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Sample records for modes structural insights

  1. Insight into structural phase transitions from the decoupled anharmonic mode approximation.

    Science.gov (United States)

    Adams, Donat J; Passerone, Daniele

    2016-08-03

    We develop a formalism (decoupled anharmonic mode approximation, DAMA) that allows calculation of the vibrational free energy using density functional theory even for materials which exhibit negative curvature of the potential energy surface with respect to atomic displacements. We investigate vibrational modes beyond the harmonic approximation and approximate the potential energy surface with the superposition of the accurate potential along each normal mode. We show that the free energy can stabilize crystal structures at finite temperatures which appear dynamically unstable at T  =  0. The DAMA formalism is computationally fast because it avoids statistical sampling through molecular dynamics calculations, and is in principle completely ab initio. It is free of statistical uncertainties and independent of model parameters, but can give insight into the mechanism of a structural phase transition. We apply the formalism to the perovskite cryolite, and investigate the temperature-driven phase transition from the P21/n to the Immm space group. We calculate a phase transition temperature between 710 and 950 K, in fair agreement with the experimental value of 885 K. This can be related to the underestimation of the interaction of the vibrational states. We also calculate the main axes of the thermal ellipsoid and can explain the experimentally observed increase of its volume for the fluorine by 200-300% throughout the phase transition. Our calculations suggest the appearance of tunneling states in the high temperature phase. The convergence of the vibrational DOS and of the critical temperature with respect of reciprocal space sampling is investigated using the polarizable-ion model.

  2. The vaccinia virus DNA polymerase structure provides insights into the mode of processivity factor binding

    Czech Academy of Sciences Publication Activity Database

    Tarbouriech, N.; Ducournau, C.; Hutin, S.; Mas, P.J.; Man, Petr; Forest, E.; Hart, D.J.; Peyrefitte, Ch.N.; Burmeister, W.P.; Iseni, F.

    2017-01-01

    Roč. 8, NOV 13 (2017), s. 1-12, č. článku 1455. ISSN 2041-1723 R&D Projects: GA MŠk(CZ) LQ1604 Institutional support: RVO:61388971 Keywords : PROTEIN SECONDARY STRUCTURE * CRYSTAL-STRUCTURE * GENETIC-CHARACTERIZATION Subject RIV: CE - Biochemistry OBOR OECD: Biochemistry and molecular biology Impact factor: 12.124, year: 2016

  3. Structure-guided approach identifies a novel class of HIV-1 ribonuclease H inhibitors: binding mode insights through magnesium complexation and site-directed mutagenesis studies

    DEFF Research Database (Denmark)

    Poongavanam, Vasanthanathan; Corona, Angela; Steinmann, Casper

    2018-01-01

    is a long and expensive process that can be speeded up by in silico methods. In the present study, a structure-guided screening is coupled with a similarity-based search on the Specs database to identify a new class of HIV-1 RNase H inhibitors. Out of the 45 compounds selected for experimental testing, 15...... inhibited the RNase H function below 100 μM with three hits exhibiting IC50 values active compound, AA, inhibits HIV-1 RNase H with an IC50 of 5.1 μM and exhibits a Mg-independent mode of inhibition. Site-directed mutagenesis studies provide valuable insight into the binding mode of newly...

  4. Hyperons: Insights into baryon structures

    International Nuclear Information System (INIS)

    Lach, J.

    1991-08-01

    The baryon octet is composed mainly of hyperons. Modern high energy hyperon beams provide a tool for the study of hyperon static properties and interactions. Experiments with these beams have provided new insights into hyperon rare decays, magnetic moments, and interactions. These experiments provide us with insights into the strong, weak, and electromagnetic structure of the baryons. 65 refs., 45 figs., 5 tabs

  5. A structural insight into the P1S1 binding mode of diaminoethylphosphonic and phosphinic acids, selective inhibitors of alanine aminopeptidases

    Energy Technology Data Exchange (ETDEWEB)

    Węglarz-Tomczak, Ewelina; Berlicki, Łukasz; Pawełczak, Małgorzata; Nocek, Bogusław; Joachimiak, Andrzej; Mucha, Artur

    2016-07-01

    N0 -substituted 1,2-diaminoethylphosphonic acids and 1,2-diaminoethylphosphinic dipeptides were explored to unveil the structural context of the unexpected selectivity of these inhibitors of M1 alanine aminopeptidases (APNs) versus M17 leucine aminopeptidase (LAP). The diaminophosphonic acids were obtained via aziridines in an improved synthetic procedure that was further expanded for the phosphinic pseudodipeptide system. The inhibitory activity, measured for three M1 and one M17 metalloaminopeptidases of different sources (bacterial, human and porcine), revealed several potent compounds (e.g., Ki ¼ 65 nM of 1u for HsAPN). Two structures of an M1 representative (APN from Neisseria meningitidis) in complex with N-benzyl-1,2-diaminoethylphosphonic acid and N-cyclohexyl-1,2- diaminoethylphosphonic acid were determined by the X-ray crystallography. The analysis of these structures and the models of the phosphonic acid complexes of the human ortholog provided an insight into the role of the additional amino group and the hydrophobic substituents of the ligands within the S1 active site region.

  6. Mode structure of active resonators

    NARCIS (Netherlands)

    Ernst, G.J.; Witteman, W.J.

    1973-01-01

    An analysis is made of the mode structure of lasers when the interaction with the active medium is taken into account. We consider the combined effect of gain and refractive-index variations for arbitrary mirror configurations. Using a dimensionless round-trip matrix for a medium with a quadratic

  7. New insights into the structure and mode of action of Mo-CBP3, an antifungal chitin-binding protein of Moringa oleifera seeds.

    Directory of Open Access Journals (Sweden)

    Adelina B Batista

    Full Text Available Mo-CBP3 is a chitin-binding protein purified from Moringa oleifera Lam. seeds that displays inhibitory activity against phytopathogenic fungi. This study investigated the structural properties and the antifungal mode of action of this protein. To this end, circular dichroism spectroscopy, antifungal assays, measurements of the production of reactive oxygen species and microscopic analyses were utilized. Mo-CBP3 is composed of 30.3% α-helices, 16.3% β-sheets, 22.3% turns and 30.4% unordered forms. The Mo-CBP3 structure is highly stable and retains its antifungal activity regardless of temperature and pH. Fusarium solani was used as a model organism for studying the mechanisms by which this protein acts as an antifungal agent. Mo-CBP3 significantly inhibited spore germination and mycelial growth at 0.05 mg.mL-1. Mo-CBP3 has both fungistatic and fungicidal effects, depending on the concentration used. Binding of Mo-CBP3 to the fungal cell surface is achieved, at least in part, via electrostatic interactions, as salt was able to reduce its inhibitory effect. Mo-CBP3 induced the production of ROS and caused disorganization of both the cytoplasm and the plasma membrane in F. solani cells. Based on its high stability and specific toxicity, with broad-spectrum efficacy against important phytopathogenic fungi at low inhibitory concentrations but not to human cells, Mo-CBP3 has great potential for the development of new antifungal drugs or transgenic crops with enhanced resistance to phytopathogens.

  8. Functional Insights from Structural Genomics

    Energy Technology Data Exchange (ETDEWEB)

    Forouhar,F.; Kuzin, A.; Seetharaman, J.; Lee, I.; Zhou, W.; Abashidze, M.; Chen, Y.; Montelione, G.; Tong, L.; et al

    2007-01-01

    Structural genomics efforts have produced structural information, either directly or by modeling, for thousands of proteins over the past few years. While many of these proteins have known functions, a large percentage of them have not been characterized at the functional level. The structural information has provided valuable functional insights on some of these proteins, through careful structural analyses, serendipity, and structure-guided functional screening. Some of the success stories based on structures solved at the Northeast Structural Genomics Consortium (NESG) are reported here. These include a novel methyl salicylate esterase with important role in plant innate immunity, a novel RNA methyltransferase (H. influenzae yggJ (HI0303)), a novel spermidine/spermine N-acetyltransferase (B. subtilis PaiA), a novel methyltransferase or AdoMet binding protein (A. fulgidus AF{_}0241), an ATP:cob(I)alamin adenosyltransferase (B. subtilis YvqK), a novel carboxysome pore (E. coli EutN), a proline racemase homolog with a disrupted active site (B. melitensis BME11586), an FMN-dependent enzyme (S. pneumoniae SP{_}1951), and a 12-stranded {beta}-barrel with a novel fold (V. parahaemolyticus VPA1032).

  9. Production in Pichia pastoris, antifungal activity and crystal structure of a class I chitinase from cowpea (Vigna unguiculata): Insights into sugar binding mode and hydrolytic action.

    Science.gov (United States)

    Landim, Patrícia G Castro; Correia, Tuana O; Silva, Fredy D A; Nepomuceno, Denise R; Costa, Helen P S; Pereira, Humberto M; Lobo, Marina D P; Moreno, Frederico B M B; Brandão-Neto, José; Medeiros, Suelen C; Vasconcelos, Ilka M; Oliveira, José T A; Sousa, Bruno L; Barroso-Neto, Ito L; Freire, Valder N; Carvalho, Cristina P S; Monteiro-Moreira, Ana C O; Grangeiro, Thalles B

    2017-04-01

    A cowpea class I chitinase (VuChiI) was expressed in the methylotrophic yeast P. pastoris. The recombinant protein was secreted into the culture medium and purified by affinity chromatography on a chitin matrix. The purified chitinase migrated on SDS-polyacrylamide gel electrophoresis as two closely-related bands with apparent molecular masses of 34 and 37 kDa. The identity of these bands as VuChiI was demonstrated by mass spectrometry analysis of tryptic peptides and N-terminal amino acid sequencing. The recombinant chitinase was able to hydrolyze colloidal chitin but did not exhibit enzymatic activity toward synthetic substrates. The highest hydrolytic activity of the cowpea chitinase toward colloidal chitin was observed at pH 5.0. Furthermore, most VuChiI activity (approximately 92%) was retained after heating to 50 °C for 30 min, whereas treatment with 5 mM Cu 2+ caused a reduction of 67% in the enzyme's chitinolytic activity. The recombinant protein had antifungal activity as revealed by its ability to inhibit the spore germination and mycelial growth of Penicillium herquei. The three-dimensional structure of VuChiI was resolved at a resolution of 1.55 Å by molecular replacement. The refined model had 245 amino acid residues and 381 water molecules, and the final R-factor and R free values were 14.78 and 17.22%, respectively. The catalytic domain of VuChiI adopts an α-helix-rich fold, stabilized by 3 disulfide bridges and possessing a wide catalytic cleft. Analysis of the crystallographic model and molecular docking calculations using chito-oligosaccharides provided evidences about the VuChiI residues involved in sugar binding and catalysis, and a possible mechanism of antifungal action is suggested. Copyright © 2017 Elsevier B.V. and Société Française de Biochimie et Biologie Moléculaire (SFBBM). All rights reserved.

  10. Component mode synthesis in structural dynamics

    International Nuclear Information System (INIS)

    Reddy, G.R.; Vaze, K.K.; Kushwaha, H.S.

    1993-01-01

    In seismic analysis of Nuclear Reactor Structures and equipments eigen solution requires large computer time. Component mode synthesis is an efficient technique with which one can evaluate dynamic characteristics of a large structure with minimum computer time. Due to this reason it is possible to do a coupled analysis of structure and equipment which takes into account the interaction effects. Basically in this the method large size structure is divided into small substructures and dynamic characteristics of individual substructure are determined. The dynamic characteristics of entire structure are evaluated by synthesising the individual substructure characteristics. Component mode synthesis has been applied in this paper to the analysis of a tall heavy water upgrading tower. Use of fixed interface normal modes, constrained modes, attachment modes in the component mode synthesis using energy principle and using Ritz vectors have been discussed. The validity of this method is established by solving fixed-fixed beam and comparing the results obtained by conventional and classical method. The eigen value problem has been solved using simultaneous iteration method. (author)

  11. Structural insights into transcription complexes

    NARCIS (Netherlands)

    Berger, I.; Blanco, A.G.; Boelens, R.; Cavarelli, J.; Coll, M.; Folkers, G.E.; Nie, Y.; Pogenberg, V.; Schultz, P.; Wilmanns, M.; Moras, D.; Poterszman, A.

    2011-01-01

    Control of transcription allows the regulation of cell activity in response to external stimuli and research in the field has greatly benefited from efforts in structural biology. In this review, based on specific examples from the European SPINE2-COMPLEXES initiative, we illustrate the impact of

  12. Mode structure of a quantum cascade laser

    Science.gov (United States)

    Bogdanov, A. A.; Suris, R. A.

    2011-03-01

    We analyze the mode structure of a quantum cascade laser (QCL) cavity considering the surface plasmon-polariton modes and familiar modes of hollow resonator jointly, within a single model. We present a comprehensive mode structure analysis of the laser cavity, varying its geometric parameters and free electron concentration inside cavity layers within a wide range. Our analysis covers, in particular, the cases of metal-insulator-metal and insulator-metal-insulator waveguides. We discuss the phenomenon of negative dispersion for eigenmodes in detail and explain the nature of this phenomenon. We specify a waveguide parameters domain in which negative dispersion exists. The mode structure of QCL cavity is considered in the case of the anisotropic electrical properties of the waveguide materials. We show that anisotropy of the waveguide core results in propagation of Langmuir modes that are degenerated in the case of the isotropic core. Comparative analysis of optical losses due to free carrier absorption is presented for different modes within the frequency range from terahertz to ultraviolet frequencies.

  13. Boundary modes in quasiperiodic elastic structures

    Science.gov (United States)

    Rosa, Matheus I. N.; Pal, Raj K.; Arruda, José R. F.; Ruzzene, Massimo

    2018-03-01

    Topological metamaterials are a new class of materials that support topological modes such as edge modes and interface modes, which are commonly immune to scattering and imperfections. This novelty has been the subject of extensive research in many branches of physics such as electronics, photonics, phononics, and acoustics. The nontrivial topological properties related to the presence of topological modes are tipically found in periodic media. However, it was recently demonstrated that structures called quasicrystals may also exhibit nontrivial topological behavior attributed to dimensions higher than that of the quasicrystal. While quasiperiodicity has received a lot of attention in the fields of crystallography and photonics, research into quasiperiodic elastic structures has been scarce. In this paper, we show how the concepts of quasiperiodicity may be applied to the design of topological mechanical metamaterials. We start by investigating the boundary modes present in quasiperiodic 1D phononic lattices. These modes have the interesting property of being localized at either one of the two different boundaries depending on the value of an additional parameter, which is remnant of the higher dimension. A smooth variation of this parameter in either time or a spatial dimension can lead to a robust transfer of energy between two sites of the structure. We present an idealized mechanical system composed by an array of coupled rods that may be used as a platform for realizing this kind of robust transfer of energy. These are preliminary investigations into a entirely new class of structures which may lead to novel engineering applications.

  14. Failure modes of laminate structures

    Energy Technology Data Exchange (ETDEWEB)

    Gordon, L.B.; Druce, R.L.; Wilson, M.J.

    1987-06-01

    Laminate structures composed of alternating thin layers of conductor and dielectric material are commonly used in energy storage and transmission components. The failure of the dielectric layers in regions of high field stress, with applied 60 Hz ac, dc and impulse voltages, was studied. Several geometries were compared, including staggered and flush edges. Electrical trees developed between the laminated dielectric layers. The visual characteristics and growth rates of the electrical trees under ac, dc and impulse stresses were different. Partial discharge detection and analysis was used to measure the inception voltage and discharge activity at the conductor edge voids, to observe tree formation and growth, and to predict impending failure due to dielectric erosion. Electric field distributions were modeled and partial discharge inception levels were estimated from known void geometries. The staggered edge geometry appears to enhance the electric field stress at the recessed electrode.

  15. Soft modes and structural phase transitions

    Energy Technology Data Exchange (ETDEWEB)

    Venkataraman, G [Reactor Research Centre, Kalpakkam (India)

    1979-12-01

    A survey of soft modes and their relationship to structural phase transitions is presented. After introducing the concept of a soft mode, the origin of softening is considered from a lattice-dynamical point. The Landau theory approach to structural transitions is then discussed, followed by a generalisation of the soft-mode concept through the use of the dynamic order-parameter susceptibility. The relationship of soft modes to broken symmetry is also examined. Experimental results for several classes of crystals are next presented, bringing out various features such as the co-operative Jahn-Teller effect. The survey concludes with a discussion of the central peak, touching upon both the experimental results and the theoretical speculations.

  16. Mode Interaction in Structures - An Overview

    DEFF Research Database (Denmark)

    Byskov, Esben

    2004-01-01

    Abstract Koiter [1] was the first to formulate an asymptotic expansion to investigate postbuckling behavior and imperfection sensitivity of elastic structures. Since then, a large number of analyses of particular structures have appeared as well as some new expansions aimed at specific problems, ...... analyses must always be preferred because asymptotic expansions are obsolete. Keywords: stability, elastic, mode interaction....

  17. IPE data base structure and insights

    International Nuclear Information System (INIS)

    Lehner, J.; Youngblood, R.

    1993-01-01

    A data base (the ''IPE Insights Data Base''), has been developed that stores data obtained from the Individual Plant Examinations (IPEs) which licensees of nuclear power plants are conducting in response to the Nuclear Regulatory Commission's (NRC) Generic Letter GL88-20. The data base, which is a collection of linked dbase files, stores information about individual plant designs, core damage frequency, and containment performance in a uniform, structured way. This data base can be queried and used as a computational tool to derive insights regarding the plants for which data is stored. This paper sets out the objectives of the IPE Insights Data Base, describes its structure and contents, illustrates sample queries, and discusses possible future uses

  18. IPE data base structure and insights

    International Nuclear Information System (INIS)

    Lehner, J.; Youngblood, R.

    1994-01-01

    A data base (the open-quotes IPE Insights Data Baseclose quotes), has been developed that stores data obtained from the Individual Plant Examinations (IPEs) which licensees of nuclear power plants are conducting in response to the Nuclear Regulatory Commission's (NRC) Generic Letter GL88-20. The data base, which is a collection of linked dBase files, stores information about individual plant designs, core damage frequency, and containment performance in a uniform, structured way. This data base can be queried and used as a computational tool to derive insights regarding the plants for which data is stored. This paper sets out the objectives of the IPE Insights Data Base, describes its structure and contents, illustrates sample queries, and discusses possible future uses

  19. Multi-Mode Cavity Accelerator Structure

    International Nuclear Information System (INIS)

    Jiang, Yong; Hirshfield, Jay Leonard

    2016-01-01

    This project aimed to develop a prototype for a novel accelerator structure comprising coupled cavities that are tuned to support modes with harmonically-related eigenfrequencies, with the goal of reaching an acceleration gradient >200 MeV/m and a breakdown rate <10"-"7/pulse/meter. Phase I involved computations, design, and preliminary engineering of a prototype multi-harmonic cavity accelerator structure; plus tests of a bimodal cavity. A computational procedure was used to design an optimized profile for a bimodal cavity with high shunt impedance and low surface fields to maximize the reduction in temperature rise Δ T. This cavity supports the TM010 mode and its 2nd harmonic TM011 mode. Its fundamental frequency is at 12 GHz, to benchmark against the empirical criteria proposed within the worldwide High Gradient collaboration for X-band copper structures; namely, a surface electric field E_s_u_r"m"a"x< 260 MV/m and pulsed surface heating Δ T"m"a"x< 56 °K. With optimized geometry, amplitude and relative phase of the two modes, reductions are found in surface pulsed heating, modified Poynting vector, and total RF power - as compared with operation at the same acceleration gradient using only the fundamental mode.

  20. Multi-Mode Cavity Accelerator Structure

    Energy Technology Data Exchange (ETDEWEB)

    Jiang, Yong [Yale Univ., New Haven, CT (United States); Hirshfield, Jay Leonard [Omega-P R& D, Inc., New Haven, CT (United States)

    2016-11-10

    This project aimed to develop a prototype for a novel accelerator structure comprising coupled cavities that are tuned to support modes with harmonically-related eigenfrequencies, with the goal of reaching an acceleration gradient >200 MeV/m and a breakdown rate <10-7/pulse/meter. Phase I involved computations, design, and preliminary engineering of a prototype multi-harmonic cavity accelerator structure; plus tests of a bimodal cavity. A computational procedure was used to design an optimized profile for a bimodal cavity with high shunt impedance and low surface fields to maximize the reduction in temperature rise ΔT. This cavity supports the TM010 mode and its 2nd harmonic TM011 mode. Its fundamental frequency is at 12 GHz, to benchmark against the empirical criteria proposed within the worldwide High Gradient collaboration for X-band copper structures; namely, a surface electric field Esurmax< 260 MV/m and pulsed surface heating ΔTmax< 56 °K. With optimized geometry, amplitude and relative phase of the two modes, reductions are found in surface pulsed heating, modified Poynting vector, and total RF power—as compared with operation at the same acceleration gradient using only the fundamental mode.

  1. The structure of ideal MHD Alfven modes

    International Nuclear Information System (INIS)

    Turnbull, A.D.; Chu, M.S.; Lao, L.L.; Greene, J.M.; Strait, E.J.; Chance, M.S.

    1991-01-01

    Continuum Alfven modes have undergone a resurgence in interest with the recent realization that so-called Toroidicity-Induced Alfven Eigenmodes (TAE modes) can be destabilized either by energetic beam ions in a strongly heated plasma or by alpha particles in a burning plasma. The GATO Ideal MHD Stability code, which minimizes the potential energy according to a variational formulation, has now been modified to isolate and calculate stable continuum eigenmodes. The existence of the TAE mode and its associated gap has been verified, using this code, for a circular cross-section, finite aspect ratio equilibrium. Moreover, the eigenfrequencies and eigenmodes obtained from this variational calculation are found to be in extremely good quantitative agreement with those obtained from the non-variational NOVA code. A systematic survey of the stable continuum has further revealed a surprising diversity in the structure of the continuum Alfven modes; the logarithmic singularity can be so broad, in some cases, as to occupy the whole cross-section. This has important implications for heating experiments which aim to locally excite the plasma by rf waves in the Alfven frequency range. The structure of several representative examples is discussed. The Alfven continuum, in general, and the TAE mode and its associated gap, in particular, are also found to be strongly modified by cross-sectional shaping. The dependence of the spectrum on various shaping factors is explored

  2. Atomic resolution crystal structure of VcLMWPTP-1 from Vibrio cholerae O395: Insights into a novel mode of dimerization in the low molecular weight protein tyrosine phosphatase family

    Energy Technology Data Exchange (ETDEWEB)

    Nath, Seema; Banerjee, Ramanuj; Sen, Udayaditya, E-mail: udayaditya.sen@saha.ac.in

    2014-07-18

    Highlights: • VcLMWPTP-1 forms dimer in solution. • The dimer is catalytically active unlike other reported dimeric LMWPTPs. • The formation of extended dimeric surface excludes the active site pocket. • The surface bears closer resemblance to eukaryotic LMWPTPs. - Abstract: Low molecular weight protein tyrosine phosphatase (LMWPTP) is a group of phosphotyrosine phosphatase ubiquitously found in a wide range of organisms ranging from bacteria to mammals. Dimerization in the LMWPTP family has been reported earlier which follows a common mechanism involving active site residues leading to an enzymatically inactive species. Here we report a novel form of dimerization in a LMWPTP from Vibrio cholera 0395 (VcLMWPTP-1). Studies in solution reveal the existence of the dimer in solution while kinetic study depicts the active form of the enzyme. This indicates that the mode of dimerization in VcLMWPTP-1 is different from others where active site residues are not involved in the process. A high resolution (1.45 Å) crystal structure of VcLMWPTP-1 confirms a different mode of dimerization where the active site is catalytically accessible as evident by a tightly bound substrate mimicking ligand, MOPS at the active site pocket. Although being a member of a prokaryotic protein family, VcLMWPTP-1 structure resembles very closely to LMWPTP from a eukaryote, Entamoeba histolytica. It also delineates the diverse surface properties around the active site of the enzyme.

  3. Latest Insights on Adenovirus Structure and Assembly

    Directory of Open Access Journals (Sweden)

    Carmen San Martín

    2012-05-01

    Full Text Available Adenovirus (AdV capsid organization is considerably complex, not only because of its large size (~950 Å and triangulation number (pseudo T = 25, but also because it contains four types of minor proteins in specialized locations modulating the quasi-equivalent icosahedral interactions. Up until 2009, only its major components (hexon, penton, and fiber had separately been described in atomic detail. Their relationships within the virion, and the location of minor coat proteins, were inferred from combining the known crystal structures with increasingly more detailed cryo-electron microscopy (cryoEM maps. There was no structural information on assembly intermediates. Later on that year, two reports described the structural differences between the mature and immature adenoviral particle, starting to shed light on the different stages of viral assembly, and giving further insights into the roles of core and minor coat proteins during morphogenesis [1,2]. Finally, in 2010, two papers describing the atomic resolution structure of the complete virion appeared [3,4]. These reports represent a veritable tour de force for two structural biology techniques: X-ray crystallography and cryoEM, as this is the largest macromolecular complex solved at high resolution by either of them. In particular, the cryoEM analysis provided an unprecedented clear picture of the complex protein networks shaping the icosahedral shell. Here I review these latest developments in the field of AdV structural studies.

  4. Structural insights into microtubule doublet interactions inaxonemes

    Energy Technology Data Exchange (ETDEWEB)

    Downing, Kenneth H.; Sui, Haixin

    2007-06-06

    Coordinated sliding of microtubule doublets, driven by dynein motors, produces periodic beating of the axoneme. Recent structural studies of the axoneme have used cryo-electron tomography to reveal new details of the interactions among some of the multitude of proteins that form the axoneme and regulate its movement. Connections among the several sets of dyneins, in particular, suggest ways in which their actions may be coordinated. Study of the molecular architecture of isolated doublets has provided a structural basis for understanding the doublet's mechanical properties that are related to the bending of the axoneme, and has also offered insight into its potential role in the mechanism of dynein activity regulation.

  5. Polarization Characterization of a Multi-Moded Feed Structure

    Data.gov (United States)

    National Aeronautics and Space Administration — The Polarization Characterization of a Multi-Moded Feed Structure projects characterize the polarization response of a multi-moded feed horn as an innovative...

  6. Structural resonance and mode of flutter of hummingbird tail feathers.

    Science.gov (United States)

    Clark, Christopher J; Elias, Damian O; Girard, Madeline B; Prum, Richard O

    2013-09-15

    Feathers can produce sound by fluttering in airflow. This flutter is hypothesized to be aeroelastic, arising from the coupling of aerodynamic forces to one or more of the feather's intrinsic structural resonance frequencies. We investigated how mode of flutter varied among a sample of hummingbird tail feathers tested in a wind tunnel. Feather vibration was measured directly at ~100 points across the surface of the feather with a scanning laser Doppler vibrometer (SLDV), as a function of airspeed, Uair. Most feathers exhibited multiple discrete modes of flutter, which we classified into types including tip, trailing vane and torsional modes. Vibratory behavior within a given mode was usually stable, but changes in independent variables such as airspeed or orientation sometimes caused feathers to abruptly 'jump' from one mode to another. We measured structural resonance frequencies and mode shapes directly by measuring the free response of 64 feathers stimulated with a shaker and recorded with the SLDV. As predicted by the aeroelastic flutter hypothesis, the mode shape (spatial distribution) of flutter corresponded to a bending or torsional structural resonance frequency of the feather. However, the match between structural resonance mode and flutter mode was better for tip or torsional mode shapes, and poorer for trailing vane modes. Often, the 3rd bending structural harmonic matched the expressed mode of flutter, rather than the fundamental. We conclude that flutter occurs when airflow excites one or more structural resonance frequencies of a feather, most akin to a vibrating violin string.

  7. Mode structure symmetry breaking of energetic particle driven beta-induced Alfvén eigenmode

    Science.gov (United States)

    Lu, Z. X.; Wang, X.; Lauber, Ph.; Zonca, F.

    2018-01-01

    The mode structure symmetry breaking of energetic particle driven Beta-induced Alfvén Eigenmode (BAE) is studied based on global theory and simulation. The weak coupling formula gives a reasonable estimate of the local eigenvalue compared with global hybrid simulation using XHMGC. The non-perturbative effect of energetic particles on global mode structure symmetry breaking in radial and parallel (along B) directions is demonstrated. With the contribution from energetic particles, two dimensional (radial and poloidal) BAE mode structures with symmetric/asymmetric tails are produced using an analytical model. It is demonstrated that the symmetry breaking in radial and parallel directions is intimately connected. The effects of mode structure symmetry breaking on nonlinear physics, energetic particle transport, and the possible insight for experimental studies are discussed.

  8. Radial mode structure of curvature-driven instabilities in EBT

    International Nuclear Information System (INIS)

    Spong, D.A.

    1983-01-01

    Viewgraphs describe the theoretical treatment of the radial mode structure of plasma instabilities in the Elmo Bumpy Torus. The calculation retains nonlocal structure of the modes, connects inner and outer ring regions together, uses a self-consistent finite β, includes the relativistic effects for the hot electron ring, and examines a wide range of parameters

  9. High frequency single mode traveling wave structure for particle acceleration

    Energy Technology Data Exchange (ETDEWEB)

    Ivanyan, M.I.; Danielyan, V.A.; Grigoryan, B.A.; Grigoryan, A.H. [CANDLE Synchrotron Research Institute, 0040 Yerevan (Armenia); Tsakanian, A.V. [CANDLE Synchrotron Research Institute, 0040 Yerevan (Armenia); Technische Universität Darmstadt, Institut TEMF, 64289 Darmstadt (Germany); Tsakanov, V.M., E-mail: tsakanov@asls.candle.am [CANDLE Synchrotron Research Institute, 0040 Yerevan (Armenia); Vardanyan, A.S.; Zakaryan, S.V. [CANDLE Synchrotron Research Institute, 0040 Yerevan (Armenia)

    2016-09-01

    The development of the new high frequency slow traveling wave structures is one of the promising directions in accomplishment of charged particles high acceleration gradient. The disc and dielectric loaded structures are the most known structures with slowly propagating modes. In this paper a large aperture high frequency metallic two-layer accelerating structure is studied. The electrodynamical properties of the slowly propagating TM{sub 01} mode in a metallic tube with internally coated low conductive thin layer are examined.

  10. The intrinsically disordered structural platform of the plant defence hub protein RPM1-interacting protein 4 provides insights into its mode of action in the host-pathogen interface and evolution of the nitrate-induced domain protein family.

    Science.gov (United States)

    Sun, Xiaolin; Greenwood, David R; Templeton, Matthew D; Libich, David S; McGhie, Tony K; Xue, Bin; Yoon, Minsoo; Cui, Wei; Kirk, Christopher A; Jones, William T; Uversky, Vladimir N; Rikkerink, Erik H A

    2014-09-01

    Arabidopsis thaliana (At) RPM1-interacting protein 4 (RIN4), targeted by many defence-suppressing bacterial type III effectors and monitored by several resistance proteins, regulates plant immune responses to pathogen-associated molecular patterns and type III effectors. Little is known about the overall protein structure of AtRIN4, especially in its unbound form, and the relevance of structure to its diverse biological functions. AtRIN4 contains two nitrate-induced (NOI) domains and is a member of the NOI family. Using experimental and bioinformatic approaches, we demonstrate that the unbound AtRIN4 is intrinsically disordered under physiological conditions. The intrinsically disordered polypeptide chain of AtRIN4 is interspersed with molecular recognition features (MoRFs) and anchor-identified long-binding regions, potentially allowing it to undergo disorder-to-order transitions upon binding to partner(s). A poly-l-proline II structure, often responsible for protein recognition, is also identified in AtRIN4. By performing bioinformatics analyses on RIN4 homologues from different plant species and the NOI proteins from Arabidopsis, we infer the conservation of intrinsic disorder, MoRFs and long-binding regions of AtRIN4 in other plant species and the NOI family. Intrinsic disorder and MoRFs could provide RIN4 proteins with the binding promiscuity and plasticity required to act as hubs in a pivotal position within plant defence signalling cascades. © 2014 FEBS.

  11. A Bloch mode expansion approach for analyzing quasi-normal modes in open nanophotonic structures

    DEFF Research Database (Denmark)

    de Lasson, Jakob Rosenkrantz; Kristensen, Philip Trøst; Mørk, Jesper

    2014-01-01

    We present a new method for determining quasi-normal modes in open nanophotonic structures using a modal ex- pansion technique. The outgoing wave boundary condition of the quasi-normal modes is satisfied automatically without absorbing boundaries, representing a significant advantage compared...

  12. Insight into nucleon structure from generalized parton distributions

    International Nuclear Information System (INIS)

    J.W. Negele; R.C. Brower; P. Dreher; R. Edwards; G. Fleming; Ph. Hagler; Th. Lippert; A.V.Pochinsky; D.B. Renner; D. Richards; K. Schilling; W. Schroers

    2004-01-01

    The lowest three moments of generalized parton distributions are calculated in full QCD and provide new insight into the behavior of nucleon electromagnetic form factors, the origin of the nucleon spin, and the transverse structure of the nucleon

  13. Edge-localized mode avoidance and pedestal structure in I-mode plasmas

    Energy Technology Data Exchange (ETDEWEB)

    Walk, J. R., E-mail: jrwalk@psfc.mit.edu; Hughes, J. W.; Hubbard, A. E.; Terry, J. L.; Whyte, D. G.; White, A. E.; Baek, S. G.; Reinke, M. L.; Theiler, C.; Churchill, R. M.; Rice, J. E. [MIT Plasma Science and Fusion Center, Cambridge, MA 02139-4307 (United States); Snyder, P. B.; Osborne, T. [General Atomics, San Diego, CA 92186-5608 (United States); Dominguez, A [Princeton Plasma Physics Laboratory, Princeton, NJ 08543-0451 (United States); Cziegler, I. [UCSD Center for Momentum Transport and Flow Organization, La Jolla, CA 92093-0417 (United States)

    2014-05-15

    I-mode is a high-performance tokamak regime characterized by the formation of a temperature pedestal and enhanced energy confinement, without an accompanying density pedestal or drop in particle and impurity transport. I-mode operation appears to have naturally occurring suppression of large Edge-Localized Modes (ELMs) in addition to its highly favorable scalings of pedestal structure and overall performance. Extensive study of the ELMy H-mode has led to the development of the EPED model, which utilizes calculations of coupled peeling-ballooning MHD modes and kinetic-ballooning mode (KBM) stability limits to predict the pedestal structure preceding an ELM crash. We apply similar tools to the structure and ELM stability of I-mode pedestals. Analysis of I-mode discharges prepared with high-resolution pedestal data from the most recent C-Mod campaign reveals favorable pedestal scalings for extrapolation to large machines—pedestal temperature scales strongly with power per particle P{sub net}/n{sup ¯}{sub e}, and likewise pedestal pressure scales as the net heating power (consistent with weak degradation of confinement with heating power). Matched discharges in current, field, and shaping demonstrate the decoupling of energy and particle transport in I-mode, increasing fueling to span nearly a factor of two in density while maintaining matched temperature pedestals with consistent levels of P{sub net}/n{sup ¯}{sub e}. This is consistent with targets for increased performance in I-mode, elevating pedestal β{sub p} and global performance with matched increases in density and heating power. MHD calculations using the ELITE code indicate that I-mode pedestals are strongly stable to edge peeling-ballooning instabilities. Likewise, numerical modeling of the KBM turbulence onset, as well as scalings of the pedestal width with poloidal beta, indicates that I-mode pedestals are not limited by KBM turbulence—both features identified with the trigger for large ELMs

  14. Cell Secretion: Current Structural and Biochemical Insights

    Directory of Open Access Journals (Sweden)

    Saurabh Trikha

    2010-01-01

    Full Text Available Essential physiological functions in eukaryotic cells, such as release of hormones and digestive enzymes, neurotransmission, and intercellular signaling, are all achieved by cell secretion. In regulated (calcium-dependent secretion, membrane-bound secretory vesicles dock and transiently fuse with specialized, permanent, plasma membrane structures, called porosomes or fusion pores. Porosomes are supramolecular, cup-shaped lipoprotein structures at the cell plasma membrane that mediate and control the release of vesicle cargo to the outside of the cell. The sizes of porosomes range from 150nm in diameter in acinar cells of the exocrine pancreas to 12nm in neurons. In recent years, significant progress has been made in our understanding of the porosome and the cellular activities required for cell secretion, such as membrane fusion and swelling of secretory vesicles. The discovery of the porosome complex and the molecular mechanism of cell secretion are summarized in this article.

  15. New insights into apoptosome structure and function.

    Science.gov (United States)

    Dorstyn, Loretta; Akey, Christopher W; Kumar, Sharad

    2018-05-15

    The apoptosome is a platform that activates apical procaspases in response to intrinsic cell death signals. Biochemical and structural studies in the past two decades have extended our understanding of apoptosome composition and structure, while illuminating the requirements for initiator procaspase activation. A number of studies have now provided high-resolution structures for apoptosomes from C. elegans (CED-4), D. melanogaster (Dark), and H. sapiens (Apaf-1), which define critical protein interfaces, including intra and interdomain interactions. This work also reveals interactions of apoptosomes with their respective initiator caspases, CED-3, Dronc and procaspase-9. Structures of the human apoptosome have defined the requirements for cytochrome c binding, which triggers the conversion of inactive Apaf-1 molecules to an extended, assembly competent state. While recent data have provided a detailed understanding of apoptosome formation and procaspase activation, they also highlight important evolutionary differences with functional implications for caspase activation. CARD/CARD interactions in the CED-4, Dark and Apaf-1 apoptosomes. Type I, II and III interfaces that stabilize CARD-CARD interactions are indicated (left column). Note that the Type I interface appears to be unique to Apaf-1/pc-9 CARD interactions. Middle column shows cartoons of the active states of the CARD-CARD disks, illustrating the two CED-4 tetrameric ring layers (top) and the recruitment of 8 Dronc CARDs and between 3-4 pc-9 CARDs, to the Dark and Apaf-1 apoptosomes respectively (middle and lower panels). Ribbon diagrams of the CED-4, Dark and Apaf-1 apoptosomes are shown (right column).

  16. Alcohol sensor based on single-mode-multimode-single-mode fiber structure

    Science.gov (United States)

    Mefina Yulias, R.; Hatta, A. M.; Sekartedjo, Sekartedjo

    2016-11-01

    Alcohol sensor based on Single-mode -Multimode-Single-mode (SMS) fiber structure is being proposed to sense alcohol concentration in alcohol-water mixtures. This proposed sensor uses refractive index sensing as its sensing principle. Fabricated SMS fiber structure had 40 m of multimode length. With power input -6 dBm and wavelength 1550 nm, the proposed sensor showed good response with sensitivity 1,983 dB per % v/v with measurement range 05 % v/v and measurement span 0,5% v/v.

  17. Structural failure modes in vertical tanks: reinforcement evaluation and solutions

    International Nuclear Information System (INIS)

    Alcantud Abellan, M.; Orden Martinez, A.

    1995-01-01

    Vertical storage tanks are essential components in the safety of nuclear plant systems. It has been shown that the traditional method of analysing seismic loads is not conservative, as it does not take account of the interaction between fluid and tank structure. This paper identifies different possible structural failure modes in tanks due to seismic load, and methods devised by various authors to evaluate tank structure capacity under different failure modes. These methods are based on experimental data relating to the structural behaviour of tanks during actual seismic events, tests, and theoretical analyses. The paper describes the problems of these structures under seismic loads in nuclear plants. It proposes solutions to the main structural problem, tank anchorage, for which the re-evaluation of the anchorage capacity is required, using methods (finite element) less conservative than those proposed by other authors. Also proposed is the local reinforcement of anchorages to increase their capacity. (Author) 4 refs

  18. Cellullar insights into cerebral cortical development: focusing on the locomotion mode of neuronal migration

    Directory of Open Access Journals (Sweden)

    Takeshi eKawauchi

    2015-10-01

    Full Text Available The mammalian brain consists of numerous compartments that are closely connected with each other via neural networks, comprising the basis of higher order brain functions. The highly specialized structure originates from simple pseudostratified neuroepithelium-derived neural progenitors located near the ventricle. A long journey by neurons from the ventricular side is essential for the formation of a sophisticated brain structure, including a mammalian-specific six-layered cerebral cortex. Neuronal migration consists of several contiguous steps, but the locomotion mode comprises a large part of the migration. The locomoting neurons exhibit unique features; a radial glial fiber-dependent migration requiring the endocytic recycling of N-cadherin and a neuron-specific migration mode with dilation/swelling formation that requires the actin and microtubule organization possibly regulated by cyclin-dependent kinase 5 (Cdk5, Dcx, p27kip1, Rac1 and POSH. Here I will introduce the roles of various cellular events, such as cytoskeletal organization, cell adhesion and membrane trafficking, in the regulation of the neuronal migration, with particular focus on the locomotion mode.

  19. Mode decomposition and Lagrangian structures of the flow dynamics in orbitally shaken bioreactors

    Science.gov (United States)

    Weheliye, Weheliye Hashi; Cagney, Neil; Rodriguez, Gregorio; Micheletti, Martina; Ducci, Andrea

    2018-03-01

    In this study, two mode decomposition techniques were applied and compared to assess the flow dynamics in an orbital shaken bioreactor (OSB) of cylindrical geometry and flat bottom: proper orthogonal decomposition and dynamic mode decomposition. Particle Image Velocimetry (PIV) experiments were carried out for different operating conditions including fluid height, h, and shaker rotational speed, N. A detailed flow analysis is provided for conditions when the fluid and vessel motions are in-phase (Fr = 0.23) and out-of-phase (Fr = 0.47). PIV measurements in vertical and horizontal planes were combined to reconstruct low order models of the full 3D flow and to determine its Finite-Time Lyapunov Exponent (FTLE) within OSBs. The combined results from the mode decomposition and the FTLE fields provide a useful insight into the flow dynamics and Lagrangian coherent structures in OSBs and offer a valuable tool to optimise bioprocess design in terms of mixing and cell suspension.

  20. The split coaxial linac structure and its RF modes

    International Nuclear Information System (INIS)

    Mueller, R.W.

    1989-01-01

    The Split Coaxial Cavity structure has been invented and applied for the first time in the heavy-ion RFQ linac MAXILAC of GSI. It has an ideally flat RF voltage distribution and a good power economy. From another standpoint, it is a member of the small family of linac structures where the two modes, the wanted one and the unflatness mode, are clearly and strictly separable. The unflatness or ''Q Line'' mode is analyzed in more detail in this paper. It is necessary for the understanding of the interaction of the beam with the cavity, possible beam instabilities resulting from it, and for curing these instabilities with the chance of obtaining improved beams. (orig.)

  1. Mechanism-based Inhibitors of the Human Sirtuin 5 Deacylase: Structure-Activity Relationship, Biostructural, and Kinetic Insight

    DEFF Research Database (Denmark)

    Rajabi, Nima; Auth, Marina; Troelsen, Kathrin Rentzius

    2017-01-01

    to date. We provide rationalization of the mode of binding by solving co-crystal structures of selected inhibitors in complex with both human and zebrafish SIRT5, which provide insight for future optimization of inhibitors with more "drug-like" properties. Importantly, enzyme kinetic evaluation revealed...

  2. Planned Products of the Mars Structure Service for the InSight Mission to Mars

    Science.gov (United States)

    Panning, Mark P.; Lognonné, Philippe; Bruce Banerdt, W.; Garcia, Raphaël; Golombek, Matthew; Kedar, Sharon; Knapmeyer-Endrun, Brigitte; Mocquet, Antoine; Teanby, Nick A.; Tromp, Jeroen; Weber, Renee; Beucler, Eric; Blanchette-Guertin, Jean-Francois; Bozdağ, Ebru; Drilleau, Mélanie; Gudkova, Tamara; Hempel, Stefanie; Khan, Amir; Lekić, Vedran; Murdoch, Naomi; Plesa, Ana-Catalina; Rivoldini, Atillio; Schmerr, Nicholas; Ruan, Youyi; Verhoeven, Olivier; Gao, Chao; Christensen, Ulrich; Clinton, John; Dehant, Veronique; Giardini, Domenico; Mimoun, David; Thomas Pike, W.; Smrekar, Sue; Wieczorek, Mark; Knapmeyer, Martin; Wookey, James

    2017-10-01

    The InSight lander will deliver geophysical instruments to Mars in 2018, including seismometers installed directly on the surface (Seismic Experiment for Interior Structure, SEIS). Routine operations will be split into two services, the Mars Structure Service (MSS) and Marsquake Service (MQS), which will be responsible, respectively, for defining the structure models and seismicity catalogs from the mission. The MSS will deliver a series of products before the landing, during the operations, and finally to the Planetary Data System (PDS) archive. Prior to the mission, we assembled a suite of a priori models of Mars, based on estimates of bulk composition and thermal profiles. Initial models during the mission will rely on modeling surface waves and impact-generated body waves independent of prior knowledge of structure. Later modeling will include simultaneous inversion of seismic observations for source and structural parameters. We use Bayesian inversion techniques to obtain robust probability distribution functions of interior structure parameters. Shallow structure will be characterized using the hammering of the heatflow probe mole, as well as measurements of surface wave ellipticity. Crustal scale structure will be constrained by measurements of receiver function and broadband Rayleigh wave ellipticity measurements. Core interacting body wave phases should be observable above modeled martian noise levels, allowing us to constrain deep structure. Normal modes of Mars should also be observable and can be used to estimate the globally averaged 1D structure, while combination with results from the InSight radio science mission and orbital observations will allow for constraint of deeper structure.

  3. Structural system identification based on variational mode decomposition

    Science.gov (United States)

    Bagheri, Abdollah; Ozbulut, Osman E.; Harris, Devin K.

    2018-03-01

    In this paper, a new structural identification method is proposed to identify the modal properties of engineering structures based on dynamic response decomposition using the variational mode decomposition (VMD). The VMD approach is a decomposition algorithm that has been developed as a means to overcome some of the drawbacks and limitations of the empirical mode decomposition method. The VMD-based modal identification algorithm decomposes the acceleration signal into a series of distinct modal responses and their respective center frequencies, such that when combined their cumulative modal responses reproduce the original acceleration response. The decaying amplitude of the extracted modal responses is then used to identify the modal damping ratios using a linear fitting function on modal response data. Finally, after extracting modal responses from available sensors, the mode shape vector for each of the decomposed modes in the system is identified from all obtained modal response data. To demonstrate the efficiency of the algorithm, a series of numerical, laboratory, and field case studies were evaluated. The laboratory case study utilized the vibration response of a three-story shear frame, whereas the field study leveraged the ambient vibration response of a pedestrian bridge to characterize the modal properties of the structure. The modal properties of the shear frame were computed using analytical approach for a comparison with the experimental modal frequencies. Results from these case studies demonstrated that the proposed method is efficient and accurate in identifying modal data of the structures.

  4. A Simple Laser Teaching Aid for Transverse Mode Structure Demonstration

    Science.gov (United States)

    Ren, Cheng; Zhang, Shulian

    2009-01-01

    A teaching aid for demonstrating the transverse mode structure in lasers is described. A novel device called "multi-dimension adjustable combined cat-eye reflector" has been constructed from easily available materials to form a He-Ne laser resonator. By finely adjusting the cat-eye, the boundary conditions of the laser cavity can be altered, which…

  5. Factorial Structure and Preliminary Validation of the Schema Mode Inventory for Eating Disorders (SMI-ED).

    Science.gov (United States)

    Simpson, Susan G; Pietrabissa, Giada; Rossi, Alessandro; Seychell, Tahnee; Manzoni, Gian Mauro; Munro, Calum; Nesci, Julian B; Castelnuovo, Gianluca

    2018-01-01

    Objective: The aim of this study was to examine the psychometric properties and factorial structure of the Schema Mode Inventory for Eating Disorders (SMI-ED) in a disordered eating population. Method: 573 participants with disordered eating patterns as measured by the Eating Disorder Examination Questionnaire (EDE-Q) completed the 190-item adapted version of the Schema Mode Inventory (SMI). The new SMI-ED was developed by clinicians/researchers specializing in the treatment of eating disorders, through combining items from the original SMI with a set of additional questions specifically representative of the eating disorder population. Psychometric testing included Confirmatory Factor Analysis (CFA) and internal consistency (Cronbach's α). Multivariate Analyses of Covariance (MANCOVA) was also run to test statistical differences between the EDE-Q subscales on the SMI-ED modes, while controlling for possible confounding variables. Results: Factorial analysis confirmed an acceptable 16-related-factors solution for the SMI-ED, thus providing preliminary evidence for the adequate validity of the new measure based on internal structure. Concurrent validity was also established through moderate to high correlations on the modes most relevant to eating disorders with EDE-Q subscales. This study represents the first step in creating a psychometrically sound instrument for measuring schema modes in eating disorders, and provides greater insight into the relevant schema modes within this population. Conclusion: This research represents an important preliminary step toward understanding and labeling the schema mode model for this clinical group. Findings from the psychometric evaluation of SMI-ED suggest that this is a useful tool which may further assist in the measurement and conceptualization of schema modes in this population.

  6. Factorial Structure and Preliminary Validation of the Schema Mode Inventory for Eating Disorders (SMI-ED

    Directory of Open Access Journals (Sweden)

    Susan G. Simpson

    2018-04-01

    Full Text Available Objective: The aim of this study was to examine the psychometric properties and factorial structure of the Schema Mode Inventory for Eating Disorders (SMI-ED in a disordered eating population.Method: 573 participants with disordered eating patterns as measured by the Eating Disorder Examination Questionnaire (EDE-Q completed the 190-item adapted version of the Schema Mode Inventory (SMI. The new SMI-ED was developed by clinicians/researchers specializing in the treatment of eating disorders, through combining items from the original SMI with a set of additional questions specifically representative of the eating disorder population. Psychometric testing included Confirmatory Factor Analysis (CFA and internal consistency (Cronbach's α. Multivariate Analyses of Covariance (MANCOVA was also run to test statistical differences between the EDE-Q subscales on the SMI-ED modes, while controlling for possible confounding variables.Results: Factorial analysis confirmed an acceptable 16-related-factors solution for the SMI-ED, thus providing preliminary evidence for the adequate validity of the new measure based on internal structure. Concurrent validity was also established through moderate to high correlations on the modes most relevant to eating disorders with EDE-Q subscales. This study represents the first step in creating a psychometrically sound instrument for measuring schema modes in eating disorders, and provides greater insight into the relevant schema modes within this population.Conclusion: This research represents an important preliminary step toward understanding and labeling the schema mode model for this clinical group. Findings from the psychometric evaluation of SMI-ED suggest that this is a useful tool which may further assist in the measurement and conceptualization of schema modes in this population.

  7. Factorial Structure and Preliminary Validation of the Schema Mode Inventory for Eating Disorders (SMI-ED)

    Science.gov (United States)

    Simpson, Susan G.; Pietrabissa, Giada; Rossi, Alessandro; Seychell, Tahnee; Manzoni, Gian Mauro; Munro, Calum; Nesci, Julian B.; Castelnuovo, Gianluca

    2018-01-01

    Objective: The aim of this study was to examine the psychometric properties and factorial structure of the Schema Mode Inventory for Eating Disorders (SMI-ED) in a disordered eating population. Method: 573 participants with disordered eating patterns as measured by the Eating Disorder Examination Questionnaire (EDE-Q) completed the 190-item adapted version of the Schema Mode Inventory (SMI). The new SMI-ED was developed by clinicians/researchers specializing in the treatment of eating disorders, through combining items from the original SMI with a set of additional questions specifically representative of the eating disorder population. Psychometric testing included Confirmatory Factor Analysis (CFA) and internal consistency (Cronbach's α). Multivariate Analyses of Covariance (MANCOVA) was also run to test statistical differences between the EDE-Q subscales on the SMI-ED modes, while controlling for possible confounding variables. Results: Factorial analysis confirmed an acceptable 16-related-factors solution for the SMI-ED, thus providing preliminary evidence for the adequate validity of the new measure based on internal structure. Concurrent validity was also established through moderate to high correlations on the modes most relevant to eating disorders with EDE-Q subscales. This study represents the first step in creating a psychometrically sound instrument for measuring schema modes in eating disorders, and provides greater insight into the relevant schema modes within this population. Conclusion: This research represents an important preliminary step toward understanding and labeling the schema mode model for this clinical group. Findings from the psychometric evaluation of SMI-ED suggest that this is a useful tool which may further assist in the measurement and conceptualization of schema modes in this population. PMID:29740379

  8. Insights into the structural biology of Gaucher disease.

    Science.gov (United States)

    Smith, Laura; Mullin, Stephen; Schapira, Anthony H V

    2017-12-01

    Gaucher disease, the most common lysosomal storage disorder, is caused by mutations in the gene encoding the acid-β-glucosidase lysosomal hydrolase enzyme that cleaves glucocerebroside into glucose and ceramide. Reduced enzyme activity and impaired structural stability arise due to >300 known disease-causing mutations. Several of these mutations have also been associated with an increased risk of Parkinson disease (PD). Since the discovery of the acid-β-glucosidase X-ray structure, there have been major advances in our understanding of the structural properties of the protein. Analysis of specific residues has provided insight into their functional and structural importance and provided insight into the pathogenesis of Gaucher disease and the contribution to PD. Disease-causing mutations are positioned throughout the acid-β-glucosidase structure, with many located far from the active site and thus retaining some enzymatic activity however, thus far no clear relationship between mutation location and disease severity has been established. Here, we review the crystal structure of acid-β-glucosidase, while highlighting important structural aspects of the protein in detail. This review discusses the structural stability of acid-β-glucosidase, which can be altered by pH and glycosylation, and explores the relationship between known Gaucher disease and PD mutations, structural stability and disease severity. Copyright © 2017. Published by Elsevier Inc.

  9. Structural insight into catalytic mechanism of PET hydrolase

    OpenAIRE

    Han, Xu; Liu, Weidong; Huang, Jian-Wen; Ma, Jiantao; Zheng, Yingying; Ko, Tzu-Ping; Xu, Limin; Cheng, Ya-Shan; Chen, Chun-Chi; Guo, Rey-Ting

    2017-01-01

    PET hydrolase (PETase), which hydrolyzes polyethylene terephthalate (PET) into soluble building blocks, provides an attractive avenue for the bioconversion of plastics. Here we present the structures of a novel PETase from the PET-consuming microbe Ideonella sakaiensis in complex with substrate and product analogs. Through structural analyses, mutagenesis, and activity measurements, a substrate-binding mode is proposed, and several features critical for catalysis are elucidated.

  10. Structural insight into catalytic mechanism of PET hydrolase.

    Science.gov (United States)

    Han, Xu; Liu, Weidong; Huang, Jian-Wen; Ma, Jiantao; Zheng, Yingying; Ko, Tzu-Ping; Xu, Limin; Cheng, Ya-Shan; Chen, Chun-Chi; Guo, Rey-Ting

    2017-12-13

    PET hydrolase (PETase), which hydrolyzes polyethylene terephthalate (PET) into soluble building blocks, provides an attractive avenue for the bioconversion of plastics. Here we present the structures of a novel PETase from the PET-consuming microbe Ideonella sakaiensis in complex with substrate and product analogs. Through structural analyses, mutagenesis, and activity measurements, a substrate-binding mode is proposed, and several features critical for catalysis are elucidated.

  11. Deflecting modes of the side-coupled cavity structure

    Energy Technology Data Exchange (ETDEWEB)

    Inagaki, Shigemi.

    1990-11-01

    The deflecting modes of the 805 MHz side-coupled cavity structure with the relativistic factor 0.566 are studied. Our main concern is the dispersion properties among different configurations of side-coupling cells and their interpretations. It is shown that the ninety degree side-coupling cell configuration, so to speak, the Mickey Mouse configuration has a merit in reducing the HEM{sub 1} passband. Another concern is the magnitude of the transverse coupling impedance around the synchronization condition. It is shown that the existence of the coupling cell introduces the nonuniformity of the deflecting mode and gives different impedance relative to the beam axis and that the coupling impedance at {pi}/10 exceeds 50 M{Omega}/m if the quality value of the mode is around 12000.

  12. Deflecting modes of the side-coupled cavity structure

    International Nuclear Information System (INIS)

    Inagaki, Shigemi.

    1990-11-01

    The deflecting modes of the 805 MHz side-coupled cavity structure with the relativistic factor 0.566 are studied. Our main concern is the dispersion properties among different configurations of side-coupling cells and their interpretations. It is shown that the ninety degree side-coupling cell configuration, so to speak, the Mickey Mouse configuration has a merit in reducing the HEM 1 passband. Another concern is the magnitude of the transverse coupling impedance around the synchronization condition. It is shown that the existence of the coupling cell introduces the nonuniformity of the deflecting mode and gives different impedance relative to the beam axis and that the coupling impedance at π/10 exceeds 50 MΩ/m if the quality value of the mode is around 12000

  13. Structural mode significance using INCA. [Interactive Controls Analysis computer program

    Science.gov (United States)

    Bauer, Frank H.; Downing, John P.; Thorpe, Christopher J.

    1990-01-01

    Structural finite element models are often too large to be used in the design and analysis of control systems. Model reduction techniques must be applied to reduce the structural model to manageable size. In the past, engineers either performed the model order reduction by hand or used distinct computer programs to retrieve the data, to perform the significance analysis and to reduce the order of the model. To expedite this process, the latest version of INCA has been expanded to include an interactive graphical structural mode significance and model order reduction capability.

  14. Molecular Dynamics Insights into Polyamine-DNA Binding Modes: Implications for Cross-Link Selectivity.

    Science.gov (United States)

    Bignon, Emmanuelle; Chan, Chen-Hui; Morell, Christophe; Monari, Antonio; Ravanat, Jean-Luc; Dumont, Elise

    2017-09-18

    Biogenic polyamines, which play a role in DNA condensation and stabilization, are ubiquitous and are found at millimolar concentration in the nucleus of eukaryotic cells. The interaction modes of three polyamines-putrescine (Put), spermine (Spm), and spermidine (Spd)-with a self-complementary 16 base pair (bp) duplex, are investigated by all-atom explicit-solvent molecular dynamics. The length of the amine aliphatic chain leads to a change of the interaction mode from minor groove binding to major groove binding. Through all-atom dynamics, noncovalent interactions that stabilize the polyamine-DNA complex and prefigure the reactivity, leading to the low-barrier formation of deleterious DNA-polyamine cross-links, after one-electron oxidation of a guanine nucleobase, are unraveled. The binding strength is quantified from the obtained trajectories by molecular mechanics generalized Born surface area post-processing (MM-GBSA). The values of binding free energies provide the same affinity order, Putstructural predictions. The binding modes and carbon-nitrogen distances along the series of polyamines illustrate the selectivity towards deleterious DNA-polyamine cross-link formation through the extraction of average approaching distances between the C8 atom of guanines and the ammonium group. These results imply that the formation of DNA-polyamine cross-links involves deprotonation of the guanine radical cation to attack the polyamines, which must be positively charged to lie in the vicinity of the B-helix. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. Physically-insightful equivalent circuit models for electromagnetic periodic structures

    Science.gov (United States)

    Mesa, F.; Rodríguez-Berral, R.; Medina, F.

    2018-02-01

    In this presentation it will be discussed how to obtain analytical or quasi-analytical equivalent circuits to deal with periodic structures such as frequency selective surfaces and/or metasurfaces. Both the topology and the values of the involved elements of these circuits are obtained from a basic rationale to solve the corresponding integral equation. This procedure, besides providing a very efficient analysis/design tool, allows for a good physical insight into the operating mechanisms of the structure in contrast with the almost blind numerical scheme of commercial simulators.

  16. Homology modeling of Homo sapiens lipoic acid synthase: Substrate docking and insights on its binding mode.

    Science.gov (United States)

    Krishnamoorthy, Ezhilarasi; Hassan, Sameer; Hanna, Luke Elizabeth; Padmalayam, Indira; Rajaram, Rama; Viswanathan, Vijay

    2017-05-07

    Lipoic acid synthase (LIAS) is an iron-sulfur cluster mitochondrial enzyme which catalyzes the final step in the de novo pathway for the biosynthesis of lipoic acid, a potent antioxidant. Recently there has been significant interest in its role in metabolic diseases and its deficiency in LIAS expression has been linked to conditions such as diabetes, atherosclerosis and neonatal-onset epilepsy, suggesting a strong inverse correlation between LIAS reduction and disease status. In this study we use a bioinformatics approach to predict its structure, which would be helpful to understanding its role. A homology model for LIAS protein was generated using X-ray crystallographic structure of Thermosynechococcus elongatus BP-1 (PDB ID: 4U0P). The predicted structure has 93% of the residues in the most favour region of Ramachandran plot. The active site of LIAS protein was mapped and docked with S-Adenosyl Methionine (SAM) using GOLD software. The LIAS-SAM complex was further refined using molecular dynamics simulation within the subsite 1 and subsite 3 of the active site. To the best of our knowledge, this is the first study to report a reliable homology model of LIAS protein. This study will facilitate a better understanding mode of action of the enzyme-substrate complex for future studies in designing drugs that can target LIAS protein. Copyright © 2017 Elsevier Ltd. All rights reserved.

  17. Structural insights into the intertwined dimer of fyn SH2.

    Science.gov (United States)

    Huculeci, Radu; Garcia-Pino, Abel; Buts, Lieven; Lenaerts, Tom; van Nuland, Nico

    2015-12-01

    Src homology 2 domains are interaction modules dedicated to the recognition of phosphotyrosine sites incorporated in numerous proteins found in intracellular signaling pathways. Here we provide for the first time structural insight into the dimerization of Fyn SH2 both in solution and in crystalline conditions, providing novel crystal structures of both the dimer and peptide-bound structures of Fyn SH2. Using nuclear magnetic resonance chemical shift analysis, we show how the peptide is able to eradicate the dimerization, leading to monomeric SH2 in its bound state. Furthermore, we show that Fyn SH2's dimer form differs from other SH2 dimers reported earlier. Interestingly, the Fyn dimer can be used to construct a completed dimer model of Fyn without any steric clashes. Together these results extend our understanding of SH2 dimerization, giving structural details, on one hand, and suggesting a possible physiological relevance of such behavior, on the other hand. © 2015 The Protein Society.

  18. Ordinary mode auroral kilometric radiation fine structure observed by DE 1

    International Nuclear Information System (INIS)

    Benson, R.F.; Mellott, M.M.; Huff, R.L.; Gurnett, D.A.

    1988-01-01

    The fine structure observed with intense right-hand extraordinary (R-X) mode auroral kilometric radiation (AKR) has received major theoretical attention. Data from the Dynamics Explorer 1 plasma wave instrument indicate that left-hand ordinary (L-O) mode AKR posses similar fine structure. Several theories have been proposed to explain the fine structure of the R-X mode AKR. In order to account for the L-O mode fine structure, these theories will have to be modified to produce the L-O mode directly or will have to rely on mode conversion processes from the R-X to the L-O mode

  19. New insight in magnetic saturation behavior of nickel hierarchical structures

    Science.gov (United States)

    Ma, Ji; Zhang, Jianxing; Liu, Chunting; Chen, Kezheng

    2017-09-01

    It is unanimously accepted that non-ferromagnetic inclusions in a ferromagnetic system will lower down total saturation magnetization in unit of emu/g. In this study, ;lattice strain; was found to be another key factor to have critical impact on magnetic saturation behavior of the system. The lattice strain determined assembling patterns of primary nanoparticles in hierarchical structures and was intimately related with the formation process of these architectures. Therefore, flower-necklace-like and cauliflower-like nickel hierarchical structures were used as prototype systems to evidence the relationship between assembling patterns of primary nanoparticles and magnetic saturation behaviors of these architectures. It was found that the influence of lattice strain on saturation magnetization outperformed that of non-ferromagnetic inclusions in these hierarchical structures. This will enable new insights into fundamental understanding of related magnetic effects.

  20. Identification of multiple modes of axisymmetric or circularly repetitive structures

    International Nuclear Information System (INIS)

    Kopff, P.

    1983-01-01

    The axisymmetric structures, or those composed with circularly repetitive elements, often display multiple modes, which are not easy to separate by modal identification of experimental responses. To be able to solve in situ some problems related to the vibrational behaviour of reactor vessels or other such huge structures, ELECTRICITY DE FRANCE developed a few years ago, experimental capabilities providing heavy harmonic driving forces, and elaborate data acquisition, signal processing and modal identification software, self-contained in an integrated mobile test facility. The modal analysis techniques we have developed with the LABORATOIRE DE MECANIQUE Appliquee of University of BESANCON (FRANCE) were especially suited for identification of multiple or separation of quasi-multiple modes, i.e. very close and strongly coupled resonances. Besides, the curve fitting methods involved, compute the same complex eigen-frequencies for all the vibration pick-ups, for better accuracy of the related eigen-vector components. Moreover, the latest extensions of these algorithms give us the means to deal with non-linear behaviour. The performances of these programs are drawn from some experimental results on axisymmetric or circularly repetitive structure, we tested in our laboratory to validate the computational hypothesis used in models for seismic responses of breeder reactor vessels. (orig.)

  1. Quantification of Structural Isomers via Mode-Selective Irmpd

    Science.gov (United States)

    Polfer, Nicolas C.

    2016-06-01

    Mixtures of structural isomers can pose a challenge for vibrational ion spectroscopy. In cases where particular structures display diagnostic vibrations, these structures can be selectively "burned away". In ion traps, the ion population can be subjected to multiple laser shots, in order to fully deplete a particular structure, in effect allowing a quantification of this structure. Protonated para-amino benzoic acid (PABA) serves as an illustrative example. PABA is known to preferentially exist in the N-protonated (N-prot) form in solution, but in the gas phase it is energetically favorable in the O-protonated (O-prot) form. As shown in Figure 1, the N-prot structure can be kinetically trapped in the gas phase when sprayed from non-protic solvent, whereas the O-prot structure is obtained when sprayed from protic solvents, analogous to results by others [1,2]. y parking the light source on the diagnostic 3440 wn mode, the percentage of the O-prot structure can be determined, and by default the remainder is assumed to adopt the N-prot structure. It will be shown that the relative percentages of O-prot vs N-prot are highly dependent on the solvent mixture, going from close to 0% O-prot in non-protic solvents, to 99% in protic solvents. Surprisingly, water behaves much more like a non-protic solvent than methanol. It is observed that the capillary temperature, which aids droplet desolvation by black-body radiation in the ESI source, is critical to promote the appearance of O-prot structures. These results are consistent with the picture that a protic bridge mechanism is at play to facilitate proton transfer, and thus allow conversion from N-prot to O-prot, but that this mechanism is subject to appreciable kinetic barriers on the timescale of solvent evaporation. 1. J. Phys. Chem. A 2011, 115, 7625. 2. Anal. Chem. 2012, 84, 7857.

  2. Magnetic apatite for structural insights on the plasma membrane

    International Nuclear Information System (INIS)

    Stanca, Sarmiza E; Müller, Robert; Dellith, Jan; Deckert, Volker; Krafft, Christoph; Popp, Jürgen; Fritzsche, Wolfgang; Nietzsche, Sandor; Stöckel, Stephan; Biskup, Christoph

    2015-01-01

    The iron oxide-hydroxyapatite (FeOxHA) nanoparticles reported here differ from those reported before by their advantage of homogeneity and simple preparation; moreover, the presence of carboxymethyldextran (CMD), together with hydroxyapatite (HA), allows access to the cellular membrane, which makes our magnetic apatite unique. These nanoparticles combine magnetic behavior, Raman label ability and the property of interaction with the cellular membrane; they therefore represent an interesting material for structural differentiation of the cell membrane. It was observed by Raman spectroscopy, scanning electron microscopy (SEM) and fluorescence microscopy that FeOxHA adheres to the plasma membrane and does not penetrate the membrane. These insights make the nanoparticles a promising material for magnetic cell sorting, e.g. in microfluidic device applications. (paper)

  3. Magnetic apatite for structural insights on the plasma membrane

    Science.gov (United States)

    Stanca, Sarmiza E.; Müller, Robert; Dellith, Jan; Nietzsche, Sandor; Stöckel, Stephan; Biskup, Christoph; Deckert, Volker; Krafft, Christoph; Popp, Jürgen; Fritzsche, Wolfgang

    2015-01-01

    The iron oxide-hydroxyapatite (FeOxHA) nanoparticles reported here differ from those reported before by their advantage of homogeneity and simple preparation; moreover, the presence of carboxymethyldextran (CMD), together with hydroxyapatite (HA), allows access to the cellular membrane, which makes our magnetic apatite unique. These nanoparticles combine magnetic behavior, Raman label ability and the property of interaction with the cellular membrane; they therefore represent an interesting material for structural differentiation of the cell membrane. It was observed by Raman spectroscopy, scanning electron microscopy (SEM) and fluorescence microscopy that FeOxHA adheres to the plasma membrane and does not penetrate the membrane. These insights make the nanoparticles a promising material for magnetic cell sorting, e.g. in microfluidic device applications.

  4. Oligomeric protein structure networks: insights into protein-protein interactions

    Directory of Open Access Journals (Sweden)

    Brinda KV

    2005-12-01

    Full Text Available Abstract Background Protein-protein association is essential for a variety of cellular processes and hence a large number of investigations are being carried out to understand the principles of protein-protein interactions. In this study, oligomeric protein structures are viewed from a network perspective to obtain new insights into protein association. Structure graphs of proteins have been constructed from a non-redundant set of protein oligomer crystal structures by considering amino acid residues as nodes and the edges are based on the strength of the non-covalent interactions between the residues. The analysis of such networks has been carried out in terms of amino acid clusters and hubs (highly connected residues with special emphasis to protein interfaces. Results A variety of interactions such as hydrogen bond, salt bridges, aromatic and hydrophobic interactions, which occur at the interfaces are identified in a consolidated manner as amino acid clusters at the interface, from this study. Moreover, the characterization of the highly connected hub-forming residues at the interfaces and their comparison with the hubs from the non-interface regions and the non-hubs in the interface regions show that there is a predominance of charged interactions at the interfaces. Further, strong and weak interfaces are identified on the basis of the interaction strength between amino acid residues and the sizes of the interface clusters, which also show that many protein interfaces are stronger than their monomeric protein cores. The interface strengths evaluated based on the interface clusters and hubs also correlate well with experimentally determined dissociation constants for known complexes. Finally, the interface hubs identified using the present method correlate very well with experimentally determined hotspots in the interfaces of protein complexes obtained from the Alanine Scanning Energetics database (ASEdb. A few predictions of interface hot

  5. Nonlinear eigen-mode structures in complex astroclouds

    International Nuclear Information System (INIS)

    Karmakar, P K; Haloi, A

    2017-01-01

    The evolutionary dynamics of strongly nonlinear waves (of arbitrary amplitude) in an inhomogeneous complex astrophysical viscous cloud is investigated without recourse to any kind of swindle. It consists of warm lighter electrons and ions (Boltzmanian); and cold massive bi-polar dust grains (inertial fluids) alongside vigorous neutral dynamics in quasi-neural hydrodynamic equilibrium. Application of the Sagdeev pseudo-potential method transforms the analytic model into a conjugated pair of intermixed non-integrable energy integral laws. A natural excitation of electrostatic quasi-monotonic compressive dispersive shock-like eigen-modes is numerically demonstrated. In contrast, the self-gravitational waves grow purely as non-monotonic compressive oscillatory shock-like structures. The unique features of both the distinct classes are depicted. Their non-trivial significance in the astro-context is emphasized. (paper)

  6. Nonlinear eigen-mode structures in complex astroclouds

    Science.gov (United States)

    Karmakar, P. K.; Haloi, A.

    2017-05-01

    The evolutionary dynamics of strongly nonlinear waves (of arbitrary amplitude) in an inhomogeneous complex astrophysical viscous cloud is investigated without recourse to any kind of swindle. It consists of warm lighter electrons and ions (Boltzmanian); and cold massive bi-polar dust grains (inertial fluids) alongside vigorous neutral dynamics in quasi-neural hydrodynamic equilibrium. Application of the Sagdeev pseudo-potential method transforms the analytic model into a conjugated pair of intermixed non-integrable energy integral laws. A natural excitation of electrostatic quasi-monotonic compressive dispersive shock-like eigen-modes is numerically demonstrated. In contrast, the self-gravitational waves grow purely as non-monotonic compressive oscillatory shock-like structures. The unique features of both the distinct classes are depicted. Their non-trivial significance in the astro-context is emphasized.

  7. Structural characterisation of Tpx from Yersinia pseudotuberculosis reveals insights into the binding of salicylidene acylhydrazide compounds.

    Directory of Open Access Journals (Sweden)

    Mads Gabrielsen

    Full Text Available Thiol peroxidase, Tpx, has been shown to be a target protein of the salicylidene acylhydrazide class of antivirulence compounds. In this study we present the crystal structures of Tpx from Y. pseudotuberculosis (ypTpx in the oxidised and reduced states, together with the structure of the C61S mutant. The structures solved are consistent with previously solved atypical 2-Cys thiol peroxidases, including that for "forced" reduced states using the C61S mutant. In addition, by investigating the solution structure of ypTpx using small angle X-ray scattering (SAXS, we have confirmed that reduced state ypTpx in solution is a homodimer. The solution structure also reveals flexibility around the dimer interface. Notably, the conformational changes observed between the redox states at the catalytic triad and at the dimer interface have implications for substrate and inhibitor binding. The structural data were used to model the binding of two salicylidene acylhydrazide compounds to the oxidised structure of ypTpx. Overall, the study provides insights into the binding of the salicylidene acylhydrazides to ypTpx, aiding our long-term strategy to understand the mode of action of this class of compounds.

  8. The Very Model of a Modern PI-Mode Structure

    CERN Document Server

    Katarina Anthony

    2014-01-01

    Linac4's PI-Mode Structures (PIMS) are the first structures of their kind to accelerate protons. Now, over three years after work began on production, over 180 PIMS elements have been rough-machined and the first new PIMS cavity is being assembled at CERN.   The newly assembled PIMS cavity undergoes testing in CERN's Main Workshop. As the final accelerating structures of Linac4, located 53 m to 74 m downstream of the source, the state-of-the-art PIMS cavities will take protons from 100 to 160 MeV. While the first cavity was built entirely at CERN, construction of the remaining cavities has become a larger, multi-national operation. The newest PIMS cavity is being assembled and validated at CERN's Main Workshop. Built in collaboration with the National Centre for Nuclear Research (NCBJ, Poland) and the Jülich Research Centre (Germany), it is the first of its kind to be produced outside the Organization. Sharing all the required know...

  9. Stronger default mode network connectivity is associated with poorer clinical insight in youth at ultra high-risk for psychotic disorders.

    Science.gov (United States)

    Clark, Sarah V; Mittal, Vijay A; Bernard, Jessica A; Ahmadi, Aral; King, Tricia Z; Turner, Jessica A

    2018-03-01

    Impaired clinical insight (CI) is a common symptom of psychotic disorders and a promising treatment target. However, to date, our understanding of how variability in CI is tied to underlying brain dysfunction in the clinical high-risk period is limited. Developing a stronger conception of this link will be a vital first step for efforts to determine if CI can serve as a useful prognostic indicator. The current study investigated whether variability in CI is related to major brain networks in adolescents and young adults at ultra high-risk (UHR) of developing psychosis. Thirty-five UHR youth were administered structured clinical interviews as well as an assessment for CI and underwent resting-state magnetic resonance imaging scans. Functional connectivity was calculated in the default mode network (DMN) and fronto-parietal network (FPN), two major networks that are dysfunctional in psychosis and are hypothesized to affect insight. Greater DMN connectivity between the posterior cingulate/precuneus and ventromedial prefrontal cortex (DMN) was related to poorer CI (R 2 =0.399). There were no significant relationships between insight and the FPN. This is the first study to relate a major brain network to clinical insight before the onset of psychosis. Findings are consistent with evidence if a hyperconnected DMN in schizophrenia and UHR, and similar to a previous study of insight and connectivity in schizophrenia. Results suggest that a strongly connected DMN may be related to poor self-awareness of subthreshold psychotic symptoms in UHR adolescents and young adults. Copyright © 2017 Elsevier B.V. All rights reserved.

  10. Unified approach for calculating the number of confined modes in multilayered waveguiding structures

    Science.gov (United States)

    Ruschin, S.; Griffel, G.; Hardy, A.; Croitoru, N.

    1986-01-01

    A general formalism is developed in order to find the number of modes and mode cutoff conditions in multilayer waveguiding structures. An explicit expression is presented for the number of confined modes that allows the modes to be counted without having to analyze the specific eigenvalue equation of the structure. The method is illustrated by its application to several structures: the buried layer, the directional coupler, and the three-guide symmetrical arrangement. By a suitable extension of the formalism, the number of well-confined modes is found for a four-layer structure.

  11. Insight into the Disciplinary Structure of Nanoscience & Nanotechnology

    Directory of Open Access Journals (Sweden)

    Chunjuan Luan

    2017-01-01

    Full Text Available Purpose: This paper aims to gain an insight into the disciplinary structure of nanoscience & nanotechnology (N&N: What is the disciplinary network of N&N like? Which disciplines are being integrated into N&N over time? For a specific discipline, how many other disciplines have direct or indirect connections with it? What are the distinct subgroups of N&N at different evolutionary stages? Such critical issues are to be addressed in this paper. Design/methodology/approach: We map the disciplinary network structure of N&N by employing the social network analysis tool, Netdraw, identifying which Web of Science Categories (WCs mediate nbetweenness centrality in different stages of nano development. Cliques analysis embedded in the Ucinet program is applied to do the disciplinary cluster analysis in the study according to the path of “Network-Subgroup-Cliques,” and a tree diagram is selected as the visualizing type. Findings: The disciplinary network structure reveals the relationships among different disciplines in the N&N developing process clearly, and it is easy for us to identify which disciplines are connected with the core “N&N” directly or indirectly. The tree diagram showing N&N related disciplines provides an interesting perspective on nano research and development (R&D structure. Research limitations: The matrices used to draw the N&N disciplinary network are the original ones, and normalized matrix could be tried in future similar studies. Practical implications: Results in this paper can help us better understand the disciplinary structure of N&N, and the dynamic evolution of N&N related disciplines over time. The findings could benefit R&D decision making. It can support policy makers from government agencies engaging in science and technology (S&T management or S&T strategy planners to formulate efficient decisions according to a perspective of converging sciences and technologies. Originality/value: The novelty of this study

  12. Constraining the reversing and non-reversing modes of the geodynamo. New insights from magnetostratigraphy.

    Science.gov (United States)

    Gallet, Y.; Pavlov, V.; Shatsillo, A.; Hulot, G.

    2015-12-01

    Constraining the evolution in the geomagnetic reversal frequency over hundreds of million years is not a trivial matter. Beyond the fact that there are long periods without reversals, known as superchrons, and periods with many reversals, the way the reversal frequency changes through time during reversing periods is still debated. A smooth evolution or a succession of stationary segments have both been suggested to account for the geomagnetic polarity time scale since the Middle-Late Jurassic. Sudden changes from a reversing mode to a non-reversing mode of the geodynamo may also well have happened, the switch between the two modes having then possibly been controlled by the thermal conditions at the core-mantle boundary. There is, nevertheless, a growing set of magnetostratigraphic data, which could help decipher a proper interpretation of the reversal history, in particular in the early Paleozoic and even during the Precambrian. Although yielding a fragmentary record, these data reveal the occurrence of both additional superchrons and periods characterized by extremely high, not to say extraordinary, magnetic reversal frequencies. In this talk, we will present a synthesis of these data, mainly obtained from Siberia, and discuss their implication for the magnetic reversal behavior over the past billion years.

  13. Insights into structural variations and genome rearrangements in prokaryotic genomes.

    Science.gov (United States)

    Periwal, Vinita; Scaria, Vinod

    2015-01-01

    Structural variations (SVs) are genomic rearrangements that affect fairly large fragments of DNA. Most of the SVs such as inversions, deletions and translocations have been largely studied in context of genetic diseases in eukaryotes. However, recent studies demonstrate that genome rearrangements can also have profound impact on prokaryotic genomes, leading to altered cell phenotype. In contrast to single-nucleotide variations, SVs provide a much deeper insight into organization of bacterial genomes at a much better resolution. SVs can confer change in gene copy number, creation of new genes, altered gene expression and many other functional consequences. High-throughput technologies have now made it possible to explore SVs at a much refined resolution in bacterial genomes. Through this review, we aim to highlight the importance of the less explored field of SVs in prokaryotic genomes and their impact. We also discuss its potential applicability in the emerging fields of synthetic biology and genome engineering where targeted SVs could serve to create sophisticated and accurate genome editing. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  14. MEMS Reliability: Infrastructure, Test Structures, Experiments, and Failure Modes

    Energy Technology Data Exchange (ETDEWEB)

    TANNER,DANELLE M.; SMITH,NORMAN F.; IRWIN,LLOYD W.; EATON,WILLIAM P.; HELGESEN,KAREN SUE; CLEMENT,J. JOSEPH; MILLER,WILLIAM M.; MILLER,SAMUEL L.; DUGGER,MICHAEL T.; WALRAVEN,JEREMY A.; PETERSON,KENNETH A.

    2000-01-01

    The burgeoning new technology of Micro-Electro-Mechanical Systems (MEMS) shows great promise in the weapons arena. We can now conceive of micro-gyros, micro-surety systems, and micro-navigators that are extremely small and inexpensive. Do we want to use this new technology in critical applications such as nuclear weapons? This question drove us to understand the reliability and failure mechanisms of silicon surface-micromachined MEMS. Development of a testing infrastructure was a crucial step to perform reliability experiments on MEMS devices and will be reported here. In addition, reliability test structures have been designed and characterized. Many experiments were performed to investigate failure modes and specifically those in different environments (humidity, temperature, shock, vibration, and storage). A predictive reliability model for wear of rubbing surfaces in microengines was developed. The root causes of failure for operating and non-operating MEMS are discussed. The major failure mechanism for operating MEMS was wear of the polysilicon rubbing surfaces. Reliability design rules for future MEMS devices are established.

  15. Dielectric structures with bound modes for microcavity lasers

    NARCIS (Netherlands)

    Visser, P.M.; Allaart, K.; Lenstra, D.

    2002-01-01

    Cavity modes of dielectric microsphcres and vertical cavity surface emitting lasers, in spite of their high Q, are never exactly bound, but have a finite width due to leakage at the borders. We propose types of microstructures that sustain three-dimensionally bound modes of the radiation field when

  16. On Kinetic Slow Modes, Fluid Slow Modes, and Pressure-balanced Structures in the Solar Wind

    Energy Technology Data Exchange (ETDEWEB)

    Verscharen, Daniel [Space Science Center and Department of Physics, University of New Hampshire, Durham, NH 03824 (United States); Chen, Christopher H. K. [Department of Physics, Imperial College London, London SW7 2AZ (United Kingdom); Wicks, Robert T., E-mail: daniel.verscharen@unh.edu, E-mail: christopher.chen@imperial.ac.uk, E-mail: r.wicks@ucl.ac.uk [Mullard Space Science Laboratory, University College London, London WC1E 6BT (United Kingdom)

    2017-05-10

    Observations in the solar wind suggest that the compressive component of inertial-range solar-wind turbulence is dominated by slow modes. The low collisionality of the solar wind allows for nonthermal features to survive, which suggests the requirement of a kinetic plasma description. The least-damped kinetic slow mode is associated with the ion-acoustic (IA) wave and a nonpropagating (NP) mode. We derive analytical expressions for the IA-wave dispersion relation in an anisotropic plasma in the framework of gyrokinetics and then compare them to fully kinetic numerical calculations, results from two-fluid theory, and magnetohydrodynamics (MHD). This comparison shows major discrepancies in the predicted wave phase speeds from MHD and kinetic theory at moderate to high β . MHD and kinetic theory also dictate that all plasma normal modes exhibit a unique signature in terms of their polarization. We quantify the relative amplitude of fluctuations in the three lowest particle velocity moments associated with IA and NP modes in the gyrokinetic limit and compare these predictions with MHD results and in situ observations of the solar-wind turbulence. The agreement between the observations of the wave polarization and our MHD predictions is better than the kinetic predictions, which suggests that the plasma behaves more like a fluid in the solar wind than expected.

  17. On Kinetic Slow Modes, Fluid Slow Modes, and Pressure-balanced Structures in the Solar Wind

    International Nuclear Information System (INIS)

    Verscharen, Daniel; Chen, Christopher H. K.; Wicks, Robert T.

    2017-01-01

    Observations in the solar wind suggest that the compressive component of inertial-range solar-wind turbulence is dominated by slow modes. The low collisionality of the solar wind allows for nonthermal features to survive, which suggests the requirement of a kinetic plasma description. The least-damped kinetic slow mode is associated with the ion-acoustic (IA) wave and a nonpropagating (NP) mode. We derive analytical expressions for the IA-wave dispersion relation in an anisotropic plasma in the framework of gyrokinetics and then compare them to fully kinetic numerical calculations, results from two-fluid theory, and magnetohydrodynamics (MHD). This comparison shows major discrepancies in the predicted wave phase speeds from MHD and kinetic theory at moderate to high β . MHD and kinetic theory also dictate that all plasma normal modes exhibit a unique signature in terms of their polarization. We quantify the relative amplitude of fluctuations in the three lowest particle velocity moments associated with IA and NP modes in the gyrokinetic limit and compare these predictions with MHD results and in situ observations of the solar-wind turbulence. The agreement between the observations of the wave polarization and our MHD predictions is better than the kinetic predictions, which suggests that the plasma behaves more like a fluid in the solar wind than expected.

  18. Competition between modes with different axial structures in gyrotrons

    International Nuclear Information System (INIS)

    Khutoryan, Eduard M.; Nusinovich, Gregory S.; Sinitsyn, Oleksandr V.

    2014-01-01

    This study was motivated by some experiments in which it was found that during the voltage rise, instead of expected excitation of a high-frequency parasitic mode, the excitation of a lower-frequency parasitic mode takes place in a certain range of voltages. For explaining this fact, the dependence of start currents of possible competing modes on the beam voltage was carried out in the cold-cavity approximation and by using the self-consistent approach. It was found that in the case of cavities, which consist of the combination of a section of constant radius waveguide and a slightly uptapered waveguide, these two approaches yield completely different results. Thus, experimentally observed excitation of the low-frequency parasitic mode can be explained by the self-consistent modification of the axial profile of the excited field, which has strong influence on the diffractive quality factor of competing modes. This modification is especially pronounced in the case of excitation of modes with many axial variations which can be excited in the region of beam interaction with the backward-wave component of such modes

  19. Spatial mode structures of electrostatic drift waves in a collisional cylindrical helicon plasma

    DEFF Research Database (Denmark)

    Schröder, C.; Grulke, O.; Klinger, T.

    2004-01-01

    In a cylindrical helicon plasma, mode structures of coherent drift waves are studied in the poloidal plane, the plane perpendicular to the ambient magnetic field. The mode structures rotate with a constant angular velocity in the direction of the electron diamagnetic drift and show significant...... radial bending. The experimental observations are compared with numerical solutions of a linear nonlocal cylindrical model for drift waves [ Ellis , Plasma Phys. 22, 113 (1980) ]. In the numerical model, a transition to bended mode structures is found if the plasma collisionality is increased....... This finding proves that the experimentally observed bended mode structures are the result of high electron collisionality. (C) 2004 American Institute of Physics....

  20. Global structures of Alfven-ballooning modes in magnetospheric plasmas

    International Nuclear Information System (INIS)

    Vetoulis, G.; Chen, Liu.

    1994-03-01

    The authors show that a steep plasma pressure gradient can lead to radially localized Alfven modes, which are damped through coupling to filed line resonances. These have been called drift Alfven balloning modes (DABM) and are the prime candidates to explain Pc4-Pc5 geomagnetic pulsations observed during storms. A strong dependence of the damping rate on the azimuthal wave number m is established, as well as on the equilibrium profile. A minimum azimuthal mode number can be found for the DABM to be radially trapped. The authors find that higher m DABMs are better localized, which is consistent with high-m observations

  1. Effect of boundary conditions on radial mode structure of whistlers

    International Nuclear Information System (INIS)

    Boswell, R.W.

    1983-01-01

    The dispersion of the radical eigen modes of a cylindrical m=1 whistler wave with Ωsub(i) << ω << Ωsub(e) << ωsub(pe) are investigated for both conducting and insulating boundaries, where Ωsub(e) and Ωsub(i) are the electron and ion gyro frequencies, Ωsub(pe) is the electron plasma frequency. The effects of electron inertia and resistivity on the modes are discussed

  2. Structures and functions in the crowded nucleus: new biophysical insights

    Directory of Open Access Journals (Sweden)

    Ronald eHancock

    2014-09-01

    Full Text Available Concepts and methods from the physical sciences have catalysed remarkable progress in understanding the cell nucleus in recent years. To share this excitement with physicists and encourage their interest in this field, this review offers an overview of how the physics which underlies structures and functions in the nucleus is becoming more clear thanks to methods which have been developed to simulate and study macromolecules, polymers, and colloids. The environment in the nucleus is very crowded with macromolecules, making entropic (depletion forces major determinants of interactions. Simulation and experiments are consistent with their key role in forming membraneless compartments such as nucleoli, PML and Cajal bodies, and discrete territories for chromosomes. The chromosomes, giant linear polyelectrolyte polymers, exist in vivo in a state like a polymer melt. Looped conformations are predicted in crowded conditions, and have been confirmed experimentally and are central to the regulation of gene expression. Polymer theory has revealed how the chromosomes are so highly compacted in the nucleus, forming a crumpled globule with fractal properties which avoids knots and entanglements in DNA while allowing facile accessibility for its replication and transcription. Entropic repulsion between looped polymers can explain the confinement of each chromosome to a discrete region of the nucleus. Crowding and looping are predicted to facilitate finding the specific targets of factors which modulate activities of DNA. Simulation shows that entropic effects contribute to finding and repairing potentially lethal double-strand breaks in DNA by increasing the mobility of the broken ends, favouring their juxtaposition for repair. Signaling pathways are strongly influenced by crowding, which favours a processive mode of response (consecutive reactions without releasing substrates. This new information contributes to understanding the sometimes counter

  3. Revealing New Structural Insights from Surfactant Micelles through DLS, Microrheology and Raman Spectroscopy

    Directory of Open Access Journals (Sweden)

    Samiul Amin

    2015-06-01

    Full Text Available The correlation between molecular changes and microstructural evolution of rheological properties has been demonstrated for the first time in a mixed anionic/zwitterionic surfactant-based wormlike micellar system. Utilizing a novel combination of DLS-microrheology and Raman Spectroscopy, the effect of electrostatic screening on these properties of anionic (SLES and zwitterionic (CapB surfactant mixtures was studied by modulating the NaCl concentration. As Raman Spectroscopy delivers information about the molecular structure and DLS-microrheology characterizes viscoelastic properties, the combination of data delivered allows for a deeper understanding of the molecular changes underlying the viscoelastic ones. The high frequency viscoelastic response obtained through DLS-microrheology has shown the persistence of the Maxwell fluid response for low viscosity solutions at high NaCl concentrations. The intensity of the Raman band at 170 cm−1 exhibits very strong correlation with the viscosity variation. As this Raman band is assigned to hydrogen bonding, its variation with NaCl concentration additionally indicates differences in water structuring due to potential microstructural differences at low and high NaCl concentrations. The microstructural differences at low and high NaCl concentrations are further corroborated by persistence of a slow mode at the higher NaCl concentrations as seen through DLS measurements. The study illustrates the utility of the combined DLS, DLS-optical microrheology and Raman Spectroscopy in providing new molecular structural insights into the self-assembly process in complex fluids.

  4. Structural insights into the binding mechanism of IDO1 with hydroxylamidine based inhibitor INCB14943

    International Nuclear Information System (INIS)

    Wu, You; Xu, Tingting; Liu, Jinsong; Ding, Ke; Xu, Jinxin

    2017-01-01

    IDO1 (indoleamine 2, 3-dioxygenase 1), a well characterized immunosuppressive enzyme, has attracted growing attention as a potential target for cancer immunotherapy. Hydroxylamidine compounds INCB024360 and INCB14943 (INCB024360 analogue) are highly effective IDO1 inhibitors. INCB024360 is undergoing clinical trials for treatment of various types of human cancer. Here, we determined the co-crystal structure of IDO1 and INCB14943, and elucidate the detailed binding mode. INCB14943 binds to heme iron in IDO1 protein through the oxime nitrogen. Further analysis also reveals that a halogen bonding interaction between the chlorine atom (3-Cl) of INCB14943 and the sulphur atom of C129 significantly improves the inhibition activity against IDO1. Comparing with the other reported inhibitors, the oxime nitrogen and halogen bond interaction are identified as the unique features of INCB14943 among the IDO1 inhibitors. Thus, our study provides novel insights into the interaction between a small molecule inhibitor INCB14943 and IDO1 protein. The structural information will facilitate future IDO1 inhibitor design. - Highlights: • This is the first co-crystal structure of IDO1 with hydroxylamidine compound. • INCB14943 binds to heme iron through oxime nitrogen instead of imidazole nitrogen. • Halogen bond interaction with C129 is another unique feature of INCB14943.

  5. Higher‐order mode absorption measurement of X-band choke-mode cavities in a radial line structure

    Energy Technology Data Exchange (ETDEWEB)

    Zha, Hao [Department of Engineering Physics, Tsinghua University, Beijing CN-100086 (China); Key Laboratory of Particle and Radiation Imaging, Tsinghua University, Ministry of Education, Beijing (China); The European Organization for Nuclear Research, Geneva CH-1211 (Switzerland); Shi, Jiaru, E-mail: shij@mail.tsinghua.edu.cn [Department of Engineering Physics, Tsinghua University, Beijing CN-100086 (China); Key Laboratory of Particle and Radiation Imaging, Tsinghua University, Ministry of Education, Beijing (China); The European Organization for Nuclear Research, Geneva CH-1211 (Switzerland); Wu, Xiaowei; Chen, Huaibi [Department of Engineering Physics, Tsinghua University, Beijing CN-100086 (China); Key Laboratory of Particle and Radiation Imaging, Tsinghua University, Ministry of Education, Beijing (China)

    2016-04-01

    An experiment is presented to study the higher-order mode (HOM) suppression of X-band choke-mode structures with a vector network analyzer (VNA). Specific radial line disks were built to test the reflection from the corresponding damping load and different choke geometries. The mismatch between the radial lines and the VNA was calibrated through a special multi-short-load calibration method. The measured reflections of different choke geometries showed good agreement with the theoretical calculations and verified the HOM absorption feature of each geometric design.

  6. Higher‐order mode absorption measurement of X-band choke-mode cavities in a radial line structure

    International Nuclear Information System (INIS)

    Zha, Hao; Shi, Jiaru; Wu, Xiaowei; Chen, Huaibi

    2016-01-01

    An experiment is presented to study the higher-order mode (HOM) suppression of X-band choke-mode structures with a vector network analyzer (VNA). Specific radial line disks were built to test the reflection from the corresponding damping load and different choke geometries. The mismatch between the radial lines and the VNA was calibrated through a special multi-short-load calibration method. The measured reflections of different choke geometries showed good agreement with the theoretical calculations and verified the HOM absorption feature of each geometric design.

  7. Global structure of mirror modes in the magnetosheath

    International Nuclear Information System (INIS)

    Johnson, J.R.; Cheng, C.Z.

    1996-01-01

    A global stability analysis of mirror modes in the magnetosheath is presented. The analysis is based upon the kinetic-MHD formulation which includes relevant kinetic effects such as Landau resonance and gradient drift effects related to inhomogeneities in the background density, temperature, pressure and its anisotropy, magnetic field, and plasma flow velocity. Pressure anisotropy provides the free energy for the global mirror mode. The local theory of mirror modes predicts purely growing modes confined in the unstable magnetosheath region; however, the nonlocal theory that includes the effects of gradients and plasma flow predicts modes with real frequencies which propagate with the flow from the magnetosheath toward the magnetopause boundary. The real frequency is on the order of a combination of the diamagnetic drift frequency and the Doppler shift frequency associated with plasma flow. The diamagnetic drift frequency provides a wave phase velocity in the direction of the magnetopause so that wave energy accumulates against the magnetopause boundary, and the amplitude is skewed in that direction. On the other hand, plasma flow also gives rise to a real phase velocity, but the phase velocity is smaller than the flow velocity. As a result, the wave amplitude is increased in the wake of the plasma flow and piles up against the bow shock boundary

  8. Global structure of mirror modes in the magnetosheath

    Energy Technology Data Exchange (ETDEWEB)

    Johnson, J.R.; Cheng, C.Z.

    1996-11-01

    A global stability analysis of mirror modes in the magnetosheath is presented. The analysis is based upon the kinetic-MHD formulation which includes relevant kinetic effects such as Landau resonance and gradient drift effects related to inhomogeneities in the background density, temperature, pressure and its anisotropy, magnetic field, and plasma flow velocity. Pressure anisotropy provides the free energy for the global mirror mode. The local theory of mirror modes predicts purely growing modes confined in the unstable magnetosheath region; however, the nonlocal theory that includes the effects of gradients and plasma flow predicts modes with real frequencies which propagate with the flow from the magnetosheath toward the magnetopause boundary. The real frequency is on the order of a combination of the diamagnetic drift frequency and the Doppler shift frequency associated with plasma flow. The diamagnetic drift frequency provides a wave phase velocity in the direction of the magnetopause so that wave energy accumulates against the magnetopause boundary, and the amplitude is skewed in that direction. On the other hand, plasma flow also gives rise to a real phase velocity, but the phase velocity is smaller than the flow velocity. As a result, the wave amplitude is increased in the wake of the plasma flow and piles up against the bow shock boundary.

  9. Static contribution of the higher modes in the dynamic response of structures

    International Nuclear Information System (INIS)

    Barbosa, H.J.C.

    1982-03-01

    In the dynamic response of structures by the modal superposition method usually only the lower modes are taken into account and a procedure that could estimate the contribution due to the higher modes without calculating them would be useful. The technique which consists of assuming that the higher modes respond statically is discussed here. Structures subjected to support motion which are analysed by response spectra techniques are considered and some numerical results are presented. (Author) [pt

  10. An Innovative Structural Mode Selection Methodology: Application for the X-33 Launch Vehicle Finite Element Model

    Science.gov (United States)

    Hidalgo, Homero, Jr.

    2000-01-01

    An innovative methodology for determining structural target mode selection and mode selection based on a specific criterion is presented. An effective approach to single out modes which interact with specific locations on a structure has been developed for the X-33 Launch Vehicle Finite Element Model (FEM). We presented Root-Sum-Square (RSS) displacement method computes resultant modal displacement for each mode at selected degrees of freedom (DOF) and sorts to locate modes with highest values. This method was used to determine modes, which most influenced specific locations/points on the X-33 flight vehicle such as avionics control components, aero-surface control actuators, propellant valve and engine points for use in flight control stability analysis and for flight POGO stability analysis. Additionally, the modal RSS method allows for primary or global target vehicle modes to also be identified in an accurate and efficient manner.

  11. Modeling Insight into Battery Electrolyte Electrochemical Stability and Interfacial Structure.

    Science.gov (United States)

    Borodin, Oleg; Ren, Xiaoming; Vatamanu, Jenel; von Wald Cresce, Arthur; Knap, Jaroslaw; Xu, Kang

    2017-12-19

    Electroactive interfaces distinguish electrochemistry from chemistry and enable electrochemical energy devices like batteries, fuel cells, and electric double layer capacitors. In batteries, electrolytes should be either thermodynamically stable at the electrode interfaces or kinetically stable by forming an electronically insulating but ionically conducting interphase. In addition to a traditional optimization of electrolytes by adding cosolvents and sacrificial additives to preferentially reduce or oxidize at the electrode surfaces, knowledge of the local electrolyte composition and structure within the double layer as a function of voltage constitutes the basis of manipulating an interphase and expanding the operating windows of electrochemical devices. In this work, we focus on how the molecular-scale insight into the solvent and ion partitioning in the electrolyte double layer as a function of applied potential could predict changes in electrolyte stability and its initial oxidation and reduction reactions. In molecular dynamics (MD) simulations, highly concentrated lithium aqueous and nonaqueous electrolytes were found to exclude the solvent molecules from directly interacting with the positive electrode surface, which provides an additional mechanism for extending the electrolyte oxidation stability in addition to the well-established simple elimination of "free" solvent at high salt concentrations. We demonstrate that depending on their chemical structures, the anions could be designed to preferentially adsorb or desorb from the positive electrode with increasing electrode potential. This provides additional leverage to dictate the order of anion oxidation and to effectively select a sacrificial anion for decomposition. The opposite electrosorption behaviors of bis(trifluoromethane)sulfonimide (TFSI) and trifluoromethanesulfonate (OTF) as predicted by MD simulation in highly concentrated aqueous electrolytes were confirmed by surface enhanced infrared

  12. Identifying the default mode network structure using dynamic causal modeling on resting-state functional magnetic resonance imaging.

    Science.gov (United States)

    Di, Xin; Biswal, Bharat B

    2014-02-01

    The default mode network is part of the brain structure that shows higher neural activity and energy consumption when one is at rest. The key regions in the default mode network are highly interconnected as conveyed by both the white matter fiber tracing and the synchrony of resting-state functional magnetic resonance imaging signals. However, the causal information flow within the default mode network is still poorly understood. The current study used the dynamic causal modeling on a resting-state fMRI data set to identify the network structure underlying the default mode network. The endogenous brain fluctuations were explicitly modeled by Fourier series at the low frequency band of 0.01-0.08Hz, and those Fourier series were set as driving inputs of the DCM models. Model comparison procedures favored a model wherein the MPFC sends information to the PCC and the bilateral inferior parietal lobule sends information to both the PCC and MPFC. Further analyses provide evidence that the endogenous connectivity might be higher in the right hemisphere than in the left hemisphere. These data provided insight into the functions of each node in the DMN, and also validate the usage of DCM on resting-state fMRI data. © 2013.

  13. Canonical failure modes of real-time control systems: insights from cognitive theory

    Science.gov (United States)

    Wallace, Rodrick

    2016-04-01

    Newly developed necessary conditions statistical models from cognitive theory are applied to generalisation of the data-rate theorem for real-time control systems. Rather than graceful degradation under stress, automatons and man/machine cockpits appear prone to characteristic sudden failure under demanding fog-of-war conditions. Critical dysfunctions span a spectrum of phase transition analogues, ranging from a ground state of 'all targets are enemies' to more standard data-rate instabilities. Insidious pathologies also appear possible, akin to inattentional blindness consequent on overfocus on an expected pattern. Via no-free-lunch constraints, different equivalence classes of systems, having structure and function determined by 'market pressures', in a large sense, will be inherently unreliable under different but characteristic canonical stress landscapes, suggesting that deliberate induction of failure may often be relatively straightforward. Focusing on two recent military case histories, these results provide a caveat emptor against blind faith in the current path-dependent evolutionary trajectory of automation for critical real-time processes.

  14. New insight into the binding modes of TNP-AMP to human liver fructose-1,6-bisphosphatase.

    Science.gov (United States)

    Han, Xinya; Huang, Yunyuan; Zhang, Rui; Xiao, San; Zhu, Shuaihuan; Qin, Nian; Hong, Zongqin; Wei, Lin; Feng, Jiangtao; Ren, Yanliang; Feng, Lingling; Wan, Jian

    2016-08-05

    Human liver fructose-1,6-bisphosphatase (FBPase) contains two binding sites, a substrate fructose-1,6-bisphosphate (FBP) active site and an adenosine monophosphate (AMP) allosteric site. The FBP active site works by stabilizing the FBPase, and the allosteric site impairs the activity of FBPase through its binding of a nonsubstrate molecule. The fluorescent AMP analogue, 2',3'-O-(2,4,6-trinitrophenyl)adenosine 5'-monophosphate (TNP-AMP) has been used as a fluorescent probe as it is able to competitively inhibit AMP binding to the AMP allosteric site and, therefore, could be used for exploring the binding modes of inhibitors targeted on the allosteric site. In this study, we have re-examined the binding modes of TNP-AMP to FBPase. However, our present enzyme kinetic assays show that AMP and FBP both can reduce the fluorescence from the bound TNP-AMP through competition for FBPase, suggesting that TNP-AMP binds not only to the AMP allosteric site but also to the FBP active site. Mutagenesis assays of K274L (located in the FBP active site) show that the residue K274 is very important for TNP-AMP to bind to the active site of FBPase. The results further prove that TNP-AMP is able to bind individually to the both sites. Our present study provides a new insight into the binding mechanism of TNP-AMP to the FBPase. The TNP-AMP fluorescent probe can be used to exam the binding site of an inhibitor (the active site or the allosteric site) using FBPase saturated by AMP and FBP, respectively, or the K247L mutant FBPase. Copyright © 2016 Elsevier B.V. All rights reserved.

  15. Nonlinear evolution of the mode structure of ELMs in realistic ASDEX Upgrade geometry

    Energy Technology Data Exchange (ETDEWEB)

    Krebs, Isabel; Hoelzl, Matthias; Lackner, Karl; Guenter, Sibylle [Max-Planck-Institut fuer Plasmaphysik, EURATOM Association, Boltzmannstr. 2, Garching (Germany); Collaboration: The ASDEX Upgrade Team

    2013-07-01

    Edge-localized modes (ELMs) are edge instabilities in H-mode plasmas, which eject particles and energy. The suitability of the H-mode for future fusion reactors depends crucially on the exact ELM dynamics as they can damage plasma facing components if too large. We have simulated ELMs in ASDEX Upgrade geometry using the nonlinear MHD code JOREK. Emphasis was put on the mode structure evolution in the early ELM phase which is characterized by the exponential growth of the unstable toroidal Fourier harmonics followed by a phase of saturation. In the linear phase, toroidal harmonics grow independently, whereas at larger amplitudes, the nonlinear interaction between the toroidal harmonics influences their growth and structure. Prior to mode saturation, the evolution of the mode structure can be reproduced well by a simple quadratic mode-interaction model, which yields a possible explanation for the strong n=1 component of type-I ELMs observed in ASDEX Upgrade. In the linear phase of the simulations, intermediate toroidal mode numbers (n 6-14) are most unstable as predicted by the peeling-ballooning model. But non-linearly, the n=1 component becomes important due to an energy transfer from pairs of linearly dominant toroidal harmonics with neighboring mode numbers to the n=1. The latter thereby changes its spatial structure.

  16. Sensitivity analysis of the stiffness between the frame structure and the frequency and vibration mode

    Science.gov (United States)

    Chen, Wenyuan

    2018-03-01

    The modal parameters such as natural frequency and vibration mode of the frame structure of the layer stiffness sensitivity is inconsistent. This article focuses on the theoretical derivation of the frequency and mode of the frame structure layer stiffness of the first-order sensitivity. The numerical examples show that the frame structure of layer stiffness higher than with the first order sensitivity vibration frequency.

  17. True photonic band-gap mode-control in VCSEL structures

    DEFF Research Database (Denmark)

    Romstad, F.; Madsen, M.; Birkedal, Dan

    2003-01-01

    Photonic band-gap mode confinement in novel nano-structured large area VCSEL structures is confirmed by the amplified spontaneous emission spectrum. Both guide and anti-guide VCSEL structures are experimentally characterised to verify the photonic band-gap effect.......Photonic band-gap mode confinement in novel nano-structured large area VCSEL structures is confirmed by the amplified spontaneous emission spectrum. Both guide and anti-guide VCSEL structures are experimentally characterised to verify the photonic band-gap effect....

  18. Simple countermeasures against the TM110-beam-blowup-mode in biperiodic structures

    International Nuclear Information System (INIS)

    Euteneuer, H.; Herminghaus, H.; Schoeler, H.

    1984-01-01

    The two fundamental methods of fighting beam blow-up in rf-accelerating-structures are staggered detuning and selective Q-spoiling of their higher order modes. Biperiodic structures offer a very simple way of applying the latter technique of the most dangerous TM 110 -like blowup mode at 1.7 times the accelerating frequency: letting this mode propagate but giving a large gap to the TM 110 -passband. This gap must be positive for electric coupling (f(phi=0) =1.7c. With asymmetric coupling elements between the cavities of a structure, one has a simple tool for staggered detuning: a change of the relative orientation of these elements spreads the resonance frequencies not only of the TM 110 -mode, but of at least all dipole modes. (orig.)

  19. New insights into the structure and composition of technical lignins : A comparative characterisation study

    NARCIS (Netherlands)

    Constant, Sandra|info:eu-repo/dai/nl/374650519; Wienk, Hans L J|info:eu-repo/dai/nl/203884884; Frissen, Augustinus E.; Peinder, Peter De|info:eu-repo/dai/nl/325810818; Boelens, Rolf|info:eu-repo/dai/nl/070151407; Van Es, Daan S.; Grisel, Ruud J H; Weckhuysen, Bert M.|info:eu-repo/dai/nl/285484397; Huijgen, Wouter J J; Gosselink, Richard J A; Bruijnincx, Pieter C A|info:eu-repo/dai/nl/33799529X

    2016-01-01

    Detailed insight into the structure and composition of industrial (technical) lignins is needed to devise efficient thermal, bio- or chemocatalytic valorisation strategies. Six such technical lignins covering three main industrial pulping methods (Indulin AT Kraft, Protobind 1000 soda lignin and

  20. New insights into the structure and composition of technical lignins: a comparative characterisation study

    NARCIS (Netherlands)

    Constant, Sandra; Wienk, Hans L.J.; Frissen, A.E.; Peinder, de Peter; Boelens, Rolf; Es, van D.S.; Grisel, Ruud J.H.; Weckhuysen, Bert M.; Huijgen, W.J.J.; Gosselink, R.J.A.; Bruijnincx, Pieter C.A.

    2016-01-01

    Detailed insight into the structure and composition of industrial (technical) lignins is needed to devise efficient thermal, bio- or chemocatalytic valorisation strategies. Six such technical lignins covering three main industrial pulping methods (Indulin AT Kraft, Protobind 1000 soda lignin and

  1. Canonical structure and extra mode of generalized unimodular gravity

    Science.gov (United States)

    Bufalo, Rodrigo; Oksanen, Markku

    2018-02-01

    We consider a recently proposed generalization of unimodular gravity, where the lapse function is constrained to be equal to a function of the determinant of the spatial metric f (h ), as a potential origin of a dark fluid with a generally h -dependent equation of state parameter. We establish the Hamiltonian analysis and the canonical path integral for the theory. All the special cases that do not match unimodular gravity involve the violation of general covariance, and consequently the physical content of the theory is changed significantly. Particularly, the case of a constant function f is shown to contain an extra physical degree of freedom in each point of space. Physical consequences of the extra degree of freedom are studied in a linearized theory, where the extra mode is carried by the trace of the metric perturbation. The trace mode does not propagate as a wave, since it satisfies an elliptic partial differential equation in spacetime. Consequently, the trace perturbation is shown to grow exponentially with time, which implies instability. The case of a general f (h ) involves additional second-class constraints, which implies the presence of an extra global degree of freedom that depends only on time (instead of the extra local degree of freedom in the case of a constant f ).

  2. Mixed-mode loading of the structural elements with defect

    Directory of Open Access Journals (Sweden)

    Larisa V. Stepanova

    2015-06-01

    Full Text Available In the article the problem of determining the stress-strain state near the mixed-mode crack tip in a power-law material under plane stress conditions is considered. The eigenfunction method is used for the mixed-mode crack tip problem. It is shown that the eigenfunction expansion method results in the nonlinear eigenvalue problem. The numeric solution of the nonlinear eigenvalue problem formulated is obtained. The power of the distance from the crack tip is the eigenvalue of the nonlinear eigenvalue problem considered whereas the angular distributions of the stress components are the eigenfunctions. The new eigenvalues different from the eigenvalues of the Hutchinson–Rice–Rosengren are found. It is shown that the new asymptotic solution can be interpreted as the self-similar intermediate asymptotics of the stress field in the vicinity of the crack tip at distances which are very small compared to the crack length or the size of the specimen and at distances which are large compared to the length of the completely damaged zone. The developed method allows us to construct the geometry of the completely damaged zone in vicinity of the crack tip.

  3. Mode shape combination in a two-dimensional vibration energy harvester through mass loading structural modification

    Energy Technology Data Exchange (ETDEWEB)

    Sharpes, Nathan; Kumar, Prashant [Center for Energy Harvesting Materials and Systems (CEHMS), Virginia Tech, Blacksburg, Virginia 24061 (United States); Abdelkefi, Abdessattar; Abdelmoula, Hichem [Department of Mechanical and Aerospace Engineering, New Mexico State University, Las Cruces, New Mexico 88003 (United States); Adler, Jan [Center for Energy Harvesting Materials and Systems (CEHMS), Virginia Tech, Blacksburg, Virginia 24061 (United States); Institute of Dynamics and Vibration Research (IDS), Leibniz Universität, Hannover 30167 (Germany); Priya, Shashank [Center for Energy Harvesting Materials and Systems (CEHMS), Virginia Tech, Blacksburg, Virginia 24061 (United States); Bio-Inspired Materials and Devices Laboratory (BMDL), Virginia Tech, Blacksburg, Virginia 24061 (United States)

    2016-07-18

    Mode shapes in the design of mechanical energy harvesters, as a means of performance increase, have been largely overlooked. Currently, the vast majority of energy harvester designs employ some variation of a single-degree-of-freedom cantilever, and the mode shapes of such beams are well known. This is especially true for the first bending mode, which is almost exclusively the chosen vibration mode for energy harvesting. Two-dimensional beam shapes (those which curve, meander, spiral, etc., in a plane) have recently gained research interest, as they offer freedom to modify the vibration characteristics of the harvester beam for achieving higher power density. In this study, the second bending mode shape of the “Elephant” two-dimensional beam shape is examined, and its interaction with the first bending mode is evaluated. A combinatory mode shape created by using mass loading structural modification to lower the second bending modal frequency was found to interact with the first bending mode. This is possible since the first two bending modes do not share common areas of displacement. The combined mode shape is shown to produce the most power of any of the considered mode shapes.

  4. Transverse kick in misaligned traveling wave structures driven at the fundamental mode

    International Nuclear Information System (INIS)

    Whittum, D.H.

    1998-04-01

    Fabrication errors in traveling wave structures result in non-axisymmetric RF fields that couple to the rf drive at the fundamental mode frequency. The authors calculate the excitation of the dipole mode and the integrated effect on the beam, using the thin iris and small hole approximation

  5. Roundtrip matrix method for calculating the leaky resonant modes of open nanophotonic structures

    DEFF Research Database (Denmark)

    de Lasson, Jakob Rosenkrantz; Kristensen, Philip Trøst; Mørk, Jesper

    2014-01-01

    We present a numerical method for calculating quasi-normal modes of open nanophotonic structures. The method is based on scattering matrices and a unity eigenvalue of the roundtrip matrix of an internal cavity, and we develop it in detail with electromagnetic fields expanded on Bloch modes...

  6. Insights into Chromatin Structure and Dynamics in Plants

    Directory of Open Access Journals (Sweden)

    Stefanie Rosa

    2013-11-01

    Full Text Available The packaging of chromatin into the nucleus of a eukaryotic cell requires an extraordinary degree of compaction and physical organization. In recent years, it has been shown that this organization is dynamically orchestrated to regulate responses to exogenous stimuli as well as to guide complex cell-type-specific developmental programs. Gene expression is regulated by the compartmentalization of functional domains within the nucleus, by distinct nucleosome compositions accomplished via differential modifications on the histone tails and through the replacement of core histones by histone variants. In this review, we focus on these aspects of chromatin organization and discuss novel approaches such as live cell imaging and photobleaching as important tools likely to give significant insights into our understanding of the very dynamic nature of chromatin and chromatin regulatory processes. We highlight the contribution plant studies have made in this area showing the potential advantages of plants as models in understanding this fundamental aspect of biology.

  7. Electron Microscopy Structural Insights into CPAP Oligomeric Behavior

    DEFF Research Database (Denmark)

    Alvarez-Cabrera, Ana L; Delgado, Sandra; Gil-Carton, David

    2017-01-01

    Centrosomal P4.1-associated protein (CPAP) is a cell cycle regulated protein fundamental for centrosome assembly and centriole elongation. In humans, the region between residues 897-1338 of CPAP mediates interactions with other proteins and includes a homodimerization domain. CPAP mutations cause...... into clearly different regular 3D maps (putatively corresponding to dimers and tetramers) and direct observation of individual images representing other complexes of HsCPAP(897-1338) (i.e., putative flexible monomers and higher-order multimers), we report a dynamic oligomeric behavior of this protein, where...... of different oligomers of CPAP, suggesting further insights to understand how this protein works, contributing to the elucidation of control mechanisms for centriole biogenesis....

  8. High spatial sampling global mode structure measurements via multichannel reflectometry in NSTX

    Energy Technology Data Exchange (ETDEWEB)

    Crocker, N A; Peebles, W A; Kubota, S; Zhang, J [Department of Physics and Astronomy, University of California-Los Angeles, Los Angeles, CA 90095-7099 (United States); Bell, R E; Fredrickson, E D; Gorelenkov, N N; LeBlanc, B P; Menard, J E; Podesta, M [Princeton Plasma Physics Laboratory, PO Box 451, Princeton, NJ 08543-0451 (United States); Sabbagh, S A [Department of Applied Physics and Applied Mathematics, Columbia University, New York, NY 10027 (United States); Tritz, K [Johns Hopkins University, Baltimore, MD 21218 (United States); Yuh, H [Nova Photonics, Princeton, NJ 08540 (United States)

    2011-10-15

    Global modes-including kinks and tearing modes (f <{approx} 50 kHz), toroidicity-induced Alfven eigenmodes (TAE; f {approx} 50-250 kHz) and global and compressional Alfven eigenmodes (GAE and CAE; f >{approx} 400 kHz)-play critical roles in many aspects of plasma performance. Their investigation on NSTX is aided by an array of fixed-frequency quadrature reflectometers used to determine their radial density perturbation structure. The array has been recently upgraded to 16 channels spanning 30-75 GHz (n{sub cutoff} = (1.1-6.9) x 10{sup 19} m{sup -3} in O-mode), improving spatial sampling and access to the core of H-mode plasmas. The upgrade has yielded significant new results that advance the understanding of global modes in NSTX. The GAE and CAE structures have been measured for the first time in the core of an NSTX high-power (6 MW) beam-heated H-mode plasma. The CAE structure is strongly core-localized, which has important implications for electron thermal transport. The TAE structure has been measured with greatly improved spatial sampling, and measurements of the TAE phase, the first in NSTX, show strong radial variation near the midplane, indicating radial propagation caused by non-ideal MHD effects. Finally, the tearing mode structure measurements provide unambiguous evidence of coupling to an external kink.

  9. Structural Damage Localization by Outlier Analysis of Signal-processed Mode Shapes

    DEFF Research Database (Denmark)

    Ulriksen, Martin Dalgaard; Damkilde, Lars

    2016-01-01

    Contrary to global modal parameters such as eigenfrequencies, mode shapes inherently provide structural information on a local level. Therefore, this particular modal parameter and its derivatives are utilized extensively for damage identification. Typically, more or less advanced mathematical...

  10. Reduction of Flight Control System/Structural Mode Interaction, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — A novel approach is proposed for reducing the degree of interaction of a high gain flight control system with the airframe structural vibration modes, representing a...

  11. Waveguide resonance mode response of stacked structures of metallic sub-wavelength slit arrays

    Science.gov (United States)

    Tokuda, Yasunori; Takano, Keisuke; Sakaguchi, Koichiro; Kato, Kosaku; Nakajima, Makoto; Akiyama, Koichi

    2018-05-01

    Detailed measurements of the optical properties of two-tier systems composed of metallic plates perforated with periodic sub-wavelength slit patterns were carried out using terahertz time-domain spectroscopy. We demonstrate that the transmission properties observed experimentally for various configurations can be reproduced successfully by simulations based on the finite-differential time-domain method. Fabry-Perot-like waveguide resonance mode behaviors specific to this quasi-dielectric system were then investigated. For structures with no lateral displacement between the slit-array plates, mode disappearance phenomena, which are caused by destructive interference between the odd-order mode and the blue- or red-shifted even-order modes, were observed experimentally. The uncommon behavior of the even-order modes was examined precisely to explain the slit-width dependence. For structures with half-pitched displacement between the plates, extraordinarily strong transmission was observed experimentally, even when the optical paths were shut off. This result was interpreted in terms of the propagation of surface plasmon polaritons through very thin and labyrinthine spacings that inevitably exist between the metallic plates. Furthermore, the optical mode disappearance phenomena are revealed to be characterized by anticrossing of the two mixing modes formed by even- and odd-order modes. These experimental observations that are supported theoretically are indispensable to the practical use of this type of artificial dielectric and are expected to encourage interest in optical mode behaviors that are not typically observed in conventional dielectric systems.

  12. Mode structure in an optically pumped D2O far infrared ring laser

    International Nuclear Information System (INIS)

    Yuan, D.C.; Soumagne, G.; Siegrist, M.R.

    1989-07-01

    The mode structures in an optically pumped D 2 O far infrared ring laser and a corresponding linear resonator have been compared. While single mode operation can be obtained over the whole useful pressure range in the ring structure, this is only possible at pressures greater than 8 Torr in the linear resonator case. A numerical model predicts quite well the pulse shape, pressure dependence and influence of the resonator quality in the ring cavity. (author) 12 figs., 8 refs

  13. Tomography and Purification of the Temporal-Mode Structure of Quantum Light

    Science.gov (United States)

    Ansari, Vahid; Donohue, John M.; Allgaier, Markus; Sansoni, Linda; Brecht, Benjamin; Roslund, Jonathan; Treps, Nicolas; Harder, Georg; Silberhorn, Christine

    2018-05-01

    High-dimensional quantum information processing promises capabilities beyond the current state of the art, but addressing individual information-carrying modes presents a significant experimental challenge. Here we demonstrate effective high-dimensional operations in the time-frequency domain of nonclassical light. We generate heralded photons with tailored temporal-mode structures through the pulse shaping of a broadband parametric down-conversion pump. We then implement a quantum pulse gate, enabled by dispersion-engineered sum-frequency generation, to project onto programmable temporal modes, reconstructing the quantum state in seven dimensions. We also manipulate the time-frequency structure by selectively removing temporal modes, explicitly demonstrating the effectiveness of engineered nonlinear processes for the mode-selective manipulation of quantum states.

  14. Soft x-ray measurement of internal tearing mode structure in a reversed-field pinch

    International Nuclear Information System (INIS)

    Chartas, G.; Hokin, S.

    1991-01-01

    The structure of internally resonant tearing modes has been studied in the Madison Symmetric Torus reversed-field pinch with a soft x-ray detector system consisting of an imaging array at one toroidal location and several detectors at different toroidal locations. The toroidal mode numbers of m = 1 structures are in the range n = -5, -6, -7. The modes propagate with phase velocity v = 1--6 x 10 6 cm/s, larger than the diamagnetic drift velocity v d ∼ 5 x 10 5 cm/s. Phase locking between modes with different n in manifested as a beating of soft x-ray signals which is found to be strongest near the resonant surfaces of the modes (r/a = 0.1 -- 0.5). 15 refs., 5 figs

  15. Zero-mode waveguide nanophotonic structures for single molecule characterization

    Science.gov (United States)

    Crouch, Garrison M.; Han, Donghoon; Bohn, Paul W.

    2018-05-01

    Single-molecule characterization has become a crucial research tool in the chemical and life sciences, but limitations, such as limited concentration range, inability to control molecular distributions in space, and intrinsic phenomena, such as photobleaching, present significant challenges. Recent developments in non-classical optics and nanophotonics offer promising routes to mitigating these restrictions, such that even low affinity (K D ~ mM) biomolecular interactions can be studied. Here we introduce and review specific nanophotonic devices used to support single molecule studies. Optical nanostructures, such as zero-mode waveguides (ZMWs), are usually fabricated in thin gold or aluminum films and serve to confine the observation volume of optical microspectroscopy to attoliter to zeptoliter volumes. These simple nanostructures allow individual molecules to be isolated for optical and electrochemical analysis, even when the molecules of interest are present at high concentration (µM–mM) in bulk solution. Arrays of ZMWs may be combined with optical probes such as single molecule fluorescence, single molecule fluorescence resonance energy transfer, and fluorescence correlation spectroscopy for distributed analysis of large numbers of single-molecule reactions or binding events in parallel. Furthermore, ZMWs may be used as multifunctional devices, for example by combining optical and electrochemical functions in a single discrete architecture to achieve electrochemical ZMWs. In this review, we will describe the optical properties, fabrication, and applications of ZMWs for single-molecule studies, as well as the integration of ZMWs into systems for chemical and biochemical analysis.

  16. Topology optimization of continuum structure with dynamic constraints using mode identification

    International Nuclear Information System (INIS)

    Li, Jianhongyu; Chen, Shenyan; Huang, Hai

    2015-01-01

    For the problems such as mode exchange and localized modes in topology optimization of continuum structure with dynamic constraints, it is difficult to apply the traditional optimization model which considers fixed order mode frequencies as constraints in optimization calculation. A new optimization model is established, in which the dynamical constraints are changed as frequencies of structural principal vibrations. The order of the principal vibrations is recognized through modal identification in the optimization process, and the constraints are updated to make the optimization calculation execute smoothly. Localized mode elimination techniques are introduced to reduce the localized modes induced by the low density elements, which could improve the optimization efficiency. A new optimization process is designed, which achieves the purpose of overcoming mode exchange problem and localized mode problem at the cost of increasing several structural analyses. Optimization system is developed by using Nastran to perform structural analysis and sensitivity analysis and two-level multipoint approximation algorithm as optimizer. Numerical results verified that the presented method is effective and reasonable.

  17. Inverse boundary element calculations based on structural modes

    DEFF Research Database (Denmark)

    Juhl, Peter Møller

    2007-01-01

    The inverse problem of calculating the flexural velocity of a radiating structure of a general shape from measurements in the field is often solved by combining a Boundary Element Method with the Singular Value Decomposition and a regularization technique. In their standard form these methods sol...

  18. New Insight into Carbon Nanotube Electronic Structure Selectivity

    Energy Technology Data Exchange (ETDEWEB)

    Sumpter, Bobby G [ORNL; Meunier, Vincent [ORNL; Jiang, Deen [ORNL

    2009-01-01

    The fundamental role of aryl diazonium salts for post synthesis selectivity of carbon nanotubes is investigated using extensive electronic structure calculations. The resulting understanding for diazonium salt based selective separation of conducting and semiconducting carbon nanotubes shows how the primary contributions come from the interplay between the intrinsic electronic structure of the carbon nanotubes and that of the anion of the salt. We demonstrate how the electronic transport properties change upon the formation of charge transfer complexes and upon their conversion into covalently attached functional groups. Our results are found to correlate well with experiments and provide for the first time an atomistic description for diazonium salt based chemical separation of carbon nanotubes

  19. Structural insight into the UNC-45–myosin complex

    DEFF Research Database (Denmark)

    Fratev, Filip; Jonsdottir, Svava Osk; Pajeva, Ilza

    2013-01-01

    The UNC-45 chaperone protein interacts with and affects the folding, stability, and the ATPase activity of myosins. It plays a critical role in the cardiomyopathy development and in the breast cancer tumor growth. Here we propose the first structural model of the UNC-45–myosin complex using various...... is mainly stabilized by electrostatic interactions. Remarkably, the contact surface area is similar to that of the myosinactin complex. A significant interspecies difference in the myosin binding epitope is observed. Our results reveal the structural basis of MYH7 exons 15–16 hypertrophic cardiomyopathy...... mutations and provide directions for drug targeting. © 2013 Wiley Periodicals, Inc....

  20. Complex modes and frequencies in damped structural vibrations

    DEFF Research Database (Denmark)

    Krenk, Steen

    2004-01-01

    It is demonstrated that the state space formulation of the equation of motion of damped structural elements like cables and beams leads to a symmetric eigenvalue problem if the stiffness and damping operators are self-adjoint, and that this is typically the case in the absence of gyroscopic forces....... The corresponding theory of complex modal analysis of continuous systems is developed and illustrated in relation to optimal damping and impulse response of cables and beams with discrete dampers....

  1. New insight on bismuth cuprates with incommensurate modulated structures

    Czech Academy of Sciences Publication Activity Database

    Mironov, A. V.; Petříček, Václav; Khasanova, N. R.; Antipov, E. V.

    2016-01-01

    Roč. 72, č. 3 (2016), s. 395-403 ISSN 2052-5206 Institutional support: RVO:68378271 Keywords : modulated structure * high Tc superconductor * superspace approach Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 2.032, year: 2016

  2. Choke-mode damped structure design for the Compact Linear Collider main linac

    CERN Document Server

    Zha, Hao; Grudiev, Alexej; Huang, Wenhui; Shi, Jiaru; Tang, Chuanxiang; Wuensch, Walter

    2012-01-01

    Choke-mode damped structures are being studied as an alternative design to waveguide damped structures for the main linac of the Compact Linear Collider (CLIC). Choke-mode structures have the potential for lower pulsed temperature rise and simpler and less expensive fabrication. An equivalent circuit model based on transmission line theory for higher-order-mode damping is presented. Using this model, a new choke geometry is proposed and the wakefield performance is verified using GDFIDL. This structure has a comparable wakefield damping effect to the baseline design which uses waveguide damping. A prototype structure with the same iris dimensions and accelerating gradient as the nominal CLIC design, but with the new choke geometry, has been designed for high-power tests. DOI: 10.1103/PhysRevSTAB.15.122003

  3. Structural Insights Into The Bacterial Carbon-Phosphorus Lyase Machinery

    DEFF Research Database (Denmark)

    Brodersen, Ditlev Egeskov

    the proteins encoded in the phn operon act in concert to catabolise phosphonate remain unknown. We have determined the crystal structure of a 240 kDa Escherichia coli carbon-phosphorus lyase core complex at 1.7 Å and show that it comprises a highly intertwined network of subunits with several unexpected......Phosphonate compounds act as a nutrient source for some microorganisms when phosphate is limiting but require a specialised enzymatic machinery due to the presence of the highly stable carbon-phosphorus bond. Despite the fundamental importance to microbial metabolism, the details of how...... structural features. The complex contains at least two different active sites and suggest a revision of current models of carbon-phosphorus bond cleavage. Using electron microscopy, we map the binding site of an additional protein subunit, which may use ATP for driving conformational changes during...

  4. Structural Insights into Ail-Mediated Adhesion in Yersinia pestis

    Energy Technology Data Exchange (ETDEWEB)

    Yamashita, Satoshi; Lukacik, Petra; Barnard, Travis J.; Noinaj, Nicholas; Felek, Suleyman; Tsang, Tiffany M.; Krukonis, Eric S.; Hinnebusch, B. Joseph; Buchanan, Susan K. (Michigan); (NIH); (Michigan-Med)

    2012-01-30

    Ail is an outer membrane protein from Yersinia pestis that is highly expressed in a rodent model of bubonic plague, making it a good candidate for vaccine development. Ail is important for attaching to host cells and evading host immune responses, facilitating rapid progression of a plague infection. Binding to host cells is important for injection of cytotoxic Yersinia outer proteins. To learn more about how Ail mediates adhesion, we solved two high-resolution crystal structures of Ail, with no ligand bound and in complex with a heparin analog called sucrose octasulfate. We identified multiple adhesion targets, including laminin and heparin, and showed that a 40 kDa domain of laminin called LG4-5 specifically binds to Ail. We also evaluated the contribution of laminin to delivery of Yops to HEp-2 cells. This work constitutes a structural description of how a bacterial outer membrane protein uses a multivalent approach to bind host cells.

  5. Insight into the Geothermal Structure in Chingshui, Ilan, Taiwan

    OpenAIRE

    Lun-Tao Tong; Shoung Ouyang; Tai-Rong Guo; Ching-Ray Lee; Kou-Hsin Hu; Chun-Li Lee; Chun-Jao Wang

    2008-01-01

    The Chingshui geothermal field is the largest known productive geothermal area in Taiwan. The purpose of this paper is to delineate this geothermal structure by integrating geophysical data and borehole information. The existence of a magma chamber in the shallow crust and shallow intrusive igneous rock results in a high heat flow and geothermal gradient; furthermore, the NE deep fault system within the meta-sandstones provides meteoric recharge from a higher elevation to artesianally drive t...

  6. Insight into mitochondrial structure and function from electron tomography.

    Science.gov (United States)

    Frey, T G; Renken, C W; Perkins, G A

    2002-09-10

    In recent years, electron tomography has provided detailed three-dimensional models of mitochondria that have redefined our concept of mitochondrial structure. The models reveal an inner membrane consisting of two components, the inner boundary membrane (IBM) closely apposed to the outer membrane and the cristae membrane that projects into the matrix compartment. These two components are connected by tubular structures of relatively uniform size called crista junctions. The distribution of crista junction sizes and shapes is predicted by a thermodynamic model based upon the energy of membrane bending, but proteins likely also play a role in determining the conformation of the inner membrane. Results of structural studies of mitochondria during apoptosis demonstrate that cytochrome c is released without detectable disruption of the outer membrane or extensive swelling of the mitochondrial matrix, suggesting the formation of an outer membrane pore large enough to allow passage of holo-cytochrome c. The possible compartmentation of inner membrane function between the IBM and the cristae membrane is also discussed.

  7. Hyperactive antifreeze proteins from longhorn beetles: some structural insights.

    Science.gov (United States)

    Kristiansen, Erlend; Wilkens, Casper; Vincents, Bjarne; Friis, Dennis; Lorentzen, Anders Blomkild; Jenssen, Håvard; Løbner-Olesen, Anders; Ramløv, Hans

    2012-11-01

    This study reports on structural characteristics of hyperactive antifreeze proteins (AFPs) from two species of longhorn beetles. In Rhagium mordax, eight unique mRNAs coding for five different mature AFPs were identified from cold-hardy individuals. These AFPs are apparently homologues to a previously characterized AFP from the closely related species Rhagium inquisitor, and consist of six identifiable repeats of a putative ice binding motif TxTxTxT spaced irregularly apart by segments varying in length from 13 to 20 residues. Circular dichroism spectra show that the AFPs from both species have a high content of β-sheet and low levels of α-helix and random coil. Theoretical predictions of residue-specific secondary structure locate these β-sheets within the putative ice-binding motifs and the central parts of the segments separating them, consistent with an overall β-helical structure with the ice-binding motifs stacked in a β-sheet on one side of the coil. Molecular dynamics models based on these findings show that these AFPs would be energetically stable in a β-helical conformation. Copyright © 2012 Elsevier Ltd. All rights reserved.

  8. Amyloid Structure and Assembly: Insights from Scanning Transmission Electron Microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Goldsbury, C.; Wall, J.; Baxa, U.; Simon, M. N.; Steven, A. C.; Engel, A.; Aebi, U.; Muller, S. A.

    2011-01-01

    Amyloid fibrils are filamentous protein aggregates implicated in several common diseases such as Alzheimer's disease and type II diabetes. Similar structures are also the molecular principle of the infectious spongiform encephalopathies such as Creutzfeldt-Jakob disease in humans, scrapie in sheep, and of the so-called yeast prions, inherited non-chromosomal elements found in yeast and fungi. Scanning transmission electron microscopy (STEM) is often used to delineate the assembly mechanism and structural properties of amyloid aggregates. In this review we consider specifically contributions and limitations of STEM for the investigation of amyloid assembly pathways, fibril polymorphisms and structural models of amyloid fibrils. This type of microscopy provides the only method to directly measure the mass-per-length (MPL) of individual filaments. Made on both in vitro assembled and ex vivo samples, STEM mass measurements have illuminated the hierarchical relationships between amyloid fibrils and revealed that polymorphic fibrils and various globular oligomers can assemble simultaneously from a single polypeptide. The MPLs also impose strong constraints on possible packing schemes, assisting in molecular model building when combined with high-resolution methods like solid-state nuclear magnetic resonance (NMR) and electron paramagnetic resonance (EPR).

  9. Structural insights into the recognition of phosphopeptide by the FHA domain of kanadaptin

    DEFF Research Database (Denmark)

    Xu, Qingping; Deller, Marc C; Nielsen, Tine K

    2014-01-01

    with a phosphopeptide mimic derived from a peptide segment from the N-terminus of a symmetry-related molecule as well as a sulfate bound to the structurally conserved phosphothreonine recognition cleft. This structure provides insights into the molecular recognition features utilized by this family of proteins...

  10. Structural insight into the Clostridium difficile ethanolamine utilisation microcompartment.

    Directory of Open Access Journals (Sweden)

    Alison C Pitts

    Full Text Available Bacterial microcompartments form a protective proteinaceous barrier around metabolic enzymes that process unstable or toxic chemical intermediates. The genome of the virulent, multidrug-resistant Clostridium difficile 630 strain contains an operon, eut, encoding a bacterial microcompartment with genes for the breakdown of ethanolamine and its utilisation as a source of reduced nitrogen and carbon. The C. difficile eut operon displays regulatory genetic elements and protein encoding regions in common with homologous loci found in the genomes of other bacteria, including the enteric pathogens Salmonella enterica and Enterococcus faecalis. The crystal structures of two microcompartment shell proteins, CD1908 and CD1918, and an uncharacterised protein with potential enzymatic activity, CD1925, were determined by X-ray crystallography. CD1908 and CD1918 display the same protein fold, though the order of secondary structure elements is permuted in CD1908 and this protein displays an N-terminal β-strand extension. These proteins form hexamers with molecules related by crystallographic and non-crystallographic symmetry. The structure of CD1925 has a cupin β-barrel fold and a putative active site that is distinct from the metal-ion dependent catalytic cupins. Thin-section transmission electron microscopy of Escherichia coli over-expressing eut proteins indicates that CD1918 is capable of self-association into arrays, suggesting an organisational role for CD1918 in the formation of this microcompartment. The work presented provides the basis for further study of the architecture and function of the C. difficile eut microcompartment, its role in metabolism and the wider consequences of intestinal colonisation and virulence in this pathogen.

  11. Structural insights into the bacterial carbon - phosphorus lyase machinery

    DEFF Research Database (Denmark)

    Seweryn, Paulina; Van, Lan Bich; Kjeldgaard, Morten

    2015-01-01

    Phosphorus is required for all life and microorganisms can extract it from their environment through several metabolic pathways. When phosphate is in limited supply, some bacteria are able to use phosphonate compounds, which require specialized enzymatic machinery to break the stable carbon......–phosphorus (C–P) bond. Despite its importance, the details of how this machinery catabolizes phosphonates remain unknown. Here we determine the crystal structure of the 240-kilodalton Escherichia coli C–P lyase core complex (PhnG–PhnH–PhnI–PhnJ; PhnGHIJ), and show that it is a two-fold symmetric hetero...

  12. Structural insights into the β-xylosidase from Trichoderma reesei

    International Nuclear Information System (INIS)

    Rojas, Adriana L.; Fischer, Hannes; Polikarpov, Igor; Craievich, Aldo Felix

    2005-01-01

    Xylan is a major structural polysaccharide in plant cells, and is the second most abundant polysaccharide in nature, accounting for approximately one-third of all renewable organic carbon on earth. Xylan together with cellulose (1,4-β-glucan) and lignin (a complex polyphenolic compound) make up the major polymeric constituents of plant cell walls, recently, there was a significant industrial interest in Xylan and its hydrolytic enzymatic complex, as a supplement in animal feed, for the manufacture of bread, food and drinks, textiles, bleaching of cellulose pulp, ethanol and xylitol production. (author)

  13. Structural insights into the {beta}-xylosidase from Trichoderma reesei

    Energy Technology Data Exchange (ETDEWEB)

    Rojas, Adriana L.; Fischer, Hannes; Polikarpov, Igor [Sao Paulo Univ. (USP), Sao Carlos, SP (Brazil). Inst. de Fisica; Eneiskaya, Elena V.; Kulminskaya, Anna A.; Shabalin, Konstantin A.; Neustroev, Kirill N.; Golubev, Alexander M. [Petersburg Nuclear Physics Inst., Moskow (Russian Federation); Craievich, Aldo Felix [Sao Paulo Univ. (USP), SP (Brazil). Inst. de Fisica

    2005-07-01

    Xylan is a major structural polysaccharide in plant cells, and is the second most abundant polysaccharide in nature, accounting for approximately one-third of all renewable organic carbon on earth. Xylan together with cellulose (1,4-{beta}-glucan) and lignin (a complex polyphenolic compound) make up the major polymeric constituents of plant cell walls, recently, there was a significant industrial interest in Xylan and its hydrolytic enzymatic complex, as a supplement in animal feed, for the manufacture of bread, food and drinks, textiles, bleaching of cellulose pulp, ethanol and xylitol production. (author)

  14. Structural and Functional Insights into Foamy Viral Integrase

    Directory of Open Access Journals (Sweden)

    Cha-Gyun Shin

    2013-07-01

    Full Text Available Successful integration of retroviral DNA into the host chromosome is an essential step for viral replication. The process is mediated by virally encoded integrase (IN and orchestrated by 3'-end processing and the strand transfer reaction. In vitro reaction conditions, such as substrate specificity, cofactor usage, and cellular binding partners for such reactions by the three distinct domains of prototype foamy viral integrase (PFV-IN have been described well in several reports. Recent studies on the three‑dimensional structure of the interacting complexes between PFV-IN and DNA, cofactors, binding partners, or inhibitors have explored the mechanistic details of such interactions and shown its utilization as an important target to develop anti-retroviral drugs. The presence of a potent, non-transferable nuclear localization signal in the PFV C-terminal domain extends its use as a model for investigating cellular trafficking of large molecular complexes through the nuclear pore complex and also to identify novel cellular targets for such trafficking. This review focuses on recent advancements in the structural analysis and in vitro functional aspects of PFV-IN.

  15. Artemin Crystal Structure Reveals Insights into Heparan Sulfate Binding

    Energy Technology Data Exchange (ETDEWEB)

    Silvian,L.; Jin, P.; Carmillo, P.; Boriack-Sjodin, P.; Pelletier, C.; Rushe, M.; Gong, B.; Sah, D.; Pepinsky, B.; Rossomando, A.

    2006-01-01

    Artemin (ART) promotes the growth of developing peripheral neurons by signaling through a multicomponent receptor complex comprised of a transmembrane tyrosine kinase receptor (cRET) and a specific glycosylphosphatidylinositol-linked co-receptor (GFR{alpha}3). Glial cell line-derived neurotrophic factor (GDNF) signals through a similar ternary complex but requires heparan sulfate proteoglycans (HSPGs) for full activity. HSPG has not been demonstrated as a requirement for ART signaling. We crystallized ART in the presence of sulfate and solved its structure by isomorphous replacement. The structure reveals ordered sulfate anions bound to arginine residues in the pre-helix and amino-terminal regions that were organized in a triad arrangement characteristic of heparan sulfate. Three residues in the pre-helix were singly or triply substituted with glutamic acid, and the resulting proteins were shown to have reduced heparin-binding affinity that is partly reflected in their ability to activate cRET. This study suggests that ART binds HSPGs and identifies residues that may be involved in HSPG binding.

  16. Development of structure design program for venturi scrubber working at self-priming mode

    International Nuclear Information System (INIS)

    Wang Meng; Sun Zhongning; Gu Haifeng

    2012-01-01

    A structure design program was developed for Venturi scrubber working at the self-priming mode. This program proposed a complete logic for thermal parameters calculation and structure design of the throat. A revised calculation for resistance relationship was carried out based on experimental study. The relative error between revised results and experimental values is within 8.6%. (authors)

  17. Introduction to structural failure modes for nuclear power facilities

    International Nuclear Information System (INIS)

    Reed, J.W.; Gurbuz, O.

    1993-01-01

    This introduction provides a background of the evaluation methods for earthquakes larger than design basis. Seismic probabilistic risk assessment (SPRA) and seismic margin assessment (SMA) methods are introduced to the reader. The basic parameters used to define seismic capacity for each method are explained. The objectives of both evaluation methods and how they can be used to evaluate the adequacy of a seismic design are discussed. General issues related to computing seismic capacity are reviewed relative to SPRA and SMA. Four companion papers presented in the journal following this introduction discuss the types of information (i.e., dynamic tests, earthquake experience, and analytical data) that are used to determine the real capacity of structures and equipment in nuclear power plants to resist earthquakes. The motivation for discussing these three types of information is presented as an introduction to these papers that following in this journal edition. The purpose of the present paper is to lay the groundwork and provide motivation for these papers

  18. Connecting structural relaxation with the low frequency modes in a hard-sphere colloidal glass.

    Science.gov (United States)

    Ghosh, Antina; Chikkadi, Vijayakumar; Schall, Peter; Bonn, Daniel

    2011-10-28

    Structural relaxation in hard-sphere colloidal glasses has been studied using confocal microscopy. The motion of individual particles is followed over long time scales to detect the rearranging regions in the system. We have used normal mode analysis to understand the origin of the rearranging regions. The low-frequency modes, obtained over short time scales, show strong spatial correlation with the rearrangements that happen on long time scales.

  19. Insight into the Geothermal Structure in Chingshui, Ilan, Taiwan

    Directory of Open Access Journals (Sweden)

    Lun-Tao Tong

    2008-01-01

    Full Text Available The Chingshui geothermal field is the largest known productive geothermal area in Taiwan. The purpose of this paper is to delineate this geothermal structure by integrating geophysical data and borehole information. The existence of a magma chamber in the shallow crust and shallow intrusive igneous rock results in a high heat flow and geothermal gradient; furthermore, the NE deep fault system within the meta-sandstones provides meteoric recharge from a higher elevation to artesianally drive the geothermal system. There is evidence that geothermal fluid deeply circulated within the fracture zone and was heated by a deeply located body of hot rock. The geothermal reservoir of the Chingshui geothermal field might be related to the fracture zone of the Chingshuihsi fault. It is bounded by the C-fault in the north and Xiaonanao fault in the south. Based on information obtained from geophysical interpretations and well logs, a 3-D geothermal conceptual model is constructed in this study. Further, the geothermal reservoir is confined to an area that is 260 m in width, N21°W, 1.5 km in length, and has an 80° dip toward the NE. Ahigh-temperature zone is found in the SE region of the reservoir, which is about 500 m in length; this zone is located near the intersection of the Chingshuihsi and Xiaonanao faults. An area on the NE side of the high-temperature zone has been recommended for the drilling of production wells for future geothermal development.

  20. Structural insights into central hypertension regulation by human aminopeptidase A.

    Science.gov (United States)

    Yang, Yang; Liu, Chang; Lin, Yi-Lun; Li, Fang

    2013-08-30

    Hypertension is regulated through both the central and systemic renin-angiotensin systems. In the central renin-angiotensin system, zinc-dependent aminopeptidase A (APA) up-regulates blood pressure by specifically cleaving the N-terminal aspartate, but not the adjacent arginine, from angiotensin II, a process facilitated by calcium. Here, we determined the crystal structures of human APA and its complexes with different ligands and identified a calcium-binding site in the S1 pocket of APA. Without calcium, the S1 pocket can bind both acidic and basic residues through formation of salt bridges with the charged side chains. In the presence of calcium, the binding of acidic residues is enhanced as they ligate the cation, whereas the binding of basic residues is no longer favorable due to charge repulsion. Of the peptidomimetic inhibitors of APA, amastatin has higher potency than bestatin by fitting better in the S1 pocket and interacting additionally with the S3' subsite. These results explain the calcium-modulated substrate specificity of APA in central hypertension regulation and can guide the design and development of brain-targeting antihypertensive APA inhibitors.

  1. Structural Insights into Central Hypertension Regulation by Human Aminopeptidase A*

    Science.gov (United States)

    Yang, Yang; Liu, Chang; Lin, Yi-Lun; Li, Fang

    2013-01-01

    Hypertension is regulated through both the central and systemic renin-angiotensin systems. In the central renin-angiotensin system, zinc-dependent aminopeptidase A (APA) up-regulates blood pressure by specifically cleaving the N-terminal aspartate, but not the adjacent arginine, from angiotensin II, a process facilitated by calcium. Here, we determined the crystal structures of human APA and its complexes with different ligands and identified a calcium-binding site in the S1 pocket of APA. Without calcium, the S1 pocket can bind both acidic and basic residues through formation of salt bridges with the charged side chains. In the presence of calcium, the binding of acidic residues is enhanced as they ligate the cation, whereas the binding of basic residues is no longer favorable due to charge repulsion. Of the peptidomimetic inhibitors of APA, amastatin has higher potency than bestatin by fitting better in the S1 pocket and interacting additionally with the S3′ subsite. These results explain the calcium-modulated substrate specificity of APA in central hypertension regulation and can guide the design and development of brain-targeting antihypertensive APA inhibitors. PMID:23888046

  2. Optimal sensor configuration for flexible structures with multi-dimensional mode shapes

    International Nuclear Information System (INIS)

    Chang, Minwoo; Pakzad, Shamim N

    2015-01-01

    A framework for deciding the optimal sensor configuration is implemented for civil structures with multi-dimensional mode shapes, which enhances the applicability of structural health monitoring for existing structures. Optimal sensor placement (OSP) algorithms are used to determine the best sensor configuration for structures with a priori knowledge of modal information. The signal strength at each node is evaluated by effective independence and modified variance methods. Euclidean norm of signal strength indices associated with each node is used to expand OSP applicability into flexible structures. The number of sensors for each method is determined using the threshold for modal assurance criterion (MAC) between estimated (from a set of observations) and target mode shapes. Kriging is utilized to infer the modal estimates for unobserved locations with a weighted sum of known neighbors. A Kriging model can be expressed as a sum of linear regression and random error which is assumed as the realization of a stochastic process. This study presents the effects of Kriging parameters for the accurate estimation of mode shapes and the minimum number of sensors. The feasible ranges to satisfy MAC criteria are investigated and used to suggest the adequate searching bounds for associated parameters. The finite element model of a tall building is used to demonstrate the application of optimal sensor configuration. The dynamic modes of flexible structure at centroid are appropriately interpreted into the outermost sensor locations when OSP methods are implemented. Kriging is successfully used to interpolate the mode shapes from a set of sensors and to monitor structures associated with multi-dimensional mode shapes. (paper)

  3. Insight, self-stigma and psychosocial outcomes in Schizophrenia: a structural equation modelling approach.

    Science.gov (United States)

    Lien, Y-J; Chang, H-A; Kao, Y-C; Tzeng, N-S; Lu, C-W; Loh, C-H

    2018-04-01

    Poor insight is prevalent in patients with schizophrenia and has been associated with acute illness severity, medication non-adherence and poor treatment outcomes. Paradoxically, high insight has been associated with various undesirable outcomes, including low self-esteem, depression and low subjective quality of life (QoL) in patients with schizophrenia. Despite the growing body of studies conducted in Western countries supporting the pernicious effects of improved insight in psychosis, which bases on the level of self-stigma, the effects are unclear in non-Western societies. The current study examined the role of self-stigma in the relationship between insight and psychosocial outcomes in a Chinese population. A total of 170 outpatients with schizophrenia spectrum disorders were recruited from two general university hospitals. Sociodemographic data and clinical variables were recorded and self-report scales were employed to measure self-stigma, depression, insight, self-esteem and subjective QoL. Structural equation modelling (SEM) was used to analyse the cross-sectional data. High levels of self-stigma were reported by 39% of the participants (n = 67). The influences of insight, self-stigma, self-esteem and depression on subjective QoL were confirmed by the SEM results. Our model with the closest fit to the data (χ 2 = 33.28; df = 20; p = 0.03; χ 2/df = 1.66; CFI = 0.98; TLI = 0.97; RMSEA = 0.06) demonstrated that self-stigma might fully mediate the association of insight with low self-esteem, depression and poor subjective QoL. High insight into illness contributed to self-stigma, which caused low self-esteem and depression and, consequently, low QoL. Notably, insight did not directly affect self-esteem, depression or QoL. Furthermore, the association of insight with poor psychosocial outcomes was not moderated by self-stigma. Our findings support the mediating model of insight relevant to the poor psychosocial outcomes of individuals diagnosed with

  4. Mode structure and continuum damping of high-n toroidal Alfven eigenmodes

    International Nuclear Information System (INIS)

    Rosenbluth, M.N.; Berk, H.L.; Van Dam, J.W.; Lindberg, D.M.

    1992-02-01

    An asymptotic theory is described for calculating the mode structure and continuum damping of short wave-length toroidal Alfven eigenmodes (TAE). The formalism somewhat resembles the treatment used for describing low-frequency toroidal modes with singular structure at a rational surface, where an inner solution, which for the TAE mode has toroidal coupling, is matched to an outer toroidally uncoupled solution. A three-term recursion relation among coupled poloidal harmonic amplitudes is obtained, whose solution gives the structure of the global wavefunction and the complex eigenfrequency, including continuum damping. Both analytic and numerical solutions are presented. The magnitude of the damping is essential for determining the thresholds for instability driven by the spatial gradients of energetic particles (e.g., neutral beam-injected ions or fusion-product alpha particles) contained in a tokamak plasma

  5. Online channel operation mode: Game theoretical analysis from the supply chain power structure

    Directory of Open Access Journals (Sweden)

    Song Huang

    2015-11-01

    Full Text Available Purpose: Dual-channels have been widely used in practice, and the pricing decisions and the online channel operation mode choice have been the core problems in dual-channel supply chain management. This paper focuses on the online channel operation mode choice from the supply chain power structures based on game theoretical analysis. Design/methodology/approach: This paper utilizes three kinds of game theoretical models to analyze the impact of supply chain power structures on the optimal pricing and online channel operation mode choice. Findings: Results derived in this paper indicate that when the self-price elasticity is large, the power structures have no direct impact on the decisions. However, when the self-price elasticity is small and customers’ preference for the online channel is low, then in the MS market, it is better for the retailer to operate the online channel, while in the RS market or in the VN market, it is better for the manufacturer to operate the online channel. Research limitations/implications: In this paper, we do not consider stochastic demand and asymmetric information, which may not well suit the reality. Originality/value: This paper provides a different perspective to analyze the impact of supply chain power structures on the pricing decisions and online channel operation mode choice. The comparison of these two online channel operation modes in this paper is also a unique point.

  6. Optimization of hardening/softening behavior of plane frame structures using nonlinear normal modes

    DEFF Research Database (Denmark)

    Dou, Suguang; Jensen, Jakob Søndergaard

    2016-01-01

    Devices that exploit essential nonlinear behavior such as hardening/softening and inter-modal coupling effects are increasingly used in engineering and fundamental studies. Based on nonlinear normal modes, we present a gradient-based structural optimization method for tailoring the hardening...... involving plane frame structures where the hardening/softening behavior is qualitatively and quantitatively tuned by simple changes in the geometry of the structures....

  7. Towards a single European electricity market. A structured approach to regulatory mode decision-making

    International Nuclear Information System (INIS)

    De Jong, H.M.

    2009-01-01

    This study focuses on the processes through which the rules and regulations that govern European electricity markets - and inherently, their integration process - are established. So far, European policy makers have largely followed a 'trial-and-error' approach to finding an appropriate regulatory mode (process) for dealing effectively with market integration issues. This unstructured approach to regulatory mode selection leads to several problems: - Today's trial-and-error strategy of shifting from one regulatory mode to another is time-consuming. - In the regulatory mode selection process, certain key principles of good governance are insufficiently considered. - European regulatory processes are experienced as vague, intransparent, and illegitimate by 'outside' stakeholders. This study develops a 'structured approach to regulatory mode decision-making' (STARMODE) based on the theory of decision modelling in policy management and a case study exploring three key market integration issues in the field of electricity markets: interconnector investment, congestion management and market transparency. The main objective is to present a systematic and comprehensive framework for analysing and improving regulatory mode decision-making in the context of the European Union, focusing on electricity market integration. The STARMODE approach is generally applicable to (and relevant for) European market integration issues in industries characterized by a natural monopoly and/or an essential service. The approach may also contribute to national regulatory mode decision-making and multi-state decision-making in other continents.

  8. Active power filter for harmonic compensation using a digital dual-mode-structure repetitive control approach

    DEFF Research Database (Denmark)

    Zou, Zhixiang; Wang, Zheng; Cheng, Ming

    2012-01-01

    This paper presents an digital dual-mode-structure repetitive control approach for the single-phase shunt active power filter (APF), which aims to enhance the tracking ability and eliminate arbitrary order harmonic. The proposed repetitive control scheme blends the characteristics of both odd......-harmonic repetitive control and even-harmonic repetitive control. Moreover, the convergence rate is faster than conventional repetitive controller. Additionally, the parameters have been designed and optimized for the dual-mode structure repetitive control to improve the performance of APF system. Experimental...

  9. Method of adiabatic modes in studying problems of smoothly irregular open waveguide structures

    International Nuclear Information System (INIS)

    Sevastianov, L. A.; Egorov, A. A.; Sevastyanov, A. L.

    2013-01-01

    Basic steps in developing an original method of adiabatic modes that makes it possible to solve the direct and inverse problems of simulating and designing three-dimensional multilayered smoothly irregular open waveguide structures are described. A new element in the method is that an approximate solution of Maxwell’s equations is made to obey “inclined” boundary conditions at the interfaces between themedia being considered. These boundary conditions take into account the obliqueness of planes tangent to nonplanar boundaries between the media and lead to new equations for coupled vector quasiwaveguide hybrid adiabatic modes. Solutions of these equations describe the phenomenon of “entanglement” of two linear polarizations of an irregular multilayered waveguide, the appearance of a new mode in an entangled state, and the effect of rotation of the polarization plane of quasiwaveguide modes. The efficiency of the method is demonstrated by considering the example of numerically simulating a thin-film generalized waveguide Lüneburg lens.

  10. Mechanistic insights into mode of action of potent natural antagonists of BACE-1 for checking Alzheimer’s plaque pathology

    Energy Technology Data Exchange (ETDEWEB)

    Dhanjal, Jaspreet Kaur [School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067 (India); Goyal, Sukriti [Apaji Institute of Mathematics and Applied Computer Technology, Banasthali University, Tonk 304022, Rajasthan (India); Sharma, Sudhanshu [Department of Biotechnology, Delhi Technological University, New Delhi 110042 (India); Hamid, Rabia [Department of Biochemistry, University of Kashmir, Srinagar 190006 (India); Grover, Abhinav, E-mail: abhinavgr@gmail.com [School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067 (India)

    2014-01-17

    Highlights: •Accumulation of Aβ plaques is one of the major pathology associated with Alzheimer’s disease. •Inhibition of β-Secretase or BACE-1 offers a viable prospect to check the growth of these plaques. •A large virtual dataset of natural compounds was screened against BACE-1. •Top two hits were analyzed for thermodynamic and structural stability using MD simulations. •Their detailed binding mode of actions were elucidated. -- Abstract: Alzheimer’s is a neurodegenerative disorder resulting in memory loss and decline in cognitive abilities. Accumulation of extracellular beta amyloidal plaques is one of the major pathology associated with this disease. β-Secretase or BACE-1 performs the initial and rate limiting step of amyloidic pathway in which 37–43 amino acid long peptides are generated which aggregate to form plaques. Inhibition of this enzyme offers a viable prospect to check the growth of these plaques. Numerous efforts have been made in recent years for the generation of BACE-1 inhibitors but many of them failed during the preclinical or clinical trials due to drug related or drug induced toxicity. In the present work, we have used computational methods to screen a large dataset of natural compounds to search for small molecules having BACE-1 inhibitory activity with low toxicity to normal cells. Molecular dynamics simulations were performed to analyze molecular interactions between the screened compounds and the active residues of the enzyme. Herein, we report two natural compounds of inhibitory nature active against β-secretase enzyme of amyloidic pathway and are potent lead molecules against Alzheimer’s disease.

  11. Mechanistic insights into mode of action of potent natural antagonists of BACE-1 for checking Alzheimer’s plaque pathology

    International Nuclear Information System (INIS)

    Dhanjal, Jaspreet Kaur; Goyal, Sukriti; Sharma, Sudhanshu; Hamid, Rabia; Grover, Abhinav

    2014-01-01

    Highlights: •Accumulation of Aβ plaques is one of the major pathology associated with Alzheimer’s disease. •Inhibition of β-Secretase or BACE-1 offers a viable prospect to check the growth of these plaques. •A large virtual dataset of natural compounds was screened against BACE-1. •Top two hits were analyzed for thermodynamic and structural stability using MD simulations. •Their detailed binding mode of actions were elucidated. -- Abstract: Alzheimer’s is a neurodegenerative disorder resulting in memory loss and decline in cognitive abilities. Accumulation of extracellular beta amyloidal plaques is one of the major pathology associated with this disease. β-Secretase or BACE-1 performs the initial and rate limiting step of amyloidic pathway in which 37–43 amino acid long peptides are generated which aggregate to form plaques. Inhibition of this enzyme offers a viable prospect to check the growth of these plaques. Numerous efforts have been made in recent years for the generation of BACE-1 inhibitors but many of them failed during the preclinical or clinical trials due to drug related or drug induced toxicity. In the present work, we have used computational methods to screen a large dataset of natural compounds to search for small molecules having BACE-1 inhibitory activity with low toxicity to normal cells. Molecular dynamics simulations were performed to analyze molecular interactions between the screened compounds and the active residues of the enzyme. Herein, we report two natural compounds of inhibitory nature active against β-secretase enzyme of amyloidic pathway and are potent lead molecules against Alzheimer’s disease

  12. Identification of dominant flow structures in rapidly rotating convection of liquid metals using Dynamic Mode Decomposition

    Science.gov (United States)

    Horn, S.; Schmid, P. J.; Aurnou, J. M.

    2016-12-01

    The Earth's metal core acts as a dynamo whose efficiency in generating and maintaining the magnetic field is essentially determined by the rotation rate and the convective motions occurring in its outer liquid part. For the description of the primary physics in the outer core the idealized system of rotating Rayleigh-Bénard convection is often invoked, with the majority of studies considering only working fluids with Prandtl numbers of Pr ≳ 1. However, liquid metals are characterized by distinctly smaller Prandtl numbers which in turn result in an inherently different type of convection. Here, we will present results from direct numerical simulations of rapidly rotating convection in a fluid with Pr ≈ 0.025 in cylindrical containers and Ekman numbers as low as 5 × 10-6. In this system, the Coriolis force is the source of two types of inertial modes, the so-called wall modes, that also exist at moderate Prandtl numbers, and cylinder-filling oscillatory modes, that are a unique feature of small Prandtl number convection. The obtained flow fields were analyzed using the Dynamic Mode Decomposition (DMD). This technique allows to extract and identify the structures that govern the dynamics of the system as well as their corresponding frequencies. We have investigated both the regime where the flow is purely oscillatory and the regime where wall modes and oscillatory modes co-exist. In the purely oscillatory regime, high and low frequency oscillatory modes characterize the flow. When both types of modes are present, the DMD reveals that the wall-attached modes dominate the flow dynamics. They precess with a relatively low frequency in retrograde direction. Nonetheless, also in this case, high frequency oscillations have a significant contribution.

  13. Rayleigh Wave Ellipticity Modeling and Inversion for Shallow Structure at the Proposed InSight Landing Site in Elysium Planitia, Mars

    Science.gov (United States)

    Knapmeyer-Endrun, Brigitte; Golombek, Matthew P.; Ohrnberger, Matthias

    2017-10-01

    The SEIS (Seismic Experiment for Interior Structure) instrument onboard the InSight mission will be the first seismometer directly deployed on the surface of Mars. From studies on the Earth and the Moon, it is well known that site amplification in low-velocity sediments on top of more competent rocks has a strong influence on seismic signals, but can also be used to constrain the subsurface structure. Here we simulate ambient vibration wavefields in a model of the shallow sub-surface at the InSight landing site in Elysium Planitia and demonstrate how the high-frequency Rayleigh wave ellipticity can be extracted from these data and inverted for shallow structure. We find that, depending on model parameters, higher mode ellipticity information can be extracted from single-station data, which significantly reduces uncertainties in inversion. Though the data are most sensitive to properties of the upper-most layer and show a strong trade-off between layer depth and velocity, it is possible to estimate the velocity and thickness of the sub-regolith layer by using reasonable constraints on regolith properties. Model parameters are best constrained if either higher mode data can be used or additional constraints on regolith properties from seismic analysis of the hammer strokes of InSight's heat flow probe HP3 are available. In addition, the Rayleigh wave ellipticity can distinguish between models with a constant regolith velocity and models with a velocity increase in the regolith, information which is difficult to obtain otherwise.

  14. Research on the Diesel Engine with Sliding Mode Variable Structure Theory

    Science.gov (United States)

    Ma, Zhexuan; Mao, Xiaobing; Cai, Le

    2018-05-01

    This study constructed the nonlinear mathematical model of the diesel engine high-pressure common rail (HPCR) system through two polynomial fitting which was treated as a kind of affine nonlinear system. Based on sliding-mode variable structure control (SMVSC) theory, a sliding-mode controller for affine nonlinear systems was designed for achieving the control of common rail pressure and the diesel engine’s rotational speed. Finally, on the simulation platform of MATLAB, the designed nonlinear HPCR system was simulated. The simulation results demonstrated that sliding-mode variable structure control algorithm shows favourable control performances which are overcoming the shortcomings of traditional PID control in overshoot, parameter adjustment, system precision, adjustment time and ascending time.

  15. Damage detection and quantification using mode curvature variation on framed structures: analysis of the preliminary results

    Science.gov (United States)

    Iacovino, Chiara; Ditommaso, Rocco; Auletta, Gianluca; Ponzo, Felice C.

    2017-04-01

    Continuous monitoring based on vibrational identification methods is increasingly employed for the evaluation of the state of health of existing buildings after strong motion earthquake. Different damage identification methods are based on the variations of damage indices defined in terms modal (eigenfrequencies, mode shapes, and modal damping) and/or non-modal parameters. Most of simplified methods for structural health monitoring and damage detection are based on the evaluation of the dynamic characteristics evolution associated to the fundamental mode of vibration of a monitored structure. Aim of this work is the upgrade of an existing method for damage localization on framed structures during a moderate/destructive earthquake. The existing version of the method is based on the comparison of the geometric characteristics (with particular reference to the mode curvature) exhibited by the structures, related to fundamental mode of vibration, before and during an earthquake. The approach is based on the use of a nonlinear filter, the band-variable filter, based on the Stockwell Transform able to extract the nonlinear response of each mode of vibration. The new version of the method provides the possibility to quantify a possible damage occurred on the monitored structure linking the mode curvature variation with the maximum inter-story drift. This paper shows the preliminary results obtained from several simulations on nonlinear numerical models of reinforced concrete framed structures, designed for only gravity loads, without and with the presence of infill panels. Furthermore, a correlation between maximum mode curvature difference and maximum inter-story drift has been defined for the different numerical models in order to quantify the structural damage. Acknowledgements This study was partially funded by the Italian Department of Civil Protection within the project DPC-RELUIS 2016 - RS4 ''Seismic observatory of structures and health monitoring'' and by the

  16. Comparative research on the transmission-mode GaAs photocathodes of exponential-doping structures

    International Nuclear Information System (INIS)

    Chen Liang; Qian Yun-Sheng; Zhang Yi-Jun; Chang Ben-Kang

    2012-01-01

    Early research has shown that the varied doping structures of the active layer of GaAs photocathodes have been proven to have a higher quantum efficiency than uniform doping structures. On the basis of our early research on the surface photovoltage of GaAs photocathodes, and comparative research before and after activation of reflection-mode GaAs photocathodes, we further the comparative research on transmission-mode GaAs photocathodes. An exponential doping structure is the typical varied doping structure that can form a uniform electric field in the active layer. By solving the one-dimensional diffusion equation for no equilibrium minority carriers of transmission-mode GaAs photocathodes of the exponential doping structure, we can obtain the equations for the surface photovoltage (SPV) curve before activation and the spectral response curve (SRC) after activation. Through experiments and fitting calculations for the designed material, the body-material parameters can be well fitted by the SPV before activation, and proven by the fitting calculation for SRC after activation. Through the comparative research before and after activation, the average surface escape probability (SEP) can also be well fitted. This comparative research method can measure the body parameters and the value of SEP for the transmission-mode GaAs photocathode more exactly than the early method, which only measures the body parameters by SRC after activation. It can also help us to deeply study and exactly measure the parameters of the varied doping structures for transmission-mode GaAs photocathodes, and optimize the Cs-O activation technique in the future. (electromagnetism, optics, acoustics, heat transfer, classical mechanics, and fluid dynamics)

  17. Highly Selective Phosphatidylinositol 4-Kinase III beta Inhibitors and Structural Insight into Their Mode of Action

    Czech Academy of Sciences Publication Activity Database

    Mejdrová, Ivana; Chalupská, Dominika; Kögler, Martin; Šála, Michal; Plačková, Pavla; Bäumlová, Adriana; Hřebabecký, Hubert; Procházková, Eliška; Dejmek, Milan; Guillon, Rémi; Strunin, Dmytro; Weber, Jan; Lee, G.; Birkuš, G.; Mertlíková-Kaiserová, Helena; Bouřa, Evžen; Nencka, Radim

    2015-01-01

    Roč. 58, č. 9 (2015), s. 3767-3793 ISSN 0022-2623 R&D Projects: GA MŠk LO1302; GA ČR GA15-09310S; GA ČR GJ15-21030Y EU Projects: European Commission(XE) 333916 - STARPI4K Institutional support: RVO:61388963 Keywords : phosphatidylinositol 4-kinase III beta * broad-spectrum antiviral agents * positive-sense RNA viruses Subject RIV: CC - Organic Chemistry Impact factor: 5.589, year: 2015

  18. Sub-Tg enthalpy relaxation in an unstable oxide glass former: insights into the structural heterogeneity

    DEFF Research Database (Denmark)

    Yue, Yuanzheng; Zhang, Yanfei

    Structural heterogeneity plays a crucial role in determining functionality of glasses. In this work we have found that the sub-Tg enthalpy relaxation pattern in a hyperquenched glass is highly sensitive to structural heterogeneity. As a consequence, the former can be used as an effective approach...... to detect and quantify the structural heterogeneity in glass-forming liquids. However, the chemical nature of structural heterogeneity should be revealed by other means such as high resolution microscopic and spectroscopic methods. To study the impact of the structural heterogeneity on the sub-Tg relaxation...... chemical features and degrees of structural heterogeneity in glass-forming liquids. This finding contributes to the microscopic origin of both the primary and secondary relaxation in terms of structural heterogeneity. Finally the results provide insights into the relation between structural heterogeneity...

  19. The Relative Effects of Explicit Correction and Recasts on Two Target Structures via Two Communication Modes

    Science.gov (United States)

    Yilmaz, Yucel

    2012-01-01

    This study investigated the effects of negative feedback type (i.e., explicit correction vs. recasts), communication mode (i.e., face-to-face communication vs. synchronous computer-mediated communication), and target structure salience (i.e., salient vs. nonsalient) on the acquisition of two Turkish morphemes. Forty-eight native speakers of…

  20. Connecting structural relaxation with the low frequency modes in a hard-sphere colloidal glass

    NARCIS (Netherlands)

    Ghosh, A.; Chikkadi, V.; Schall, P.; Bonn, D.

    2011-01-01

    Structural relaxation in hard-sphere colloidal glasses has been studied using confocal microscopy. The motion of individual particles is followed over long time scales to detect the rearranging regions in the system. We have used normal mode analysis to understand the origin of the rearranging

  1. Scaling Mode Shapes in Output-Only Structure by a Mass-Change-Based Method

    Directory of Open Access Journals (Sweden)

    Liangliang Yu

    2017-01-01

    Full Text Available A mass-change-based method based on output-only data for the rescaling of mode shapes in operational modal analysis (OMA is introduced. The mass distribution matrix, which is defined as a diagonal matrix whose diagonal elements represent the ratios among the diagonal elements of the mass matrix, is calculated using the unscaled mode shapes. Based on the theory of null space, the mass distribution vector or mass distribution matrix is obtained. A small mass with calibrated weight is added to a certain location of the structure, and then the mass distribution vector of the modified structure is estimated. The mass matrix is identified according to the difference of the mass distribution vectors between the original and modified structures. Additionally, the universal set of modes is unnecessary when calculating the mass distribution matrix, indicating that modal truncation is allowed in the proposed method. The mass-scaled mode shapes estimated in OMA according to the proposed method are compared with those obtained by experimental modal analysis. A simulation is employed to validate the feasibility of the method. Finally, the method is tested on output-only data from an experiment on a five-storey structure, and the results confirm the effectiveness of the method.

  2. LALAGE - a computer program to calculate the TM01 modes of cylindrically symmetrical multicell resonant structures

    International Nuclear Information System (INIS)

    Fernandes, P.

    1982-01-01

    An improvement has been made to the LALA program to compute resonant frequencies and fields for all the modes of the lowest TM 01 band-pass of multicell structures. The results are compared with those calculated by another popular rf cavity code and with experimentally measured quantities. (author)

  3. Contribution of the higher modes in the dynamic analysis of reticulate structures

    International Nuclear Information System (INIS)

    Torres, A.L.F.L.; Lima, E.C.P. de

    1982-01-01

    The approximation obtained using the high mode static contribution technique in the stress calculation, is analyzed. The results are compared to those obtained by a direct method using the structure movement differential equations. Several numerical examples are presented and discussed. (E.G.) [pt

  4. On the Theory of Coupled Modes in Optical Cavity-Waveguide Structures

    DEFF Research Database (Denmark)

    Kristensen, Philip Trøst; de Lasson, Jakob Rosenkrantz; Heuck, Mikkel

    2017-01-01

    Light propagation in systems of optical cavities coupled to waveguides can be conveniently described by a general rate equation model known as (temporal) coupled mode theory (CMT). We present an alternative derivation of the CMT for optical cavitywaveguide structures, which explicitly relies...... in the coupled systems. Practical application of the theory is illustrated using example calculations in one and two dimensions....

  5. Design of tunable surface mode waveguide based on photonic crystal composite structure using organic liquid*

    International Nuclear Information System (INIS)

    Zhang Lan-Lan; Liu Wei; Li Ping; Yang Xi; Cao Xu

    2017-01-01

    With the method of replacing the surface layer of photonic crystal with tubes, a novel photonic crystal composite structure used as a tunable surface mode waveguide is designed. The tubes support tunable surface states. The tunable propagation capabilities of the structure are investigated by using the finite-difference time-domain. Simulation results show that the beam transmission distributions of the composite structure are sensitive to the frequency range of incident light and the surface morphology which can be modified by filling the tubes with different organic liquids. By adjusting the filler in tubes, the T-shaped, Y-shaped, and L-shaped propagations can be realized. The property can be applied to the tunable surface mode waveguide. Compared with a traditional single function photonic crystal waveguide, our designed structure not only has a small size, but also is a tunable device. (paper)

  6. Nonlinear asteroseismology: insight from amplitude and frequency modulations of oscillation modes in compact pulsators from Kepler photometry

    Directory of Open Access Journals (Sweden)

    Zong Weikai

    2017-01-01

    Full Text Available Nonlinear mode interactions are difficult to observe from ground-based telescopes as the typical periods of the modulations induced by those nonlinear phenomena are on timescales of weeks, months, even years. The launch of space telescopes, e.g., Kepler, has tremendously changed the situation and shredded new light on this research field. We present results from Kepler photometry showing evidence that nonlinear interactions between modes occur in the two compact pulsators KIC 8626021, a DB white dwarf, and KIC 10139564, a short period hot B subdwarf. KIC 8626021 and KIC 10139564 had been monitored by Kepler in short-cadence for nearly two years and more than three years without interruption, respectively. By analyzing these high-quality photometric data, we found that the modes within the triplets induced by rotation clearly reveal different behaviors: their frequencies and amplitudes may exhibit either periodic or irregular modulations, or remain constant. These various behaviors of the amplitude and of the frequency modulations of the oscillation modes observed in these two stars are in good agreement with those predicted within the amplitude equation formalism in the case of the nonlinear resonant mode coupling mechanism.

  7. A pilot study of cognitive insight and structural covariance in first-episode psychosis.

    Science.gov (United States)

    Kuang, Corin; Buchy, Lisa; Barbato, Mariapaola; Makowski, Carolina; MacMaster, Frank P; Bray, Signe; Deighton, Stephanie; Addington, Jean

    2017-01-01

    Cognitive insight is described as a balance between one's self-reflectiveness (recognition and correction of dysfunctional reasoning), and self-certainty (overconfidence). Neuroimaging studies have linked the ventrolateral prefrontal cortex (VLPFC) to cognitive insight in people with psychosis. However, the relationship between cognitive insight and structural connectivity between the VLPFC and other brain areas is unknown. Here, we investigated the modulation of cognitive insight on structural covariance networks involving the VLPFC in a first-episode psychosis sample. Fifteen patients with a first-episode psychosis provided magnetic resonance (MR) scans and completed the Beck Cognitive Insight Scale (BCIS). MR scans were also available for 15 historical controls. Seed-based analysis of structural covariance was conducted using the Mapping Anatomical Correlations Across the Cerebral Cortex (MACACC) methodology, whereby Pearson correlation coefficients were extracted between seed regions in left and right VLPFC and cortical thickness across the brain. Structural covariance maps between groups were compared at each vertex. In first-episode subjects, we evaluated the modulation of BCIS scores on cortical covariance between VLPFC and every other vertex. Findings showed no significant group difference between first-episode psychosis subjects and controls in thickness covariance seeded from left or right VLPFC. However, in first-episode psychosis subjects, a positive association with self-certainty was found in networks seeded from both left and right VLPFC with thickness in medial frontal cortex and right pars triangularis. No significant associations were found for self-reflectiveness. These results suggest that self-certainty, but not self-reflectiveness, positively modulated cortical covariance in a frontal network in patients with a first-episode psychosis. Copyright © 2016 Elsevier B.V. All rights reserved.

  8. Two-dimensional spatial structure of the dissipative trapped-electron mode

    International Nuclear Information System (INIS)

    Rewoldt, G.; Tang, W.M.; Frieman, E.A.

    1976-09-01

    This paper deals with the complete two-dimensional structure of the dissipative trapped-electron mode over its full width, which may extend over several mode-rational surfaces. The complete integro-differential equation is studied in the limit k/sub r/rho/sub i/ less than 1, where rho/sub i/ is the ion gyroradius, and k/sub r/, the radial wavenumber, is regarded as a differential operator. This is converted into a matrix equation which is then solved by standard numerical methods

  9. SnoRNAs from the filamentous fungus Neurospora crassa: structural, functional and evolutionary insights

    Directory of Open Access Journals (Sweden)

    Chen Chun-Long

    2009-11-01

    Full Text Available Abstract Background SnoRNAs represent an excellent model for studying the structural and functional evolution of small non-coding RNAs involved in the post-transcriptional modification machinery for rRNAs and snRNAs in eukaryotic cells. Identification of snoRNAs from Neurospora crassa, an important model organism playing key roles in the development of modern genetics, biochemistry and molecular biology will provide insights into the evolution of snoRNA genes in the fungus kingdom. Results Fifty five box C/D snoRNAs were identified and predicted to guide 71 2'-O-methylated sites including four sites on snRNAs and three sites on tRNAs. Additionally, twenty box H/ACA snoRNAs, which potentially guide 17 pseudouridylations on rRNAs, were also identified. Although not exhaustive, the study provides the first comprehensive list of two major families of snoRNAs from the filamentous fungus N. crassa. The independently transcribed strategy dominates in the expression of box H/ACA snoRNA genes, whereas most of the box C/D snoRNA genes are intron-encoded. This shows that different genomic organizations and expression modes have been adopted by the two major classes of snoRNA genes in N. crassa . Remarkably, five gene clusters represent an outstanding organization of box C/D snoRNA genes, which are well conserved among yeasts and multicellular fungi, implying their functional importance for the fungus cells. Interestingly, alternative splicing events were found in the expression of two polycistronic snoRNA gene hosts that resemble the UHG-like genes in mammals. Phylogenetic analysis further revealed that the extensive separation and recombination of two functional elements of snoRNA genes has occurred during fungus evolution. Conclusion This is the first genome-wide analysis of the filamentous fungus N. crassa snoRNAs that aids in understanding the differences between unicellular fungi and multicellular fungi. As compared with two yeasts, a more complex

  10. Pedestal structure and stability in H-mode and I-mode: a comparative study on Alcator C-Mod

    International Nuclear Information System (INIS)

    Hughes, J.W.; Walk, J.R.; Davis, E.M.; LaBombard, B.; Baek, S.G.; Churchill, R.M.; Greenwald, M.; Hubbard, A.E.; Lipschultz, B.; Marmar, E.S.; Reinke, M.L.; Rice, J.E.; Theiler, C.; Terry, J.; White, A.E.; Whyte, D.G.; Snyder, P.B.; Groebner, R.J.; Osborne, T.; Diallo, A.

    2013-01-01

    New experimental data from the Alcator C-Mod tokamak are used to benchmark predictive modelling of the edge pedestal in various high-confinement regimes, contributing to greater confidence in projection of pedestal height and width in ITER and reactors. ELMy H-modes operate near stability limits for ideal peeling–ballooning modes, as shown by calculations with the ELITE code. Experimental pedestal width in ELMy H-mode scales as the square root of β pol at the pedestal top, i.e. the dependence expected from theory if kinetic ballooning modes (KBMs) were responsible for limiting the pedestal width. A search for KBMs in experiment has revealed a short-wavelength electromagnetic fluctuation in the pedestal that is a candidate driver for inter-edge localized mode (ELM) pedestal regulation. A predictive pedestal model (EPED) has been tested on an extended set of ELMy H-modes from C-Mod, reproducing pedestal height and width reasonably well across the data set, and extending the tested range of EPED to the highest absolute pressures available on any existing tokamak and to within a factor of three of the pedestal pressure targeted for ITER. In addition, C-Mod offers access to two regimes, enhanced D-alpha (EDA) H-mode and I-mode, that have high pedestals, but in which large ELM activity is naturally suppressed and, instead, particle and impurity transport are regulated continuously. Pedestals of EDA H-mode and I-mode discharges are found to be ideal magnetohydrodynamic (MHD) stable with ELITE, consistent with the general absence of ELM activity. Invocation of alternative physics mechanisms may be required to make EPED-like predictions of pedestals in these kinds of intrinsically ELM-suppressed regimes, which would be very beneficial to operation in burning plasma devices. (paper)

  11. Microwave measurements of energy lost to longitudinal modes by single electron bunches traversing periodic structures

    International Nuclear Information System (INIS)

    Wang, J.W.; Loew, G.A.; Weaver, J.N.; Wilson, P.B.

    1981-10-01

    In the design of future linear colliders, it will be important to minimize the loss of beam energy due to the excitation of higher-order modes in the accelerator structure by single bunches of electrons or positrons. This loss is not only detrimental in itself but also gives rise to energy spectrum widening and transverse emittance growth. Microwave measurements made on disk-loaded and alternating-spoke structures to determine the loss to the longitudinal modes are described. In these measurements the Gaussian bunch is simulated by a current pulse of the same shape transmitted through the structure on an axial center conductor. Results to date are presented for the total longitudinal loss parameter per period K in volts per picocoulomb

  12. Flutter Analysis of RX-420 Balistic Rocket Fin Involving Rigid Body Modes of Rocket Structures

    Directory of Open Access Journals (Sweden)

    Novi Andria

    2013-03-01

    Full Text Available Flutter is a phenomenon that has brought a catastrophic failure to the flight vehicle structure. In this experiment, flutter was analyzed for its symmetric and antisymmetric configuration to understand the effect of rocket rigid modes to the fin flutter characteristic. This research was also expected to find out the safety level of RX-420 structure design. The analysis was performed using half rocket model. Fin structure used in this research was a fin which has semispan 600 mm, thickness 12 mm, chord root 700 mm, chord tip 400 mm, made by Al 6061-T651, double spar configuration with skin thickness of 2 mm. Structural dynamics and flutter stability were analyzed using finite element software implemented on MSC. Nastran. The analysis shows that the antisymmetric flutter mode is more critical than symmetric flutter mode. At sea level altitude, antisymmetric flutter occurs at 6.4 Mach, and symmetric flutter occurs at 10.15 Mach. Compared to maximum speed of RX-420 which is 4.5 Mach at altitude 11 km or equivalent to 2.1 Mach at sea level, it can be concluded that the RX-420 structure design is safe, and flutter will not occur during flight.

  13. New Insights about Enzyme Evolution from Large Scale Studies of Sequence and Structure Relationships*

    Science.gov (United States)

    Brown, Shoshana D.; Babbitt, Patricia C.

    2014-01-01

    Understanding how enzymes have evolved offers clues about their structure-function relationships and mechanisms. Here, we describe evolution of functionally diverse enzyme superfamilies, each representing a large set of sequences that evolved from a common ancestor and that retain conserved features of their structures and active sites. Using several examples, we describe the different structural strategies nature has used to evolve new reaction and substrate specificities in each unique superfamily. The results provide insight about enzyme evolution that is not easily obtained from studies of one or only a few enzymes. PMID:25210038

  14. New insights about enzyme evolution from large scale studies of sequence and structure relationships.

    Science.gov (United States)

    Brown, Shoshana D; Babbitt, Patricia C

    2014-10-31

    Understanding how enzymes have evolved offers clues about their structure-function relationships and mechanisms. Here, we describe evolution of functionally diverse enzyme superfamilies, each representing a large set of sequences that evolved from a common ancestor and that retain conserved features of their structures and active sites. Using several examples, we describe the different structural strategies nature has used to evolve new reaction and substrate specificities in each unique superfamily. The results provide insight about enzyme evolution that is not easily obtained from studies of one or only a few enzymes. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

  15. Upper Mantle Shear Wave Structure Beneath North America From Multi-mode Surface Wave Tomography

    Science.gov (United States)

    Yoshizawa, K.; Ekström, G.

    2008-12-01

    The upper mantle structure beneath the North American continent has been investigated from measurements of multi-mode phase speeds of Love and Rayleigh waves. To estimate fundamental-mode and higher-mode phase speeds of surface waves from a single seismogram at regional distances, we have employed a method of nonlinear waveform fitting based on a direct model-parameter search using the neighbourhood algorithm (Yoshizawa & Kennett, 2002). The method of the waveform analysis has been fully automated by employing empirical quantitative measures for evaluating the accuracy/reliability of estimated multi-mode phase dispersion curves, and thus it is helpful in processing the dramatically increasing numbers of seismic data from the latest regional networks such as USArray. As a first step toward modeling the regional anisotropic shear-wave velocity structure of the North American upper mantle with extended vertical resolution, we have applied the method to long-period three-component records of seismic stations in North America, which mostly comprise the GSN and US regional networks as well as the permanent and transportable USArray stations distributed by the IRIS DMC. Preliminary multi-mode phase-speed models show large-scale patterns of isotropic heterogeneity, such as a strong velocity contrast between the western and central/eastern United States, which are consistent with the recent global and regional models (e.g., Marone, et al. 2007; Nettles & Dziewonski, 2008). We will also discuss radial anisotropy of shear wave speed beneath North America from multi-mode dispersion measurements of Love and Rayleigh waves.

  16. Structural and mutational analysis of Escherichia coli AlkB provides insight into substrate specificity and DNA damage searching.

    Directory of Open Access Journals (Sweden)

    Paul J Holland

    Full Text Available BACKGROUND: In Escherichia coli, cytotoxic DNA methyl lesions on the N1 position of purines and N3 position of pyrimidines are primarily repaired by the 2-oxoglutarate (2-OG iron(II dependent dioxygenase, AlkB. AlkB repairs 1-methyladenine (1-meA and 3-methylcytosine (3-meC lesions, but it also repairs 1-methylguanine (1-meG and 3-methylthymine (3-meT at a much less efficient rate. How the AlkB enzyme is able to locate and identify methylated bases in ssDNA has remained an open question. METHODOLOGY/PRINCIPAL FINDINGS: We determined the crystal structures of the E. coli AlkB protein holoenzyme and the AlkB-ssDNA complex containing a 1-meG lesion. We coupled this to site-directed mutagenesis of amino acids in and around the active site, and tested the effects of these mutations on the ability of the protein to bind both damaged and undamaged DNA, as well as catalyze repair of a methylated substrate. CONCLUSIONS/SIGNIFICANCE: A comparison of our substrate-bound AlkB-ssDNA complex with our unliganded holoenzyme reveals conformational changes of residues within the active site that are important for binding damaged bases. Site-directed mutagenesis of these residues reveals novel insight into their roles in DNA damage recognition and repair. Our data support a model that the AlkB protein utilizes at least two distinct conformations in searching and binding methylated bases within DNA: a "searching" mode and "repair" mode. Moreover, we are able to functionally separate these modes through mutagenesis of residues that affect one or the other binding state. Finally, our mutagenesis experiments show that amino acid D135 of AlkB participates in both substrate specificity and catalysis.

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

    International Nuclear Information System (INIS)

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

    2007-01-01

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

  18. The structure and binding mode of citrate in the stabilization of gold nanoparticles

    KAUST Repository

    Al-Johani, Hind

    2017-03-27

    Elucidating the binding mode of carboxylate-containing ligands to gold nanoparticles (AuNPs) is crucial to understand their stabilizing role. A detailed picture of the three-dimensional structure and coordination modes of citrate, acetate, succinate and glutarate to AuNPs is obtained by 13C and 23Na solid-state NMR in combination with computational modelling and electron microscopy. The binding between the carboxylates and the AuNP surface is found to occur in three different modes. These three modes are simultaneously present at low citrate to gold ratios, while a monocarboxylate monodentate (1κO1) mode is favoured at high citrate:gold ratios. The surface AuNP atoms are found to be predominantly in the zero oxidation state after citrate coordination, although trace amounts of Auδ+ are observed. 23Na NMR experiments show that Na+ ions are present near the gold surface, indicating that carboxylate binding occurs as a 2e− L-type interaction for each oxygen atom involved. This approach has broad potential to probe the binding of a variety of ligands to metal nanoparticles.

  19. The structure and binding mode of citrate in the stabilization of gold nanoparticles

    KAUST Repository

    Al-Johani, Hind; Abou-Hamad, Edy; Jedidi, Abdesslem; Widdifield, Cory M.; Viger-Gravel, Jasmine; Sangaru, Shiv; Gajan, David; Anjum, Dalaver H.; Ould-Chikh, Samy; Hedhili, Mohamed N.; Gurinov, Andrei; Kelly, Michael J.; El Eter, Mohamad; Cavallo, Luigi; Basset, Jean-Marie; Basset, Jean-Marie

    2017-01-01

    Elucidating the binding mode of carboxylate-containing ligands to gold nanoparticles (AuNPs) is crucial to understand their stabilizing role. A detailed picture of the three-dimensional structure and coordination modes of citrate, acetate, succinate and glutarate to AuNPs is obtained by 13C and 23Na solid-state NMR in combination with computational modelling and electron microscopy. The binding between the carboxylates and the AuNP surface is found to occur in three different modes. These three modes are simultaneously present at low citrate to gold ratios, while a monocarboxylate monodentate (1κO1) mode is favoured at high citrate:gold ratios. The surface AuNP atoms are found to be predominantly in the zero oxidation state after citrate coordination, although trace amounts of Auδ+ are observed. 23Na NMR experiments show that Na+ ions are present near the gold surface, indicating that carboxylate binding occurs as a 2e− L-type interaction for each oxygen atom involved. This approach has broad potential to probe the binding of a variety of ligands to metal nanoparticles.

  20. Phase space interrogation of the empirical response modes for seismically excited structures

    Science.gov (United States)

    Paul, Bibhas; George, Riya C.; Mishra, Sudib K.

    2017-07-01

    Conventional Phase Space Interrogation (PSI) for structural damage assessment relies on exciting the structure with low dimensional chaotic waveform, thereby, significantly limiting their applicability to large structures. The PSI technique is presently extended for structure subjected to seismic excitations. The high dimensionality of the phase space for seismic response(s) are overcome by the Empirical Mode Decomposition (EMD), decomposing the responses to a number of intrinsic low dimensional oscillatory modes, referred as Intrinsic Mode Functions (IMFs). Along with their low dimensionality, a few IMFs, retain sufficient information of the system dynamics to reflect the damage induced changes. The mutually conflicting nature of low-dimensionality and the sufficiency of dynamic information are taken care by the optimal choice of the IMF(s), which is shown to be the third/fourth IMFs. The optimal IMF(s) are employed for the reconstruction of the Phase space attractor following Taken's embedding theorem. The widely referred Changes in Phase Space Topology (CPST) feature is then employed on these Phase portrait(s) to derive the damage sensitive feature, referred as the CPST of the IMFs (CPST-IMF). The legitimacy of the CPST-IMF is established as a damage sensitive feature by assessing its variation with a number of damage scenarios benchmarked in the IASC-ASCE building. The damage localization capability, remarkable tolerance to noise contamination and the robustness under different seismic excitations of the feature are demonstrated.

  1. Recent Advances In Structural Vibration And Failure Mode Control In Mainland China: Theory, Experiments And Applications

    International Nuclear Information System (INIS)

    Li Hui; Ou Jinping

    2008-01-01

    A number of researchers have been focused on structural vibration control in the past three decades over the world and fruit achievements have been made. This paper introduces the recent advances in structural vibration control including passive, active and semiactive control in mainland China. Additionally, the co-author extends the structural vibration control to failure mode control. The research on the failure mode control is also involved in this paper. For passive control, this paper introduces full scale tests of buckling-restrained braces conducted to investigate the performance of the dampers and the second-editor of the Code of Seismic Design for Buildings. For active control, this paper introduces the HMD system for wind-induced vibration control of the Guangzhou TV tower. For semiactive control, the smart damping devices, algorithms for semi-active control, design methods and applications of semi-active control for structures are introduced in this paper. The failure mode control for bridges is also introduced

  2. On the structure and normal modes of hydrogenated Ti-fullerene compounds

    Energy Technology Data Exchange (ETDEWEB)

    Tlahuice-Flores, Alfredo, E-mail: tlahuicef@yahoo.com [Universidad Nacional Autonoma de Mexico, Instituto de Fisica (Mexico); Mejia-Rosales, Sergio, E-mail: sergio.mejiars@uanl.edu.mx [Universidad Autonoma de Nuevo Leon, CICFIM-Facultad de Ciencias Fisico Matematicas, and Centro de Innovacion, Investigacion y Desarrollo en Ingenieria y Tecnologia (Mexico); Galvan, Donald H., E-mail: donald@cnyn.unam.mx [Centro de Nanociencias y Nanotecnologia-Universidad Nacional Autonoma de Mexico (Mexico)

    2012-08-15

    When titanium covers a C{sub 60} core, the metal atoms may suppress the fullerene's capacity of storing hydrogen, depending on the number of Ti atoms covering the C{sub 60} framework, the Ti-C binding energy, and diffusion barriers. In this article, we study the structural and vibrational properties of the C{sub 60}TiH{sub n} (n = 2, 4, 6, and 8) and C{sub 60}Ti{sub 6}H{sub 48} compounds. The IR spectra of C{sub 60}TiH{sub n} compounds have a maximum attributable to the Ti-H stretching mode, which shifts to lower values in the structures with n = 4, 8, while their Raman spectra show two peaks corresponding to the stretching modes of H{sub 2} molecules at apical and azimuthal positions. On the other hand, the IR spectrum of C{sub 60}Ti{sub 6}H{sub 48} shows an intense peak due to the Ti-H in-phase stretching mode, while its Raman spectrum has a maximum attributed to the pentagonal pinch of the C{sub 60} core. Finally, we have found that the presence of one apical H{sub 2} molecule enhances the pentagonal pinch mode, becoming the maximum in the Raman spectrum.Graphical Abstract.

  3. Structure of modes of smoothly irregular three-dimensional integrated optical four-layer waveguide

    International Nuclear Information System (INIS)

    Egorov, A.A.; Ajryan, Eh.A.; Sevast'yanov, A.L.; Sevast'yanov, L.A.

    2009-01-01

    As a method of research of an integrated optical multilayer waveguide, satisfying the condition of smooth modification of the shape of the studied three-dimensional structure, an asymptotic method is used. Three-dimensional fields of smoothly deforming modes of the integrated optical waveguide are circumscribed analytically. An evident dependence of the contributions of the first order of smallness in the amplitudes of the electrical and magnetic fields of the quasi-waveguide modes is obtained. The canonical type of the equations circumscribing propagation of quasi-TE and quasi-TM modes in the smoothly irregular part of a four-layer integrated optical waveguide is represented for an asymptotic method. With the help of the method of coupled waves and perturbation theory method, the shifts of complex propagation constants for quasi-TE and quasi-TM modes are obtained in an explicit form. The elaborated theory is applicable for the analysis of similar structures of dielectric, magnetic and metamaterials in a sufficiently broad band of electromagnetic wavelengths

  4. The Orbital Angular Momentum Modes Supporting Fibers Based on the Photonic Crystal Fiber Structure

    Directory of Open Access Journals (Sweden)

    Hu Zhang

    2017-10-01

    Full Text Available The orbital angular momentum (OAM of light can be another physical dimension that we exploit to make multiplexing in the spatial domain. The design of the OAM mode supporting fiber attracts many attentions in the field of the space division multiplexing (SDM system. This paper reviews the recent progresses in photonic crystal fiber (PCF supporting OAM modes, and summarizes why a PCF structure can be used to support stable OAM transmission modes. The emphasis is on the circular PCFs, which possess many excellent features of transmission performance, such as good-quality OAM modes, enough separation of the effective indices, low confinement loss, flat dispersion, a large effective area, and a low nonlinear coefficient. We also compare the transmission properties between the circular PCF and the ring core fiber, as well as the properties between the OAM EDFA based on circular PCF and the OAM EDFA based on the ring core fiber. At last, the challenges and prospects of OAM fibers based on the PCF structure are also discussed.

  5. The role of retrieval mode and retrieval orientation in retrieval practice: insights from comparing recognition memory testing formats and restudying.

    Science.gov (United States)

    Gao, Chuanji; Rosburg, Timm; Hou, Mingzhu; Li, Bingbing; Xiao, Xin; Guo, Chunyan

    2016-12-01

    The effectiveness of retrieval practice for aiding long-term memory, referred to as the testing effect, has been widely demonstrated. However, the specific neurocognitive mechanisms underlying this phenomenon remain unclear. In the present study, we sought to explore the role of pre-retrieval processes at initial testing on later recognition performance by using event-related potentials (ERPs). Subjects studied two lists of words (Chinese characters) and then performed a recognition task or a source memory task, or restudied the word lists. At the end of the experiment, subjects received a final recognition test based on the remember-know paradigm. Behaviorally, initial testing (active retrieval) enhanced memory retention relative to restudying (passive retrieval). The retrieval mode at initial testing was indexed by more positive-going ERPs for unstudied items in the active-retrieval tasks than in passive retrieval from 300 to 900 ms. Follow-up analyses showed that the magnitude of the early ERP retrieval mode effect (300-500 ms) was predictive of the behavioral testing effect later on. In addition, the ERPs for correctly rejected new items during initial testing differed between the two active-retrieval tasks from 500 to 900 ms, and this ERP retrieval orientation effect predicted differential behavioral testing gains between the two active-retrieval conditions. Our findings confirm that initial testing promotes later retrieval relative to restudying, and they further suggest that adopting pre-retrieval processing in the forms of retrieval mode and retrieval orientation might contribute to these memory enhancements.

  6. Insight into DEG/ENaC channel gating from genetics and structure.

    Science.gov (United States)

    Eastwood, Amy L; Goodman, Miriam B

    2012-10-01

    The founding members of the superfamily of DEG/ENaC ion channel proteins are C. elegans proteins that form mechanosensitive channels in touch and pain receptors. For more than a decade, the research community has used mutagenesis to identify motifs that regulate gating. This review integrates insight derived from unbiased in vivo mutagenesis screens with recent crystal structures to develop new models for activation of mechanically gated DEGs.

  7. New insights into the structural organization of eukaryotic and prokaryotic cytoskeletons using cryo-electron tomography

    International Nuclear Information System (INIS)

    Kuerner, Julia; Medalia, Ohad; Linaroudis, Alexandros A.; Baumeister, Wolfgang

    2004-01-01

    Cryo-electron tomography (cryo-ET) is an emerging imaging technology that combines the potential of three-dimensional (3-D) imaging at molecular resolution (<5 nm) with a close-to-life preservation of the specimen. In conjunction with pattern recognition techniques, it enables us to map the molecular landscape inside cells. The application of cryo-ET to intact cells provides novel insights into the structure and the spatial organization of the cytoskeleton in prokaryotic and eukaryotic cells

  8. Deciphering Dimerization Modes of PAS Domains: Computational and Experimental Analyses of the AhR:ARNT Complex Reveal New Insights Into the Mechanisms of AhR Transformation.

    Science.gov (United States)

    Corrada, Dario; Soshilov, Anatoly A; Denison, Michael S; Bonati, Laura

    2016-06-01

    The Aryl hydrocarbon Receptor (AhR) is a transcription factor that mediates the biochemical response to xenobiotics and the toxic effects of a number of environmental contaminants, including dioxins. Recently, endogenous regulatory roles for the AhR in normal physiology and development have also been reported, thus extending the interest in understanding its molecular mechanisms of activation. Since dimerization with the AhR Nuclear Translocator (ARNT) protein, occurring through the Helix-Loop-Helix (HLH) and PER-ARNT-SIM (PAS) domains, is needed to convert the AhR into its transcriptionally active form, deciphering the AhR:ARNT dimerization mode would provide insights into the mechanisms of AhR transformation. Here we present homology models of the murine AhR:ARNT PAS domain dimer developed using recently available X-ray structures of other bHLH-PAS protein dimers. Due to the different reciprocal orientation and interaction surfaces in the different template dimers, two alternative models were developed for both the PAS-A and PAS-B dimers and they were characterized by combining a number of computational evaluations. Both well-established hot spot prediction methods and new approaches to analyze individual residue and residue-pairwise contributions to the MM-GBSA binding free energies were adopted to predict residues critical for dimer stabilization. On this basis, a mutagenesis strategy for both the murine AhR and ARNT proteins was designed and ligand-dependent DNA binding ability of the AhR:ARNT heterodimer mutants was evaluated. While functional analysis disfavored the HIF2α:ARNT heterodimer-based PAS-B model, most mutants derived from the CLOCK:BMAL1-based AhR:ARNT dimer models of both the PAS-A and the PAS-B dramatically decreased the levels of DNA binding, suggesting this latter model as the most suitable for describing AhR:ARNT dimerization. These novel results open new research directions focused at elucidating basic molecular mechanisms underlying the

  9. Deciphering Dimerization Modes of PAS Domains: Computational and Experimental Analyses of the AhR:ARNT Complex Reveal New Insights Into the Mechanisms of AhR Transformation.

    Directory of Open Access Journals (Sweden)

    Dario Corrada

    2016-06-01

    Full Text Available The Aryl hydrocarbon Receptor (AhR is a transcription factor that mediates the biochemical response to xenobiotics and the toxic effects of a number of environmental contaminants, including dioxins. Recently, endogenous regulatory roles for the AhR in normal physiology and development have also been reported, thus extending the interest in understanding its molecular mechanisms of activation. Since dimerization with the AhR Nuclear Translocator (ARNT protein, occurring through the Helix-Loop-Helix (HLH and PER-ARNT-SIM (PAS domains, is needed to convert the AhR into its transcriptionally active form, deciphering the AhR:ARNT dimerization mode would provide insights into the mechanisms of AhR transformation. Here we present homology models of the murine AhR:ARNT PAS domain dimer developed using recently available X-ray structures of other bHLH-PAS protein dimers. Due to the different reciprocal orientation and interaction surfaces in the different template dimers, two alternative models were developed for both the PAS-A and PAS-B dimers and they were characterized by combining a number of computational evaluations. Both well-established hot spot prediction methods and new approaches to analyze individual residue and residue-pairwise contributions to the MM-GBSA binding free energies were adopted to predict residues critical for dimer stabilization. On this basis, a mutagenesis strategy for both the murine AhR and ARNT proteins was designed and ligand-dependent DNA binding ability of the AhR:ARNT heterodimer mutants was evaluated. While functional analysis disfavored the HIF2α:ARNT heterodimer-based PAS-B model, most mutants derived from the CLOCK:BMAL1-based AhR:ARNT dimer models of both the PAS-A and the PAS-B dramatically decreased the levels of DNA binding, suggesting this latter model as the most suitable for describing AhR:ARNT dimerization. These novel results open new research directions focused at elucidating basic molecular mechanisms

  10. Experimental model for neutron scattering in disordered systems: static structure factor determination of mode-softening

    International Nuclear Information System (INIS)

    Siegel, E.

    1982-01-01

    The generalized-disorder collective-boson mode-softening universality-principle (GDCBMSUP) for collective-boson mode dispersion in disordered systems (liquids, quantum liquids, glasses, powders, disordered magnets, plasmas...), a unified qualitative and semi-qualitative and semi-quantitative descriptive prescription for treating the properties of very differently disordered systems, is directly dependent upon a measurement (or calculation) of the static structure factor S(k) determined from a frequency average of the dynamic structure factor S(k,w), a multiple of the inelastic differential neutron scattering cross section d 2 sigma/dwdOMEGA. The prescription for this principle is given and, because of its universal applicability to disordered systems of any type with any type and/or degree of disorder, the neutron scattering determination of S(k) takes on renewed importance

  11. A versatile stereo photogrammetry based technique for measuring fracture mode displacements in structures

    DEFF Research Database (Denmark)

    Alvarado, Jonathan Shmueli; Eder, Martin Alexander; Tesauro, Angelo

    2015-01-01

    The measurement of fracture mode displacements in structures which are susceptible to cracking such as adhesive joints in composite components – is becoming increasingly important. Such measurements are essential for the understanding of the root causes for specific fracture damage types. Further......The measurement of fracture mode displacements in structures which are susceptible to cracking such as adhesive joints in composite components – is becoming increasingly important. Such measurements are essential for the understanding of the root causes for specific fracture damage types......-made automated image processing software (AIPS) allows a rapid and reliable evaluation of a multitude of subsequently taken measurements at a high-precision level. The SDMS is used to measure the LRDs at three different locations close to the trailing edge of a wind turbine rotor blade. In addition...

  12. Measurements of higher order modes in a 30 cm long X-band structure

    International Nuclear Information System (INIS)

    Xiao, L.; Liang, Y.; Tong, D.; Zhang, H.

    2001-01-01

    The use of a cage of metallic wires as a bead is proposed to measure the higher order modes (HOMs) in an X-band accelerating structure. These long thin wires can isolate the longitudinal electric field component from other field components and produce sufficient frequency shift in bead-pull measurements. In the setup described in this paper, the bead is made by sputtering silver film onto a thin nylon line through a specially designed fixture. The cage has a size of approximately 0.5 mm in diameter, 2 mm in length and more than six metallic wires of less than 0.1 mm in width. The fabrication and calibration of the cage are described. The longitudinal electric fields of the lowest passband dipole mode TM 110 in a 30 cm long X-band structure are measured by bead-pull measurements. Results are compared with the calculated ones obtained from URMELT-code

  13. Crystal structures from the Plasmodium peroxiredoxins: new insights into oligomerization and product binding.

    Science.gov (United States)

    Qiu, Wei; Dong, Aiping; Pizarro, Juan C; Botchkarsev, Alexei; Min, Jinrong; Wernimont, Amy K; Hills, Tanya; Hui, Raymond; Artz, Jennifer D

    2012-03-19

    Plasmodium falciparum is the protozoan parasite primarily responsible for more than one million malarial deaths, annually, and is developing resistance to current therapies. Throughout its lifespan, the parasite is subjected to oxidative attack, so Plasmodium antioxidant defences are essential for its survival and are targets for disease control. To further understand the molecular aspects of the Plasmodium redox system, we solved 4 structures of Plasmodium peroxiredoxins (Prx). Our study has confirmed PvTrx-Px1 to be a hydrogen peroxide (H2O2)-sensitive peroxiredoxin. We have identified and characterized the novel toroid octameric oligomer of PyTrx-Px1, which may be attributed to the interplay of several factors including: (1) the orientation of the conserved surface/buried arginine of the NNLA(I/L)GRS-loop; and (2) the C-terminal tail positioning (also associated with the aforementioned conserved loop) which facilitates the intermolecular hydrogen bond between dimers (in an A-C fashion). In addition, a notable feature of the disulfide bonds in some of the Prx crystal structures is discussed. Finally, insight into the latter stages of the peroxiredoxin reaction coordinate is gained. Our structure of PyPrx6 is not only in the sulfinic acid (RSO2H) form, but it is also with glycerol bound in a way (not previously observed) indicative of product binding. The structural characterization of Plasmodium peroxiredoxins provided herein provides insight into their oligomerization and product binding which may facilitate the targeting of these antioxidant defences. Although the structural basis for the octameric oligomerization is further understood, the results yield more questions about the biological implications of the peroxiredoxin oligomerization, as multiple toroid configurations are now known. The crystal structure depicting the product bound active site gives insight into the overoxidation of the active site and allows further characterization of the leaving group

  14. Structural insight to mutation effects uncover a common allosteric site in class C GPCRs

    DEFF Research Database (Denmark)

    Harpsøe, Kasper; Boesgaard, Michael W; Munk, Christian

    2017-01-01

    MOTIVATION: Class C G protein-coupled receptors (GPCRs) regulate important physiological functions and allosteric modulators binding to the transmembrane domain constitute an attractive and, due to a lack of structural insight, a virtually unexplored potential for therapeutics and the food industry....... Combining pharmacological site-directed mutagenesis data with the recent class C GPCR experimental structures will provide a foundation for rational design of new therapeutics. RESULTS: We uncover one common site for both positive and negative modulators with different amino acid layouts that can...

  15. Recent density functional studies of hydrodesulfurization catalysts: insight into structure and mechanism

    International Nuclear Information System (INIS)

    Hinnemann, Berit; Moses, Poul Georg; Noerskov, Jens K

    2008-01-01

    The present article will highlight some recent density functional theory (DFT) studies of hydrodesulfurization (HDS) catalysts. It will be summarized how DFT in combination with experimental studies can give a detailed picture of the structure of the active phase. Furthermore, we have used DFT to investigate the reaction pathway for thiophene HDS, and we find that the reaction entails a complex interplay of different active sites, depending on reaction conditions. An investigation of pyridine inhibition confirmed some of these results. These fundamental insights constitute a basis for rational improvement of HDS catalysts, as they have provided important structure-activity relationships

  16. Modified Adaptive Control for Region 3 Operation in the Presence of Wind Turbine Structural Modes

    Science.gov (United States)

    Frost, Susan Alane; Balas, Mark J.; Wright, Alan D.

    2010-01-01

    Many challenges exist for the operation of wind turbines in an efficient manner that is reliable and avoids component fatigue and failure. Turbines operate in highly turbulent environments resulting in aerodynamic loads that can easily excite turbine structural modes, possibly causing component fatigue and failure. Wind turbine manufacturers are highly motivated to reduce component fatigue and failure that can lead to loss of revenue due to turbine down time and maintenance costs. The trend in wind turbine design is toward larger, more flexible turbines that are ideally suited to adaptive control methods due to the complexity and expense required to create accurate models of their dynamic characteristics. In this paper, we design an adaptive collective pitch controller for a high-fidelity simulation of a utility-scale, variable-speed horizontal axis wind turbine operating in Region 3. The objective of the adaptive pitch controller is to regulate generator speed, accommodate wind gusts, and reduce the excitation of structural modes in the wind turbine. The control objective is accomplished by collectively pitching the turbine blades. The adaptive collective pitch controller for Region 3 was compared in simulations with a baseline classical Proportional Integrator (PI) collective pitch controller. The adaptive controller will demonstrate the ability to regulate generator speed in Region 3, while accommodating gusts, and reducing the excitation of certain structural modes in the wind turbine.

  17. Using Acoustic Structure Quantification During B-Mode Sonography for Evaluation of Hashimoto Thyroiditis.

    Science.gov (United States)

    Rhee, Sun Jung; Hong, Hyun Sook; Kim, Chul-Hee; Lee, Eun Hye; Cha, Jang Gyu; Jeong, Sun Hye

    2015-12-01

    This study aimed to evaluate the usefulness of Acoustic Structure Quantification (ASQ; Toshiba Medical Systems Corporation, Nasushiobara, Japan) values in the diagnosis of Hashimoto thyroiditis using B-mode sonography and to identify a cutoff ASQ level that differentiates Hashimoto thyroiditis from normal thyroid tissue. A total of 186 thyroid lobes with Hashimoto thyroiditis and normal thyroid glands underwent sonography with ASQ imaging. The quantitative results were reported in an echo amplitude analysis (Cm(2)) histogram with average, mode, ratio, standard deviation, blue mode, and blue average values. Receiver operating characteristic curve analysis was performed to assess the diagnostic ability of the ASQ values in differentiating Hashimoto thyroiditis from normal thyroid tissue. Intraclass correlation coefficients of the ASQ values were obtained between 2 observers. Of the 186 thyroid lobes, 103 (55%) had Hashimoto thyroiditis, and 83 (45%) were normal. There was a significant difference between the ASQ values of Hashimoto thyroiditis glands and those of normal glands (P thyroiditis were significantly greater than those in patients with normal thyroid glands. The areas under the receiver operating characteristic curves for the ratio, blue average, average, blue mode, mode, and standard deviation were: 0.936, 0.902, 0.893, 0.855, 0.846, and 0.842, respectively. The ratio cutoff value of 0.27 offered the best diagnostic performance, with sensitivity of 87.38% and specificity of 95.18%. The intraclass correlation coefficients ranged from 0.86 to 0.94, which indicated substantial agreement between the observers. Acoustic Structure Quantification is a useful and promising sonographic method for diagnosing Hashimoto thyroiditis. Not only could it be a helpful tool for quantifying thyroid echogenicity, but it also would be useful for diagnosis of Hashimoto thyroiditis. © 2015 by the American Institute of Ultrasound in Medicine.

  18. Magnetotelluric 2D Modelling Provides Insight on the Structural Characteristics of the Guadalajara (Mexico) Triple Junction Domains

    Science.gov (United States)

    Arboleda Zapata, M. D. J., Sr.; Arzate-Flores, J.; Guevara Betancourt, R. E., Sr.

    2017-12-01

    The Jalisco Block is a continental microplate produced by the extension along three large structures: the Tepic-Zacoalco rift (TZR), the Colima rift (CR) and the Chapala rift that converge in a triple junction 50 km southwest of Guadalajara, Mexico, with orientation NW-SE, N-S, and E-W respectively. The present study focuses on investigating the deep structure of the north Colima and eastern Zacoalco grabens close to the Guadalajara triple junction (GTJ). This is a first study of its type that provide insight on the grabens structures and crustal characteristics underneath. We measured along two magnetotellurics (MT) profiles that cut perpendicularly the TZR (profile ZAC), and the northern CR (profile SAY) comprising a total of 24 broad band MT soundings. The ZAC profile has 11 stations and has a NE orientation, and the SAY profile has 14 station aligned E-W. Standard processing and editing procedures were completed, and distortion analysis was applied to the data set in order to define the dimensionality and electric strike of the separated profiles. Static shift was corrected using geology information to distinguish the different types of soundings and later averaging for those soundings located over the same lithology. The Bahr dimensionality parameters showed that the medium is mainly 3D for the SAY profile and 2D for the ZAC profile; furthermore, the regional geoelectric strike azimuth calculated with Bahr methodology were -4° and -48° respectively, with good concordance with the main surface structures. The tipper analysis permitted validated these results, as the real induction vectors were nearly perpendicular to main fault structures. All soundings were rotated to the respective regional strike and a 2D simultaneous inversion of the transverse electric (TE) mode, the transvers magnetic (TM) mode and the Tipper was completed. The RMS fitting error yield 3.2% for ZAC profile and 3.7% for SAY profile. Both profiles show a shallow conductive zone at north of

  19. Frequency splitter based on the directional emission from surface modes in dielectric photonic crystal structures.

    Science.gov (United States)

    Tasolamprou, Anna C; Zhang, Lei; Kafesaki, Maria; Koschny, Thomas; Soukoulis, Costas M

    2015-06-01

    We demonstrate the numerical design and the experimental validation of frequency dependent directional emission from a dielectric photonic crystal structure. The wave propagates through a photonic crystal line-defect waveguide, while a surface layer at the termination of the photonic crystal enables the excitation of surface modes and a subsequent grating layer transforms the surface energy into outgoing propagating waves of the form of a directional beam. The angle of the beam is controlled by the frequency and the structure operates as a frequency splitter in the intermediate and far field region.

  20. Three-mode coupling interference patterns in the dynamic structure factor of a relaxor ferroelectric

    Science.gov (United States)

    Manley, M. E.; Abernathy, D. L.; Sahul, R.; Stonaha, P. J.; Budai, J. D.

    2016-09-01

    A longstanding controversy for relaxor ferroelectrics has been the origin of the "waterfall" effect in the phonon dispersion curves, in which low-energy transverse phonons cascade into vertical columns. Originally interpreted as phonons interacting with polar nanoregions (PNRs), it was later explained as an interference effect of coupling damped optic and acoustic phonons. In light of a recently discovered PNR vibrational mode near the "waterfall" wave vector [M. E. Manley, J. W. Lynn, D. L. Abernathy, E. D. Specht, O. Delaire, A. R. Bishop, R. Sahul, and J. D. Budai, Nat. Commun. 5, 3683 (2014), 10.1038/ncomms4683], we have reexamined this feature using neutron scattering on [100]-poled PMN-30%PT [0.6 Pb (M g1 /3N b2 /3 ) O3-0.3 PbTi O3] . We find that the PNR mode couples to both optic and acoustic phonons and that this results in complex patterns in the dynamic structure factor, including intensity pockets and peaks localized in momentum-energy space. These features are fully explained by extending the mode-coupling model to include three coupled damped harmonic oscillators representing the transverse optic, acoustic, and PNR modes.

  1. Method of adiabatic modes in studying problems of smoothly irregular open waveguide structures

    Energy Technology Data Exchange (ETDEWEB)

    Sevastianov, L. A., E-mail: sevast@sci.pfu.edu.ru [Peoples' Friendship University of Russia (Russian Federation); Egorov, A. A. [Russian Academy of Sciences, Prokhorov General Physics Institute (Russian Federation); Sevastyanov, A. L. [Peoples' Friendship University of Russia (Russian Federation)

    2013-02-15

    Basic steps in developing an original method of adiabatic modes that makes it possible to solve the direct and inverse problems of simulating and designing three-dimensional multilayered smoothly irregular open waveguide structures are described. A new element in the method is that an approximate solution of Maxwell's equations is made to obey 'inclined' boundary conditions at the interfaces between themedia being considered. These boundary conditions take into account the obliqueness of planes tangent to nonplanar boundaries between the media and lead to new equations for coupled vector quasiwaveguide hybrid adiabatic modes. Solutions of these equations describe the phenomenon of 'entanglement' of two linear polarizations of an irregular multilayered waveguide, the appearance of a new mode in an entangled state, and the effect of rotation of the polarization plane of quasiwaveguide modes. The efficiency of the method is demonstrated by considering the example of numerically simulating a thin-film generalized waveguide Lueneburg lens.

  2. Recursive formulae and performance comparisons for first mode dynamics of periodic structures

    Science.gov (United States)

    Hobeck, Jared D.; Inman, Daniel J.

    2017-05-01

    Periodic structures are growing in popularity especially in the energy harvesting and metastructures communities. Common types of these unique structures are referred to in the literature as zigzag, orthogonal spiral, fan-folded, and longitudinal zigzag structures. Many of these studies on periodic structures have two competing goals in common: (a) minimizing natural frequency, and (b) minimizing mass or volume. These goals suggest that no single design is best for all applications; therefore, there is a need for design optimization and comparison tools which first require efficient easy-to-implement models. All available structural dynamics models for these types of structures do provide exact analytical solutions; however, they are complex requiring tedious implementation and providing more information than necessary for practical applications making them computationally inefficient. This paper presents experimentally validated recursive models that are able to very accurately and efficiently predict the dynamics of the four most common types of periodic structures. The proposed modeling technique employs a combination of static deflection formulae and Rayleigh’s Quotient to estimate the first mode shape and natural frequency of periodic structures having any number of beams. Also included in this paper are the results of an extensive experimental validation study which show excellent agreement between model prediction and measurement. Lastly, the proposed models are used to evaluate the performance of each type of structure. Results of this performance evaluation reveal key advantages and disadvantages associated with each type of structure.

  3. Structure of the Hantavirus Nucleoprotein Provides Insights into the Mechanism of RNA Encapsidation

    Directory of Open Access Journals (Sweden)

    Daniel Olal

    2016-03-01

    Full Text Available Hantaviruses are etiological agents of life-threatening hemorrhagic fever with renal syndrome and hantavirus cardiopulmonary syndrome. The nucleoprotein (N of hantavirus is essential for viral transcription and replication, thus representing an attractive target for therapeutic intervention. We have determined the crystal structure of hantavirus N to 3.2 Å resolution. The structure reveals a two-lobed, mostly α-helical structure that is distantly related to that of orthobunyavirus Ns. A basic RNA binding pocket is located at the intersection between the two lobes. We provide evidence that oligomerization is mediated by amino- and C-terminal arms that bind to the adjacent monomers. Based on these findings, we suggest a model for the oligomeric ribonucleoprotein (RNP complex. Our structure provides mechanistic insights into RNA encapsidation in the genus Hantavirus and constitutes a template for drug discovery efforts aimed at combating hantavirus infections.

  4. Structural insights into Cydia pomonella pheromone binding protein 2 mediated prediction of potentially active semiochemicals

    Science.gov (United States)

    Tian, Zhen; Liu, Jiyuan; Zhang, Yalin

    2016-03-01

    Given the advantages of behavioral disruption application in pest control and the damage of Cydia pomonella, due progresses have not been made in searching active semiochemicals for codling moth. In this research, 31 candidate semiochemicals were ranked for their binding potential to Cydia pomonella pheromone binding protein 2 (CpomPBP2) by simulated docking, and this sorted result was confirmed by competitive binding assay. This high predicting accuracy of virtual screening led to the construction of a rapid and viable method for semiochemicals searching. By reference to binding mode analyses, hydrogen bond and hydrophobic interaction were suggested to be two key factors in determining ligand affinity, so is the length of molecule chain. So it is concluded that semiochemicals of appropriate chain length with hydroxyl group or carbonyl group at one head tended to be favored by CpomPBP2. Residues involved in binding with each ligand were pointed out as well, which were verified by computational alanine scanning mutagenesis. Progress made in the present study helps establish an efficient method for predicting potentially active compounds and prepares for the application of high-throughput virtual screening in searching semiochemicals by taking insights into binding mode analyses.

  5. Coupling analysis of energy conversion in multi-mode vibration structural control using a synchronized switch damping method

    International Nuclear Information System (INIS)

    Ji, Hongli; Qiu, Jinhao; Xia, Pinqi; Inman, Daniel

    2012-01-01

    Modal coupling is an important issue in the analysis and control of structural systems with multi-degrees of freedom (MDOF). In this paper, modal coupling induced by energy conversion in the structural control of an MDOF system using a synchronized switch damping method is investigated theoretically and validated numerically. In the analysis, it is supposed that the voltage on the piezoelectric actuator is switched at the displacement extrema of a given mode. Two types of coupling in energy conversion are considered. The first is whether the switching action based on one mode induces energy conversion of the other modes. The second is whether the vibration of one mode affects the energy conversion of the other modes. The results indicate that the modal coupling in energy conversion is very complicated. In most cases the switching action based on one mode does induce energy conversion of another mode, but the efficiency depends on the frequency ratio of the two modes. The vibration of one mode affects the energy conversion of another mode only when the frequency ratio of the two modes takes some special values. Discussions are also given on the potential application of the theoretical results in the design of an energy harvesting device. (paper)

  6. Structure of Human GIVD Cytosolic Phospholipase A2 Reveals Insights into Substrate Recognition

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Hui; Klein, Michael G.; Snell, Gyorgy; Lane, Weston; Zou, Hua; Levin, Irena; Li, Ke; Sang, Bi-Ching (Takeda Cali)

    2016-07-01

    Cytosolic phospholipases A2 (cPLA2s) consist of a family of calcium-sensitive enzymes that function to generate lipid second messengers through hydrolysis of membrane-associated glycerophospholipids. The GIVD cPLA2 (cPLA2δ) is a potential drug target for developing a selective therapeutic agent for the treatment of psoriasis. Here, we present two X-ray structures of human cPLA2δ, capturing an apo state, and in complex with a substrate-like inhibitor. Comparison of the apo and inhibitor-bound structures reveals conformational changes in a flexible cap that allows the substrate to access the relatively buried active site, providing new insight into the mechanism for substrate recognition. The cPLA2δ structure reveals an unexpected second C2 domain that was previously unrecognized from sequence alignments, placing cPLA2δ into the class of membrane-associated proteins that contain a tandem pair of C2 domains. Furthermore, our structures elucidate novel inter-domain interactions and define three potential calcium-binding sites that are likely important for regulation and activation of enzymatic activity. These findings provide novel insights into the molecular mechanisms governing cPLA2's function in signal transduction.

  7. Frustration-induced internal stresses are responsible for quasilocalized modes in structural glasses

    Science.gov (United States)

    Lerner, Edan; Bouchbinder, Eran

    2018-03-01

    It has been recently shown [E. Lerner, G. Düring, and E. Bouchbinder, Phys. Rev. Lett. 117, 035501 (2016), 10.1103/PhysRevLett.117.035501] that the nonphononic vibrational modes of structural glasses at low frequencies ω are quasilocalized and follow a universal density of states D (ω ) ˜ω4 . Here we show that the gapless nature of the observed density of states depends on the existence of internal stresses that generically emerge in glasses due to frustration, thus elucidating a basic element underlying this universal behavior. Similarly to jammed particulate packings, low-frequency modes in structural glasses emerge from a balance between a local elasticity term and an internal stress term in the dynamical matrix, where the difference between them is orders of magnitude smaller than their typical magnitude. By artificially reducing the magnitude of internal stresses in a computer glass former in three dimensions, we show that a gap is formed in the density of states below which no vibrational modes exist, thus demonstrating the crucial importance of internal stresses. Finally, we show that while better annealing the glass upon cooling from the liquid state significantly reduces its internal stresses, the self-organizational processes during cooling render the gapless D (ω ) ˜ω4 density of state unaffected.

  8. Constructive and destructive quantum interference sensitive to quantum vacuum mode structure in a metallic waveguide

    International Nuclear Information System (INIS)

    Shen Jianqi

    2011-01-01

    Quantum vacuum mode structure can be changed due to length scale fluctuation of the cross section of a metallic waveguide. Such a structure change in vacuum modes (particularly in cutoff vacuum modes) would lead to dramatic enhancement or inhibition of spontaneous emission decay of atoms and, if the waveguide is filled with a dilute atomic vapor consisting of quantum-coherent atoms of a four-level tripod-configuration system, an optical wave propagating inside the waveguide can be coherently manipulated by tunable constructive and destructive quantum interference between two control transitions (driven by two control fields) in a quite unusual way (e.g., the optical response, in which a three-level dark state is involved, is sensitive to the waveguide dimension variations at certain positions of resonance of the atomic spontaneous emission decay rate). Therefore, an intriguing effect that can be employed to designs of new photonic and quantum optical devices could be achieved based on the present mechanisms of quantum-vacuum manipulation and quantum coherence control.

  9. Temporal coupled mode analysis of one-dimensional magneto-photonic crystals with cavity structures

    Energy Technology Data Exchange (ETDEWEB)

    Saghirzadeh Darki, Behnam, E-mail: b.saghirzadeh@ec.iut.ac.ir; Zeidaabadi Nezhad, Abolghasem; Firouzeh, Zaker Hossein

    2016-12-01

    In this paper, we propose the time-dependent coupled mode analysis of one-dimensional magneto-photonic crystals including one, two or multiple defect layers. The performance of the structures, namely the total transmission, Faraday rotation and ellipticity, is obtained using the proposed method. The results of the developed analytic approach are verified by comparing them to the results of the exact numerical transfer matrix method. Unlike the widely used numerical method, our proposed analytic method seems promising for the synthesis as well as the analysis purposes. Moreover, the proposed method has not the restrictions of the previously examined analytic methods. - Highlights: • A time-dependent coupled mode analysis is proposed for the cavity-type 1D MPCs. • Analytical formalism is presented for the single, double and multiple-defect MPCs. • Transmission, Faraday rotation and ellipticity are gained using the proposed method. • The proposed analytic method has advantages over the previously examined methods.

  10. Mode analysis and structure parameter optimization of a novel SiGe-OI rib optical waveguide

    Energy Technology Data Exchange (ETDEWEB)

    Feng Song; Gao Yong; Yang Yuan [Department of Electronic Engineering, Xi' an University of Technology, Xi' an 710048 (China); Feng Yuchun, E-mail: vonfs@yahoo.com.c [Key Laboratories of Optoelectronic Devices and Systems, Shenzhen University, Shenzhen 518060 (China)

    2009-08-15

    The mode of a novel SiGe-OI optical waveguide is analyzed, and its single-mode conditions are derived. The Ge content and structure parameters of SiGe-OI optical waveguides are respectively optimized. Under an operation wavelength of 1300 nm, the structures of SiGe-OI rib optical waveguides are built and analyzed with Optiwave software, and the optical field and transmission losses of the SiGe-OI rib optical waveguides are analyzed. The optimization results show that when the structure parameters H, h, W are respectively 500 nm, 250 nm, 500 nm and the Ge content is 5%, the total power loss of SiGe-OI rib waveguides is 0.3683 dB/cm considering the loss of radiation outside the waveguides and materials, which is less than the traditional value of 0.5 dB/cm. The analytical technique for SiGe-OI optical waveguides and structure parameters computed by this paper are proved to be accurate and computationally efficient compared with the beam propagation method (BPM) and the experimental results. (semiconductor devices)

  11. Structural studies of Pseudomonas and Chromobacterium ω-aminotransferases provide insights into their differing substrate specificity

    International Nuclear Information System (INIS)

    Sayer, Christopher; Isupov, Michail N.; Westlake, Aaron; Littlechild, Jennifer A.

    2013-01-01

    The X-ray structures of two ω-aminotransferases from P. aeruginosa and C. violaceum in complex with an inhibitor offer the first detailed insight into the structural basis of the substrate specificity of these industrially important enzymes. The crystal structures and inhibitor complexes of two industrially important ω-aminotransferase enzymes from Pseudomonas aeruginosa and Chromobacterium violaceum have been determined in order to understand the differences in their substrate specificity. The two enzymes share 30% sequence identity and use the same amino acceptor, pyruvate; however, the Pseudomonas enzyme shows activity towards the amino donor β-alanine, whilst the Chromobacterium enzyme does not. Both enzymes show activity towards S-α-methylbenzylamine (MBA), with the Chromobacterium enzyme having a broader substrate range. The crystal structure of the P. aeruginosa enzyme has been solved in the holo form and with the inhibitor gabaculine bound. The C. violaceum enzyme has been solved in the apo and holo forms and with gabaculine bound. The structures of the holo forms of both enzymes are quite similar. There is little conformational difference observed between the inhibitor complex and the holoenzyme for the P. aeruginosa aminotransferase. In comparison, the crystal structure of the C. violaceum gabaculine complex shows significant structural rearrangements from the structures of both the apo and holo forms of the enzyme. It appears that the different rigidity of the protein scaffold contributes to the substrate specificity observed for the two ω-aminotransferases

  12. U6+ minerals and inorganic compounds: insights into an expanded structural hierarchy of crystal structures

    International Nuclear Information System (INIS)

    Burns, P.C.

    2005-01-01

    The crystal structures of uranyl minerals and inorganic uranyl compounds are important for understanding the genesis of U deposits, the interaction of U mine and mill tailings with the environment, transport of actinides in soils and the vadose zone, the performance of geological repositories for nuclear waste, and for the development of advanced materials with novel applications. Over the past decade, the number of inorganic uranyl compounds (including minerals) with known structures has more than doubled, and reconsideration of the structural hierarchy of uranyl compounds is warranted. Here, 368 inorganic crystal structures that contain essential U 6+ are considered (of which 89 are minerals). They are arranged on the basis of the topological details of their structural units, which are formed by the polymerization of polyhedra containing higher-valence cations. Overarching structural categories correspond to those based upon isolated polyhedra (8), finite clusters (43), chains (57), sheets (204), and frameworks (56) of polyhedra. Within these categories, structures are organized and compared upon the basis of either their graphical representations, or in the case of sheets involving sharing of edges of polyhedra, upon the topological arrangement of anions within the sheets. (author)

  13. Structural insights into FRS2α PTB domain recognition by neurotrophin receptor TrkB.

    Science.gov (United States)

    Zeng, Lei; Kuti, Miklos; Mujtaba, Shiraz; Zhou, Ming-Ming

    2014-07-01

    The fibroblast growth factor receptor (FGFR) substrate 2 (FRS2) family proteins function as scaffolding adapters for receptor tyrosine kinases (RTKs). The FRS2α proteins interact with RTKs through the phosphotyrosine-binding (PTB) domain and transfer signals from the activated receptors to downstream effector proteins. Here, we report the nuclear magnetic resonance structure of the FRS2α PTB domain bound to phosphorylated TrkB. The structure reveals that the FRS2α-PTB domain is comprised of two distinct but adjacent pockets for its mutually exclusive interaction with either nonphosphorylated juxtamembrane region of the FGFR, or tyrosine phosphorylated peptides TrkA and TrkB. The new structural insights suggest rational design of selective small molecules through targeting of the two conjunct pockets in the FRS2α PTB domain. © 2014 Wiley Periodicals, Inc.

  14. Insights into Dynamic Tuning of Magnetic-Resonant Wireless Power Transfer Receivers Based on Switch-Mode Gyrators

    Directory of Open Access Journals (Sweden)

    Mohamed Saad

    2018-02-01

    Full Text Available Magnetic-resonant wireless power transfer (WPT has become a reliable contactless source of power for a wide range of applications. WPT spans different power levels ranging from low-power implantable devices up to high-power electric vehicles (EV battery charging. The transmission range and efficiency of WPT have been reasonably enhanced by resonating the transmitter and receiver coils at a common frequency. Nevertheless, matching between resonance in the transmitter and receiver is quite cumbersome, particularly in single-transmitter multi-receiver systems. The resonance frequency in transmitter and receiver tank circuits has to be perfectly matched, otherwise power transfer capability is greatly degraded. This paper discusses the mistuning effect of parallel-compensated receivers, and thereof a novel dynamic frequency tuning method and related circuit topology and control is proposed and characterized in the system application. The proposed method is based on the concept of switch-mode gyrator emulating variable lossless inductors oriented to enable self-tunability in WPT receivers.

  15. Structural Insights into the Coupling of Virion Assembly and Rotavirus Replication

    Science.gov (United States)

    Trask, Shane D.; McDonald, Sarah M.; Patton, John T.

    2013-01-01

    Preface Viral replication is rapid and robust, but it is far from a chaotic process. Instead, successful production of infectious progeny requires that events occur in the correct place and at the correct time. Rotavirus, a segmented double-stranded RNA virus of the Reoviridae family, seems to govern its replication through ordered disassembly and assembly of a triple-layered icosahedral capsid. In recent years, high-resolution structural data have provided unprecedented insight into these events. In this Review, we explore the current understanding of rotavirus replication and how it compares to other Reoviridae family members. PMID:22266782

  16. Prediction of pressure induced structural phase transitions and internal mode frequency changes in solid N2+

    International Nuclear Information System (INIS)

    Etters, R.D.; Kobashi, K.; Chandrasekharan, V.

    1983-01-01

    A rhombohedral distortion of the Pm3n structure is introduced which shows that a low temperature phase transition occurs from P4 2 /mnm into the R3c calcite structure at P approx. = 19.2 kbar with a volume change of 0.125 cm 3 /mole. This transition agrees with recent Raman scattering measurements. Another transition from R3c into R3m is predicted at P approx. = 67.5 kbar, with a volume change of 0.1 cm 3 /mole. The pressure dependence of the intramolecular mode frequencies for the R3c structure is in reasonably good agreement with the two main branches observed experimentally

  17. Deep transcriptome sequencing provides new insights into the structural and functional organization of the wheat genome.

    Science.gov (United States)

    Pingault, Lise; Choulet, Frédéric; Alberti, Adriana; Glover, Natasha; Wincker, Patrick; Feuillet, Catherine; Paux, Etienne

    2015-02-10

    Because of its size, allohexaploid nature, and high repeat content, the bread wheat genome is a good model to study the impact of the genome structure on gene organization, function, and regulation. However, because of the lack of a reference genome sequence, such studies have long been hampered and our knowledge of the wheat gene space is still limited. The access to the reference sequence of the wheat chromosome 3B provided us with an opportunity to study the wheat transcriptome and its relationships to genome and gene structure at a level that has never been reached before. By combining this sequence with RNA-seq data, we construct a fine transcriptome map of the chromosome 3B. More than 8,800 transcription sites are identified, that are distributed throughout the entire chromosome. Expression level, expression breadth, alternative splicing as well as several structural features of genes, including transcript length, number of exons, and cumulative intron length are investigated. Our analysis reveals a non-monotonic relationship between gene expression and structure and leads to the hypothesis that gene structure is determined by its function, whereas gene expression is subject to energetic cost. Moreover, we observe a recombination-based partitioning at the gene structure and function level. Our analysis provides new insights into the relationships between gene and genome structure and function. It reveals mechanisms conserved with other plant species as well as superimposed evolutionary forces that shaped the wheat gene space, likely participating in wheat adaptation.

  18. The structural connectivity pattern of the default mode network and its association with memory and anxiety

    Directory of Open Access Journals (Sweden)

    Yan eTao

    2015-11-01

    Full Text Available The default mode network (DMN is one of the most widely studied resting state functional networks. The structural basis for the DMN is of particular interest and has been studied by several researchers using diffusion tensor imaging (DTI. Most of these previous studies focused on a few regions or white matter tracts of the DMN so that the global structural connectivity pattern and network properties of the DMN remain unclear. Moreover, evidences indicate that the DMN is involved in both memory and emotion, but how the DMN regulates memory and anxiety from the perspective of the whole DMN structural network remains unknown. We used multimodal neuroimaging methods to investigate the structural connectivity pattern of the DMN and the association of its network properties with memory and anxiety in 205 young healthy subjects. Using a probabilistic fiber tractography technique based on DTI data and graph theory methods, we constructed the global structural connectivity pattern of the DMN and found that memory quotient (MQ score was significantly positively correlated with the global and local efficiency of the DMN whereas anxiety was found to be negatively correlated with the efficiency. The strong structural connectivity between multiple brain regions within DMN may reflect that the DMN has certain structural basis. Meanwhile, we found the network efficiency of the DMN were related to memory and anxiety measures, which indicated that the DMN may play a role in the memory and anxiety.

  19. Structural insights into the mycobacteria transcription initiation complex from analysis of X-ray crystal structures

    Energy Technology Data Exchange (ETDEWEB)

    Hubin, Elizabeth A.; Lilic, Mirjana; Darst, Seth A.; Campbell, Elizabeth A.

    2017-07-13

    The mycobacteria RNA polymerase (RNAP) is a target for antimicrobials against tuberculosis, motivating structure/function studies. Here we report a 3.2 Å-resolution crystal structure of a Mycobacterium smegmatis (Msm) open promoter complex (RPo), along with structural analysis of the Msm RPo and a previously reported 2.76 Å-resolution crystal structure of an Msm transcription initiation complex with a promoter DNA fragment. We observe the interaction of the Msm RNAP α-subunit C-terminal domain (αCTD) with DNA, and we provide evidence that the αCTD may play a role in Mtb transcription regulation. Our results reveal the structure of an Actinobacteria-unique insert of the RNAP β' subunit. Finally, our analysis reveals the disposition of the N-terminal segment of Msm σA, which may comprise an intrinsically disordered protein domain unique to mycobacteria. The clade-specific features of the mycobacteria RNAP provide clues to the profound instability of mycobacteria RPo compared with E. coli.

  20. A computational analysis of the binding mode of closantel as inhibitor of the Onchocerca volvulus chitinase: insights on macrofilaricidal drug design

    Science.gov (United States)

    Segura-Cabrera, Aldo; Bocanegra-García, Virgilio; Lizarazo-Ortega, Cristian; Guo, Xianwu; Correa-Basurto, José; Rodríguez-Pérez, Mario A.

    2011-12-01

    Onchocerciasis is a leading cause of blindness with at least 37 million people infected and more than 120 million people at risk of contracting the disease; most (99%) of this population, threatened by infection, live in Africa. The drug of choice for mass treatment is the microfilaricidal Mectizan® (ivermectin); it does not kill the adult stages of the parasite at the standard dose which is a single annual dose aimed at disease control. However, multiple treatments a year with ivermectin have effects on adult worms. The discovery of new therapeutic targets and drugs directed towards the killing of the adult parasites are thus urgently needed. The chitinase of filarial nematodes is a new drug target due to its essential function in the metabolism and molting of the parasite. Closantel is a potent and specific inhibitor of chitinase of Onchocerca volvulus (OvCHT1) and other filarial chitinases. However, the binding mode and specificity of closantel towards OvCHT1 remain unknown. In the absence of a crystallographic structure of OvCHT1, we developed a homology model of OvCHT1 using the currently available X-ray structures of human chitinases as templates. Energy minimization and molecular dynamics (MD) simulation of the model led to a high quality of 3D structure of OvCHIT1. A flexible docking study using closantel as the ligand on the binding site of OvCHIT1 and human chitinases was performed and demonstrated the differences in the closantel binding mode between OvCHIT1 and human chitinase. Furthermore, molecular dynamics simulations and free-energy calculation were employed to determine and compare the detailed binding mode of closantel with OvCHT1 and the structure of human chitinase. This comparative study allowed identification of structural features and properties responsible for differences in the computationally predicted closantel binding modes. The homology model and the closantel binding mode reported herein might help guide the rational development of

  1. Adaptive Sliding Mode Control of Dynamic Systems Using Double Loop Recurrent Neural Network Structure.

    Science.gov (United States)

    Fei, Juntao; Lu, Cheng

    2018-04-01

    In this paper, an adaptive sliding mode control system using a double loop recurrent neural network (DLRNN) structure is proposed for a class of nonlinear dynamic systems. A new three-layer RNN is proposed to approximate unknown dynamics with two different kinds of feedback loops where the firing weights and output signal calculated in the last step are stored and used as the feedback signals in each feedback loop. Since the new structure has combined the advantages of internal feedback NN and external feedback NN, it can acquire the internal state information while the output signal is also captured, thus the new designed DLRNN can achieve better approximation performance compared with the regular NNs without feedback loops or the regular RNNs with a single feedback loop. The new proposed DLRNN structure is employed in an equivalent controller to approximate the unknown nonlinear system dynamics, and the parameters of the DLRNN are updated online by adaptive laws to get favorable approximation performance. To investigate the effectiveness of the proposed controller, the designed adaptive sliding mode controller with the DLRNN is applied to a -axis microelectromechanical system gyroscope to control the vibrating dynamics of the proof mass. Simulation results demonstrate that the proposed methodology can achieve good tracking property, and the comparisons of the approximation performance between radial basis function NN, RNN, and DLRNN show that the DLRNN can accurately estimate the unknown dynamics with a fast speed while the internal states of DLRNN are more stable.

  2. Optimization of TW accelerating structures for SLED type modes of operation

    International Nuclear Information System (INIS)

    Le Duff, J.

    1984-02-01

    The SLED method was invented at SLAC in order to produce more electron (and positron) energy from the existing klystrons. The LEP injector LINAC, also now is supposed to operate in the SLED-2 mode. At DESY similar developments have been undertaken too, to improve the linac performances. However in all cases the accelerating sections were not initially optimized for such a mode of operation, and in most cases the designers ended with long accelerating sections making a more efficient use of the klystron power, with rectangular pulses, sometimes at the expense of a longer linac. The present study deals with new approaches for designing linacs, and in particular compact linacs, considering from the beginning a pulse compression scheme, where the main feature consists of having an exponential pulse shape instead of rectangular. Moreover a detailed comparison is made between constant impedance and constant gradient travelling wave (TW) accelerating structures. As a matter of fact the constant impedance structure when optimized looks sligthy better than the second one. In addition short structures appear to be more efficient for a given number of RF sources. Consequently linear accelerators can be made more simple and less expensive, and if one allows for higher tolerable accelerating gradients they can be made even compact

  3. Trade structure, trade mode and the urban-rural income gap in China

    Directory of Open Access Journals (Sweden)

    Hao Wei

    2013-05-01

    Full Text Available This paper analyses the effect of foreign trade in China on the urban-rural income gap from certain angles including trade scale, trade structure and trade mode at the national and provincial levels. The empirical results indicate that, from the perspective of trade scale, the export and import in the eastern and national regions have an expansion effect on the urban-rural income gap, and, in the central regions, they have a reduction effect. Furthermore, export in the western regions has a reduction effect while import in these regions did not have a significant effect. From the perspective of trade structure, the trade of high-tech products and labour-intensive products in the national and eastern regions has an expansion effect, and the trade of the above-mentioned products in the central regions has a reduction effect. The trade of labour-intensive products in the western regions has a reduction effect, and that of high-tech products an expansion effect. From the perspective of trade mode, processing trade and general trade in the national and eastern regions have an expansion effect, while in the central regions they have a reduction effect. General trade in the western regions would expand the urban-rural income gap, and processing trade does not have a significant effect. Consequently, when the South African Government is working out trade multiplicative and corresponding policy, they should consider the development of foreign trade and should pay attention to the labour market structure.

  4. Study of higher order modes in superconducting accelerating structures for linac applications

    Energy Technology Data Exchange (ETDEWEB)

    Schuh, Marcel

    2011-06-22

    Higher Order Modes (HOMs) can severely limit the operation of superconducting cavities in a linear accelerator with high beam current, high duty factor and complex pulse structure. Therefore, the full HOM spectrum has to be analysed in detail to identify potentially dangerous modes already during the design phase and to define their damping requirements. For this purpose a dedicated beam dynamics simulation code, Simulation of higher order Mode Dynamics (SMD), focusing on beam-HOM interaction, has been developed in the frame of this project. SMD allows to analyse the beam behaviour under the presence of HOMs, taking into account many important effects, such as for example the HOM frequency spread, beam input jitter, different chopping patterns, as well as klystron and alignment errors. SMD is used to investigate in detail into the effects of HOMs in the Superconducting Proton Linac (SPL) at CERN and in particular their potential to drive beam instabilities in the longitudinal and transverse direction. Based on these results, HOM damping requirements for the HOM coupler design are then defined. In addition, the linear accelerators of the European Spallation Source (ESS) and the Spallation Neutron Source (SNS) are analysed with respect to HOM impact and the results are compared with the SPL simulations. (orig.)

  5. High gradient test of the C-band choke-mode type accelerating structure

    International Nuclear Information System (INIS)

    Inagaki, T.; Shintake, T.; Baba, H.; Togawa, K.; Onoe, K.; Marechal, X.; Takashima, T.; Takahashi, S.; Matsumoto, H.

    2004-01-01

    The C-band (5712 MHz) choke-mode type accelerating structure will be used for SPring-8 Compact SASE-FEL Source (SCSS). To make the accelerator length short, we designed the field gradient as high as 40 MV/m. Since it is higher gradient than other traditional electron accelerators, we have to carefully check its performance (RF breakdown, dark current emission, etc.) in the high gradient test stand. The first experiment will be scheduled in this summer. In this paper, we will describe the preparation progress for the test. (author)

  6. Analysis of Higher Order Modes in Large Superconducting Radio Frequency Accelerating Structures

    CERN Document Server

    Galek, Tomasz; Brackebusch, Korinna; Van Rienen, Ursula

    2015-01-01

    Superconducting radio frequency cavities used for accelerating charged particle beams are commonly used in accelerator facilities around the world. The design and optimization of modern superconducting RF cavities requires intensive numerical simulations. Vast number of operational parameters must be calculated to ensure appropriate functioning of the accelerating structures. In this study, we primarily focus on estimation and behavior of higher order modes in superconducting RF cavities connected in chains. To calculate large RF models the state-space concatenation scheme, an efficient hybrid method, is employed.

  7. Structural and functional insight into the carbohydrate receptor binding of F4 fimbriae-producing enterotoxigenic Escherichia coli.

    Science.gov (United States)

    Moonens, Kristof; Van den Broeck, Imke; De Kerpel, Maia; Deboeck, Francine; Raymaekers, Hanne; Remaut, Han; De Greve, Henri

    2015-03-27

    Enterotoxigenic Escherichia coli (ETEC) strains are important causes of intestinal disease in humans and lead to severe production losses in animal farming. A range of fimbrial adhesins in ETEC strains determines host and tissue tropism. ETEC strains expressing F4 fimbriae are associated with neonatal and post-weaning diarrhea in piglets. Three naturally occurring variants of F4 fimbriae (F4ab, F4ac, and F4ad) exist that differ in the primary sequence of their major adhesive subunit FaeG, and each features a related yet distinct receptor binding profile. Here the x-ray structure of FaeGad bound to lactose provides the first structural insight into the receptor specificity and mode of binding by the poly-adhesive F4 fimbriae. A small D'-D″-α1-α2 subdomain grafted on the immunoglobulin-like core of FaeG hosts the carbohydrate binding site. Two short amino acid stretches Phe(150)-Glu(152) and Val(166)-Glu(170) of FaeGad bind the terminal galactose in the lactosyl unit and provide affinity and specificity to the interaction. A hemagglutination-based assay with E. coli expressing mutant F4ad fimbriae confirmed the elucidated co-complex structure. Interestingly, the crucial D'-α1 loop that borders the FaeGad binding site adopts a different conformation in the two other FaeG variants and hints at a heterogeneous binding pocket among the FaeG serotypes. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  8. Electron temperature structures associated with magnetic tearing modes in the Madison Symmetric Torus

    Science.gov (United States)

    Stephens, Hillary Dianne

    Tearing mode induced magnetic islands have a significant impact on the thermal characteristics of magnetically confined plasmas such as those in the reversed-field-pinch. Using a state-of-the-art Thomson scattering (TS) diagnostic, electron temperature fluctuations correlated with magnetic tearing modes have been observed on the Madison Symmetric Torus reversed-field-pinch. The TS diagnostic consists of two independently triggerable Nd:YAG lasers that can each pulse up to 15 times each plasma discharge and 21 General Atomics polchromators equipped with avalanche photodiode modules. Detailed calibrations focusing on accuracy, ease of use and repeatability and in-situ measurements have been performed on the system. Electron temperature (Te) profiles are acquired at 25 kHz with 2 cm or less resolution along the minor radius, sufficient to measure the effect of an island on the profile as the island rotates by the measurement point. Bayesian data analysis techniques are developed and used to detect fluctuations over an ensemble of shots. Four cases are studied; standard plasmas in quiescent periods, through sawteeth, through core reconnection events and in plasmas where the tearing mode activity is decreased. With a spectrum of unstable tearing modes, remnant islands that tend to flatten the temperature profile are present in the core between sawtooth-like reconnection events. This flattening is characteristic of rapid parallel heat conduction along helical magnetic field lines. The spatial structure of the temperature fluctuations show that the location of the rational surface of the m/n = 1/6 tearing mode is significantly further in than equilibrium suggestions predict. The fluctuations also provide a measurement of the remnant island width which is significantly smaller than the predicted full island width. These correlated fluctuations disappear during both global and core reconnection events. In striking contrast to temperature flattening, a temperature gradient

  9. Structure of sulfamidase provides insight into the molecular pathology of mucopolysaccharidosis IIIA

    International Nuclear Information System (INIS)

    Sidhu, Navdeep S.; Schreiber, Kathrin; Pröpper, Kevin; Becker, Stefan; Usón, Isabel; Sheldrick, George M.; Gärtner, Jutta; Krätzner, Ralph; Steinfeld, Robert

    2014-01-01

    Mucopolysaccharidosis IIIA is a fatal neurodegenerative disease that typically manifests itself in childhood and is caused by mutations in the gene for the lysosomal enzyme sulfamidase. The first structure of this enzyme is presented, which provides insight into the molecular basis of disease-causing mutations, and the enzymatic mechanism is proposed. Mucopolysaccharidosis type IIIA (Sanfilippo A syndrome), a fatal childhood-onset neurodegenerative disease with mild facial, visceral and skeletal abnormalities, is caused by an inherited deficiency of the enzyme N-sulfoglucosamine sulfohydrolase (SGSH; sulfamidase). More than 100 mutations in the SGSH gene have been found to reduce or eliminate its enzymatic activity. However, the molecular understanding of the effect of these mutations has been confined by a lack of structural data for this enzyme. Here, the crystal structure of glycosylated SGSH is presented at 2 Å resolution. Despite the low sequence identity between this unique N-sulfatase and the group of O-sulfatases, they share a similar overall fold and active-site architecture, including a catalytic formylglycine, a divalent metal-binding site and a sulfate-binding site. However, a highly conserved lysine in O-sulfatases is replaced in SGSH by an arginine (Arg282) that is positioned to bind the N-linked sulfate substrate. The structure also provides insight into the diverse effects of pathogenic mutations on SGSH function in mucopolysaccharidosis type IIIA and convincing evidence for the molecular consequences of many missense mutations. Further, the molecular characterization of SGSH mutations will lay the groundwork for the development of structure-based drug design for this devastating neurodegenerative disorder

  10. Structure of sulfamidase provides insight into the molecular pathology of mucopolysaccharidosis IIIA

    Energy Technology Data Exchange (ETDEWEB)

    Sidhu, Navdeep S. [University of Göttingen, Robert-Koch-Strasse 40, 37075 Göttingen (Germany); University of Göttingen, Tammannstrasse 4, 37077 Göttingen (Germany); Schreiber, Kathrin [University of Göttingen, Robert-Koch-Strasse 40, 37075 Göttingen (Germany); Pröpper, Kevin [University of Göttingen, Tammannstrasse 4, 37077 Göttingen (Germany); Becker, Stefan [Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen (Germany); Usón, Isabel [Instituto de Biologia Molecular de Barcelona (IBMB–CSIC), Barcelona Science Park, Baldiri Reixach 15, 08028 Barcelona (Spain); Institucio Catalana de Recerca i Estudis Avancats (ICREA), (Spain); Sheldrick, George M. [University of Göttingen, Tammannstrasse 4, 37077 Göttingen (Germany); Gärtner, Jutta; Krätzner, Ralph, E-mail: rkraetz@gwdg.de; Steinfeld, Robert, E-mail: rkraetz@gwdg.de [University of Göttingen, Robert-Koch-Strasse 40, 37075 Göttingen (Germany)

    2014-05-01

    Mucopolysaccharidosis IIIA is a fatal neurodegenerative disease that typically manifests itself in childhood and is caused by mutations in the gene for the lysosomal enzyme sulfamidase. The first structure of this enzyme is presented, which provides insight into the molecular basis of disease-causing mutations, and the enzymatic mechanism is proposed. Mucopolysaccharidosis type IIIA (Sanfilippo A syndrome), a fatal childhood-onset neurodegenerative disease with mild facial, visceral and skeletal abnormalities, is caused by an inherited deficiency of the enzyme N-sulfoglucosamine sulfohydrolase (SGSH; sulfamidase). More than 100 mutations in the SGSH gene have been found to reduce or eliminate its enzymatic activity. However, the molecular understanding of the effect of these mutations has been confined by a lack of structural data for this enzyme. Here, the crystal structure of glycosylated SGSH is presented at 2 Å resolution. Despite the low sequence identity between this unique N-sulfatase and the group of O-sulfatases, they share a similar overall fold and active-site architecture, including a catalytic formylglycine, a divalent metal-binding site and a sulfate-binding site. However, a highly conserved lysine in O-sulfatases is replaced in SGSH by an arginine (Arg282) that is positioned to bind the N-linked sulfate substrate. The structure also provides insight into the diverse effects of pathogenic mutations on SGSH function in mucopolysaccharidosis type IIIA and convincing evidence for the molecular consequences of many missense mutations. Further, the molecular characterization of SGSH mutations will lay the groundwork for the development of structure-based drug design for this devastating neurodegenerative disorder.

  11. Bacterial Effectors and Their Functions in the Ubiquitin-Proteasome System: Insight from the Modes of Substrate Recognition

    Directory of Open Access Journals (Sweden)

    Minsoo Kim

    2014-08-01

    Full Text Available Protein ubiquitination plays indispensable roles in the regulation of cell homeostasis and pathogenesis of neoplastic, infectious, and neurodegenerative diseases. Given the importance of this modification, it is to be expected that several pathogenic bacteria have developed the ability to utilize the host ubiquitin system for their own benefit. Modulation of the host ubiquitin system by bacterial effector proteins inhibits innate immune responses and hijacks central signaling pathways. Bacterial effectors mimic enzymes of the host ubiquitin system, but may or may not be structurally similar to the mammalian enzymes. Other effectors bind and modify components of the host ubiquitin system, and some are themselves subject to ubiquitination. This review will describe recent findings, based on structural analyses, regarding how pathogens use post-translational modifications of proteins to establish an infection.

  12. Bacterial effectors and their functions in the ubiquitin-proteasome system: insight from the modes of substrate recognition.

    Science.gov (United States)

    Kim, Minsoo; Otsubo, Ryota; Morikawa, Hanako; Nishide, Akira; Takagi, Kenji; Sasakawa, Chihiro; Mizushima, Tsunehiro

    2014-08-18

    Protein ubiquitination plays indispensable roles in the regulation of cell homeostasis and pathogenesis of neoplastic, infectious, and neurodegenerative diseases. Given the importance of this modification, it is to be expected that several pathogenic bacteria have developed the ability to utilize the host ubiquitin system for their own benefit. Modulation of the host ubiquitin system by bacterial effector proteins inhibits innate immune responses and hijacks central signaling pathways. Bacterial effectors mimic enzymes of the host ubiquitin system, but may or may not be structurally similar to the mammalian enzymes. Other effectors bind and modify components of the host ubiquitin system, and some are themselves subject to ubiquitination. This review will describe recent findings, based on structural analyses, regarding how pathogens use post-translational modifications of proteins to establish an infection.

  13. Structure of uracil-DNA glycosylase from Mycobacterium tuberculosis: insights into interactions with ligands

    International Nuclear Information System (INIS)

    Kaushal, Prem Singh; Talawar, Ramappa K.; Varshney, Umesh; Vijayan, M.

    2010-01-01

    The molecule of uracil-DNA glycosylase from M. tuberculosis exhibits domain motion on binding to DNA or a proteinaceous inhibitor. The highly conserved DNA-binding region interacts with a citrate ion in the structure. Uracil N-glycosylase (Ung) is the most thoroughly studied of the group of uracil DNA-glycosylase (UDG) enzymes that catalyse the first step in the uracil excision-repair pathway. The overall structure of the enzyme from Mycobacterium tuberculosis is essentially the same as that of the enzyme from other sources. However, differences exist in the N- and C-terminal stretches and some catalytic loops. Comparison with appropriate structures indicate that the two-domain enzyme closes slightly when binding to DNA, while it opens slightly when binding to the proteinaceous inhibitor Ugi. The structural changes in the catalytic loops on complexation reflect the special features of their structure in the mycobacterial protein. A comparative analysis of available sequences of the enzyme from different sources indicates high conservation of amino-acid residues in the catalytic loops. The uracil-binding pocket in the structure is occupied by a citrate ion. The interactions of the citrate ion with the protein mimic those of uracil, in addition to providing insights into other possible interactions that inhibitors could be involved in

  14. Insights into the role of protein molecule size and structure on interfacial properties using designed sequences

    Science.gov (United States)

    Dwyer, Mirjana Dimitrijev; He, Lizhong; James, Michael; Nelson, Andrew; Middelberg, Anton P. J.

    2013-01-01

    Mixtures of a large, structured protein with a smaller, unstructured component are inherently complex and hard to characterize at interfaces, leading to difficulties in understanding their interfacial behaviours and, therefore, formulation optimization. Here, we investigated interfacial properties of such a mixed system. Simplicity was achieved using designed sequences in which chemical differences had been eliminated to isolate the effect of molecular size and structure, namely a short unstructured peptide (DAMP1) and its longer structured protein concatamer (DAMP4). Interfacial tension measurements suggested that the size and bulk structuring of the larger molecule led to much slower adsorption kinetics. Neutron reflectometry at equilibrium revealed that both molecules adsorbed as a monolayer to the air–water interface (indicating unfolding of DAMP4 to give a chain of four connected DAMP1 molecules), with a concentration ratio equal to that in the bulk. This suggests the overall free energy of adsorption is equal despite differences in size and bulk structure. At small interfacial extensional strains, only molecule packing influenced the stress response. At larger strains, the effect of size became apparent, with DAMP4 registering a higher stress response and interfacial elasticity. When both components were present at the interface, most stress-dissipating movement was achieved by DAMP1. This work thus provides insights into the role of proteins' molecular size and structure on their interfacial properties, and the designed sequences introduced here can serve as effective tools for interfacial studies of proteins and polymers. PMID:23303222

  15. Further insights on the French WISC-IV factor structure through Bayesian structural equation modeling.

    Science.gov (United States)

    Golay, Philippe; Reverte, Isabelle; Rossier, Jérôme; Favez, Nicolas; Lecerf, Thierry

    2013-06-01

    The interpretation of the Wechsler Intelligence Scale for Children--Fourth Edition (WISC-IV) is based on a 4-factor model, which is only partially compatible with the mainstream Cattell-Horn-Carroll (CHC) model of intelligence measurement. The structure of cognitive batteries is frequently analyzed via exploratory factor analysis and/or confirmatory factor analysis. With classical confirmatory factor analysis, almost all cross-loadings between latent variables and measures are fixed to zero in order to allow the model to be identified. However, inappropriate zero cross-loadings can contribute to poor model fit, distorted factors, and biased factor correlations; most important, they do not necessarily faithfully reflect theory. To deal with these methodological and theoretical limitations, we used a new statistical approach, Bayesian structural equation modeling (BSEM), among a sample of 249 French-speaking Swiss children (8-12 years). With BSEM, zero-fixed cross-loadings between latent variables and measures are replaced by approximate zeros, based on informative, small-variance priors. Results indicated that a direct hierarchical CHC-based model with 5 factors plus a general intelligence factor better represented the structure of the WISC-IV than did the 4-factor structure and the higher order models. Because a direct hierarchical CHC model was more adequate, it was concluded that the general factor should be considered as a breadth rather than a superordinate factor. Because it was possible for us to estimate the influence of each of the latent variables on the 15 subtest scores, BSEM allowed improvement of the understanding of the structure of intelligence tests and the clinical interpretation of the subtest scores. PsycINFO Database Record (c) 2013 APA, all rights reserved.

  16. Crystal structure of glucose isomerase in complex with xylitol inhibitor in one metal binding mode.

    Science.gov (United States)

    Bae, Ji-Eun; Kim, In Jung; Nam, Ki Hyun

    2017-11-04

    Glucose isomerase (GI) is an intramolecular oxidoreductase that interconverts aldoses and ketoses. These characteristics are widely used in the food, detergent, and pharmaceutical industries. In order to obtain an efficient GI, identification of novel GI genes and substrate binding/inhibition have been studied. Xylitol is a well-known inhibitor of GI. In Streptomyces rubiginosus, two crystal structures have been reported for GI in complex with xylitol inhibitor. However, a structural comparison showed that xylitol can have variable conformation at the substrate binding site, e.g., a nonspecific binding mode. In this study, we report the crystal structure of S. rubiginosus GI in a complex with xylitol and glycerol. Our crystal structure showed one metal binding mode in GI, which we presumed to represent the inactive form of the GI. The metal ion was found only at the M1 site, which was involved in substrate binding, and was not present at the M2 site, which was involved in catalytic function. The O 2 and O 4 atoms of xylitol molecules contributed to the stable octahedral coordination of the metal in M1. Although there was no metal at the M2 site, no large conformational change was observed for the conserved residues coordinating M2. Our structural analysis showed that the metal at the M2 site was not important when a xylitol inhibitor was bound to the M1 site in GI. Thus, these findings provided important information for elucidation or engineering of GI functions. Copyright © 2017 Elsevier Inc. All rights reserved.

  17. Design Principles for the Atomic and Electronic Structure of Halide Perovskite Photovoltaic Materials: Insights from Computation.

    Science.gov (United States)

    Berger, Robert F

    2018-02-09

    In the current decade, perovskite solar cell research has emerged as a remarkably active, promising, and rapidly developing field. Alongside breakthroughs in synthesis and device engineering, halide perovskite photovoltaic materials have been the subject of predictive and explanatory computational work. In this Minireview, we focus on a subset of this computation: density functional theory (DFT)-based work highlighting the ways in which the electronic structure and band gap of this class of materials can be tuned via changes in atomic structure. We distill this body of computational literature into a set of underlying design principles for the band gap engineering of these materials, and rationalize these principles from the viewpoint of band-edge orbital character. We hope that this perspective provides guidance and insight toward the rational design and continued improvement of perovskite photovoltaics. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. New insights into structural determinants of prion protein folding and stability.

    Science.gov (United States)

    Benetti, Federico; Legname, Giuseppe

    2015-01-01

    Prions are the etiological agent of fatal neurodegenerative diseases called prion diseases or transmissible spongiform encephalopathies. These maladies can be sporadic, genetic or infectious disorders. Prions are due to post-translational modifications of the cellular prion protein leading to the formation of a β-sheet enriched conformer with altered biochemical properties. The molecular events causing prion formation in sporadic prion diseases are still elusive. Recently, we published a research elucidating the contribution of major structural determinants and environmental factors in prion protein folding and stability. Our study highlighted the crucial role of octarepeats in stabilizing prion protein; the presence of a highly enthalpically stable intermediate state in prion-susceptible species; and the role of disulfide bridge in preserving native fold thus avoiding the misfolding to a β-sheet enriched isoform. Taking advantage from these findings, in this work we present new insights into structural determinants of prion protein folding and stability.

  19. Structure, dynamics, and function of the monooxygenase P450 BM-3: insights from computer simulations studies

    International Nuclear Information System (INIS)

    Roccatano, Danilo

    2015-01-01

    The monooxygenase P450 BM-3 is a NADPH-dependent fatty acid hydroxylase enzyme isolated from soil bacterium Bacillus megaterium. As a pivotal member of cytochrome P450 superfamily, it has been intensely studied for the comprehension of structure–dynamics–function relationships in this class of enzymes. In addition, due to its peculiar properties, it is also a promising enzyme for biochemical and biomedical applications. However, despite the efforts, the full understanding of the enzyme structure and dynamics is not yet achieved. Computational studies, particularly molecular dynamics (MD) simulations, have importantly contributed to this endeavor by providing new insights at an atomic level regarding the correlations between structure, dynamics, and function of the protein. This topical review summarizes computational studies based on MD simulations of the cytochrome P450 BM-3 and gives an outlook on future directions. (topical review)

  20. Structural insights into substrate and inhibitor binding sites in human indoleamine 2,3-dioxygenase 1

    Energy Technology Data Exchange (ETDEWEB)

    Lewis-Ballester, Ariel; Pham, Khoa N.; Batabyal, Dipanwita; Karkashon, Shay; Bonanno, Jeffrey B.; Poulos, Thomas L.; Yeh, Syun-Ru (Einstein); (UCI)

    2017-11-22

    Human indoleamine 2,3-dioxygenase 1 (hIDO1) is an attractive cancer immunotherapeutic target owing to its role in promoting tumoral immune escape. However, drug development has been hindered by limited structural information. Here, we report the crystal structures of hIDO1 in complex with its substrate, Trp, an inhibitor, epacadostat, and/or an effector, indole ethanol (IDE). The data reveal structural features of the active site (Sa) critical for substrate activation; in addition, they disclose a new inhibitor-binding mode and a distinct small molecule binding site (Si). Structure-guided mutation of a critical residue, F270, to glycine perturbs the Si site, allowing structural determination of an inhibitory complex, where both the Sa and Si sites are occupied by Trp. The Si site offers a novel target site for allosteric inhibitors and a molecular explanation for the previously baffling substrate-inhibition behavior of the enzyme. Taken together, the data open exciting new avenues for structure-based drug design.

  1. Spectral structure of Pc3–4 pulsations: possible signatures of cavity modes

    Directory of Open Access Journals (Sweden)

    P. R. Sutcliffe

    2013-04-01

    Full Text Available In this study we investigate the spectral structure of Pc3–4 pulsations observed at low and midlatitudes. For this purpose, ground-based magnetometer data recorded at the MM100 stations in Europe and at two low latitude stations in South Africa were used. In addition, fluxgate magnetometer data from the CHAMP (CHAllenging Minisatellite Payload low Earth orbit satellite were used. The results of our analysis suggest that at least three mechanisms contribute to the spectral content of Pc3–4 pulsations typically observed at these latitudes. We confirm that a typical Pc3–4 pulsation contains a field line resonance (FLR contribution, with latitude dependent frequency, and an upstream wave (UW contribution, with frequency proportional to the IMF (interplanetary magnetic field magnitude BIMF. Besides the FLR and UW contributions, the Pc3–4 pulsations consistently contain signals at other frequencies that are independent of latitude and BIMF. We suggest that the most likely explanation for these additional frequency contributions is that they are fast mode resonances (FMRs related to cavity, waveguide, or virtual modes. Although the above contributions to the pulsation spectral structure have been reported previously, we believe that this is the first time where evidence is presented showing that they are all present simultaneously in both ground-based and satellite data.

  2. Observer based on sliding mode variable structure for synchronization of chaotic systems

    International Nuclear Information System (INIS)

    Yin Xunhe; Shan Xiuming; Ren Yong

    2003-01-01

    In the paper an approach, based on the state observer of sliding mode variable structure, is used for synchronizing chaotic systems. It does not require either the computation of the Lyapunov exponents, or the initial conditions belonging to the same basin of attraction as the existed approaches based on the state observer for synchronizing chaotic systems. The approach is more robust against noise and parameter mismatch than the existed approaches based on the state observer for synchronizing chaotic systems, because the former uses variable structure control, which is strong robust with respect to noise and parameter mismatch in the error dynamics, the later uses an appropriate choice of the feedback gain. Two well-known chaotic systems, a chaotic Roessler system and a hyperchaotic Roessler system are considered as illustrative examples to demonstrate the effectiveness of the used approach by numerical simulations

  3. Fuzzy sliding mode controller of a pneumatic active isolating system using negative stiffness structure

    International Nuclear Information System (INIS)

    Le, Thanh Danh; Ahn, Kyoung Kwan

    2012-01-01

    A novel active vibration isolation system using negative stiffness structure (active system with NSS) for low excitation frequency ranges (< 5 Hz) is developed successfully. Here, the negative stiffness structure (NSS) is used to minimize the attraction of vibration. Then, the fuzzy sliding mode controller (FSMC) is designed to improve the vibration isolation performance of the active system with NSS. Based on Lyapunov stability theorem, the fuzzy control rules are constructed. Next, the experimental apparatus is built for evaluating the isolation efficiency of the proposed system controlled by the FSMC corresponding to various excitation conditions. In addition, the isolation performance of the active system with NSS, the active system without NSS and the passive the system with NSS is compared. The experimental results confirmed that the active system with NSS gives better isolation efficiency than the active system without NSS and the passive system with NSS in low excitation frequency areas

  4. Mode structure of delay-coupled semiconductor lasers: influence of the pump current

    International Nuclear Information System (INIS)

    Erzgraeber, Hartmut; Krauskopf, Bernd; Lenstra, Daan

    2005-01-01

    We consider two identical, mutually delay-coupled semiconductor lasers and show that their compound laser modes (CLMs)-the basic continuous wave solutions-depend rather sensitively on the pump current of the lasers. Specifically, we show with figures and accompanying animations how the underlying CLM structure and the associated locking region, where both lasers operate stably with the same frequency, change as a function of the pump current. Our results provide a natural transition between rather different CLM structures that have been reported in the literature. Moreover, we demonstrate how the locking region as well as the different types of instabilities at its boundary depend on the pump current. This is of fundamental interest for the dynamics of coupled lasers and their possible application

  5. New Insights Toward Quantitative Relationships between Lignin Reactivity to Monomers and Their Structural Characteristics.

    Science.gov (United States)

    Ma, Ruoshui; Zhang, Xiumei; Wang, Yi; Zhang, Xiao

    2018-04-27

    The heterogeneous and complex structural characteristics of lignin present a significant challenge to predict its processability (e.g. depolymerization, modifications etc) to valuable products. This study provides a detailed characterization and comparison of structural properties of seven representative biorefinery lignin samples derived from forest and agricultural residues, which were subjected to representative pretreatment methods. A range of wet chemistry and spectroscopy methods were applied to determine specific lignin structural characteristics such as functional groups, inter-unit linkages and peak molecular weight. In parallel, oxidative depolymerization of these lignin samples to either monomeric phenolic compounds or dicarboxylic acids were conducted, and the product yields were quantified. Based on these results (lignin structural characteristics and monomer yields), we demonstrated for the first time to apply multiple-variable linear estimations (MVLE) approach using R statistics to gain insight toward a quantitative correlation between lignin structural properties and their conversion reactivity toward oxidative depolymerization to monomers. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. Structural insights into the anti-HIV activity of the Oscillatoria agardhii agglutinin homolog lectin family.

    Science.gov (United States)

    Koharudin, Leonardus M I; Kollipara, Sireesha; Aiken, Christopher; Gronenborn, Angela M

    2012-09-28

    Oscillatoria agardhii agglutinin homolog (OAAH) proteins belong to a recently discovered lectin family. All members contain a sequence repeat of ~66 amino acids, with the number of repeats varying among different family members. Apart from data for the founding member OAA, neither three-dimensional structures, information about carbohydrate binding specificities, nor antiviral activity data have been available up to now for any other members of the OAAH family. To elucidate the structural basis for the antiviral mechanism of OAAHs, we determined the crystal structures of Pseudomonas fluorescens and Myxococcus xanthus lectins. Both proteins exhibit the same fold, resembling the founding family member, OAA, with minor differences in loop conformations. Carbohydrate binding studies by NMR and x-ray structures of glycan-lectin complexes reveal that the number of sugar binding sites corresponds to the number of sequence repeats in each protein. As for OAA, tight and specific binding to α3,α6-mannopentaose was observed. All the OAAH proteins described here exhibit potent anti-HIV activity at comparable levels. Altogether, our results provide structural details of the protein-carbohydrate interaction for this novel lectin family and insights into the molecular basis of their HIV inactivation properties.

  7. Structural insights into the molecular mechanisms of myasthenia gravis and their therapeutic implications

    Energy Technology Data Exchange (ETDEWEB)

    Noridomi, Kaori; Watanabe, Go; Hansen, Melissa N.; Han, Gye Won; Chen, Lin (USC)

    2017-04-25

    The nicotinic acetylcholine receptor (nAChR) is a major target of autoantibodies in myasthenia gravis (MG), an autoimmune disease that causes neuromuscular transmission dysfunction. Despite decades of research, the molecular mechanisms underlying MG have not been fully elucidated. Here, we present the crystal structure of the nAChR α1 subunit bound by the Fab fragment of mAb35, a reference monoclonal antibody that causes experimental MG and competes with ~65% of antibodies from MG patients. Our structures reveal for the first time the detailed molecular interactions between MG antibodies and a core region on nAChR α1. These structures suggest a major nAChR-binding mechanism shared by a large number of MG antibodies and the possibility to treat MG by blocking this binding mechanism. Structure-based modeling also provides insights into antibody-mediated nAChR cross-linking known to cause receptor degradation. Our studies establish a structural basis for further mechanistic studies and therapeutic development of MG.

  8. Structure of the Aeropyrum pernix L7Ae multifunctional protein and insight into its extreme thermostability

    International Nuclear Information System (INIS)

    Bhuiya, Mohammad Wadud; Suryadi, Jimmy; Zhou, Zholi; Brown, Bernard Andrew II

    2013-01-01

    The crystal structure of A. pernix L7Ae is reported, providing insight into the extreme thermostability of this protein. Archaeal ribosomal protein L7Ae is a multifunctional RNA-binding protein that directs post-transcriptional modification of archaeal RNAs. The L7Ae protein from Aeropyrum pernix (Ap L7Ae), a member of the Crenarchaea, was found to have an extremely high melting temperature (>383 K). The crystal structure of Ap L7Ae has been determined to a resolution of 1.56 Å. The structure of Ap L7Ae was compared with the structures of two homologs: hyperthermophilic Methanocaldococcus jannaschii L7Ae and the mesophilic counterpart mammalian 15.5 kD protein. The primary stabilizing feature in the Ap L7Ae protein appears to be the large number of ion pairs and extensive ion-pair network that connects secondary-structural elements. To our knowledge, Ap L7Ae is among the most thermostable single-domain monomeric proteins presently observed

  9. Crystal structure of the Epithiospecifier Protein, ESP from Arabidopsis thaliana provides insights into its product specificity.

    Science.gov (United States)

    Zhang, Weiwei; Wang, Wenhe; Liu, Zihe; Xie, Yongchao; Wang, Hao; Mu, Yajuan; Huang, Yao; Feng, Yue

    2016-09-16

    Specifier proteins are important components of the glucosinolate-myrosinase system, which mediate plant defense against herbivory and pathogen attacks. Upon tissue disruption, glucosinolates are hydrolyzed to instable aglucones by myrosinases, and then aglucones will rearrange to form defensive isothiocyanates. Specifier proteins can redirect this reaction to form other products, such as simple nitriles, epithionitriles and organic thiocyanates instead of isothiocyanates based on the side chain structure of glucosinolate and the type of the specifier proteins. Nevertheless, the molecular mechanism underlying the different product spectrums of various specifier proteins was not fully understood. Here in this study, we solved the crystal structure of the Epithiospecifier Protein, ESP from Arabidopsis thaliana (AtESP) at 2.3 Å resolution. Structural comparisons with the previously solved structure of thiocyanate forming protein, TFP from Thlaspi arvense (TaTFP) reveal that AtESP shows a dimerization pattern different from TaTFP. Moreover, AtESP harbors a slightly larger active site pocket than TaTFP and several residues around the active site are different between the two proteins, which might account for the different product spectrums of the two proteins. Together, our structural study provides important insights into the molecular mechanisms of specifier proteins and shed light on the basis of their different product spectrums. Copyright © 2016 Elsevier Inc. All rights reserved.

  10. An Insight into the Pharmacophores of Phosphodiesterase-5 Inhibitors from Synthetic and Crystal Structural Studies

    Energy Technology Data Exchange (ETDEWEB)

    Chen,G.; Wang, H.; Robinson, H.; Cai, J.; Wan, Y.; Ke, H.

    2008-01-01

    Selective inhibitors of cyclic nucleotide phosphodiesterase-5 (PDE5) have been used as drugs for treatment of male erectile dysfunction and pulmonary hypertension. An insight into the pharmacophores of PDE5 inhibitors is essential for development of second generation of PDE5 inhibitors, but has not been completely illustrated. Here we report the synthesis of a new class of the sildenafil derivatives and a crystal structure of the PDE5 catalytic domain in complex with 5-(2-ethoxy-5-(sulfamoyl)-3-thienyl)-1-methyl-3-propyl-1, 6-dihydro-7H-pyrazolo[4, 3-d]pyrimidin-7-one (12). Inhibitor 12 induces conformational change of the H-loop (residues 660-683), which is different from any of the known PDE5 structures. The pyrazolopyrimidinone groups of 12 and sildenafil are well superimposed, but their sulfonamide groups show a positional difference of as much as 1.5 Angstroms . The structure-activity analysis suggests that a small hydrophobic pocket and the H-loop of PDE5 are important for the inhibitor affinity, in addition to two common elements for binding of almost all the PDE inhibitors: the stack against the phenylalanine and the hydrogen bond with the invariant glutamine. However, the PDE5-12 structure does not provide a full explanation to affinity changes of the inhibitors. Thus alternatives such as conformational change of the M-loop are open and further structural study is required.

  11. Linker histones: novel insights into structure-specific recognition of the nucleosome.

    Science.gov (United States)

    Cutter, Amber R; Hayes, Jeffrey J

    2017-04-01

    Linker histones (H1s) are a primary component of metazoan chromatin, fulfilling numerous functions, both in vitro and in vivo, including stabilizing the wrapping of DNA around the nucleosome, promoting folding and assembly of higher order chromatin structures, influencing nucleosome spacing on DNA, and regulating specific gene expression. However, many molecular details of how H1 binds to nucleosomes and recognizes unique structural features on the nucleosome surface remain undefined. Numerous, confounding studies are complicated not only by experimental limitations, but the use of different linker histone isoforms and nucleosome constructions. This review summarizes the decades of research that has resulted in several models of H1 association with nucleosomes, with a focus on recent advances that suggest multiple modes of H1 interaction in chromatin, while highlighting the remaining questions.

  12. Kinetic, thermodynamic and X-ray structural insights into the interaction of melatonin and analogues with quinone reductase 2

    Energy Technology Data Exchange (ETDEWEB)

    Calamini, Barbara; Santarsiero, Bernard D.; Boutin, Jean A.; Mesecar, Andrew D. (IdRS); (UIC)

    2008-09-12

    Melatonin exerts its biological effects through at least two transmembrane G-protein-coupled receptors, MT1 and MT2, and a lower-affinity cytosolic binding site, designated MT3. MT3 has recently been identified as QR2 (quinone reductase 2) (EC 1.10.99.2) which is of significance since it links the antioxidant effects of melatonin to a mechanism of action. Initially, QR2 was believed to function analogously to QR1 in protecting cells from highly reactive quinones. However, recent studies indicate that QR2 may actually transform certain quinone substrates into more highly reactive compounds capable of causing cellular damage. Therefore it is hypothesized that inhibition of QR2 in certain cases may lead to protection of cells against these highly reactive species. Since melatonin is known to inhibit QR2 activity, but its binding site and mode of inhibition are not known, we determined the mechanism of inhibition of QR2 by melatonin and a series of melatonin and 5-hydroxytryptamine (serotonin) analogues, and we determined the X-ray structures of melatonin and 2-iodomelatonin in complex with QR2 to between 1.5 and 1.8 {angstrom} (1 {angstrom} = 0.1 nm) resolution. Finally, the thermodynamic binding constants for melatonin and 2-iodomelatonin were determined by ITC (isothermal titration calorimetry). The kinetic results indicate that melatonin is a competitive inhibitor against N-methyldihydronicotinamide (K{sub i} = 7.2 {mu}M) and uncompetitive against menadione (K{sub i} = 92 {mu}M), and the X-ray structures shows that melatonin binds in multiple orientations within the active sites of the QR2 dimer as opposed to an allosteric site. These results provide new insights into the binding mechanisms of melatonin and analogues to QR2.

  13. Neurocognition, insight and medication nonadherence in schizophrenia: a structural equation modeling approach.

    Directory of Open Access Journals (Sweden)

    Laurent Boyer

    Full Text Available OBJECTIVE: The aim of this study was to examine the complex relationships among neurocognition, insight and nonadherence in patients with schizophrenia. METHODS: DESIGN: Cross-sectional study. INCLUSION CRITERIA: Diagnosis of schizophrenia according to the DSM-IV-TR criteria. DATA COLLECTION: Neurocognition was assessed using a global approach that addressed memory, attention, and executive functions; insight was analyzed using the multidimensional 'Scale to assess Unawareness of Mental Disorder;' and nonadherence was measured using the multidimensional 'Medication Adherence Rating Scale.' ANALYSIS: Structural equation modeling (SEM was applied to examine the non-straightforward relationships among the following latent variables: neurocognition, 'awareness of positive symptoms' and 'negative symptoms', 'awareness of mental disorder' and nonadherence. RESULTS: One hundred and sixty-nine patients were enrolled. The final testing model showed good fit, with normed χ(2 = 1.67, RMSEA = 0.063, CFI = 0.94, and SRMR = 0.092. The SEM revealed significant associations between (1 neurocognition and 'awareness of symptoms,' (2 'awareness of symptoms' and 'awareness of mental disorder' and (3 'awareness of mental disorder' and nonadherence, mainly in the 'attitude toward taking medication' dimension. In contrast, there were no significant links between neurocognition and nonadherence, neurocognition and 'awareness of mental disorder,' and 'awareness of symptoms' and nonadherence. CONCLUSIONS: Our findings support the hypothesis that neurocognition influences 'awareness of symptoms,' which must be integrated into a higher level of insight (i.e., the 'awareness of mental disorder' to have an impact on nonadherence. These findings have important implications for the development of effective strategies to enhance medication adherence.

  14. Structural insights into viral determinants of nematode mediated Grapevine fanleaf virus transmission.

    Directory of Open Access Journals (Sweden)

    Pascale Schellenberger

    2011-05-01

    Full Text Available Many animal and plant viruses rely on vectors for their transmission from host to host. Grapevine fanleaf virus (GFLV, a picorna-like virus from plants, is transmitted specifically by the ectoparasitic nematode Xiphinema index. The icosahedral capsid of GFLV, which consists of 60 identical coat protein subunits (CP, carries the determinants of this specificity. Here, we provide novel insight into GFLV transmission by nematodes through a comparative structural and functional analysis of two GFLV variants. We isolated a mutant GFLV strain (GFLV-TD poorly transmissible by nematodes, and showed that the transmission defect is due to a glycine to aspartate mutation at position 297 (Gly297Asp in the CP. We next determined the crystal structures of the wild-type GFLV strain F13 at 3.0 Å and of GFLV-TD at 2.7 Å resolution. The Gly297Asp mutation mapped to an exposed loop at the outer surface of the capsid and did not affect the conformation of the assembled capsid, nor of individual CP molecules. The loop is part of a positively charged pocket that includes a previously identified determinant of transmission. We propose that this pocket is a ligand-binding site with essential function in GFLV transmission by X. index. Our data suggest that perturbation of the electrostatic landscape of this pocket affects the interaction of the virion with specific receptors of the nematode's feeding apparatus, and thereby severely diminishes its transmission efficiency. These data provide a first structural insight into the interactions between a plant virus and a nematode vector.

  15. Enhanced dewaterability of sludge during anaerobic digestion with thermal hydrolysis pretreatment: New insights through structure evolution.

    Science.gov (United States)

    Zhang, Jingsi; Li, Ning; Dai, Xiaohu; Tao, Wenquan; Jenkinson, Ian R; Li, Zhuo

    2017-12-19

    Comprehensive insights into the sludge digestate dewaterability were gained through porous network structure of sludge. We measured the evolution of digestate dewaterability, represented by the solid content of centrifugally dewatered cake, in high-solids sequencing batch digesters with and without thermal hydrolysis pretreatment (THP). The results show that the dewaterability of the sludge after digestion was improved by 3.5% (±0.5%) for unpretreated sludge and 5.1% (±0.4%) for thermally hydrolyzed sludge. Compared to the unpretreated sludge digestate, thermal hydrolysis pretreatment eventually resulted in an improvement of dewaterability by 4.6% (±0.5%). Smaller particle size and larger surface area of sludge were induced by thermal hydrolysis and anaerobic digestion treatments. The structure strength and compactness of sludge, represented by elastic modulus and fractal dimension respectively, decreased with increase of digestion time. The porous network structure was broken up by thermal hydrolysis pretreatment and was further weakened during anaerobic digestion, which correspondingly improved the dewaterability of digestates. The logarithm of elastic modulus increased linearly with fractal dimension regardless of the pretreatment. Both fractal dimension and elastic modulus showed linear relationship with dewaterability. The rheological characterization combined with the analysis of fractal dimension of sewage sludge porous network structure was found applicable in quantitative evaluation of sludge dewaterability, which depended positively on both thermal hydrolysis and anaerobic digestion. Copyright © 2017 Elsevier Ltd. All rights reserved.

  16. Buckling Modes of Structural Elements of Off-Axis Fiber-Reinforced Plastics

    Science.gov (United States)

    Paimushin, V. N.; Polyakova, N. V.; Kholmogorov, S. A.; Shishov, M. A.

    2018-05-01

    The structures of two types of unidirectional fiber-reinforced composites — with an ELUR-P carbon fiber tape, an XT-118 cold-cure binder with an HSE 180 REM prepreg, and a hot-cure binder — were investigated. The diameters of fibers and fiber bundles (threads) of both the types of composites were measured, and their mutual arrangement was examined both in the semifinished products (in the uncured state) and in the finished composites. The defects characteristic of both the types of binder and manufacturing technique were detected in the cured composites. Based on an analysis of the results obtained, linearized problems on the internal multiscale buckling modes of an individual fiber (with and without account of its interaction with the surrounding matrix) or of a fiber bundle are formulated. In the initial atate, these structural elements of the fibrous composites are in a subcritical (unperturbed) state under the action of shear stresses and tension (compression) in the transverse direction. Such an initial stress state is formed in them in tension and compression tests on flat specimens made of off-axis-reinforced composites with straight fibers. To formulate the problems, the equations derived earlier from a consistent variant of geometrically nonlinear equations of elasticity theory by reducing them to the one-dimensional equations of the theory of straight rods on the basis of a refined Timoshenko shear model with account of tensile-compressive strains in the transverse direction are used. It is shown that, in loading test specimens, a continuous rearrangement of composite structure can occur due to the realization and continuous change of internal buckling modes as the wave-formation parameter varies continuously, which apparently explain the decrease revealed in the tangential shear modulus of the fibrous composites with increasing shear strains.

  17. Tandem Mass Spectrometry and Ion Mobility Reveals Structural Insight into Eicosanoid Product Ion Formation.

    Science.gov (United States)

    Di Giovanni, James P; Barkley, Robert M; Jones, David N M; Hankin, Joseph A; Murphy, Robert C

    2018-04-23

    Ion mobility measurements of product ions were used to characterize the collisional cross section (CCS) of various complex lipid [M-H] - ions using traveling wave ion mobility mass spectrometry (TWIMS). TWIMS analysis of various product ions derived after collisional activation of mono- and dihydroxy arachidonate metabolites was found to be more complex than the analysis of intact molecular ions and provided some insight into molecular mechanisms involved in product ion formation. The CCS observed for the molecular ion [M-H] - and certain product ions were consistent with a folded ion structure, the latter predicted by the proposed mechanisms of product ion formation. Unexpectedly, product ions from [M-H-H 2 O-CO 2 ] - and [M-H-H 2 O] - displayed complex ion mobility profiles suggesting multiple mechanisms of ion formation. The [M-H-H 2 O] - ion from LTB 4 was studied in more detail using both nitrogen and helium as the drift gas in the ion mobility cell. One population of [M-H-H 2 O] - product ions from LTB 4 was consistent with formation of covalent ring structures, while the ions displaying a higher CCS were consistent with a more open-chain structure. Using molecular dynamics and theoretical CCS calculations, energy minimized structures of those product ions with the open-chain structures were found to have a higher CCS than a folded molecular ion structure. The measurement of product ion mobility can be an additional and unique signature of eicosanoids measured by LC-MS/MS techniques. Graphical Abstract ᅟ.

  18. Tandem Mass Spectrometry and Ion Mobility Reveals Structural Insight into Eicosanoid Product Ion Formation

    Science.gov (United States)

    Di Giovanni, James P.; Barkley, Robert M.; Jones, David N. M.; Hankin, Joseph A.; Murphy, Robert C.

    2018-04-01

    Ion mobility measurements of product ions were used to characterize the collisional cross section (CCS) of various complex lipid [M-H]- ions using traveling wave ion mobility mass spectrometry (TWIMS). TWIMS analysis of various product ions derived after collisional activation of mono- and dihydroxy arachidonate metabolites was found to be more complex than the analysis of intact molecular ions and provided some insight into molecular mechanisms involved in product ion formation. The CCS observed for the molecular ion [M-H]- and certain product ions were consistent with a folded ion structure, the latter predicted by the proposed mechanisms of product ion formation. Unexpectedly, product ions from [M-H-H2O-CO2]- and [M-H-H2O]- displayed complex ion mobility profiles suggesting multiple mechanisms of ion formation. The [M-H-H2O]- ion from LTB4 was studied in more detail using both nitrogen and helium as the drift gas in the ion mobility cell. One population of [M-H-H2O]- product ions from LTB4 was consistent with formation of covalent ring structures, while the ions displaying a higher CCS were consistent with a more open-chain structure. Using molecular dynamics and theoretical CCS calculations, energy minimized structures of those product ions with the open-chain structures were found to have a higher CCS than a folded molecular ion structure. The measurement of product ion mobility can be an additional and unique signature of eicosanoids measured by LC-MS/MS techniques. [Figure not available: see fulltext.

  19. On-orbit evaluation of the control system/structural mode interactions on OSO-8

    Science.gov (United States)

    Slafer, L. I.

    1980-01-01

    The Orbiting Solar Observatory-8 experienced severe structural mode/control loop interaction problems during the spacecraft development. Extensive analytical studies, using the hybrid coordinate modeling approach, and comprehensive ground testing were carried out in order to achieve the system's precision pointing performance requirements. A recent series of flight tests were conducted with the spacecraft in which a wide bandwidth, high resolution telemetry system was utilized to evaluate the on-orbit flexible dynamics characteristics of the vehicle along with the control system performance. This paper describes the results of these tests, reviewing the basic design problem, analytical approach taken, ground test philosophy, and on-orbit testing. Data from the tests was used to determine the primary mode frequency, damping, and servo coupling dynamics for the on-orbit condition. Additionally, the test results have verified analytically predicted differences between the on-orbit and ground test environments. The test results have led to a validation of both the analytical modeling and servo design techniques used during the development of the control system, and also verified the approach taken to vehicle and servo ground testing.

  20. Structure, stability and ELM dynamics of the H-mode pedestal in DIII-D

    International Nuclear Information System (INIS)

    Fenstermacher, M.E.; Leonard, A.W.; Osborne, T.H.

    2005-01-01

    Experiments are described that have increased understanding of the transport and stability physics that set the H-mode edge pedestal width and height, determine the onset of Type-I edge localized modes (ELMs), and produce the nonlinear dynamics of the ELM perturbation in the pedestal and scrape-off layer (SOL). Predictive models now exist for the n e pedestal profile and the p e height at the onset of Type-I ELMs, and progress has been made toward predictive models of the T e pedestal width and nonlinear ELM evolution. Similarity experiments between DIII-D and JET suggested that neutral penetration physics dominates in the relationship between the width and height of the n e pedestal while plasma physics dominates in setting the T e pedestal width. Measured pedestal conditions including edge current at ELM onset agree with intermediate-n peeling-ballooning (P-B) stability predictions. Midplane ELM dynamics data show the predicted (P-B) structure at ELM onset, large rapid variations of the SOL parameters, and fast radial propagation in later phases, similar to features in nonlinear ELM simulations. (author)

  1. Body-insensitive Multi-Mode MIMO Terminal Antenna of Double-Ring Structure

    DEFF Research Database (Denmark)

    Zhao, Kun; Zhang, Shuai; Ishimiya, Katsunori

    2015-01-01

    of mobile terminals. With the multimode excitation, the MIMO cellular antenna can operate at 830-900 MHz, 1700-2200 MHz, and 2400-2700 MHz, for 2G, 3G, and LTE bands, respectively. The MIMO Wi-Fi antenna can cover two Wi-Fi bands from 2.4 to 2.5 GHz and from 5.2 to 5.8 GHz. The effect of a user's body......In this paper, we propose a novel multimode multi-input multi-output (MIMO) antenna system composed of a dual-element MIMO cellular antenna and dual-element MIMO Wi-Fi antenna for mobile terminal applications. The antenna system has a double-ring structure and can be integrated with the metal frame...... on the MIMO cellular antenna is investigated on CTIA standard phantoms and a real user. Since our antenna mainly operates in the loop mode, it has a much lower efficiency loss than conventional mobile antennas in both talking and data modes. Our theoretical analysis and experiments have shown that our design...

  2. Insights on synergy of materials and structures in biomimetic platelet-matrix composites

    Science.gov (United States)

    Sakhavand, Navid; Shahsavari, Rouzbeh

    2018-01-01

    Hybrid materials such as biomimetic platelet-matrix composites are in high demand to confer low weight and multifunctional mechanical properties. This letter reports interfacial-bond regulated assembly of polymers on cement-an archetype model with significant infrastructure applications. We demonstrate a series of 20+ molecular dynamics studies on decoding and optimizing the complex interfacial interactions including the role and types of various heterogeneous, competing interfacial bonds that are key to adhesion and interfacial strength. Our results show an existence of an optimum overlap length scale (˜15 nm) between polymers and cement crystals, exhibiting the best balance of strength, toughness, stiffness, and ductility for the composite. This finding, combined with the fundamental insights into the nature of interfacial bonds, provides key hypotheses for selection and processing of constituents to deliberate the best synergy in the structure and materials of platelet-matrix composites.

  3. Structure of parallel-velocity-shear-driven mode in toroidal plasmas

    International Nuclear Information System (INIS)

    Dong, J.Q.; Xu, W.B.; Zhang, Y.Z.; Horton, W.

    1998-01-01

    It is shown that the Fourier-ballooning representation is appropriate for the study of short-wavelength drift-like perturbation in toroidal plasmas with a parallel velocity shear (PVS). The radial structure of the mode driven by a PVS is investigated in a torus. The Reynolds stress created by PVS turbulence, and proposed as one of the sources for a sheared poloidal plasma rotation, is analyzed. It is demonstrated that a finite ion temperature may strongly enhance the Reynolds stress creation ability from PVS-driven turbulence. The correlation of this observation with the requirement that ion heating power be higher than a threshold value for the formation of an internal transport barrier is discussed. copyright 1998 American Institute of Physics

  4. Spinor-electron wave guided modes in coupled quantum wells structures by solving the Dirac equation

    International Nuclear Information System (INIS)

    Linares, Jesus; Nistal, Maria C.

    2009-01-01

    A quantum analysis based on the Dirac equation of the propagation of spinor-electron waves in coupled quantum wells, or equivalently coupled electron waveguides, is presented. The complete optical wave equations for Spin-Up (SU) and Spin-Down (SD) spinor-electron waves in these electron guides couplers are derived from the Dirac equation. The relativistic amplitudes and dispersion equations of the spinor-electron wave-guided modes in a planar quantum coupler formed by two coupled quantum wells, or equivalently by two coupled slab electron waveguides, are exactly derived. The main outcomes related to the spinor modal structure, such as the breaking of the non-relativistic degenerate spin states, the appearance of phase shifts associated with the spin polarization and so on, are shown.

  5. Structural insights into human Kif7, a kinesin involved in Hedgehog signalling

    Energy Technology Data Exchange (ETDEWEB)

    Klejnot, Marta, E-mail: m.klejnot@beatson.gla.ac.uk; Kozielski, Frank, E-mail: m.klejnot@beatson.gla.ac.uk [The Beatson Institute for Cancer Research, Garscube Estate, Switchback Road, Glasgow G61 1BD, Scotland (United Kingdom)

    2012-02-01

    The human Kif7 motor domain structure provides insights into a kinesin of medical significance. Kif7, a member of the kinesin 4 superfamily, is implicated in a variety of diseases including Joubert, hydrolethalus and acrocallosal syndromes. It is also involved in primary cilium formation and the Hedgehog signalling pathway and may play a role in cancer. Its activity is crucial for embryonic development. Kif7 and Kif27, a closely related kinesin in the same subfamily, are orthologues of the Drosophila melano@@gaster kinesin-like protein Costal-2 (Cos2). In vertebrates, they work together to fulfil the role of the single Cos2 gene in Drosophila. Here, the high-resolution structure of the human Kif7 motor domain is reported and is compared with that of conventional kinesin, the founding member of the kinesin superfamily. These data are a first step towards structural characterization of a kinesin-4 family member and of this interesting molecular motor of medical significance.

  6. The narrative structure as a way to gain insight into peoples' experiences: one methodological approach.

    Science.gov (United States)

    Rejnö, Åsa; Berg, Linda; Danielson, Ella

    2014-09-01

    The narrative method is used in healthcare research, mostly in data collection but also in the analysis. Narrative approaches draw attention to how people tell about and create meaning of experiences. The aim of the article was to examine the narrative structure, the elements in the structure and their function and how these can be used in research to gain insights into experiences. Examples are taken from a material of narratives from a study where next of kin were asked to narrate their experiences of sudden and unexpected death from stroke. The narratives had a clear beginning, midpoint and ending. In the beginning, orientation of the narrated events was given. The narrated events were told to have a turning point constituted of complicating actions that lead to a resolution that solved the narrated event. The narratives were built up by multiple recaps into the narrated events and also consisted of asides - side narratives and flashbacks - events back in time. Use of a narrative structure can contribute with valuable information that might be missed with other analysis. The analysis can be used on its own, as a complement to other narrative analysis or even as a complement to other qualitative analysis. © 2013 Nordic College of Caring Science.

  7. Insights into Caco-2 cell culture structure using coherent anti-Stokes Raman scattering (CARS) microscopy.

    Science.gov (United States)

    Saarinen, Jukka; Sözeri, Erkan; Fraser-Miller, Sara J; Peltonen, Leena; Santos, Hélder A; Isomäki, Antti; Strachan, Clare J

    2017-05-15

    We have used coherent anti-Stokes Raman scattering (CARS) microscopy as a novel and rapid, label-free and non-destructive imaging method to gain structural insights into live intestinal epithelial cell cultures used for drug permeability testing. Specifically we have imaged live Caco-2 cells in (bio)pharmaceutically relevant conditions grown on membrane inserts. Imaging conditions were optimized, including evaluation of suitable membrane materials and media solutions, as well as tolerable laser powers for non-destructive imaging of the live cells. Lipid structures, in particular lipid droplets, were imaged within the cells on the insert membranes. The size of the individual lipid droplets increased substantially over the 21-day culturing period up to approximately 10% of the volume of the cross section of individual cells. Variation in lipid content has important implications for intestinal drug permeation testing during drug development but has received limited attention to date due to a lack of suitable analytical techniques. CARS microscopy was shown to be well suited for such analysis with the potential for in situ imaging of the same individual cell-cultures that are used for permeation studies. Overall, the method may be used to provide important information about cell monolayer structure to better understand drug permeation results. Copyright © 2017 Elsevier B.V. All rights reserved.

  8. Functional Diversity of Haloacid Dehalogenase Superfamily Phosphatases from Saccharomyces cerevisiae: BIOCHEMICAL, STRUCTURAL, AND EVOLUTIONARY INSIGHTS.

    Science.gov (United States)

    Kuznetsova, Ekaterina; Nocek, Boguslaw; Brown, Greg; Makarova, Kira S; Flick, Robert; Wolf, Yuri I; Khusnutdinova, Anna; Evdokimova, Elena; Jin, Ke; Tan, Kemin; Hanson, Andrew D; Hasnain, Ghulam; Zallot, Rémi; de Crécy-Lagard, Valérie; Babu, Mohan; Savchenko, Alexei; Joachimiak, Andrzej; Edwards, Aled M; Koonin, Eugene V; Yakunin, Alexander F

    2015-07-24

    The haloacid dehalogenase (HAD)-like enzymes comprise a large superfamily of phosphohydrolases present in all organisms. The Saccharomyces cerevisiae genome encodes at least 19 soluble HADs, including 10 uncharacterized proteins. Here, we biochemically characterized 13 yeast phosphatases from the HAD superfamily, which includes both specific and promiscuous enzymes active against various phosphorylated metabolites and peptides with several HADs implicated in detoxification of phosphorylated compounds and pseudouridine. The crystal structures of four yeast HADs provided insight into their active sites, whereas the structure of the YKR070W dimer in complex with substrate revealed a composite substrate-binding site. Although the S. cerevisiae and Escherichia coli HADs share low sequence similarities, the comparison of their substrate profiles revealed seven phosphatases with common preferred substrates. The cluster of secondary substrates supporting significant activity of both S. cerevisiae and E. coli HADs includes 28 common metabolites that appear to represent the pool of potential activities for the evolution of novel HAD phosphatases. Evolution of novel substrate specificities of HAD phosphatases shows no strict correlation with sequence divergence. Thus, evolution of the HAD superfamily combines the conservation of the overall substrate pool and the substrate profiles of some enzymes with remarkable biochemical and structural flexibility of other superfamily members. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  9. Structural Insights into DD-Fold Assembly and Caspase-9 Activation by the Apaf-1 Apoptosome.

    Science.gov (United States)

    Su, Tsung-Wei; Yang, Chao-Yu; Kao, Wen-Pin; Kuo, Bai-Jiun; Lin, Shan-Meng; Lin, Jung-Yaw; Lo, Yu-Chih; Lin, Su-Chang

    2017-03-07

    Death domain (DD)-fold assemblies play a crucial role in regulating the signaling to cell survival or death. Here we report the crystal structure of the caspase recruitment domain (CARD)-CARD disk of the human apoptosome. The structure surprisingly reveals that three 1:1 Apaf-1:procaspase-9 CARD protomers form a novel helical DD-fold assembly on the heptameric wheel-like platform of the apoptosome. The small-angle X-ray scattering and multi-angle light scattering data also support that three protomers could form an oligomeric complex similar to the crystal structure. Interestingly, the quasi-equivalent environment of CARDs could generate different quaternary CARD assemblies. We also found that the type II interaction is conserved in all DD-fold complexes, whereas the type I interaction is found only in the helical DD-fold assemblies. This study provides crucial insights into the caspase activation mechanism, which is tightly controlled by a sophisticated and highly evolved CARD assembly on the apoptosome, and also enables better understanding of the intricate DD-fold assembly. Copyright © 2017 Elsevier Ltd. All rights reserved.

  10. One-step sol-gel imprint lithography for guided-mode resonance structures.

    Science.gov (United States)

    Huang, Yin; Liu, Longju; Johnson, Michael; C Hillier, Andrew; Lu, Meng

    2016-03-04

    Guided-mode resonance (GMR) structures consisting of sub-wavelength periodic gratings are capable of producing narrow-linewidth optical resonances. This paper describes a sol-gel-based imprint lithography method for the fabrication of submicron 1D and 2D GMR structures. This method utilizes a patterned polydimethylsiloxane (PDMS) mold to fabricate the grating coupler and waveguide for a GMR device using a sol-gel thin film in a single step. An organic-inorganic hybrid sol-gel film was selected as the imprint material because of its relatively high refractive index. The optical responses of several sol-gel GMR devices were characterized, and the experimental results were in good agreement with the results of electromagnetic simulations. The influence of processing parameters was investigated in order to determine how finely the spectral response and resonant wavelength of the GMR devices could be tuned. As an example potential application, refractometric sensing experiments were performed using a 1D sol-gel device. The results demonstrated a refractive index sensitivity of 50 nm/refractive index unit. This one-step fabrication process offers a simple, rapid, and low-cost means of fabricating GMR structures. We anticipate that this method can be valuable in the development of various GMR-based devices as it can readily enable the fabrication of complex shapes and allow the doping of optically active materials into sol-gel thin film.

  11. One-step sol–gel imprint lithography for guided-mode resonance structures

    International Nuclear Information System (INIS)

    Huang, Yin; Liu, Longju; Lu, Meng; Johnson, Michael; C Hillier, Andrew

    2016-01-01

    Guided-mode resonance (GMR) structures consisting of sub-wavelength periodic gratings are capable of producing narrow-linewidth optical resonances. This paper describes a sol–gel-based imprint lithography method for the fabrication of submicron 1D and 2D GMR structures. This method utilizes a patterned polydimethylsiloxane (PDMS) mold to fabricate the grating coupler and waveguide for a GMR device using a sol–gel thin film in a single step. An organic–inorganic hybrid sol–gel film was selected as the imprint material because of its relatively high refractive index. The optical responses of several sol–gel GMR devices were characterized, and the experimental results were in good agreement with the results of electromagnetic simulations. The influence of processing parameters was investigated in order to determine how finely the spectral response and resonant wavelength of the GMR devices could be tuned. As an example potential application, refractometric sensing experiments were performed using a 1D sol–gel device. The results demonstrated a refractive index sensitivity of 50 nm/refractive index unit. This one-step fabrication process offers a simple, rapid, and low-cost means of fabricating GMR structures. We anticipate that this method can be valuable in the development of various GMR-based devices as it can readily enable the fabrication of complex shapes and allow the doping of optically active materials into sol–gel thin film. (paper)

  12. Measurement of deforming mode of lattice truss structures under impact loading

    Directory of Open Access Journals (Sweden)

    Zhao H.

    2012-08-01

    Full Text Available Lattice truss structures, which are used as a core material in sandwich panels, were widely investigated experimentally and theoretically. However, explanation of the deforming mechanism using reliable experimental results is almost rarely reported, particularly for the dynamic deforming mechanism. The present work aimed at the measurement of the deforming mode of lattice truss structures. Indeed, quasi-static and Split Hopkinson Pressure Bar (SHPB tests have been performed on the tetrahedral truss cores structures made of Aluminum 3003-O. Global values such as crushing forces and displacements between the loading platens are obtained. However, in order to understand the deforming mechanism and to explain the observed impact strength enhancement observed in the experiments, images of the truss core element during the tests are recorded. A method based on the edge detection algorithm is developed and applied to these images. The deforming profiles of one beam are extracted and it allows for calculating the length of beam. It is found that these lengths diminish to a critical value (due to compression and remain constant afterwards (because of significant bending. The comparison between quasi-static and impact tests shows that the beam were much more compressed under impact loading, which could be understood as the lateral inertia effect in dynamic bucking. Therefore, the impact strength enhancement of tetrahedral truss core sandwich panel can be explained by the delayed buckling of beam under impact (more compression reached, together with the strain hardening of base material.

  13. Structure and stability insights into tumour suppressor p53 evolutionary related proteins.

    Directory of Open Access Journals (Sweden)

    Bruno Pagano

    Full Text Available The p53 family of genes and their protein products, namely, p53, p63 and p73, have over one billion years of evolutionary history. Advances in computational biology and genomics are enabling studies of the complexities of the molecular evolution of p53 protein family to decipher the underpinnings of key biological conditions spanning from cancer through to various metabolic and developmental disorders and facilitate the design of personalised medicines. However, a complete understanding of the inherent nature of the thermodynamic and structural stability of the p53 protein family is still lacking. This is due, to a degree, to the lack of comprehensive structural information for a large number of homologous proteins and to an incomplete knowledge of the intrinsic factors responsible for their stability and how these might influence function. Here we investigate the thermal stability, secondary structure and folding properties of the DNA-binding domains (DBDs of a range of proteins from the p53 family using biophysical methods. While the N- and the C-terminal domains of the p53 family show sequence diversity and are normally targets for post-translational modifications and alternative splicing, the central DBD is highly conserved. Together with data obtained from Molecular Dynamics simulations in solution and with structure based homology modelling, our results provide further insights into the molecular properties of evolutionary related p53 proteins. We identify some marked structural differences within the p53 family, which could account for the divergence in biological functions as well as the subtleties manifested in the oligomerization properties of this family.

  14. Structures of parasite calreticulins provide insights into their flexibility and dual carbohydrate/peptide-binding properties.

    Science.gov (United States)

    Moreau, Christophe; Cioci, Gianluca; Iannello, Marina; Laffly, Emmanuelle; Chouquet, Anne; Ferreira, Arturo; Thielens, Nicole M; Gaboriaud, Christine

    2016-11-01

    Calreticulin (CRT) is a multifaceted protein, initially discovered as an endoplasmic reticulum (ER) chaperone protein, that is essential in calcium metabolism. Various implications in cancer, early development and immunology have been discovered more recently for CRT, as well as its role as a dominant 'eat-me' prophagocytic signal. Intriguingly, cell-surface exposure/secretion of CRT is among the infective strategies used by parasites such as Trypanosoma cruzi , Entamoeba histolytica , Taenia solium , Leishmania donovani and Schistosoma mansoni . Because of the inherent flexibility of CRTs, their analysis by X-ray crystallography requires the design of recombinant constructs suitable for crystallization, and thus only the structures of two very similar mammalian CRT lectin domains are known. With the X-ray structures of two distant parasite CRTs, insights into species structural determinants that might be harnessed to fight against the parasites without affecting the functions of the host CRT are now provided. Moreover, although the hypothesis that CRT can exhibit both open and closed conformations has been proposed in relation to its chaperone function, only the open conformation has so far been observed in crystal structures. The first evidence is now provided of a complex conformational transition with the junction reoriented towards P-domain closure. SAXS experiments also provided additional information about the flexibility of T. cruzi CRT in solution, thus complementing crystallographic data on the open conformation. Finally, regarding the conserved lectin-domain structure and chaperone function, evidence is provided of its dual carbohydrate/protein specificity and a new scheme is proposed to interpret such unusual substrate-binding properties. These fascinating features are fully consistent with previous experimental observations, as discussed considering the broad spectrum of CRT sequence conservations and differences.

  15. Structures of parasite calreticulins provide insights into their flexibility and dual carbohydrate/peptide-binding properties

    Directory of Open Access Journals (Sweden)

    Christophe Moreau

    2016-11-01

    Full Text Available Calreticulin (CRT is a multifaceted protein, initially discovered as an endoplasmic reticulum (ER chaperone protein, that is essential in calcium metabolism. Various implications in cancer, early development and immunology have been discovered more recently for CRT, as well as its role as a dominant `eat-me' prophagocytic signal. Intriguingly, cell-surface exposure/secretion of CRT is among the infective strategies used by parasites such as Trypanosoma cruzi, Entamoeba histolytica, Taenia solium, Leishmania donovani and Schistosoma mansoni. Because of the inherent flexibility of CRTs, their analysis by X-ray crystallography requires the design of recombinant constructs suitable for crystallization, and thus only the structures of two very similar mammalian CRT lectin domains are known. With the X-ray structures of two distant parasite CRTs, insights into species structural determinants that might be harnessed to fight against the parasites without affecting the functions of the host CRT are now provided. Moreover, although the hypothesis that CRT can exhibit both open and closed conformations has been proposed in relation to its chaperone function, only the open conformation has so far been observed in crystal structures. The first evidence is now provided of a complex conformational transition with the junction reoriented towards P-domain closure. SAXS experiments also provided additional information about the flexibility of T. cruzi CRT in solution, thus complementing crystallographic data on the open conformation. Finally, regarding the conserved lectin-domain structure and chaperone function, evidence is provided of its dual carbohydrate/protein specificity and a new scheme is proposed to interpret such unusual substrate-binding properties. These fascinating features are fully consistent with previous experimental observations, as discussed considering the broad spectrum of CRT sequence conservations and differences.

  16. Structural and molecular insights into novel surface-exposed mucus adhesins from Lactobacillus reuteri human strains.

    Science.gov (United States)

    Etzold, Sabrina; MacKenzie, Donald A; Jeffers, Faye; Walshaw, John; Roos, Stefan; Hemmings, Andrew M; Juge, Nathalie

    2014-05-01

    The mucus layer covering the gastrointestinal tract is the first point of contact of the intestinal microbiota with the host. Cell surface macromolecules are critical for adherence of commensal bacteria to mucus but structural information is scarce. Here we report the first molecular and structural characterization of a novel cell-surface protein, Lar_0958 from Lactobacillus reuteri JCM 1112(T) , mediating adhesion of L. reuteri human strains to mucus. Lar_0958 is a modular protein of 133 kDa containing six repeat domains, an N-terminal signal sequence and a C-terminal anchoring motif (LPXTG). Lar_0958 homologues are expressed on the cell-surface of L. reuteri human strains, as shown by flow-cytometry and immunogold microscopy. Adhesion of human L. reuteri strains to mucus in vitro was significantly reduced in the presence of an anti-Lar_0958 antibody and Lar_0958 contribution to adhesion was further confirmed using a L. reuteri ATCC PTA 6475 lar_0958 KO mutant (6475-KO). The X-ray crystal structure of a single Lar_0958 repeat, determined at 1.5 Å resolution, revealed a divergent immunoglobulin (Ig)-like β-sandwich fold, sharing structural homology with the Ig-like inter-repeat domain of internalins of the food borne pathogen Listeria monocytogenes. These findings provide unique structural insights into cell-surface protein repeats involved in adhesion of Gram-positive bacteria to the intestine. © 2014 John Wiley & Sons Ltd.

  17. X-ray structure reveals a new class and provides insight into evolution of alkaline phosphatases.

    Directory of Open Access Journals (Sweden)

    Subhash C Bihani

    Full Text Available The alkaline phosphatase (AP is a bi-metalloenzyme of potential applications in biotechnology and bioremediation, in which phosphate monoesters are nonspecifically hydrolysed under alkaline conditions to yield inorganic phosphate. The hydrolysis occurs through an enzyme intermediate in which the catalytic residue is phosphorylated. The reaction, which also requires a third metal ion, is proposed to proceed through a mechanism of in-line displacement involving a trigonal bipyramidal transition state. Stabilizing the transition state by bidentate hydrogen bonding has been suggested to be the reason for conservation of an arginine residue in the active site. We report here the first crystal structure of alkaline phosphatase purified from the bacterium Sphingomonas. sp. Strain BSAR-1 (SPAP. The crystal structure reveals many differences from other APs: 1 the catalytic residue is a threonine instead of serine, 2 there is no third metal ion binding pocket, and 3 the arginine residue forming bidentate hydrogen bonding is deleted in SPAP. A lysine and an aspargine residue, recruited together for the first time into the active site, bind the substrate phosphoryl group in a manner not observed before in any other AP. These and other structural features suggest that SPAP represents a new class of APs. Because of its direct contact with the substrate phosphoryl group, the lysine residue is proposed to play a significant role in catalysis. The structure is consistent with a mechanism of in-line displacement via a trigonal bipyramidal transition state. The structure provides important insights into evolutionary relationships between members of AP superfamily.

  18. Fine structure of the stimulated Raman spectrum in compressed hydrogen. The relaxation-oscillation mode of backscattered Stokes emission

    International Nuclear Information System (INIS)

    Bespalov, V.G.; Efimov, Yu.N.; Staselko, D.I.

    1992-01-01

    This paper studies the emission spectra of backscattered stimulated Raman scattering (SRS) in compressed hydrogen in the relaxation-oscillation mode and the compression SRS mode for the minimum width of the spontaneous scattering spectrum (in the region of the Dicke dip). It is shown that the generation of a train of Stokes-emission subpulses results in the appearance of fine structure in the backscattered SRS spectrum. The influence of the temporal structure of reflected Stokes pulses on this spectrum and on the appearance of fine structure in it is analyzed. The conditions for generating spectrally limited (without phase modulation), extremely coherent Stokes pulses are explained. 18 refs., 3 figs

  19. NOMAD-Ref: visualization, deformation and refinement of macromolecular structures based on all-atom normal mode analysis.

    Science.gov (United States)

    Lindahl, Erik; Azuara, Cyril; Koehl, Patrice; Delarue, Marc

    2006-07-01

    Normal mode analysis (NMA) is an efficient way to study collective motions in biomolecules that bypasses the computational costs and many limitations associated with full dynamics simulations. The NOMAD-Ref web server presented here provides tools for online calculation of the normal modes of large molecules (up to 100,000 atoms) maintaining a full all-atom representation of their structures, as well as access to a number of programs that utilize these collective motions for deformation and refinement of biomolecular structures. Applications include the generation of sets of decoys with correct stereochemistry but arbitrary large amplitude movements, the quantification of the overlap between alternative conformations of a molecule, refinement of structures against experimental data, such as X-ray diffraction structure factors or Cryo-EM maps and optimization of docked complexes by modeling receptor/ligand flexibility through normal mode motions. The server can be accessed at the URL http://lorentz.immstr.pasteur.fr/nomad-ref.php.

  20. Structural insight into the mechanism of synergistic autoinhibition of SAD kinases.

    Science.gov (United States)

    Wu, Jing-Xiang; Cheng, Yun-Sheng; Wang, Jue; Chen, Lei; Ding, Mei; Wu, Jia-Wei

    2015-12-02

    The SAD/BRSK kinases participate in various important life processes, including neural development, cell cycle and energy metabolism. Like other members of the AMPK family, SAD contains an N-terminal kinase domain followed by the characteristic UBA and KA1 domains. Here we identify a unique autoinhibitory sequence (AIS) in SAD kinases, which exerts autoregulation in cooperation with UBA. Structural studies of mouse SAD-A revealed that UBA binds to the kinase domain in a distinct mode and, more importantly, AIS nestles specifically into the KD-UBA junction. The cooperative action of AIS and UBA results in an 'αC-out' inactive kinase, which is conserved across species and essential for presynaptic vesicle clustering in C. elegans. In addition, the AIS, along with the KA1 domain, is indispensable for phospholipid binding. Taken together, these data suggest a model for synergistic autoinhibition and membrane activation of SAD kinases.

  1. Localization of Geological Inhomogeneities on the Arctic Shelf by Analysis of the Seismoacoustic Wave Field Mode Structure

    Science.gov (United States)

    Sobisevich, A. L.; Presnov, D. A.; Sobisevich, L. E.; Shurup, A. S.

    2018-03-01

    The results of analysis of wave modes in the ambient noise induced in the layered structure "lithosphere-hydrosphere-ice sheet" are presented. It is shown that instrumental monitoring over background noises in an ice-covered shallow sea allows us to apply methods of seismic tomography in order to determine the structural parameters of a layered geophysical media.

  2. ROLE OF NEUTRALS IN CORE FUELING AND PEDESTAL STRUCTURE IN H-MODE DIII-D DISCHARGES

    International Nuclear Information System (INIS)

    WOLF, NS; PETRIE, TW; PORTER, GD; ROGNLIEN, TD; GROEBNER, RJ; MAKOWSKI, MA

    2002-01-01

    OAK A271 ROLE OF NEUTRALS IN CORE FUELING AND PEDESTAL STRUCTURE IN H-MODE DIII-D DISCHARGES. The 2-D fluid code UEDGE was used to analyze DIII-D experiments to determine the role of neutrals in core fueling, core impurities, and also the H-mode pedestal structure. The authors compared the effects of divertor closure on the fueling rate and impurity density of high-triangularity, H-mode plasmas. UEDGE simulations indicate that the decrease in both deuterium core fueling (∼ 15%-20%) and core carbon density (∼ 15%-30%) with the closed divertor compared to the open divertor configuration is due to greater divertor screening of neutrals. They also compared UEDGE results with a simple analytic model of the H-mode pedestal structure. The model predicts both the width and gradient of the transport barrier in n e as a function of the pedestal density. The more sophisticated UEDGE simulations of H-mode discharges corroborate the simple analytic model, which is consistent with the hypothesis that fueling processes play a role in H-mode transport barrier formation

  3. Structural insights into lipid-dependent reversible dimerization of human GLTP

    International Nuclear Information System (INIS)

    Samygina, Valeria R.; Ochoa-Lizarralde, Borja; Popov, Alexander N.; Cabo-Bilbao, Aintzane; Goni-de-Cerio, Felipe; Molotkovsky, Julian G.; Patel, Dinshaw J.; Brown, Rhoderick E.; Malinina, Lucy

    2013-01-01

    It is shown that dimerization is promoted by glycolipid binding to human GLTP. The importance of dimer flexibility in wild-type protein is manifested by point mutation that ‘locks’ the dimer while diversifying ligand/protein adaptations. Human glycolipid transfer protein (hsGLTP) forms the prototypical GLTP fold and is characterized by a broad transfer selectivity for glycosphingolipids (GSLs). The GLTP mutation D48V near the ‘portal entrance’ of the glycolipid binding site has recently been shown to enhance selectivity for sulfatides (SFs) containing a long acyl chain. Here, nine novel crystal structures of hsGLTP and the SF-selective mutant complexed with short-acyl-chain monoSF and diSF in different crystal forms are reported in order to elucidate the potential functional roles of lipid-mediated homodimerization. In all crystal forms, the hsGLTP–SF complexes displayed homodimeric structures supported by similarly organized intermolecular interactions. The dimerization interface always involved the lipid sphingosine chain, the protein C-terminus (C-end) and α-helices 6 and 2, but the D48V mutant displayed a ‘locked’ dimer conformation compared with the hinge-like flexibility of wild-type dimers. Differences in contact angles, areas and residues at the dimer interfaces in the ‘flexible’ and ‘locked’ dimers revealed a potentially important role of the dimeric structure in the C-end conformation of hsGLTP and in the precise positioning of the key residue of the glycolipid recognition centre, His140. ΔY207 and ΔC-end deletion mutants, in which the C-end is shifted or truncated, showed an almost complete loss of transfer activity. The new structural insights suggest that ligand-dependent reversible dimerization plays a role in the function of human GLTP

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

    Science.gov (United States)

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

    2015-11-01

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

  5. Theory for passive mode-locking in semiconductor laser structures including the effects of self-phase modulation, dispersion and pulse collisions

    NARCIS (Netherlands)

    Koumans, R.G.M.P.; Roijen, van R.

    1996-01-01

    We present a theory for passive mode-locking in semiconductor laser structures using a semiconductor laser amplifier and absorber. The mode-locking system is described in terms of the different elements in the semiconductor laser structure. We derive mode-locking conditions and show how other

  6. The structure of psychological life satisfaction: insights from farmers and a general community sample in Australia

    Science.gov (United States)

    2012-01-01

    Background Psychological life satisfaction is a robust predictor of wellbeing. Public health measures to improve wellbeing would benefit from an understanding of how overall life satisfaction varies as a function of satisfaction with multiple life domains, an area that has been little explored. We examine a sample of drought-affected Australian farmers and a general community sample of Australians to investigate how domain satisfaction combines to form psychological satisfaction. In particular, we introduce a way of statistically testing for the presence of “supra-domains” of satisfaction to propose a novel way of examining the composition of psychological life satisfaction to gain insights for health promotion and policy. Methods Covariance between different perceptions of life domain satisfaction was identified by conducting correlation, regression, and exploratory factor analyses on responses to the Personal Wellbeing Index. Structural equations modelling was then used to (a) validate satisfaction supra-domain constructs emerging from different perceptions of life domain satisfaction, and (b) model relationships between supra-domains and an explicit measure of psychological life satisfaction. Results Perceived satisfaction with eight different life domains loaded onto a single unitary satisfaction construct adequately in each sample. However, in both samples, different domains better loaded onto two separate but correlated constructs (‘supra-domains’): “satisfaction with connectedness” and “satisfaction with efficacy”. Modelling reciprocal pathways between these supra-domains and an explicit measure of psychological life satisfaction revealed that efficacy mediated the link between connectedness and psychological satisfaction. Conclusions If satisfaction with connectedness underlies satisfaction with efficacy (and thus psychological satisfaction), a novel insight for health policy emerges: psychological life satisfaction, a vital part of

  7. The structure of psychological life satisfaction: insights from farmers and a general community sample in Australia

    Directory of Open Access Journals (Sweden)

    OBrien Léan V

    2012-11-01

    Full Text Available Abstract Background Psychological life satisfaction is a robust predictor of wellbeing. Public health measures to improve wellbeing would benefit from an understanding of how overall life satisfaction varies as a function of satisfaction with multiple life domains, an area that has been little explored. We examine a sample of drought-affected Australian farmers and a general community sample of Australians to investigate how domain satisfaction combines to form psychological satisfaction. In particular, we introduce a way of statistically testing for the presence of “supra-domains” of satisfaction to propose a novel way of examining the composition of psychological life satisfaction to gain insights for health promotion and policy. Methods Covariance between different perceptions of life domain satisfaction was identified by conducting correlation, regression, and exploratory factor analyses on responses to the Personal Wellbeing Index. Structural equations modelling was then used to (a validate satisfaction supra-domain constructs emerging from different perceptions of life domain satisfaction, and (b model relationships between supra-domains and an explicit measure of psychological life satisfaction. Results Perceived satisfaction with eight different life domains loaded onto a single unitary satisfaction construct adequately in each sample. However, in both samples, different domains better loaded onto two separate but correlated constructs (‘supra-domains’: “satisfaction with connectedness” and “satisfaction with efficacy”. Modelling reciprocal pathways between these supra-domains and an explicit measure of psychological life satisfaction revealed that efficacy mediated the link between connectedness and psychological satisfaction. Conclusions If satisfaction with connectedness underlies satisfaction with efficacy (and thus psychological satisfaction, a novel insight for health policy emerges: psychological life satisfaction

  8. Aberrant default-mode functional and structural connectivity in heroin-dependent individuals.

    Directory of Open Access Journals (Sweden)

    Xiaofen Ma

    Full Text Available Little is known about connectivity within the default mode network (DMN in heroin-dependent individuals (HDIs. In the current study, diffusion-tensor imaging (DTI and resting-state functional MRI (rs-fMRI were combined to investigate both structural and functional connectivity within the DMN in HDIs.Fourteen HDIs and 14 controls participated in the study. Structural (path length, tracts count, (fractional anisotropy FA and (mean diffusivity MD derived from DTI tractographyand functional (temporal correlation coefficient derived from rs-fMRI DMN connectivity changes were examined in HDIs. Pearson correlation analysis was performed to compare the structural/functional indices and duration of heroin use/Iowa gambling task(IGT performance in HDIs.HDIs had lower FA and higher MD in the tract connecting the posterior cingulate cortex/precuneus (PCC/PCUN to right parahippocampal gyrus (PHG, compared to the controls. HDIs also had decreased FA and track count in the tract connecting the PCC/PCUN and medial prefrontal cortex (MPFC, as well as decreased functional connectivity between the PCC/PCUN and bilateral PHG and MPFC, compared to controls. FA values for the tract connecting PCC/PCUN to the right PHG and connecting PCC/PCUN to the MPFC were negatively correlated to the duration of heroin use. The temporal correlation coefficients between the PCC/PCUN and the MPFC, and the FA values for the tract connecting the PCC/PCUN to the MPFC were positively correlated to IGT performance in HDIs.Structural and functional connectivity within the DMN are both disturbed in HDIs. This disturbance progresses as duration of heroin use increases and is related to deficits in decision making in HDIs.

  9. Different shades of default mode disturbance in schizophrenia: Subnodal covariance estimation in structure and function.

    Science.gov (United States)

    Lefort-Besnard, Jérémy; Bassett, Danielle S; Smallwood, Jonathan; Margulies, Daniel S; Derntl, Birgit; Gruber, Oliver; Aleman, Andre; Jardri, Renaud; Varoquaux, Gaël; Thirion, Bertrand; Eickhoff, Simon B; Bzdok, Danilo

    2018-02-01

    Schizophrenia is a devastating mental disease with an apparent disruption in the highly associative default mode network (DMN). Interplay between this canonical network and others probably contributes to goal-directed behavior so its disturbance is a candidate neural fingerprint underlying schizophrenia psychopathology. Previous research has reported both hyperconnectivity and hypoconnectivity within the DMN, and both increased and decreased DMN coupling with the multimodal saliency network (SN) and dorsal attention network (DAN). This study systematically revisited network disruption in patients with schizophrenia using data-derived network atlases and multivariate pattern-learning algorithms in a multisite dataset (n = 325). Resting-state fluctuations in unconstrained brain states were used to estimate functional connectivity, and local volume differences between individuals were used to estimate structural co-occurrence within and between the DMN, SN, and DAN. In brain structure and function, sparse inverse covariance estimates of network coupling were used to characterize healthy participants and patients with schizophrenia, and to identify statistically significant group differences. Evidence did not confirm that the backbone of the DMN was the primary driver of brain dysfunction in schizophrenia. Instead, functional and structural aberrations were frequently located outside of the DMN core, such as in the anterior temporoparietal junction and precuneus. Additionally, functional covariation analyses highlighted dysfunctional DMN-DAN coupling, while structural covariation results highlighted aberrant DMN-SN coupling. Our findings reframe the role of the DMN core and its relation to canonical networks in schizophrenia. We thus underline the importance of large-scale neural interactions as effective biomarkers and indicators of how to tailor psychiatric care to single patients. © 2017 Wiley Periodicals, Inc.

  10. Kinetic and Structural Insights into the Mechanism of AMPylation by VopS Fic Domain*

    Science.gov (United States)

    Luong, Phi; Kinch, Lisa N.; Brautigam, Chad A.; Grishin, Nick V.; Tomchick, Diana R.; Orth, Kim

    2010-01-01

    The bacterial pathogen Vibrio parahemeolyticus manipulates host signaling pathways during infections by injecting type III effectors into the cytoplasm of the target cell. One of these effectors, VopS, blocks actin assembly by AMPylation of a conserved threonine residue in the switch 1 region of Rho GTPases. The modified GTPases are no longer able to interact with downstream effectors due to steric hindrance by the covalently linked AMP moiety. Herein we analyze the structure of VopS and its evolutionarily conserved catalytic residues. Steady-state analysis of VopS mutants provides kinetic understanding on the functional role of each residue for AMPylation activity by the Fic domain. Further mechanistic analysis of VopS with its two substrates, ATP and Cdc42, demonstrates that VopS utilizes a sequential mechanism to AMPylate Rho GTPases. Discovery of a ternary reaction mechanism along with structural insight provides critical groundwork for future studies for the family of AMPylators that modify hydroxyl-containing residues with AMP. PMID:20410310

  11. Kinetic and Structural Insights into the Mechanism of AMPylation by VopS Fic Domain

    Energy Technology Data Exchange (ETDEWEB)

    Luong, Phi; Kinch, Lisa N.; Brautigam, Chad A.; Grishin, Nick V.; Tomchick, Diana R.; Orth, Kim (UTSMC)

    2010-07-19

    The bacterial pathogen Vibrio parahemeolyticus manipulates host signaling pathways during infections by injecting type III effectors into the cytoplasm of the target cell. One of these effectors, VopS, blocks actin assembly by AMPylation of a conserved threonine residue in the switch 1 region of Rho GTPases. The modified GTPases are no longer able to interact with downstream effectors due to steric hindrance by the covalently linked AMP moiety. Herein we analyze the structure of VopS and its evolutionarily conserved catalytic residues. Steady-state analysis of VopS mutants provides kinetic understanding on the functional role of each residue for AMPylation activity by the Fic domain. Further mechanistic analysis of VopS with its two substrates, ATP and Cdc42, demonstrates that VopS utilizes a sequential mechanism to AMPylate Rho GTPases. Discovery of a ternary reaction mechanism along with structural insight provides critical groundwork for future studies for the family of AMPylators that modify hydroxyl-containing residues with AMP.

  12. Structural insights and ab initio sequencing within the DING proteins family

    International Nuclear Information System (INIS)

    Elias, Mikael; Liebschner, Dorothee; Gotthard, Guillaume; Chabriere, Eric

    2011-01-01

    DING proteins constitute a recently discovered protein family that is ubiquitous in eukaryotes. The structural insights and the physiological involvements of these intriguing proteins are hereby deciphered. DING proteins constitute an intriguing family of phosphate-binding proteins that was identified in a wide range of organisms, from prokaryotes and archae to eukaryotes. Despite their seemingly ubiquitous occurrence in eukaryotes, their encoding genes are missing from sequenced genomes. Such a lack has considerably hampered functional studies. In humans, these proteins have been related to several diseases, like atherosclerosis, kidney stones, inflammation processes and HIV inhibition. The human phosphate binding protein is a human representative of the DING family that was serendipitously discovered from human plasma. An original approach was developed to determine ab initio the complete and exact sequence of this 38 kDa protein by utilizing mass spectrometry and X-ray data in tandem. Taking advantage of this first complete eukaryotic DING sequence, a immunohistochemistry study was undertaken to check the presence of DING proteins in various mice tissues, revealing that these proteins are widely expressed. Finally, the structure of a bacterial representative from Pseudomonas fluorescens was solved at sub-angstrom resolution, allowing the molecular mechanism of the phosphate binding in these high-affinity proteins to be elucidated

  13. Structural insights and ab initio sequencing within the DING proteins family

    Energy Technology Data Exchange (ETDEWEB)

    Elias, Mikael, E-mail: mikael.elias@weizmann.ac.il [Weizmann Institute of Science, Rehovot (Israel); Liebschner, Dorothee [CRM2, Nancy Université (France); Gotthard, Guillaume; Chabriere, Eric [AFMB, Université Aix-Marseille II (France)

    2011-01-01

    DING proteins constitute a recently discovered protein family that is ubiquitous in eukaryotes. The structural insights and the physiological involvements of these intriguing proteins are hereby deciphered. DING proteins constitute an intriguing family of phosphate-binding proteins that was identified in a wide range of organisms, from prokaryotes and archae to eukaryotes. Despite their seemingly ubiquitous occurrence in eukaryotes, their encoding genes are missing from sequenced genomes. Such a lack has considerably hampered functional studies. In humans, these proteins have been related to several diseases, like atherosclerosis, kidney stones, inflammation processes and HIV inhibition. The human phosphate binding protein is a human representative of the DING family that was serendipitously discovered from human plasma. An original approach was developed to determine ab initio the complete and exact sequence of this 38 kDa protein by utilizing mass spectrometry and X-ray data in tandem. Taking advantage of this first complete eukaryotic DING sequence, a immunohistochemistry study was undertaken to check the presence of DING proteins in various mice tissues, revealing that these proteins are widely expressed. Finally, the structure of a bacterial representative from Pseudomonas fluorescens was solved at sub-angstrom resolution, allowing the molecular mechanism of the phosphate binding in these high-affinity proteins to be elucidated.

  14. Human acid sphingomyelinase structures provide insight to molecular basis of Niemann–Pick disease

    Energy Technology Data Exchange (ETDEWEB)

    Zhou, Yan-Feng; Metcalf, Matthew C.; Garman, Scott C.; Edmunds, Tim; Qiu, Huawei; Wei, Ronnie R. (Sanofi Aventis); (UMASS, Amherst)

    2016-10-26

    Acid sphingomyelinase (ASM) hydrolyzes sphingomyelin to ceramide and phosphocholine, essential components of myelin in neurons. Genetic alterations in ASM lead to ASM deficiency (ASMD) and have been linked to Niemann–Pick disease types A and B. Olipudase alfa, a recombinant form of human ASM, is being developed as enzyme replacement therapy to treat the non-neurological manifestations of ASMD. Here we present the human ASM holoenzyme and product bound structures encompassing all of the functional domains. The catalytic domain has a metallophosphatase fold, and two zinc ions and one reaction product phosphocholine are identified in a histidine-rich active site. The structures reveal the underlying catalytic mechanism, in which two zinc ions activate a water molecule for nucleophilic attack of the phosphodiester bond. Docking of sphingomyelin provides a model that allows insight into the selectivity of the enzyme and how the ASM domains collaborate to complete hydrolysis. Mapping of known mutations provides a basic understanding on correlations between enzyme dysfunction and phenotypes observed in ASMD patients.

  15. Insight into the biological effects of acupuncture points by X-ray absorption fine structure.

    Science.gov (United States)

    Liu, Chenglin; Liu, Qinghua; Zhang, Dongming; Liu, Wei; Yan, Xiaohui; Zhang, Xinyi; Oyanagi, Hiroyuki; Pan, Zhiyun; Hu, Fengchun; Wei, Shiqiang

    2018-06-02

    Exploration of the biological effects of transition metal ions in acupuncture points is essential to clarify the functional mechanism of acupuncture treatment. Here we show that in the SP6 acupuncture point (Sanyinjiao) the Fe ions are in a high-spin state of approximately t 2g 4.5 e g 1.5 in an Fe-N(O) octahedral crystal field. The Fe K-edge synchrotron radiation X-ray absorption fine structure results reveal that the Fe-N and Fe-O bond lengths in the SP6 acupuncture point are 2.05 and 2.13 Å, respectively, and are 0.05-0.10 Å longer than those in the surrounding tissue. The distorted atomic structure reduces the octahedral symmetry and weakens the crystal field around the Fe ions by approximately 0.3 eV, leading to the high-spin configuration of the Fe ions, which is favorable for strengthening the magnetotransport and oxygen transportation properties in the acupuncture point by the enhanced spin coherence. This finding might provide some insight into the microscopic effect of the atomic and electronic interactions of transition metal ions in the acupuncture point. Graphical Abstract ᅟ.

  16. Identification and characterisation of a novel acylpeptide hydrolase from Sulfolobus solfataricus: structural and functional insights.

    Directory of Open Access Journals (Sweden)

    Marta Gogliettino

    Full Text Available A novel acylpeptide hydrolase, named APEH-3(Ss, was isolated from the hypertermophilic archaeon Sulfolobus solfataricus. APEH is a member of the prolyl oligopeptidase family which catalyzes the removal of acetylated amino acid residues from the N terminus of oligopeptides. The purified enzyme shows a homotrimeric structure, unique among the associate partners of the APEH cluster and, in contrast to the archaeal APEHs which show both exo/endo peptidase activities, it appears to be a "true" aminopeptidase as exemplified by its mammalian counterparts, with which it shares a similar substrate specificity. Furthermore, a comparative study on the regulation of apeh gene expression, revealed a significant but divergent alteration in the expression pattern of apeh-3(Ss and apeh(Ss (the gene encoding the previously identified APEH(Ss from S. solfataricus, which is induced in response to various stressful growth conditions. Hence, both APEH enzymes can be defined as stress-regulated proteins which play a complementary role in enabling the survival of S. solfataricus cells under different conditions. These results provide new structural and functional insights into S. solfataricus APEH, offering a possible explanation for the multiplicity of this enzyme in Archaea.

  17. Base pairing and structural insights into the 5-formylcytosine in RNA duplex

    Science.gov (United States)

    Wang, Rui; Luo, Zhipu; He, Kaizhang; Delaney, Michael O.; Chen, Doris; Sheng, Jia

    2016-01-01

    Abstract 5-Formylcytidine (f5C), a previously discovered natural nucleotide in the mitochondrial tRNA of many species including human, has been recently detected as the oxidative product of 5-methylcytidine (m5C) through 5-hydroxymethylcytidine (hm5C) in total RNA of mammalian cells. The discovery indicated that these cytosine derivatives in RNA might also play important epigenetic roles similar as in DNA, which has been intensively investigated in the past few years. In this paper, we studied the base pairing specificity of f5C in different RNA duplex contexts. We found that the 5-formyl group could increase duplex thermal stability and enhance base pairing specificity. We present three high-resolution crystal structures of an octamer RNA duplex [5′-GUA(f5C)GUAC-3′]2 that have been solved under three crystallization conditions with different buffers and pH values. Our results showed that the 5-formyl group is located in the same plane as the cytosine base and forms an intra-residue hydrogen bond with the amino group in the N4 position. In addition, this modification increases the base stacking between the f5C and the neighboring bases while not causing significant global and local structure perturbations. This work provides insights into the effects of 5-formylcytosine on RNA duplex. PMID:27079978

  18. Delivery Mode and the Transition of Pioneering Gut-Microbiota Structure, Composition and Predicted Metabolic Function

    Directory of Open Access Journals (Sweden)

    Noel T. Mueller

    2017-12-01

    Full Text Available Cesarean (C-section delivery, recently shown to cause excess weight gain in mice, perturbs human neonatal gut microbiota development due to the lack of natural mother-to-newborn transfer of microbes. Neonates excrete first the in-utero intestinal content (referred to as meconium hours after birth, followed by intestinal contents reflective of extra-uterine exposure (referred to as transition stool 2 to 3 days after birth. It is not clear when the effect of C-section on the neonatal gut microbiota emerges. We examined bacterial DNA in carefully-collected meconium, and the subsequent transitional stool, from 59 neonates [13 born by scheduled C-section and 46 born by vaginal delivery] in a private hospital in Brazil. Bacterial DNA was extracted, and the V4 region of the 16S rRNA gene was sequenced using the Illumina MiSeq (San Diego, CA, USA platform. We found evidence of bacterial DNA in the majority of meconium samples in our study. The bacterial DNA structure (i.e., beta diversity of meconium differed significantly from that of the transitional stool microbiota. There was a significant reduction in bacterial alpha diversity (e.g., number of observed bacterial species and change in bacterial composition (e.g., reduced Proteobacteria in the transition from meconium to stool. However, changes in predicted microbiota metabolic function from meconium to transitional stool were only observed in vaginally-delivered neonates. Within sample comparisons showed that delivery mode was significantly associated with bacterial structure, composition and predicted microbiota metabolic function in transitional-stool samples, but not in meconium samples. Specifically, compared to vaginally delivered neonates, the transitional stool of C-section delivered neonates had lower proportions of the genera Bacteroides, Parabacteroides and Clostridium. These differences led to C-section neonates having lower predicted abundance of microbial genes related to metabolism of

  19. Characterizing the structure-function relationship reveals the mode of action of a novel antimicrobial peptide, P1, from jumper ant Myrmecia pilosula.

    Science.gov (United States)

    Tseng, Tien-Sheng; Tsai, Keng-Chang; Chen, Chinpan

    2017-06-01

    Microbial infections of antibiotic-resistant strains cause serious diseases and have a significant impact on public health worldwide, so novel antimicrobial drugs are urgently needed. Insect venoms, a rich source of bioactive components containing antimicrobial peptides (AMPs), are attractive candidates for new therapeutic agents against microbes. Recently, a novel peptide, P1, identified from the venom of the Australian jumper ant Myrmecia pilosula, showed potent antimicrobial activities against both Gram-negative and Gram-positive bacteria, but its structure-function relationship is unknown. Here, we used biochemical and biophysical techniques coupled with computational simulations to explore the mode of action of P1 interaction with dodecylphosphocholine (DPC) micelles as a model membrane system. Our circular dichroism (CD) and NMR studies revealed an amphipathic α-helical structure for P1 upon interaction with DPC micelles. A paramagnetic relaxation enhancement approach revealed that P1 orients its α-helix segment (F6-G14) into DPC micelles. In addition, the α-helix segment could be essential for membrane permeabilization and antimicrobial activity. Moreover, the arginine residues R8, R11, and R15 significantly contribute to helix formation and membrane-binding affinity. The lysine residue K19 of the C-terminus functionally guides P1 to interact with DPC micelles in the early interaction stage. Our study provides insights into the mode of action of P1, which is valuable in modifying and developing potent AMPs as antibiotic drugs.

  20. Study of transport and micro-structural properties of magnesium di-boride strand under react and bend mode and bend and react mode

    International Nuclear Information System (INIS)

    Kundu, Ananya; Das, Subrat Kumar; Bano, Anees; Pradhan, Subrata

    2015-01-01

    I-V characterization of commercial multi-filamentary Magnesium Di-Boride (MgB 2 ) wire of diameter 0.83 mm were studied in cryocooler based self-field characterization system under both react and bent mode and bent and react mode for a range of temperature 6 K - 25 K. This study is of practical technical relevance where the heat treatment of the superconducting wire makes the sample less flexible for winding in magnet and in other applications. There are limited reported data, available on degradation of MgB 2 wire with bending induced strain in react and wind and wind and react method. In the present work the bending diameter were varied from 80 mm to 20 mm in the interval of 10 mm change of bending diameter and for each case critical current (Ic) of the strand is measured for the above range of temperature. An ETP copper made customized sample holder for mounting the MgB 2 strand was fabricated and is thermally anchored to the cooling stage of the cryocooler. It is seen from the experimental data that in react and bent mode the critical current degrades from 105 A to 87 A corresponding to bending diameter of 80 mm and 20 mm respectively. The corresponding bending strain was analytically estimated and compared with the simulation result. It is also observed that in react and bent mode, the degradation of the transport property of the strand is less as compared to react and bent mode. For bent and react mode in the same sample, the critical current (Ic) was measured to be ∼145 A at 15 K for bending diameter of 20 mm. Apart from studying the bending induced strain on MgB 2 strand, the tensile test of the strand at RT was carried out. The electrical characterizations of the samples were accompanied by the microstructure analyses of the bent strand to examine the bending induced degradation in the grain structure of the strand. All these experimental findings are expected to be used as input to fabricate prototype MgB 2 based magnet. (author)

  1. Structural insights into Rhino-Deadlock complex for germline piRNA cluster specification.

    Science.gov (United States)

    Yu, Bowen; Lin, Yu An; Parhad, Swapnil S; Jin, Zhaohui; Ma, Jinbiao; Theurkauf, William E; Zhang, Zz Zhao; Huang, Ying

    2018-06-01

    PIWI-interacting RNAs (piRNAs) silence transposons in germ cells to maintain genome stability and animal fertility. Rhino, a rapidly evolving heterochromatin protein 1 (HP1) family protein, binds Deadlock in a species-specific manner and so defines the piRNA-producing loci in the Drosophila genome. Here, we determine the crystal structures of Rhino-Deadlock complex in Drosophila melanogaster and simulans In both species, one Rhino binds the N-terminal helix-hairpin-helix motif of one Deadlock protein through a novel interface formed by the beta-sheet in the Rhino chromoshadow domain. Disrupting the interface leads to infertility and transposon hyperactivation in flies. Our structural and functional experiments indicate that electrostatic repulsion at the interaction interface causes cross-species incompatibility between the sibling species. By determining the molecular architecture of this piRNA-producing machinery, we discover a novel HP1-partner interacting mode that is crucial to piRNA biogenesis and transposon silencing. We thus explain the cross-species incompatibility of two sibling species at the molecular level. © 2018 The Authors.

  2. Crystal Structures of the Tetratricopeptide Repeat Domains of Kinesin Light Chains: Insight into Cargo Recognition Mechanisms

    Energy Technology Data Exchange (ETDEWEB)

    Zhu, Haizhong; Lee, Han Youl; Tong, Yufeng; Hong, Bum-Soo; Kim, Kyung-Phil; Shen, Yang; Lim, Kyung Jik; Mackenzie, Farrell; Tempel, Wolfram; Park, Hee-Won (SGC-Toronto); (PPCS); (Toronto)

    2012-10-23

    Kinesin-1 transports various cargos along the axon by interacting with the cargos through its light chain subunit. Kinesin light chains (KLC) utilize its tetratricopeptide repeat (TPR) domain to interact with over 10 different cargos. Despite a high sequence identity between their TPR domains (87%), KLC1 and KLC2 isoforms exhibit differential binding properties towards some cargos. We determined the structures of human KLC1 and KLC2 tetratricopeptide repeat (TPR) domains using X-ray crystallography and investigated the different mechanisms by which KLCs interact with their cargos. Using isothermal titration calorimetry, we attributed the specific interaction between KLC1 and JNK-interacting protein 1 (JIP1) cargo to residue N343 in the fourth TRP repeat. Structurally, the N343 residue is adjacent to other asparagines and lysines, creating a positively charged polar patch within the groove of the TPR domain. Whereas, KLC2 with the corresponding residue S328 did not interact with JIP1. Based on these finding, we propose that N343 of KLC1 can form 'a carboxylate clamp' with its neighboring asparagine to interact with JIP1, similar to that of HSP70/HSP90 organizing protein-1's (HOP1) interaction with heat shock proteins. For the binding of cargos shared by KLC1 and KLC2, we propose a different site located within the groove but not involving N343. We further propose a third binding site on KLC1 which involves a stretch of polar residues along the inter-TPR loops that may form a network of hydrogen bonds to JIP3 and JIP4. Together, these results provide structural insights into possible mechanisms of interaction between KLC TPR domains and various cargo proteins.

  3. Structures of foot and mouth disease virus pentamers: Insight into capsid dissociation and unexpected pentamer reassociation.

    Directory of Open Access Journals (Sweden)

    Nayab Malik

    2017-09-01

    Full Text Available Foot-and-mouth disease virus (FMDV belongs to the Aphthovirus genus of the Picornaviridae, a family of small, icosahedral, non-enveloped, single-stranded RNA viruses. It is a highly infectious pathogen and is one of the biggest hindrances to the international trade of animals and animal products. FMDV capsids (which are unstable below pH6.5 release their genome into the host cell from an acidic compartment, such as that of an endosome, and in the process dissociate into pentamers. Whilst other members of the family (enteroviruses have been visualized to form an expanded intermediate capsid with holes from which inner capsid proteins (VP4, N-termini (VP1 and RNA can be released, there has been no visualization of any such state for an aphthovirus, instead the capsid appears to simply dissociate into pentamers. Here we present the 8-Å resolution structure of isolated dissociated pentamers of FMDV, lacking VP4. We also found these pentamers to re-associate into a rigid, icosahedrally symmetric assembly, which enabled their structure to be solved at higher resolution (5.2 Å. In this assembly, the pentamers unexpectedly associate 'inside out', but still with their exposed hydrophobic edges buried. Stabilizing interactions occur between the HI loop of VP2 and its symmetry related partners at the icosahedral 3-fold axes, and between the BC and EF loops of VP3 with the VP2 βB-strand and the CD loop at the 2-fold axes. A relatively extensive but subtle structural rearrangement towards the periphery of the dissociated pentamer compared to that in the mature virus provides insight into the mechanism of dissociation of FMDV and the marked difference in antigenicity.

  4. Insights into finding a mismatch through the structure of a mispaired DNA bound by a rhodium intercalator

    Science.gov (United States)

    Pierre, Valérie C.; Kaiser, Jens T.; Barton, Jacqueline K.

    2007-01-01

    We report the 1.1-Å resolution crystal structure of a bulky rhodium complex bound to two different DNA sites, mismatched and matched in the oligonucleotide 5′-(dCGGAAATTCCCG)2-3′. At the AC mismatch site, the structure reveals ligand insertion from the minor groove with ejection of both mismatched bases and elucidates how destabilized mispairs in DNA may be recognized. This unique binding mode contrasts with major groove intercalation, observed at a matched site, where doubling of the base pair rise accommodates stacking of the intercalator. Mass spectral analysis reveals different photocleavage products associated with the two binding modes in the crystal, with only products characteristic of mismatch binding in solution. This structure, illustrating two clearly distinct binding modes for a molecule with DNA, provides a rationale for the interrogation and detection of mismatches. PMID:17194756

  5. The Coupling Structure Features Between (2,1) NTM and (1,1) Internal Mode in EAST Tokamak

    International Nuclear Information System (INIS)

    Shi Tonghui; Wan Baonian; Sun Youwen; Shen Biao; Qian Jinping; Hu Liqun; Chen Kaiyun; Liu Yong

    2015-01-01

    In the discharge of EAST tokamak, it is observed that (2,1) neoclassical tearing mode (NTM) is triggered by mode coupling with a (1,1) internal mode. Using singular value decomposition (SVD) method for soft X-ray emission and for electron cyclotron emission (ECE), the coupling spatial structures and coupling process between these two modes are analyzed in detail. The results of SVD for ECE reveal that the phase difference between these two modes equals to zero. This is consistent with the perfect coupling condition. Finally, performing statistical analysis of r 1/1 , ξ 1/1 and w 2/1 , we find that r 1/1 more accurately represents the coupling strength than ξ 1/1 , and r 1/1 is also strongly related to the (2,1) NTM triggering, where r 1/1 is the width of (1,1) internal mode, ξ 1/1 is the perturbed amplitude of (1,1) internal mode, and w 2/1 denot es the magnetic island width of (2,1) NTM. (paper)

  6. Structural Insights into Diversity and n-Alkane Biodegradation Mechanisms of Alkane Hydroxylases

    Directory of Open Access Journals (Sweden)

    Yurui eJi

    2013-03-01

    Full Text Available Environmental microbes utilize four degradation pathways for the oxidation of n-alkanes. Although the enzymes degrading n-alkanes in different microbes may vary, enzymes functioning in the first step in the aerobic degradation of alkanes all belong to the alkane hydroxylases. Alkane hydroxylases are a class of enzymes that insert oxygen atoms derived from molecular oxygen into different sites of the alkane terminus (or termini depending on the type of enzymes. In this review, we summarize the different types of alkane hydroxylases, their degrading steps and compare typical enzymes from various classes with regard to their three dimensional structures, in order to provide insights into how the enzymes mediate their different roles in the degradation of n-alkanes and what determines their different substrate ranges. Through the above analyses, the degrading mechanisms of enzymes can be elucidated and molecular biological methods can be utilized to expand their catalytic roles in the petrochemical industry or in bioremediation of oil-contaminated environments.

  7. Composition of the mitochondrial electron transport chain in acanthamoeba castellanii: structural and evolutionary insights.

    Science.gov (United States)

    Gawryluk, Ryan M R; Chisholm, Kenneth A; Pinto, Devanand M; Gray, Michael W

    2012-11-01

    The mitochondrion, derived in evolution from an α-proteobacterial progenitor, plays a key metabolic role in eukaryotes. Mitochondria house the electron transport chain (ETC) that couples oxidation of organic substrates and electron transfer to proton pumping and synthesis of ATP. The ETC comprises several multiprotein enzyme complexes, all of which have counterparts in bacteria. However, mitochondrial ETC assemblies from animals, plants and fungi are generally more complex than their bacterial counterparts, with a number of 'supernumerary' subunits appearing early in eukaryotic evolution. Little is known, however, about the ETC of unicellular eukaryotes (protists), which are key to understanding the evolution of mitochondria and the ETC. We present an analysis of the ETC proteome from Acanthamoeba castellanii, an ecologically, medically and evolutionarily important member of Amoebozoa (sister to Opisthokonta). Data obtained from tandem mass spectrometric (MS/MS) analyses of purified mitochondria as well as ETC complexes isolated via blue native polyacrylamide gel electrophoresis are combined with the results of bioinformatic queries of sequence databases. Our bioinformatic analyses have identified most of the ETC subunits found in other eukaryotes, confirming and extending previous observations. The assignment of proteins as ETC subunits by MS/MS provides important insights into the primary structures of ETC proteins and makes possible, through the use of sensitive profile-based similarity searches, the identification of novel constituents of the ETC along with the annotation of highly divergent but phylogenetically conserved ETC subunits. © 2012 Elsevier B.V. All rights reserved.

  8. The sights and insights of examiners in objective structured clinical examinations

    Directory of Open Access Journals (Sweden)

    Lauren Chong

    2017-12-01

    Full Text Available Purpose The objective structured clinical examination (OSCE is considered to be one of the most robust methods of clinical assessment. One of its strengths lies in its ability to minimise the effects of examiner bias due to the standardisation of items and tasks for each candidate. However, OSCE examiners’ assessment scores are influenced by several factors that may jeopardise the assumed objectivity of OSCEs. To better understand this phenomenon, the current review aims to determine and describe important sources of examiner bias and the factors affecting examiners’ assessments. Methods We performed a narrative review of the medical literature using Medline. All articles meeting the selection criteria were reviewed, with salient points extracted and synthesised into a clear and comprehensive summary of the knowledge in this area. Results OSCE examiners’ assessment scores are influenced by factors belonging to 4 different domains: examination context, examinee characteristics, examinee-examiner interactions, and examiner characteristics. These domains are composed of several factors including halo, hawk/dove and OSCE contrast effects; the examiner’s gender and ethnicity; training; lifetime experience in assessing; leadership and familiarity with students; station type; and site effects. Conclusion Several factors may influence the presumed objectivity of examiners’ assessments, and these factors need to be addressed to ensure the objectivity of OSCEs. We offer insights into directions for future research to better understand and address the phenomenon of examiner bias.

  9. Cyclotide Evolution: Insights from the Analyses of Their Precursor Sequences, Structures and Distribution in Violets (Viola

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    Sungkyu Park

    2017-12-01

    Full Text Available Cyclotides are a family of plant proteins that are characterized by a cyclic backbone and a knotted disulfide topology. Their cyclic cystine knot (CCK motif makes them exceptionally resistant to thermal, chemical, and enzymatic degradation. By disrupting cell membranes, the cyclotides function as host defense peptides by exhibiting insecticidal, anthelmintic, antifouling, and molluscicidal activities. In this work, we provide the first insight into the evolution of this family of plant proteins by studying the Violaceae, in particular species of the genus Viola. We discovered 157 novel precursor sequences by the transcriptomic analysis of six Viola species: V. albida var. takahashii, V. mandshurica, V. orientalis, V. verecunda, V. acuminata, and V. canadensis. By combining these precursor sequences with the phylogenetic classification of Viola, we infer the distribution of cyclotides across 63% of the species in the genus (i.e., ~380 species. Using full precursor sequences from transcriptomes, we show an evolutionary link to the structural diversity of the cyclotides, and further classify the cyclotides by sequence signatures from the non-cyclotide domain. Also, transcriptomes were compared to cyclotide expression on a peptide level determined using liquid chromatography-mass spectrometry. Furthermore, the novel cyclotides discovered were associated with the emergence of new biological functions.

  10. Structural, mechanistic and functional insight into gliotoxin bis-thiomethylation in Aspergillus fumigatus.

    Science.gov (United States)

    Dolan, Stephen K; Bock, Tobias; Hering, Vanessa; Owens, Rebecca A; Jones, Gary W; Blankenfeldt, Wulf; Doyle, Sean

    2017-02-01

    Gliotoxin is an epipolythiodioxopiperazine (ETP) class toxin, contains a disulfide bridge that mediates its toxic effects via redox cycling and is produced by the opportunistic fungal pathogen Aspergillus fumigatus Self-resistance against gliotoxin is effected by the gliotoxin oxidase GliT, and attenuation of gliotoxin biosynthesis is catalysed by gliotoxin S -methyltransferase GtmA. Here we describe the X-ray crystal structures of GtmA-apo (1.66 Å), GtmA complexed to S -adenosylhomocysteine (1.33 Å) and GtmA complexed to S -adenosylmethionine (2.28 Å), providing mechanistic insights into this important biotransformation. We further reveal that simultaneous elimination of the ability of A. fumigatus to dissipate highly reactive dithiol gliotoxin, via deletion of GliT and GtmA, results in the most significant hypersensitivity to exogenous gliotoxin observed to date. Indeed, quantitative proteomic analysis of Δ gliT ::Δ gtmA reveals an uncontrolled over-activation of the gli -cluster upon gliotoxin exposure. The data presented herein reveal, for the first time, the extreme risk associated with intracellular dithiol gliotoxin biosynthesis-in the absence of an efficient dismutation capacity. Significantly, a previously concealed protective role for GtmA and functionality of ETP bis -thiomethylation as an ancestral protection strategy against dithiol compounds is now evident. © 2017 The Authors.

  11. NMR structure of temporin-1 ta in lipopolysaccharide micelles: mechanistic insight into inactivation by outer membrane.

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    Rathi Saravanan

    Full Text Available BACKGROUND: Antimicrobial peptides (AMPs play important roles in the innate defense mechanism. The broad spectrum of activity of AMPs requires an efficient permeabilization of the bacterial outer and inner membranes. The outer leaflet of the outer membrane of Gram negative bacteria is made of a specialized lipid called lipopolysaccharide (LPS. The LPS layer is an efficient permeability barrier against anti-bacterial agents including AMPs. As a mode of protection, LPS can induce self associations of AMPs rendering them inactive. Temporins are a group of short-sized AMPs isolated from frog skin, and many of them are inactive against Gram negative bacteria as a result of their self-association in the LPS-outer membrane. PRINCIPAL FINDINGS: Using NMR spectroscopy, we have determined atomic resolution structure and characterized localization of temporin-1Ta or TA (FLPLIGRVLSGIL-amide in LPS micelles. In LPS micelles, TA adopts helical conformation for residues L4-I12, while residues F1-L3 are found to be in extended conformations. The aromatic sidechain of residue F1 is involved in extensive packing interactions with the sidechains of residues P3, L4 and I5. Interestingly, a number of long-range NOE contacts have been detected between the N-terminal residues F1, P3 with the C-terminal residues S10, I12, L13 of TA in LPS micelles. Saturation transfer difference (STD NMR studies demonstrate close proximity of residues including F1, L2, P3, R7, S10 and L13 with the LPS micelles. Notably, the LPS bound structure of TA shows differences with the structures of TA determined in DPC and SDS detergent micelles. SIGNIFICANCE: We propose that TA, in LPS lipids, forms helical oligomeric structures employing N- and C-termini residues. Such oligomeric structures may not be translocated across the outer membrane; resulting in the inactivation of the AMP. Importantly, the results of our studies will be useful for the development of antimicrobial agents with a

  12. Insights on Forest Structure and Composition from Long-Term Research in the Luquillo Mountains

    Directory of Open Access Journals (Sweden)

    Tamara Heartsill Scalley

    2017-06-01

    Full Text Available The science of ecology fundamentally aims to understand species and their relation to the environment. At sites where hurricane disturbance is part of the environmental context, permanent forest plots are critical to understand ecological vegetation dynamics through time. An overview of forest structure and species composition from two of the longest continuously measured tropical forest plots is presented. Long-term measurements, 72 years at the leeward site, and 25 years at windward site, of stem density are similar to initial and pre-hurricane values at both sites. For 10 years post-hurricane Hugo (1989, stem density increased at both sites. Following that increase period, stem density has remained at 1400 to 1600 stems/ha in the leeward site, and at 1200 stems/ha in the windward site. The forests had similar basal area values before hurricane Hugo in 1989, but these sites are following different patterns of basal area accumulation. The leeward forest site continues to accumulate and increase basal area with each successive measurement, currently above 50 m2/ha. The windward forest site maintains its basal area values close to an asymptote of 35 m2/ha. Currently, the most abundant species at both sites is the sierra palm. Ordinations to explore variation in tree species composition through time present the leeward site with a trajectory of directional change, while at the windward site, the composition of species seems to be converging to pre-hurricane conditions. The observed differences in forest structure and composition from sites differently affected by hurricane disturbance provide insight into how particular forest characteristics respond at shorter or longer time scales in relation to previous site conditions and intensity of disturbance effects.

  13. Structural and dynamical insights into the membrane-bound α-synuclein.

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    Neha Jain

    Full Text Available Membrane-induced disorder-to-helix transition of α-synuclein, a presynaptic protein, has been implicated in a number of important neuronal functions as well as in the etiology of Parkinson's disease. In order to obtain structural insights of membrane-bound α-synuclein at the residue-specific resolution, we took advantage of the fact that the protein is devoid of tryptophan and incorporated single tryptophan at various residue positions along the sequence. These tryptophans were used as site-specific markers to characterize the structural and dynamical aspects of α-synuclein on the negatively charged small unilamellar lipid vesicles. An array of site-specific fluorescence readouts, such as the spectral-shift, quenching efficiency and anisotropy, allowed us to discern various features of the conformational rearrangements occurring at different locations of α-synuclein on the lipid membrane. In order to define the spatial localization of various regions of the protein near the membrane surface, we utilized a unique and sensitive indicator, namely, red-edge excitation shift (REES, which originates when a fluorophore is located in a highly ordered micro-environment. The extent of REES observed at different residue positions allowed us to directly identify the residues that are localized at the membrane-water interface comprising a thin (∼ 15 Å layer of motionally restrained water molecules and enabled us to construct a dynamic hydration map of the protein. The combination of site-specific fluorescence readouts allowed us to unravel the intriguing molecular details of α-synuclein on the lipid membrane in a direct model-free fashion. Additionally, the combination of methodologies described here are capable of distinguishing subtle but important structural alterations of α-synuclein bound to different negatively charged lipids with varied head-group chemistry. We believe that the structural modulations of α-synuclein on the membrane could

  14. Sorption of structurally different ionized pharmaceutical and illicit drugs to a mixed-mode coated microsampler.

    Science.gov (United States)

    Peltenburg, Hester; Timmer, Niels; Bosman, Ingrid J; Hermens, Joop L M; Droge, Steven T J

    2016-05-20

    The mixed-mode (C18/strong cation exchange-SCX) solid-phase microextraction (SPME) fiber has recently been shown to have increased sensitivity for ionic compounds compared to more conventional sampler coatings such as polyacrylate and polydimethylsiloxane (PDMS). However, data for structurally diverse compounds to this (prototype) sampler coating are too limited to define its structural limitations. We determined C18/SCX fiber partitioning coefficients of nineteen cationic structures without hydrogen bonding capacity besides the charged group, stretching over a wide hydrophobicity range (including amphetamine, amitriptyline, promazine, chlorpromazine, triflupromazine, difenzoquat), and eight basic pharmaceutical and illicit drugs (pKa>8.86) with additional hydrogen bonding moieties (MDMA, atenolol, alprenolol, metoprolol, morphine, nicotine, tramadol, verapamil). In addition, sorption data for three neutral benzodiazepines (diazepam, temazepam, and oxazepam) and the anionic NSAID diclofenac were collected to determine the efficiency to sample non-basic drugs. All tested compounds showed nonlinear isotherms above 1mmol/L coating, and linear isotherms below 1mmol/L. The affinity for C18/SCX-SPME for tested organic cations without Hbond capacities increased with longer alkyl chains, ranging from logarithmic fiber-water distribution coefficients (log Dfw) of 1.8 (benzylamine) to 5.8 (triflupromazine). Amines smaller than benzylamine may thus have limited detection levels, while cationic surfactants with alkyl chain lengths >12 carbon atoms may sorb too strong to the C18/SCX sampler which hampers calibration of the fiber-water relationship in the linear range. The log Dfw for these simple cation structures closely correlates with the octanol-water partition coefficient of the neutral form (Kow,N), and decreases with increased branching and presence of multiple aromatic rings. Oxygen moieties in organic cations decreased the affinity for C18/SCX-SPME. Log Dfw values of

  15. Structural improvement of unliganded simian immunodeficiency virus gp120 core by normal-mode-based X-ray crystallographic refinement

    International Nuclear Information System (INIS)

    Chen, Xiaorui; Lu, Mingyang; Poon, Billy K.; Wang, Qinghua; Ma, Jianpeng

    2009-01-01

    The structural model of the unliganded and fully glycosylated simian immunodeficiency virus gp120 core determined to 4.0 Å resolution was substantially improved using a recently developed normal-mode-based anisotropic B-factor refinement method. The envelope protein gp120/gp41 of simian and human immunodeficiency viruses plays a critical role in viral entry into host cells. However, the extraordinarily high structural flexibility and heavy glycosylation of the protein have presented enormous difficulties in the pursuit of high-resolution structural investigation of some of its conformational states. An unliganded and fully glycosylated gp120 core structure was recently determined to 4.0 Å resolution. The rather low data-to-parameter ratio limited refinement efforts in the original structure determination. In this work, refinement of this gp120 core structure was carried out using a normal-mode-based refinement method that has been shown in previous studies to be effective in improving models of a supramolecular complex at 3.42 Å resolution and of a membrane protein at 3.2 Å resolution. By using only the first four nonzero lowest-frequency normal modes to construct the anisotropic thermal parameters, combined with manual adjustments and standard positional refinement using REFMAC5, the structural model of the gp120 core was significantly improved in many aspects, including substantial decreases in R factors, better fitting of several flexible regions in electron-density maps, the addition of five new sugar rings at four glycan chains and an excellent correlation of the B-factor distribution with known structural flexibility. These results further underscore the effectiveness of this normal-mode-based method in improving models of protein and nonprotein components in low-resolution X-ray structures

  16. Tamm-plasmon and surface-plasmon hybrid-mode based refractometry in photonic bandgap structures.

    Science.gov (United States)

    Das, Ritwick; Srivastava, Triranjita; Jha, Rajan

    2014-02-15

    The transverse magnetic (TM) polarized hybrid modes formed as a consequence of coupling between Tamm plasmon polariton (TM-TPP) mode and surface plasmon polariton (SPP) mode exhibit interesting dispersive features for realizing a highly sensitive and accurate surface plasmon resonance (SPR) sensor. We found that the TM-TPP modes, formed at the interface of distributed Bragg reflector and metal, are strongly dispersive as compared to SPP modes at optical frequencies. This causes an appreciably narrow interaction bandwidth between TM-TPP and SPP modes, which leads to highly accurate sensing. In addition, appropriate tailoring of dispersion characteristics of TM-TPP as well as SPP modes could ensure high sensitivity of a novel SPR platform. By suitably designing the Au/TiO₂/SiO₂-based geometry, we propose a TM-TPP/SPP hybrid-mode sensor and achieve a sensitivity ≥900  nm/RIU with high detection accuracy (≥30  μm⁻¹) for analyte refractive indices varying between 1.330 and 1.345 in 600-700 nm wavelength range. The possibility to achieve desired dispersive behavior in any spectral band makes the sensing configuration an extremely attractive candidate to design sensors depending on the availability of optical sources.

  17. Fatigue Debond Growth in Sandwich Structures Loaded in Mixed Mode Bending (MMB)

    DEFF Research Database (Denmark)

    Quispitupa, Amilcar; Berggreen, Christian; Carlsson, Leif A.

    2008-01-01

    Static and cyclic debond growth in sandwich specimens loaded in mixed mode bending (MMB) is examined. The MMB sandwich specimens were manufactured using H100 PVC foam core and E-glass/polyester non-crimp quadro-axial [0/45/90/-45]s DBLT-850 face sheets. Static test were performed to determine...... the fracture toughness of the debonded sandwich specimens at different mixed mode loadings. The mixed mode ratio (mode I to mode II) was controlled by changing the lever arm distance of the MMB test rig. Compliance technique and visual inspection was employed to measure the crack length during fatigue. Fatigue...... tests were performed at 90% of the static fracture toughness at a loading ratio of R=0.1. Fatigue results revealed higher debond crack growth rates when the lever arm distance was increased. For some specimens, the crack propagated just below the face/core interface in the foam core and for others...

  18. Insights into the Structure of the Vip3Aa Insecticidal Protein by Protease Digestion Analysis

    Directory of Open Access Journals (Sweden)

    Yolanda Bel

    2017-04-01

    Full Text Available Vip3 proteins are secretable proteins from Bacillus thuringiensis whose mode of action is still poorly understood. In this study, the activation process for Vip3 proteins was closely examined in order to better understand the Vip3Aa protein stability and to shed light on its structure. The Vip3Aa protoxin (of 89 kDa was treated with trypsin at concentrations from 1:100 to 120:100 (trypsin:Vip3A, w:w. If the action of trypsin was not properly neutralized, the results of SDS-PAGE analysis (as well as those with Agrotis ipsilon midgut juice equivocally indicated that the protoxin could be completely processed. However, when the proteolytic reaction was efficiently stopped, it was revealed that the protoxin was only cleaved at a primary cleavage site, regardless of the amount of trypsin used. The 66 kDa and the 19 kDa peptides generated by the proteases co-eluted after gel filtration chromatography, indicating that they remain together after cleavage. The 66 kDa fragment was found to be extremely resistant to proteases. The trypsin treatment of the protoxin in the presence of SDS revealed the presence of secondary cleavage sites at S-509, and presumably at T-466 and V-372, rendering C-terminal fragments of approximately 29, 32, and 42 kDa, respectively. The fact that the predicted secondary structure of the Vip3Aa protein shows a cluster of beta sheets in the C-terminal region of the protein might be the reason behind the higher stability to proteases compared to the rest of the protein, which is mainly composed of alpha helices.

  19. Gain analysis of higher-order-mode amplification in a dielectric-implanted multi-beam traveling wave structure

    Energy Technology Data Exchange (ETDEWEB)

    Gee, Anthony; Shin, Young-Min

    2013-01-01

    A multi-beam traveling wave amplifier designed with an overmoded staggered double grating array was examined by small signal analysis combined with simulation. Eigenmode and S-parameter analyses show that the 2cm long slow wave structure (SWS) has 1-5dB insertion loss over the passband (TM31 mode) with ~28% cold bandwidth. Analytic gain calculation indicates that in the SWS, TM31-mode is amplified with 15–20 dB/beam at 64–84GHz with three elliptical beams of 10kV and 150mA/beam, which was compared with particle-in-cell (PIC) simulations. PIC analysis on the analysis of instability with zero-input driving excitations demonstrated that background noises and non-operating lower order modes are noticeably suppressed by implanting equidistant dielectric absorbers; the overmoded structure only allowed the desired 3rd order mode to propagate in the structure. The designed circuit structure can be widely applied to multi-beam devices for high power RF generation.

  20. Gain analysis of higher-order-mode amplification in a dielectric-implanted multi-beam traveling wave structure

    International Nuclear Information System (INIS)

    Gee, Anthony; Shin, Young-Min

    2013-01-01

    A multi-beam traveling wave amplifier designed with an overmoded staggered double grating array was examined by small signal analysis combined with simulation. Eigenmode and S-parameter analyses show that the 2 cm long slow wave structure (SWS) has 1–5 dB insertion loss over the passband (TM 31 mode) with ∼28% cold bandwidth. Analytic gain calculation indicates that in the SWS, TM 31 -mode is amplified with 15–20 dB/beam at 64–84 GHz with three elliptical beams of 10 kV and 150 mA/beam, which was compared with particle-in-cell (PIC) simulations. PIC analysis on the analysis of instability with zero-input driving excitations demonstrated that background noises and non-operating lower order modes are noticeably suppressed by implanting equidistant dielectric absorbers; the overmoded structure only allowed the desired 3rd order mode to propagate in the structure. The designed circuit structure can be widely applied to multi-beam devices for high power RF generation

  1. Amplified emission and modified spectral features in an opal hetero-structure mediated by passive defect mode localization

    Science.gov (United States)

    Rout, Dipak; Kumar, Govind; Vijaya, R.

    2018-01-01

    A photonic crystal hetero-structure consisting of a passive planar defect of SiO2 thin film sandwiched between two identical opals grown by inward growing self-assembly method using Rhodamine-B dye-doped polystyrene microspheres is studied for the characteristics of dye emission. The optical properties and the defect mode characteristics of the hetero-structure are studied from the reflection and transmission measurements. Laser-induced fluorescence from the hetero-structure showed amplified and spectrally narrowed emission compared to the photonic crystal emphasizing the role of the defect mode and distributed feedback. The enhanced emission is also complemented by the reduction in fluorescence decay time in the case of the hetero-structure in comparison to the 3D photonic crystals.

  2. Optimal design for crosstalk analysis in 12-core 5-LP mode homogeneous multicore fiber for different lattice structure

    Science.gov (United States)

    Kumar, Dablu; Ranjan, Rakesh

    2018-03-01

    12-Core 5-LP mode homogeneous multicore fibers have been proposed for analysis of inter-core crosstalk and dispersion, with four different lattice structures (circular, 2-ring, square lattice, and triangular lattice) having cladding diameter of 200 μm and a fixed cladding thickness of 35 μm. The core-to-core crosstalk impact has been studied numerically with respect to bending radius, core pitch, transmission distance, wavelength, and core diameter for all 5-LP modes. In anticipation of further reduction in crosstalk levels, the trench-assisted cores have been incorporated for all respective designs. Ultra-low crosstalk (-138 dB/100 km) has been achieved through the triangular lattice arrangement, with trench depth Δ2 = -1.40% for fundamental (LP01) mode. It has been noted that the impact of mode polarization on crosstalk behavior is minor, with difference in crosstalk levels between two polarized spatial modes as ≤0.2 dB. Moreover, the optimized cladding diameter has been obtained for all 5-LP modes for a target value of crosstalk of -50 dB/100 km, with all the core arrangements. The dispersion characteristic has also been analyzed with respect to wavelength, which is nearly 2.5 ps/nm km at operating wavelength 1550 nm. The relative core multiplicity factor (RCMF) for the proposed design is obtained as 64.

  3. Single-crystal structure determination of hydrous minerals and insights into a wet deep lower mantle

    Science.gov (United States)

    Zhang, L.; Yuan, H.; Meng, Y.; Popov, D.

    2017-12-01

    Water enters the Earth's interior through hydrated subducting slabs. How deep within the lower mantle (670-2900 km depth) can water be transported down and stored depends upon the availability of hydrous phases that is thermodynamically stable under the high P-T conditions and have a sufficiently high density to sink through the lower mantle. Phase H [MgSiH2O4] (1) and the δ-AlOOH (2) form solid solutions that are stable in the deep lower mantle (3), but the solid solution phase is 10% lighter than the corresponding lower mantle. Recent experimental discoveries of the pyrite (Py) structured FeO2 and FeOOH (4-6) suggest that these Fe-enriched phases can be transported to the deepest lower mantle owing to their high density. We have further discovered a very dense hydrous phase in (Fe,Al)OOH with a previously unknown hexagonal symmetry and this phase is stable relative to the Py-phase under extreme high P-T conditions in the deep lower mantle. Through in situ multigrain analysis (7) and single-crystal structure determination of the hydrous minerals at P-Tconditions of the deep lower mantle, we can obtain detailed structure information of the hydrous phases and therefore provide insights into the hydration mechanism in the deep lower mantle. These highly stable hydrous minerals extend the water cycle at least to the depth of 2900 km. 1. M. Nishi et al., Nature Geoscience 7, 224-227 (2014). 2. E. Ohtani, K. Litasov, A. Suzuki, T. Kondo, Geophysical Research Letters 28, 3991-3993 (2001). 3. I. Ohira et al., Earth and Planetary Science Letters 401, 12-17 (2014). 4. Q. Hu et al., Proceedings of the National Academy of Sciences of the United States of America 114, 1498-1501 (2017). 5. M. Nishi, Y. Kuwayama, J. Tsuchiya, T. Tsuchiya, Nature 547, 205-208 (2017). 6. Q. Hu et al., Nature 534, 241-244 (2016). 7. L. Zhang et al., American Mineralogist 101, 231-234 (2016).

  4. Heteroleptic Copper(I) Complexes of "Scorpionate" Bis-pyrazolyl Carboxylate Ligand with Auxiliary Phosphine as Potential Anticancer Agents: An Insight into Cytotoxic Mode.

    Science.gov (United States)

    Khan, Rais Ahmad; Usman, Mohammad; Dhivya, Rajakumar; Balaji, Perumalsamy; Alsalme, Ali; AlLohedan, Hamad; Arjmand, Farukh; AlFarhan, Khalid; Akbarsha, Mohammad Abdulkader; Marchetti, Fabio; Pettinari, Claudio; Tabassum, Sartaj

    2017-03-24

    New copper(I) complexes [CuCl(PPh 3 )(L)] (1: L = L A  = 4-carboxyphenyl)bis(3,5-dimethylpyrazolyl)methane; (2: L = L B  = 3-carboxyphenyl)bis(3,5-dimethylpyrazolyl)methane) were prepared and characterised by elemental analysis and various spectroscopic techniques such as FT-IR, NMR, UV-Vis, and ESI-MS. The molecular structures of complexes 1 and 2 were analyzed by theoretical B3LYP/DFT method. Furthermore, in vitro DNA binding studies were carried out to check the ability of complexes 1 and 2 to interact with native calf thymus DNA (CT-DNA) using absorption titration, fluorescence quenching and circular dichroism, which is indicative of more avid binding of the complex 1. Moreover, DNA mobility assay was also conducted to study the concentration-dependent cleavage pattern of pBR322 DNA by complex 1, and the role of ROS species to have a mechanistic insight on the cleavage pattern, which ascertained substantial roles by both hydrolytic and oxidative pathways. Additionally, we analyzed the potential of the interaction of complex 1 with DNA and enzyme (Topo I and II) with the aid of molecular modeling. Furthermore, cytotoxic activity of complex 1 was tested against HepG2 cancer cell lines. Thus, the potential of the complex 1 is promising though further in vivo investigations may be required before subjecting it to clinical trials.

  5. B-GATA transcription factors - insights into their structure, regulation and role in plant development

    Directory of Open Access Journals (Sweden)

    Claus eSchwechheimer

    2015-02-01

    Full Text Available GATA transcription factors are evolutionarily conserved transcriptional regulators that recognize promoter elements with a G-A-T-A core sequence. In comparison to animal genomes, the GATA transcription factor family in plants is comparatively large with approximately 30 members. In spite of a long-standing interest of plant molecular biologists in GATA factors, only research conducted in the last years has led to reliable insights into their functions during plant development. Here, we review the current knowledge on B-GATAs, one of four GATA factor subfamilies from Arabidopsis thaliana. We show that B-GATAs can be subdivided based on structural features and their biological function into family members with a C-terminal LLM- (leucine-leucine-methionine domain or an N-terminal HAN- (HANABA TARANU domain. The paralogous GNC (GATA, NITRATE-INDUCIBLE, CARBON-METABOLISM INVOLVED and CGA1/GNL (CYTOKININ-INDUCED GATA1/GNC-LIKE are introduced as LLM-domain containing B-GATAs from Arabidopsis that control germination, greening, senescence and flowering time downstream from several growth regulatory signals including light and the hormones gibberellin, auxin, and cytokinin. Arabidopsis HAN and its monocot-specific paralogs from rice (NECK LEAF1, maize (TASSEL SHEATH1, and barley (THIRD OUTER GLUME are HAN-domain-containing B-GATAs with a predominant role in embryo development and floral development. We also review GATA23, a regulator of lateral root initiation from Arabidopsis, that is closely related to GNC and GNL but has a degenerate LLM-domain that is seemingly specific for the Brassicaceae family. The Brassicaceae-specific GATA23 together with the above-mentioned monocot-specific HAN-domain GATAs provide evidence that neofunctionalization of the B-GATAs was used during plant evolution to expand the functional repertoire of these transcription factors.

  6. CYANOMETHANIMINE ISOMERS IN COLD INTERSTELLAR CLOUDS: INSIGHTS FROM ELECTRONIC STRUCTURE AND KINETIC CALCULATIONS

    Energy Technology Data Exchange (ETDEWEB)

    Vazart, Fanny; Latouche, Camille; Skouteris, Dimitrios; Barone, Vincenzo [Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56125 Pisa (Italy); Balucani, Nadia [Dipartimento di Chimica, Biologia e Biotecnologie, Universitá degli Studi di Perugia, Via Elce di Sotto 8, I-06123 Perugia (Italy)

    2015-09-10

    New insights into the formation of interstellar cyanomethanimine, a species of great relevance in prebiotic chemistry, are provided by electronic structure and kinetic calculations for the reaction CN + CH{sub 2} = NH. This reaction is a facile formation route of Z,E-C-cyanomethanimine, even under the extreme conditions of density and temperature typical of cold interstellar clouds. E-C-cyanomethanimine has been recently identified in Sgr B2(N) in the Green Bank Telescope (GBT) PRIMOS survey by P. Zaleski et al. and no efficient formation routes have been envisaged so far. The rate coefficient expression for the reaction channel leading to the observed isomer E-C-cyanomethanimine is 3.15 × 10-10 × (T/300){sup 0.152} × e{sup (−0.0948/T)}. According to the present study, the more stable Z-C-cyanomethanimine isomer is formed with a slightly larger yield (4.59 × 10{sup −10} × (T/300){sup 0.153} × e{sup (−0.0871/T)}. As the detection of E-isomer is favored due to its larger dipole moment, the missing detection of the Z-isomer can be due to the sensitivity limit of the GBT PRIMOS survey and the detection of the Z-isomer should be attempted with more sensitive instrumentation. The CN + CH{sub 2} = NH reaction can also play a role in the chemistry of the upper atmosphere of Titan where the cyanomethanimine products can contribute to the buildup of the observed nitrogen-rich organic aerosols that cover the moon.

  7. Structural insights into mechanisms for inhibiting amyloid β42 aggregation by non-catechol-type flavonoids.

    Science.gov (United States)

    Hanaki, Mizuho; Murakami, Kazuma; Akagi, Ken-ichi; Irie, Kazuhiro

    2016-01-15

    The prevention of 42-mer amyloid β-protein (Aβ42) aggregation is promising for the treatment of Alzheimer's disease. We previously described the site-specific inhibitory mechanism for Aβ42 aggregation by a catechol-type flavonoid, (+)-taxifolin, targeting Lys16,28 after its autoxidation. In contrast, non-catechol-type flavonoids (morin, datiscetin, and kaempferol) inhibited Aβ42 aggregation without targeting Lys16,28 with almost similar potencies to that of (+)-taxifolin. We herein provided structural insights into their mechanisms for inhibiting Aβ42 aggregation. Physicochemical analyses revealed that their inhibition did not require autoxidation. The (1)H-(15)N SOFAST-HMQC NMR of Aβ42 in the presence of morin and datiscetin revealed the significant perturbation of chemical shifts of His13,14 and Gln15, which were close to the intermolecular β-sheet region, Gln15-Ala21. His13,14 also played a role in radical formation at Tyr10, thereby inducing the oxidation of Met35, which has been implicated in Aβ42 aggregation. These results suggest the direct interaction of morin and datiscetin with the Aβ42 monomer. Although only kaempferol was oxidatively-degraded during incubation, its degradation products as well as kaempferol itself suppressed Aβ42 aggregation. However, neither kaempferol nor its decomposed products perturbed the chemical shifts of the Aβ42 monomer. Aggregation experiments using 1,1,1,3,3,3-hexafluoro-2-propanol-treated Aβ42 demonstrated that kaempferol and its degradation products inhibited the elongation rather than nucleation phase, implying that they interacted with small aggregates of Aβ42, but not with the monomer. In contrast, morin and datiscetin inhibited both phases. The position and number of hydroxyl groups on the B-ring of non-catechol-type flavonoids could be important for their inhibitory potencies and mechanisms against Aβ42 aggregation. Copyright © 2015 Elsevier Ltd. All rights reserved.

  8. 3D-structured illumination microscopy provides novel insight into architecture of human centrosomes

    Directory of Open Access Journals (Sweden)

    Katharina F. Sonnen

    2012-08-01

    Centrioles are essential for the formation of cilia and flagella. They also form the core of the centrosome, which organizes microtubule arrays important for cell shape, polarity, motility and division. Here, we have used super-resolution 3D-structured illumination microscopy to analyse the spatial relationship of 18 centriole and pericentriolar matrix (PCM components of human centrosomes at different cell cycle stages. During mitosis, PCM proteins formed extended networks with interspersed γ-Tubulin. During interphase, most proteins were arranged at specific distances from the walls of centrioles, resulting in ring staining, often with discernible density masses. Through use of site-specific antibodies, we found the C-terminus of Cep152 to be closer to centrioles than the N-terminus, illustrating the power of 3D-SIM to study protein disposition. Appendage proteins showed rings with multiple density masses, and the number of these masses was strongly reduced during mitosis. At the proximal end of centrioles, Sas-6 formed a dot at the site of daughter centriole assembly, consistent with its role in cartwheel formation. Plk4 and STIL co-localized with Sas-6, but Cep135 was associated mostly with mother centrioles. Remarkably, Plk4 formed a dot on the surface of the mother centriole before Sas-6 staining became detectable, indicating that Plk4 constitutes an early marker for the site of nascent centriole formation. Our study provides novel insights into the architecture of human centrosomes and illustrates the power of super-resolution microscopy in revealing the relative localization of centriole and PCM proteins in unprecedented detail.

  9. The Nucleus 59Cu. Complex Structure, Shape Evolution, Exotic Decay Modes

    International Nuclear Information System (INIS)

    Andreoiu, Corina

    2002-08-01

    High-spin states in the mass A∼60 region were populated using the state-of-art γ-ray spectrometers Gammasphere, Euroball, and GASP in conjunction with dedicated ancillary detectors. In particular, the 59 Cu nucleus was studied in several experiments, and a very extensive level scheme was determined. It comprises more than 320 transitions connecting about 150 excited states. Relative to mass, it is the most extensive level scheme known to date. Next to the spherical states at low excitation energy eight regular sequences of high-energy γ-ray transitions have been observed. They form rotational bands with various degree of deformation, which are interpreted in the light of the shell model and the configuration-dependent Cranked Nilsson-Strutinsky approach. One of the experiments was dedicated to the study of prompt particle decays. It revealed five prompt proton decays connecting five deformed states in three of the rotational bands in 59 Cu with three spherical states in the daughter nucleus 58 Ni. It is the first observation of the fine structure of the newly discovered prompt proton decay mode. The proton decays compete with the γ decay-out from the second minimum of the nuclear potential into the low-spin spherical states in the first minimum of the potential. The discrete γ decay-out mechanism of the yrast superdeformed band is investigated in detail. The nucleus 59 Zn, the mirror partner of 59 Cu, was identified for the first time, and the mirror symmetry of the T=1/2 A=59 pair is discussed

  10. Optical-cell model based on the lasing competition of mode structures with different Q-factors in high-power semiconductor lasers

    Energy Technology Data Exchange (ETDEWEB)

    Podoskin, A. A., E-mail: podoskin@mail.ioffe.ru; Shashkin, I. S.; Slipchenko, S. O.; Pikhtin, N. A.; Tarasov, I. S. [Russian Academy of Sciences, Ioffe Institute (Russian Federation)

    2015-08-15

    A model describing the operation of a completely optical cell, based on the competition of lasing of Fabry-Perot cavity modes and the high-Q closed mode in high-power semiconductor lasers is proposed. Based on rate equations, the conditions of lasing switching between Fabry-Perot modes for ground and excited lasing levels and the closed mode are considered in the case of increasing internal optical loss under conditions of high current pump levels. The optical-cell operation conditions in the mode of a high-power laser radiation switch (reversible mode-structure switching) and in the mode of a memory cell with bistable irreversible lasing switching between mode structures with various Q-factors are considered.

  11. Design and prototyping of self-centering optical single-mode fiber alignment structures

    International Nuclear Information System (INIS)

    Ebraert, Evert; Gao, Fei; Thienpont, Hugo; Van Erps, Jürgen; Beri, Stefano; Watté, Jan

    2016-01-01

    The European Commission’s goal of providing each European household with at least a 30 Mb s −1 Internet connection by 2020 would be facilitated by a widespread deployment of fibre-to-the-home, which would in turn be sped up by the development of connector essential components, such as high-precision alignment features. Currently, the performance of state-of-the-art physical contact optical fiber connectors is limited by the tolerance on the cladding of standard telecom-grade single-mode fiber (SMF), which is typically smaller than  ±1 μ m. We propose to overcome this limit by developing micro-spring-based self-centering alignment structures (SCAS) for SMF-connectors. We design these alignment structures with robustness and low-cost replication in mind, allowing for large-scale deployment. Both theoretical and finite element analysis (FEA) models are used to determine the optimal dimensions of the beams of which the micro-springs of the SCAS are comprised. Two topologies of the SCAS, consisting of three and four micro-springs respectively, are investigated for two materials: polysulfone (PSU) and polyetherimide (PEI). These materials hold great potential for high-performance fiber connectors while being compatible with low-cost production and with the harsh environmental operation conditions of those connectors. The theory and FEA agree well (<3% difference) for a simple micro-spring. When including a pedestal on the micro-spring (to bring it further away from the fiber) and for shorter spring lengths the agreement worsens. This is due to spring compression effects not being taken into account in our theoretical model. Prototypes are successfully fabricated using deep proton writing and subsequently characterized. The controlled insertion of an SMF in the SCAS is investigated and we determine that a force of 0.11 N is required. The fiber insertion also causes an out-of-plane deformation of the micro-springs in the SCAS of about 7 μ m, which is no

  12. Seismic analysis of structures of nuclear power plants by Lanczos mode superposition method

    International Nuclear Information System (INIS)

    Coutinho, A.L.G.A.; Alves, J.L.D.; Landau, L.; Lima, E.C.P. de; Ebecken, N.F.F.

    1986-01-01

    The Lanczos Mode Superposition Method is applied in the seismic analysis of nuclear power plants. The coordinate transformation matrix is generated by the Lanczos algorithm. It is shown that, through a convenient choice of the starting vector of the algorithm, modes with participation factors are automatically selected. It is performed the Response Spectra analysis of a typical reactor building. The obtained results are compared with those determined by the classical aproach stressing the remarkable computer effectiveness of the proposed methodology. (Author) [pt

  13. Edge transport and mode structure of a QCM-like fluctuation driven by the Shoelace antenna

    Science.gov (United States)

    Golfinopoulos, T.; LaBombard, B.; Brunner, D.; Terry, J. L.; Baek, S. G.; Ennever, P.; Edlund, E.; Han, W.; Burke, W. M.; Wolfe, S. M.; Irby, J. H.; Hughes, J. W.; Fitzgerald, E. W.; Granetz, R. S.; Greenwald, M. J.; Leccacorvi, R.; Marmar, E. S.; Pierson, S. Z.; Porkolab, M.; Vieira, R. F.; Wukitch, S. J.; The Alcator C-Mod Team

    2018-05-01

    The Shoelace antenna was built to drive edge fluctuations in the Alcator C-Mod tokamak, matching the wavenumber (k\\perp≈1.5 cm‑1) and frequency (30≲ f ≲ 200 kHz) of the quasi-coherent mode (QCM), which is responsible for regulating transport across the plasma boundary in the steady-state, ELM-free Enhanced D α (EDA) H-mode. Initial experiments in 2012 demonstrated that the antenna drove a resonant response in the edge plasma in steady-state EDA and transient, non-ELMy H-modes, but transport measurements were unavailable. In 2016, the Shoelace antenna was relocated to enable direct measurements of driven transport by a reciprocating Mirror Langmuir Probe, while also making available gas puff imaging and reflectometer data to provide additional radial localization of the driven fluctuation. This new data suggests a  ∼4 mm-wide mode layer centered on or just outside the separatrix. Fluctuations coherent with the antenna produced a radial electron flux with {Γ_e}/{n_e}∼4 m s‑1 in EDA H-mode, smaller than but comparable to the QCM level. But in transient ELM-free H-mode, {Γ_e}/{n_e} was an order of magnitude smaller, and driven fluctuations reduced by a factor of ≳ 3. The driven mode is quantitatively similar to the intrinsic QCM across measured spectral quantities, except that it is more coherent and weaker. This work informs the prospect of achieving control of edge transport by direct coupling to edge modes, as well as the use of such active coupling for diagnostic purposes.

  14. Structure of picosecond pulses of a Q-switched and mode-locked diode-pumped Nd:YAG laser

    Energy Technology Data Exchange (ETDEWEB)

    Donin, V I; Yakovin, D V; Gribanov, A V [Institute of Automation and Electrometry, Siberian Branch of the Russian Academy of Sciences, Novosibirsk (Russian Federation)

    2015-12-31

    The pulse duration of a diode-pumped Nd:YAG laser, in which Q-switching with mode-locking (QML regime) is achieved using a spherical mirror and a travelling-wave acousto-optic modulator, is directly measured with a streak camera. It is found that the picosecond pulses can have a non-single-pulse structure, which is explained by excitation of several competing transverse modes in the Q-switching regime with a pulse repetition rate of 1 kHz. In the case of cw mode-locking (without Q-switching), a new (auto-QML) regime is observed, in which the pulse train repetition rate is determined by the frequency of the relaxation oscillations of the laser field while the train contains single picosecond pulses. (control of laser radiation parameters)

  15. Insight into the Dzyaloshinskii-Moriya interaction through first-principles study of chiral magnetic structures

    Science.gov (United States)

    Sandratskii, L. M.

    2017-07-01

    The purpose of the paper is to gain deeper insight into microscopic formation of the Dzyaloshinskii-Moriya interaction (DMI). The paper aims at the development of the physical picture able to address apparently contradicting conclusions of recent studies concerning the location of the DMI energy in the real and reciprocal spaces as well as the relation between values of the atomic moments and the DMI strength. The main tools of our study are the first-principles calculations of the energies of the spiral magnetic states with opposite chiralities. We suggest a method of the calculation of the spiral structures with account for the spin-orbit coupling (SOC). It is based on the application of the generalized Bloch theorem and generalized Bloch functions and allows to reduce the consideration of arbitrary incommensurate spiral to small chemical unit cell. The method neglects the anisotropy in the plane orthogonal to the rotation axis of the spirals that does not influence importantly the DMI energy. For comparison, the supercell calculation with full account for the SOC is performed. The concrete calculations are performed for the Co/Pt bilayer. We consider the distribution of the DMI energy in both real and reciprocal spaces and the dependence of the DMI on the number of electrons. The results of the calculations reveal a number of energy compensations in the formation of the DMI. Thus, the partial atomic contributions as functions of the spiral wave vector q are nonmonotonic and have strongly varying slopes. However, in the total DMI energy these atom-related features compensate each other, resulting in a smooth q dependence. The reason for the peculiar form of the partial DMI contributions is a q -dependent difference in the charge distribution between q and -q spirals. The strongly q -dependent relation between atomic contributions shows that the real-space distribution of the DMI energy obtained for a selected q value cannot be considered as a general

  16. Influencing Mechanism of Potential Factors on Passengers’ Long-Distance Travel Mode Choices Based on Structural Equation Modeling

    Directory of Open Access Journals (Sweden)

    Yun Wang

    2017-10-01

    Full Text Available Understanding the public transportation users’ preferences to long-distance travel modes would contribute to reasonable developing policies and resource allocation. This paper aims to explore the influencing mechanism of potential factors on the long-distance travel mode choice. A survey was conducted to collect the data. The analysis of variance (ANOVA approach was applied to analyze the correlation relationship between potential factors and travel mode choice behavior. The results showed that, except gender, service demand for safety and departure time, all of the other factors significantly influenced the travel mode choice behavior. Specifically, passengers with higher education level and income level were more likely to choose high-speed railway (HSR and plane; passengers caring about travel expense were more likely to choose ordinary train, whereas plane and HSR may be chosen more by passengers caring more about comfort, punctuality and efficiency; the more passengers were satisfied with travel modes’ service performance, the more they would be likely to choose them; the most competitive distance ranges for coach, ordinary train, HSR and plane were below 500 km, 500–1000 km, 500–1500 km and over 1500 km, respectively. Besides, the structural equation modeling (SEM technique was applied to investigate the influencing mechanism of factors on the long-distance travel mode choice. The results revealed that travel distance was the most significant variable directly influencing passengers’ mode choices, followed by the service demand, performance evaluation, and personal attributes. Furthermore, personal attributes were verified to have an indirect effect on travel mode choice behavior by significantly affecting the service demand and performance evaluation.

  17. DC Voltage Droop Control Structures and its Impact on the Interaction Modes in Interconnected AC-HVDC Systems

    DEFF Research Database (Denmark)

    Thams, Florian; Chatzivasileiadis, Spyros; Eriksson, Robert

    2017-01-01

    Different dc voltage droop control structures for future multi-terminal HVDC systems have been proposed in literature. This paper contributes to the evaluation of those structures by an analysis of their impact on the coupling of the interconnected subsystems. In particular, the modes...... of the systems are classified in different subsets according to the participation of the various subsystems. Those subsets are then evaluated qualitatively and quantitatively indicating which impact the choice of the droop control structure has on the degree of coupling between the connected ac and dc systems...

  18. Field profile and loading measurements on higher order modes in a two cell 500 MHz superconducting structure

    International Nuclear Information System (INIS)

    Barry, W.; Edighoffer, J.; Chattopadhyay, S.; Fornaco, S.

    1992-01-01

    The Infrared Free Electron Laser, being designed at LBL as part of the Chemical Dynamics Research Laboratory, is based on a 500 MHz superconducting linac driver that consists of five 4-cell structures of the CERN/DESY type. A 500 MHz, 2-cell version of this structure is being used in a joint Stanford/LBL/BNL program to study accelerator issues relevant to the FEL applications. As part of this study, field profile and loading measurements of higher order modes have been made on the prototype structure. (Author) 3 refs., 2 figs., tab

  19. Field profile and loading measurements on higher order modes in a two cell 500 MHz superconducting structure

    International Nuclear Information System (INIS)

    Barry, W.; Edighoffer, J.; Chattopadhyay, S.; Fornaca, S.

    1992-08-01

    The Infrared Free Electron Laser, being designed at LBL as part of the Chemical Dynamics Research Laboratory, is based on a 500 MHz superconducting linac driver that consists of five 4-cell structures of the CERN/DESY type. A 500 MHz, 2-cell version of this structure is being used in a joint Stanford/LBL/BNL program to study accelerator issues relevant to the FEL applications. As part of this study, field profile and loading measurements of higher order modes have been made on the prototype structure

  20. Insight into Evolution, Processing and Performance of Multi-length-scale Structures in Planar Heterojunction Perovskite Solar Cells.

    Science.gov (United States)

    Huang, Yu-Ching; Tsao, Cheng-Si; Cho, Yi-Ju; Chen, Kuan-Chen; Chiang, Kai-Ming; Hsiao, Sheng-Yi; Chen, Chang-Wen; Su, Chun-Jen; Jeng, U-Ser; Lin, Hao-Wu

    2015-09-04

    The structural characterization correlated to the processing control of hierarchical structure of planar heterojunction perovskite layer is still incomplete due to the limitations of conventional microscopy and X-ray diffraction. This present study performed the simultaneously grazing-incidence small-angle scattering and wide-angle scattering (GISAXS/GIWAXS) techniques to quantitatively probe the hierarchical structure of the planar heterojunction perovskite solar cells. The result is complementary to the currently microscopic study. Correlation between the crystallization behavior, crystal orientation, nano- and meso-scale internal structure and surface morphology of perovskite film as functions of various processing control parameters is reported for the first time. The structural transition from the fractal pore network to the surface fractal can be tuned by the chloride percentage. The GISAXS/GIWAXS measurement provides the comprehensive understanding of concurrent evolution of the film morphology and crystallization correlated to the high performance. The result can provide the insight into formation mechanism and rational synthesis design.

  1. Insight into Evolution, Processing and Performance of Multi-length-scale Structures in Planar Heterojunction Perovskite Solar Cells

    Science.gov (United States)

    Huang, Yu-Ching; Tsao, Cheng-Si; Cho, Yi-Ju; Chen, Kuan-Chen; Chiang, Kai-Ming; Hsiao, Sheng-Yi; Chen, Chang-Wen; Su, Chun-Jen; Jeng, U.-Ser; Lin, Hao-Wu

    2015-09-01

    The structural characterization correlated to the processing control of hierarchical structure of planar heterojunction perovskite layer is still incomplete due to the limitations of conventional microscopy and X-ray diffraction. This present study performed the simultaneously grazing-incidence small-angle scattering and wide-angle scattering (GISAXS/GIWAXS) techniques to quantitatively probe the hierarchical structure of the planar heterojunction perovskite solar cells. The result is complementary to the currently microscopic study. Correlation between the crystallization behavior, crystal orientation, nano- and meso-scale internal structure and surface morphology of perovskite film as functions of various processing control parameters is reported for the first time. The structural transition from the fractal pore network to the surface fractal can be tuned by the chloride percentage. The GISAXS/GIWAXS measurement provides the comprehensive understanding of concurrent evolution of the film morphology and crystallization correlated to the high performance. The result can provide the insight into formation mechanism and rational synthesis design.

  2. Experimental Characterization of Electron-Beam-Driven Wakefield Modes in a Dielectric-Woodpile Cartesian Symmetric Structure

    Science.gov (United States)

    Hoang, P. D.; Andonian, G.; Gadjev, I.; Naranjo, B.; Sakai, Y.; Sudar, N.; Williams, O.; Fedurin, M.; Kusche, K.; Swinson, C.; Zhang, P.; Rosenzweig, J. B.

    2018-04-01

    Photonic structures operating in the terahertz (THz) spectral region enable the essential characteristics of confinement, modal control, and electric field shielding for very high gradient accelerators based on wakefields in dielectrics. We report here an experimental investigation of THz wakefield modes in a three-dimensional photonic woodpile structure. Selective control in exciting or suppressing of wakefield modes with a nonzero transverse wave vector is demonstrated by using drive beams of varying transverse ellipticity. Additionally, we show that the wakefield spectrum is insensitive to the offset position of strongly elliptical beams. These results are consistent with analytic theory and three-dimensional simulations and illustrate a key advantage of wakefield systems with Cartesian symmetry: the suppression of transverse wakes by elliptical beams.

  3. Influence of Secondary Cooling Mode on Solidification Structure and Macro-segregation Behavior for High-carbon Continuous Casting Bloom

    Science.gov (United States)

    Dou, Kun; Yang, Zhenguo; Liu, Qing; Huang, Yunhua; Dong, Hongbiao

    2017-07-01

    A cellular automaton-finite element coupling model for high-carbon continuously cast bloom of GCr15 steel is established to simulate the solidification structure and to investigate the influence of different secondary cooling modes on characteristic parameters such as equiaxed crystal ratio, grain size and secondary dendrite arm spacing, in which the effect of phase transformation and electromagnetic stirring is taken into consideration. On this basis, evolution of carbon macro-segregation for GCr15 steel bloom is researched correspondingly via industrial tests. Based on above analysis, the relationship among secondary cooling modes, characteristic parameters for solidification structure as well as carbon macro-segregation is illustrated to obtain optimum secondary cooling strategy and alleviate carbon macro-segregation degree for GCr15 steel bloom in continuous casting process. The evaluating method for element macro-segregation is applicable in various steel types.

  4. Structural models of zebrafish (Danio rerio NOD1 and NOD2 NACHT domains suggest differential ATP binding orientations: insights from computational modeling, docking and molecular dynamics simulations.

    Directory of Open Access Journals (Sweden)

    Jitendra Maharana

    Full Text Available Nucleotide-binding oligomerization domain-containing protein 1 (NOD1 and NOD2 are cytosolic pattern recognition receptors playing pivotal roles in innate immune signaling. NOD1 and NOD2 recognize bacterial peptidoglycan derivatives iE-DAP and MDP, respectively and undergoes conformational alternation and ATP-dependent self-oligomerization of NACHT domain followed by downstream signaling. Lack of structural adequacy of NACHT domain confines our understanding about the NOD-mediated signaling mechanism. Here, we predicted the structure of NACHT domain of both NOD1 and NOD2 from model organism zebrafish (Danio rerio using computational methods. Our study highlighted the differential ATP binding modes in NOD1 and NOD2. In NOD1, γ-phosphate of ATP faced toward the central nucleotide binding cavity like NLRC4, whereas in NOD2 the cavity was occupied by adenine moiety. The conserved 'Lysine' at Walker A formed hydrogen bonds (H-bonds and Aspartic acid (Walker B formed electrostatic interaction with ATP. At Sensor 1, Arg328 of NOD1 exhibited an H-bond with ATP, whereas corresponding Arg404 of NOD2 did not. 'Proline' of GxP motif (Pro386 of NOD1 and Pro464 of NOD2 interacted with adenine moiety and His511 at Sensor 2 of NOD1 interacted with γ-phosphate group of ATP. In contrast, His579 of NOD2 interacted with the adenine moiety having a relatively inverted orientation. Our findings are well supplemented with the molecular interaction of ATP with NLRC4, and consistent with mutagenesis data reported for human, which indicates evolutionary shared NOD signaling mechanism. Together, this study provides novel insights into ATP binding mechanism, and highlights the differential ATP binding modes in zebrafish NOD1 and NOD2.

  5. What affects commute mode choice: Physical neighborhood structure or preferences toward neighborhoods?

    NARCIS (Netherlands)

    Schwanen, T.; Mokhtarian, P.L.

    2005-01-01

    The academic literature on the impact of urban form on travel behavior has increasingly recognized that residential location choice and travel choices may be interconnected. We contribute to the understanding of this interrelation by studying to what extent commute mode choice differs by

  6. Temporal genetic structure in a poecilogonous polychaete: the interplay of developmental mode and environmental stochasticity

    DEFF Research Database (Denmark)

    Hansen, Benni Winding; Kesäniemi, Jenni E; Mustonen, Marina

    2014-01-01

    elegans, a poecilogonous polychaete with within-species variation in developmental mode. P. elegans produces either planktonic, benthic, or intermediate larvae, varying both among and within populations, providing a within-species test of the generality of a relationship between temporal genetic variation...

  7. Variable Structure Disturbance Rejection Control for Nonlinear Uncertain Systems with State and Control Delays via Optimal Sliding Mode Surface Approach

    Directory of Open Access Journals (Sweden)

    Jing Lei

    2013-01-01

    Full Text Available The paper considers the problem of variable structure control for nonlinear systems with uncertainty and time delays under persistent disturbance by using the optimal sliding mode surface approach. Through functional transformation, the original time-delay system is transformed into a delay-free one. The approximating sequence method is applied to solve the nonlinear optimal sliding mode surface problem which is reduced to a linear two-point boundary value problem of approximating sequences. The optimal sliding mode surface is obtained from the convergent solutions by solving a Riccati equation, a Sylvester equation, and the state and adjoint vector differential equations of approximating sequences. Then, the variable structure disturbance rejection control is presented by adopting an exponential trending law, where the state and control memory terms are designed to compensate the state and control delays, a feedforward control term is designed to reject the disturbance, and an adjoint compensator is designed to compensate the effects generated by the nonlinearity and the uncertainty. Furthermore, an observer is constructed to make the feedforward term physically realizable, and thus the dynamical observer-based dynamical variable structure disturbance rejection control law is produced. Finally, simulations are demonstrated to verify the effectiveness of the presented controller and the simplicity of the proposed approach.

  8. Effect of Thermal Fields on the Structure of Corrosion-Resistant Steels Under Different Modes of Laser Treatment

    Science.gov (United States)

    Tarasova, T. V.; Gusarov, A. V.; Protasov, K. E.; Filatova, A. A.

    2017-11-01

    The influence of temperature fields on the structure and properties of corrosion-resistant chromium steels under different modes of laser treatment is investigated. A model of heat transfer under laser impact on target is used to plot thermal fields and cycles and cooling rates. It is shown that the model used for computing thermal fields gives tentative geometric sizes of the fusion zones under laser treatment and selective laser fusion. The cooling rate is shown to have decisive influence on the structure of corrosion-resistant steels after laser treatment with surface fusion in devices for pulsed, continuous, and selective laser melting.

  9. Structural properties, crystal quality and growth modes of MOCVD-grown AlN with TMAl pretreatment of sapphire substrate

    KAUST Repository

    Sun, Haiding; Wu, Feng; Altahtamouni, Talal Mohammed Ahmad; Alfaraj, Nasir; Li, Kun; Detchprohm, Theeradetch; Dupuis, Russell; Li, Xiaohang

    2017-01-01

    The growth of high quality AlN epitaxial films relies on precise control of the initial growth stages. In this work, we examined the influence of the trimethylaluminum (TMAl) pretreatment of sapphire substrates on the structural properties, crystal quality and growth modes of heteroepitaxial AlN films on (0001) sapphire substrates. Without the pretreatment, the AlN films nucleated on the smooth surface but exhibited mixed crystallographic Al- (N-) polarity, resulting in rough AlN film surfaces. With increasing the pretreatment time from 1 to 5 s, the N-polarity started to be impeded. However, small islands were formed on sapphire surface due to the decompostion of TMAl. As a result, small voids became noticeable at the nucleation layer (NL) because the growth started as quasi three-dimensional (3D) but transformed to 2D mode as the film grew thicker and got coalesced, leading to smoother and Al-polar films. On the other hand, longer pretreatment time of 40 s formed large 3D islands on sapphire, and thus initiated a 3D-growth mode of the AlN film, generating Al-polar AlN nanocolumns with different facets, which resulted into rougher film surfaces. The epitaxial growth modes and their correlation with the AlN film crystal quality under different TMAl pretreatments are also discussed.

  10. Electromagnetic waves in a topological insulator thin film stack: helicon-like wave mode and photonic band structure.

    Science.gov (United States)

    Inoue, Jun-ichi

    2013-09-09

    We theoretically explore the electromagnetic modes specific to a topological insulator superlattice in which topological and conventional insulator thin films are stacked periodically. In particular, we obtain analytic formulas for low energy mode that corresponds to a helicon wave, as well as those for photonic bands. We illustrate that the system can be modeled as a stack of quantum Hall layers whose conductivity tensors alternately change signs, and then we analyze the photonic band structures. This subject is a natural extension of a previous study by Tselis et al., which took into consideration a stack of identical quantum Hall layers but their discussion was limited into a low energy mode. Thus we provide analytic formulas for photonic bands and compare their features between the two systems. Our central findings in the topological insulator superlattice are that a low energy mode corresponding to a helicon wave has linear dispersion instead of the conventional quadratic form, and that a robust gapless photonic band appears although the system considered has spacial periodicity. In addition, we demonstrate that the photonic bands agree with the numerically calculated transmission spectra.

  11. Structural properties, crystal quality and growth modes of MOCVD-grown AlN with TMAl pretreatment of sapphire substrate

    KAUST Repository

    Sun, Haiding

    2017-08-08

    The growth of high quality AlN epitaxial films relies on precise control of the initial growth stages. In this work, we examined the influence of the trimethylaluminum (TMAl) pretreatment of sapphire substrates on the structural properties, crystal quality and growth modes of heteroepitaxial AlN films on (0001) sapphire substrates. Without the pretreatment, the AlN films nucleated on the smooth surface but exhibited mixed crystallographic Al- (N-) polarity, resulting in rough AlN film surfaces. With increasing the pretreatment time from 1 to 5 s, the N-polarity started to be impeded. However, small islands were formed on sapphire surface due to the decompostion of TMAl. As a result, small voids became noticeable at the nucleation layer (NL) because the growth started as quasi three-dimensional (3D) but transformed to 2D mode as the film grew thicker and got coalesced, leading to smoother and Al-polar films. On the other hand, longer pretreatment time of 40 s formed large 3D islands on sapphire, and thus initiated a 3D-growth mode of the AlN film, generating Al-polar AlN nanocolumns with different facets, which resulted into rougher film surfaces. The epitaxial growth modes and their correlation with the AlN film crystal quality under different TMAl pretreatments are also discussed.

  12. New Insights into HTLV-1 Particle Structure, Assembly, and Gag-Gag Interactions in Living Cells

    Directory of Open Access Journals (Sweden)

    Jolene L. Johnson

    2011-06-01

    Full Text Available Human T-cell leukemia virus type 1 (HTLV-1 has a reputation for being extremely difficult to study in cell culture. The challenges in propagating HTLV-1 has prevented a rigorous analysis of how these viruses replicate in cells, including the detailed steps involved in virus assembly. The details for how retrovirus particle assembly occurs are poorly understood, even for other more tractable retroviral systems. Recent studies on HTLV-1 using state-of-the-art cryo-electron microscopy and fluorescence-based biophysical approaches explored questions related to HTLV-1 particle size, Gag stoichiometry in virions, and Gag-Gag interactions in living cells. These results provided new and exciting insights into fundamental aspects of HTLV-1 particle assembly—which are distinct from those of other retroviruses, including HIV-1. The application of these and other novel biophysical approaches promise to provide exciting new insights into HTLV-1 replication.

  13. Divergent modes of enzyme inhibition in a homologous structure-activity series.

    Science.gov (United States)

    Ferreira, Rafaela S; Bryant, Clifford; Ang, Kenny K H; McKerrow, James H; Shoichet, Brian K; Renslo, Adam R

    2009-08-27

    A docking screen identified reversible, noncovalent inhibitors (e.g., 1) of the parasite cysteine protease cruzain. Chemical optimization of 1 led to a series of oxadiazoles possessing interpretable SAR and potencies as much as 500-fold greater than 1. Detailed investigation of the SAR series subsequently revealed that many members of the oxadiazole class (and surprisingly also 1) act via divergent modes of inhibition (competitive or via colloidal aggregation) depending on the assay conditions employed.

  14. Absolute Molecular Orientation of Isopropanol at Ceria (100) Surfaces: Insight into Catalytic Selectivity from the Interfacial Structure

    Energy Technology Data Exchange (ETDEWEB)

    Doughty, Benjamin [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Goverapet Srinivasan, Sriram [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Indian Inst. of Technology (IIT), Rajasthan (India); Bryantsev, Vyacheslav S. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Lee, Dongkyu [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Lee, Ho Nyung [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Ma, Ying-Zhong [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Lutterman, Daniel A. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

    2017-06-12

    The initial mechanistic steps underlying heterogeneous chemical catalysis can be described in a framework where the composition, structure, and orientation of molecules adsorbed to reactive interfaces are known. However, extracting this vital information is the limiting step in most cases due in part to challenges in probing the interfacial monolayer with enough chemical specificity to characterize the surface molecular constituents. These challenges are exacerbated at complex or spatially heterogeneous interfaces where competing processes and a distribution of local environments can uniquely drive chemistry. To address these limitations, this work presents a distinctive combination of materials synthesis, surface specific optical experiments, and theory to probe and understand molecular structure at catalytic interfaces. Specifically, isopropanol was adsorbed to surfaces of the model CeO2 catalyst that were synthesized with only the (100) facet exposed. Vibrational sum-frequency generation was used to probe the molecular monolayer, and with the guidance of density functional theory calculations, was used to extract the structure and absolute molecular orientation of isopropanol at the CeO2 (100) surface. Our results show that isopropanol is readily deprotonated at the surface, and through the measured absolute molecular orientation of isopropanol, we obtain new insight into the selectivity of the (100) surface to form propylene. Our findings reveal key insight into the chemical and physical phenomena taking place at pristine interfaces thereby pointing to intuitive structural arguments to describe catalytic selectivity in more complex systems.

  15. Structural insight into RNA recognition motifs: versatile molecular Lego building blocks for biological systems.

    Science.gov (United States)

    Muto, Yutaka; Yokoyama, Shigeyuki

    2012-01-01

    'RNA recognition motifs (RRMs)' are common domain-folds composed of 80-90 amino-acid residues in eukaryotes, and have been identified in many cellular proteins. At first they were known as RNA binding domains. Through discoveries over the past 20 years, however, the RRMs have been shown to exhibit versatile molecular recognition activities and to behave as molecular Lego building blocks to construct biological systems. Novel RNA/protein recognition modes by RRMs are being identified, and more information about the molecular recognition by RRMs is becoming available. These RNA/protein recognition modes are strongly correlated with their biological significance. In this review, we would like to survey the recent progress on these versatile molecular recognition modules. Copyright © 2012 John Wiley & Sons, Ltd.

  16. Insight to structural subsite recognition in plant thiol protease-inhibitor complexes : Understanding the basis of differential inhibition and the role of water

    Directory of Open Access Journals (Sweden)

    Mukhopadhayay Bishnu P

    2001-09-01

    Full Text Available Abstract Background This work represents an extensive MD simulation / water-dynamics studies on a series of complexes of inhibitors (leupeptin, E-64, E-64-C, ZPACK and plant cysteine proteases (actinidin, caricain, chymopapain, calotropin DI of papain family to understand the various interactions, water binding mode, factors influencing it and the structural basis of differential inhibition. Results The tertiary structure of the enzyme-inhibitor complexes were built by visual interactive modeling and energy minimization followed by dynamic simulation of 120 ps in water environment. DASA study with and without the inhibitor revealed the potential subsite residues involved in inhibition. Though the interaction involving main chain atoms are similar, critical inspection of the complexes reveal significant differences in the side chain interactions in S2-P2 and S3-P3 pairs due to sequence differences in the equivalent positions of respective subsites leading to differential inhibition. Conclusion The key finding of the study is a conserved site of a water molecule near oxyanion hole of the enzyme active site, which is found in all the modeled complexes and in most crystal structures of papain family either native or complexed. Conserved water molecules at the ligand binding sites of these homologous proteins suggest the structural importance of the water, which changes the conventional definition of chemical geometry of inhibitor binding domain, its shape and complimentarity. The water mediated recognition of inhibitor to enzyme subsites (Pn...H2O....Sn of leupeptin acetyl oxygen to caricain, chymopapain and calotropinDI is an additional information and offer valuable insight to potent inhibitor design.

  17. Can CFMIP2 models reproduce the leading modes of cloud vertical structure in the CALIPSO-GOCCP observations?

    Science.gov (United States)

    Wang, Fang; Yang, Song

    2018-02-01

    Using principal component (PC) analysis, three leading modes of cloud vertical structure (CVS) are revealed by the GCM-Oriented CALIPSO Cloud Product (GOCCP), i.e. tropical high, subtropical anticyclonic and extratropical cyclonic cloud modes (THCM, SACM and ECCM, respectively). THCM mainly reflect the contrast between tropical high clouds and clouds in middle/high latitudes. SACM is closely associated with middle-high clouds in tropical convective cores, few-cloud regimes in subtropical anticyclonic clouds and stratocumulus over subtropical eastern oceans. ECCM mainly corresponds to clouds along extratropical cyclonic regions. Models of phase 2 of Cloud Feedback Model Intercomparison Project (CFMIP2) well reproduce the THCM, but SACM and ECCM are generally poorly simulated compared to GOCCP. Standardized PCs corresponding to CVS modes are generally captured, whereas original PCs (OPCs) are consistently underestimated (overestimated) for THCM (SACM and ECCM) by CFMIP2 models. The effects of CVS modes on relative cloud radiative forcing (RSCRF/RLCRF) (RSCRF being calculated at the surface while RLCRF at the top of atmosphere) are studied in terms of principal component regression method. Results show that CFMIP2 models tend to overestimate (underestimated or simulate the opposite sign) RSCRF/RLCRF radiative effects (REs) of ECCM (THCM and SACM) in unit global mean OPC compared to observations. These RE biases may be attributed to two factors, one of which is underestimation (overestimation) of low/middle clouds (high clouds) (also known as stronger (weaker) REs in unit low/middle (high) clouds) in simulated global mean cloud profiles, the other is eigenvector biases in CVS modes (especially for SACM and ECCM). It is suggested that much more attention should be paid on improvement of CVS, especially cloud parameterization associated with particular physical processes (e.g. downwelling regimes with the Hadley circulation, extratropical storm tracks and others), which

  18. Fault-controlled development of shallow hydrothermal systems: Structural and mineralogical insights from the Southern Andes

    Science.gov (United States)

    Roquer, T.; Arancibia, G.; Rowland, J. V.; Iturrieta, P. C.; Morata, D.; Cembrano, J. M.

    2017-12-01

    Paleofluid-transporting systems can be recognized as meshes of fracture-filled veins in eroded zones of extinct hydrothermal systems. Here we conducted meso-microstructural analysis and mechanical modeling from two exhumed exposures of the faults governing regional tectonics of the Southern Andes: the Liquiñe-Ofqui Fault System (LOFS) and the Andean Transverse Faults (ATF). A total of 107 fractures in both exposures were analyzed. The ATF specific segment shows two tectonic solutions that can be modeled as Andersonian and non-Andersonian tectonic regimes: (1) shear (mode II/III) failure occurs at differential stresses > 28 MPa and fluid pressures 85-98% lithostatic in the non-Andersonian regime. Additionally, the LOFS exposure cyclically fails in extension (mode I) or extension + shear (modes I + II/III) in the Andersonian regime, at differential stresses 40-80% lithostatic. In areas of spatial interaction between ATF and LOFS, these conditions might favor: (1) the storage of overpressured fluids in hydrothermal systems associated with the ATF faults, and (2) continuous fluid flow through vertical conduits in the LOFS faults. These observations suggest that such intersections are highly probable locations for concentrated hydrothermal activity, which must be taken into consideration for further geothermal exploration. ACKNOWLEDGEMENTS. PhD CONICYT grants, Centro de Excelencia en Geotermia de los Andes (CEGA-FONDAP/CONICYT Project #15090013), FONDECYT Project #1130030 and Project CONICYT REDES #140036.

  19. Imaging the Earth's anisotropic structure with Bayesian Inversion of fundamental and higher mode surface-wave dispersion data

    Science.gov (United States)

    Ravenna, Matteo; Lebedev, Sergei; Celli, Nicolas

    2017-04-01

    We develop a Markov Chain Monte Carlo inversion of fundamental and higher mode phase-velocity curves for radially and azimuthally anisotropic structure of the crust and upper mantle. In the inversions of Rayleigh- and Love-wave dispersion curves for radially anisotropic structure, we obtain probabilistic 1D radially anisotropic shear-velocity profiles of the isotropic average Vs and anisotropy (or Vsv and Vsh) as functions of depth. In the inversions for azimuthal anisotropy, Rayleigh-wave dispersion curves at different azimuths are inverted for the vertically polarized shear-velocity structure (Vsv) and the 2-phi component of azimuthal anisotropy. The strength and originality of the method is in its fully non-linear approach. Each model realization is computed using exact forward calculations. The uncertainty of the models is a part of the output. In the inversions for azimuthal anisotropy, in particular, the computation of the forward problem is performed separately at different azimuths, with no linear approximations on the relation of the Earth's elastic parameters to surface wave phase velocities. The computations are performed in parallel in order reduce the computing time. We compare inversions of the fundamental mode phase-velocity curves alone with inversions that also include overtones. The addition of higher modes enhances the resolving power of the anisotropic structure of the deep upper mantle. We apply the inversion method to phase-velocity curves in a few regions, including the Hangai dome region in Mongolia. Our models provide constraints on the Moho depth, the Lithosphere-Asthenosphere Boundary, and the alignment of the anisotropic fabric and the direction of current and past flow, from the crust down to the deep asthenosphere.

  20. A new surface fractal dimension for displacement mode shape-based damage identification of plate-type structures

    Science.gov (United States)

    Shi, Binkai; Qiao, Pizhong

    2018-03-01

    Vibration-based nondestructive testing is an area of growing interest and worthy of exploring new and innovative approaches. The displacement mode shape is often chosen to identify damage due to its local detailed characteristic and less sensitivity to surrounding noise. Requirement for baseline mode shape in most vibration-based damage identification limits application of such a strategy. In this study, a new surface fractal dimension called edge perimeter dimension (EPD) is formulated, from which an EPD-based window dimension locus (EPD-WDL) algorithm for irregularity or damage identification of plate-type structures is established. An analytical notch-type damage model of simply-supported plates is proposed to evaluate notch effect on plate vibration performance; while a sub-domain of notch cases with less effect is selected to investigate robustness of the proposed damage identification algorithm. Then, fundamental aspects of EPD-WDL algorithm in term of notch localization, notch quantification, and noise immunity are assessed. A mathematical solution called isomorphism is implemented to remove false peaks caused by inflexions of mode shapes when applying the EPD-WDL algorithm to higher mode shapes. The effectiveness and practicability of the EPD-WDL algorithm are demonstrated by an experimental procedure on damage identification of an artificially-induced notched aluminum cantilever plate using a measurement system of piezoelectric lead-zirconate (PZT) actuator and scanning laser Doppler vibrometer (SLDV). As demonstrated in both the analytical and experimental evaluations, the new surface fractal dimension technique developed is capable of effectively identifying damage in plate-type structures.

  1. Assessment of soil-structure interaction effects based on simple modes

    International Nuclear Information System (INIS)

    Philippacopoulos, A.J.; Miller, C.A.

    1983-01-01

    Soil-structure interaction effects are investigated using a simple mathematical model which employs three degrees-of-freedom. The foundation is approximated by a homogeneous, isotropic, elastic half-space. Harmonic functions and a recorded earthquake are used to represent the free-field input motion. Variations of the response characteristics due to structural and interaction parameters are demonstrated. Response spectra are presented that display the magnitude of the maximum structural response for a range of fixed-base structural frequencies, interaction frequencies and damping. Conclusions are obtained regarding the behavior of the response of the soil-structure system. The findings reported herein can be used for the interpretation of the results of soil-structure interaction analyses of nuclear plant structures that are performed with available computer codes

  2. Potential seismic structural failure modes associated with the Zion Nuclear Plant. Seismic safety margins research program (Phase I). Project VI. Fragilities

    International Nuclear Information System (INIS)

    1979-10-01

    The Zion 1 and 2 Nuclear Power Plant consists of a number of structures. The most important of these from the viewpoint of safety are the containment buildings, the auxiliary building, the turbine building, and the crib house (or intake structure). The evaluation of the potential seismic failure modes and determination of the ultimate seismic capacity of the structures is a complex undertaking which will require a large number of detailed calculations. As the first step in this evaluation, a number of potential modes of structural failure have been determined and are discussed. The report is principally directed towards seismically induced failure of structures. To some extent, modes involving soil foundation failures are discussed in so far as they affect the buildings. However, failure modes involving soil liquefaction, surface faulting, tsunamis, etc., are considered outside the scope of this evaluation

  3. Influences of the Living World on Architectural Structures: An Analytical Insight

    Directory of Open Access Journals (Sweden)

    Gülcan MİNSOLMAZ YELER

    2015-01-01

    Full Text Available Structures in the nature motivate innovation in architectural and engineering disciplines in termsof aesthetical, functional and structural advantages. Using efficient, lightweight structural forms similar tothose in nature reduces material and energy usage and waste amount. In this sense, it can be clearly seenthat based on learning from nature in relation to meeting gradually increasing and changing requirementsthrough limited resources and creating modern structural designs, biomimicry will provide much morecontribution on architecture and related fields. In this direction, in the study based on comprehensiveliterature research, lots of varying living organisms in the nature have been analyzed in terms of structure;architectural structures developed by inspiring from natural structures have been sampled and influencesof solutions inspired from nature on architectural environment have been focused.

  4. Accelerator structure for a charged particle linear accelerator working in standing wave mode

    International Nuclear Information System (INIS)

    Tran, D.T.; Tronc, Dominique.

    1977-01-01

    Charged particle accelerators generally include a pre-grouping or pre-accelerating structure associated with the accelerator structure itself. But pre-grouping or pre-accelerating structures of known type (Patent application No. 70 39261 for example) present electric and dimensional characteristics that rule them out for accelerators working at high frequencies (C or X bands for example), since the distance separating the interaction spaces becomes very small in this case. The accelerator structure mentioned in this invention can be used to advantage for such accelerators [fr

  5. Effects of Different Working Modes of Ultrasound on Structural Characteristics of Zein and ACE Inhibitory Activity of Hydrolysates

    Directory of Open Access Journals (Sweden)

    Xiaofeng Ren

    2017-01-01

    Full Text Available Ultrasound was used as a new technology to pretreat protein prior to proteolysis to improve enzymolysis efficiency. The effects of different working modes of ultrasound on the angiotensin I-converting enzyme (ACE inhibitory activity of zein hydrolysates and the structural characteristics of zein were investigated. The solubility, surface hydrophobicity (H0, ultraviolet-visible (UV-Vis spectra, intrinsic fluorescence spectra, and circular dichroism (CD spectra of zein pretreated with ultrasound were determined. All ultrasound pretreatments significantly improved the ACE inhibitory activity of zein hydrolysates (p<0.05. The highest ACE inhibitory activity, representing an increase of 99.21% over the control, was obtained with dual sweeping frequency ultrasound of 33±2 and 68±2 kHz. The effects of single sweeping frequency and dual fixed frequency ultrasound were stronger than those of single fixed frequency ultrasound for improving the ACE inhibitory activity of zein. Structural changes in zein were induced by ultrasound, as confirmed by changes in the solubility, H0, UV-Vis spectra, intrinsic fluorescence spectra, and CD spectra of zein, and these were consistent with the corresponding ACE inhibitory activities of zein hydrolysates. Thus, ultrasound working mode and frequency have significant effects on the structure of zein and the ACE inhibitory activity of zein hydrolysates.

  6. The crystal structure of full-length Sizzled from Xenopus laevis yields insights into Wnt-antagonistic function of secreted Frizzled-related proteins.

    Science.gov (United States)

    Bu, Qixin; Li, Zhiqiang; Zhang, Junying; Xu, Fei; Liu, Jianmei; Liu, Heli

    2017-09-29

    The Wnt-signaling pathway is crucial to cell proliferation, differentiation, and migration. The secreted Frizzled-related proteins (sFRPs) represent the largest family of secreted Wnt inhibitors. However, their function in antagonizing Wnt signaling has remained somewhat controversial. Here, we report the crystal structure of Sizzled from Xenopus laevis , the first full-length structure of an sFRP. Tethered by an inter-domain disulfide bond and a linker, the N-terminal cysteine-rich domain (CRD) and the C-terminal netrin-like domain (NTR) of Sizzled are arranged in a tandem fashion, with the NTR domain occluding the groove of CRD for Wnt accessibility. A Dual-Luciferase assay demonstrated that removing the NTR domain and replacing the CRD groove residues His-116 and His-118 with aromatic residues may significantly enhance antagonistic function of Sizzled in inhibiting Wnt3A signaling. Sizzled is a monomer in solution, and Sizzled CRD exhibited different packing in the crystal, suggesting that sFRPs do not have a conserved CRD dimerization mode. Distinct from the canonical NTR domain, the Sizzled NTR adopts a novel α/β folding with two perpendicular helices facing the central mixed β-sheet. The subgroup of human sFRP1/2/5 and Sizzled should have a similar NTR domain that features a highly positively charged region, opposite the NTR-CRD interface, suggesting that the NTR domain in human sFRPs, at least sFRP1/2/5, is unlikely to bind to Wnt but is likely involved in biphasic Wnt signaling modulation. In summary, the Sizzled structure provides the first insights into how the CRD and the NTR domains relate to each other for modulating Wnt-antagonistic function of sFRPs. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  7. Theoretical and experimental study on active sound transmission control based on single structural mode actuation using point force actuators.

    Science.gov (United States)

    Sanada, Akira; Tanaka, Nobuo

    2012-08-01

    This study deals with the feedforward active control of sound transmission through a simply supported rectangular panel using vibration actuators. The control effect largely depends on the excitation method, including the number and locations of actuators. In order to obtain a large control effect at low frequencies over a wide frequency, an active transmission control method based on single structural mode actuation is proposed. Then, with the goal of examining the feasibility of the proposed method, the (1, 3) mode is selected as the target mode and a modal actuation method in combination with six point force actuators is considered. Assuming that a single input single output feedforward control is used, sound transmission in the case minimizing the transmitted sound power is calculated for some actuation methods. Simulation results showed that the (1, 3) modal actuation is globally effective at reducing the sound transmission by more than 10 dB in the low-frequency range for both normal and oblique incidences. Finally, experimental results also showed that a large reduction could be achieved in the low-frequency range, which proves the validity and feasibility of the proposed method.

  8. Binding Mode and Structure-Activity Relationships of ITE as an Aryl Hydrocarbon Receptor (AhR) Agonist.

    Science.gov (United States)

    Dolciami, Daniela; Gargaro, Marco; Cerra, Bruno; Scalisi, Giulia; Bagnoli, Luana; Servillo, Giuseppe; Fazia, Maria Agnese Della; Puccetti, Paolo; Quintana, Francisco J; Fallarino, Francesca; Macchiarulo, Antonio

    2018-02-06

    Discovered as a modulator of the toxic response to environmental pollutants, aryl hydrocarbon receptor (AhR) has recently gained attention for its involvement in various physiological and pathological pathways. AhR is a ligand-dependent transcription factor activated by a large array of chemical compounds, which include metabolites of l-tryptophan (l-Trp) catabolism as endogenous ligands of the receptor. Among these, 2-(1'H-indole-3'-carbonyl)thiazole-4-carboxylic acid methyl ester (ITE) has attracted interest in the scientific community, being endowed with nontoxic, immunomodulatory, and anticancer AhR-mediated functions. So far, no information about the binding mode and interactions of ITE with AhR is available. In this study, we used docking and molecular dynamics to propose a putative binding mode of ITE into the ligand binding pocket of AhR. Mutagenesis studies were then instrumental in validating the proposed binding mode, identifying His 285 and Tyr 316 as important key residues for ligand-dependent receptor activation. Finally, a set of ITE analogues was synthesized and tested to further probe molecular interactions of ITE to AhR and characterize the relevance of specific functional groups in the chemical structure for receptor activity. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. Parameters Designing of Slide Mode Variable Structure Controller of Bus Voltage of DC Microgrid Based on Proportion Switching Function

    Directory of Open Access Journals (Sweden)

    Sun Zhenchuan

    2017-01-01

    Full Text Available Constant value control of the DC-bus voltage is a essential problem of the control system of the DC microgrids. DC-DC converters are applied in parallel to realize the transform of energy from the distributed generations (DGs to the DC-bus. Droop control methods are applied to the DC-bus voltage while PI controllers are used in controlling the duty ratios of the converters. This method may bring out the slow response speed of the system accompanied by the large ripple of the voltage. The slide mode variable structure control can speed up the response and reduce the ripple of the voltage as well. In the traditional slide mode control based on the proportion switching function, the denominator of the transfer function of the controlled plant is a second-order characteristic polynomial without the constant term. The denominators of the transfer functions of the buck DC-DC converters contain the constant terms. The designing of the parameters of the slide mode control based on the proportion switching function is analyzed based on mathematics deductions. Simulation results show that the selected parameters can not only speed up the response of the system but also greatly reduce the ripple of the voltage.

  10. Key performance outcomes of patient safety curricula: root cause analysis, failure mode and effects analysis, and structured communications skills.

    Science.gov (United States)

    Fassett, William E

    2011-10-10

    As colleges and schools of pharmacy develop core courses related to patient safety, course-level outcomes will need to include both knowledge and performance measures. Three key performance outcomes for patient safety coursework, measured at the course level, are the ability to perform root cause analyses and healthcare failure mode effects analyses, and the ability to generate effective safety communications using structured formats such as the Situation-Background-Assessment-Recommendation (SBAR) situational briefing model. Each of these skills is widely used in patient safety work and competence in their use is essential for a pharmacist's ability to contribute as a member of a patient safety team.

  11. Project of the electron linear accelerator on the biperiodical accelerating structure with deep energy retuning in a pulse mode

    International Nuclear Information System (INIS)

    Bogdanovich, B.Yu.; Zavadtsev, D.A.; Kaminskij, V.I.; Sobenin, N.P.; Fadin, A.I.; Zavadtsev, A.A.

    2001-01-01

    The schemes of the electron linear accelerator (ELA), realized on the basis of a biperiodical accelerating structure and ensuring the possibility of deep retuning of the beam energy in a pulse mode, are considered. Advantages and shortcomings of the proposed methods of pulse regulation of the electron energy are discussed. A project of a two-section ELA with two levels of energy (10 and 4 MeV) is presented as a base version. The beam dynamics is calculated for two versions of the ELA. Their main parameters are given [ru

  12. Structural insights into the backbone-circularized granulocyte colony-stimulating factor containing a short connector.

    Science.gov (United States)

    Miyafusa, Takamitsu; Shibuya, Risa; Honda, Shinya

    2018-06-02

    Backbone circularization is a powerful approach for enhancing the structural stability of polypeptides. Herein, we present the crystal structure of the circularized variant of the granulocyte colony-stimulating factor (G-CSF) in which the terminal helical region was circularized using a short, two-amino acid connector. The structure revealed that the N- and C-termini were indeed connected by a peptide bond. The local structure of the C-terminal region transited from an α helix to 3 10 helix with a bend close to the N-terminal region, indicating that the structural change offset the insufficient length of the connector. This is the first-ever report of a crystal structure of the backbone of a circularized protein. It will facilitate the development of backbone circularization methodology. Copyright © 2018 Elsevier Inc. All rights reserved.

  13. Insights into function of PSI domains from structure of the Met receptor PSI domain

    International Nuclear Information System (INIS)

    Kozlov, Guennadi; Perreault, Audrey; Schrag, Joseph D.; Park, Morag; Cygler, Miroslaw; Gehring, Kalle; Ekiel, Irena

    2004-01-01

    PSI domains are cysteine-rich modules found in extracellular fragments of hundreds of signaling proteins, including plexins, semaphorins, integrins, and attractins. Here, we report the solution structure of the PSI domain from the human Met receptor, a receptor tyrosine kinase critical for proliferation, motility, and differentiation. The structure represents a cysteine knot with short regions of secondary structure including a three-stranded antiparallel β-sheet and two α-helices. All eight cysteines are involved in disulfide bonds with the pattern consistent with that for the PSI domain from Sema4D. Comparison with the Sema4D structure identifies a structurally conserved core comprising the N-terminal half of the PSI domain. Interestingly, this part links adjacent SEMA and immunoglobulin domains in the Sema4D structure, suggesting that the PSI domain serves as a wedge between propeller and immunoglobulin domains and is responsible for the correct positioning of the ligand-binding site of the receptor

  14. Preliminary design of offshore wind turbine support structures : The importance of proper mode shape estimation

    NARCIS (Netherlands)

    Van der Male, P.

    2013-01-01

    Offshore wind turbines are highly exposed to timevarying loads. For support structures, estimation of the fatigue damage during the lifetime of the structure is an essential design aspect. This already applies for the preliminary design stage. In determining the dynamic amplification in the

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

    DEFF Research Database (Denmark)

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

    2013-01-01

    In pelagic species inhabiting large oceans, genetic differentiation tends to be mild and populations devoid of structure. However, large cetaceans have provided many examples of structuring. Here we investigate whether the sperm whale, a pelagic species with large population sizes and reputedly......, use of habitat and/or migratory destinations are dissimilar between whales from the two regions and suggest that the North Atlantic population of sperm whales is more structured than traditionally accepted....

  16. Exploring the potential of a structural alphabet-based tool for mining multiple target conformations and target flexibility insight.

    Science.gov (United States)

    Regad, Leslie; Chéron, Jean-Baptiste; Triki, Dhoha; Senac, Caroline; Flatters, Delphine; Camproux, Anne-Claude

    2017-01-01

    Protein flexibility is often implied in binding with different partners and is essential for protein function. The growing number of macromolecular structures in the Protein Data Bank entries and their redundancy has become a major source of structural knowledge of the protein universe. The analysis of structural variability through available redundant structures of a target, called multiple target conformations (MTC), obtained using experimental or modeling methods and under different biological conditions or different sources is one way to explore protein flexibility. This analysis is essential to improve the understanding of various mechanisms associated with protein target function and flexibility. In this study, we explored structural variability of three biological targets by analyzing different MTC sets associated with these targets. To facilitate the study of these MTC sets, we have developed an efficient tool, SA-conf, dedicated to capturing and linking the amino acid and local structure variability and analyzing the target structural variability space. The advantage of SA-conf is that it could be applied to divers sets composed of MTCs available in the PDB obtained using NMR and crystallography or homology models. This tool could also be applied to analyze MTC sets obtained by dynamics approaches. Our results showed that SA-conf tool is effective to quantify the structural variability of a MTC set and to localize the structural variable positions and regions of the target. By selecting adapted MTC subsets and comparing their variability detected by SA-conf, we highlighted different sources of target flexibility such as induced by binding partner, by mutation and intrinsic flexibility. Our results support the interest to mine available structures associated with a target using to offer valuable insight into target flexibility and interaction mechanisms. The SA-conf executable script, with a set of pre-compiled binaries are available at http://www.mti.univ-paris-diderot.fr/recherche/plateformes/logiciels.

  17. Exploring the potential of a structural alphabet-based tool for mining multiple target conformations and target flexibility insight.

    Directory of Open Access Journals (Sweden)

    Leslie Regad

    Full Text Available Protein flexibility is often implied in binding with different partners and is essential for protein function. The growing number of macromolecular structures in the Protein Data Bank entries and their redundancy has become a major source of structural knowledge of the protein universe. The analysis of structural variability through available redundant structures of a target, called multiple target conformations (MTC, obtained using experimental or modeling methods and under different biological conditions or different sources is one way to explore protein flexibility. This analysis is essential to improve the understanding of various mechanisms associated with protein target function and flexibility. In this study, we explored structural variability of three biological targets by analyzing different MTC sets associated with these targets. To facilitate the study of these MTC sets, we have developed an efficient tool, SA-conf, dedicated to capturing and linking the amino acid and local structure variability and analyzing the target structural variability space. The advantage of SA-conf is that it could be applied to divers sets composed of MTCs available in the PDB obtained using NMR and crystallography or homology models. This tool could also be applied to analyze MTC sets obtained by dynamics approaches. Our results showed that SA-conf tool is effective to quantify the structural variability of a MTC set and to localize the structural variable positions and regions of the target. By selecting adapted MTC subsets and comparing their variability detected by SA-conf, we highlighted different sources of target flexibility such as induced by binding partner, by mutation and intrinsic flexibility. Our results support the interest to mine available structures associated with a target using to offer valuable insight into target flexibility and interaction mechanisms. The SA-conf executable script, with a set of pre-compiled binaries are available at

  18. Hierarchical super-structure identified by polarized light microscopy, electron microscopy and nanoindentation: Implications for the limits of biological control over the growth mode of abalone sea shells

    Directory of Open Access Journals (Sweden)

    Schneider Andreas S

    2012-09-01

    Full Text Available Abstract Background Mollusc shells are commonly investigated using high-resolution imaging techniques based on cryo-fixation. Less detailed information is available regarding the light-optical properties. Sea shells of Haliotis pulcherina were embedded for polishing in defined orientations in order to investigate the interface between prismatic calcite and nacreous aragonite by standard materialographic methods. A polished thin section of the interface was prepared with a defined thickness of 60 μm for quantitative birefringence analysis using polarized light and LC-PolScope microscopy. Scanning electron microscopy images were obtained for comparison. In order to study structural-mechanical relationships, nanoindentation experiments were performed. Results Incident light microscopy revealed a super-structure in semi-transparent regions of the polished cross-section under a defined angle. This super-structure is not visible in transmitted birefringence analysis due to the blurred polarization of small nacre platelets and numerous organic interfaces. The relative orientation and homogeneity of calcite prisms was directly identified, some of them with their optical axes exactly normal to the imaging plane. Co-oriented "prism colonies" were identified by polarized light analyses. The nacreous super-structure was also visualized by secondary electron imaging under defined angles. The domains of the super-structure were interpreted to consist of crystallographically aligned platelet stacks. Nanoindentation experiments showed that mechanical properties changed with the same periodicity as the domain size. Conclusions In this study, we have demonstrated that insights into the growth mechanisms of nacre can be obtained by conventional light-optical methods. For example, we observed super-structures formed by co-oriented nacre platelets as previously identified using X-ray Photo-electron Emission Microscopy (X-PEEM [Gilbert et al., Journal of the

  19. Impact of acoustic airflow on intrasinus drug deposition: New insights into the vibrating mode and the optimal acoustic frequency to enhance the delivery of nebulized antibiotic.

    Science.gov (United States)

    Leclerc, Lara; Merhie, Amira El; Navarro, Laurent; Prévôt, Nathalie; Durand, Marc; Pourchez, Jérémie

    2015-10-15

    We investigated the impact of vibrating acoustic airflow, the high frequency (f≥100 Hz) and the low frequency (f≤45 Hz) sound waves, on the enhancement of intrasinus drug deposition. (81m)Kr-gas ventilation study was performed in a plastinated human cast with and without the addition of vibrating acoustic airflow. Similarly, intrasinus drug deposition in a nasal replica using gentamicin as a marker was studied with and without the superposition of different modes of acoustic airflow. Ventilation experiments demonstrate that no sinus ventilation was observed without acoustic airflow although sinus ventilation occurred whatever the modes of acoustic airflow applied. Intrasinus drug deposition experiments showed that the high frequency acoustic airflow led to 4-fold increase in gentamicin deposition into the left maxillary sinus and to 2-fold deposition increase into the right maxillary sinus. Besides, the low frequency acoustic airflow demonstrated a significant increase of 4-fold and 2-fold in the right and left maxillary sinuses, respectively. We demonstrated the benefit of different modes of vibrating acoustic airflow for maxillary sinus ventilation and intrasinus drug deposition. The degree of gentamicin deposition varies as a function of frequency of the vibrating acoustic airflow and the geometry of the ostia. Copyright © 2015 Elsevier B.V. All rights reserved.

  20. Mode of production of monomolecular structuring water in liquid crystalline form

    International Nuclear Information System (INIS)

    Hasanov, A.M.

    2011-01-01

    Full text : Mode to protect living organisms from the biological effects of electromagnetic radiation of mobile phones and personal computers, including the determination of the energy absorbed by the body over time, depending on the biological factors of the body, characterized in that a biological factor using the total amount of water contained in the body, with time corresponding to the absorbed energy is equated to the maximum allowable rate, determined by the formula dt=dEBBNH/EodEeksp. Here K is the coefficient of the percentage of water in biological tissues, dEeksp. - Experimentally established energy flux density of the mobile phone or personal computer, dEBBNH ∼10mkVt/si 2 - maximum permissible rate of absorbed energy.

  1. Structural insights into RISC assembly facilitated by dsRNA-binding domains of human RNA helicase A (DHX9).

    Science.gov (United States)

    Fu, Qinqin; Yuan, Y Adam

    2013-03-01

    Intensive research interest has focused on small RNA-processing machinery and the RNA-induced silencing complex (RISC), key cellular machines in RNAi pathways. However, the structural mechanism regarding RISC assembly, the primary step linking small RNA processing and RNA-mediated gene silencing, is largely unknown. Human RNA helicase A (DHX9) was reported to function as an RISC-loading factor, and such function is mediated mainly by its dsRNA-binding domains (dsRBDs). Here, we report the crystal structures of human RNA helicase A (RHA) dsRBD1 and dsRBD2 domains in complex with dsRNAs, respectively. Structural analysis not only reveals higher siRNA duplex-binding affinity displayed by dsRBD1, but also identifies a crystallographic dsRBD1 pair of physiological significance in cooperatively recognizing dsRNAs. Structural observations are further validated by isothermal titration calorimetric (ITC) assay. Moreover, co-immunoprecipitation (co-IP) assay coupled with mutagenesis demonstrated that both dsRBDs are required for RISC association, and such association is mediated by dsRNA. Hence, our structural and functional efforts have revealed a potential working model for siRNA recognition by RHA tandem dsRBDs, and together they provide direct structural insights into RISC assembly facilitated by RHA.

  2. Neutron irradiation effects in fusion or spallation structural materials: Some recent insights related to neutron spectra

    International Nuclear Information System (INIS)

    Garner, F.A.; Greenwood, L.R.

    1998-01-01

    A review is presented of recent insights on the role of transmutation in the development of radiation-induced changes in dimension or radiation-induced changes in physical or mechanical properties. It is shown that, in some materials and some neutron spectra, transmutation can significantly affect or even dominate a given property change process. When the process under study is also sensitive to displacement rate, and especially if it involves radiation-induced segregation and precipitation, it becomes much more difficult to separate the transmutation and displacement rate dependencies. This complicates the application of data derived from 'surrogate' spectra to predictions in other flux-spectra environments. It is also shown in this paper that one must be sensitive to the impact of previously -ignored 'small' variations in neutron spectra within a given reactor. In some materials these small variations have major consequences. (author)

  3. Water versus DNA: new insights into proton track-structure modelling in radiobiology and radiotherapy.

    Science.gov (United States)

    Champion, C; Quinto, M A; Monti, J M; Galassi, M E; Weck, P F; Fojón, O A; Hanssen, J; Rivarola, R D

    2015-10-21

    Water is a common surrogate of DNA for modelling the charged particle-induced ionizing processes in living tissue exposed to radiations. The present study aims at scrutinizing the validity of this approximation and then revealing new insights into proton-induced energy transfers by a comparative analysis between water and realistic biological medium. In this context, a self-consistent quantum mechanical modelling of the ionization and electron capture processes is reported within the continuum distorted wave-eikonal initial state framework for both isolated water molecules and DNA components impacted by proton beams. Their respective probability of occurrence-expressed in terms of total cross sections-as well as their energetic signature (potential and kinetic) are assessed in order to clearly emphasize the differences existing between realistic building blocks of living matter and the controverted water-medium surrogate. Consequences in radiobiology and radiotherapy will be discussed in particular in view of treatment planning refinement aiming at better radiotherapy strategies.

  4. Crystal structure mediates mode of cell death in TiO2 nanotoxicity

    International Nuclear Information System (INIS)

    Braydich-Stolle, Laura K.; Schaeublin, Nicole M.; Murdock, Richard C.; Jiang, Jingkun; Biswas, Pratim; Schlager, John J.; Hussain, Saber M.

    2009-01-01

    Certain properties that nanoparticles possess differentiate them from their bulk counterparts, and these characteristics must be evaluated prior to nanoparticle studies and include: size, shape, dispersion, physical and chemical properties, surface area, and surface chemistry. Early nanotoxicity studies evaluating TiO 2 have yielded conflicting data which identify either size or crystal structure as the mediating property for nano-TiO 2 toxicity. However, it is important to note that none of these studies examined size with the crystal structure composition controlled for or examined crystal structure while controlling the nanoparticle size. The goal of this study was to evaluate the role of size and crystal structure in TiO 2 nanotoxicity while controlling for as many other nanoproperties as possible using the HEL-30 mouse keratinocyte cell line as a model for dermal exposure. In the size-dependent studies, all the nanoparticles are 100% anatase, and aggregate sizes were determined in order to take into account the effect of agglomeration on size-dependent toxicity. In addition, varying crystal structures were assessed while the size of the nanoparticles was controlled. We were able to identify that both size and crystal structure contribute to cytotoxicity and that the mechanism of cell death varies based on crystal structure. The 100% anatase TiO 2 nanoparticles, regardless of size, induced cell necrosis, while the rutile TiO 2 nanoparticles initiated apoptosis through formation of reactive oxygen species (ROS).

  5. Crystal structure mediates mode of cell death in TiO{sub 2} nanotoxicity

    Energy Technology Data Exchange (ETDEWEB)

    Braydich-Stolle, Laura K.; Schaeublin, Nicole M.; Murdock, Richard C. [Wright-Patterson AFB, Applied Biotechnology Branch, Human Effectiveness Directorate, Air Force Research Laboratory (United States); Jiang, Jingkun; Biswas, Pratim [Washington University in St. Louis, Department of Energy, Environmental, and Chemical Engineering (United States); Schlager, John J.; Hussain, Saber M., E-mail: Saber.Hussain@wpafb.af.mi [Wright-Patterson AFB, Applied Biotechnology Branch, Human Effectiveness Directorate, Air Force Research Laboratory (United States)

    2009-08-15

    Certain properties that nanoparticles possess differentiate them from their bulk counterparts, and these characteristics must be evaluated prior to nanoparticle studies and include: size, shape, dispersion, physical and chemical properties, surface area, and surface chemistry. Early nanotoxicity studies evaluating TiO{sub 2} have yielded conflicting data which identify either size or crystal structure as the mediating property for nano-TiO{sub 2} toxicity. However, it is important to note that none of these studies examined size with the crystal structure composition controlled for or examined crystal structure while controlling the nanoparticle size. The goal of this study was to evaluate the role of size and crystal structure in TiO{sub 2} nanotoxicity while controlling for as many other nanoproperties as possible using the HEL-30 mouse keratinocyte cell line as a model for dermal exposure. In the size-dependent studies, all the nanoparticles are 100% anatase, and aggregate sizes were determined in order to take into account the effect of agglomeration on size-dependent toxicity. In addition, varying crystal structures were assessed while the size of the nanoparticles was controlled. We were able to identify that both size and crystal structure contribute to cytotoxicity and that the mechanism of cell death varies based on crystal structure. The 100% anatase TiO{sub 2} nanoparticles, regardless of size, induced cell necrosis, while the rutile TiO{sub 2} nanoparticles initiated apoptosis through formation of reactive oxygen species (ROS).

  6. Finite element modeling of temperature load effects on the vibration of local modes in multi-cable structures

    Science.gov (United States)

    Treyssède, Fabien

    2018-01-01

    Understanding thermal effects on the vibration of local (cable-dominant) modes in multi-cable structures is a complicated task. The main difficulty lies in the modification by temperature change of cable tensions, which are then undetermined. This paper applies a finite element procedure to investigate the effects of thermal loads on the linear dynamics of prestressed self-weighted multi-cable structures. Provided that boundary conditions are carefully handled, the discretization of cables with nonlinear curved beam elements can properly represent the thermoelastic behavior of cables as well as their linearized dynamics. A three-step procedure that aims to replace applied pretension forces with displacement continuity conditions is used. Despite an increase in the computational cost related to beam rotational degrees of freedom, such an approach has several advantages. Nonlinear beam finite elements are usually available in commercial codes. The overall method follows a thermoelastic geometrically non-linear analysis and hereby includes the main sources of non-linearities in multi-cable structures. The effects of cable bending stiffness, which can be significant, are also naturally accounted for. The accuracy of the numerical approach is assessed thanks to an analytical model for the vibration of a single inclined cable under temperature change. Then, the effects of thermal loads are investigated for two cable bridges, highlighting how natural frequencies can be affected by temperature. Although counterintuitive, a reverse relative change of natural frequency may occur for certain local modes. This phenomenon can be explained by two distinct mechanisms, one related to the physics intrinsic to cables and the other related to the thermal deflection of the superstructure. Numerical results show that cables cannot be isolated from the rest of the structure and the importance of modeling the whole structure for a quantitative analysis of temperature effects on the

  7. Local Fine Structural Insight into Mechanism of Electrochemical Passivation of Titanium.

    Science.gov (United States)

    Wang, Lu; Yu, Hongying; Wang, Ke; Xu, Haisong; Wang, Shaoyang; Sun, Dongbai

    2016-07-20

    Electrochemically formed passive film on titanium in 1.0 M H2SO4 solution and its thickness, composition, chemical state, and local fine structure are examined by Auger electron spectroscopy (AES), X-ray photoelectron spectroscopy (XPS), and X-ray absorption fine structure. AES analysis reveals that the thickness and composition of oxide film are proportional to the reciprocal of current density in potentiodynamic polarization. XPS depth profiles of the chemical states of titanium exhibit the coexistence of various valences cations in the surface. Quantitative X-ray absorption near edge structure analysis of the local electronic structure of the topmost surface (∼5.0 nm) shows that the ratio of [TiO2]/[Ti2O3] is consistent with that of passivation/dissolution of electrochemical activity. Theoretical calculation and analysis of extended X-ray absorption fine structure spectra at Ti K-edge indicate that both the structures of passivation and dissolution are distorted caused by the appearance of two different sites of Ti-O and Ti-Ti. And the bound water in the topmost surface plays a vital role in structural disorder confirmed by XPS. Overall, the increase of average Ti-O coordination causes the electrochemical passivation, and the dissolution is due to the decrease of average Ti-Ti coordination. The structural variations of passivation in coordination number and interatomic distance are in good agreement with the prediction of point defect model.

  8. An Insight towards Conceptual Understanding: Looking into the Molecular Structures of Compounds

    Science.gov (United States)

    Uyulgan, Melis Arzu; Akkuzu, Nalan

    2016-01-01

    The subject of molecular structures is one of the most important and complex subject in chemistry which a majority of the undergraduate students have difficulties to understand its concepts and characteristics correctly. To comprehend the molecular structures and their characteristics the students need to understand related subjects such as Lewis…

  9. Anti-symmetrized molecular dynamics: a new insight into the structure of nuclei

    International Nuclear Information System (INIS)

    Yoshiko, Kanada-En'yo; Masaaki, Kimura; Hisashi, Horiuchi

    2003-01-01

    The AMD (anti-symmetrized molecular dynamics) theory for nuclear structure is explained by showing its actual applications. First the formulation of AMD including various refined versions is briefly presented and its characteristics are discussed, putting a stress on its nature as an 'ab initio' theory. Then we demonstrate fruitful applications to various structure problems in stable nuclei, in order to explicitly verify the 'ab initio' nature of AMD, especially the ability to describe both mean-field-type structure and cluster structure. Finally, we show the results of applications of AMD to unstable nuclei, from which we see that AMD is powerful in elucidating and understanding various types of nuclear structure of unstable nuclei. (authors)

  10. Insight into the microscopic structure of an AdS black hole from a thermodynamical phase transition.

    Science.gov (United States)

    Wei, Shao-Wen; Liu, Yu-Xiao

    2015-09-11

    Comparing with an ordinary thermodynamic system, we investigate the possible microscopic structure of a charged anti-de Sitter black hole completely from the thermodynamic viewpoint. The number density of the black hole molecules is introduced to measure the microscopic degrees of freedom of the black hole. We found that the number density suffers a sudden change accompanied by a latent heat when the black hole system crosses the small-large black hole coexistence curve, while when the system passes the critical point, it encounters a second-order phase transition with a vanishing latent heat due to the continuous change of the number density. Moreover, the thermodynamic scalar curvature suggests that there is a weak attractive interaction between two black hole molecules. These phenomena might cast new insight into the underlying microscopic structure of a charged anti-de Sitter black hole.

  11. On the structure of the two-stream instability–complex G-Hamiltonian structure and Krein collisions between positive- and negative-action modes

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Ruili; Liu, Jian; Xiao, Jianyuan [Department of Modern Physics and School of Nuclear Science and Technology, University of Science and Technology of China, Hefei, Anhui 230026 (China); Key Laboratory of Geospace Environment, CAS, Hefei, Anhui 230026 (China); Qin, Hong, E-mail: hongqin@princeton.edu [Plasma Physics Laboratory, Princeton University, Princeton, New Jersey 08543 (United States); Department of Modern Physics and School of Nuclear Science and Technology, University of Science and Technology of China, Hefei, Anhui 230026 (China); Davidson, Ronald C. [Plasma Physics Laboratory, Princeton University, Princeton, New Jersey 08543 (United States)

    2016-07-15

    The two-stream instability is probably the most important elementary example of collective instabilities in plasma physics and beam-plasma systems. For a warm plasma with two charged particle species, the instability diagram of the two-stream instability based on a 1D warm-fluid model exhibits an interesting band structure that has not been explained. We show that the band structure for this instability is the consequence of the Hamiltonian nature of the warm two-fluid system. Interestingly, the Hamiltonian nature manifests as a complex G-Hamiltonian structure in wave-number space, which directly determines the instability diagram. Specifically, it is shown that the boundaries between the stable and unstable regions are locations for Krein collisions between eigenmodes with different Krein signatures. In terms of physics, this rigorously implies that the system is destabilized when a positive-action mode resonates with a negative-action mode, and that this is the only mechanism by which the system can be destabilized. It is anticipated that this physical mechanism of destabilization is valid for other collective instabilities in conservative systems in plasma physics, accelerator physics, and fluid dynamics systems, which admit infinite-dimensional Hamiltonian structures.

  12. Mechanical low-frequency filter via modes separation in 3D periodic structures

    Science.gov (United States)

    D'Alessandro, L.; Belloni, E.; Ardito, R.; Braghin, F.; Corigliano, A.

    2017-12-01

    This work presents a strategy to design three-dimensional elastic periodic structures endowed with complete bandgaps, the first of which is ultra-wide, where the top limits of the first two bandgaps are overstepped in terms of wave transmission in the finite structure. Thus, subsequent bandgaps are merged, approaching the behaviour of a three-dimensional low-pass mechanical filter. This result relies on a proper organization of the modal characteristics, and it is validated by performing numerical and analytical calculations over the unit cell. A prototype of the analysed layout, made of Nylon by means of additive manufacturing, is experimentally tested to assess the transmission spectrum of the finite structure, obtaining good agreement with numerical predictions. The presented strategy paves the way for the development of a class of periodic structures to be used in robust and reliable wave attenuation over a wide frequency band.

  13. Coupling Neumann development and component mode synthesis methods for stochastic analysis of random structures

    Directory of Open Access Journals (Sweden)

    Driss Sarsri

    2014-05-01

    Full Text Available In this paper, we propose a method to calculate the first two moments (mean and variance of the structural dynamics response of a structure with uncertain variables and subjected to random excitation. For this, Newmark method is used to transform the equation of motion of the structure into a quasistatic equilibrium equation in the time domain. The Neumann development method was coupled with Monte Carlo simulations to calculate the statistical values of the random response. The use of modal synthesis methods can reduce the dimensions of the model before integration of the equation of motion. Numerical applications have been developed to highlight effectiveness of the method developed to analyze the stochastic response of large structures.

  14. Loading mode dependent effective properties of octet-truss lattice structures using 3D-printing

    Science.gov (United States)

    Challapalli, Adithya

    Cellular materials, often called lattice materials, are increasingly receiving attention for their ultralight structures with high specific strength, excellent impact absorption, acoustic insulation, heat dissipation media and compact heat exchangers. In alignment with emerging additive manufacturing (AM) technology, realization of the structural applications of the lattice materials appears to be becoming faster. Considering the direction dependent material properties of the products with AM, by directionally dependent printing resolution, effective moduli of lattice structures appear to be directionally dependent. In this paper, a constitutive model of a lattice structure, which is an octet-truss with a base material having an orthotropic material property considering AM is developed. In a case study, polyjet based 3D printing material having an orthotropic property with a 9% difference in the principal direction provides difference in the axial and shear moduli in the octet-truss by 2.3 and 4.6%. Experimental validation for the effective properties of a 3D printed octet-truss is done for uniaxial tension and compression test. The theoretical value based on the micro-buckling of truss member are used to estimate the failure strength. Modulus value appears a little overestimate compared with the experiment. Finite element (FE) simulations for uniaxial compression and tension of octettruss lattice materials are conducted. New effective properties for the octet-truss lattice structure are developed considering the observed behavior of the octet-truss structure under macroscopic compression and tension trough simulations.

  15. Characterizing structures on borehole images and logging data of the Nankai trough accretionary prism: new insights

    Science.gov (United States)

    Jurado, Maria Jose

    2016-04-01

    IODP has extensively used the D/V Chikyu to drill the Kumano portion of the Nankai Trough, including two well sites within the Kumano Basin. IODP Expeditions 338 and 348 drilled deep into the inner accretionary prism south of the Kii Peninsula collecting a suite of LWD data, including natural gamma ray, electrical resistivity logs and borehole images, suitable to characterize structures (fractures and faults) inside the accretionary prism. Structural interpretation and analysis of logging-while-drilling data in the deep inner prism revealed intense deformation of a generally homogenous lithology characterized by bedding that dips steeply (60-90°) to the NW, intersected by faults and fractures. Multiple phases of deformation are characterized. IODP Expedition borehole images and LWD data acquired in the last decade in previous and results of NantroSEIZE IODP Expeditions (314, 319) were also analyzed to investigate the internal geometries and structures of the Nankai Trough accretionary prism. This study focused mainly on the characterization of the different types of structures and their specific position within the accretionary prism structures. New structural constraints and methodologies as well as a new approach to the characterization of study of active structures inside the prism will be presented.

  16. Expression, purification and insights into structure and folding of the ADAM22 pro domain

    DEFF Research Database (Denmark)

    Sørensen, Hans Peter; Jacobsen, Jonas; Nielbo, Steen

    2008-01-01

    . To understand the functions of human ADAM pro domains and to determine three-dimensional structures, we have screened promising targets for expression and purification properties when using Escherichia coli as the host. The pro domain of ADAM22 (ADAM22-P) expressed in E. coli was folded, as determined by CD...... and NMR spectroscopy. An ADAM22-P fragment encoding residues 26-199 could be expressed in high amounts, remained soluble above 1 mM, and was suitable for structural studies by NMR spectroscopy. CD spectroscopy and predictions suggest that the secondary structure in ADAM22-P consists of beta...

  17. New insight into the solution structures of wheat gluten proteins from Raman optical activity

    DEFF Research Database (Denmark)

    Blanch, E.W.; Kasarda, D.D.; Hecht, L.

    2003-01-01

    Vibrational Raman optical activity (ROA) spectra of the wheat proteins a-gliadin (A-gliadin), omega-liadin, and a 30 kDa peptide called T-A-1 from the high molecular weight glutenin subunit (HMW-GS) Dx5 were measured to obtain new information about their solution structures. The spectral data show...... that, under the conditions investigated, A-gliadin contains a considerable amount of hydrated alpha-helix, most of which probably lies within a relatively structured C-terminal domain. Smaller quantities of beta-structure and poly(L-proline) II (PPII) helix were also identified. Addition of methanol...

  18. Kinetic and structural studies reveal a unique binding mode of sulfite to the nickel center in urease.

    Science.gov (United States)

    Mazzei, Luca; Cianci, Michele; Benini, Stefano; Bertini, Leonardo; Musiani, Francesco; Ciurli, Stefano

    2016-01-01

    Urease is the most efficient enzyme known to date, and catalyzes the hydrolysis of urea using two Ni(II) ions in the active site. Urease is a virulence factor in several human pathogens, while causing severe environmental and agronomic problems. Sporosarcina pasteurii urease has been used extensively in the structural characterization of the enzyme. Sodium sulfite has been widely used as a preservative in urease solutions to prevent oxygen-induced oxidation, but its role as an inhibitor has also been suggested. In the present study, isothermal titration microcalorimetry was used to establish sulfite as a competitive inhibitor for S. pasteurii urease, with an inhibition constant of 0.19mM at pH7. The structure of the urease-sulfite complex, determined at 1.65Å resolution, shows the inhibitor bound to the dinuclear Ni(II) center of urease in a tridentate mode involving bonds between the two Ni(II) ions in the active site and all three oxygen atoms of the inhibitor, supporting the observed competitive inhibition kinetics. This coordination mode of sulfite has never been observed, either in proteins or in small molecule complexes, and could inspire synthetic coordination chemists as well as biochemists to develop urease inhibitors based on this chemical moiety. Copyright © 2015 Elsevier Inc. All rights reserved.

  19. Stable single longitudinal mode erbium-doped silica fiber laser based on an asymmetric linear three-cavity structure

    International Nuclear Information System (INIS)

    Feng Ting; Yan Feng-Ping; Li Qi; Peng Wan-Jing; Feng Su-Chun; Tan Si-Yu; Wen Xiao-Dong

    2013-01-01

    We present a stable linear-cavity single longitudinal mode (SLM) erbium-doped silica fiber laser. It consists of four fiber Bragg gratings (FBGs) directly written in a section of photosensitive erbium-doped fiber (EDF) to form an asymmetric three-cavity structure. The stable SLM operation at a wavelength of 1545.112 nm with a 3-dB bandwidth of 0.012 nm and an optical signal-to-noise ratio (OSNR) of about 60 dB is verified experimentally. Under laboratory conditions, the performance of a power fluctuation of less than 0.05 dB observed from the power meter for 6 h and a wavelength variation of less than 0.01 nm obtained from the optical spectrum analyzer (OSA) for about 1.5 h are demonstrated. The gain fiber length is no longer limited to only several centimeters for SLM operation because of the excellent mode-selecting ability of the asymmetric three-cavity structure. The proposed scheme provides a simple and cost-effective approach to realizing a stable SLM fiber laser. (electromagnetism, optics, acoustics, heat transfer, classical mechanics, and fluid dynamics)

  20. An integrated approach to the probabilistic assessments of aircraft strikes and structural mode of damages to nuclear power plants

    International Nuclear Information System (INIS)

    Godbout, P.; Brais, A.

    1975-01-01

    The possibilities of an aircraft striking a Canadian nuclear power plant in the vicinity of an airport and of inducing structural failure modes have been evaluated. This evaluation, together with other studies, may enhance decisions in the development of general criteria for the siting of reactors near airports. The study made use, for assessment, of the probabilistic approach and made judicious applications of the finite Canadian, French, German, American and English resources that were available. The tools, techniques and methods used for achieving the above, form what may be called an integrated approach. This method of approach requires that the study be made in six consecutive steps as follows: the qualitative evaluation of having an aircraft strike on a site situated near an airport with the use of the logic model technique; the statistical data gathering on aircraft movements and accidents; evaluating the probability distribution and calculating the basic event probabilities; evaluating the probability of an aircraft strike and the application of the sensitivity approach; generating the probability density distribution versus strike impact energy, that is, the evaluation of the energy envelope; and the probabilistic evaluation of structural failure mode inducements

  1. Experimental demonstration of a simple displacement sensor based on a bent single-mode–multimode–single-mode fiber structure

    International Nuclear Information System (INIS)

    Wu, Qiang; Semenova, Yuliya; Wang, Pengfei; Hatta, Agus Muhamad; Farrell, Gerald

    2011-01-01

    A simple displacement sensor based on a bent single-mode–multimode–single-mode (SMS) fiber structure is proposed and experimentally investigated. The sensor offers a wider displacement range, not limited by the risk of fiber breakage, as well as a three-fold increase in displacement sensitivity by comparison with a straight SMS structure sensor. This sensor can be interrogated by either an optical spectral analyzer (OSA) or a ratiometric interrogation system: (1) if interrogated by an OSA assuming a resolution of 1 pm, it has a sensitivity of 28.2 nm for a displacement measurement range from 0 to 280 µm; (2) if interrogated by a ratiometric interrogation system, it has worst and best case resolutions of 556 and 38 nm, respectively, for a displacement measurement range from 0 to 520 µm

  2. Hepatoprotective amide constituents from the fruit of Piper chaba: Structural requirements, mode of action, and new amides.

    Science.gov (United States)

    Matsuda, Hisashi; Ninomiya, Kiyofumi; Morikawa, Toshio; Yasuda, Daisuke; Yamaguchi, Itadaki; Yoshikawa, Masayuki

    2009-10-15

    The 80% aqueous acetone extract from the fruit of Piper chaba (Piperaceae) was found to have hepatoprotective effects on D-galactosamine (D-GalN)/lipopolysaccharide-induced liver injury in mice. From the ethyl acetate-soluble fraction, three new amides, piperchabamides E, G, and H, 33 amides, and four aromatic constituents were isolated. Among the isolates, several amide constituents inhibited D-GalN/tumor necrosis factor-alpha (TNF-alpha)-induced death of hepatocytes, and the following structural requirements were suggested: (i) the amide moiety is essential for potent activity; and (ii) the 1,9-decadiene structure between the benzene ring and the amide moiety tended to enhance the activity. Moreover, a principal constituent, piperine, exhibited strong in vivo hepatoprotective effects at doses of 5 and 10 mg/kg, po and its mode of action was suggested to depend on the reduced sensitivity of hepatocytes to TNF-alpha.

  3. Molecular details of secretory phospholipase A2 from flax (Linum usitatissimum L.) provide insight into its structure and function.

    Science.gov (United States)

    Gupta, Payal; Dash, Prasanta K

    2017-09-11

    Secretory phospholipase A 2 (sPLA 2 ) are low molecular weight proteins (12-18 kDa) involved in a suite of plant cellular processes imparting growth and development. With myriad roles in physiological and biochemical processes in plants, detailed analysis of sPLA 2 in flax/linseed is meagre. The present work, first in flax, embodies cloning, expression, purification and molecular characterisation of two distinct sPLA 2 s (I and II) from flax. PLA 2 activity of the cloned sPLA 2 s were biochemically assayed authenticating them as bona fide phospholipase A 2 . Physiochemical properties of both the sPLA 2 s revealed they are thermostable proteins requiring di-valent cations for optimum activity.While, structural analysis of both the proteins revealed deviations in the amino acid sequence at C- & N-terminal regions; hydropathic study revealed LusPLA 2 I as a hydrophobic protein and LusPLA 2 II as a hydrophilic protein. Structural analysis of flax sPLA 2 s revealed that secondary structure of both the proteins are dominated by α-helix followed by random coils. Modular superimposition of LusPLA 2 isoforms with rice sPLA 2 confirmed monomeric structural preservation among plant phospholipase A 2 and provided insight into structure of folded flax sPLA 2 s.

  4. The structural flexibility of the human copper chaperone Atox1: Insights from combined pulsed EPR studies and computations.

    Science.gov (United States)

    Levy, Ariel R; Turgeman, Meital; Gevorkyan-Aiapetov, Lada; Ruthstein, Sharon

    2017-08-01

    Metallochaperones are responsible for shuttling metal ions to target proteins. Thus, a metallochaperone's structure must be sufficiently flexible both to hold onto its ion while traversing the cytoplasm and to transfer the ion to or from a partner protein. Here, we sought to shed light on the structure of Atox1, a metallochaperone involved in the human copper regulation system. Atox1 shuttles copper ions from the main copper transporter, Ctr1, to the ATP7b transporter in the Golgi apparatus. Conventional biophysical tools such as X-ray or NMR cannot always target the various conformational states of metallochaperones, owing to a requirement for crystallography or low sensitivity and resolution. Electron paramagnetic resonance (EPR) spectroscopy has recently emerged as a powerful tool for resolving biological reactions and mechanisms in solution. When coupled with computational methods, EPR with site-directed spin labeling and nanoscale distance measurements can provide structural information on a protein or protein complex in solution. We use these methods to show that Atox1 can accommodate at least four different conformations in the apo state (unbound to copper), and two different conformations in the holo state (bound to copper). We also demonstrate that the structure of Atox1 in the holo form is more compact than in the apo form. Our data provide insight regarding the structural mechanisms through which Atox1 can fulfill its dual role of copper binding and transfer. © 2017 The Protein Society.

  5. Insights from the structure of a smallpox virus topoisomerase-DNA transition state mimic

    Science.gov (United States)

    Perry, Kay; Hwang, Young; Bushman, Frederic D.; Van Duyne, Gregory D.

    2010-01-01

    Summary Poxviruses encode their own type IB topoisomerases (TopIBs) which release superhelical tension generated by replication and transcription of their genomes. To investigate the reaction catalyzed viral TopIBs, we have determined the structure of a variola virus topoisomerase-DNA complex trapped as a vanadate transition state mimic. The structure reveals how the viral TopIB enzymes are likely to position the DNA duplex for ligation following relaxation of supercoils and identifies the sources of friction observed in single molecule experiments that argue against free rotation. The structure also identifies a conformational change in the leaving group sugar that must occur prior to cleavage and reveals a mechanism for promoting ligation following relaxation of supercoils that involves a novel Asp-minor groove interaction. Overall, the new structural data support a common catalytic mechanism for the TopIB superfamily but indicate distinct methods for controlling duplex rotation in the small vs. large enzyme subfamilies. PMID:20152159

  6. New Insight into the Toughening Mechanisms of Seashell: From Arch Shape to Multilayer Structure

    Directory of Open Access Journals (Sweden)

    Quan Yuan

    2016-01-01

    Full Text Available A seashell is a closed three-dimensional curved surface formed by two symmetrical open shells. Three-point bending is performed on a pure aragonite straight beam (PASB model and a multilayer structure curved beam (MSCB model to elucidate the structure-property relationships of seashells. The integrity of the PASB is broken because of the introduction of a soft layer, but this drawback is compensated by the peculiar arch shape and the internal multilayer structure. The effective modulus, stiffness, and fracture energy of MSCB increase with an increase in volume fraction, aspect ratio of aragonite platelet, overlap ratio of hard layers, and ratio of the elastic modulus of the hard layer to the shear modulus of the soft layer. New design disciplines drawn from the MSCB model are peculiar arch shape, internal multilayer structure of larger volume fraction, and aspect ratio of hard layers and nanoscaled soft layers.

  7. New insights about enzyme evolution from large scale studies of sequence and structure relationships

    OpenAIRE

    Babbitt, Patricia; Brown, SD; Babbitt, PC

    2014-01-01

    © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.Understanding how enzymes have evolved offers clues about their structure-function relationships and mechanisms. Here, we describe evolution of functionally diverse enzyme superfami

  8. Optimized expression and purification of NavAb provide the structural insight into the voltage dependence.

    Science.gov (United States)

    Irie, Katsumasa; Haga, Yukari; Shimomura, Takushi; Fujiyoshi, Yoshinori

    2018-01-01

    Voltage-gated sodium channels are crucial for electro-signalling in living systems. Analysis of the molecular mechanism requires both fine electrophysiological evaluation and high-resolution channel structures. Here, we optimized a dual expression system of NavAb, which is a well-established standard of prokaryotic voltage-gated sodium channels, for E. coli and insect cells using a single plasmid vector to analyse high-resolution protein structures and measure large ionic currents. Using this expression system, we evaluated the voltage dependence and determined the crystal structures of NavAb wild-type and two mutants, E32Q and N49K, whose voltage dependence were positively shifted and essential interactions were lost in voltage sensor domain. The structural and functional comparison elucidated the molecular mechanisms of the voltage dependence of prokaryotic voltage-gated sodium channels. © 2017 Federation of European Biochemical Societies.

  9. Insights into Brain Glycogen Metabolism: THE STRUCTURE OF HUMAN BRAIN GLYCOGEN PHOSPHORYLASE.

    Science.gov (United States)

    Mathieu, Cécile; Li de la Sierra-Gallay, Ines; Duval, Romain; Xu, Ximing; Cocaign, Angélique; Léger, Thibaut; Woffendin, Gary; Camadro, Jean-Michel; Etchebest, Catherine; Haouz, Ahmed; Dupret, Jean-Marie; Rodrigues-Lima, Fernando

    2016-08-26

    Brain glycogen metabolism plays a critical role in major brain functions such as learning or memory consolidation. However, alteration of glycogen metabolism and glycogen accumulation in the brain contributes to neurodegeneration as observed in Lafora disease. Glycogen phosphorylase (GP), a key enzyme in glycogen metabolism, catalyzes the rate-limiting step of glycogen mobilization. Moreover, the allosteric regulation of the three GP isozymes (muscle, liver, and brain) by metabolites and phosphorylation, in response to hormonal signaling, fine-tunes glycogenolysis to fulfill energetic and metabolic requirements. Whereas the structures of muscle and liver GPs have been known for decades, the structure of brain GP (bGP) has remained elusive despite its critical role in brain glycogen metabolism. Here, we report the crystal structure of human bGP in complex with PEG 400 (2.5 Å) and in complex with its allosteric activator AMP (3.4 Å). These structures demonstrate that bGP has a closer structural relationship with muscle GP, which is also activated by AMP, contrary to liver GP, which is not. Importantly, despite the structural similarities between human bGP and the two other mammalian isozymes, the bGP structures reveal molecular features unique to the brain isozyme that provide a deeper understanding of the differences in the activation properties of these allosteric enzymes by the allosteric effector AMP. Overall, our study further supports that the distinct structural and regulatory properties of GP isozymes contribute to the different functions of muscle, liver, and brain glycogen. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  10. Research resource: novel structural insights bridge gaps in glycoprotein hormone receptor analyses.

    Science.gov (United States)

    Kreuchwig, Annika; Kleinau, Gunnar; Krause, Gerd

    2013-08-01

    The first version of a glycoprotein hormone receptor (GPHR) information resource was designed to link functional with structural GPHR information, in order to support sequence-structure-function analysis of the LH, FSH, and TSH receptors (http://ssfa-gphr.de). However, structural information on a binding- and signaling-sensitive extracellular fragment (∼100 residues), the hinge region, had been lacking. A new FSHR crystal structure of the hormone-bound extracellular domain has recently been solved. The structure comprises the leucine-rich repeat domain and most parts of the hinge region. We have not only integrated the new FSHR/FSH structure and the derived homology models of TSHR/TSH, LHCGR/CG, and LHCGR/LH into our web-based information resource, but have additionally provided novel tools to analyze the advanced structural features, with the common characteristics and distinctions between GPHRs, in a more precise manner. The hinge region with its second hormone-binding site allows us to assign functional data to the new structural features between hormone and receptor, such as binding details of a sulfated tyrosine (conserved throughout the GPHRs) extending into a pocket of the hormone. We have also implemented a protein interface analysis tool that enables the identification and visualization of extracellular contact points between interaction partners. This provides a starting point for comparing the binding patterns of GPHRs. Together with the mutagenesis data stored in the database, this will help to decipher the essential residues for ligand recognition and the molecular mechanisms of signal transduction, extending from the extracellular hormone-binding site toward the intracellular G protein-binding sites.

  11. The NMR structure of human obestatin in membrane-like environments: insights into the structure-bioactivity relationship of obestatin.

    Science.gov (United States)

    Alén, Begoña O; Nieto, Lidia; Gurriarán-Rodríguez, Uxía; Mosteiro, Carlos S; Álvarez-Pérez, Juan C; Otero-Alén, María; Camiña, Jesús P; Gallego, Rosalía; García-Caballero, Tomás; Martín-Pastor, Manuel; Casanueva, Felipe F; Jiménez-Barbero, Jesús; Pazos, Yolanda

    2012-01-01

    The quest for therapeutic applications of obestatin involves, as a first step, the determination of its 3D solution structure and the relationship between this structure and the biological activity of obestatin. On this basis, we have employed a combination of circular dichroism (CD), nuclear magnetic resonance (NMR) spectroscopy, and modeling techniques to determine the solution structure of human obestatin (1). Other analogues, including human non-amidated obestatin (2) and the fragment peptides (6-23)-obestatin (3), (11-23)-obestatin (4), and (16-23)-obestatin (5) have also been scrutinized. These studies have been performed in a micellar environment to mimic the cell membrane (sodium dodecyl sulfate, SDS). Furthermore, structural-activity relationship studies have been performed by assessing the in vitro proliferative capabilities of these peptides in the human retinal pigmented epithelial cell line ARPE-19 (ERK1/2 and Akt phosphorylation, Ki67 expression, and cellular proliferation). Our findings emphasize the importance of both the primary structure (composition and size) and particular segments of the obestatin molecule that posses significant α-helical characteristics. Additionally, details of a species-specific role for obestatin have also been hypothesized by comparing human and mouse obestatins (1 and 6, respectively) at both the structural and bioactivity levels.

  12. The NMR structure of human obestatin in membrane-like environments: insights into the structure-bioactivity relationship of obestatin.

    Directory of Open Access Journals (Sweden)

    Begoña O Alén

    Full Text Available The quest for therapeutic applications of obestatin involves, as a first step, the determination of its 3D solution structure and the relationship between this structure and the biological activity of obestatin. On this basis, we have employed a combination of circular dichroism (CD, nuclear magnetic resonance (NMR spectroscopy, and modeling techniques to determine the solution structure of human obestatin (1. Other analogues, including human non-amidated obestatin (2 and the fragment peptides (6-23-obestatin (3, (11-23-obestatin (4, and (16-23-obestatin (5 have also been scrutinized. These studies have been performed in a micellar environment to mimic the cell membrane (sodium dodecyl sulfate, SDS. Furthermore, structural-activity relationship studies have been performed by assessing the in vitro proliferative capabilities of these peptides in the human retinal pigmented epithelial cell line ARPE-19 (ERK1/2 and Akt phosphorylation, Ki67 expression, and cellular proliferation. Our findings emphasize the importance of both the primary structure (composition and size and particular segments of the obestatin molecule that posses significant α-helical characteristics. Additionally, details of a species-specific role for obestatin have also been hypothesized by comparing human and mouse obestatins (1 and 6, respectively at both the structural and bioactivity levels.

  13. Thermodynamic heuristics with case-based reasoning: combined insights for RNA pseudoknot secondary structure.

    Science.gov (United States)

    Al-Khatib, Ra'ed M; Rashid, Nur'Aini Abdul; Abdullah, Rosni

    2011-08-01

    The secondary structure of RNA pseudoknots has been extensively inferred and scrutinized by computational approaches. Experimental methods for determining RNA structure are time consuming and tedious; therefore, predictive computational approaches are required. Predicting the most accurate and energy-stable pseudoknot RNA secondary structure has been proven to be an NP-hard problem. In this paper, a new RNA folding approach, termed MSeeker, is presented; it includes KnotSeeker (a heuristic method) and Mfold (a thermodynamic algorithm). The global optimization of this thermodynamic heuristic approach was further enhanced by using a case-based reasoning technique as a local optimization method. MSeeker is a proposed algorithm for predicting RNA pseudoknot structure from individual sequences, especially long ones. This research demonstrates that MSeeker improves the sensitivity and specificity of existing RNA pseudoknot structure predictions. The performance and structural results from this proposed method were evaluated against seven other state-of-the-art pseudoknot prediction methods. The MSeeker method had better sensitivity than the DotKnot, FlexStem, HotKnots, pknotsRG, ILM, NUPACK and pknotsRE methods, with 79% of the predicted pseudoknot base-pairs being correct.

  14. Model representations of kerogen structures: An insight from density functional theory calculations and spectroscopic measurements.

    Science.gov (United States)

    Weck, Philippe F; Kim, Eunja; Wang, Yifeng; Kruichak, Jessica N; Mills, Melissa M; Matteo, Edward N; Pellenq, Roland J-M

    2017-08-01

    Molecular structures of kerogen control hydrocarbon production in unconventional reservoirs. Significant progress has been made in developing model representations of various kerogen structures. These models have been widely used for the prediction of gas adsorption and migration in shale matrix. However, using density functional perturbation theory (DFPT) calculations and vibrational spectroscopic measurements, we here show that a large gap may still remain between the existing model representations and actual kerogen structures, therefore calling for new model development. Using DFPT, we calculated Fourier transform infrared (FTIR) spectra for six most widely used kerogen structure models. The computed spectra were then systematically compared to the FTIR absorption spectra collected for kerogen samples isolated from Mancos, Woodford and Marcellus formations representing a wide range of kerogen origin and maturation conditions. Limited agreement between the model predictions and the measurements highlights that the existing kerogen models may still miss some key features in structural representation. A combination of DFPT calculations with spectroscopic measurements may provide a useful diagnostic tool for assessing the adequacy of a proposed structural model as well as for future model development. This approach may eventually help develop comprehensive infrared (IR)-fingerprints for tracing kerogen evolution.

  15. Novel complex MAD phasing and RNase H structural insights using selenium oligonucleotides

    Energy Technology Data Exchange (ETDEWEB)

    Abdur, Rob; Gerlits, Oksana O.; Gan, Jianhua; Jiang, Jiansheng; Salon, Jozef; Kovalevsky, Andrey Y.; Chumanevich, Alexander A.; Weber, Irene T.; Huang, Zhen, E-mail: huang@gsu.edu [Georgia State University, Atlanta, GA 30303 (United States)

    2014-02-01

    Selenium-derivatized oligonucleotides may facilitate phase determination and high-resolution structure determination for protein–nucleic acid crystallography. The Se atom-specific mutagenesis (SAM) strategy may also enhance the study of nuclease catalysis. The crystal structures of protein–nucleic acid complexes are commonly determined using selenium-derivatized proteins via MAD or SAD phasing. Here, the first protein–nucleic acid complex structure determined using selenium-derivatized nucleic acids is reported. The RNase H–RNA/DNA complex is used as an example to demonstrate the proof of principle. The high-resolution crystal structure indicates that this selenium replacement results in a local subtle unwinding of the RNA/DNA substrate duplex, thereby shifting the RNA scissile phosphate closer to the transition state of the enzyme-catalyzed reaction. It was also observed that the scissile phosphate forms a hydrogen bond to the water nucleophile and helps to position the water molecule in the structure. Consistently, it was discovered that the substitution of a single O atom by a Se atom in a guide DNA sequence can largely accelerate RNase H catalysis. These structural and catalytic studies shed new light on the guide-dependent RNA cleavage.

  16. Insights into the molecular mechanism of dehalogenation catalyzed by D-2-haloacid dehalogenase from crystal structures.

    Science.gov (United States)

    Wang, Yayue; Feng, Yanbin; Cao, Xupeng; Liu, Yinghui; Xue, Song

    2018-01-23

    D-2-haloacid dehalogenases (D-DEXs) catalyse the hydrolytic dehalogenation of D-2-haloacids, releasing halide ions and producing the corresponding 2-hydroxyacids. A structure-guided elucidation of the catalytic mechanism of this dehalogenation reaction has not been reported yet. Here, we report the catalytic mechanism of a D-DEX, HadD AJ1 from Pseudomonas putida AJ1/23, which was elucidated by X-ray crystallographic analysis and the H 2 18 O incorporation experiment. HadD AJ1 is an α-helical hydrolase that forms a homotetramer with its monomer including two structurally axisymmetric repeats. The product-bound complex structure was trapped with L-lactic acid in the active site, which is framed by the structurally related helices between two repeats. Site-directed mutagenesis confirmed the importance of the residues lining the binding pocket in stabilizing the enzyme-substrate complex. Asp205 acts as a key catalytic residue and is responsible for activating a water molecule along with Asn131. Then, the hydroxyl group of the water molecule directly attacks the C2 atom of the substrate to release the halogen ion instead of forming an enzyme-substrate ester intermediate as observed in L-2-haloacid dehalogenases. The newly revealed structural and mechanistic information on D-DEX may inspire structure-based mutagenesis to engineer highly efficient haloacid dehalogenases.

  17. Insight into the structures and stabilities of Tc and Re DMSA complexes: A computational study

    International Nuclear Information System (INIS)

    Blanco González, Alejandro; Hernández Valdés, Daniel; García Fleitas, Ariel; Rodríguez Riera, Zalua; Jáuregui Haza, Ulises

    2016-01-01

    Meso-2,3-dimercaptosuccinic acid (DMSA) is used in nuclear medicine as ligand for preparation of radiopharmaceuticals for diagnostic and therapy. DMSA has been the subject of numerous investigations during the past three decades and new and significant information of the chemistry and pharmacology of DMSA complexes have emerged. In comparison to other ligands, the structure of some DMSA complexes is unclear up today. The structures and applications of DMSA complexes are strictly dependent on the chemical conditions of their preparation, especially pH and the ratio of components. A computational study of M-DMSA (M = Tc, Re) complexes has been performed using density functional theory. Different isomers for M(V) and M(III) complexes were study. The pH influence over ligand structures was taken into account and the solvent effect was evaluated using an implicit solvation model. The fully optimized complex syn-endo Re(V)-DMSA shows a geometry similar to the X-ray data and was used to validate the methodology. Moreover, new alternative structures for the renal agent 99mTc(III)-DMSA were proposed and computationally studied. For two complex structures, a larger stability respect to that proposed in the literature was obtained. Furthermore, Tc(V)-DMSA complexes are more stable than the Tc(III)-DMSA proposed structures. In general, Re complexes are more stables than the corresponding Tc ones. (author)

  18. Seismotectonics of Taiwan Shoal region in northeastern SCS: Insights from crustal structure

    Science.gov (United States)

    Kuiyuan, Wan; Jinlong, Sun; Shaohong, Xia; Xiaoling, Xie; Xiang, Zhang; Huilong, Xu; Jinghe, Cao

    2017-04-01

    A seismicity cluster and a great 16 September 1994 earthquake occur in the Taiwan Shoal region, outer rise of the Manila subduction zone. To understand what mechanisms control and generate the earthquake cluster, it is important to investigate the deep crustal structure of the Taiwan Shoal region. We present a 2-D seismic tomographic image of the crustal structure along the OBS2012 profile based on ocean bottom seismographic (OBS) data. The structure exhibits that a high velocity anomaly in the upper crust beneath the Taiwan Shoal is flanked by lower velocity anomalies. Based on the crustal structure, we study the 765 earthquakes, which occurred in the period 1991-2015. These epicenters, combined with the regional faults, and crustal structure, allow us to better understand the nature of the active tectonics in this region. The high velocity area is interpreted as representing stronger, defining major asperities where stress is concentrated corresponding to the location of the earthquake cluster. The earthquake cluster is influenced by the fault interactions. However, the 16 September 1994 earthquake is independents of the seismic activities but associated with the reactivation of the preexisting fault. In Taiwan region, the slab-pull was resisted by the exposed pre-collision accretionary prism and the resistive force caused the in-plane compressive stress accumulation. This condition may favor the triggering of future damaging earthquakes in this region. Key words: earthquake cluster; crustal structure; fault interactions; outer rise; Taiwan Shoal

  19. Crystal structure of the thioesterification conformation of Bacillus subtilis o-succinylbenzoyl-CoA synthetase reveals a distinct substrate-binding mode.

    Science.gov (United States)

    Chen, Yaozong; Li, Tin Lok; Lin, Xingbang; Li, Xin; Li, Xiang David; Guo, Zhihong

    2017-07-21

    o -Succinylbenzoyl-CoA (OSB-CoA) synthetase (MenE) is an essential enzyme in bacterial vitamin K biosynthesis and an important target in the development of new antibiotics. It is a member of the adenylating enzymes (ANL) family, which reconfigure their active site in two different active conformations, one for the adenylation half-reaction and the other for a thioesterification half-reaction, in a domain-alternation catalytic mechanism. Although several aspects of the adenylating mechanism in MenE have recently been uncovered, its thioesterification conformation remains elusive. Here, using a catalytically competent Bacillus subtilis mutant protein complexed with an OSB-CoA analogue, we determined MenE high-resolution structures to 1.76 and 1.90 Å resolution in a thioester-forming conformation. By comparison with the adenylation conformation, we found that MenE's C-domain rotates around the Ser-384 hinge by 139.5° during domain-alternation catalysis. The structures also revealed a thioesterification active site specifically conserved among MenE orthologues and a substrate-binding mode distinct from those of many other acyl/aryl-CoA synthetases. Of note, using site-directed mutagenesis, we identified several residues that specifically contribute to the thioesterification half-reaction without affecting the adenylation half-reaction. Moreover, we observed a substantial movement of the activated succinyl group in the thioesterification half-reaction. These findings provide new insights into the domain-alternation catalysis of a bacterial enzyme essential for vitamin K biosynthesis and of its adenylating homologues in the ANL enzyme family. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  20. Separate structure of two branches of sheared slab ηi mode and effects of plasma rotation shear in weak magnetic shear region

    International Nuclear Information System (INIS)

    Jiquan Li; Kishimoto, Y.; Tuda, T.

    2000-01-01

    The separate structure of two branches of the sheared slab η i mode near the minimum-q magnetic surface is analysed and the effects of plasma rotation shears are considered in the weak magnetic shear region. Results show that the separation condition depends on the non-monotonous q profile and the deviation of rational surface from the minimum-q surface. Furthermore, it is found that the diamagnetic rotation shear may suppress the perturbation of the sheared slab η i mode at one side of the minimum-q surface, the poloidal rotation shear from the sheared E-vector x B-vector flow has a similar role to the slab mode structure when it possesses a direction same as the diamagnetic shear. A plausible interrelation between the separate structures of the two branches of the sheared slab mode and the discontinuity or gap of the radially global structure of the drift wave near the minimum-q surface observed in the toroidal particle simulation (Kishimoto Y et al 1998 Plasma Phys. Control. Fusion 40 A663) is discussed. It seems to support such a viewpoint: the double or/and global branches of the sheared slab η i mode near the minimum-q surface may become a bridge to connect the radially global structures of the drift wave at two sides of the minimum-q surface and the discontinuity may originate from the separate structures of these slab modes for a flatter q profile. (author)

  1. Crystal structure of inulosucrase from Lactobacillus: insights into the substrate specificity and product specificity of GH68 fructansucrases.

    Science.gov (United States)

    Pijning, Tjaard; Anwar, Munir A; Böger, Markus; Dobruchowska, Justyna M; Leemhuis, Hans; Kralj, Slavko; Dijkhuizen, Lubbert; Dijkstra, Bauke W

    2011-09-09

    Fructansucrases (FSs) catalyze a transfructosylation reaction with sucrose as substrate to produce fructo-oligosaccharides and fructan polymers that contain either β-2,1 glycosidic linkages (inulin) or β-2,6 linkages (levan). Levan-synthesizing FSs (levansucrases) have been most extensively investigated, while detailed information on inulosucrases is limited. Importantly, the molecular basis of the different product specificities of levansucrases and inulosucrases is poorly understood. We have elucidated the three-dimensional structure of a truncated active bacterial GH68 inulosucrase, InuJ of Lactobacillus johnsonii NCC533 (residues 145-708), in its apo form, with a bound substrate (sucrose), and with a transfructosylation product. The sucrose binding pocket and the sucrose binding mode are virtually identical with those of GH68 levansucrases, confirming that both enzyme types use the same fully conserved structural framework for the binding and cleavage of the donor substrate sucrose in the active site. The binding mode of the first transfructosylation product 1-kestose (Fru-β(2-1)-Fru-α(2-1)-Glc, where Fru=fructose and Glc=glucose) in subsites -1 to +2 shows for the first time how inulin-type fructo-oligosaccharide bind in GH68 FS and how an inulin-type linkage can be formed. Surprisingly, observed interactions with the sugar in subsites +1 and +2 are provided by residues that are also present in levansucrases. The binding mode of 1-kestose and the presence of a more distant sucrose binding site suggest that residues beyond the +2 subsite, in particular residues from the nonconserved 1B-1C loop, determine product linkage type specificity in GH68 FSs. Copyright © 2011 Elsevier Ltd. All rights reserved.

  2. Failure mode prediction for composite structural insulated panels with MgO board facings

    Science.gov (United States)

    Smakosz, Łukasz; Kreja, Ireneusz

    2018-01-01

    Sandwich panels are readily used in civil engineering due to their high strength to weight ratio and the ease and speed of assembly. The idea of a sandwich section is to combine thin and durable facings with a light-weight core and the choice of materials used allows obtaining the desired behaviour. Panels in consideration consist of MgO (magnesium oxide) board facings and expanded polystyrene core and are characterized by immunity to biological corrosion, a high thermal insulation and a relatively low impact on environment. Customizing the range of panels to meet market needs requires frequent size changes, leading to different failure modes, which are identified in a series of costly full-scale laboratory tests. A nonlinear numerical model was created with a use of a commercial ABAQUS code and a user-defined procedure, which is able to reproduce observed failure mechanisms; its parameters were established on the basis of small-scale tests and numerical experiments. The model was validated by a comparison with the results of the full-scale bending and compression tests. The results obtained were in satisfactory agreement with the test data.

  3. Monolithic mode locked DBR laser with multiple-bandgap MQW structure realized by selective area growth

    Energy Technology Data Exchange (ETDEWEB)

    Schilling, M.; Bouayad-Amine, J.; Feeser, T.; Haisch, H.; Kuehn, E.; Lach, E.; Satzke, K.; Weber, J.; Zielinski, E. [Alcatel Telecom, Stuttgart (Germany). Research Div.

    1996-12-31

    The realization of novel monolithically integrated multiple-segment pulse laser sources in InGaAsP MQW technology is reported. The MQW layers for all functional sections of these devices, the modulator, the active (gain) and the passive waveguide, as well as the Bragg section were grown in a single selective area growth (SAG) step by LP-MOVPE on SiO{sub 2} patterned 2 inch InP substrates. Due to a properly selected pattern geometry 3 different bandgap regions with smooth interfaces are thereby formed along the laser cavity. The more than 4 mm long DBR lasers which exhibit a threshold current as low as 30 mA were mode locked by an intra-cavity electroabsorption modulator applying a sinusoidal voltage at around 10 GHz. In this way an optical pulse train with pulse widths < 13 ps (measured with a streak camera) and high extinction ratio was generated. A time-bandwidth product of 0.5 close to the Fourier limit is obtained. This device is very attractive for signal generation in 40 Gb/s OTDM transmission systems at 1.55 {micro}m wavelength.

  4. Rhabdovirus matrix protein structures reveal a novel mode of self-association.

    Directory of Open Access Journals (Sweden)

    Stephen C Graham

    2008-12-01

    Full Text Available The matrix (M proteins of rhabdoviruses are multifunctional proteins essential for virus maturation and budding that also regulate the expression of viral and host proteins. We have solved the structures of M from the vesicular stomatitis virus serotype New Jersey (genus: Vesiculovirus and from Lagos bat virus (genus: Lyssavirus, revealing that both share a common fold despite sharing no identifiable sequence homology. Strikingly, in both structures a stretch of residues from the otherwise-disordered N terminus of a crystallographically adjacent molecule is observed binding to a hydrophobic cavity on the surface of the protein, thereby forming non-covalent linear polymers of M in the crystals. While the overall topology of the interaction is conserved between the two structures, the molecular details of the interactions are completely different. The observed interactions provide a compelling model for the flexible self-assembly of the matrix protein during virion morphogenesis and may also modulate interactions with host proteins.

  5. SFM-FDTD analysis of triangular-lattice AAA structure: Parametric study of the TEM mode

    Science.gov (United States)

    Hamidi, M.; Chemrouk, C.; Belkhir, A.; Kebci, Z.; Ndao, A.; Lamrous, O.; Baida, F. I.

    2014-05-01

    This theoretical work reports a parametric study of enhanced transmission through annular aperture array (AAA) structure arranged in a triangular lattice. The effect of the incidence angle in addition to the inner and outer radii values on the evolution of the transmission spectra is carried out. To this end, a 3D Finite-Difference Time-Domain code based on the Split Field Method (SFM) is used to calculate the spectral response of the structure for any angle of incidence. In order to work through an orthogonal unit cell which presents the advantage to reduce time and space of computation, special periodic boundary conditions are implemented. This study provides a new modeling of AAA structures useful for producing tunable ultra-compact devices.

  6. Combining QSAR Modeling and Text-Mining Techniques to Link Chemical Structures and Carcinogenic Modes of Action.

    Science.gov (United States)

    Papamokos, George; Silins, Ilona

    2016-01-01

    There is an increasing need for new reliable non-animal based methods to predict and test toxicity of chemicals. Quantitative structure-activity relationship (QSAR), a computer-based method linking chemical structures with biological activities, is used in predictive toxicology. In this study, we tested the approach to combine QSAR data with literature profiles of carcinogenic modes of action automatically generated by a text-mining tool. The aim was to generate data patterns to identify associations between chemical structures and biological mechanisms related to carcinogenesis. Using these two methods, individually and combined, we evaluated 96 rat carcinogens of the hematopoietic system, liver, lung, and skin. We found that skin and lung rat carcinogens were mainly mutagenic, while the group of carcinogens affecting the hematopoietic system and the liver also included a large proportion of non-mutagens. The automatic literature analysis showed that mutagenicity was a frequently reported endpoint in the literature of these carcinogens, however, less common endpoints such as immunosuppression and hormonal receptor-mediated effects were also found in connection with some of the carcinogens, results of potential importance for certain target organs. The combined approach, using QSAR and text-mining techniques, could be useful for identifying more detailed information on biological mechanisms and the relation with chemical structures. The method can be particularly useful in increasing the understanding of structure and activity relationships for non-mutagens.

  7. Combining QSAR Modeling and Text-Mining Techniques to Link Chemical Structures and Carcinogenic Modes of Action

    Science.gov (United States)

    Papamokos, George; Silins, Ilona

    2016-01-01

    There is an increasing need for new reliable non-animal based methods to predict and test toxicity of chemicals. Quantitative structure-activity relationship (QSAR), a computer-based method linking chemical structures with biological activities, is used in predictive toxicology. In this study, we tested the approach to combine QSAR data with literature profiles of carcinogenic modes of action automatically generated by a text-mining tool. The aim was to generate data patterns to identify associations between chemical structures and biological mechanisms related to carcinogenesis. Using these two methods, individually and combined, we evaluated 96 rat carcinogens of the hematopoietic system, liver, lung, and skin. We found that skin and lung rat carcinogens were mainly mutagenic, while the group of carcinogens affecting the hematopoietic system and the liver also included a large proportion of non-mutagens. The automatic literature analysis showed that mutagenicity was a frequently reported endpoint in the literature of these carcinogens, however, less common endpoints such as immunosuppression and hormonal receptor-mediated effects were also found in connection with some of the carcinogens, results of potential importance for certain target organs. The combined approach, using QSAR and text-mining techniques, could be useful for identifying more detailed information on biological mechanisms and the relation with chemical structures. The method can be particularly useful in increasing the understanding of structure and activity relationships for non-mutagens. PMID:27625608

  8. Structural relaxation of polydisperse hard spheres: comparison of the mode-coupling theory to a Langevin dynamics simulation.

    Science.gov (United States)

    Weysser, F; Puertas, A M; Fuchs, M; Voigtmann, Th

    2010-07-01

    We analyze the slow glassy structural relaxation as measured through collective and tagged-particle density correlation functions obtained from Brownian dynamics simulations for a polydisperse system of quasi-hard spheres in the framework of the mode-coupling theory (MCT) of the glass transition. Asymptotic analyses show good agreement for the collective dynamics when polydispersity effects are taken into account in a multicomponent calculation, but qualitative disagreement at small q when the system is treated as effectively monodisperse. The origin of the different small-q behavior is attributed to the interplay between interdiffusion processes and structural relaxation. Numerical solutions of the MCT equations are obtained taking properly binned partial static structure factors from the simulations as input. Accounting for a shift in the critical density, the collective density correlation functions are well described by the theory at all densities investigated in the simulations, with quantitative agreement best around the maxima of the static structure factor and worst around its minima. A parameter-free comparison of the tagged-particle dynamics however reveals large quantitative errors for small wave numbers that are connected to the well-known decoupling of self-diffusion from structural relaxation and to dynamical heterogeneities. While deviations from MCT behavior are clearly seen in the tagged-particle quantities for densities close to and on the liquid side of the MCT glass transition, no such deviations are seen in the collective dynamics.

  9. Structural insights into transient receptor potential vanilloid type 1 (TRPV1) from homology modeling, flexible docking, and mutational studies.

    Science.gov (United States)

    Lee, Jin Hee; Lee, Yoonji; Ryu, HyungChul; Kang, Dong Wook; Lee, Jeewoo; Lazar, Jozsef; Pearce, Larry V; Pavlyukovets, Vladimir A; Blumberg, Peter M; Choi, Sun

    2011-04-01

    The transient receptor potential vanilloid subtype 1 (TRPV1) is a non-selective cation channel composed of four monomers with six transmembrane helices (TM1-TM6). TRPV1 is found in the central and peripheral nervous system, and it is an important therapeutic target for pain relief. We describe here the construction of a tetrameric homology model of rat TRPV1 (rTRPV1). We experimentally evaluated by mutational analysis the contribution of residues of rTRPV1 contributing to ligand binding by the prototypical TRPV1 agonists, capsaicin and resiniferatoxin (RTX). We then performed docking analysis using our homology model. The docking results with capsaicin and RTX showed that our homology model was reliable, affording good agreement with our mutation data. Additionally, the binding mode of a simplified RTX (sRTX) ligand as predicted by the modeling agreed well with those of capsaicin and RTX, accounting for the high binding affinity of the sRTX ligand for TRPV1. Through the homology modeling, docking and mutational studies, we obtained important insights into the ligand-receptor interactions at the molecular level which should prove of value in the design of novel TRPV1 ligands.

  10. Endoscopic mode for three-dimensional CT display of normal and pathologic laryngeal structures

    International Nuclear Information System (INIS)

    Sanuki, Tetsuji; Hyodo, Masamitsu; Yumoto, Eiji; Yasuhara, Yoshifumi; Ochi, Takashi

    1997-01-01

    The recent development of helical (spiral) computed tomography allows collection of volumetric data to obtain high quality three-dimensional (3D) reconstructed images. The authors applied the 3D CT endoscopic imaging technique to asses normal and pathologic laryngeal structures. The latter included trauma, vocal fold atrophy, cancer of the larynx and recurrent nerve palsy. This technique was able to show normal laryngeal structures and characteristic findings of each pathology. The 3D CT endoscopic images can be rotated around any axis, allowing optimal depiction of pathologic lesion. The use of 3D CT endoscopic technique provides the display of the location and extent of pathology and affords accurate therapeutic planning. (author)

  11. Structural insight into the binding interactions of modeled structure of Arabidopsis thaliana urease with urea: an in silico study.

    Science.gov (United States)

    Yata, Vinod Kumar; Thapa, Arun; Mattaparthi, Venkata Satish Kumar

    2015-01-01

    Urease (EC 3.5.1.5., urea amidohydrolase) catalyzes the hydrolysis of urea to ammonia and carbon dioxide. Urease is present to a greater abundance in plants and plays significant role related to nitrogen recycling from urea. But little is known about the structure and function of the urease derived from the Arabidopsis thaliana, the model system of choice for research in plant biology. In this study, a three-dimensional structural model of A. thaliana urease was constructed using computer-aided molecular modeling technique. The characteristic structural features of the modeled structure were then studied using atomistic molecular dynamics simulation. It was observed that the modeled structure was stable and regions between residues index (50-80, 500-700) to be significantly flexible. From the docking studies, we detected the possible binding interactions of modeled urease with urea. Ala399, Ile675, Thr398, and Thr679 residues of A. thaliana urease were observed to be significantly involved in binding with the substrate urea. We also compared the docking studies of ureases from other sources such as Canavalia ensiformis, Helicobacter pylori, and Bacillus pasteurii. In addition, we carried out mutation analysis to find the highly mutable amino acid residues of modeled A. thaliana urease. In this particular study, we observed Met485, Tyr510, Ser786, Val426, and Lys765 to be highly mutable amino acids. These results are significant for the mutagenesis analysis. As a whole, this study expounds the salient structural features as well the binding interactions of the modeled structure of A. thaliana urease.

  12. The human otubain2-ubiquitin structure provides insights into the cleavage specificity of poly-ubiquitin-linkages.

    Directory of Open Access Journals (Sweden)

    Mikael Altun

    Full Text Available Ovarian tumor domain containing proteases cleave ubiquitin (Ub and ubiquitin-like polypeptides from proteins. Here we report the crystal structure of human otubain 2 (OTUB2 in complex with a ubiquitin-based covalent inhibitor, Ub-Br2. The ubiquitin binding mode is oriented differently to how viral otubains (vOTUs bind ubiquitin/ISG15, and more similar to yeast and mammalian OTUs. In contrast to OTUB1 which has exclusive specificity towards Lys48 poly-ubiquitin chains, OTUB2 cleaves different poly-Ub linked chains. N-terminal tail swapping experiments between OTUB1 and OTUB2 revealed how the N-terminal structural motifs in OTUB1 contribute to modulating enzyme activity and Ub-chain selectivity, a trait not observed in OTUB2, supporting the notion that OTUB2 may affect a different spectrum of substrates in Ub-dependent pathways.

  13. Cortical Thinning and Altered Cortico-Cortical Structural Covariance of the Default Mode Network in Patients with Persistent Insomnia Symptoms.

    Science.gov (United States)

    Suh, Sooyeon; Kim, Hosung; Dang-Vu, Thien Thanh; Joo, Eunyeon; Shin, Chol

    2016-01-01

    Recent studies have suggested that structural abnormalities in insomnia may be linked with alterations in the default-mode network (DMN). This study compared cortical thickness and structural connectivity linked to the DMN in patients with persistent insomnia (PI) and good sleepers (GS). The current study used a clinical subsample from the longitudinal community-based Korean Genome and Epidemiology Study (KoGES). Cortical thickness and structural connectivity linked to the DMN in patients with persistent insomnia symptoms (PIS; n = 57) were compared to good sleepers (GS; n = 40). All participants underwent MRI acquisition. Based on literature review, we selected cortical regions corresponding to the DMN. A seed-based structural covariance analysis measured cortical thickness correlation between each seed region of the DMN and other cortical areas. Association of cortical thickness and covariance with sleep quality and neuropsychological assessments were further assessed. Compared to GS, cortical thinning was found in PIS in the anterior cingulate cortex, precentral cortex, and lateral prefrontal cortex. Decreased structural connectivity between anterior and posterior regions of the DMN was observed in the PIS group. Decreased structural covariance within the DMN was associated with higher PSQI scores. Cortical thinning in the lateral frontal lobe was related to poor performance in executive function in PIS. Disrupted structural covariance network in PIS might reflect malfunctioning of antero-posterior disconnection of the DMN during the wake to sleep transition that is commonly found during normal sleep. The observed structural network alteration may further implicate commonly observed sustained sleep difficulties and cognitive impairment in insomnia. © 2016 Associated Professional Sleep Societies, LLC.

  14. Insight into microtubule destabilization mechanism of 3,4,5-trimethoxyphenyl indanone derivatives using molecular dynamics simulation and conformational modes analysis

    Science.gov (United States)

    Tripathi, Shubhandra; Srivastava, Gaurava; Singh, Aastha; Prakasham, A. P.; Negi, Arvind S.; Sharma, Ashok

    2018-03-01

    Colchicine site inhibitors are microtubule destabilizers having promising role in cancer therapeutics. In the current study, four such indanone derivatives (t1, t9, t14 and t17) with 3,4,5-trimethoxyphenyl fragment (ring A) and showing significant microtubule destabilization property have been explored. The interaction mechanism and conformational modes triggered by binding of these indanone derivatives and combretastatin at colchicine binding site (CBS) of αβ-tubulin dimer were studied using molecular dynamics (MD) simulation, principle component analysis and free energy landscape analysis. In the MD results, t1 showed binding similar to colchicine interacting in the deep hydrophobic core at the CBS. While t9, t14 and t17 showed binding conformation similar to combretastatin, with ring A superficially binding at the CBS. Results demonstrated that ring A played a vital role in binding via hydrophobic interactions and got anchored between the S8 and S9 sheets, H8 helix and T7 loop at the CBS. Conformational modes study revealed that twisting and bending conformational motions (as found in the apo system) were nearly absent in the ligand bound systems. Absence of twisting motion might causes loss of lateral contacts in microtubule, thus promoting microtubule destabilization. This study provides detailed account of microtubule destabilization mechanism by indanone ligands and combretastatin, and would be helpful for designing microtubule destabilizers with higher activity.

  15. Structural Insights into the Molecular Design of Flutolanil Derivatives Targeted for Fumarate Respiration of Parasite Mitochondria

    Directory of Open Access Journals (Sweden)

    Daniel Ken Inaoka

    2015-07-01

    Full Text Available Recent studies on the respiratory chain of Ascaris suum showed that the mitochondrial NADH-fumarate reductase system composed of complex I, rhodoquinone and complex II plays an important role in the anaerobic energy metabolism of adult A. suum. The system is the major pathway of energy metabolism for adaptation to a hypoxic environment not only in parasitic organisms, but also in some types of human cancer cells. Thus, enzymes of the pathway are potential targets for chemotherapy. We found that flutolanil is an excellent inhibitor for A. suum complex II (IC50 = 0.058 μM but less effectively inhibits homologous porcine complex II (IC50 = 45.9 μM. In order to account for the specificity of flutolanil to A. suum complex II from the standpoint of structural biology, we determined the crystal structures of A. suum and porcine complex IIs binding flutolanil and its derivative compounds. The structures clearly demonstrated key interactions responsible for its high specificity to A. suum complex II and enabled us to find analogue compounds, which surpass flutolanil in both potency and specificity to A. suum complex II. Structures of complex IIs binding these compounds will be helpful to accelerate structure-based drug design targeted for complex IIs.

  16. Structural Insights into the Molecular Design of Flutolanil Derivatives Targeted for Fumarate Respiration of Parasite Mitochondria.

    Science.gov (United States)

    Inaoka, Daniel Ken; Shiba, Tomoo; Sato, Dan; Balogun, Emmanuel Oluwadare; Sasaki, Tsuyoshi; Nagahama, Madoka; Oda, Masatsugu; Matsuoka, Shigeru; Ohmori, Junko; Honma, Teruki; Inoue, Masayuki; Kita, Kiyoshi; Harada, Shigeharu

    2015-07-07

    Recent studies on the respiratory chain of Ascaris suum showed that the mitochondrial NADH-fumarate reductase system composed of complex I, rhodoquinone and complex II plays an important role in the anaerobic energy metabolism of adult A. suum. The system is the major pathway of energy metabolism for adaptation to a hypoxic environment not only in parasitic organisms, but also in some types of human cancer cells. Thus, enzymes of the pathway are potential targets for chemotherapy. We found that flutolanil is an excellent inhibitor for A. suum complex II (IC50 = 0.058 μM) but less effectively inhibits homologous porcine complex II (IC50 = 45.9 μM). In order to account for the specificity of flutolanil to A. suum complex II from the standpoint of structural biology, we determined the crystal structures of A. suum and porcine complex IIs binding flutolanil and its derivative compounds. The structures clearly demonstrated key interactions responsible for its high specificity to A. suum complex II and enabled us to find analogue compounds, which surpass flutolanil in both potency and specificity to A. suum complex II. Structures of complex IIs binding these compounds will be helpful to accelerate structure-based drug design targeted for complex IIs.

  17. Protic ammonium carboxylate ionic liquids: insight into structure, dynamics and thermophysical properties by alkyl group functionalization.

    Science.gov (United States)

    Reddy, Th Dhileep N; Mallik, Bhabani S

    2017-04-19

    This study is aimed at characterising the structure, dynamics and thermophysical properties of five alkylammonium carboxylate ionic liquids (ILs) from classical molecular dynamics simulations. The structural features of these ILs were characterised by calculating the site-site radial distribution functions, g(r), spatial distribution functions and structure factors. The structural properties demonstrate that ILs show greater interaction between cations and anions when alkyl chain length increases on the cation or anion. In all ILs, spatial distribution functions show that the anion is close to the acidic hydrogen atoms of the ammonium cation. We determined the role of alkyl group functionalization of the charged entities, cations and anions, in the dynamical behavior and the transport coefficients of this family of ionic liquids. The dynamics of ILs are described by studying the mean square displacement (MSD) of the centres of mass of the ions, diffusion coefficients, ionic conductivities and hydrogen bonds as well as residence dynamics. The diffusion coefficients and ionic conductivity decrease with an increase in the size of the cation or anion. The effect of alkyl chain length on ionic conductivity calculated in this article is consistent with the findings of other experimental studies. Hydrogen bond lifetimes and residence times along with structure factors were also calculated, and are related to alkyl chain length.

  18. Body size and dispersal mode as key traits determining metacommunity structure of aquatic organisms

    NARCIS (Netherlands)

    De Bie, T.; De Meester, L.; Brendonck, L.; Martens, K.; Goddeeris, B.; Ercken, D.; Hampel, H.; Denys, L.; Vanhecke, L.; Van der Gucht, K.; Van Wichelen, J.; Vyverman, W.; Declerck, S.A.J.

    2012-01-01

    Relationships between traits of organisms and the structure of their metacommunities have so far mainly been explored with meta-analyses. We compared metacommunities of a wide variety of aquatic organism groups (12 groups, ranging from bacteria to fish) in the same set of 99 ponds to minimise biases

  19. Atomic structure and phason modes of the Sc–Zn icosahedral quasicrystal

    Directory of Open Access Journals (Sweden)

    Tsunetomo Yamada

    2016-07-01

    Full Text Available The detailed atomic structure of the binary icosahedral (i ScZn7.33 quasicrystal has been investigated by means of high-resolution synchrotron single-crystal X-ray diffraction and absolute scale measurements of diffuse scattering. The average atomic structure has been solved using the measured Bragg intensity data based on a six-dimensional model that is isostructural to the i-YbCd5.7 one. The structure is described with a quasiperiodic packing of large Tsai-type rhombic triacontahedron clusters and double Friauf polyhedra (DFP, both resulting from a close-packing of a large (Sc and a small (Zn atom. The difference in chemical composition between i-ScZn7.33 and i-YbCd5.7 was found to lie in the icosahedron shell and the DFP where in i-ScZn7.33 chemical disorder occurs on the large atom sites, which induces a significant distortion to the structure units. The intensity in reciprocal space displays a substantial amount of diffuse scattering with anisotropic distribution, located around the strong Bragg peaks, that can be fully interpreted as resulting from phason fluctuations, with a ratio of the phason elastic constants K2/K1 = −0.53, i.e. close to a threefold instability limit. This induces a relatively large perpendicular (or phason Debye–Waller factor, which explains the vanishing of `high-Qperp' reflections.

  20. Sperm competition and reproductive mode influence sperm dimensions and structure among snakes.

    Science.gov (United States)

    Tourmente, Maximiliano; Gomendio, Montserrat; Roldan, Eduardo R S; Giojalas, Laura C; Chiaraviglio, Margarita

    2009-10-01

    The role of sperm competition in increasing sperm length is a controversial issue, because findings from different taxa seem contradictory. We present a comparative study of 25 species of snakes with different levels of sperm competition to test whether it influences the size and structure of different sperm components. We show that, as levels of sperm competition increase, so does sperm length, and that this elongation is largely explained by increases in midpiece length. In snakes, the midpiece is comparatively large and it contains structures, which in other taxa are present in the rest of the flagellum, suggesting that it may integrate some of its functions. Thus, increases in sperm midpiece size would result in more energy as well as greater propulsion force. Sperm competition also increases the area occupied by the fibrous sheath and outer dense fibers within the sperm midpiece, revealing for the first time an effect upon structural elements within the sperm. Finally, differences in male-male encounter rates between oviparous and viviparous species seem to lead to differences in levels of sperm competition. We conclude that the influence of sperm competition upon different sperm components varies between taxa, because their structure and function is different.

  1. Insights into the Structures of DNA Damaged by Hydroxyl Radical: Crystal Structures of DNA Duplexes Containing 5-Formyluracil

    Directory of Open Access Journals (Sweden)

    Masaru Tsunoda

    2010-01-01

    Full Text Available Hydroxyl radicals are potent mutagens that attack DNA to form various base and ribose derivatives. One of the major damaged thymine derivatives is 5-formyluracil (fU, which induces pyrimidine transition during replication. In order to establish the structural basis for such mutagenesis, the crystal structures of two kinds of DNA d(CGCGRATfUCGCG with R = A/G have been determined by X-ray crystallography. The fU residues form a Watson-Crick-type pair with A and two types of pairs (wobble and reversed wobble with G, the latter being a new type of base pair between ionized thymine base and guanine base. In silico structural modeling suggests that the DNA polymerase can accept the reversed wobble pair with G, as well as the Watson-Crick pair with A.

  2. Orientation of aromatic residues in amyloid cores: Structural insights into prion fiber diversity

    KAUST Repository

    Reymer, Anna

    2014-11-17

    Structural conversion of one given protein sequence into different amyloid states, resulting in distinct phenotypes, is one of the most intriguing phenomena of protein biology. Despite great efforts the structural origin of prion diversity remains elusive, mainly because amyloids are insoluble yet noncrystalline and therefore not easily amenable to traditional structural-biology methods. We investigate two different phenotypic prion strains, weak and strong, of yeast translation termination factor Sup35 with respect to angular orientation of tyrosines using polarized light spectroscopy. By applying a combination of alignment methods the degree of fiber orientation can be assessed, which allows a relatively accurate determination of the aromatic ring angles. Surprisingly, the strains show identical average orientations of the tyrosines, which are evenly spread through the amyloid core. Small variations between the two strains are related to the local environment of a fraction of tyrosines outside the core, potentially reflecting differences in fibril packing.

  3. Recognition of damaged DNA by Escherichia coli Fpg protein: insights from structural and kinetic data

    International Nuclear Information System (INIS)

    Zharkov, Dmitry O.; Ishchenko, Alexander A.; Douglas, Kenneth T.; Nevinsky, Georgy A.

    2003-01-01

    Formamidopyrimidine-DNA glycosylase (Fpg) excises oxidized purines from damaged DNA. The recent determination of the three-dimensional structure of the covalent complex of DNA with Escherichia coli Fpg, obtained by reducing the Schiff base intermediate formed during the reaction [Gilboa et al., J. Biol. Chem. 277 (2002) 19811] has revealed a number of potential specific and non-specific interactions between Fpg and DNA. We analyze the structural data for Fpg in the light of the kinetic and thermodynamic data obtained by the method of stepwise increase in ligand complexity to estimate relative contributions of individual nucleotide units of lesion-containing DNA to its total affinity for this enzyme [Ishchenko et al., Biochemistry 41 (2002) 7540]. Stopped-flow kinetic analysis that has allowed the dissection of Fpg catalysis in time [Fedorova et al., Biochemistry 41 (2002) 1520] is also correlated with the structural data

  4. Investigating dynamical information transfer in the brain following a TMS pulse: Insights from structural architecture.

    Science.gov (United States)

    Amico, Enrico; Van Mierlo, Pieter; Marinazzo, Daniele; Laureys, Steven

    2015-01-01

    Transcranial magnetic stimulation (TMS) has been used for more than 20 years to investigate connectivity and plasticity in the human cortex. By combining TMS with high-density electroencephalography (hd-EEG), one can stimulate any cortical area and measure the effects produced by this perturbation in the rest of the cerebral cortex. The purpose of this paper is to investigate changes of information flow in the brain after TMS from a functional and structural perspective, using multimodal modeling of source reconstructed TMS/hd-EEG recordings and DTI tractography. We prove how brain dynamics induced by TMS is constrained and driven by its structure, at different spatial and temporal scales, especially when considering cross-frequency interactions. These results shed light on the function-structure organization of the brain network at the global level, and on the huge variety of information contained in it.

  5. Structure insight of GSDMD reveals the basis of GSDMD autoinhibition in cell pyroptosis.

    Science.gov (United States)

    Kuang, Siyun; Zheng, Jun; Yang, Hui; Li, Suhua; Duan, Shuyan; Shen, Yanfang; Ji, Chaoneng; Gan, Jianhua; Xu, Xue-Wei; Li, Jixi

    2017-10-03

    Recent findings have revealed that the protein gasdermin D (GSDMD) plays key roles in cell pyroptosis. GSDMD binds lipids and forms pore structures to induce pyroptosis upon microbial infection and associated danger signals. However, detailed structural information for GSDMD remains unknown. Here, we report the crystal structure of the C-terminal domain of human GSDMD (GSDMD-C) at 2.64-Å resolution. The first loop on GSDMD-C inserts into the N-terminal domain (GSDMD-N), which helps stabilize the conformation of the full-length GSDMD. Substitution of this region by a short linker sequence increased levels of cell death. Mutants F283A and F283R can increase protein heterogeneity in vitro and are capable of undergoing cell pyroptosis in 293T cells. The small-angle X-ray-scattering envelope of human GSDMD is consistent with the modeled GSDMD structure and mouse GSDMA3 structure, which suggests that GSDMD adopts an autoinhibited conformation in solution. The positive potential surface of GSDMD-N covered by GSDMD-C is exposed after being released from the autoinhibition state and can form high-order oligomers via a charge-charge interaction. Furthermore, by mapping different regions of GSDMD, we determined that one short segment is sufficient to kill bacteria in vitro and can efficiently inhibit cell growth in Escherichia coli and Mycobacterium Smegmatis These findings reveal that GSDMD-C acts as an auto-inhibition executor and GSDMD-N could form pore structures via a charge-charge interaction upon cleavage by caspases during cell pyroptosis.

  6. Insights into the fold organization of TIM barrel from interaction energy based structure networks.

    Science.gov (United States)

    Vijayabaskar, M S; Vishveshwara, Saraswathi

    2012-01-01

    There are many well-known examples of proteins with low sequence similarity, adopting the same structural fold. This aspect of sequence-structure relationship has been extensively studied both experimentally and theoretically, however with limited success. Most of the studies consider remote homology or "sequence conservation" as the basis for their understanding. Recently "interaction energy" based network formalism (Protein Energy Networks (PENs)) was developed to understand the determinants of protein structures. In this paper we have used these PENs to investigate the common non-covalent interactions and their collective features which stabilize the TIM barrel fold. We have also developed a method of aligning PENs in order to understand the spatial conservation of interactions in the fold. We have identified key common interactions responsible for the conservation of the TIM fold, despite high sequence dissimilarity. For instance, the central beta barrel of the TIM fold is stabilized by long-range high energy electrostatic interactions and low-energy contiguous vdW interactions in certain families. The other interfaces like the helix-sheet or the helix-helix seem to be devoid of any high energy conserved interactions. Conserved interactions in the loop regions around the catalytic site of the TIM fold have also been identified, pointing out their significance in both structural and functional evolution. Based on these investigations, we have developed a novel network based phylogenetic analysis for remote homologues, which can perform better than sequence based phylogeny. Such an analysis is more meaningful from both structural and functional evolutionary perspective. We believe that the information obtained through the "interaction conservation" viewpoint and the subsequently developed method of structure network alignment, can shed new light in the fields of fold organization and de novo computational protein design.

  7. Structural insights into GDP-mediated regulation of a bacterial acyl-CoA thioesterase.

    Science.gov (United States)

    Khandokar, Yogesh B; Srivastava, Parul; Cowieson, Nathan; Sarker, Subir; Aragao, David; Das, Shubagata; Smith, Kate M; Raidal, Shane R; Forwood, Jade K

    2017-12-15

    Thioesterases catalyze the cleavage of thioester bonds within many activated fatty acids and acyl-CoA substrates. They are expressed ubiquitously in both prokaryotes and eukaryotes and are subdivided into 25 thioesterase families according to their catalytic active site, protein oligomerization, and substrate specificity. Although many of these enzyme families are well-characterized in terms of function and substrate specificity, regulation across most thioesterase families is poorly understood. Here, we characterized a TE6 thioesterase from the bacterium Neisseria meningitidis Structural analysis with X-ray crystallographic diffraction data to 2.0-Å revealed that each protein subunit harbors a hot dog-fold and that the TE6 enzyme forms a hexamer with D3 symmetry. An assessment of thioesterase activity against a range of acyl-CoA substrates revealed the greatest activity against acetyl-CoA, and structure-guided mutagenesis of putative active site residues identified Asn 24 and Asp 39 as being essential for activity. Our structural analysis revealed that six GDP nucleotides bound the enzyme in close proximity to an intersubunit disulfide bond interactions that covalently link thioesterase domains in a double hot dog dimer. Structure-guided mutagenesis of residues within the GDP-binding pocket identified Arg 93 as playing a key role in the nucleotide interaction and revealed that GDP is required for activity. All mutations were confirmed to be specific and not to have resulted from structural perturbations by X-ray crystallography. This is the first report of a bacterial GDP-regulated thioesterase and of covalent linkage of thioesterase domains through a disulfide bond, revealing structural similarities with ADP regulation in the human ACOT12 thioesterase. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  8. Protein kinase CK2 in health and disease: Protein kinase CK2: from structures to insights

    DEFF Research Database (Denmark)

    Niefind, K; Raaf, J; Issinger, Olaf-Georg

    2009-01-01

    the critical region of CK2alpha recruitment is pre-formed in the unbound state. In CK2alpha the activation segment - a key element of protein kinase regulation - adapts invariably the typical conformation of the active enzymes. Recent structures of human CK2alpha revealed a surprising plasticity in the ATP......Within the last decade, 40 crystal structures corresponding to protein kinase CK2 (former name 'casein kinase 2'), to its catalytic subunit CK2alpha and to its regulatory subunit CK2beta were published. Together they provide a valuable, yet by far not complete basis to rationalize the biochemical...

  9. Epoxide hydrolase-lasalocid a structure provides mechanistic insight into polyether natural product biosynthesis.

    Science.gov (United States)

    Wong, Fong T; Hotta, Kinya; Chen, Xi; Fang, Minyi; Watanabe, Kenji; Kim, Chu-Young

    2015-01-14

    Biosynthesis of some polyether natural products involves a kinetically disfavored epoxide-opening cyclic ether formation, a reaction termed anti-Baldwin cyclization. One such example is the biosynthesis of lasalocid A, an ionophore antibiotic polyether. During lasalocid A biosynthesis, an epoxide hydrolase, Lsd19, converts the bisepoxy polyketide intermediate into the tetrahydrofuranyl-tetrahydropyran product. We report the crystal structure of Lsd19 in complex with lasalocid A. The structure unambiguously shows that the C-terminal domain of Lsd19 catalyzes the intriguing anti-Baldwin cyclization. We propose a general mechanism for epoxide selection by ionophore polyether epoxide hydrolases.

  10. Structural and Functional Insights into the Pilotin-Secretin Complex of the Type II Secretion System

    OpenAIRE

    Gu, Shuang; Rehman, Saima; Wang, Xiaohui; Shevchik, Vladimir E.; Pickersgill, Richard W.

    2012-01-01

    Gram-negative bacteria secrete virulence factors and assemble fibre structures on their cell surface using specialized secretion systems. Three of these, T2SS, T3SS and T4PS, are characterized by large outer membrane channels formed by proteins called secretins. Usually, a cognate lipoprotein pilot is essential for the assembly of the secretin in the outer membrane. The structures of the pilotins of the T3SS and T4PS have been described. However in the T2SS, the molecular mechanism of this pr...

  11. Role of charged lipids in membrane structuresInsight given by simulations

    DEFF Research Database (Denmark)

    Pöyry, Sanja; Vattulainen, Ilpo

    2016-01-01

    Lipids and proteins are the main components of cell membranes. It is becoming increasingly clear that lipids, in addition to providing an environment for proteins to work in, are in many cases also able to modulate the structure and function of those proteins. Particularly charged lipids...... to fruitful directions. In this paper, we review studies that have utilized molecular dynamics simulations to unravel the roles of charged lipids in membrane structures. We focus on lipids as active constituents of the membranes, affecting both general membrane properties as well as non-lipid membrane...

  12. Systems level insights into alternate methane cycling modes in a freshwater lake via community transcriptomics, metabolomics and nano-SIMS analysis

    Energy Technology Data Exchange (ETDEWEB)

    Lidstrom, Mary E. [Univ. of Washington, Seattle, WA (United States); Chistoserdova, Ludmila [Univ. of Washington, Seattle, WA (United States); Kalyuzhnaya, Marina G. [Univ. of Washington, Seattle, WA (United States); Orphan, Victoria J. [California Inst. of Technology (CalTech), Pasadena, CA (United States); Beck, David A. [Univ. of Washington, Seattle, WA (United States)

    2014-08-07

    The research conducted as part of this project contributes significantly to the understanding of the microbes and their activities involved in methane metabolism in freshwater lake sediments and in the environment in a more global sense. Significant new insights have been gained into the identity of the species that are most active in methane oxidation. New concepts have been developed based on the new data on how these organisms metabolize methane, impacting not only environmental microbiology but also biotechnology, including biotechnology of next generation biofuels. Novel approaches have been developed for studying functional microbial communities, via holistic approaches, such as metagenomics, metatrancriptomics and metabolite analysis. As a result, a novel outlook has been obtained at how such communities operate in nature. Understanding methane-oxidizing communities in lakes and other environments is of significant benefit to the public, in terms of methane emission mitigation and in terms of potential biotechnological applications.

  13. Optical and mode-locking properties of InGaN/GaN based hetero-structures

    International Nuclear Information System (INIS)

    Irshad, A.

    2011-01-01

    Short wavelength pulsed lasers are indispensable for high density and high speed optical data acquisition, storage and transfer applications. Passively mode-locked blue lasers are an attractive alternative for blue laser sources achieved by non-linear frequency conversion techniques. Although over the recent years it has been shown that InGaN/GaN based hetero-structures can be used as potential material for the fabrication of saturable absorbers, passive mode-locking in the blue spectral range has not been realized yet. The main reason for that is the complicated microscopic nature of InGaN/GaN materials and the difficulty to control the dynamics of photo-induced carriers which determine mode-locking properties of the material. In this work, we have characterized different InGaN based hetero-structures as potential saturable absorbers. Three different groups of the samples have been investigated: i) quantum well samples with different numbers of quantum wells grown under optimal conditions; ii)quantum well samples with modified optical properties due to different buffer layer thickness and postgrowth treatment; iii) a multilayered quantum dot sample. The characterized quantum well samples exhibit relatively high optical quality and sufficiently high saturable losses (which can be controlled by alternating a number of the quantum wells). Nevertheless, they have two major disadvantages as saturable absorbers, namely, a very long absorption recovery time (in the order of a few nanoseconds) and a rather high saturation fluence. The long recovery times are not desirable for achieving a stable and self-starting mode-locking without Q-switching. In order to understand the relaxation processes of photo-induced carriers that determine the absorption recovery times of the saturable absorbers, optical properties of the hetero-structures have been extensively studied by using the frequency and time resolved photo-luminescence technique. The obtained data reveal that, directly

  14. Mechanistic insights into validoxylamine A 7'-phosphate synthesis by VldE using the structure of the entire product complex.

    Directory of Open Access Journals (Sweden)

    Michael C Cavalier

    Full Text Available The pseudo-glycosyltransferase VldE catalyzes non-glycosidic C-N coupling between an unsaturated cyclitol and a saturated aminocyclitol with the conservation of the stereochemical configuration of the substrates to form validoxylamine A 7'-phosphate, the biosynthetic precursor of the antibiotic validamycin A. To study the molecular basis of its mechanism, the three-dimensional structures of VldE from Streptomyces hygroscopicus subsp. limoneus was determined in apo form, in complex with GDP, in complex with GDP and validoxylamine A 7'-phosphate, and in complex with GDP and trehalose. The structure of VldE with the catalytic site in both an "open" and "closed" conformation is also described. With these structures, the preferred binding of the guanine moiety by VldE, rather than the uracil moiety as seen in OtsA could be explained. The elucidation of the VldE structure in complex with the entirety of its products provides insight into the internal return mechanism by which catalysis occurs with a net retention of the stereochemical configuration of the donated cyclitol.

  15. Insights into structural and dynamical features of water at halloysite interfaces probed by DFT and classical molecular dynamics simulations.

    Science.gov (United States)

    Presti, Davide; Pedone, Alfonso; Mancini, Giordano; Duce, Celia; Tiné, Maria Rosaria; Barone, Vincenzo

    2016-01-21

    Density functional theory calculations and classical molecular dynamics simulations have been used to investigate the structure and dynamics of water molecules on kaolinite surfaces and confined in the interlayer of a halloysite model of nanometric dimension. The first technique allowed us to accurately describe the structure of the tetrahedral-octahedral slab of kaolinite in vacuum and in interaction with water molecules and to assess the performance of two widely employed empirical force fields to model water/clay interfaces. Classical molecular dynamics simulations were used to study the hydrogen bond network structure and dynamics of water adsorbed on kaolinite surfaces and confined in the halloysite interlayer. The results are in nice agreement with the few experimental data available in the literature, showing a pronounced ordering and reduced mobility of water molecules at the hydrophilic octahedral surfaces of kaolinite and confined in the halloysite interlayer, with respect to water interacting with the hydrophobic tetrahedral surfaces and in the bulk. Finally, this investigation provides new atomistic insights into the structural and dynamical properties of water-clay interfaces, which are of fundamental importance for both natural processes and industrial applications.

  16. Structural insights into the elevator-like mechanism of the sodium/citrate symporter CitS.

    Science.gov (United States)

    Kim, Ji Won; Kim, Subin; Kim, Songwon; Lee, Haerim; Lee, Jie-Oh; Jin, Mi Sun

    2017-05-31

    The sodium-dependent citrate transporter of Klebsiella pneumoniae (KpCitS) belongs to the 2-hydroxycarboxylate transporter (2-HCT) family and allows the cell to use citrate as sole carbon and energy source in anaerobic conditions. Here we present crystal structures of KpCitS in citrate-bound outward-facing, citrate-bound asymmetric, and citrate-free inward-facing state. The structures reveal that the KpCitS dimerization domain remains stationary throughout the transport cycle due to a hydrogen bond network as well as extensive hydrophobic interactions. In contrast, its transport domain undergoes a ~35° rigid-body rotation and a ~17 Å translocation perpendicular to the membrane to expose the substrate-binding site alternately to either side of the membrane. Furthermore, homology models of two other 2-HCT proteins based on the KpCitS structure offer structural insights into their differences in substrate specificity at a molecular level. On the basis of our results and previous biochemical data, we propose that the activity of the 2-HCT CitS involves an elevator-like movement in which the transport domain itself traverses the lipid bilayer, carrying the substrate into the cell in a sodium-dependent manner.

  17. Structural insights of the ssDNA binding site in the multifunctional endonuclease AtBFN2 from Arabidopsis thaliana.

    Directory of Open Access Journals (Sweden)

    Tsung-Fu Yu

    Full Text Available The multi S1/P1 nuclease AtBFN2 (EC 3.1.30.1 encoded by the Arabidopsis thaliana At1g68290 gene is a glycoprotein that digests RNA, ssDNA, and dsDNA. AtBFN2 depends on three zinc ions for cleaving DNA and RNA at 3'-OH to yield 5'-nucleotides. In addition, AtBFN2's enzymatic activity is strongly glycan dependent. Plant Zn(2+-dependent endonucleases present a unique fold, and belong to the Phospholipase C (PLC/P1 nuclease superfamily. In this work, we present the first complete, ligand-free, AtBFN2 crystal structure, along with sulfate, phosphate and ssDNA co-crystal structures. With these, we were able to provide better insight into the glycan structure and possible enzymatic mechanism. In comparison with other nucleases, the AtBFN2/ligand-free and AtBFN2/PO4 models suggest a similar, previously proposed, catalytic mechanism. Our data also confirm that the phosphate and vanadate can inhibit the enzyme activity by occupying the active site. More importantly, the AtBFN2/A5T structure reveals a novel and conserved secondary binding site, which seems to be important for plant Zn(2+-dependent endonucleases. Based on these findings, we propose a rational ssDNA binding model, in which the ssDNA wraps itself around the protein and the attached surface glycan, in turn, reinforces the binding complex.

  18. Crystal Structure of the FGFR4/LY2874455 Complex Reveals Insights into the Pan-FGFR Selectivity of LY2874455.

    Science.gov (United States)

    Wu, Daichao; Guo, Ming; Philips, Michael A; Qu, Lingzhi; Jiang, Longying; Li, Jun; Chen, Xiaojuan; Chen, Zhuchu; Chen, Lin; Chen, Yongheng

    2016-01-01

    Aberrant FGFR4 signaling has been documented abundantly in various human cancers. The majority of FGFR inhibitors display significantly reduced potency toward FGFR4 compared to FGFR1-3. However, LY2874455 has similar inhibition potency for FGFR1-4 with IC50 less than 6.4 nM. To date, there is no published crystal structure of LY2874455 in complex with any kinase. To better understand the pan-FGFR selectivity of LY2874455, we have determined the crystal structure of the FGFR4 kinase domain bound to LY2874455 at a resolution of 2.35 Å. LY2874455, a type I inhibitor for FGFR4, binds to the ATP-binding pocket of FGFR4 in a DFG-in active conformation with three hydrogen bonds and a number of van der Waals contacts. After alignment of the kinase domain sequence of 4 FGFRs, and superposition of the ATP binding pocket of 4 FGFRs, our structural analyses reveal that the interactions of LY2874455 to FGFR4 are largely conserved in 4 FGFRs, explaining at least partly, the broad inhibitory activity of LY2874455 toward 4 FGFRs. Consequently, our studies reveal new insights into the pan-FGFR selectivity of LY2874455 and provide a structural basis for developing novel FGFR inhibitors that target FGFR1-4 broadly.

  19. Structure of EspB from the ESX-1 type VII secretion system and insights into its export mechanism.

    Science.gov (United States)

    Solomonson, Matthew; Setiaputra, Dheva; Makepeace, Karl A T; Lameignere, Emilie; Petrotchenko, Evgeniy V; Conrady, Deborah G; Bergeron, Julien R; Vuckovic, Marija; DiMaio, Frank; Borchers, Christoph H; Yip, Calvin K; Strynadka, Natalie C J

    2015-03-03

    Mycobacterium tuberculosis (Mtb) uses the ESX-1 type VII secretion system to export virulence proteins across its lipid-rich cell wall, which helps permeabilize the host's macrophage phagosomal membrane, facilitating the escape and cell-to-cell spread of Mtb. ESX-1 membranolytic activity depends on a set of specialized secreted Esp proteins, the structure and specific roles of which are not currently understood. Here, we report the X-ray and electron microscopic structures of the ESX-1-secreted EspB. We demonstrate that EspB adopts a PE/PPE-like fold that mediates oligomerization with apparent heptameric symmetry, generating a barrel-shaped structure with a central pore that we propose contributes to the macrophage killing functions of EspB. Our structural data also reveal unexpected direct interactions between the EspB bipartite secretion signal sequence elements that form a unified aromatic surface. These findings provide insight into how specialized proteins encoded within the ESX-1 locus are targeted for secretion, and for the first time indicate an oligomerization-dependent role for Esp virulence factors. Copyright © 2015 Elsevier Ltd. All rights reserved.

  20. Structural Insights into the Mechanisms of Action of Short-Peptide HIV-1 Fusion Inhibitors Targeting the Gp41 Pocket

    Directory of Open Access Journals (Sweden)

    Xiujuan Zhang

    2018-02-01

    Full Text Available The deep hydrophobic pocket of HIV-1 gp41 has been considered a drug target, but short-peptides targeting this site usually lack potent antiviral activity. By applying the M-T hook structure, we previously generated highly potent short-peptide fusion inhibitors that specifically targeted the pocket site, such as MT-SC22EK, HP23L, and LP-11. Here, the crystal structures of HP23L and LP-11 bound to the target mimic peptide N36 demonstrated the critical intrahelical and interhelical interactions, especially verifying that the hook-like conformation was finely adopted while the methionine residue was replaced by the oxidation-less prone residue leucine, and that addition of an extra glutamic acid significantly enhanced the binding and inhibitory activities. The structure of HP23L bound to N36 with two mutations (E49K and L57R revealed the critical residues and motifs mediating drug resistance and provided new insights into the mechanism of action of inhibitors. Therefore, the present data help our understanding for the structure-activity relationship (SAR of HIV-1 fusion inhibitors and facilitate the development of novel antiviral drugs.

  1. Communication: Supramolecular structures in monohydroxy alcohols: Insights from shear-mechanical studies of a systematic series of octanol structural isomers

    DEFF Research Database (Denmark)

    Hecksher, Tina; Jakobsen, Bo

    2014-01-01

    response, also has a mechanical signature. In this work, we apply broadband shear-mechanical spectroscopy to a systematic series of octanol structural isomers, x-methyl-3-heptanol (with x ranging from 2 to 6). We find that the characteristics of the mechanical signature overall follow the systematic...

  2. Biochemical and structural insights into xylan utilization by the thermophilic bacterium Caldanaerobius polysaccharolyticus.

    Science.gov (United States)

    Han, Yejun; Agarwal, Vinayak; Dodd, Dylan; Kim, Jason; Bae, Brian; Mackie, Roderick I; Nair, Satish K; Cann, Isaac K O

    2012-10-12

    Hemicellulose is the next most abundant plant cell wall component after cellulose. The abundance of hemicellulose such as xylan suggests that their hydrolysis and conversion to biofuels can improve the economics of bioenergy production. In an effort to understand xylan hydrolysis at high temperatures, we sequenced the genome of the thermophilic bacterium Caldanaerobius polysaccharolyticus. Analysis of the partial genome sequence revealed a gene cluster that contained both hydrolytic enzymes and also enzymes key to the pentose-phosphate pathway. The hydrolytic enzymes in the gene cluster were demonstrated to convert products from a large endoxylanase (Xyn10A) predicted to anchor to the surface of the bacterium. We further use structural and calorimetric studies to demonstrate that the end products of Xyn10A hydrolysis of xylan are recognized and bound by XBP1, a putative solute-binding protein, likely for transport into the cell. The XBP1 protein showed preference for xylo-oligosaccharides as follows: xylotriose > xylobiose > xylotetraose. To elucidate the structural basis for the oligosaccharide preference, we solved the co-crystal structure of XBP1 complexed with xylotriose to a 1.8-Å resolution. Analysis of the biochemical data in the context of the co-crystal structure reveals the molecular underpinnings of oligosaccharide length specificity.

  3. Structure of active IspH enzyme from escherichia coli provides mechanistic insights into substrate reduction

    KAUST Repository

    Grä wert, Tobias; Rohdich, Felix; Span, Lngrid; Backer, Adelbert; Eisenreich, Wolfgang; Eppinger, Jö rg; Groll, Michael

    2009-01-01

    The terminal step of the non-mevalonate pathway of terpene biosynthesis is catalyzed by IspH (see scheme). In the crystal structure of IspH from E. coli, a bound inorganic diphosphate ligand occupies the position of the diphosphate residue

  4. Hierarchical population structure in greater sage-grouse provides insight into management boundary delineation

    Science.gov (United States)

    Todd B. Cross; David E. Naugle; John C. Carlson; Michael K. Schwartz

    2016-01-01

    Understanding population structure is important for guiding ongoing conservation and restoration efforts. The greater sage-grouse (Centrocercus urophasianus) is a species of concern distributed across 1.2 million km2 of western North America. We genotyped 1499 greater sagegrouse from 297 leks across Montana, North Dakota and South Dakota using a 15 locus...

  5. GPCR engineering yields high-resolution structural insights into beta2-adrenergic receptor function

    DEFF Research Database (Denmark)

    Rosenbaum, Daniel M; Cherezov, Vadim; Hanson, Michael A

    2007-01-01

    The beta2-adrenergic receptor (beta2AR) is a well-studied prototype for heterotrimeric guanine nucleotide-binding protein (G protein)-coupled receptors (GPCRs) that respond to diffusible hormones and neurotransmitters. To overcome the structural flexibility of the beta2AR and to facilitate its cr...

  6. Structural insights into human peroxisome proliferator activated receptor delta (PPAR-delta selective ligand binding.

    Directory of Open Access Journals (Sweden)

    Fernanda A H Batista

    Full Text Available Peroxisome proliferator activated receptors (PPARs δ, α and γ are closely related transcription factors that exert distinct effects on fatty acid and glucose metabolism, cardiac disease, inflammatory response and other processes. Several groups developed PPAR subtype specific modulators to trigger desirable effects of particular PPARs without harmful side effects associated with activation of other subtypes. Presently, however, many compounds that bind to one of the PPARs cross-react with others and rational strategies to obtain highly selective PPAR modulators are far from clear. GW0742 is a synthetic ligand that binds PPARδ more than 300-fold more tightly than PPARα or PPARγ but the structural basis of PPARδ:GW0742 interactions and reasons for strong selectivity are not clear. Here we report the crystal structure of the PPARδ:GW0742 complex. Comparisons of the PPARδ:GW0742 complex with published structures of PPARs in complex with α and γ selective agonists and pan agonists suggests that two residues (Val312 and Ile328 in the buried hormone binding pocket play special roles in PPARδ selective binding and experimental and computational analysis of effects of mutations in these residues confirms this and suggests that bulky substituents that line the PPARα and γ ligand binding pockets as structural barriers for GW0742 binding. This analysis suggests general strategies for selective PPARδ ligand design.

  7. New insights into structure and function of the different types of fatty acid-binding protein

    NARCIS (Netherlands)

    Zimmerman, Augusta Wilhelmina

    2002-01-01

    Fatty acid binding proteins (FABPs) are small cytosolic proteins with virtually identical backbone structures that facilitate the solubility and intracellular transport of fatty acids. They may also modulate the effect of fatty acids on various metabolic enzymes and receptors and on cellular

  8. Insights on Forest Structure and Composition from Long-Term Research in the Luquillo Mountains

    Science.gov (United States)

    Tamara Heartsill Scalley

    2017-01-01

    The science of ecology fundamentally aims to understand species and their relation to the environment. At sites where hurricane disturbance is part of the environmental context, permanent forest plots are critical to understand ecological vegetation dynamics through time. An overview of forest structure and species composition from two of the longest continuously...

  9. Structural and mechanistic insight into Holliday-junction dissolution by topoisomerase IIIα and RMI1

    DEFF Research Database (Denmark)

    Bocquet, Nicolas; Bizard, Anna H; Abdulrahman, Wassim

    2014-01-01

    to TopIIIα influences it to behave as a hemicatenane dissolvase, rather than as an enzyme that relaxes DNA topology, is unknown. Here, we present the crystal structure of human TopIIIα complexed to the first oligonucleotide-binding domain (OB fold) of RMI1. TopIII assumes a toroidal type 1A topoisomerase...

  10. Structural insights into leishmanolysins encoded on chromosome 10 of Leishmania (Viannia braziliensis

    Directory of Open Access Journals (Sweden)

    Amanda Sutter

    Full Text Available BACKGROUND Leishmanolysins have been described as important parasite virulence factors because of their roles in the infection of promastigotes and resistance to host’s defenses. Leishmania (Viannia braziliensis contains several leishmanolysin genes in its genome, especially in chromosome 10. However, the functional impact of such diversity is not understood, but may be attributed partially to the lack of structural data for proteins from this parasite. OBJECTIVES This works aims to compare leishmanolysin sequences from L. (V. braziliensis and to understand how the diversity impacts in their structural and dynamic features. METHODS Leishmanolysin sequences were retrieved from GeneDB. Subsequently, 3D models were built using comparative modeling methods and their dynamical behavior was studied using molecular dynamic simulations. FINDINGS We identified three subgroups of leishmanolysins according to sequence variations. These differences directly affect the electrostatic properties of leishmanolysins and the geometry of their active sites. We identified two levels of structural heterogeneity that might be related to the ability of promastigotes to interact with a broad range of substrates. MAIN CONCLUSION Altogether, the structural plasticity of leishmanolysins may constitute an important evolutionary adaptation rarely explored when considering the virulence of L. (V. braziliensis parasites.

  11. Wannier–Stark electro-optical effect, quasi-guided and photonic modes in 2D macroporous silicon structures with SiO_2 coatings

    International Nuclear Information System (INIS)

    Karachevtseva, L.; Goltviansky, Yu.; Sapelnikova, O.; Lytvynenko, O.; Stronska, O.; Bo, Wang; Kartel, M.

    2016-01-01

    Highlights: • The IR absorption spectra of oxidized macroporous silicon were studied. • The Wannier–Stark electro-optical effect on Si-SiO_2 boundary was confirmed. • An additional electric field of quasi-guided optical modes was evaluated. • The photonic modes and band gaps were measured as peculiarities in absorption spectra. - Abstract: Opportunities to enhance the properties of structured surfaces were demonstrated on 2D macroporous silicon structures with SiO_2 coatings. We investigated the IR light absorption oscillations in macroporous silicon structures with SiO2 coatings 0–800 nm thick. The Wannier–Stark electro-optical effect due to strong electric field on Si-SiO_2boundary and an additional electric field of quasi-guided optical modes were taken into account. The photonic modes and band gaps were also considered as peculiarities in absorbance spectra of macroporous silicon structures with a thick SiO_2 coating. The photonic modes do not coincide with the quasi-guided modes in the silicon matrix and do not appear in absorption spectra of 2D macroporous silicon structures with surface nanocrystals.

  12. Introduction to structural and mechanical failure modes for nuclear power facilities

    International Nuclear Information System (INIS)

    Reed, J.W.

    1991-01-01

    The three papers presented in this section discuss the types of information (i.e., dynamic tests, earthquake experience and analytical data) which are used in predicting the capacity of structures and equipment in nuclear power plants to resist earthquakes. The background and motivation for discussing these three types of information is presented in this paper as an introduction to the papers which follow in this section

  13. The effect of the solidification mode on eutectic structure in Fe-C-V alloys

    International Nuclear Information System (INIS)

    Fras, E.; Guzik, E.

    1980-01-01

    The aim of the study was to determine such a chemical composition of Fe-C-V alloys which would ensure the formation of perfectly eutectic structures as well as to investigate the eutectic morphology of these alloys when undergoing bulk and directional solidification. Attempts have been done to get in situ composites from Fe-C-V alloys. The adopted testing methods as well as obtained results are described in detail. (H.M.)

  14. A fast anharmonic mode in electrooptical switching of liquid crystal structures based on chiral nematics

    Energy Technology Data Exchange (ETDEWEB)

    Palto, S. P., E-mail: palto@online.ru; Barnik, M I; Blinov, L M; Umanskii, B. A., E-mail: umanskii@yahoo.com; Shtykov, N M [Russian Academy of Sciences, Shubnikov Institute of Crystallography (Russian Federation)

    2010-09-15

    Polarization, spectral, and relaxation features of a new electrooptical effect in oriented layers of chiral nematic liquid crystals (LCs) are considered. The physics behind this electrooptical effect is the induction of higher order spatial harmonics in the helical distribution of the director field, which ensures the high speed of electrooptical response. It is shown that the spectral properties of the electrooptical response can be effectively controlled by varying the optical anisotropy of the LC and the pitch of the helical structure.

  15. Insights from the Structure of Mycobacterium tuberculosis Topoisomerase I with a Novel Protein Fold.

    Science.gov (United States)

    Tan, Kemin; Cao, Nan; Cheng, Bokun; Joachimiak, Andrzej; Tse-Dinh, Yuk-Ching

    2016-01-16

    The DNA topoisomerase I enzyme of Mycobacterium tuberculosis (MtTOP1) is essential for the viability of the organism and survival in a murine model. This topoisomerase is being pursued as a novel target for the discovery of new therapeutic agents for the treatment of drug-resistant tuberculosis. In this study, we succeeded in obtaining a structure of MtTOP1 by first predicting that the C-terminal region of MtTOP1 contains four repeated domains that do not involve the Zn-binding tetracysteine motifs seen in the C-terminal domains of Escherichia coli topoisomerase I. A construct (amino acids A2-T704), MtTOP1-704t, that includes the N-terminal domains (D1-D4) and the first predicted C-terminal domain (D5) of MtTOP1 was expressed and found to retain DNA cleavage-religation activity and catalyze single-stranded DNA catenation. MtTOP1-704t was crystallized, and a structure of 2.52Å resolution limit was obtained. The structure of the MtTOP1 N-terminal domains has features that have not been observed in other previously available bacterial topoisomerase I crystal structures. The first C-terminal domain D5 forms a novel protein fold of a four-stranded antiparallel β-sheet stabilized by a crossing-over α-helix. Since there is only one type IA topoisomerase present in Mycobacteriaceae and related Actinobacteria, this subfamily of type IA topoisomerase may be required for multiple functions in DNA replication, transcription, recombination, and repair. The unique structural features observed for MtTOP1 may allow these topoisomerase I enzymes to carry out physiological functions associated with topoisomerase III enzyme in other bacteria. Copyright © 2015 Elsevier Ltd. All rights reserved.

  16. Genetic diversity and population structure in Polygonum cespitosum: insights to an ongoing plant invasion.

    Directory of Open Access Journals (Sweden)

    Silvia Matesanz

    Full Text Available Molecular markers can help elucidate how neutral evolutionary forces and introduction history contribute to genetic variation in invaders. We examined genetic diversity, population structure and colonization patterns in the invasive Polygonum cespitosum, a highly selfing, tetraploid Asian annual introduced to North America. We used nine diploidized polymorphic microsatellite markers to study 16 populations in the introduced range (northeastern North America, via the analyses of 516 individuals, and asked the following questions: 1 Do populations have differing levels of within-population genetic diversity? 2 Do populations form distinct genetic clusters? 3 Does population structure reflect either geographic distances or habitat similarities? We found low heterozygosity in all populations, consistent with the selfing mating system of P. cespitosum. Despite the high selfing levels, we found substantial genetic variation within and among P. cespitosum populations, based on the percentage of polymorphic loci, allelic richness, and expected heterozygosity. Inferences from individual assignment tests (Bayesian clustering and pairwise FST values indicated high among-population differentiation, which indicates that the effects of gene flow are limited relative to those of genetic drift, probably due to the high selfing rates and the limited seed dispersal ability of P. cespitosum. Population structure did not reflect a pattern of isolation by distance nor was it related to habitat similarities. Rather, population structure appears to be the result of the random movement of propagules across the introduced range, possibly associated with human dispersal. Furthermore, the high population differentiation, genetic diversity, and fine-scale genetic structure (populations founded by individuals from different genetic sources in the introduced range suggest that multiple introductions to this region may have occurred. High genetic diversity may further

  17. Plant Biodiversity Drivers in Brazilian Campos Rupestres: Insights from Phylogenetic Structure.

    Science.gov (United States)

    Zappi, Daniela C; Moro, Marcelo F; Meagher, Thomas R; Nic Lughadha, Eimear

    2017-01-01

    Old, climate-buffered infertile landscapes (Ocbils) have attracted increasing levels of interest in recent years because of their exceptionally diverse plant communities. Brazil's campos rupestres (rupestrian grasslands) are home to almost 15% of Brazil's native flora in less than 0.8% of Brazil's territory: an ideal study system for exploring variation in floristic diversity and phylogenetic structure in sites differing in geology and phytophysiognomy. We found significant differences in floristic diversity and phylogenetic structure across a range of study sites encompassing open vegetation and forest on quartzite (FQ) and on ironstone substrates, commonly termed canga . Substrate and physiognomy were key in structuring floristic diversity in the Espinhaço and physiognomy was more important than substrate in structuring phylogenetic diversity, with neither substrate nor its interaction with physiognomy accounting for significant variation in phylogenetic structure. Phylogenetic clustering was significant in open vegetation on both canga and quartzite, reflecting the potential role of environmental filtering in these exposed montane communities adapted to multiple environmental stressors. In forest communities, phylogenetic clustering was significant only at relatively deep nodes of the phylogeny in FQ while no significant phylogenetic clustering was detected across forest on canga (FC), which may be attributable to proximity to the megadiverse Atlantic forest biome and/or comparatively benign environmental conditions in FC with relatively deep, nutrient-rich soils and access to edaphic water reliable in comparison to those for open vegetation on canga and open or forest communities on quartzite. Clades representing relatively old lineages are significantly over-represented in campos rupestres on quartzite, consistent with the Gondwanan Heritage Hypothesis of Ocbil theory. In contrast, forested sites on canga are recognized as Yodfels. To be effective

  18. Plant Biodiversity Drivers in Brazilian Campos Rupestres: Insights from Phylogenetic Structure

    Directory of Open Access Journals (Sweden)

    Daniela C. Zappi

    2017-12-01

    Full Text Available Old, climate-buffered infertile landscapes (Ocbils have attracted increasing levels of interest in recent years because of their exceptionally diverse plant communities. Brazil’s campos rupestres (rupestrian grasslands are home to almost 15% of Brazil’s native flora in less than 0.8% of Brazil’s territory: an ideal study system for exploring variation in floristic diversity and phylogenetic structure in sites differing in geology and phytophysiognomy. We found significant differences in floristic diversity and phylogenetic structure across a range of study sites encompassing open vegetation and forest on quartzite (FQ and on ironstone substrates, commonly termed canga. Substrate and physiognomy were key in structuring floristic diversity in the Espinhaço and physiognomy was more important than substrate in structuring phylogenetic diversity, with neither substrate nor its interaction with physiognomy accounting for significant variation in phylogenetic structure. Phylogenetic clustering was significant in open vegetation on both canga and quartzite, reflecting the potential role of environmental filtering in these exposed montane communities adapted to multiple environmental stressors. In forest communities, phylogenetic clustering was significant only at relatively deep nodes of the phylogeny in FQ while no significant phylogenetic clustering was detected across forest on canga (FC, which may be attributable to proximity to the megadiverse Atlantic forest biome and/or comparatively benign environmental conditions in FC with relatively deep, nutrient-rich soils and access to edaphic water reliable in comparison to those for open vegetation on canga and open or forest communities on quartzite. Clades representing relatively old lineages are significantly over-represented in campos rupestres on quartzite, consistent with the Gondwanan Heritage Hypothesis of Ocbil theory. In contrast, forested sites on canga are recognized as Yodfels. To be

  19. Insights from the Structure of Mycobacterium tuberculosis Topoisomerase I with a Novel Protein Fold

    Energy Technology Data Exchange (ETDEWEB)

    Tan, Kemin; Cao, Nan; Cheng, Bokun; Joachimiak, Andrzej; Tse-Dinh, Yuk-Ching

    2016-01-16

    The DNA topoisomerase I enzyme of Mycobacterium tuberculosis (MtTOP1) is essential for the viability of the organism and survival in a murine model. This topoisomerase is being pursued as a novel target for the discovery of new therapeutic agents for the treatment of drug-resistant tuberculosis. In this study, we succeeded in obtaining a structure of MtTOP1 by first predicting that the C-terminal region of MtTOP1 contains four repeated domains that do not involve the Zn-binding tetracysteine motifs seen in the C-terminal domains of Escherichia coli topoisomerase I. A construct (amino acids A2-T704), MtTOP1-704t, that includes the N-terminal domains (D1-D4) and the first predicted C-terminal domain (D5) of MtTOP1 was expressed and found to retain DNA cleavage-religation activity and catalyze single-stranded DNA catenation. MtTOP1-704t was crystallized, and a structure of 2.52 angstrom resolution limit was obtained. The structure of the MtTOP1 N-terminal domains has features that have not been observed in other previously available bacterial topoisomerase I crystal structures. The first C-terminal domain D5 forms a novel protein fold of a four-stranded antiparallel beta-sheet stabilized by a crossing-over alpha-helix. Since there is only one type IA topoisomerase present in Mycobacteriaceae and related Actinobacteria, this subfamily of type IA topoisomerase may be required for multiple functions in DNA replication, transcription, recombination, and repair. The unique structural features observed for MtTOP1 may allow these topoisomerase I enzymes to carry out physiological functions associated with topoisomerase III enzyme in other bacteria.

  20. Comparing Two Modes of Instruction in English Passive Structures (Processing and Meaning-Based Output Instruction

    Directory of Open Access Journals (Sweden)

    Asma Dabiri

    2018-04-01

    Full Text Available This research compared the effects of two types of instruction: Processing Instruction (PI and Meaning-based Output Instruction (MOI on the interpretation and production of English passive structures.  Ninety EFL intermediate tertiary level female students (PI group= 30, MOI group= 30 and control group = 30 participated in this study. The instruments were a proficiency test, a test to assess English passive structures and two instructional materials (PI and MOI. The data were analyzed by running one-way analysis of variance (ANOVA and mixed between-within ANOVA. The study indicated the effectiveness of PI and MOI on English passive structures. PI had considerable enhancement on interpretation tasks all the time. It supported the use of PI rather than the use of traditional instructions in which mechanical components were emphasized. Also, the PI and MOI had long term effects on the interpretation and production of English passive sentences.  This study supported the use of PI and MOI rather than the use of traditional instruction (TI in EFL settings. The implication for particularly classroom teaching is that successful grammar instruction has to related to ultimate learning outcomes. Also, creating communicative tasks to offer opportunities for teaching grammar can lead to long-lasting learning effects.

  1. Compressive failure modes and parameter optimization of the trabecular structure of biomimetic fully integrated honeycomb plates.

    Science.gov (United States)

    Chen, Jinxiang; Tuo, Wanyong; Zhang, Xiaoming; He, Chenglin; Xie, Juan; Liu, Chang

    2016-12-01

    To develop lightweight biomimetic composite structures, the compressive failure and mechanical properties of fully integrated honeycomb plates were investigated experimentally and through the finite element method. The results indicated that: fracturing of the fully integrated honeycomb plates primarily occurred in the core layer, including the sealing edge structure. The morphological failures can be classified into two types, namely dislocations and compactions, and were caused primarily by the stress concentrations at the interfaces between the core layer and the upper and lower laminations and secondarily by the disordered short-fiber distribution in the material; although the fully integrated honeycomb plates manufactured in this experiment were imperfect, their mass-specific compressive strength was superior to that of similar biomimetic samples. Therefore, the proposed bio-inspired structure possesses good overall mechanical properties, and a range of parameters, such as the diameter of the transition arc, was defined for enhancing the design of fully integrated honeycomb plates and improving their compressive mechanical properties. Copyright © 2016 Elsevier B.V. All rights reserved.

  2. Structural Insight into the Gene Expression Profiling of the hcn Operon in Pseudomonas aeruginosa.

    Science.gov (United States)

    Chowdhury, Nilkanta; Bagchi, Angshuman

    2017-07-01

    Pseudomonas aeruginosa is a common opportunistic human pathogen. It generally attacks immunosuppressed patients like AIDS, cancer, cystic fibrosis, etc. The virulence of P. aeruginosa is mediated by various virulence factors. One of such potential virulence factors is HCN synthesized by HCN synthase enzyme, which is encoded by the hcnABC operon. The expressions of the genes of this operon are regulated by three transcriptional regulators, viz., LasR, ANR, and RhlR. In our previous work, we analyzed the molecular details of the functionalities of LasR. In this work, we focused on ANR. ANR is a regulatory protein which belongs to the FNR family and works in anaerobic condition. ANR binds to the promoter DNA, named ANR box, as a dimer. The dimerization of this ANR protein is regulated by Fe 4 S 4 , an iron-sulfur cluster. This dimer of ANR (ANR-Fe 4 S 4 /ANR-Fe 4 S 4 ) recognizes and binds the promoter DNA sequence and regulates the transcription of this hcnABC operon. Till date, the biomolecular details of the interactions of ANR dimer with the promoter DNA are not fully understood. Thus, we built the molecular model of ANR-Fe 4 S 4 /ANR-Fe 4 S 4 . We docked the complex with the corresponding promoter DNA region. We analyzed the mode of interactions with the promoter DNA under different conditions. Thus, we tried to analyze the functionality of the ANR protein during the expressions of the genes of the hcnABC operon. So far, this is the first report to detail the molecular mechanism of the gene expression in P. aeruginosa.

  3. New Insights on the Structure of the Cascadia Subduction Zone from Amphibious Seismic Data

    Science.gov (United States)

    Janiszewski, Helen Anne

    A new onshore-offshore seismic dataset from the Cascadia subduction zone was used to characterize mantle lithosphere structure from the ridge to the volcanic arc, and plate interface structure offshore within the seismogenic zone. The Cascadia Initiative (CI) covered the Juan de Fuca plate offshore the northwest coast of the United States with an ocean bottom seismometer (OBS) array for four years; this was complemented by a simultaneous onshore seismic array. Teleseismic data recorded by this array allows the unprecedented imaging of an entire tectonic plate from its creation at the ridge through subduction initiation and back beyond the volcanic arc along the entire strike of the Cascadia subduction zone. Higher frequency active source seismic data also provides constraints on the crustal structure along the plate interface offshore. Two seismic datasets were used to image the plate interface structure along a line extending 100 km offshore central Washington. These are wide-angle reflections from ship-to-shore seismic data from the Ridge-To-Trench seismic cruise and receiver functions calculated from a densely spaced CI OBS focus array in a similar region. Active source seismic observations are consistent with reflections from the plate interface offshore indicating the presence of a P-wave velocity discontinuity. Until recently, there has been limited success in using the receiver function technique on OBS data. I avoid these traditional challenges by using OBS constructed with shielding deployed in shallow water on the continental shelf. These data have quieter horizontals and avoid water- and sediment-multiple contamination at the examined frequencies. The receiver functions are consistently modeled with a velocity structure that has a low velocity zone (LVZ) with elevated P to S-wave velocity ratios at the plate interface. A similar LVZ structure has been observed onshore and interpreted as a combination of elevated pore-fluid pressures or metasediments

  4. Crystal structure of bassetite and saleeite. New insight into autunite-group minerals

    Energy Technology Data Exchange (ETDEWEB)

    Dal Bo, Fabrice; Hatert, Frederic [Liege Univ. (Belgium). Lab. de Mineralogie; Mees, Florias [Royal Museum for Central Africa, Tervuren (Belgium); Philippo, Simon [Musee National d' Histoire Naturelle, Luxembourg (Luxembourg). Section Mineralogie; Baijot, Maxime; Fontaine, Francois [Liege Univ. (Belgium). Dept. de Geologie

    2016-06-15

    The crystal structures of two autunite-group minerals have been solved recently. The crystal structure of bassetite, Fe{sup 2+}[(UO{sub 2})(PO{sub 4})]{sub 2}(H{sub 2}O){sub 10}, from the type locality in Cornwall, United Kingdom (Basset Mines) was solved for the first time. Bassetite is monoclinic, space group P2{sub 1}/n, a = 6.961(1), b = 20.039(2), c = 6.974(1) Aa and β = 90.46(1) . The crystal structure of saleeite, Mg[(UO{sub 2})(PO{sub 4})]{sub 2}(H{sub 2}O){sub 10}, from Shinkolobwe, Democratic Republic of Congo, was also solved. Saleeite is monoclinic, space group P2{sub 1}/n, a = 6.951(1), b = 19.942(1), c = 6.967(1) Aa and β = 90.58(1) . The crystal structure investigation of bassetite (R{sub 1} = 0.0658 for 1879 observed reflections with vertical stroke F{sub o} vertical stroke ≥ 4σ{sub F}) and saleeite (R{sub 1} = 0.0307 for 1990 observed reflections with vertical stroke F{sub o} vertical stroke ≥ 4σ{sub F}) confirms that both minerals are topologically identical and that bassetite contains ten water molecules per formula unit. Their structure contains autunite-type sheets, [(UO{sub 2})(PO{sub 4})]{sup -}, consisting of corner-sharing UO{sub 6} square bipyramids and PO{sub 4} tetrahedra. Iron and magnesium are surrounded by water molecules to form Fe(H{sub 2}O){sub 6} or Mg(H{sub 2}O){sub 6} octahedra located in interlayer, between the autunite-type sheets. Two isolated independent water molecules are also located in interlayer. Energy-dispersive X-ray spectroscopy analysis confirmed the chemical composition obtained from structure refinement. These new data prompt a re-assessment of minerals of the autunite and meta-autunite groups.

  5. Cross-over between discrete and continuous protein structure space: insights into automatic classification and networks of protein structures.

    Directory of Open Access Journals (Sweden)

    Alberto Pascual-García

    2009-03-01

    Full Text Available Structural classifications of proteins assume the existence of the fold, which is an intrinsic equivalence class of protein domains. Here, we test in which conditions such an equivalence class is compatible with objective similarity measures. We base our analysis on the transitive property of the equivalence relationship, requiring that similarity of A with B and B with C implies that A and C are also similar. Divergent gene evolution leads us to expect that the transitive property should approximately hold. However, if protein domains are a combination of recurrent short polypeptide fragments, as proposed by several authors, then similarity of partial fragments may violate the transitive property, favouring the continuous view of the protein structure space. We propose a measure to quantify the violations of the transitive property when a clustering algorithm joins elements into clusters, and we find out that such violations present a well defined and detectable cross-over point, from an approximately transitive regime at high structure similarity to a regime with large transitivity violations and large differences in length at low similarity. We argue that protein structure space is discrete and hierarchic classification is justified up to this cross-over point, whereas at lower similarities the structure space is continuous and it should be represented as a network. We have tested the qualitative behaviour of this measure, varying all the choices involved in the automatic classification procedure, i.e., domain decomposition, alignment algorithm, similarity score, and clustering algorithm, and we have found out that this behaviour is quite robust. The final classification depends on the chosen algorithms. We used the values of the clustering coefficient and the transitivity violations to select the optimal choices among those that we tested. Interestingly, this criterion also favours the agreement between automatic and expert classifications

  6. From DNA to proteins via the ribosome: Structural insights into the workings of the translation machinery

    Directory of Open Access Journals (Sweden)

    Agirrezabala Xabier

    2010-04-01

    Full Text Available Abstract Understanding protein synthesis in bacteria and humans is important for understanding the origin of many human diseases and devising treatments for them. Over the past decade, the field of structural biology has made significant advances in the visualisation of the molecular machinery involved in protein synthesis. It is now possible to discern, at least in outline, the way that interlocking ribosomal components and factors adapt their conformations throughout this process. The determination of structures in various functional contexts, along with the application of kinetic and fluorescent resonance energy transfer approaches to the problem, has given researchers the frame of reference for what remains as the greatest challenge: the complete dynamic portrait of protein synthesis in the cell.

  7. Designer biomass for next-generation biorefineries: leveraging recent insights into xylan structure and biosynthesis.

    Science.gov (United States)

    Smith, Peter J; Wang, Hsin-Tzu; York, William S; Peña, Maria J; Urbanowicz, Breeanna R

    2017-01-01

    Xylans are the most abundant noncellulosic polysaccharides in lignified secondary cell walls of woody dicots and in both primary and secondary cell walls of grasses. These polysaccharides, which comprise 20-35% of terrestrial biomass, present major challenges for the efficient microbial bioconversion of lignocellulosic feedstocks to fuels and other value-added products. Xylans play a significant role in the recalcitrance of biomass to degradation, and their bioconversion requires metabolic pathways that are distinct from those used to metabolize cellulose. In this review, we discuss the key differences in the structural features of xylans across diverse plant species, how these features affect their interactions with cellulose and lignin, and recent developments in understanding their biosynthesis. In particular, we focus on how the combined structural and biosynthetic knowledge can be used as a basis for biomass engineering aimed at developing crops that are better suited as feedstocks for the bioconversion industry.

  8. Collagenolytic Matrix Metalloproteinase Structure-Function Relationships: Insights From Molecular Dynamics Studies.

    Science.gov (United States)

    Karabencheva-Christova, Tatyana G; Christov, Christo Z; Fields, Gregg B

    2017-01-01

    Several members of the zinc-dependent matrix metalloproteinase (MMP) family catalyze collagen degradation. Experimental data reveal a collaboration between different MMP domains in order to achieve efficient collagenolysis. Molecular dynamics (MD) simulations have been utilized to provide atomistic details of the collagenolytic process. The triple-helical structure of collagen exhibits local regions of flexibility, with modulation of interchain salt bridges and water bridges contributing to accessibility of individual chains by the enzyme. In turn, the hemopexin-like (HPX) domain of the MMP initially binds the triple helix and facilitates the presentation of individual strands to active site in the catalytic (CAT) domain. Extensive positive and negative correlated motions are observed between the CAT and HPX domains when collagen is bound. Ultimately, the MD simulation studies have complemented structural (NMR spectroscopy, X-ray crystallography) and kinetic analyses to provide a more detailed mechanistic view of MMP-catalyzed collagenolysis. © 2017 Elsevier Inc. All rights reserved.

  9. First principles insight into the α-glucan structures of starch

    DEFF Research Database (Denmark)

    Damager, Iben; Engelsen, Søren Balling; Blennow, Andreas

    2010-01-01

    A study was conducted to demonstrate the synthesis, conformation, and hydration of the α-glucan structures of starch. Starch and glycogen were synthesized by sets of specific enzyme activities that directly determined their molecular structures and physical properties. It was demonstrated...... that the extent of crystallinity, aggregation and hydration was of fundamental importance for starch and its human analogue glycogen. Starch was deposited in the plant as a stable form in highly organized and semicrystalline granules having specific crystalline polymorphs as determined by powder X......-ray crystallography. The investigations mainly focused on the bottom-up approach of synthesis, conformation, and hydration of starch. Starch and glycogen were found to be polymers that were built up from a single monomer, D-glucopyranose, or for short D-glucose....

  10. Designing Probes for Immunodiagnostics: Structural Insights into an Epitope Targeting Burkholderia Infections.

    Science.gov (United States)

    Capelli, Riccardo; Matterazzo, Elena; Amabili, Marco; Peri, Claudio; Gori, Alessandro; Gagni, Paola; Chiari, Marcella; Lertmemongkolchai, Ganjana; Cretich, Marina; Bolognesi, Martino; Colombo, Giorgio; Gourlay, Louise J

    2017-10-13

    Structure-based epitope prediction drives the design of diagnostic peptidic probes to reveal specific antibodies elicited in response to infections. We previously identified a highly immunoreactive epitope from the peptidoglycan-associated lipoprotein (Pal) antigen from Burkholderia pseudomallei, which could also diagnose Burkholderia cepacia infections. Here, considering the high phylogenetic conservation within Burkholderia species, we ask whether cross-reactivity can be reciprocally displayed by the synthetic epitope from B. cenocepacia. We perform comparative analyses of the conformational preferences and diagnostic performances of the corresponding epitopes from the two Burkholderia species when presented in the context of the full-length proteins or as isolated peptides. The effects of conformation on the diagnostic potential and cross-reactivity of Pal peptide epitopes are rationalized on the basis of the 1.8 Å crystal structure of B. cenocepacia Pal and through computational analyses. Our results are discussed in the context of designing new diagnostic molecules for the early detection of infectious diseases.

  11. Insights on Structural Characteristics and Ligand Binding Mechanisms of CDK2

    Directory of Open Access Journals (Sweden)

    Yan Li

    2015-04-01

    Full Text Available Cyclin-dependent kinase 2 (CDK2 is a crucial regulator of the eukaryotic cell cycle. However it is well established that monomeric CDK2 lacks regulatory activity, which needs to be aroused by its positive regulators, cyclins E and A, or be phosphorylated on the catalytic segment. Interestingly, these activation steps bring some dynamic changes on the 3D-structure of the kinase, especially the activation segment. Until now, in the monomeric CDK2 structure, three binding sites have been reported, including the adenosine triphosphate (ATP binding site (Site I and two non-competitive binding sites (Site II and III. In addition, when the kinase is subjected to the cyclin binding process, the resulting structural changes give rise to a variation of the ATP binding site, thus generating an allosteric binding site (Site IV. All the four sites are demonstrated as being targeted by corresponding inhibitors, as is illustrated by the allosteric binding one which is targeted by inhibitor ANS (fluorophore 8-anilino-1-naphthalene sulfonate. In the present work, the binding mechanisms and their fluctuations during the activation process attract our attention. Therefore, we carry out corresponding studies on the structural characterization of CDK2, which are expected to facilitate the understanding of the molecular mechanisms of kinase proteins. Besides, the binding mechanisms of CDK2 with its relevant inhibitors, as well as the changes of binding mechanisms following conformational variations of CDK2, are summarized and compared. The summary of the conformational characteristics and ligand binding mechanisms of CDK2 in the present work will improve our understanding of the molecular mechanisms regulating the bioactivities of CDK2.

  12. Insights on Forest Structure and Composition from Long-Term Research in the Luquillo Mountains

    OpenAIRE

    Tamara Heartsill Scalley

    2017-01-01

    The science of ecology fundamentally aims to understand species and their relation to the environment. At sites where hurricane disturbance is part of the environmental context, permanent forest plots are critical to understand ecological vegetation dynamics through time. An overview of forest structure and species composition from two of the longest continuously measured tropical forest plots is presented. Long-term measurements, 72 years at the leeward site, and 25 years at windward site, o...

  13. Structural insights into SUN-KASH complexes across the nuclear envelope

    Institute of Scientific and Technical Information of China (English)

    Wenjia Wang; Zhaocai Zhou; Zhubing Shi; Shi Jiao; Cuicui Chen; Huizhen Wang; Guoguang Liu; Qiang Wang; Yun Zhao; Mark I Greene

    2012-01-01

    Linker of the nucleoskeleton and the cytoskeleton (LINC) complexes are composed of SUN and KASH domaincontaining proteins and bridge the inner and outer membranes of the nuclear envelope.LINC complexes play critical roles in nuclear positioning,cell polarization and cellular stiffness.Previously,we reported the homotrimeric structure of human SUN2.We have now determined the crystal structure of the human SUN2-KASH complex.In the complex structure,the SUN domain homotrimer binds to three independent "hook"-like KASH peptides.The overall conformation of the SUN domain in the complex closely resembles the SUN domain in its apo state.A major conformational change involves the AA'-loop of KASH-bound SUN domain,which rearranges to form a mini β-sheet that interacts with the KASH peptide.The PPPT motif of the KASH domain fits tightly into a hydrophobic pocket on the homotrimeric interface of the SUN domain,which we termed the BI-pocket.Moreover,two adjacent protomers of the SUN domain homotrimer sandwich the KASH domain by hydrophobic interaction and hydrogen bonding.Mutations of these binding sites disrupt or reduce the association between the SUN and KASH domains in vitro.In addition,transfection of wild-type,but not mutant,SUN2 promotes cell migration in Ovcar-3 cells.These results provide a structural model of the LINC complex,which is essential for additional study of the physical and functional coupling between the cytoplasm and the nucleoplasm.

  14. Structural insight into mechanism and diverse substrate selection strategy of L-ribulokinase

    Energy Technology Data Exchange (ETDEWEB)

    Agarwal R.; Swaminathan S.; Burley, S. K.

    2012-01-01

    The araBAD operon encodes three different enzymes required for catabolism of L-arabinose, which is one of the most abundant monosaccharides in nature. L-ribulokinase, encoded by the araB gene, catalyzes conversion of L-ribulose to L-ribulose-5-phosphate, the second step in the catabolic pathway. Unlike other kinases, ribulokinase exhibits diversity in substrate selectivity and catalyzes phosphorylation of all four 2-ketopentose sugars with comparable k{sub cat} values. To understand ribulokinase recognition and phosphorylation of a diverse set of substrates, we have determined the X-ray structure of ribulokinase from