling's protein α-helix and of Crick and Pauling's protein coiled-coil are revisited. This is followed by a non-technical comparison between the historic x-ray diffraction patterns of the A and B conformations of DNA, which were crucial for the discovery of the double helix. The qualitative analysis of the diffraction images is supported by novel optical simulation experiments designed to pinpoint the gross structural informational content of the patterns. The spectacular helical structure of the tobacco mosaic virus determined by Rosalind Franklin and co-workers will then be described as an early example of the great power of x-ray crystallography in determining the structure of a large biomolecular edifice. After these mostly historical and didactic case studies, this paper will consider electron diffraction and transmission electron microscopy of CNTs of great current interest, focusing particularly on recent data obtained for single-wall, double-wall and scrolled nanotubes. Several points of convergence between the interpretations of the diffraction patterns of biological helices and CNTs will be emphasized.

  1. Diffraction by DNA, carbon nanotubes and other helical nanostructures

    Energy Technology Data Exchange (ETDEWEB)

    Lucas, Amand A; Lambin, Philippe [Physics Department, FUNDP, 61 Rue de Bruxelles, B5000 Namur (Belgium)

    2005-05-01

    This review discusses the diffraction patterns of x-rays or electrons scattered by fibres of helical biological molecules and by carbon nanotubes (CNTs) from the unified point of view of the Fourier-Bessel transform of an atomic helix. This paper is intended for scientists who are not professional crystallographers. X-ray fibre diffraction patterns of Pauling's protein {alpha}-helix and of Crick and Pauling's protein coiled-coil are revisited. This is followed by a non-technical comparison between the historic x-ray diffraction patterns of the A and B conformations of DNA, which were crucial for the discovery of the double helix. The qualitative analysis of the diffraction images is supported by novel optical simulation experiments designed to pinpoint the gross structural informational content of the patterns. The spectacular helical structure of the tobacco mosaic virus determined by Rosalind Franklin and co-workers will then be described as an early example of the great power of x-ray crystallography in determining the structure of a large biomolecular edifice. After these mostly historical and didactic case studies, this paper will consider electron diffraction and transmission electron microscopy of CNTs of great current interest, focusing particularly on recent data obtained for single-wall, double-wall and scrolled nanotubes. Several points of convergence between the interpretations of the diffraction patterns of biological helices and CNTs will be emphasized.

  2. The emerging role of triple helices in RNA biology.

    Science.gov (United States)

    Conrad, Nicholas K

    2014-01-01

    The ability of RNA to form sophisticated secondary and tertiary structures enables it to perform a wide variety of cellular functions. One tertiary structure, the RNA triple helix, was first observed in vitro over 50 years ago, but biological activities for triple helices are only beginning to be appreciated. The recent determination of several RNA structures has implicated triple helices in distinct biological functions. For example, the SAM-II riboswitch forms a triple helix that creates a highly specific binding pocket for S-adenosylmethionine. In addition, a triple helix in the conserved pseudoknot domain of the telomerase-associated RNA TER is essential for telomerase activity. A viral RNA cis-acting RNA element called the ENE contributes to the nuclear stability of a viral noncoding RNA by forming a triple helix with the poly(A) tail. Finally, a cellular noncoding RNA, MALAT1, includes a triple helix at its 3'-end that contributes to RNA stability, but surprisingly also supports translation. These examples highlight the diverse roles that RNA triple helices play in biology. Moreover, the dissection of triple helix mechanisms has the potential to uncover fundamental pathways in cell biology.

  3. Stabilized helical peptides: a strategy to target protein-protein interactions.

    Science.gov (United States)

    Klein, Mark A

    2014-08-14

    Protein-protein interactions are critical for cell proliferation, differentiation, and function. Peptides hold great promise for clinical applications focused on targeting protein-protein interactions. Advantages of peptides include a large chemical space and potential diversity of sequences and structures. However, peptides do present well-known challenges for drug development. Progress has been made in the development of stabilizing alpha helices for potential therapeutic applications. Advantages and disadvantages of different methods of helical peptide stabilization are discussed.

  4. Realizing topological stability of magnetic helices in exchange-coupled multilayers for all-spin-based system

    Science.gov (United States)

    Fust, Sergej; Mukherjee, Saumya; Paul, Neelima; Stahn, Jochen; Kreuzpaintner, Wolfgang; Böni, Peter; Paul, Amitesh

    2016-09-01

    Topologically stabilized spin configurations like helices in the form of planar domain walls (DWs) or vortex-like structures with magnetic functionalities are more often a theoretical prediction rather than experimental realization. In this paper we report on the exchange coupling and helical phase characteristics within Dy-Fe multilayers. The magnetic hysteresis loops with temperature show an exchange bias field of around 1.0 kOe at 10 K. Polarized neutron reflectivity reveal (i) ferrimagnetic alignment of the layers at low fields forming twisted magnetic helices and a more complicated but stable continuous helical arrangement at higher fields (ii) direct evidence of helices in the form of planar 2π-DWs within both layers of Fe and Dy. The helices within the Fe layers are topologically stabilized by the reasonably strong induced in-plane magnetocrystalline anisotropy of Dy and the exchange coupling at the Fe-Dy interfaces. The helices in Dy are plausibly reminiscent of the helical ordering at higher temperatures induced by the field history and interfacial strain. Stability of the helical order even at large fields have resulted in an effective modulation of the periodicity of the spin-density like waves and subsequent increase in storage energy. This opens broad perspectives for future scientific and technological applications in increasing the energy density for systems in the field of all-spin-based engineering which has the potential for energy-storing elements on nanometer length scales.

  5. Magnetic Helicity in a Cyclic Convective Dynamo

    Science.gov (United States)

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

    2016-05-01

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

  6. Investigation of backfire monofilar helical antenna

    DEFF Research Database (Denmark)

    Smith, Thomas Gunst; Larsen, Niels Vesterdal; Gothelf, Ulrich Vesterager

    2011-01-01

    This paper presents a numerical investigation of the electromagnetic properties of the backfire monofilar helical antenna. The current distribution along the helical conductor, the input impedance, and the front-to-back ratio are calculated and analyzed for the backfire operation of the antenna....... A parametric study of the helical geometry and the resulting antenna characteristics will be described and discussed. The currents and fields are calculated using the simulation software AWAS based on the Method of Moments with a wire representation of the ground plane....

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

    Science.gov (United States)

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

    2013-05-21

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

  8. Nucleon Helicity and Transversity Parton Distributions from Lattice QCD

    CERN Document Server

    Chen, Jiunn-Wei; Ji, Xiangdong; Lin, Huey-Wen; Zhang, Jian-Hui

    2016-01-01

    We present the first lattice-QCD calculation of the isovector polarized parton distribution functions (both helicity and transversity) using the large-momentum effective field theory (LaMET) approach for direct Bjorken-$x$ dependence. We first review the detailed steps of the procedure in the unpolarized case, then generalize to the helicity and transversity cases. We also derive a new mass-correction formulation for all three cases. We then compare the effects of each finite-momentum correction using lattice data calculated at $M_\\pi\\approx 310$ MeV. Finally, we discuss the implications of these results for the poorly known antiquark structure and predict the sea-flavor asymmetry in the transversely polarized nucleon.

  9. 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.

  10. The inverse cascade of magnetic helicity in magnetohydrodynamic turbulence

    CERN Document Server

    Müller, Wolf-Christian; Busse, Angela

    2012-01-01

    The nonlinear dynamics of magnetic helicity, $H^M$, which is responsible for large-scale magnetic structure formation in electrically conducting turbulent media is investigated in forced and decaying three-dimensional magnetohydrodynamic turbulence. This is done with the help of high resolution direct numerical simulations and statistical closure theory. The numerically observed spectral scaling of $H^M$ is at variance with earlier work using a statistical closure model [Pouquet et al., J. Fluid Mech. \\textbf{77} 321 (1976)]. By revisiting this theory a universal dynamical balance relation is found that includes effects of kinetic helicity, as well as kinetic and magnetic energy on the inverse cascade of $H^M$ and explains the above-mentioned discrepancy. Considering the result in the context of mean-field dynamo theory suggests a nonlinear modification of the $\\alpha$-dynamo effect important in the context of magnetic field excitation in turbulent plasmas.

  11. Helicity selection rules and noninterference for BSM amplitudes

    Science.gov (United States)

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

    2017-03-01

    Precision studies of scattering processes at colliders provide powerful indirect constraints on new physics. We study the helicity structure of scattering amplitudes in the standard model (SM) and in the context of an effective Lagrangian description of beyond-the-SM (BSM) dynamics. Our analysis reveals a novel set of helicity selection rules according to which, in the majority of 2 →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. Inverse cascade of magnetic helicity in magnetohydrodynamic turbulence.

    Science.gov (United States)

    Müller, Wolf-Christian; Malapaka, Shiva Kumar; Busse, Angela

    2012-01-01

    The nonlinear dynamics of magnetic helicity HM, which is responsible for large-scale magnetic structure formation in electrically conducting turbulent media, is investigated in forced and decaying three-dimensional magnetohydrodynamic turbulence. This is done with the help of high-resolution direct numerical simulations and statistical closure theory. The numerically observed spectral scaling of HM is at variance with earlier work using a statistical closure model [Pouquet et al., J. Fluid Mech. 77, 321 (1976)]. By revisiting this theory, a universal dynamical balance relation is found that includes the effects of kinetic helicity as well as kinetic and magnetic energies on the inverse cascade of HM and explains the above-mentioned discrepancy. Consideration of the result in the context of mean-field dynamo theory suggests a nonlinear modification of the α-dynamo effect, which is important in the context of magnetic-field excitation in turbulent plasmas.

  13. On helical behavior of turbulence in the ship wake

    Institute of Scientific and Technical Information of China (English)

    GOLBRAIKH Ephim; EIDELMAN Alexander; SOLOVIEV Alex

    2013-01-01

    Turbulent ship wake conservation at a long distance is among unsolved problems at present.It is well known that far wakes have a vortical structure and slowly expand with distance.As was obtained by Dubrovin et al.,slow expansion of the wake may be related to the distribution of turbulent viscosity in it.In our work we study the effect of helicity in the wake on the behavior of turbulent viscosity.Taking into account the helical nature of the wake,we can clarify the difference between turbulence inside and outside the wake on the one hand and slowing down of its expansion with time on the other hand.

  14. 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/.

  15. Microbunch preserving in-line system for an APPLE II helical radiator at the LCLS baseline

    CERN Document Server

    Geloni, Gianluca; Saldin, Evgeni

    2011-01-01

    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 sl...

  16. Particle-in-cell Simulations of Global Relativistic Jets with Helical Magnetic Fields

    CERN Document Server

    Duţan, Ioana; Mizuno, Yosuke; Niemiec, Jacek; Kobzar, Oleh; Pohl, Martin; Gómez, Jose L; Pe'er, Asaf; Frederiksen, Jacob T; Nordlund, Åke; Meli, Athina; Sol, Helene; Hardee, Philip E; Hartmann, Dieter H

    2016-01-01

    We study the interaction of relativistic jets with their environment, using 3-dimensional relativistic particle-in-cell simulations for two cases of jet composition: (i) electron-proton ($e^{-}-p^{+}$) and (ii) electron-positron ($e^{\\pm}$) plasmas containing helical magnetic fields. 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 and the Mushroom instability. We have found that these kinetic instabilities are suppressed and new types of instabilities can grow. For the $e^{-}-p^{+}$ jet, a recollimation-like instability occurs and jet electrons are strongly perturbed, whereas for the $e^{\\pm}$ jet, a recollimation-like instability occurs at early times followed by kinetic instability and the general structure is similar to a simulation without a helical magnetic field. We plan to perform further simulations using much larger sys...

  17. Role of van der Waals interactions for the intrinsic stability of polyalanine helices

    Science.gov (United States)

    Tkatchenko, Alexandre; Blum, Volker; Ireta, Joel; Scheffler, Matthias

    2009-03-01

    The helical motif is an ubiquitous conformation adopted by aminoacid residues in a protein structure and helix formation is the simplest example of the protein folding process. How stable is the folded peptide helix in comparison to a random coil structure? What are the interactions responsible for stabilizing the helical conformation? Answering these questions has thus a direct implication for understanding protein folding. In this work we use density functional theory (DFT) augmented with a non-empirical correction for van der Waals (vdW) forces to study the stability of alanine polypeptide helices in vacuo. We find a large stabilization of the native helical forms when vdW correction is used. It amounts to 121%, 157% and 83% on top of the Perdew-Burke-Ernzerhof (PBE) functional in the case of infinite α, π and 310 helices, respectively. Thus, the experimentally observed α helix is significantly stabilized by vdW forces both over the fully extended and the 310 conformations. Our findings also suggest an explanation to the remarkable stability of gas-phase alanine helices up to high temperatures [M. Kohtani et al. JACS 126, 7420 (2004)].

  18. Shielding requirements in helical tomotherapy

    Science.gov (United States)

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

    2007-08-01

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

  19. Motion of a helical vortex

    CERN Document Server

    Fuentes, Oscar Velasco

    2015-01-01

    We study the motion of a single helical vortex in an unbounded, inviscid, incompressible fluid. The vortex is an infinite tube whose centerline is a helix and whose cross section is a circle of small radius (compared to the radius of curvature) where the vorticity is uniform and parallel to the centerline. Ever since Joukowsky (1912) deduced that this vortex translates and rotates steadily without change of form, numerous attempts have been made to compute these self-induced velocities. Here we use Hardin's (1982) solution for the velocity field to find new expressions for the vortex's linear and angular velocities. Our results, verified by numerically computing the Helmholtz integral and the Rosenhead-Moore approximation to the Biot-Savart law, are more accurate than previous results over the whole range of values of the vortex pitch and cross-section. We then use the new formulas to study the advection of passive particles near the vortex; we find that the vortex's motion and capacity to transport fluid dep...

  20. Helical Two-Revolutional Cyclical Surface

    Directory of Open Access Journals (Sweden)

    Tatiana Olejníková

    2009-12-01

    Full Text Available Paper presents a family of helical two-revolutional cyclical surfaces, which arecreated by movement of the circle alongside the helical cycloidal curve, where circle islocated in the curve normal plane and its centre is on this curve. Helical cycloidal curvecan be created by simultaneous revolution of a point about two different axes 3o, 2o and byscrewing about axis 1o in the space. Form of the helical cycloidal curve and also of thehelical two-revolutional cyclical surface is dependent on the relative position of the threeaxes of revolutions, on multiples of angular velocities and orientations of separaterevolutions. Analytic representation, classification of surfaces and some of their geometricproperties are derived.

  1. Helicity at Photospheric and Chromospheric Heights

    CERN Document Server

    Tiwari, S K; Sankarasubramanian, K

    2009-01-01

    In the solar atmosphere the twist parameter $\\alpha$ has the same sign as magnetic helicity. It has been observed using photospheric vector magnetograms that negative/positive helicity is dominant in the northern/southern hemisphere of the Sun. Chromospheric features show dextral/sinistral dominance in the northern/southern hemisphere and sigmoids observed in X-rays also have a dominant sense of reverse-S/forward-S in the northern/southern hemisphere. It is of interest whether individual features have one-to-one correspondence in terms of helicity at different atmospheric heights. We use UBF \\Halpha images from the Dunn Solar Telescope (DST) and other \\Halpha data from Udaipur Solar Observatory and Big Bear Solar Observatory. Near-simultaneous vector magnetograms from the DST are used to establish one-to-one correspondence of helicity at photospheric and chromospheric heights. We plan to extend this investigation with more data including coronal intensities.

  2. 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.

  3. Magnetic Helicity Conservation and Astrophysical Dynamos

    CERN Document Server

    Vishniac, E T; Vishniac, Ethan T.; Cho, Jungyeon

    2000-01-01

    We construct a magnetic helicity conserving dynamo theory which incorporates a calculated magnetic helicity current. In this model the fluid helicity plays a small role in large scale magnetic field generation. Instead, the dynamo process is dominated by a new quantity, derived from asymmetries in the second derivative of the velocity correlation function, closely related to the `twist and fold' dynamo model. The turbulent damping term is, as expected, almost unchanged. Numerical simulations with a spatially constant fluid helicity and vanishing resistivity are not expected to generate large scale fields in equipartition with the turbulent energy density. In fact, there seems to be little prospect for driving a fast dynamo in a closed box containing homogeneous turbulence. On the other hand, there is an efficient analog to the $\\alpha-\\Omega$ dynamo. Systems whose turbulence is driven by some anisotropic local instability in shearing flow, like real stars and accretion disks, and some computer simulations, ma...

  4. STUDY ON A NOVEL ELLIPSOIDAL HELICAL ANTENNA

    Institute of Scientific and Technical Information of China (English)

    Xia Dongyu; Zhang Hou; Wang Chong; Zhang Qianyue

    2007-01-01

    A novel ellipsoidal helical antenna is proposed and studied in this letter.As a special instance,the hemispherical helical antennas are analyzed firstly,which indicates that the characteristics of a two-arm unit are better than that of a single-arm unit.Based on this,the ellipsoidal helical antenna,formed by changing the axial direction's dimension of the two-arm hemispherical helical antenna,is analyzed by the moment method with curved basic and testing function.The effects to VSWR (Voltage Standing Wave Ratio),gain,polarization and patterns by the axial direction's dimensions are investigated.The study results provide dependable gist to the choice of antenna format according to the practical requirements.

  5. Kinematic dynamo induced by helical waves

    OpenAIRE

    Wei, Xing

    2014-01-01

    We investigate numerically the kinematic dynamo induced by the superposition of two helical waves in a periodic box as a simplified model to understand the dynamo action in astronomical bodies. The effects of magnetic Reynolds number, wavenumber and wave frequency on the dynamo action are studied. It is found that this helical-wave dynamo is a slow dynamo. There exists an optimal wavenumber for the dynamo growth rate. A lower wave frequency facilitates the dynamo action and the oscillations o...

  6. Cosmological Magnetic Fields from Primordial Helical Seeds

    CERN Document Server

    Sigl, G

    2002-01-01

    Most early Universe scenarios predict negligible magnetic fields on cosmological scales if they are unprocessed during subsequent expansion of the Universe. We present a new numerical treatment of the evolution of primordial fields and apply it to weakly helical seeds as they occur in certain early Universe scenarios. We find that initial helicities not much larger than the baryon to photon number can lead to fields of about 10^{-13} Gauss with coherence scales slightly below a kilo-parsec today.

  7. Duality and helicity: A symplectic viewpoint

    Science.gov (United States)

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

    2016-10-01

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

  8. 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.

  9. The AGS with four helical magnets

    Energy Technology Data Exchange (ETDEWEB)

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

    2010-02-25

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

  10. Computational design and characterization of a monomeric helical dinuclear metalloprotein.

    Science.gov (United States)

    Calhoun, Jennifer R; Kono, Hidetoshi; Lahr, Steven; Wang, Wei; DeGrado, William F; Saven, Jeffery G

    2003-12-12

    The de novo design of di-iron proteins is an important step towards understanding the diversity of function among this complex family of metalloenzymes. Previous designs of due ferro (DF) proteins have resulted in tetrameric and dimeric four-helix bundles having crystallographically well-defined structures and active-site geometries. Here, the design and characterization of DFsc, a 114 residue monomeric four-helix bundle, is presented. The backbone was modeled using previous oligomeric structures and appropriate inter-helical turns. The identities of 26 residues were predetermined, including the primary and secondary ligands in the active site, residues involved in active site accessibility, and the gamma beta gamma beta turn between helices 2 and 3. The remaining 88 amino acid residues were determined using statistical computer aided design, which is based upon a recent statistical theory of protein sequences. Rather than sampling sequences, the theory directly provides the site-specific amino acid probabilities, which are then used to guide sequence design. The resulting sequence (DFsc) expresses well in Escherichia coli and is highly soluble. Sedimentation studies confirm that the protein is monomeric in solution. Circular dichroism spectra are consistent with the helical content of the target structure. The protein is structured in both the apo and the holo forms, with the metal-bound form exhibiting increased stability. DFsc stoichiometrically binds a variety of divalent metal ions, including Zn(II), Co(II), Fe(II), and Mn(II), with micromolar affinities. 15N HSQC NMR spectra of both the apo and Zn(II) proteins reveal excellent dispersion with evidence of a significant structural change upon metal binding. DFsc is then a realization of complete de novo design, where backbone structure, activity, and sequence are specified in the design process.

  11. Spin Helicity in Chiral Lanthanide Chains.

    Science.gov (United States)

    Mihalcea, Ionut; Perfetti, Mauro; Pineider, Francesco; Tesi, Lorenzo; Mereacre, Valeriu; Wilhelm, Fabrice; Rogalev, Andrei; Anson, Christopher E; Powell, Annie K; Sessoli, Roberta

    2016-10-17

    We report here the determination of the helical spin structure of three Ln-based chiral chains of the formula [Ln(Hnic)(nic)2(NO3)]n (Hnic = nicotinic acid; Ln = Tb, Dy, and Er) by means of cantilever torque magnetometry. While the Dy and Er derivatives are strongly axial (easy-axis and easy-plane anisotropy, respectively), the Tb derivative is characterized by a remarkable rhombicity. In agreement with these findings, alternating-current susceptibility reveals slow magnetic relaxation only in the Dy derivative. Dilution of Dy(III) ions in the diamagnetic Y-based analogue shows that the weak ferromagnetic intrachain interactions do not contribute significantly to the energy barrier for the reversal of magnetization, which is better described as a single-ion process. Single crystals of the two enantiomers of the Dy derivative have also been investigated using hard X-ray synchrotron radiation at the L-edge of the metal revealing optical activity although with negligible involvement of the 4f electrons of the Dy(III) ion.

  12. Towards online patient imaging during helical radiotherapy.

    Science.gov (United States)

    Yu, L; Poole, C M; Lancaster, C M; Sylvander, S R

    2015-03-01

    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.

  13. Alternative Methods for Field Corrections in 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)

    2015-05-01

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

  14. Evidence of Magnetic Helicity in Emerging Flux and Associated Flare

    CERN Document Server

    Chandra, R; Aulanier, G; Malherbe, J M

    2009-01-01

    The aim of this paper is to look at the magnetic helicity structure of an emerging active region and show that both emergence and flaring signatures are consistent with a same sign for magnetic helicity. We present a multi-wavelength analysis of an M1.6 flare occurring in the active region NOAA 10365 on 27 May, 2003, in which a large new bipole emerges in a decaying active region. The diverging flow pattern and the "tongue" shape of the magnetic field in the photosphere with elongated polarities are highly suggestive of the emergence of a twisted flux tube. The orientation of these tongues indicates the emergence of a flux tube with a right hand twist, i.e. positive magnetic helicity. The flare signatures in the chromosphere are ribbons observed in H-alpha by the MSDP spectrograph in the Meudon solar tower and in 1600 A by TRACE. These ribbons have a `J' shape and are shifted along the inversion line. The pattern of these ribbons suggests that the flare was triggered by magnetic reconnection at coronal height...

  15. 浅谈螺旋聚合物%A Brief Introduction on Helical Polymers

    Institute of Scientific and Technical Information of China (English)

    张立芬; 代海存; 周建; 李晗; 范群福; 周慧云; 徐晓冬

    2013-01-01

    螺旋聚合物广泛存在于自然界中,天然大分子如DNA、蛋白质和胶原等都呈现出神奇的螺旋结构,这些规整的二级结构对于生命体维持正常的生命活动至关重要.螺旋结构存在手性特征并具有旋光性,奇特的结构赋予了螺旋聚合物独特的性质和功能,使得螺旋聚合物在手性识别、不对称催化、手性响应和数据存储等领域显示了广阔的应用前景.本文简要介绍了螺旋聚合物研究概况,综述了动态和静态螺旋聚合物的研究进展,以及螺旋聚合物的功能和应用.%The high functionalities of naturally occurring macromolecules such as DNA,proteins and collagen arise from their supernatural helical structures.The precisely ordered secondary structure plays important roles in realizing biological activities and is the ubiquitous object in nature.Helical structure is chiral and optically active,and the unique structure provides sophisticated properties and functions for helical polymers,which allows the potential applications of helical polymers in chiral recognition and asymmetric catalysis together with chirality response and data storage.In this paper,the overview of helical polymers is provided,and the research progress of static and dynamic helical polymers,as well as functions and applications of helical polymers,is reviewed in detail.

  16. Chiral charge erasure via thermal fluctuations of magnetic helicity

    Energy Technology Data Exchange (ETDEWEB)

    Long, Andrew J. [Kavli Institute for Cosmological Physics, University of Chicago,Chicago, Illinois 60637 (United States); Sabancilar, Eray [Institut de Théorie des Phénoménes Physiques, Ecole Polytechnique Fédérale de Lausanne,CH-1015 Lausanne (Switzerland)

    2016-05-11

    We consider a relativistic plasma of fermions coupled to an Abelian gauge field and carrying a chiral charge asymmetry, which might arise in the early Universe through baryogenesis. It is known that on large length scales, λ≳1/(αμ{sub 5}), the chiral anomaly opens an instability toward the erasure of chiral charge and growth of magnetic helicity. Here the chemical potential μ{sub 5} parametrizes the chiral asymmetry and α is the fine-structure constant. We study the process of chiral charge erasure through the thermal fluctuations of magnetic helicity and contrast with the well-studied phenomenon of Chern-Simons number diffusion. Through the fluctuation-dissipation theorem we estimate the amplitude and time scale of helicity fluctuations on the length scale λ, finding δ H∼λT and τ∼αλ{sup 3}T{sup 2} for a relativistic plasma at temperature T. We argue that the presence of a chiral asymmetry allows the helicity to grow diffusively for a time t∼T{sup 3}/(α{sup 5}μ{sub 5}{sup 4}) until it reaches an equilibrium value H∼μ{sub 5}T{sup 2}/α, and the chiral asymmetry is partially erased. If the chiral asymmetry is small, μ{sub 5}

  17. MHD and Reconnection Activity During Local Helicity Injection

    Science.gov (United States)

    Barr, J. L.; Bongard, M. W.; Burke, M. G.; Fonck, R. J.; Reusch, J. A.; Richner, N. J.

    2016-10-01

    Scaling local helicity injection (LHI) to larger devices requires a validated, predictive model of its current drive mechanism. NIMROD simulations predict the injected helical current streams persist in the edge and periodically reconnect to form axisymmetric current rings that travel into the bulk plasma to grow Ip and poloidal flux. In simulation, these events result in discrete bursts of Alfvénic-frequency MHD activity and jumps in Ip of order ΔIp Iinj , in qualitative agreement with large n = 1 activity found in experiment. Fast imaging prior to tokamak formation supports the instability of, and apparent reconnection between, adjacent helical streams. The bursts exhibit toroidal amplitude asymmetries consistent with a kink structure singly line-tied to the injectors. Internal measurements localize this activity to the injector radial location. Pairwise correlations of poloidal Mirnov coil amplitude and phase match expectations of an edge-localized current stream carrying Iinj. Prior to tokamak formation, reconnection from both adjacent helical windings and co-injected current streams are shown to strongly heat impurity ions. After tokamak formation, strong anomalous ion heating in the plasma edge is attributed to continuous reconnection between colinear streams. The n = 1 bursts occur less frequently as Ip rises, likely caused by increased stream stability as Bv rises and qedge drops. This evidence supports the general NIMROD model of LHI, confirms the persistence and role of the edge current streams, and motivates experiments at higher Iinj and BT. Supported by US DOE Grants DE-FG02-96ER54375, DE-SC0006928.

  18. Chiral charge erasure via thermal fluctuations of magnetic helicity

    Science.gov (United States)

    Long, Andrew J.; Sabancilar, Eray

    2016-05-01

    We consider a relativistic plasma of fermions coupled to an Abelian gauge field and carrying a chiral charge asymmetry, which might arise in the early Universe through baryogenesis. It is known that on large length scales, λ gtrsim 1/(αμ5), the chiral anomaly opens an instability toward the erasure of chiral charge and growth of magnetic helicity. Here the chemical potential μ5 parametrizes the chiral asymmetry and α is the fine-structure constant. We study the process of chiral charge erasure through the thermal fluctuations of magnetic helicity and contrast with the well-studied phenomenon of Chern-Simons number diffusion. Through the fluctuation-dissipation theorem we estimate the amplitude and time scale of helicity fluctuations on the length scale λ, finding δScript H ~ λT and τ ~ αλ3T2 for a relativistic plasma at temperature T. We argue that the presence of a chiral asymmetry allows the helicity to grow diffusively for a time t ~ T3/(α5μ54) until it reaches an equilibrium value Script H ~ μ5T2/α, and the chiral asymmetry is partially erased. If the chiral asymmetry is small, μ5 < T/α, this avenue for chiral charge erasure is found to be slower than the chiral magnetic effect for which t ~ T/(α3μ52). This mechanism for chiral charge erasure can be important for the hypercharge sector of the Standard Model as well as extensions including U(1) gauge interactions, such as asymmetric dark matter models.

  19. The use of low-radius circular-cross-section helical strakes for the reduction of VIV of tapered cylinders at high Reynolds numbers

    DEFF Research Database (Denmark)

    Johansson, Jens; Christensen, Silas Sverre

    2017-01-01

    Helical strakes are known to reduce or suppress vortex-induced vibrations, VIV, of circular structures. The design of the strakes is generally recommended to be a triple-start helical strake system, with a strake height corresponding to approximately 10% of the diameter of the structure and 15% f...

  20. Evolution of magnetic helicity in the course of kinetic magnetic reconnection

    Directory of Open Access Journals (Sweden)

    T. Wiegelmann

    2001-01-01

    Full Text Available We investigate the evolution of magnetic helicity density in the course of 2D and 3D kinetic magnetic reconnection through thin current sheets. In 2D, the helicity density near a reconnection X-line becomes purely quadrupolar structured, while in 3D, an additional dipolar structure occurs. This dipolar structure is related to kinetic current instabilities and becomes dominant for spontaneous 3D reconnection, in accordance with the dominating current instabilities. The 2D simulations have been carried out with a newly developed Vlasov-code and the 3D simulations with the particle-in-cell code GISMO.

  1. 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

  2. Microbunch preserving in-line system for an APPLE II helical radiator at the LCLS baseline

    Energy Technology Data Exchange (ETDEWEB)

    Geloni, Gianluca [European XFEL Project Team, Hamburg (Germany); Kocharyan, Vitali; Saldin, Evgeni [Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany)

    2011-05-15

    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.)

  3. 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.

  4. Matched elastic constants for a perfect helical planar state and a fast switching time in chiral nematic liquid crystals.

    Science.gov (United States)

    Yu, Meina; Zhou, Xiaochen; Jiang, Jinghua; Yang, Huai; Yang, Deng-Ke

    2016-05-11

    Chiral nematic liquid crystals possess a self-assembled helical structure and exhibit unique selective reflection in visible and infrared light regions. Their optical properties can be electrically tuned. The tuning involves the unwinding and restoring of the helical structure. We carried out an experimental study on the mechanism of the restoration of the helical structure. We constructed chiral nematic liquid crystals with variable elastic constants by doping bent-dimers and studied their impact on the restoration. With matched twist and bend elastic constants, the helical structure can be restored dramatically fast from the field-induced homeotropic state. Furthermore, defects can be eliminated to produce a perfect planar state which exhibits high selective reflection.

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

    Science.gov (United States)

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

    2013-10-30

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

  6. Seeded and unseeded helical modes in magnetized, non-imploding cylindrical liner-plasmas

    Science.gov (United States)

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

    2016-10-01

    In this research, we generated helical instability modes using unseeded and kink-seeded, non-imploding liner-plasmas at the 1 MA Linear Transformer Driver facility at the University of Michigan in order to determine the effects of externally applied, axial magnetic fields. In order to minimize the coupling of sausage and helical modes to the magneto Rayleigh-Taylor instability, the 400 nm-thick aluminum liners were placed directly around straight-cylindrical (unseeded) or threaded-cylindrical (kink-seeded) support structures to prevent implosion. The evolution of the instabilities was imaged using a combination of laser shadowgraphy and visible self-emission, collected by a 12-frame fast intensified CCD camera. With no axial magnetic field, the unseeded liners developed an azimuthally correlated m = 0 sausage instability (m is the azimuthal mode number). Applying a small external axial magnetic field of 1.1 T (compared to peak azimuthal field of 30 T) generated a smaller amplitude, helically oriented instability structure that is interpreted as an m = +2 helical mode. The kink-seeded liners showed highly developed helical structures growing at the seeded wavelength of λ = 1.27 mm. It was found that the direction of the axial magnetic field played an important role in determining the overall stabilization effects; modes with helices spiraling in the opposite direction of the global magnetic field showed the strongest stabilization. Finally, the Weis-Zhang analytic theory [Weis et al., Phys. Plasmas 22, 032706 (2015)] is used to calculate sausage and helical growth rates for experimental parameters in order to study the effects of axial magnetic fields.

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

    Science.gov (United States)

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

    2017-03-01

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

  8. Paramagnetic Response of Helical Carbon Fibers%螺旋碳纤维的顺磁响应

    Institute of Scientific and Technical Information of China (English)

    朱俊廷; 简贤; 王定川; 周祚万

    2012-01-01

    采用化学气相沉积法制备了螺旋碳纤维,通过XRD、EDX和SEM对样品进行了表征和分析,采用研磨方法考察了螺旋结构的破坏情况,并对比了研磨前后样品的低温磁性.结果表明,在有效去除催化剂的情况下,螺旋形貌被破坏以后,碳纤维的抗磁性信号增强.基于单电子受缚于螺旋线的物理模型对实验结果进行分析和讨论,认为螺旋形貌具有顺磁响应,并阐释了其产生机理.%The helical carbon fibers were fabricated using chemical vapor deposition (CVD) process and were characterized by XRD, EDX and SEM. The magnetic properties of helical carbon fibers were studied experimentally. The response to external magnetic field was tested by SQUID at 3K. It showed that the magnetization of helical carbon fiber response negatively to external magnetic field, and the diamagnetism of the carbon fibers without helical structure was stronger than helical carbon fibers. The observation of experiments indicated that paramagnetism was caused by helical structure. In addition, the mechanism of the magnetic property of helical structure was qualitative studied by the model of a free electron constrained on a helical coil. The results showed paramagnetism induced by electronic bro-ken-chirality in mesoscale can be realized in a helical structure.

  9. 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.

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

    Science.gov (United States)

    Screpanti, Emanuela; Hunte, Carola

    2007-08-01

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

  11. Electromagnetic gyrokinetic turbulence in high-beta helical plasmas

    Science.gov (United States)

    Ishizawa, Akihiro

    2013-10-01

    Gyrokinetic simulation of electromagnetic turbulence in finite-beta plasmas is important for predicting the performance of fusion reactors. Whereas in low-beta tokamaks the zonal flow shear acts to regulate ion temperature gradient (ITG) driven turbulence, it has often been observed that the kinetic ballooning mode (KBM) and, at moderate-beta, the ITG mode continue to grow without reaching a physically relevant level of saturation. The corresponding problem in helical high-beta plasmas, the identification of a saturation mechanism for microturbulence in regimes where zonal flow generation is too weak, is the subject of the present work. This problem has not been previously explored because of numerical difficulties associated with complex three-dimensional magnetic structures as well as multiple spatio-temporal scales related to electromagnetic ion and electron dynamics. The present study identifies a new saturation process of the KBM turbulence originating from the spatial structure of the KBM instabilities in a high-beta Large Helical Device (LHD) plasma. Specifically, the most unstable KBM in LHD has an inclined mode structure with respect to the mid-plane of a torus, i.e. it has finite radial wave-number in flux tube coordinates, in contrast to KBMs in tokamaks as well as ITG modes in tokamaks and helical systems. The simulations reveal that the growth of KBMs in LHD is saturated by nonlinear interactions of oppositely inclined convection cells through mutual shearing, rather than by the zonal flow shear. The mechanism is quantitatively evaluated by analysis of the nonlinear entropy transfer.

  12. FLUID FLOW IN ROTATING HELICAL SQUARE DUCTS

    Institute of Scientific and Technical Information of China (English)

    Chen Hua-jun; Zhang Ben-zhao; Zhang Jin-suo

    2003-01-01

    A numerical study is made for a fully developed laminar flow in rotating helical pipes.Due to the rotation, the Coriolis force can also contribute to the secondary flow.The interaction between rotation, torsion, and curvature complicates the flow characteristics.The effects of rotation and torsion on the flow transitions are studied in details.The results show that there are obvious differences between the flow in rotating ducts and in helical ducts without rotation.Certain hitherto unknown flow patterns are found.The effects of rotation and torsion on the friction factor are also examined.Present results show the characteristics of the fluid flow in rotating helical square ducts.

  13. Large-scale dynamics of magnetic helicity

    Science.gov (United States)

    Linkmann, Moritz; Dallas, Vassilios

    2016-11-01

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

  14. A helically distorted MHD flux rope model

    Science.gov (United States)

    Theobald, Michael L.; Montgomery, David

    1990-01-01

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

  15. Turbulent dynamo with advective magnetic helicity flux

    CERN Document Server

    Del Sordo, Fabio; Brandenburg, Axel

    2012-01-01

    Many astrophysical bodies harbor magnetic fields that are thought to be sustained by dynamo processes. However, it has been argued that the production of large-scale magnetic fields by a mean-field dynamo is strongly suppressed at large magnetic Reynolds numbers owing to the conservation of magnetic helicity. This phenomenon is known as catastrophic quenching. Advection of magnetic field toward the outer boundaries and away from the dynamo is expected to alleviate such quenching. Examples are stellar and galactic winds. Such advection might be able to overcome the constraint imposed by the conservation of magnetic helicity, transporting a fraction of it outside the domain in which the dynamo operates. We study how the dynamo process is affected by advection. In particular, we study the relative roles played by advective and diffusive fluxes of magnetic helicity. We do this by performing direct numerical simulations of a turbulent dynamo of alpha^2 type driven by forced turbulence in a Cartesian domain in the ...

  16. Demonstration of steady inductive helicity injection

    Science.gov (United States)

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

    2006-02-01

    Initial results demonstrating the concept of constant inductive helicity injection are presented. Constant helicity injection is achieved using two oscillating inductive helicity injectors, with the goal of producing a bow tie spheromak. Each injector is a 180° segment of a reverse field pinch and they are driven 90° out of phase. Approximately 5 MW of power is injected during the 6 ms pulse, and the input power has been maintained at a fairly constant value by directly fuelling the injectors with neutral gas. Motivation for the experiment is given, including beta-limit calculations for the bow tie spheromak. Fuelling the injectors with neutral gas during the discharge is shown to produce injector parameters that are more constant in time. A series of discharges with increasing power input shows a promising increase in toroidal current. Unique construction techniques of the experiment are also described.

  17. 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

  18. Current helicity and electromotive force of magnetoconvection influenced by helical background fields

    CERN Document Server

    Ruediger, Guenther

    2016-01-01

    Motivated by the empirical finding that the known hemispheric rules for the current helicity at the solar surface are not strict, the excitation of small-scale current helicity by the influence of a large-scale helical magnetic background fields on nonrotating magnetoconvection is demonstrated. It is shown within a quasilinear analytic theory of driven turbulence and by nonlinear simulations of magnetoconvection that the resulting small-scale current helicity has the same sign as the large-scale current helicity while the ratio of both pseudo-scalars is of the order of the magnetic Reynolds number of the convection. The same models do not provide finite values of the small-scale kinetic helicity. On the other hand, a turbulence-induced electromotive force is produced including the diamagnetic pumping term as well as the eddy diffusivity but no alpha effect. It is thus argued that the relations by Pouquet & Patterson (1978) and Keinigs (1983) for the simultaneous existence of small-scale current helicity a...

  19. Helicity and nuclear $\\beta$ decay correlations

    CERN Document Server

    Hong, Ran; García, Alejandro

    2016-01-01

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

  20. 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.

  1. Assembly of transmembrane helices of simple polytopic membrane proteins from sequence conservation patterns.

    Science.gov (United States)

    Park, Yungki; Helms, Volkhard

    2006-09-01

    The transmembrane (TM) domains of most membrane proteins consist of helix bundles. The seemingly simple task of TM helix bundle assembly has turned out to be extremely difficult. This is true even for simple TM helix bundle proteins, i.e., those that have the simple form of compact TM helix bundles. Herein, we present a computational method that is capable of generating native-like structural models for simple TM helix bundle proteins having modest numbers of TM helices based on sequence conservation patterns. Thus, the only requirement for our method is the presence of more than 30 homologous sequences for an accurate extraction of sequence conservation patterns. The prediction method first computes a number of representative well-packed conformations for each pair of contacting TM helices, and then a library of tertiary folds is generated by overlaying overlapping TM helices of the representative conformations. This library is scored using sequence conservation patterns, and a subsequent clustering analysis yields five final models. Assuming that neighboring TM helices in the sequence contact each other (but not that TM helices A and G contact each other), the method produced structural models of Calpha atom root-mean-square deviation (CA RMSD) of 3-5 A from corresponding crystal structures for bacteriorhodopsin, halorhodopsin, sensory rhodopsin II, and rhodopsin. In blind predictions, this type of contact knowledge is not available. Mimicking this, predictions were made for the rotor of the V-type Na(+)-adenosine triphosphatase without such knowledge. The CA RMSD between the best model and its crystal structure is only 3.4 A, and its contact accuracy reaches 55%. Furthermore, the model correctly identifies the binding pocket for sodium ion. These results demonstrate that the method can be readily applied to ab initio structure prediction of simple TM helix bundle proteins having modest numbers of TM helices.

  2. Eikonal slant helices and eikonal Darboux helices in 3-dimensional pseudo-Riemannian manifolds

    OpenAIRE

    Önder, Mehmet; Ziplar, Evren

    2013-01-01

    In this study, we give definitions and characterizations of eikonal slant helices, eikonal Darboux helices and non-normed eikonal Darboux helices in 3-dimensional pseudo- Riemannian manifold M . We show that every eikonal slant helix is also an eikonal Darboux helix for timelike and spacelike curves. Furthermore, we obtain that if the non-null curve a is a non-normed eikonal Darboux helix, then a is an eikonal slant helix if and only if 2 2 e 3k +e1t = constant, where k and t are curvature an...

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

    Energy Technology Data Exchange (ETDEWEB)

    Perucho, M.; Kovalev, Y. Y. [Departament d' Astronomia i Astrofisica, Universitat de Valencia, 46100 Burjassot (Valencia) (Spain); Lobanov, A. P. [Max-Planck-Institut fuer Radioastronomie, Auf dem Huegel 69, 53121 Bonn (Germany); Hardee, P. E. [Department of Physics and Astronomy, The University of Alabama, Tuscaloosa, AL 35487 (United States); Agudo, I., E-mail: manel.perucho@uv.es [Instituto de Astrofisica de Andalucia, Apartado 3004, 18080 Granada (Spain)

    2012-04-10

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

  4. Anatomy of helical relativistic jets: The case of S5 0836+710

    CERN Document Server

    Perucho, Manel; Lobanov, Andrei P; Hardee, Philip E; Agudo, Ivan

    2012-01-01

    Helical structures are common in extragalactic jets. They are usually attributed in the literature to periodical phenomena in the source (e.g., precession). In this work, we use VLBI data of the radio-jet in the quasar S5 0836+710 and hypothesize that the ridge-line of helical jets like this corresponds to a pressure maximum in the jet and assume that the helically twisted pressure maximum is the result of a helical wave pattern. For our study, we use observations of the jet in S5 0836+710 at different frequencies and epochs. The results show that the structures observed are physical and not generated artificially by the observing arrays. Our hypothesis that the observed intensity ridge-line can correspond to a helically twisted pressure maximum is confirmed by our observational tests. This interpretation allows us to explain jet misalignment between parsec and kiloparsec scales when the viewing angle is small, and also brings us to the conclusion that high-frequency observations may show only a small region ...

  5. The membrane integration of a naturally occurring alpha-helical hairpin.

    Science.gov (United States)

    Nagy, Akos; Turner, R James

    2007-05-04

    Helical hairpins, two closely spaced helical membrane spanning segments separated by a short surface turn, are thought to be common in integral membrane proteins. Here, we study the membrane integration of a naturally occurring helical hairpin from the secretory Na(+)-K(+)-2Cl(-) cotransporter NKCC1. This sequence is only slightly longer and significantly less hydrophobic than a previously identified minimal poly-leucine model hairpin structure. Using site directed mutagenesis we document the importance of the turn propensity of the amino acids in the intervening surface turn but, somewhat surprisingly, our results indicate that the formation of this natural hairpin apparently does not depend on specific helix-helix interactions. Our results suggest that helical hairpins may be formed quite readily from even minimally hydrophobic sequences separated by a short, sufficiently strong, turn signal, and that current methods for predicting integral membrane protein topology may miss many similar short helical hairpin sequences. Thus the occurrence of these structures may be much more common than presently thought.

  6. Electromagnetic gyrokinetic turbulence in finite-beta helical plasmasa)

    Science.gov (United States)

    Ishizawa, A.; Watanabe, T.-H.; Sugama, H.; Maeyama, S.; Nakajima, N.

    2014-05-01

    A saturation mechanism for microturbulence in a regime of weak zonal flow generation is investigated by means of electromagnetic gyrokinetic simulations. The study identifies a new saturation process of the kinetic ballooning mode (KBM) turbulence originating from the spatial structure of the KBM instabilities in a finite-beta Large Helical Device (LHD) plasma. Specifically, the most unstable KBM in LHD has an inclined mode structure with respect to the mid-plane of a torus, i.e., it has a finite radial wave-number in flux tube coordinates, in contrast to KBMs in tokamaks as well as ion-temperature gradient modes in tokamaks and helical systems. The simulations reveal that the growth of KBMs in LHD is saturated by nonlinear interactions of oppositely inclined convection cells through mutual shearing as well as by the zonal flow. The saturation mechanism is quantitatively investigated by analysis of the nonlinear entropy transfer that shows not only the mutual shearing but also a self-interaction with an elongated mode structure along the magnetic field line.

  7. Helix dynamics in LacY: helices II/IV

    Science.gov (United States)

    Liu, Zhenyu; Madej, M. Gregor; Kaback, H. Ronald

    2011-01-01

    Biochemical and biophysical studies based upon crystal structures of both a mutant and wild-type lactose permease from Escherichia coli (LacY) in an inward-facing conformation have led to a model for the symport mechanism in which both sugar- and H+-binding sites are alternatively accessible to either side of the membrane. Previous findings indicate that the face of helix II with Asp68 is important for the conformational changes that occur during turnover. As shown here, replacement of Asp68 at the cytoplasmic end of helix II, particularly with Glu, abolishes active transport, but the mutants retain the ability to bind galactopyranoside. In the x-ray structure, Asp68 and Lys131 (helix IV) lie within ∼4.2 Å of each other. Although a double mutant with Cys replacements at both position 68 and 131 cross-links efficiently, single replacements for Lys131 exhibit very significant transport activity. Site-directed alkylation studies show that sugar binding by the Asp68 mutants causes closure of the cytoplasmic cavity, like wild-type LacY; but strikingly, the probability of opening the periplasmic pathway upon sugar binding is markedly reduced. Taken together with previous mutagenesis and cross-linking studies, the findings lead to a model in which replacement of Asp68 blocks a conformational transition involving helices II and IV that is important for opening the periplasmic cavity. Evidence is also presented suggesting that movements of helices II and IV are coupled functionally with movements in the pseudo-symmetrically paired helices VIII and X. PMID:20043916

  8. 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.

  9. Energy and helicity budgets of solar quiet regions

    CERN Document Server

    Tziotziou, K; Georgoulis, M K; Kontogiannis, I

    2014-01-01

    We investigate the free magnetic energy and relative magnetic helicity budgets of solar quiet regions. Using a novel non-linear force-free method requiring single solar vector magnetograms we calculate the instantaneous free magnetic energy and relative magnetic helicity budgets in 55 quiet-Sun vector magnetograms. As in a previous work on active regions, we construct here for the first time the (free) energy-(relative) helicity diagram of quiet-Sun regions. We find that quiet-Sun regions have no dominant sense of helicity and show monotonic correlations a) between free magnetic energy/relative helicity and magnetic network area and, consequently, b) between free magnetic energy and helicity. Free magnetic energy budgets of quiet-Sun regions represent a rather continuous extension of respective active-region budgets towards lower values, but the corresponding helicity transition is discontinuous due to the incoherence of the helicity sense contrary to active regions. We further estimate the instantaneous free...

  10. Helical mode interactions and spectral transfer processes in magnetohydrodynamic turbulence

    CERN Document Server

    Linkmann, Moritz F; McKay, Mairi E; Jäger, Julia

    2015-01-01

    Spectral transfer processes in magnetohydrodynamic (MHD) turbulence are investigated analytically by decomposition of the velocity and magnetic fields in Fourier space into helical modes. Steady solutions of the dynamical system which governs the evolution of the helical modes are determined, and a stability analysis of these solutions is carried out. The interpretation of the analysis is that unstable solutions lead to energy transfer between the interacting modes while stable solutions do not. From this, a dependence of possible interscale energy and helicity transfers on the helicities of the interacting modes is derived. As expected from the inverse cascade of magnetic helicity in 3D MHD turbulence, mode interactions with like helicities lead to transfer of energy and magnetic helicity to smaller wavenumbers. However, some interactions of modes with unlike helicities also contribute to an inverse energy transfer. As such, an inverse energy cascade for nonhelical magnetic fields is shown to be possible. Fu...

  11. In vivo mechanical study of helical cardiac pacing electrode interacting with canine myocardium

    Institute of Scientific and Technical Information of China (English)

    Xiangming Zhang; Nianke Ma; Hualin Fan; Guodong Niu; Wei Yang

    2007-01-01

    Cardiac pacing is a medical device to help human to overcome arrhythmia and to recover the regular beats of heart. A helical configuration of electrode tip is a new type of cardiac pacing lead distal tip. The helical electrode attaches itself to the desired site of heart by screwing its helical tip into the myocardium. In vivo experiments on anesthetized dogs were carried out to measure the acute interactions between helical electrode and myocardium during screw-in and pull-out processes. These data would be helpful for electrode tip design and electrode/myocardium adherence safety evaluation. They also provide reliability data for clinical site choice of human heart to implant and to fix the pacing lead.A special design of the helical tip using strain gauges is instrumented for the measurement of the screw-in and pull-out forces. We obtained the data of screw-in torques and pull-out forces for five different types of helical electrodes at nine designed sites on ten canine hearts. The results indicate that the screw-in torques increased steplike while the torque-time curves presente saw-tooth fashion. The maximum torque has a range of 0.3-1.9N mm. Obvious differences are observed for different types of helical tips and for different test sites.Large pull-out forces are frequently obtained at epicardium of left ventricle and right ventricle lateral wall, and the forces obtained at right ventricle apex and outflow tract of right ventricle are normally small. The differences in pull-out forces are dictated by the geometrical configuration of helix and regional structures of heart muscle.

  12. LAMINAR FLUID FLOW IN HELICAL ELLIPTICAL PIPE

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    In this paper, using an orthogonal curvilinear coordinate system and solving the complete N-S equations, we analyzed the flow in a helical elliptical duct by the perturbation method. The first-order solutions of the stream function Ψ, axial velocity w and the velocity of secondary flow (u, v) were obtained. The effects of torsion, curvature and the axial pressure gradient on the secondary flow were discussed in detail. The study indicates that the torsion has first-order effect on the secondary flow in a helical elliptical pipe, the secondary flow is dominated by torsion when the axial pressure gradient is small and for increasing gradient the secondary flow is eventually dominated by the effect due to curvature. The fact that the torsion has no effect on fluid flow in a helical pipe with a circular cross section was also confirmed. The most important conclusion is that the flow in a helical elliptical pipe to the first-order can be obtained as a combination of the flow in a toroidal pipe and the flow in a twisted pipe.

  13. Coulomb drag between helical Luttinger liquids

    Science.gov (United States)

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

    2017-01-01

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

  14. Helical Gears Modified To Decrease Transmission Errors

    Science.gov (United States)

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

    1993-01-01

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

  15. Muon Beam Helical Cooling Channel Design

    Energy Technology Data Exchange (ETDEWEB)

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

    2013-06-01

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

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

    Science.gov (United States)

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

    2012-12-19

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

  17. 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.

  18. Helicity of Solar Active Regions from a Dynamo Model

    Indian Academy of Sciences (India)

    Piyali Chatterjee

    2006-06-01

    We calculate helicities of solar active regions based on the idea that poloidal flux lines get wrapped around a toroidal flux tube rising through the convection zone, thereby giving rise to the helicity. We use our solar dynamo model based on the Babcock–Leighton -effect to study how helicity varies with latitude and time.

  19. Sign of helicity in the alpha-Omega geodynamo

    CERN Document Server

    Wei, Xing

    2010-01-01

    In this paper we investigate the sign of helicity in the alpha-Omega dynamo and point out that the alpha effect in the geodynamo is induced by helical wave but not helical flow as in the solar dynamo. We then postulate the mechanisms of the Earth's magnetic tilt angle, westward drift and dipole reversals.

  20. Field-theoretic calculation of kinetic helicity flux

    Indian Academy of Sciences (India)

    V Avinash; Mahendra K Verma; Amar K Chandra

    2006-02-01

    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.

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

    Science.gov (United States)

    Koch Ocker, Stella; Petrie, Gordon

    2016-05-01

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

  2. Native like helices in a specially designed β peptide in the gas phase.

    Science.gov (United States)

    Schubert, Franziska; Pagel, Kevin; Rossi, Mariana; Warnke, Stephan; Salwiczek, Mario; Koksch, Beate; von Helden, Gert; Blum, Volker; Baldauf, Carsten; Scheffler, Matthias

    2015-02-21

    In the natural peptides, helices are stabilized by hydrogen bonds that point backward along the sequence direction. Until now, there is only little evidence for the existence of analogous structures in oligomers of conformationally unrestricted β amino acids. We specifically designed the β peptide Ac-(β(2)hAla)6-LysH(+) to form native like helical structures in the gas phase. The design follows the known properties of the peptide Ac-Ala6-LysH(+) that forms a α helix in isolation. We perform ion-mobility mass-spectrometry and vibrational spectroscopy in the gas phase, combined with state-of-the-art density-functional theory simulations of these molecular systems in order to characterize their structure. We can show that the straightforward exchange of alanine residues for the homologous β amino acids generates a system that is generally capable of adopting native like helices with backward oriented H-bonds. By pushing the limits of theory and experiments, we show that one cannot assign a single preferred structure type due to the densely populated energy landscape and present an interpretation of the data that suggests an equilibrium of three helical structures.

  3. Dynamo effect in a driven helical flow.

    Science.gov (United States)

    Feudel, F; Gellert, M; Rüdiger, S; Witt, A; Seehafer, N

    2003-10-01

    The Roberts flow, a helical flow in the form of convectionlike rolls, is known to be capable of both kinematic and nonlinear dynamo action. We study the Roberts dynamo with particular attention being paid to the spatial structure of the generated magnetic field and its back-reaction on the flow. The dynamo bifurcation is decisively determined by the symmetry group of the problem, which is given by a subgroup of discrete transformations and a continuous translational invariance of the flow. In the bifurcation the continuous symmetry is broken while the discrete subgroup symmetry completely survives. Its actions help in understanding the spatial structures of the magnetic field and of the modified flow. In accordance with experimental observations, the magnetic field component perpendicular to the originally invariant direction is much stronger than the component in this direction. Furthermore, the magnetic field is largely concentrated in layers separating the convectionlike rolls of the flow and containing, in particular, its stagnation points, which are isolated for the modified flow while they are line filling for the original Roberts flow. The magnetic field is strongest near beta-type stagnation points, with a two-dimensional unstable and a one-dimensional stable manifold, and is weak near alpha-type stagnation points, with a two-dimensional stable and a one-dimensional unstable manifold. This contrasts with the usual picture that dynamo action is promoted at the alpha points and impeded at the beta points. Both the creation of isolated stagnation points and the concentration of strong fields at the beta points may be understood as a result of the way in which the Roberts dynamo saturates. It is also found that, while the original Roberts flow is regular, the modified flow is chaotic in the layers between the convectionlike rolls where the magnetic field is concentrated. This chaoticity, which results from the back-reaction of the magnetic field on the flow

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

    Science.gov (United States)

    Shelar, Ashish; Bansal, Manju

    2014-12-01

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

  5. 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.

  6. Helical vortices generated by flapping wings of bumblebees

    Science.gov (United States)

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

    2016-11-01

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

  7. Chaotic and regular instantons in helical shell models of turbulence

    CERN Document Server

    De Pietro, Massimo; Biferale, Luca

    2016-01-01

    Shell models of turbulence have a finite-time blowup, i.e. the enstrophy diverges while the single shell velocities stay finite, in the inviscid limit. The signature of this blowup is represented by self-similar instantonic structures traveling coherently through the inertial range. These solutions might influence the energy transfer and the anomalous scaling properties empirically observed for the forced and viscous models. In this paper we present a study of the instantonic solutions for a class of shell-models of turbulence based on the exact decomposition of the Navier-Stokes equations in helical eigenstates. We found that depending on the helical structure of the shell interactions instantons are chaotic or regular. Some instantonic solutions tend to recover mirror symmetry for scales small enough. All models that have anomalous scaling develop regular non-chaotic instantons. Vice-versa, models that have mean field non-anomalous scaling in the stationary regime are those that have chaotic instantons. Fin...

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

    Science.gov (United States)

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

    2016-09-01

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

  9. Double twist helical nanofilaments in bent-core liquid crystals

    Science.gov (United States)

    Zhang, Cuiyu; Diorio, Nicholas; Lavrentovich, Oleg D.; Jakli, Antal

    2014-03-01

    Cryo-TEM observations on 40-150 nm films of four bent-core liquid crystal materials in their helical nanofilament (HNF) phase show that the filaments get deformed near the substrate, and the subsequent arrays of nanofilaments are not parallel, but twisted with respect to each other. The effect can explain the mysterious properties of the HNF materials, such as structural color and ambidextrous optical activity. The observed double twist structure was not expected in the previous models of this phase. Being principally different from the packing of molecules in the twist grain boundary (TGB) and blue (BP) phases, the double-twist structure of HNF expands the rich word of nanostructured organic materials. This work was financially supported by NSF DMR-0964765 and DMR 1104850. The cryo-TEM facility was supported by the Ohio Research Scholars Program. We are grateful for Prof. G. Heppke and Dr. D. Lotsch for providing the PnOPIMB materials for us.

  10. Helical conformations of hexapeptides containing N-terminus diproline segments.

    Science.gov (United States)

    Raghothama, Srinivasarao; Aravinda, Subrayashastry; Shamala, Narayanaswamy; Balaram, Padmanabhan

    2010-01-01

    The role of N-terminus diproline segments in facilitating helical folding in short peptides has been investigated in a set of model hexapeptides of the type Piv-Xxx-Yyy-Aib-Leu-Aib-Phe-OMe (Piv, pivaloyl). Nine sequences have been investigated with the following N-terminus dipeptide segments: (D)Pro-Ala (4) and Pro-PsiPro (5, Psi, pseudoproline), Ala-Ala (6), Ala-Pro (7), Pro-Ala (8), Aib-Ala (9), Ala-Aib (10). The analog sequences Piv-Pro-Pro-Ala-Leu-Aib-Phe-OMe (2) and Piv-Pro-Pro-Ala-Aib-Ala-Aib-OMe (3) have also been studied. Solid state conformations have been determined by X-ray crystallography for peptides 4, 6, and 8 and compared with the previously determined crystal structure of peptide 1 (Boc-Pro-Pro-Aib-Leu-Aib-Val-OMe); (Rai et al., JACS 2006, 128, 7916-7928). Peptides 1 and 6 adopt almost identical helical conformations with unfolding of the helix at the N-terminus Pro (1) residue. Peptide 4 reveals the anticipated (D)Pro-Ala type II' beta-turn, followed by a stretch of 3(10)-helix. Peptide 8 adopts a folded conformation stabilized by four successive 4-->1 intramolecular hydrogen bonds. Ala (2) adopts an alpha(L) conformation, resulting in a type II beta-turn conformation followed by a stretch of 3(10)-helix. Conformational properties in solution were probed using solvent perturbation of NH chemical shifts which permit delineation of hydrogen bonded NH groups and nuclear Overhauser effects (NOEs) between backbone protons, which are diagnostic of local residue conformations. The results suggest that, continuous helical conformations are indeed significantly populated for peptides 2 and 3. Comparison of the results for peptides 1 and 2, suggest that there is a significant influence of the residue that follows diproline segments in influencing backbone folding.

  11. Impact of histidine residues on the transmembrane helices of viroporins.

    Science.gov (United States)

    Wang, Yan; Park, Sang Ho; Tian, Ye; Opella, Stanley J

    2013-11-01

    Abstract The role of histidine in channel-forming transmembrane (TM) helices was investigated by comparing the TM helices from Virus protein 'u' (Vpu) and the M2 proton channel. Both proteins are members of the viroporin family of small membrane proteins that exhibit ion channel activity, and have a single TM helix that is capable of forming oligomers. The TM helices from both proteins have a conserved tryptophan towards the C-terminus. Previously, alanine 18 of Vpu was mutated to histidine in order to artificially introduce the same HXXXW motif that is central to the proton channel activity of M2. Interestingly, the mutated Vpu TM resulted in an increase in helix tilt angle of 11° in lipid bilayers compared to the wild-type Vpu TM. Here, we find the reverse, when histidine 37 of the HXXXW motif in M2 was mutated to alanine, it decreased the helix tilt by 10° from that of wild-type M2. The tilt change is independent of both the helix length and the presence of tryptophan. In addition, compared to wild-type M2, the H37A mutant displayed lowered sensitivity to proton concentration. We also found that the solvent accessibility of histidine-containing M2 is greater than without histidine. This suggests that the TM helix may increase the solvent exposure by changing its tilt angle in order to accommodate a polar/charged residue within the hydrophobic membrane region. The comparative results of M2, Vpu and their mutants demonstrated the significance of histidine in a transmembrane helix and the remarkable plasticity of the function and structure of ion channels stemming from changes at a single amino acid site.

  12. Helical mode lung 4D-CT reconstruction using Bayesian model.

    Science.gov (United States)

    He, Tiancheng; Xue, Zhong; Nitsch, Paige L; Teh, Bin S; Wong, Stephen T

    2013-01-01

    4D computed tomography (CT) has been widely used for treatment planning of thoracic and abdominal cancer radiotherapy. Current 4D-CT lung image reconstruction methods rely on respiratory gating to rearrange the large number of axial images into different phases, which may be subject to external surrogate errors due to poor reproducibility of breathing cycles. New image-matching-based reconstruction works better for the cine mode of 4D-CT acquisition than the helical mode because the table position of each axial image is different in helical mode and image matching might suffer from bigger errors. In helical mode, not only the phases but also the un-uniform table positions of images need to be considered. We propose a Bayesian method for automated 4D-CT lung image reconstruction in helical mode 4D scans. Each axial image is assigned to a respiratory phase based on the Bayesian framework that ensures spatial and temporal smoothness of surfaces of anatomical structures. Iterative optimization is used to reconstruct a series of 3D-CT images for subjects undergoing 4D scans. In experiments, we compared visually and quantitatively the results of the proposed Bayesian 4D-CT reconstruction algorithm with the respiratory surrogate and the image matching-based method. The results showed that the proposed algorithm yielded better 4D-CT for helical scans.

  13. Stitched α-helical peptides via bis ring-closing metathesis.

    Science.gov (United States)

    Hilinski, Gerard J; Kim, Young-Woo; Hong, Jooyeon; Kutchukian, Peter S; Crenshaw, Charisse M; Berkovitch, Shaunna S; Chang, Andrew; Ham, Sihyun; Verdine, Gregory L

    2014-09-03

    Conformationally stabilized α-helical peptides are capable of inhibiting disease-relevant intracellular or extracellular protein-protein interactions in vivo. We have previously reported that the employment of ring-closing metathesis to introduce a single all-hydrocarbon staple along one face of an α-helical peptide greatly increases α-helical content, binding affinity to a target protein, cell penetration through active transport, and resistance to proteolytic degradation. In an effort to improve upon this technology for stabilizing a peptide in a bioactive α-helical conformation, we report the discovery of an efficient and selective bis ring-closing metathesis reaction leading to peptides bearing multiple contiguous staples connected by a central spiro ring junction. Circular dichroism spectroscopy, NMR, and computational analyses have been used to investigate the conformation of these "stitched" peptides, which are shown to exhibit remarkable thermal stabilities. Likewise, trypsin proteolysis assays confirm the achievement of a structural rigidity unmatched by peptides bearing a single staple. Furthermore, fluorescence-activated cell sorting (FACS) and confocal microscopy assays demonstrate that stitched peptides display superior cell penetrating ability compared to their stapled counterparts, suggesting that this technology may be useful not only in the context of enhancing the drug-like properties of α-helical peptides but also in producing potent agents for the intracellular delivery of proteins and oligonucleotides.

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

    Energy Technology Data Exchange (ETDEWEB)

    Toi, K. [National Institute for Fusion Science, Toki, Japan; Ogawa, K. [Nagoya University, Japan; Isobe, M. [National Institute for Fusion Science, Toki, Japan; Osakabe, M. [National Institute for Fusion Science, Toki, Japan; Spong, Donald A [ORNL; Todo, Yasushi [National Institute for Fusion Science, Toki, Japan

    2011-01-01

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

  15. 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.

  16. 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.

  17. Measurement of W-Boson Helicity Fractions in Top-Quark Decays Using costheta*

    CERN Document Server

    Aaltonen, T; Adelman, J; Akimoto, T; Alvarez Gonzlez, B; Ameriow, a S; Amidei, D; Anastassov, A; Annovi, A; Antos, J; Apollinari, G; Apresyan, A; Arisawa, T; Artikov, A; Ashmanskas, W; Attal, A; Aurisano, A; Azfar, F; Azzurriz, P; Badgett, W; Barbaro-Galtieri, A; Barnes, V E; Barnett, B A; Bartsch, V; Bauer, G; Beauchemin, P H; Bedeschi, F; Beecher, D; Behari, S; Bellettini, Giorgio; Bellinger, J; Benjamin, D; Beretvas, A; Beringer, J; Bhatti, A; Binkley, M; Bisellow, D; Bizjakcc, I; Blair, R E; Blocker, C; Blumenfeld, B; Bocci, A; Bodek, A; Boisvert, V; Bölla, G; Bortoletto, D; Boudreau, J; Boveia, A; Braua, B; Bridgeman, A; Brigliadori, L; Bromberg, C; Brubaker, E; Budagov, Yu; Budd, H S; Budd, S; Burke, S; Burkett, K; Busettow, G; Busseyk, P; Buzatu, A; Byrum, K L; Cabrerau, S; Calancha, C; Campanelli, M; Campbell, M; Canelli, F; Canepa, A; Carls, B; Carlsmith, D; Carosi, R; Carrillom, S; Carron, S; Casal, B; Casarsa, M; Castrov, A; Catastiniy, P; Cauzbb, D; Cavalierey, V; Cavalli-Sforza, M; Cerri, A; Cerriton, L; Chang, S H; Chen, Y C; Chertok, M; Chiarelli, G; Chlachidze, G; Chlebana, F; Cho, K; Chokheli, D; Chou, J P; Choudalakis, G; Chuang, S H; Chung, K; Chung, W H; Chung, Y S; Chwalek, T; Ciobanu, C I; Ciocciy, M A; Clark, A; Clark, D; Compostella, G; Convery, M E; Conway, J; Cordelli, M; Cortianaw, G; Cox, C A; Cox, D J; Cresciolix, F; Cuenca Almenaru, C; Cuevasr, J; Culbertson, R; Cully, J C; Dagenhart, D; Datta, M; Davies, T; De Barbaro, P; De Cecco, S; Deisher, A; De Lorenzo, G; Dell'Orsox, M; Deluca, C; Demortier, L; Deng, J; Deninno, M; Derwent, P F; di Giovanni, G P; Dionisiaa, C; Di Ruzzabb, B; Dittmann, J R; D'Onofrio, M; Donatix, S; Dong, P; Donini, J; Dorigo, T; Dube, S; Efron, J; Elagin, A; Erbacher, R; Errede, D; Errede, S; Eusebi, R; Fang, H C; Farrington, S; Fedorko, W T; Feild, R G; Feindt, M; Fernández, J P; Ferrazzaz, C; Field, R; Flanagan, G; Forrest, R; Frank, M J; Franklin, M; Freeman, J C; Furic, I; Gallinaro, M; Galyardt, J; Garberson, F; García, J E; Garfinkel, A F; Genser, K; Gerberich, H; Gerdes, D; Gessler, A; Giaguaa, S; Giakoumopoulou, V; Giannetti, P; Gibson, K; Gimmell, J L; Ginsburg, C M; Giokaris, N; Giordanibb, M; Giromini, P; Giuntax, M; Giurgiu, G; Glagolev, V; Glenzinski, D; Gold, M; Goldschmidt, N; Golossanov, A; Gómez, G; Gómez-Ceballos, G; Goncharov, M; Gonzlez, O; Gorelov, I; Goshaw, a A T; Goulianos, K; Greselew, A; Grinstein, S; Grosso-Pilcher, C; Group, R C; Grundler, U; Guimarães da Costa, J; Gunay-Unalan, Z; Haber, C; Hahn, K; Hahn, S R; Halkiadakis, E; Han, B Y; Han, J Y; Happacher, F; Hara, K; Hare, D; Hare, M; Harper, S; Harr, R F; Harris, R M; Hartz, M; Hatakeyama, K; Hays, C; Heck, M; Heijboer, A; Heinrich, J; Henderson, C; Herndon, M; Heuser, J; Hewamanage, S; Hidas, D; Hillc, C S; Hirschbuehl, D; Höcker, A; Hou, S; Houlden, M; Hsu, S C; Huffman, B T; Hughes, R E; Husemann, U; Hussein, M; Huston, J; Incandela, J; Introzzi, G; Ioriaa, M; Ivanov, A; James, E; Jayatilaka, B; Jeon, E J; Jha, M K; Jindariani, S; Johnson, W; Jones, M; Joo, K K; Jun, S Y; Jung, J E; Junk, T R; Kamon, T; Kar, D; Karchin, P E; Kato, Y; Kephart, R; Keung, J; Khotilovich, V; Kilminster, B; Kim, D H; Kim, H S; Kim, H W; Kim, J E; Kim, M J; Kim, S B; Kim, S H; Kim, Y K; Kimura, N; Kirsch, L; Klimenko, S; Knuteson, B; Ko, B R; Kondo, K; Kong, D J; Konigsberg, J; Korytov, A; Kotwal, A V; Kreps, M; Kroll, J; Krop, D; Krumnack, N; Kruse, M; Krutelyov, V; Kubo, T; Kuhr, T; Kulkarni, N P; Kurata, M; Kwang, S; Laasanen, A T; Lami, S; Lammel, S; Lancaster, M; Lander, R L; Lannonq, K; Lath, A; Latinoy, G; Lazzizzeraw, I; LeCompte, T; Lee, E; Lee, H S; Leet, S W; Leone, S; Lewis, J D; Lin, C S; Linacre, J; Lindgren, M; Lipeles, E; Lister, A; Litvintsev, D O; Liu, C; Liu, T; Lockyer, N S; Loginov, A; Loretiw, M; Lovas, L; Lucchesiw, D; Luciaa, C; Lueck, J; Lujan, P; Lukens, P; Lungu, G; Lyons, L; Lys, J; Lysak, R; MacQueen, D; Madrak, R; Maeshima, K; Makhoul, K; Mäki, T; Maksimovic, P; Malde, S; Malik, S; Mancae, G; Manousakis-Katsikakis, A; Margaroli, F; Marino, C; Marino, C P; Martin, A; Martinl, V; Martínez, M; Martinez-Ballarin, R; Maruyama, T; Mastrandrea, P; Masubuchi, T; Mathis, ii M; Mattson, M E; Mazzanti, P; McFarland, K S; McIntyre, P; McNultyj, R; Mehta, A; Mehtälä, P; Menzione, A; Merkel, P; Mesropian, C; Miao, T; Miladinovic, N; Miller, R; Mills, C; Milnik, M; Mitra, A; Mitselmakher, G; Miyake, H; Moed, S; Moggi, N; Moon, C S; Moore, R; Morellox, M J; Morlok, J; Movilla-Fernández, P A; Mülmenstädt, J; Mukherjee, A; Müller, T; Mumford, R; Murat, P; Mussiniv, M; Nachtman, J; Nagai, Y; Nagano, A; Naganoma, J; Nakamura, K; Nakano, I; Napier, A; Necula, V; Nett, J; Neuv, C; Neubauer, M S; Neubauer, S; Nielseng, J; Nodulman, L; Norman, M; Norniella, O; Nurse, E; Oakes, L; Oh, S H; Oh, Y D; Oksuzian, I; Okusawa, T; Orava, R; Pagan Grisow, S; Palencia, E; Papadimitriou, V; Papaikonomou, A; Paramonov, A A; Parks, B; Pashapour, S; Patrick, J; Paulettabb, G; Paulini, M; Paus, C; Peiffer, T; Pellett, D E; Penzo, Aldo L; Phillips, T J; Piacentino, G; Pianori, E; Pinera, L; Pitts, K; Plager, C; Pondrom, L; Poukhov, O; Pounder, N; Prakoshyn, F; Pronko, A; Proudfoot, J; Ptohosi, F; Pueschel, E; Punzix, G; Pursley, J; Rademackerc, J; Rahaman, A; Ramakrishnan, V; Ranjan, N; Redondo, I; Renton, P B; Renz, M; Rescigno, M; Richter, S; Rimondiv, F; Ristori, L; Robson, A; Rodrigo, T; Rodríguez, T; Rogers, E; Rolli, S; Roser, R; Rossi, M; Rossin, R; Roy, P; Ruiz, A; Russ, J; Rusu, V; Safonov, A; Sakumoto, W K; Salt, O; Santibb, L; Sarkaraa, S; Sartori, L; Sato, o K; Savoy-Navarro, A; Schlabach, P; Schmidt, A; Schmidt, E E; Schmidt, M A; Schmidt, M P; Schmitt, M; Schwarz, T; Scodellaro, L; Scribanoy, A; Scuri, F; Sedov, A; Seidel, S; Seiya, Y; Semenov, A; Sexton-Kennedy, L; Sforza, F; Sfyrla, A; Shalhout, S Z; Shears, T G; Shepard, P F; Shimojimap, M; Shiraishi, S; Shochet, M; Shon, Y; Shreyber, I; Sidoti, A; Sinervo, P; Sisakian, A; Slaughter, A J; Slaunwhite, J; Sliwa, K; Smith, J R; Snider, F D; Snihur, R; Soha, A; Somalwar, S; Sorin, V; Spalding, J; Spreitzer, T; Squillaciotiy, P; Stanitzki, M; Saint-Denis, R; Stelzer, B; Stelzer-Chilton, O; Stentz, D; Strologas, J; Strycker, G L; Stuart, D; Suh, J S; Sukhanov, A; Suslov, I; Suzuki, T; Taffardf, A; Takashima, R; Takeuchi, Y; Tanaka, R; Tecchio, M; Teng, P K; Terashi, K; Thomh, J; Thompson, A S; Thompson, G A; Thomson, E; Tipton, P; Ttito-Guzmn, P; Tkaczyk, S; Toback, D; Tokar, a S; Tollefson, K; Tomura, T; Tonelli, D; Torre, S; Torretta, D; Totarobb, P; Tourneur, S; Trovato, M; Tsai, S Y; Tu, Y; Turiniy, N; Ukegawa, F; Vallecorsa, S; van Remortelb, N; Varganov, A; Vatagaz, E; Vazquezm, F; Velev, G; Vellidis, C; Veszpremi, V; Vidal, M; Vidal, R; Vila, I; Vilar, R; Vine, T; Vogel, M; Volobouevt, I; Volpix, G; Wagner, P; Wagner, R G; Wagner, R L; Wagner, W; Wagner-Kuhr, J; Wakisaka, T; Wallny, R; Wang, S M; Warburton, A; Waters, D; Weinberger, M; Weinelt, J; Wester, W C; Whitehouse, B; Whitesonf, D; Wicklund, A B; Wicklund, E; Wilbur, S; Williams, G; Williams, H H; Wilson, P; Winer, B L; Wittichh, P; Wolbers, S; Wolfe, C; Wright, T; Wu, X; Würthwein, F; Wynne, S M; Xie, S; Yagil, A; Yamamoto, K; Yamaoka, J; Yango, U K; Yang, Y C; Yao, W M; Yeh, G P; Yoh, J; Yorita, K; Yoshida, T; Yu, G B; Yu, I; Yu, S S; Yun, J C; Zanelloaa, L; Zanetti, A; Zhang, X; Zhengd, Y; Zucchelliv, S

    2008-01-01

    Fully reconstructed top-antitop-events are used to determine the fractions of right-handed and longitudinally polarized W bosons produced in top-quark decays. The helicity fractions are sensitive to the couplings and the Dirac structure of the Wtb vertex. This paper reports measurements of the W-boson helicity fractions from two different methods using data corresponding to an integrated luminosity of 1.9 fb-1 of proton-antiproton collisions collected by the CDF II detector operating at the Fermilab Tevatron.

  18. Evolution and breakdown of helical vortex wakes behind a wind turbine

    Science.gov (United States)

    Nemes, A.; Sherry, M.; Lo Jacono, D.; Blackburn, H. M.; Sheridan, J.

    2014-12-01

    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.

  19. Human Skin as Arrays of Helical Antennas in the Millimeter and Submillimeter Wave Range

    Science.gov (United States)

    Feldman, Yuri; Puzenko, Alexander; Ben Ishai, Paul; Caduff, Andreas; Agranat, Aharon J.

    2008-03-01

    Recent studies of the minute morphology of the skin by optical coherence tomography showed that the sweat ducts in human skin are helically shaped tubes, filled with a conductive aqueous solution. A computer simulation study of these structures in millimeter and submillimeter wave bands show that the human skin functions as an array of low-Q helical antennas. Experimental evidence is presented that the spectral response in the sub-Terahertz region is governed by the level of activity of the perspiration system. It is also correlated to physiological stress as manifested by the pulse rate and the systolic blood pressure.

  20. 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.

  1. Bifurcation to 3D helical magnetic equilibrium in an axisymmetric toroidal device.

    Science.gov (United States)

    Bergerson, W F; Auriemma, F; Chapman, B E; Ding, W X; Zanca, P; Brower, D L; Innocente, P; Lin, L; Lorenzini, R; Martines, E; Momo, B; Sarff, J S; Terranova, D

    2011-12-16

    We report the first direct measurement of the internal magnetic field structure associated with a 3D helical equilibrium generated spontaneously in the core of an axisymmetric toroidal plasma containment device. Magnetohydrodynamic equilibrium bifurcation occurs in a reversed-field pinch when the innermost resonant magnetic perturbation grows to a large amplitude, reaching up to 8% of the mean field strength. Magnetic topology evolution is determined by measuring the Faraday effect, revealing that, as the perturbation grows, toroidal symmetry is broken and a helical equilibrium is established. © 2011 American Physical Society

  2. Bifurcation to 3D Helical Magnetic Equilibrium in an Axisymmetric Toroidal Device

    Science.gov (United States)

    Bergerson, W. F.; Auriemma, F.; Chapman, B. E.; Ding, W. X.; Zanca, P.; Brower, D. L.; Innocente, P.; Lin, L.; Lorenzini, R.; Martines, E.; Momo, B.; Sarff, J. S.; Terranova, D.

    2011-12-01

    We report the first direct measurement of the internal magnetic field structure associated with a 3D helical equilibrium generated spontaneously in the core of an axisymmetric toroidal plasma containment device. Magnetohydrodynamic equilibrium bifurcation occurs in a reversed-field pinch when the innermost resonant magnetic perturbation grows to a large amplitude, reaching up to 8% of the mean field strength. Magnetic topology evolution is determined by measuring the Faraday effect, revealing that, as the perturbation grows, toroidal symmetry is broken and a helical equilibrium is established.

  3. Evolution of Magnetic Helicity During Eruptive Flares and Coronal Mass Ejections

    CERN Document Server

    Priest, Eric; Janvier, Miho

    2016-01-01

    During eruptive solar flares and coronal mass ejections, a non-pot{\\-}ential magnetic arcade with much excess magnetic energy goes unstable and reconnects. It produces a twisted erupting flux rope and leaves behind a sheared arcade of hot coronal loops. We suggest that: the twist of the erupting flux rope can be determined from conservation of magnetic flux and magnetic helicity and equipartition of magnetic helicity. It depends on the geometry of the initial pre-eruptive structure. Two cases are considered, in the first of which a flux rope is not present initially but is created during the eruption by the reconnection. In the second case, a flux rope is present under the arcade in the pre-eruptive state, and the effect of the eruption and reconnection is to add an amount of magnetic helicity that depends on the fluxes of the rope and arcade and the geometry.

  4. All One-loop Maximally Helicity Violating Gluonic Amplitudes in QCD

    Energy Technology Data Exchange (ETDEWEB)

    Berger, Carola F.; Bern, Zvi; Dixon, Lance J.; Forde, Darren; Kosower, David A.

    2006-07-05

    We use on-shell recursion relations to compute analytically the one-loop corrections to maximally-helicity-violating n-gluon amplitudes in QCD. The cut-containing parts have been computed previously; our work supplies the remaining rational parts for these amplitudes, which contain two gluons of negative helicity and the rest positive, in an arbitrary color ordering. We also present formulae specific to the six-gluon cases, with helicities (-+-+++) and (-++-++), as well as numerical results for six, seven, and eight gluons. Our construction of the n-gluon amplitudes illustrates the relatively modest growth in complexity of the on-shell-recursive calculation as the number of external legs increases. These amplitudes add to the growing body of one-loop amplitudes known for all n, which are useful for studies of general properties of amplitudes, including their twistor-space structure.

  5. Spontaneous helicity of a polymer with side-loops confined to a cylinder

    CERN Document Server

    Chaudhuri, Debasish

    2011-01-01

    Inspired by recent experiments on the spatial organization of bacterial chromosomes, we consider a type of "bottle brush" polymer consisting of a flexible backbone chain, to which flexible side loops are connected. We show that such a model with an open linear backbone spontaneously adopts a helical structure with a well-defined pitch when confined to small cylindrical volume. This helicity persists over a range of sizes and aspect-ratios of the cylinder, provided the packing fraction of the chain is suitably large. We analyze this results in terms of the interplay between the effective stiffness and actual intra-chain packing effects caused by the side-loops in response to the confinement. For the case of a circular backbone, mimicking e.g. the E. coli chromosome, the polymer adopts a linearized configuration of two parallel helices connected at the cylinder poles.

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

    Science.gov (United States)

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

    2014-12-01

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

  7. STEADY STATE RESPONSE ANALYSIS ON HELICAL SPRING IMPACTED BY SHORT WAVE

    Institute of Scientific and Technical Information of China (English)

    FU Chaoxing; WANG Xiulun; WANG Jirong; LIU Dawei

    2006-01-01

    The wave transmission character of helical spring is applied to establish 2-DOF model of impacted vehicle on the wave impact theory. Considering the concrete structure of helical spring,corresponding responses under different impact frequency of the vehicle are imitated. The reason why the vehicle floor overresponds in some special frequency fields is explored based on analyzing the responses. When the impactions are in low frequency, the change of the spring has not been considered, but this does not affect the results. Because the transmission characters of velocity and acceleration are unanimous in helical spring, the responses characters of velocity and acceleration are also unanimous, the only difference is the magnitude, which can make use of acceleration responses to analyse velocity responses.

  8. What Helicity Can Tell Us about Solar Magnetic Fields

    Indian Academy of Sciences (India)

    Alexei A. Pevtsov

    2008-03-01

    Concept of magnetic/current helicity was introduced to solar physics about 15 years ago. Earlier studies led to discovery of such fundamental properties as hemispheric helicity rule, and role of helicity in magnetic reconnection and solar eruptions. Later, the concept was successfully applied in studies of different solar processes from solar dynamo to flare and CME phenomena. Although no silver bullet, helicity has proven to be a very useful “tool” in answering many still-puzzling questions about origin and evolution of solar magnetic fields. I present an overview of some helicity studies and briefly analyze their findings.

  9. Ion temperature gradient modes in toroidal helical systems

    Energy Technology Data Exchange (ETDEWEB)

    Kuroda, T. [Graduate University for Advanced Studies, Toki, Gifu (Japan); Sugama, H.; Kanno, R.; Okamoto, M.

    2000-04-01

    Linear properties of ion temperature gradient (ITG) modes in helical systems are studied. The real frequency, growth rate, and eigenfunction are obtained for both stable and unstable cases by solving a kinetic integral equation with proper analytic continuation performed in the complex frequency plane. Based on the model magnetic configuration for toroidal helical systems like the Large Helical Device (LHD), dependences of the ITG mode properties on various plasma equilibrium parameters are investigated. Particularly, relative effects of {nabla}B-curvature drifts driven by the toroidicity and by the helical ripples are examined in order to compare the ITG modes in helical systems with those in tokamaks. (author)

  10. Kinematic equations to grind a helical drill point on a virtual axis drill sharpener

    Institute of Scientific and Technical Information of China (English)

    陈五一; 陈鼎昌

    2000-01-01

    The basic structure of a virtual axis drill grinder is presented in terms of the spatial vectors and thegrinding parameters calculated according to the geometry of a helical drill point. The kinematic equations for sharpening the drills on the virtual axis grinder are deduced using the grinding parameters via vector-matrix txansformation.

  11. Stabilization of peptide helices by length and vibrational free energies: Ab initio case study of polyalanine

    Science.gov (United States)

    Rossi, Mariana; Blum, Volker; Scheffler, Matthias

    2012-02-01

    Helices are one of the most abundant secondary structure ``building blocks" of polypeptides and proteins. Here, we explore helix stabilization as a function of peptide length and temperature [harmonic approximation to the vibrational free energy (FE)], for the alanine-based peptide, Ac-Alan-LysH^+ n=4-15, in the gas phase. For n=4-8, we predict the lowest energy structures in density-functional theory, using the van der Waals (vdW) corrected[1] PBE exchange-correlation potential. α-helices become the lowest energy structures at n 7-8 on the potential energy surface, but only barely and if including vdW interactions. At finite temperatures, the helices are further stabilized over compact conformers. While the vibrational entropy is the leading stabilizing term at 300 K, also the zero-point-energies favor the helical structures. For n>=8, the α-helix should be the only accessible conformer in the FE surface at 300 K, in agreement with experiment[2] and with our own comparison[3] of calculated ab initio anharmonic IR spectra to experimental IR multiple photon dissociation data for n=5, 10, and 15. [1] Tkatchenko and Scheffler, PRL 102, 073055 (2009); [2] Kohtani and Jarrold, JACS 108, 8454 (2004); [3] Rossi et al., JPCL 1, 3465 (2010).

  12. 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.

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

    Science.gov (United States)

    Overfelt, P L

    2001-08-01

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

  14. Magnetic helicity balance in the Sustained Spheromak Plasma Experiment

    Science.gov (United States)

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

    2003-07-01

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

  15. Large-scale flow generation by inhomogeneous helicity

    CERN Document Server

    Yokoi, Nobumitsu

    2015-01-01

    The effect of kinetic helicity (velocity--vorticity correlation) on turbulent momentum transport is investigated. The turbulent kinetic helicity (pseudoscalar) enters into the Reynolds stress (mirrorsymmetric tensor) expression in the form of a helicity gradient as the coupling coefficient for the mean vorticity and/or the angular velocity (axial vector), which suggests the possibility of mean-flow generation in the presence of inhomogeneous helicity. This inhomogeneous helicity effect, which was previously confirmed at the level of a turbulence- or closure-model simulation, is examined with the aid of direct numerical simulations of rotating turbulence with non-uniform helicity sustained by an external forcing. The numerical simulations show that the spatial distribution of the Reynolds stress is in agreement with the helicity-related term coupled with the angular velocity, and that a large-scale flow is generated in the direction of angular velocity. Such a large-scale flow is not induced in the case of hom...

  16. Helicity, Topology and Kelvin Waves in reconnecting quantum knots

    CERN Document Server

    di Leoni, P Clark; Brachet, M E

    2016-01-01

    Helicity is a topological invariant that measures the linkage and knottedness of lines, tubes and ribbons. As such, it has found myriads of applications in astrophysics and solar physics, in fluid dynamics, in atmospheric sciences, and in biology. In quantum flows, where topology-changing reconnection events are a staple, helicity appears as a key quantity to study. However, the usual definition of helicity is not well posed in quantum vortices, and its computation based on counting links and crossings of vortex lines can be downright impossible to apply in complex and turbulent scenarios. We present a new definition of helicity which overcomes these problems. With it, we show that only certain reconnection events conserve helicity. In other cases helicity can change abruptly during reconnection. Furthermore, we show that these events can also excite Kelvin waves, which slowly deplete helicity as they interact nonlinearly, thus linking the theory of vortex knots with observations of quantum turbulence.

  17. Evolution of field line helicity during magnetic reconnection

    CERN Document Server

    Russell, Alexander J B; Hornig, Gunnar; Wilmot-Smith, Antonia L

    2015-01-01

    We investigate the evolution of field line helicity for non-zero magnetic fields that connect two boundaries, with emphasis on localized finite-B magnetic reconnection. Total (relative) magnetic helicity is already recognized as an important topological constraint on magnetohydrodynamic processes. Field line helicity offers further advantages because it preserves all topological information and can distinguish between different magnetic fields with the same total helicity. Magnetic reconnection changes field topology and field line helicity reflects these changes; the goal of this paper is to characterize that evolution. We start by deriving the evolution equation for field line helicity and examining its terms, also obtaining a simplified form for cases where dynamics are localized within the domain. The main result, which we support using kinematic examples, is that during localized reconnection in a topologically complex magnetic field, the evolution of field line helicity is dominated by a work-like term ...

  18. Magnetic Energy and Helicity Budgets in the Active-Region Solar Corona. I. Linear Force-Free Approximation

    CERN Document Server

    Georgoulis, M K

    2007-01-01

    We self-consistently derive the magnetic energy and relative magnetic helicity budgets of a three-dimensional linear force-free magnetic structure rooted in a lower boundary plane. For the potential magnetic energy we derive a general expression that gives results practically equivalent to those of the magnetic Virial theorem. All magnetic energy and helicity budgets are formulated in terms of surface integrals applied to the lower boundary, thus avoiding computationally intensive three-dimensional magnetic field extrapolations. We analytically and numerically connect our derivations with classical expressions for the magnetic energy and helicity, thus presenting a so-far lacking unified treatment of the energy/helicity budgets in the constant-alpha approximation. Applying our derivations to photospheric vector magnetograms of an eruptive and a noneruptive solar active regions, we find that the most profound quantitative difference between these regions lies in the estimated free magnetic energy and relative ...

  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. Weaving knotted vector fields with tunable helicity

    CERN Document Server

    Kedia, Hridesh; Dennis, Mark R; Irvine, William T M

    2016-01-01

    We present a general construction of divergence-free knotted vector fields from complex scalar fields, whose closed field lines encode many kinds of knots and links, including torus knots, their cables, the figure-8 knot and its generalizations. As finite-energy physical fields they represent initial states for fields such as the magnetic field in a plasma, or the vorticity field in a fluid. We give a systematic procedure for calculating the vector potential, starting from complex scalar functions with knotted zero filaments, thus enabling an explicit computation of the helicity of these knotted fields. The construction can be used to generate isolated knotted flux tubes, filled by knots encoded in the lines of the vector field. Lastly we give examples of manifestly knotted vector fields with vanishing helicity. Our results provide building blocks for analytical models and simulations alike.

  1. Helicity of the toroidal vortex with swirl

    CERN Document Server

    Bannikova, Elena Yu; Poslavsky, Sergey A

    2016-01-01

    On the basis of solutions of the Bragg-Hawthorne equations we discuss the helicity of thin toroidal vortices with the swirl - the orbital motion along the torus diretrix. It is shown that relationship of the helicity with circulations along the small and large linked circles - directrix and generatrix of the torus - depends on distribution of the azimuthal velocity in the core of the swirling vortex ring. In the case of non-homogeneous swirl this relationship differs from the well-known Moffat relationship - the doubled product of such circulations multiplied by the number of links. The results can be applied to vortices in planetary atmospheres and to vortex movements in the vicinity of active galactic nuclei.

  2. Driving Solar Eruptions via Helicity Condensation

    Science.gov (United States)

    Dahlin, Joel Timothy; Antiochos, Spiro K.; DeVore, C. Richard

    2017-08-01

    One of the important questions in solar physics is, “How does the Sun store and release energy in coronal mass ejections"? Key to answering this question is understanding how the sun (a) stores magnetic energy in the form of a solar filament and (b) suddenly releases this energy as a coronal mass ejection. An important model for the energy release is the ‘magnetic breakout’ - a positive-feedback mechanism between filament ejection and magnetic reconnection. Recent theory and numerical calculations have demonstrated that helicity injected into the corona via photospheric driving can accumulate in the form of a filament channel of strongly sheared magnetic fields that can provide the free energy for a coronal mass ejection. We present preliminary calculations that, for the first time, incorporate helicity injection in a breakout topology to model a fully self-consistent eruption, from filament formation to ejection.

  3. Weyl spinors and the helicity formalism

    CERN Document Server

    Diaz-Cruz, J Lorenzo; Meza-Aldama, O; Perez, Jonathan Reyes

    2015-01-01

    In this work we give a review of the original formulation of the relativistic wave equation for particles with spin one-half. Traditionally \\`a la Dirac, it's proposed that the ``square root'' of the Klein-Gordon (K-G) equation involves a 4 component (Dirac) spinor and in the non-relativistic limit it can be written as 2 equations for two 2 component spinors. On the other hand, there exists Weyl's formalism, in which one works from the beginning with 2 component Weyl spinors, which are the fundamental objects of the helicity formalism. In this work we rederive Weyl's equations directly, starting from K-G equation. We also obtain the electromagnetic interaction through minimal coupling and we get the interaction with the magnetic moment. As an example of the use of that formalism, we calculate Compton scattering using the helicity methods.

  4. Helical apodizers for tunable hyper Gaussian masks

    Science.gov (United States)

    Ojeda-Castañeda, J.; Ledesma, Sergio; Gómez-Sarabia, Cristina M.

    2013-09-01

    We discuss an optical method for controlling the half-width of Gaussian like transmittance windows, by using a pair of absorption masks that have both radial and helical amplitude variations. For describing the radial part of the proposed masks, we employ amplitude transmittance profiles of the form T(ρ) = exp(- ρ s ). For s = 2, one has an amplitude transmittance that is proportional to a Gaussian function. A sub Gaussian mask is defined by a value of s 2, one has super Gaussian masks. Our discussion considers that any of these radially varying masks has also helical modulations. We show that by using a suitable pair of this type of masks, one can control the halfwidth of Gaussian like windows.

  5. Instabilities of a rotating helical rod

    Science.gov (United States)

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

    2016-11-01

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

  6. Helical propulsion in shear-thinning fluids

    CERN Document Server

    Gomez, Saul; Lauga, Eric; Zenit, Roberto

    2016-01-01

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

  7. Helical Muon Beam Cooling Channel Engineering Design

    Energy Technology Data Exchange (ETDEWEB)

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

    2012-05-01

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

  8. Helicity evolution at small x : Flavor singlet and nonsinglet observables

    Science.gov (United States)

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

    2017-01-01

    We extend our earlier results for the quark helicity evolution at small x [J. High Energy Phys. 01 (2016) 072, 10.1007/JHEP01(2016)072] to derive the small-x asymptotics of the flavor singlet and flavor nonsinglet quark helicity TMDs and PDFs and of the g1 structure function. In the flavor singlet case we rederive the evolution equations obtained in our previous paper on the subject [J. High Energy Phys. 01 (2016) 072, 10.1007/JHEP01(2016)072], performing additional cross-checks of our results. In the flavor nonsinglet case we construct new small-x evolution equations by employing the large-Nc limit. All evolution equations resum double-logarithmic powers of αsln2(1 /x ) in the polarization-dependent evolution along with the single-logarithmic powers of αsln (1 /x ) in the unpolarized evolution which includes saturation effects. We solve the linearized flavor nonsinglet equation analytically, obtaining an intercept which agrees with the one calculated earlier by Bartels, Ermolaev and Ryskin [Z. Phys. C 70, 273 (1996)] using the infrared evolution equations. Our numerical solution of the linearized large-Nc evolution equations for the flavor singlet case is presented in the accompanying Letter [Phys. Rev. Lett. 118, 052001 (2017), 10.1103/PhysRevLett.118.052001] and is further discussed here.

  9. A new self-propelled magnetic bearing with helical windings

    Science.gov (United States)

    Shayak, B.

    2016-12-01

    In this work, a design is proposed for an active, permanent magnet based, self-propelled magnetic bearing, i.e. levitating motor having the following features: (i) simple winding structure, (ii) high load supporting capacity, (iii) no eccentricity sensors, (iv) stable confinement in all translational dimensions, (v) stable confinement in all rotational dimensions, and (vi) high efficiency. This design uses an architecture consisting of a helically wound three-phase stator, and a rotor with the magnets also arranged in a helical manner. Active control is used to excite the rotor at a torque angle lying in the second quadrant. This torque angle is independent of the rotor's position inside the stator cavity; hence the control algorithm is similar to that of a conventional permanent magnet synchronous motor. It is motivated through a physical argument that the bearing rotor develops a lift force proportional to the output torque and that it remains stably confined in space. These assertions are then proved rigorously through a calculation of the magnetic fields, forces and torques. The stiffness matrix of the system is presented and a discussion of stable and unstable operating regions is given.

  10. Modal properties of three-dimensional helical planetary gears

    Science.gov (United States)

    Eritenel, Tugan; Parker, Robert G.

    2009-08-01

    The structured modal properties of single-stage helical planetary gears with equally spaced planets are categorized and mathematically proved. Compared to prior two-dimensional analyses of spur gears, this study examines the three-dimensional motion of the helical gears and shafts. A lumped-parameter model is formulated to obtain the equations of motion. The gear-shaft bodies are modeled as rigid bodies with compliant bearings at arbitrary axial locations on the shafts. A translational and a tilting stiffness account for the force and moment transmission at the gear mesh interface. The derived modal properties generalize those of two-dimensional spur planetary gears; there are twice as many degrees of freedom and natural frequencies due to the added tilting and axial motion. All vibration modes are categorized as rotational-axial, translational-tilting, and planet modes. The modal properties are shown to hold even for configurations that are not symmetric about the gear plane, due to, for example, shaft bearings not being equidistant from the gear plane.

  11. 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}.

  12. 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...

  13. A Chiral Helical Compound Based on Achiral Components

    Institute of Scientific and Technical Information of China (English)

    ZHANG Qi-Wei; WANG Gui-Xian

    2007-01-01

    The title compound, [Cu(dpa)(2,2'-bipy)(H2O)2]n 1 (H2dpa = diphenic acid and 2,2'- bipy = 2,2'-bipyridine), has been synthesized and its structure was determined by single-crystal X-ray diffraction. The crystal is of orthorhombic, space group P212121 with a = 10.597(4), b = 11.317(4), c = 17.630(7) (A), V = 2114.3(14)(A)3, C24H20CuN2O6, Mr = 495.97, Z = 4, Dc = 1.558 g/cm3, μ = 1.079 mm-1, F(000) = 1020, Flack value = 0.052(18), R = 0.0430 and wR = 0.1016 for 3381 observed reflections (Ⅰ > 2σ(Ⅰ)). In compound 1, the dpa ligands link metal ions into helical structures in the same direction.

  14. Field of a helical Siberian Snake

    Energy Technology Data Exchange (ETDEWEB)

    Luccio, A. [Brookhaven National Lab., Upton, NY (United States)

    1995-02-01

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

  15. Automatic generation of tree level helicity amplitudes

    CERN Document Server

    Stelzer, T

    1994-01-01

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

  16. Droplets climbing a rotating helical fiber

    CERN Document Server

    Texier, Baptiste Darbois

    2015-01-01

    A liquid droplet is placed on a rotating helical fiber. We find that the droplet may slide down, attach or climb up the fiber. We inspect experimentally the domain of existence of these three behaviors as a function of the geometrical characteristics of the fiber, its angle relatively to the horizontal, the wetting properties of the fluid and the rotating speed of the helix. A theoretical model is proposed in order to capture the boundaries of the experimental phase diagram.

  17. Helicity formalism for spin-2 particles

    Energy Technology Data Exchange (ETDEWEB)

    Gleisberg, Tanju [Institut fuer Theoretische Physik, TU Dresden, D-01062 Dresden (Germany); Physics Department, University of Florida, Gainesville, FL 32611 (United States); Krauss, Frank [Theory Division, CERN, CH-1211 Geneva 23 (Switzerland); Matchev, Konstantin T. [Physics Department, University of Florida, Gainesville, FL 32611 (United States) and LEPP, Cornell University, Ithaca, NY 14853 (United States)]. E-mail: matchev@mail.lns.cornell.edu; Schaelicke, Andreas [Institut fuer Theoretische Physik, TU Dresden, D-01062 Dresden (Germany); Schumann, Steffen [Institut fuer Theoretische Physik, TU Dresden, D-01062 Dresden (Germany); Soff, Gerhard [Institut fuer theoretische Physik, TU Dresden, D-01062 Dresden (Germany)

    2003-09-01

    We develop the helicity formalism for spin-2 particles and apply it to the case of gravity in flat extra dimensions. We then implement the large extra dimensions scenario of Arkani-Hamed, Dimopoulos and Dvali in the program AMEGIC++, allowing for an easy calculation of arbitrary processes involving the emission or exchange of gravitons. We complete the set of Feynman rules derived by Han, Lykken and Zhang, and perform several consistency checks of our implementation. (author)

  18. Physics of collapses in toroidal helical plasmas

    Energy Technology Data Exchange (ETDEWEB)

    Itoh, Kimitaka [National Inst. for Fusion Science, Toki, Gifu (Japan); Itoh, Sanae; Fukuyama, Atsushi; Yagi, Masatoshi

    1998-12-31

    Theoretical model for the collapse events in toroidal helical plasmas with magnetic hill is presented. There exists a turbulent-turbulent transition at a critical pressure gradient, leading to a sudden increase of the anomalous transport. When the magnetic shear is low, the nonlinear excitation of the global mode is possible. This model explains an abrupt growth of the perturbations, i.e., the trigger phenomena. Achievable limit of the plasma beta value is discussed. (author)

  19. Glycine and beta-branched residues support and modulate peptide helicity in membrane environments.

    Science.gov (United States)

    Li, S C; Deber, C M

    1992-10-26

    Transmembrane (TM) segments of integral membrane proteins are putatively alpha-helical in conformation once inserted into the membrane, yet consist of primary sequences rich in residues known in soluble proteins as helix-breakers (Gly) and beta-sheet promoters (Ile, Val, Thr). To examine the specific 2 degrees structure propensities of such residues in membrane environments, we have designed and synthesized a series of 20-residue peptides with 'guest' hydrophobic segments--expected to provide three turns of incipient alpha-helix content--embedded in 'host' hydrophilic (Lys-Ser) matrices. Circular dichroism (CD) spectra of the model peptides in water showed that significant helical content was observed only for peptides with high Ala content; others behaved as 'random coils'. However, in the membrane-mimetic environment of sodium dodecylsulfate (SDS) micelles, it was found that Gly can be accommodated as readily as Ala, and Ile or Val as readily as Leu, in hydrophobic alpha-helices. Further subtleties of structural preferences could be observed in electrically-neutral lyso-phosphatidylcholine (LPC) micelles, where helical propensity decreased in the order Ala-Leu-rich > Gly-Leu-rich > Gly-Ile(Val)-rich hydrophobic segments. The results conjure a role of environment-dependent helix-modulation for Gly, Ile, and Val residues--and suggest that these residues may provide, in part, the structural basis for conformational transitions within or adjacent to membrane domains, such as those accompanying membrane insertion and/or required for transport or signalling functions.

  20. Propulsion by Helical Strips in Circular Channels

    Science.gov (United States)

    Yesilyurt, Serhat; Demir, Ebru

    2016-11-01

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