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Sample records for backbone dihedral angles

  1. Using Excel To Study The Relation Between Protein Dihedral Angle Omega And Backbone Length

    Science.gov (United States)

    Shew, Christopher; Evans, Samari; Tao, Xiuping

    How to involve the uninitiated undergraduate students in computational biophysics research? We made use of Microsoft Excel to carry out calculations of bond lengths, bond angles and dihedral angles of proteins. Specifically, we studied protein backbone dihedral angle omega by examining how its distribution varies with the length of the backbone length. It turns out Excel is a respectable tool for this task. An ordinary current-day desktop or laptop can handle the calculations for midsized proteins in just seconds. Care has to be taken to enter the formulas for the spreadsheet column after column to minimize the computing load. Supported in part by NSF Grant #1238795.

  2. Constructing euclidean simplex with prescribed dihedral angles

    International Nuclear Information System (INIS)

    Given 1/2n (n + 1) dihedral angles, what is the condition under which there exists an n-dimensional simplex with the prescribed dihedral angles? A complete solution for this problem is given with application demonstrated. (author). 3 refs

  3. On Dihedral Angles of a Simplex

    OpenAIRE

    Maehara, H.

    2013-01-01

    For an $n$-simplex, let $\\alpha,\\,\\beta$ denote the maximum, and the minimum dihedral angles of the simplex, respectively. It is proved that the inequality $\\alpha\\le \\arccos(1/n)\\le \\beta$ always holds, and either side equality implies that the $n$-simplex is a regular simplex. Similar inequalities are also given for a star-simplex, which is defined as a simplex that has a vertex (apex) such that the angles between distinct edges incident to the apex are all equal. Further, an explicit formu...

  4. Predicting dihedral angle probability distributions for protein coil residues from primary sequence using neural networks

    DEFF Research Database (Denmark)

    Helles, Glennie; Fonseca, Rasmus

    2009-01-01

    residue in the input-window. The trained neural network shows a significant improvement (4-68%) in predicting the most probable bin (covering a 30°×30° area of the dihedral angle space) for all amino acids in the data set compared to first order statistics. An accuracy comparable to that of secondary...... local context dependent dihedral angle propensities in coil-regions. This predicted distribution can potentially improve tertiary structure prediction methods that are based on sampling the backbone dihedral angles of individual amino acids. The predicted distribution may also help predict local...

  5. Cooling Rate Controls Dihedral Angles in Dolerite Sills

    Science.gov (United States)

    Holness, M. B.; Richardson, C.

    2011-12-01

    The median of the population of augite-plagioclase-plagioclase dihedral angles in mafic rocks (Θcpp) varies systematically within layered intrusions. It is not clear from previous work how much of this variation is caused by composition and how much is the consequence of different thermal histories. However, the effect of temperature can be isolated by studying a family of non-fractionated planar-sided mafic bodies of various size (and hence cooling rate). Formation of augite-plag-plag dihedral angles involves the growth of augite into the melt-filled space created by the juxtaposition of two plagioclase grains. Examination of the Kiluaea Iki lava lake demonstrates that growth of interstitial augite grains preferentially occurs where the two plagioclase grains meet at a high angle, while narrower melt pockets tend to cool through the glass transition before the melt crystallizes. Θcpp in the lava lake crust and in other rapidly cooled dolerites is ~78°, higher than the 60° expected if augite perfectly pseudomorphed the melt geometry. In more slowly cooled bodies, augite-plag-plag junctions are not formed by the intersection of two planar augite-plag boundaries, but are curved towards higher angles: Θcpp > 78° and, in the most slowly cooled dolerites, may approach the equilibrium value of 109°. Comparison with layered intrusions demonstrates that the change in geometry with decreased cooling rate is not due to sub-solidus modification but is a consequence of simultaneous growth of the two minerals during the last stages of solidification at the three-grain junction. While this is not yet fully quantified it is likely that the controls on the geometry of three-grain junctions, and therefore the dihedral angle, are the effects of confinement on crystal growth rate and mass transport, together with the variable effects of undercooling on crystal growth mechanisms. We measured Θcpp from 10-15 samples across each of a family of non-fractionated basaltic sills

  6. Role of the dihedral angle potential in the nucleation pathway of protein folding

    CERN Document Server

    Djikaev, Y S

    2006-01-01

    A kinetic model for the nucleation mechanism of protein folding is proposed. A protein is modeled as a heteropolymer consisting of hydrophobic and hydrophilic beads with equal constant bond lengths and bond angles. The total energy of the heteropolymer is determined by the repulsive/attractive interactions of non-linked beads and the contribution from the dihedral angles involved. Their parameters can be rigorously defined, unlike the ill defined surface tension of a cluster of protein residues which is the basis of the previous model. As a crucial idea of the model, the dihedral potential in which a selected bead is involved is averaged over all possible configurations of neighboring beads along the protein chain. The resulting average dihedral potential of the residue is constant far enough from the cluster, but increases monotonically with decreasing distance below a threshold value. An overall potential around the cluster wherein a residue performs a chaotic motion is a combination of the average dihedral...

  7. Protein Structure Idealization: How accurately is it possible to model protein structures with dihedral angles?

    OpenAIRE

    Cui, Xuefeng; Li, Shuai Cheng; Bu, Dongbo; Alipanahi, Babak; Li, Ming

    2013-01-01

    Previous studies show that the same type of bond lengths and angles fit Gaussian distributions well with small standard deviations on high resolution protein structure data. The mean values of these Gaussian distributions have been widely used as ideal bond lengths and angles in bioinformatics. However, we are not aware of any research done to evaluate how accurately we can model protein structures with dihedral angles and ideal bond lengths and angles. Here, we introduce the protein structur...

  8. Time dependent correlation between dihedral angles as probe for long range communication in proteins

    Science.gov (United States)

    Das, Amit; Ghosh, Mahua; Chakrabarti, J.

    2016-02-01

    We calculate the time dependent correlation functions (TDCF) between the dihedral angles of a protein calmodulin (CaM), an important protein involved in calcium ion binding in eukaryotic cells. The linker between the calcium binding domains of CaM shows structural changes due to calcium binding at far distances which enables the protein to function. We show that the TDCF between the dihedral angles in these regions are correlated temporally prior to ion binding which are lost upon ion binding. Thus the TDCFs connect the structural changes with ion binding, and can be useful to understand coupled phenomena in bio-macromolecules.

  9. HYPER: A hierarchical algorithm for automatic determination of protein dihedral-angle constraints and stereospecific CβH2 resonance assignments from NMR data

    International Nuclear Information System (INIS)

    A new computer program, HYPER, has been developed for automated analysis of protein dihedral angle values and CβH2 stereospecific assignments from NMR data. HYPER uses a hierarchical grid-search algorithm to determine allowed values of φ, Ψ, and χ1 dihedral angles and CβH2 stereospecific assignments based on a set of NMR-derived distance and/or scalar-coupling constraints. Dihedral-angle constraints are valuable for restricting conformational space and improving convergence in three-dimensional structure calculations. HYPER computes the set of φ, Ψ, and χ1dihedral angles and CβH2 stereospecific assignments that are consistent with up to nine intraresidue and sequential distance bounds, two pairs of relative distance bounds, thirteen homo- and heteronuclear scalar coupling bounds, and two pairs of relative scalar coupling constant bounds. The program is designed to be very flexible, and provides for simple user modification of Karplus equations and standard polypeptide geometries, allowing it to accommodate recent and future improved calibrations of Karplus curves. The C code has been optimized to execute rapidly (0.3-1.5 CPU-sec residue-1 using a 5 deg. grid) on Silicon Graphics R8000, R10000 and Intel Pentium CPUs, making it useful for interactive evaluation of inconsistent experimental constraints. The HYPER program has been tested for internal consistency and reliability using both simulated and real protein NMR data sets

  10. Protein backbone and sidechain torsion angles predicted from NMR chemical shifts using artificial neural networks

    International Nuclear Information System (INIS)

    A new program, TALOS-N, is introduced for predicting protein backbone torsion angles from NMR chemical shifts. The program relies far more extensively on the use of trained artificial neural networks than its predecessor, TALOS+. Validation on an independent set of proteins indicates that backbone torsion angles can be predicted for a larger, ≥90 % fraction of the residues, with an error rate smaller than ca 3.5 %, using an acceptance criterion that is nearly two-fold tighter than that used previously, and a root mean square difference between predicted and crystallographically observed (φ, ψ) torsion angles of ca 12º. TALOS-N also reports sidechain χ1 rotameric states for about 50 % of the residues, and a consistency with reference structures of 89 %. The program includes a neural network trained to identify secondary structure from residue sequence and chemical shifts

  11. Protein backbone and sidechain torsion angles predicted from NMR chemical shifts using artificial neural networks

    Energy Technology Data Exchange (ETDEWEB)

    Shen Yang; Bax, Ad, E-mail: bax@nih.gov [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States)

    2013-07-15

    A new program, TALOS-N, is introduced for predicting protein backbone torsion angles from NMR chemical shifts. The program relies far more extensively on the use of trained artificial neural networks than its predecessor, TALOS+. Validation on an independent set of proteins indicates that backbone torsion angles can be predicted for a larger, {>=}90 % fraction of the residues, with an error rate smaller than ca 3.5 %, using an acceptance criterion that is nearly two-fold tighter than that used previously, and a root mean square difference between predicted and crystallographically observed ({phi}, {psi}) torsion angles of ca 12 Masculine-Ordinal-Indicator . TALOS-N also reports sidechain {chi}{sup 1} rotameric states for about 50 % of the residues, and a consistency with reference structures of 89 %. The program includes a neural network trained to identify secondary structure from residue sequence and chemical shifts.

  12. Assessing protein conformational sampling methods based on bivariate lag-distributions of backbone angles

    KAUST Repository

    Maadooliat, Mehdi

    2012-08-27

    Despite considerable progress in the past decades, protein structure prediction remains one of the major unsolved problems in computational biology. Angular-sampling-based methods have been extensively studied recently due to their ability to capture the continuous conformational space of protein structures. The literature has focused on using a variety of parametric models of the sequential dependencies between angle pairs along the protein chains. In this article, we present a thorough review of angular-sampling-based methods by assessing three main questions: What is the best distribution type to model the protein angles? What is a reasonable number of components in a mixture model that should be considered to accurately parameterize the joint distribution of the angles? and What is the order of the local sequence-structure dependency that should be considered by a prediction method? We assess the model fits for different methods using bivariate lag-distributions of the dihedral/planar angles. Moreover, the main information across the lags can be extracted using a technique called Lag singular value decomposition (LagSVD), which considers the joint distribution of the dihedral/planar angles over different lags using a nonparametric approach and monitors the behavior of the lag-distribution of the angles using singular value decomposition. As a result, we developed graphical tools and numerical measurements to compare and evaluate the performance of different model fits. Furthermore, we developed a web-tool (http://www.stat.tamu. edu/~madoliat/LagSVD) that can be used to produce informative animations. © The Author 2012. Published by Oxford University Press.

  13. Improving the performance of the PLB index for ligand-binding site prediction using dihedral angles and the solvent-accessible surface area.

    Science.gov (United States)

    Cao, Chen; Xu, Shutan

    2016-01-01

    Protein ligand-binding site prediction is highly important for protein function determination and structure-based drug design. Over the past twenty years, dozens of computational methods have been developed to address this problem. Soga et al. identified ligand cavities based on the preferences of amino acids for the ligand-binding site (RA) and proposed the propensity for ligand binding (PLB) index to rank the cavities on the protein surface. However, we found that residues exhibit different RAs in response to changes in solvent exposure. Furthermore, previous studies have suggested that some dihedral angles of amino acids in specific regions of the Ramachandran plot are preferred at the functional sites of proteins. Based on these discoveries, the amino acid solvent-accessible surface area and dihedral angles were combined with the RA and PLB to obtain two new indexes, multi-factor RA (MF-RA) and multi-factor PLB (MF-PLB). MF-PLB, PLB and other methods were tested using two benchmark databases and two particular ligand-binding sites. The results show that MF-PLB can improve the success rate of PLB for both ligand-bound and ligand-unbound structures, particularly for top choice prediction. PMID:27619067

  14. Protein backbone chemical shifts predicted from searching a database for torsion angle and sequence homology

    International Nuclear Information System (INIS)

    Chemical shifts of nuclei in or attached to a protein backbone are exquisitely sensitive to their local environment. A computer program, SPARTA, is described that uses this correlation with local structure to predict protein backbone chemical shifts, given an input three-dimensional structure, by searching a newly generated database for triplets of adjacent residues that provide the best match in φ/ψ/χ1 torsion angles and sequence similarity to the query triplet of interest. The database contains 15N, 1HN, 1Hα, 13Cα, 13Cβ and 13C' chemical shifts for 200 proteins for which a high resolution X-ray (≤2.4 A) structure is available. The relative importance of the weighting factors for the φ/ψ/χ1 angles and sequence similarity was optimized empirically. The weighted, average secondary shifts of the central residues in the 20 best-matching triplets, after inclusion of nearest neighbor, ring current, and hydrogen bonding effects, are used to predict chemical shifts for the protein of known structure. Validation shows good agreement between the SPARTA-predicted and experimental shifts, with standard deviations of 2.52, 0.51, 0.27, 0.98, 1.07 and 1.08 ppm for 15N, 1HN, 1Hα, 13Cα, 13Cβ and 13C', respectively, including outliers

  15. Refinement of the protein backbone angle {psi} in NMR structure calculations

    Energy Technology Data Exchange (ETDEWEB)

    Sprangers, R.; Bottomley, M.J.; Linge, J.P.; Schultz, J.; Nilges, M.; Sattler, M. [European Molecular Biology Laboratory (Germany)

    2000-01-15

    Cross-correlated relaxation rates involving the C{sup {alpha}}-H{sup {alpha}} dipolar interaction and the carbonyl (C') chemical shift anisotropy (CSA) have been measured using two complementary 3D experiments. We show that the protein backbone angle {psi} can be directly refined against such cross-correlated relaxation rates ({gamma}{sup H{alpha}}{sup C{alpha}}{sup ,C'}) and the three-bond H/D isotope effect on the C{sup {alpha}} chemical shifts ({sup 3}{delta}C{sup {alpha}}{sub (ND)}). By simultaneously using both experimental parameters as restraints during NMR structure calculations, a unique value for the backbone angle {psi} is defined. We have applied the new refinement method to the {alpha}-Spectrin SH3 domain (a {beta}-sheet protein) and to the Sgs1p HRDC domain (an {alpha}-helical protein) and show that the quality of the NMR structures is substantially improved, judging from the atomic coordinate precision and the Ramachandran map. In addition, the {psi}-refined NMR structures of the SH3 domain deviate less from the 1.8 A crystal structure, suggesting an improved accuracy. The proposed refinement method can be used to significantly improve the quality of NMR structures and will be applicable to larger proteins.

  16. Dihedral flavor symmetries

    International Nuclear Information System (INIS)

    This thesis deals with the possibility of describing the flavor sector of the Standard Model of Particle Physics (with neutrino masses), that is the fermion masses and mixing matrices, with a discrete, non-abelian flavor symmetry. In particular, mass independent textures are considered, where one or several of the mixing angles are determined by group theory alone and are independent of the fermion masses. To this end a systematic analysis of a large class of discrete symmetries, the dihedral groups, is analyzed. Mass independent textures originating from such symmetries are described and it is shown that such structures arise naturally from the minimization of scalar potentials, where the scalars are gauge singlet flavons transforming non-trivially only under the flavor group. Two models are constructed from this input, one describing leptons, based on the group D4, the other describing quarks and employing the symmetry D14. In the latter model it is the quark mixing matrix element Vud - basically the Cabibbo angle - which is at leading order predicted from group theory. Finally, discrete flavor groups are discussed as subgroups of a continuous gauge symmetry and it is shown that this implies that the original gauge symmetry is broken by fairly large representations. (orig.)

  17. Dihedral flavor symmetries

    Energy Technology Data Exchange (ETDEWEB)

    Blum, Alexander Simon

    2009-06-10

    This thesis deals with the possibility of describing the flavor sector of the Standard Model of Particle Physics (with neutrino masses), that is the fermion masses and mixing matrices, with a discrete, non-abelian flavor symmetry. In particular, mass independent textures are considered, where one or several of the mixing angles are determined by group theory alone and are independent of the fermion masses. To this end a systematic analysis of a large class of discrete symmetries, the dihedral groups, is analyzed. Mass independent textures originating from such symmetries are described and it is shown that such structures arise naturally from the minimization of scalar potentials, where the scalars are gauge singlet flavons transforming non-trivially only under the flavor group. Two models are constructed from this input, one describing leptons, based on the group D{sub 4}, the other describing quarks and employing the symmetry D{sub 14}. In the latter model it is the quark mixing matrix element V{sub ud} - basically the Cabibbo angle - which is at leading order predicted from group theory. Finally, discrete flavor groups are discussed as subgroups of a continuous gauge symmetry and it is shown that this implies that the original gauge symmetry is broken by fairly large representations. (orig.)

  18. The determinants of bond angle variability in protein/peptide backbones: A comprehensive statistical/quantum mechanics analysis.

    Science.gov (United States)

    Improta, Roberto; Vitagliano, Luigi; Esposito, Luciana

    2015-11-01

    The elucidation of the mutual influence between peptide bond geometry and local conformation has important implications for protein structure refinement, validation, and prediction. To gain insights into the structural determinants and the energetic contributions associated with protein/peptide backbone plasticity, we here report an extensive analysis of the variability of the peptide bond angles by combining statistical analyses of protein structures and quantum mechanics calculations on small model peptide systems. Our analyses demonstrate that all the backbone bond angles strongly depend on the peptide conformation and unveil the existence of regular trends as function of ψ and/or φ. The excellent agreement of the quantum mechanics calculations with the statistical surveys of protein structures validates the computational scheme here employed and demonstrates that the valence geometry of protein/peptide backbone is primarily dictated by local interactions. Notably, for the first time we show that the position of the H(α) hydrogen atom, which is an important parameter in NMR structural studies, is also dependent on the local conformation. Most of the trends observed may be satisfactorily explained by invoking steric repulsive interactions; in some specific cases the valence bond variability is also influenced by hydrogen-bond like interactions. Moreover, we can provide a reliable estimate of the energies involved in the interplay between geometry and conformations. PMID:26264789

  19. Multiplicities of dihedral discriminants

    Science.gov (United States)

    Mayer, Daniel C.

    1992-04-01

    Given the discriminant {d_k} of a quadratic field k, the number of cyclic relative extensions N\\vert k of fixed odd prime degree p with dihedral absolute Galois group of order 2p, which share a common conductor f, is called the multiplicity of the dihedral discriminant {d_N} = {f^{2(p - 1)}}d_k^p . In this paper, general formulas for multiplicities of dihedral discriminants are derived by analyzing the p-rank of the ring class group mod f of k. For the special case p = 3,{d_k} = - 3 , an elementary proof is given additionally. The theory is illustrated by a discussion of all known discriminants of multiplicity ≥ 5 of totally real and complex cubic fields.

  20. On correlation between protein secondary structure, backbone bond angles, and side-chain orientations

    CERN Document Server

    Lundgren, Martin

    2012-01-01

    We investigate the fine structure of the sp3 hybridized covalent bond geometry that governs the tetrahedral architecture around the central C$_\\alpha$ carbon of a protein backbone, and for this we develop new visualization techniques to analyze high resolution X-ray structures in Protein Data Bank. We observe that there is a correlation between the deformations of the ideal tetrahedral symmetry and the local secondary structure of the protein. We propose a universal coarse grained energy function to describe the ensuing side-chain geometry in terms of the C$_\\beta$ carbon orientations. The energy function can model the side-chain geometry with a sub-atomic precision. As an example we construct the C$_\\alpha$-C$_\\beta$ structure of HP35 chicken villin headpiece. We obtain a configuration that deviates less than 0.4 \\.A in root-mean-square distance from the experimental X-ray structure.

  1. HMM-based prediction for protein structural motifs' two local properties: solvent accessibility and backbone torsion angles.

    Science.gov (United States)

    Yu, Jianyong; Xiang, Leijun; Hong, Jiang; Zhang, Weidong

    2013-02-01

    Protein structure prediction is often assisted by predicting one-dimensional structural properties including relative solvent accessibility (RSA) surface and backbone torsion angles (BTA) of residues, and these two properties are continuously varying variables because proteins can move freely in a three-dimensional space. Instead of subdividing them into a few arbitrarily defined states that many popular approaches used, this paper proposes an integrated system for realvalue prediction of protein structural motifs' two local properties, based on the modified Hidden Markov Model that we previously presented. The model was used to capture the relevance of RSA and the dependency of BTA between adjacent residues along the local protein chain in motifs with definite probabilities. These two properties were predicted according to their own probability distribution. The method was applied to a protein fragment library. For nine different classes of motifs, real values of RSA were predicted with mean absolute error (MAE) of 0.122-0.175 and Pearson's correlation coefficient (PCC) of 0.623-0.714 between predicted and actual RSA. Meanwhile, real values of BTA were obtained with MAE of 8.5⁰-29.4⁰ for Φ angles, 11.2⁰-38.5⁰ for ψ angles and PCC of 0.601-0.716 for Φ, 0.597-0.713 for ψ. The results were compared with well-known Real-SPINE Server, and indicate the proposed method may at least serve as the foundation to obtain better local properties from structural motifs for protein structure prediction. PMID:22894152

  2. Reconstructing the free-energy landscape of Met-enkephalin using dihedral principal component analysis and well-tempered metadynamics

    Science.gov (United States)

    Sicard, François; Senet, Patrick

    2013-06-01

    Well-Tempered Metadynamics (WTmetaD) is an efficient method to enhance the reconstruction of the free-energy surface of proteins. WTmetaD guarantees a faster convergence in the long time limit in comparison with the standard metadynamics. It still suffers, however, from the same limitation, i.e., the non-trivial choice of pertinent collective variables (CVs). To circumvent this problem, we couple WTmetaD with a set of CVs generated from a dihedral Principal Component Analysis (dPCA) on the Ramachandran dihedral angles describing the backbone structure of the protein. The dPCA provides a generic method to extract relevant CVs built from internal coordinates, and does not depend on the alignment to an arbitrarily chosen reference structure as usual in Cartesian PCA. We illustrate the robustness of this method in the case of a reference model protein, the small and very diffusive Met-enkephalin pentapeptide. We propose a justification a posteriori of the considered number of CVs necessary to bias the metadynamics simulation in terms of the one-dimensional free-energy profiles associated with Ramachandran dihedral angles along the amino-acid sequence.

  3. Dihedral symmetries of multiple logarithms

    OpenAIRE

    Agarwala, Susama

    2011-01-01

    This paper finds relationships between multiple logarithms with a dihedral group action on the arguments. I generalize the combinatorics developed in Gangl, Goncharov and Levin's R-deco polygon representation of multiple logarithms to find these relations. By writing multiple logarithms as iterated integrals, my arguments are valid for iterated integrals as over an arbitrary field.

  4. Polynomials Associated with Dihedral Groups

    Directory of Open Access Journals (Sweden)

    Charles F. Dunkl

    2007-03-01

    Full Text Available There is a commutative algebra of differential-difference operators, with two parameters, associated to any dihedral group with an even number of reflections. The intertwining operator relates this algebra to the algebra of partial derivatives. This paper presents an explicit form of the action of the intertwining operator on polynomials by use of harmonic and Jacobi polynomials. The last section of the paper deals with parameter values for which the formulae have singularities.

  5. MERA: a webserver for evaluating backbone torsion angle distributions in dynamic and disordered proteins from NMR data

    Energy Technology Data Exchange (ETDEWEB)

    Mantsyzov, Alexey B. [M.V. Lomonosov Moscow State University, Faculty of Fundamental Medicine (Russian Federation); Shen, Yang; Lee, Jung Ho [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States); Hummer, Gerhard [Max Planck Institute of Biophysics (Germany); Bax, Ad, E-mail: bax@nih.gov [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States)

    2015-09-15

    MERA (Maximum Entropy Ramachandran map Analysis from NMR data) is a new webserver that generates residue-by-residue Ramachandran map distributions for disordered proteins or disordered regions in proteins on the basis of experimental NMR parameters. As input data, the program currently utilizes up to 12 different parameters. These include three different types of short-range NOEs, three types of backbone chemical shifts ({sup 15}N, {sup 13}C{sup α}, and {sup 13}C′), six types of J couplings ({sup 3}J{sub HNHα}, {sup 3}J{sub C′C′}, {sup 3}J{sub C′Hα}, {sup 1}J{sub HαCα}, {sup 2}J{sub CαN} and {sup 1}J{sub CαN}), as well as the {sup 15}N-relaxation derived J(0) spectral density. The Ramachandran map distributions are reported in terms of populations of their 15° × 15° voxels, and an adjustable maximum entropy weight factor is available to ensure that the obtained distributions will not deviate more from a newly derived coil library distribution than required to account for the experimental data. MERA output includes the agreement between each input parameter and its distribution-derived value. As an application, we demonstrate performance of the program for several residues in the intrinsically disordered protein α-synuclein, as well as for several static and dynamic residues in the folded protein GB3.

  6. MERA: a webserver for evaluating backbone torsion angle distributions in dynamic and disordered proteins from NMR data

    International Nuclear Information System (INIS)

    MERA (Maximum Entropy Ramachandran map Analysis from NMR data) is a new webserver that generates residue-by-residue Ramachandran map distributions for disordered proteins or disordered regions in proteins on the basis of experimental NMR parameters. As input data, the program currently utilizes up to 12 different parameters. These include three different types of short-range NOEs, three types of backbone chemical shifts (15N, 13Cα, and 13C′), six types of J couplings (3JHNHα, 3JC′C′, 3JC′Hα, 1JHαCα, 2JCαN and 1JCαN), as well as the 15N-relaxation derived J(0) spectral density. The Ramachandran map distributions are reported in terms of populations of their 15° × 15° voxels, and an adjustable maximum entropy weight factor is available to ensure that the obtained distributions will not deviate more from a newly derived coil library distribution than required to account for the experimental data. MERA output includes the agreement between each input parameter and its distribution-derived value. As an application, we demonstrate performance of the program for several residues in the intrinsically disordered protein α-synuclein, as well as for several static and dynamic residues in the folded protein GB3

  7. Reconstructing the free-energy landscape of Met-enkephalin using dihedral Principal Component Analysis and Well-tempered Metadynamics

    CERN Document Server

    Sicard, Francois

    2012-01-01

    Well-Tempered Metadynamics (WTmetaD) is an efficient method to enhance the reconstruction of the free-energy surface of proteins. WTmetaD guarantees a faster convergence in the long time limit in comparison with the standard metadynamics. It still suffers however from the same limitation, i.e. the non trivial choice of pertinent collective variables (CVs). To circumvent this problem, we couple WTmetaD with a set of CVs generated from a dihedral Principal Component Analysis (dPCA) on the Ramachadran dihedral angles describing the backbone structure of the protein. The dPCA provides a generic method to extract relevant CVs built from internal coordinates. We illustrate the robustness of this method in the case of the small and very diffusive Metenkephalin pentapeptide, and highlight a criterion to limit the number of CVs necessary to biased the metadynamics simulation. The free-energy landscape (FEL) of Met-enkephalin built on CVs generated from dPCA is found rugged compared with the FEL built on CVs extracted ...

  8. Dihedral-like constructions of automorphic loops

    Science.gov (United States)

    Aboras, Mouna

    In this dissertation we study dihedral-like constructions of automorphic loops. Automorphic loops are loops in which all inner mappings are automorphisms. We start by describing a generalization of the dihedral construction for groups. Namely, if (G, +) is an abelian group, m > 1 and alpha ∈2 Aut(G), let Dih(m, G, alpha) on Zm x G be defined by. (i, u)(j, v) = (i + j, ((--1)ju + v)alpha ij). We prove that the resulting loop is automorphic if and only if m = 2 or (alpha2 = 1 and m is even) or (m is odd, alpha = 1 and exp(G) ≤ 2). In the last case, the loop is a group. The case m = 2 was introduced by Kinyon, Kunen, Phillips, and Vojtechovsky. We study basic structural properties of dihedral-like automorphic loops. We describe certain subloops, including: nucleus, commutant, center, associator subloop and derived subloop. We prove theorems for dihedral-like automorphic loops analogous to the Cauchy and Lagrange theorems for groups, and further we discuss the coset decomposition in dihedral-like automorphic loops. We show that two finite dihedral-like automorphic loops Dih( m, G, alpha) and Dih(m¯, G¯, [special character omitted]) are isomorphic if and only if m = m¯, G ≅ G¯ and alpha is conjugate to [special character omitted] in Aut(G). We describe the automorphism group of Q and its subgroup consisting of inner mappings of Q. Finally, due to the solution to the isomorphism problem, we are interested in studying conjugacy classes of automorphism groups of finite abelian groups. Then we describe all dihedral-like automorphic loops of order < 128 up to isomorphism. We conclude with a description of all dihedral-like automorphic loops of order < 64 up to isotopism.

  9. $EE_8$-lattices and dihedral groups

    OpenAIRE

    Griess Jr., Robert L.; lam, Ching Hung

    2008-01-01

    We classify integral rootless lattices which are sums of pairs of $EE_8$-lattices (lattices isometric to $\\sqrt 2$ times the $E_8$-lattice) and which define dihedral groups of orders less than or equal to 12. Most of these may be seen in the Leech lattice. Our classification may help understand Miyamoto involutions on lattice type vertex operator algebras and give a context for the dihedral groups which occur in the Glauberman-Norton moonshine theory.

  10. Characterizing universal gate sets via dihedral benchmarking

    Science.gov (United States)

    Carignan-Dugas, Arnaud; Wallman, Joel J.; Emerson, Joseph

    2015-12-01

    We describe a practical experimental protocol for robustly characterizing the error rates of non-Clifford gates associated with dihedral groups, including small single-qubit rotations. Our dihedral benchmarking protocol is a generalization of randomized benchmarking that relaxes the usual unitary 2-design condition. Combining this protocol with existing randomized benchmarking schemes enables practical universal gate sets for quantum information processing to be characterized in a way that is robust against state-preparation and measurement errors. In particular, our protocol enables direct benchmarking of the π /8 gate even under the gate-dependent error model that is expected in leading approaches to fault-tolerant quantum computation.

  11. Automorphic Lie algebras with dihedral symmetry

    International Nuclear Information System (INIS)

    The concept of automorphic Lie algebras arises in the context of reduction groups introduced in the early 1980s in the field of integrable systems. automorphic Lie algebras are obtained by imposing a discrete group symmetry on a current algebra of Krichever–Novikov type. Past work shows remarkable uniformity between algebras associated to different reduction groups. For example, if the base Lie algebra is sl2(C) and the poles of the automorphic Lie algebra are restricted to an exceptional orbit of the symmetry group, changing the reduction group does not affect the Lie algebra structure. In this research we fix the reduction group to be the dihedral group and vary the orbit of poles as well as the group action on the base Lie algebra. We find a uniform description of automorphic Lie algebras with dihedral symmetry, valid for poles at exceptional and generic orbits. (paper)

  12. Measurement of micro-V-groove dihedral using white light interferometry

    Science.gov (United States)

    Fang, Fengzhou; Zeng, Zhen; Zhang, Xiaodong; Jiang, Lili

    2016-01-01

    This study presents a micro-V-grooves dihedral measurement method using white light interferometry on multiple reflection phenomena. When an optical instrument is used to measure microstructures with steep large gradient faces with high reflection rate, considerable measurement errors caused by multiple scattering or multiple reflecting can be observed. These difficulties have limited the application of white light interferometry in the measurement of microstructures. However, the study has found that the multiple-reflection phenomena can be utilized to measure V-groove dihedral angle. The precision of dihedral measurement is a guarantee of ultra-precise machining of retro-reflection mirrors which requires a non-contact measurement to avoid scratches and surface defects caused by the contact probe. The proposed method is capable of obtaining more accurate surface profile data compared to common white light interferometry. Experimental results verify the method and the consistence between the proposed method and contact mode profilometer.

  13. Geometry motivated alternative view on local protein backbone structures

    OpenAIRE

    Zacharias, Jan; Knapp, Ernst Walter

    2013-01-01

    We present an alternative to the classical Ramachandran plot (R-plot) to display local protein backbone structure. Instead of the (ϕ, ψ)-backbone angles relating to the chemical architecture of polypeptides generic helical parameters are used. These are the rotation or twist angle ϑ and the helical rise parameter d. Plots with these parameters provide a different view on the nature of local protein backbone structures. It allows to display the local structures in polar (d, ϑ)-coordinates, whi...

  14. General trends of dihedral conformational transitions in a globular protein

    OpenAIRE

    Y. Miao; Baudry, J.; Smith, JC; McCammon, JA

    2016-01-01

    Dihedral conformational transitions are analyzed systematically in a model globular protein, cytochrome P450cam, to examine their structural and chemical dependences through combined conventional molecular dynamics (cMD), accelerated molecular dynamics (aMD) and adaptive biasing force (ABF) simulations. The aMD simulations are performed at two acceleration levels, using dihedral and dual boost, respectively. In comparison with cMD, aMD samples protein dihedral transitions approximately two ti...

  15. Reflexive and dihedral (cohomology of a pre-additive category

    Directory of Open Access Journals (Sweden)

    Yasien Gh. Gouda

    2001-08-01

    Full Text Available The group dihedral homology of an algebra over a field with characteristic zero was introduced by Tsygan (1983. The dihedral homology and cohomology of an algebra with involution over commutative ring with identity, associated with the small category, were studied by Krasauskas et al. (1988, Loday (1987, and Lodder (1993. The aim of this work is concerned with dihedral and reflexive (cohomology of small pre-additive category. We also define the free product of involutive algebras associated with this category and study its dihedral homology group. Finally, following Perelygin (1990, we show that a small pre-additive category is Morita equivalence.

  16. Testing Backbone.js

    CERN Document Server

    Roemer, Ryan

    2013-01-01

    This book is packed with the step by step tutorial and instructions in recipe format helping you setup test infrastructure and gradually advance your skills to plan, develop, and test your backbone applications.If you are a JavaScript developer looking for recipes to create and implement test support for your backbone application, then this book is ideal for you.

  17. Backbone amide linker strategy

    DEFF Research Database (Denmark)

    Shelton, Anne Pernille Tofteng; Jensen, Knud Jørgen

    2013-01-01

    In the backbone amide linker (BAL) strategy, the peptide is anchored not at the C-terminus but through a backbone amide, which leaves the C-terminal available for various modifications. This is thus a very general strategy for the introduction of C-terminal modifications. The BAL strategy was...... assemble the final peptide. One useful application of this strategy is in the synthesis of C-terminal peptide aldehydes. The C-terminal aldehyde is masked as an acetal during synthesis and then conveniently demasked in the final cleavage step to generate the free aldehyde. Another application is in the...

  18. Local backbone structure prediction of proteins.

    Science.gov (United States)

    de Brevern, Alexandre G; Benros, Cristina; Gautier, Romain; Valadié, Héléne; Hazout, Serge; Etchebest, Catherine

    2004-01-01

    A statistical analysis of the PDB structures has led us to define a new set of small 3D structural prototypes called Protein Blocks (PBs). This structural alphabet includes 16 PBs, each one is defined by the (phi, psi) dihedral angles of 5 consecutive residues. The amino acid distributions observed in sequence windows encompassing these PBs are used to predict by a Bayesian approach the local 3D structure of proteins from the sole knowledge of their sequences. LocPred is a software which allows the users to submit a protein sequence and performs a prediction in terms of PBs. The prediction results are given both textually and graphically. PMID:15724288

  19. Modularity of nearly ordinary 2-adic residually dihedral Galois representations

    OpenAIRE

    Allen, Patrick

    2012-01-01

    We prove modularity of some two dimensional 2-adic Galois representations over a totally real field that are nearly ordinary at all places above 2 and that are residually dihedral. We do this by employing the strategy of Skinner and Wiles using Hida families together with the 2-adic patching method of Khare and Wintenberger. As an application we deduce modularity of some elliptic curves over totally real fields that have good ordinary or multiplicative reduction at places above 2.

  20. Registration of Images with N-fold Dihedral Blur

    Czech Academy of Sciences Publication Activity Database

    Pedone, M.; Flusser, Jan; Heikkila, J.

    2015-01-01

    Roč. 24, č. 3 (2015), s. 1036-1045. ISSN 1057-7149 R&D Projects: GA ČR GA13-29225S; GA ČR GA15-16928S Institutional support: RVO:67985556 Keywords : Image registration * blurred image s * N-fold rotational symmetry * dihedral symmetry * phase correlation Subject RIV: JD - Computer Applications, Robotics Impact factor: 3.625, year: 2014 http://library.utia.cas.cz/separaty/2015/ZOI/flusser-0441247.pdf

  1. Invariants to symmetrical convolution with application to dihedral kernel symmetry

    Czech Academy of Sciences Publication Activity Database

    Boldyš, Jiří; Flusser, Jan

    Berlin: Springer-Verlag, 2013 - (Petrosino, A.), s. 369-378. (Lecture Notes in Computer Science. Image Processing , Computer Vision, Pattern Recognition, and Graphics. 8157). ISBN 978-3-642-41183-0. [ Image Analysis and Processing – ICIAP 2013. Neapol (IT), 11.09.2013-13.09.2013] R&D Projects: GA ČR GAP103/11/1552 Institutional support: RVO:67985556 Keywords : moment invariants * dihedral symmetry * symmetrical blur Subject RIV: BD - Theory of Information http://library.utia.cas.cz/separaty/2013/ZOI/boldys-0397178.pdf

  2. Getting started with Backbone Marionette

    CERN Document Server

    Armendariz, Raymundo

    2014-01-01

    This book is written with an easy-to-understand approach with the intention of giving small but concrete examples that will help you to quickly understand each component of Marionette. Follow along as we work together to build a practical application using Backbone Marionette.If you are a web application developer interested in using Backbone Marionette for a real-life project, then this book is for you. As a prerequisite, knowledge of JavaScript and a working knowledge of Backbone.js is required.

  3. A sampling approach for protein backbone fragment conformations.

    Science.gov (United States)

    Yu, J Y; Zhang, W

    2013-01-01

    In protein structure prediction, backbone fragment bias information can narrow down the conformational space of the whole polypeptide chain significantly. Unlike existing methods that use fragments as building blocks, the paper presents a probabilistic sampling approach for protein backbone torsion angles by modelling angular correlation of (phi, psi) with a directional statistics distribution. Given a protein sequence and secondary structure information, this method samples backbone fragments conformations by using a backtrack sampling algorithm for the hidden Markov model with multiple inputs and a single output. The proposed approach is applied to a fragment library, and some well-known structural motifs are sampled very well on the optimal path. Computational results show that the method can help to obtain native-like backbone fragments conformations. PMID:23777175

  4. A vault ribonucleoprotein particle exhibiting 39-fold dihedral symmetry

    Energy Technology Data Exchange (ETDEWEB)

    Kato, Koji; Tanaka, Hideaki [Insutitute for Protein Research, Osaka University, 3-2 Yamada-oka, Suita 565-0871 (Japan); Sumizawa, Tomoyuki [Department of Environmental Toxicology, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, 1-1 Iseigaoka, Yahatanishi, Kitakyushu 807-8555 (Japan); Yoshimura, Masato; Yamashita, Eiki [Insutitute for Protein Research, Osaka University, 3-2 Yamada-oka, Suita 565-0871 (Japan); Iwasaki, Kenji [Insutitute for Protein Research, Osaka University, 3-2 Yamada-oka, Suita 565-0871 (Japan); Bio-multisome Research Team, Structural Physiology Research Group, RIKEN Harima Institute, Mikazuki Sayo, Hyogo 679-5148 (Japan); Core Research for Evolution Science and Technology, Japan Science and Technology Agency (Japan); Tsukihara, Tomitake, E-mail: tsuki@protein.osaka-u.ac.jp [Insutitute for Protein Research, Osaka University, 3-2 Yamada-oka, Suita 565-0871 (Japan)

    2008-05-01

    A vault from rat liver was crystallized in space group C2. Rotational symmetry searches indicated that the particle has 39-fold dihedral symmetry. Vault is a 12.9 MDa ribonucleoprotein particle with a barrel-like shape, two protruding caps and an invaginated waist structure that is highly conserved in a wide variety of eukaryotes. Multimerization of the major vault protein (MVP) is sufficient to assemble the entire exterior shell of the barrel-shaped vault particle. Multiple copies of two additional proteins, vault poly(ADP-ribose) polymerase (VPARP) and telomerase-associated protein 1 (TEP1), as well as a small vault RNA (vRNA), are also associated with vault. Here, the crystallization of vault particles is reported. The crystals belong to space group C2, with unit-cell parameters a = 708.0, b = 385.0, c = 602.9 Å, β = 124.8°. Rotational symmetry searches based on the R factor and correlation coefficient from noncrystallographic symmetry (NCS) averaging indicated that the particle has 39-fold dihedral symmetry.

  5. A vault ribonucleoprotein particle exhibiting 39-fold dihedral symmetry

    International Nuclear Information System (INIS)

    A vault from rat liver was crystallized in space group C2. Rotational symmetry searches indicated that the particle has 39-fold dihedral symmetry. Vault is a 12.9 MDa ribonucleoprotein particle with a barrel-like shape, two protruding caps and an invaginated waist structure that is highly conserved in a wide variety of eukaryotes. Multimerization of the major vault protein (MVP) is sufficient to assemble the entire exterior shell of the barrel-shaped vault particle. Multiple copies of two additional proteins, vault poly(ADP-ribose) polymerase (VPARP) and telomerase-associated protein 1 (TEP1), as well as a small vault RNA (vRNA), are also associated with vault. Here, the crystallization of vault particles is reported. The crystals belong to space group C2, with unit-cell parameters a = 708.0, b = 385.0, c = 602.9 Å, β = 124.8°. Rotational symmetry searches based on the R factor and correlation coefficient from noncrystallographic symmetry (NCS) averaging indicated that the particle has 39-fold dihedral symmetry

  6. Detection of closed influenza virus hemagglutinin fusion peptide structures in membranes by backbone {sup 13}CO-{sup 15}N rotational-echo double-resonance solid-state NMR

    Energy Technology Data Exchange (ETDEWEB)

    Ghosh, Ujjayini; Xie Li; Weliky, David P., E-mail: weliky@chemistry.msu.edu [Michigan State University, Department of Chemistry (United States)

    2013-02-15

    The influenza virus fusion peptide is the N-terminal {approx}20 residues of the HA2 subunit of the hemagglutinin protein and this peptide plays a key role in the fusion of the viral and endosomal membranes during initial infection of a cell. The fusion peptide adopts N-helix/turn/C-helix structure in both detergent and membranes with reports of both open and closed interhelical topologies. In the present study, backbone {sup 13}CO-{sup 15}N REDOR solid-state NMR was applied to the membrane-associated fusion peptide to detect the distribution of interhelical distances. The data clearly showed a large fraction of closed and semi-closed topologies and were best-fitted to a mixture of two structures that do not exchange. One of the earlier open structural models may have incorrect G13 dihedral angles derived from TALOS analysis of experimentally correct {sup 13}C shifts.

  7. Unique interplay between electronic states and dihedral angle for the molecular rotor diphenyldiacetylene

    DEFF Research Database (Denmark)

    Thulstrup, Peter W.; Hoffmann, Søren Vrønning; Hansen, Bjarke K.V.; Spanget-Larsen, Jens

    2011-01-01

    A new analysis of the optical properties of the molecular rotor 1,4-diphenyl-1,3-butadiyne (diphenyl-diacetylene, DPDA) is presented, taking account of the conformational dynamics. The absorption spectra are interpreted in terms of simultaneous contributions from planar as well as non-planar rota......A new analysis of the optical properties of the molecular rotor 1,4-diphenyl-1,3-butadiyne (diphenyl-diacetylene, DPDA) is presented, taking account of the conformational dynamics. The absorption spectra are interpreted in terms of simultaneous contributions from planar as well as non...

  8. Universal deformation rings and dihedral blocks with two simple modules

    CERN Document Server

    Bleher, Frauke M; Schaefer, Jennifer B

    2010-01-01

    Let k be an algebraically closed field of characteristic 2, and let W be the ring of infinite Witt vectors over k. Suppose G is a finite group and B is a block of kG with a dihedral defect group D such that there are precisely two isomorphism classes of simple B-modules. We determine the universal deformation ring R(G,V) for every finitely generated kG-module V which belongs to B and whose stable endomorphism ring is isomorphic to k. The description by Erdmann of the quiver and relations of the basic algebra of B is usually only determined up to a certain parameter c which is either 0 or 1. We show that R(G,V) is isomorphic to a subquotient ring of WD for all V as above if and only if c=0, giving an answer to a question raised by the first author and Chinburg in this case. Moreover, we prove that c=0 if and only if B is Morita equivalent to a principal block.

  9. Adding diverse noncanonical backbones to rosetta: enabling peptidomimetic design.

    Directory of Open Access Journals (Sweden)

    Kevin Drew

    Full Text Available Peptidomimetics are classes of molecules that mimic structural and functional attributes of polypeptides. Peptidomimetic oligomers can frequently be synthesized using efficient solid phase synthesis procedures similar to peptide synthesis. Conformationally ordered peptidomimetic oligomers are finding broad applications for molecular recognition and for inhibiting protein-protein interactions. One critical limitation is the limited set of design tools for identifying oligomer sequences that can adopt desired conformations. Here, we present expansions to the ROSETTA platform that enable structure prediction and design of five non-peptidic oligomer scaffolds (noncanonical backbones, oligooxopiperazines, oligo-peptoids, [Formula: see text]-peptides, hydrogen bond surrogate helices and oligosaccharides. This work is complementary to prior additions to model noncanonical protein side chains in ROSETTA. The main purpose of our manuscript is to give a detailed description to current and future developers of how each of these noncanonical backbones was implemented. Furthermore, we provide a general outline for implementation of new backbone types not discussed here. To illustrate the utility of this approach, we describe the first tests of the ROSETTA molecular mechanics energy function in the context of oligooxopiperazines, using quantum mechanical calculations as comparison points, scanning through backbone and side chain torsion angles for a model peptidomimetic. Finally, as an example of a novel design application, we describe the automated design of an oligooxopiperazine that inhibits the p53-MDM2 protein-protein interaction. For the general biological and bioengineering community, several noncanonical backbones have been incorporated into web applications that allow users to freely and rapidly test the presented protocols (http://rosie.rosettacommons.org. This work helps address the peptidomimetic community's need for an automated and expandable

  10. On the special values of Artin $L$-functions for dihedral extensions

    OpenAIRE

    Konomi, Yutaka

    2015-01-01

    We study special values of Artin $L$-functions for dihedral extensions at negative integers. We give a relation between these values and orders of the $\\chi$-parts of certain étale cohomology groups.

  11. Dihedral f-tilings of the sphere by rhombi and triangles

    Directory of Open Access Journals (Sweden)

    Ana M. Breda

    2005-12-01

    Full Text Available We classify, up to an isomorphism, the class of all dihedral f-tilings of S 2, whose prototiles are a spherical triangle and a spherical rhombus. The equiangular case was considered and classified in Ana M. Breda and Altino F. Santos, Dihedral f-tilings of the sphere by spherical triangles and equiangular well-centered quadrangles. Here we complete the classification considering the case of non-equiangular rhombi.

  12. A direct electrifying algorithm for backbone identification

    International Nuclear Information System (INIS)

    This paper proposes a new algorithm for identifying backbones in the application of percolation theory. This algorithm is based on the current-carrying definition of backbone and is carried out on the predetermined spanning cluster. It is fairly easy to implement and further parallelize. The efficiency is enhanced by the fact that the conductivity of a percolating system can be obtained in the same processing of backbone identification. The critical exponents of backbone mass, red bonds (sites) and conductivity obtained by this algorithm are in very good agreement with the existing results

  13. Green Network Planning Model for Optical Backbones

    DEFF Research Database (Denmark)

    Gutierrez Lopez, Jose Manuel; Riaz, M. Tahir; Jensen, Michael;

    2010-01-01

    Communication networks are becoming more essential for our daily lives and critically important for industry and governments. The intense growth in the backbone traffic implies an increment of the power demands of the transmission systems. This power usage might have a significant negative effect...... an analytical model to consider environmental aspects in the planning stage of backbones design....

  14. Exercise: The Backbone of Spine Treatment

    Medline Plus

    Full Text Available Exercise: The Backbone of Spine Treatment | View Video Back Purchase Video Struggling with Low Back Pain? Many people are surprised to learn that carefully selected exercise can ...

  15. Exercise: The Backbone of Spine Treatment

    Science.gov (United States)

    Exercise: The Backbone of Spine Treatment | View Video Back Purchase Video Struggling with Low Back Pain? Many people are surprised to learn that carefully selected exercise can actually reduce back pain. Some exercises can ...

  16. Exercise: The Backbone of Spine Treatment

    Medline Plus

    Full Text Available Exercise: The Backbone of Spine Treatment | View Video Back Purchase Video Struggling with Low Back Pain? Many people are surprised to learn that carefully selected exercise can actually reduce back pain. Some exercises can ...

  17. G-graphs and special representations for binary dihedral groups in GL(2,C)

    OpenAIRE

    de Celis, Álvaro Nolla

    2009-01-01

    We give the classification of all possible G-graphs for any small binary dihedral subgroup G in GL(2,C) and use this classification to give the combinatorial description of the special representations of G in terms of its maximal cyclic normal subgroup.

  18. Regular Balanced Cayley Maps for Cyclic, Dihedral and Generalized Quaternion Groups

    Institute of Scientific and Technical Information of China (English)

    Yan WANG; Rong Quan FENG

    2005-01-01

    A Cayley map is a Cayley graph embedded in an orientable surface such that the local rotations at every vertex are identical. In this paper, balanced regular Cayley maps for cyclic groups,dihedral groups, and generalized quaternion groups are classified.

  19. A restraint molecular dynamics and simulated annealing approach for protein homology modeling utilizing mean angles

    Directory of Open Access Journals (Sweden)

    Maurer Till

    2005-04-01

    Full Text Available Abstract Background We have developed the program PERMOL for semi-automated homology modeling of proteins. It is based on restrained molecular dynamics using a simulated annealing protocol in torsion angle space. As main restraints defining the optimal local geometry of the structure weighted mean dihedral angles and their standard deviations are used which are calculated with an algorithm described earlier by Döker et al. (1999, BBRC, 257, 348–350. The overall long-range contacts are established via a small number of distance restraints between atoms involved in hydrogen bonds and backbone atoms of conserved residues. Employing the restraints generated by PERMOL three-dimensional structures are obtained using standard molecular dynamics programs such as DYANA or CNS. Results To test this modeling approach it has been used for predicting the structure of the histidine-containing phosphocarrier protein HPr from E. coli and the structure of the human peroxisome proliferator activated receptor γ (Ppar γ. The divergence between the modeled HPr and the previously determined X-ray structure was comparable to the divergence between the X-ray structure and the published NMR structure. The modeled structure of Ppar γ was also very close to the previously solved X-ray structure with an RMSD of 0.262 nm for the backbone atoms. Conclusion In summary, we present a new method for homology modeling capable of producing high-quality structure models. An advantage of the method is that it can be used in combination with incomplete NMR data to obtain reasonable structure models in accordance with the experimental data.

  20. Calibration of a polarimetric radar using a rotatable dihedral corner reflector

    Science.gov (United States)

    Unal, C. M. H.; Niemeijer, R. J.; van Sinttruyen, J. S.; Ligthart, L. P.

    1994-07-01

    Based on the existing mathematical formalisms of radar polarimetry, it is necessary to perform accurate and diversified polarimetric measurements in the real world to thoroughly investigate signature definition, identification, and classification of radar targets. For this study the Delft Atmospheric Research Radar (DARR) is used. This ground-based polarimetric FM-CW radar operates in the S-band. The purpose of the present paper is the polarimetric calibration of the DARR. Among the passive reflectors, a rotatable dihedral corner reflector is a suitable calibration object. It enables one to measure different scattering matrices with only one reflector. One alignment must be performed and the scattering matrices are measured at the same range. By measuring several scattering matrices, the accuracy of the calibration result can be estimated. A measurement campaign with a rotatable dihedral corner reflector was therefore performed. The experimental results and the calibration procedure are presented in this paper.

  1. Electronic Transitions in Conformationally Controlled Tetrasilanes with a Wide Range of SiSiSiSi Dihedral Angles

    Czech Academy of Sciences Publication Activity Database

    Tsuji, H.; Fogarty, H. A.; Ehara, M.; Fukuda, R.; Casher, D. L.; Tamao, K.; Nakatsuji, H.; Michl, Josef

    2014-01-01

    Roč. 20, č. 30 (2014), s. 9431-9441. ISSN 0947-6539 Institutional support: RVO:61388963 Keywords : conformational effects * electronic spectra * SAC-CI calculations * silicon * UV/ Vis spectroscopy Subject RIV: CC - Organic Chemistry Impact factor: 5.731, year: 2014

  2. Orientation-dependent backbone-only residue pair scoring functions for fixed backbone protein design

    Directory of Open Access Journals (Sweden)

    Bordner Andrew J

    2010-04-01

    Full Text Available Abstract Background Empirical scoring functions have proven useful in protein structure modeling. Most such scoring functions depend on protein side chain conformations. However, backbone-only scoring functions do not require computationally intensive structure optimization and so are well suited to protein design, which requires fast score evaluation. Furthermore, scoring functions that account for the distinctive relative position and orientation preferences of residue pairs are expected to be more accurate than those that depend only on the separation distance. Results Residue pair scoring functions for fixed backbone protein design were derived using only backbone geometry. Unlike previous studies that used spherical harmonics to fit 2D angular distributions, Gaussian Mixture Models were used to fit the full 3D (position only and 6D (position and orientation distributions of residue pairs. The performance of the 1D (residue separation only, 3D, and 6D scoring functions were compared by their ability to identify correct threading solutions for a non-redundant benchmark set of protein backbone structures. The threading accuracy was found to steadily increase with increasing dimension, with the 6D scoring function achieving the highest accuracy. Furthermore, the 3D and 6D scoring functions were shown to outperform side chain-dependent empirical potentials from three other studies. Next, two computational methods that take advantage of the speed and pairwise form of these new backbone-only scoring functions were investigated. The first is a procedure that exploits available sequence data by averaging scores over threading solutions for homologs. This was evaluated by applying it to the challenging problem of identifying interacting transmembrane alpha-helices and found to further improve prediction accuracy. The second is a protein design method for determining the optimal sequence for a backbone structure by applying Belief Propagation

  3. Net neutrality at internet backbone provider level

    OpenAIRE

    Baglioni, Laura; Calabrese, Armando; Ghiron, Nathan Levialdi

    2013-01-01

    This paper analysis the Internet interconnection market and combine the main technical (i.e. service quality) and economic aspects (i.e. profits and utility) characterizing relations between market players (end users, EUs; Internet Service Providers, ISPs; Internet Backbone Providers, IBPs) in order to determine possible economic outcomes in the strategic interaction between them. The proposed model enables a comparison to be made between expected values of social welfare (i.e. EU utility and...

  4. Backbone Dynamics of Triple-helical Collagen-like Structure

    OpenAIRE

    Lazarev, Yu.A.; Lazareva, A.V.; Komarov, V.M.

    1999-01-01

    Some details of the backbone dynamics in the collagen-like triple helix is discussed and the role of backbone dynamics in functioning collagen proteins is illustrated. On a series of oligotripeptides synthetic analogs of collagen formation of high-frequency vibrational backbone dynamics and low-frequency nonlinear backbone dynamics upon stepwise elongation of peptide chain have been described using infrared spectroscopy and hydrogen-exchange method. In the fully completed triple helix the lev...

  5. Porous solid backbone impregnation for electrochemical energy conversion systems

    KAUST Repository

    Boulfrad, Samir

    2013-09-19

    An apparatus and method for impregnating a porous solid backbone. The apparatus may include a platform for holding a porous solid backbone, an ink jet nozzle configured to dispense a liquid solution onto the porous solid backbone, a positioning mechanism configured to position the ink jet nozzle proximate to a plurality of locations of the porous solid backbone, and a control unit configured to control the positioning mechanism to position the ink jet nozzle proximate to the plurality of locations and cause the ink jet nozzle to dispense the liquid solution onto the porous solid backbone.

  6. Backbone Guided Local Search for the Weighted Maximum Satisfiability Problem

    OpenAIRE

    Jiang, He; Xuan, Jifeng

    2009-01-01

    In this chapter, analytical results on the backbone in weighted MAX-SAT were presented in this paper. We showed that it is intractable to retrieve the backbone in weighted MAX-SAT with any performance guarantee under the assumption that P NP . And a backbone guided local search algorithm was proposed for weighted MAX-SAT. Results of this paper imply a new way to incorporate the backbone in heuristics. The approximate backbone used to guide the flipping of literals in those local search based...

  7. Understanding VoIP from Backbone Measurements

    OpenAIRE

    Birke, Robert Rene' Maria; Petracca, Michele; Mellia, Marco

    2007-01-01

    VoIP has widely been addressed as the technology that will change the Telecommunication model opening the path for convergence. Still today this revolution is far from being complete, since the majority of telephone calls are originated by circuit-oriented networks. In this paper for the first time to the best of our knowledge, we present a large dataset of measurements collected from the FastWeb backbone, which is one of the first worldwide Telecom operator to offer VoIP and high-speed data ...

  8. Peptoid-Peptide hybrid backbone architectures

    DEFF Research Database (Denmark)

    Olsen, Christian Adam

    2010-01-01

    Peptidomimetic oligomers and foldamers have received considerable attention for over a decade, with beta-peptides and the so-called peptoids (N-alkylglycine oligomers) representing prominent examples of such architectures. Lately, hybrid or mixed backbones consisting of both alpha- and beta......-amino acids (alpha/beta-peptides) have been investigated in some detail as well. The present Minireview is a survey of the literature concerning hybrid structures of alpha-amino acids and peptoids, including beta-peptoids (N-alkyl-beta-alanine oligomers), and is intended to give an overview of this area...

  9. High Performance Infiltrated Backbones for Cathode-Supported SOFC's

    DEFF Research Database (Denmark)

    Gil, Vanesa; Kammer Hansen, Kent

    2014-01-01

    A four-step infiltration method has been developed to infiltrate La0.75Sr0.25MnO3+δ (LSM25) nanoparticles into porous structures (YSZ or LSM-YSZ backbones). The pore size distribution in the backbones is obtained either by using PMMA and/or graphites as pore formers or by leaching treatment of...

  10. Determination of Protein Backbone Structures from Residual Dipolar Couplings

    OpenAIRE

    Prestegard, J H; Mayer, K. L.; Valafar, H.; Benison, G. C.

    2005-01-01

    There are a number of circumstances where a focus on determination of the backbone structure of a protein, as opposed to a complete all-atom structure, may be appropriate. This is particularly the case for structures determined as a part of a structural genomics initiative where computational modeling of many sequentially related structures from the backbone of a single family representative is anti...

  11. Free backbone carbonyls mediate rhodopsin activation.

    Science.gov (United States)

    Kimata, Naoki; Pope, Andreyah; Sanchez-Reyes, Omar B; Eilers, Markus; Opefi, Chikwado A; Ziliox, Martine; Reeves, Philip J; Smith, Steven O

    2016-08-01

    Conserved prolines in the transmembrane helices of G-protein-coupled receptors (GPCRs) are often considered to function as hinges that divide the helix into two segments capable of independent motion. Depending on their potential to hydrogen-bond, the free C=O groups associated with these prolines can facilitate conformational flexibility, conformational switching or stabilization of the receptor structure. To address the role of conserved prolines in family A GPCRs through solid-state NMR spectroscopy, we focus on bovine rhodopsin, a GPCR in the visual receptor subfamily. The free backbone C=O groups on helices H5 and H7 stabilize the inactive rhodopsin structure through hydrogen-bonds to residues on adjacent helices. In response to light-induced isomerization of the retinal chromophore, hydrogen-bonding interactions involving these C=O groups are released, thus facilitating repacking of H5 and H7 onto the transmembrane core of the receptor. These results provide insights into the multiple structural and functional roles of prolines in membrane proteins. PMID:27376589

  12. A data acquisition backbone core library

    International Nuclear Information System (INIS)

    For the new experiments at FAIR new concepts of data acquisition systems have to be developed like the distribution of self-triggered, time stamped data streams over high performance networks for event building. The data acquisition backbone core (DABC) is a general purpose software framework designed for the implementation of such data acquisition systems. It provides the event building over networks like InfiniBand or Gigabit Ethernet. All kinds of data channels (front-end systems) are supported by program plug-ins into functional components of DABC like data input, combiner, scheduler, event builder, analysis and storage components. Commands and parameters of DABC and its application plug-ins are published by DIM servers. A Java based Graphical User Interface provides the dynamic control and visualization of these components. Application specific GUIs can be added. After a testing phase, DABC can be used to develop high performance data acquisition systems. Besides that DABC will be used for the implementation of various test beds needed for the final design of data acquisition systems at FAIR like detector tests, readout components test, and data flow investigations

  13. Backbone flexibility in protein design theory and experiment

    Science.gov (United States)

    Su, Alyce

    The role of backbone flexibility in protein design was studied. First, the effect of explicit backbone motion on the selection of amino acids in protein design was assessed in the core of the streptococcal protein Gβ1 domain (Gβ1). Concerted backbone motion was introduced by varying Gβ1's supersecondary structure parameter values. The stability and structural flexibility of seven of the redesigned proteins were determined experimentally. Core variants containing as many as six of ten possible mutations retained native-like properties. This result demonstrates that backbone flexibility can be combined with amino acid side-chain selection and that the selection algorithm is sufficiently robust to tolerate perturbations as large as 15% of the native parameter values. Second, a general, quantitative design method for computing de novo backbone templates was developed. The method had to compute atomic resolution backbones compatible with the atomistic sequence selection algorithm we were using and it had to be applicable to all protein motifs. We again developed a method that uses super-secondary structure parameters to determine the orientation among secondary structural elements, given a target protein fold. Possible backbone arrangements were screened using a cost function which evaluates core packing, hydrogen bonding, loop closure, and backbone torsional geometry. Given a specified number of residues for each secondary structural element, a family of optimal configurations was found. We chose three motifs to test our method (ββα, βαβ, and αα) since their combination could be used to approximate most possible backbone fold. The best structure found for the ββα motif is similar to a zinc finger, and the best structure for the ββα motif is similar to a segment of a β-barrel. The backbone obtained for the αα motif resembles minimized protein A. Last, our backbone design method was evaluated by testing the thermal stability and structural properties

  14. Identical repeated backbone of the human genome

    Directory of Open Access Journals (Sweden)

    Gonzaga-Jauregui Claudia

    2010-01-01

    Full Text Available Abstract Background Identical sequences with a minimal length of about 300 base pairs (bp have been involved in the generation of various meiotic/mitotic genomic rearrangements through non-allelic homologous recombination (NAHR events. Genomic disorders and structural variation, together with gene remodelling processes have been associated with many of these rearrangements. Based on these observations, we identified and integrated all the 100% identical repeats of at least 300 bp in the NCBI version 36.2 human genome reference assembly into non-overlapping regions, thus defining the Identical Repeated Backbone (IRB of the reference human genome. Results The IRB sequences are distributed all over the genome in 66,600 regions, which correspond to ~2% of the total NCBI human genome reference assembly. Important structural and functional elements such as common repeats, segmental duplications, and genes are contained in the IRB. About 80% of the IRB bp overlap with known copy-number variants (CNVs. By analyzing the genes embedded in the IRB, we were able to detect some identical genes not previously included in the Ensembl release 50 annotation of human genes. In addition, we found evidence of IRB gene copy-number polymorphisms in raw sequence reads of two diploid sequenced genomes. Conclusions In general, the IRB offers new insight into the complex organization of the identical repeated sequences of the human genome. It provides an accurate map of potential NAHR sites which could be used in targeting the study of novel CNVs, predicting DNA copy-number variation in newly sequenced genomes, and improve genome annotation.

  15. Efficient Algorithms for Extension of Mobile Backbone Networks

    Directory of Open Access Journals (Sweden)

    Eswaramoorthi. R

    2012-03-01

    Full Text Available Network wide communication is an essential criterion for all wireless sensor networks, to transmit the collected data from environment to base station (sink node in an efficient way. The wide network coverage is provided by constructing Mobile Backbone Networks (MBN, which are dynamic networks. These networks have two types of nodes. They are Mobile backbone nodes and Regular nodes. The Mobile backbone nodes have superior mobility and communication capability than regular nodes. All the information needs to be routed through mobile backbone nodes to regular nodes. The communication between clusters is done through backbone node so that transmission overhead is less. In this paper, we are mainly concentrates on throughput optimization and assigning new regular nodes. First the throughput range is calculated for each cluster, and then data packets are transmitted in such a way that the calculated range of throughput for each cluster is satisfied. The number of regular nodes that can be successfully assigned to mobile backbone nodes can be improved by means of adopting network design formulation technique. In case of any failure of mobile backbone node ,new cluster head is elected based on high energy first (HEF algorithm, where the residual energy of the nodes are considered for election.

  16. Radiation safety system (RSS) backbones: Design, engineering, fabrication and installation

    Energy Technology Data Exchange (ETDEWEB)

    Wilmarth, J.E.; Sturrock, J.C.; Gallegos, F.R.

    1998-12-01

    The Radiation Safety System (RSS) Backbones are part of an electrical/electronic/mechanical system insuring safe access and exclusion of personnel to areas at the Los Alamos Neutron Science Center (LANSCE) accelerator. The RSS Backbones control the safety fusible beam plugs which terminate transmission of accelerated ion beams in response to predefined conditions. Any beam or access fault of the backbone inputs will cause insertion of the beam plugs in the low energy beam transport. The Backbones serve the function of tying the beam plugs to the access control systems, beam spill monitoring systems and current-level limiting systems. In some ways the Backbones may be thought of as a spinal column with beam plugs at the head and nerve centers along the spinal column. The two Linac Backbone segments and experimental area segments form a continuous cable plant over 3,500 feet from beam plugs to the tip on the longest tail. The Backbones were installed in compliance with current safety standards, such as installation of the two segments in separate conduits or tray. Monitoring for ground-faults and input wiring verification was an added enhancement to the system. The system has the capability to be tested remotely.

  17. Radiation safety system (RSS) backbones: Design, engineering, fabrication and installation

    International Nuclear Information System (INIS)

    The Radiation Safety System (RSS) Backbones are part of an electrical/electronic/mechanical system insuring safe access and exclusion of personnel to areas at the Los Alamos Neutron Science Center (LANSCE) accelerator. The RSS Backbones control the safety fusible beam plugs which terminate transmission of accelerated ion beams in response to predefined conditions. Any beam or access fault of the backbone inputs will cause insertion of the beam plugs in the low energy beam transport. The Backbones serve the function of tying the beam plugs to the access control systems, beam spill monitoring systems and current-level limiting systems. In some ways the Backbones may be thought of as a spinal column with beam plugs at the head and nerve centers along the spinal column. The two Linac Backbone segments and experimental area segments form a continuous cable plant over 3,500 feet from beam plugs to the tip on the longest tail. The Backbones were installed in compliance with current safety standards, such as installation of the two segments in separate conduits or tray. Monitoring for ground-faults and input wiring verification was an added enhancement to the system. The system has the capability to be tested remotely

  18. Scoliosis angle

    International Nuclear Information System (INIS)

    The most commonly used methods of assessing the scoliotic deviation measure angles that are not clearly defined in relation to the anatomy of the patient. In order to give an anatomic basis for such measurements it is proposed to define the scoliotic deviation as the deviation the vertebral column makes with the sagittal plane. Both the Cobb and the Ferguson angles may be based on this definition. The present methods of measurement are then attempts to measure these angles. If the plane of these angles is parallel to the film, the measurement will be correct. Errors in the measurements may be incurred by the projection. A hypothetical projection, called a 'rectified orthogonal projection', is presented, which correctly represents all scoliotic angles in accordance with these principles. It can be constructed in practice with the aid of a computer and by performing measurements on two projections of the vertebral column; a scoliotic curve can be represented independent of the kyphosis and lordosis. (Auth.)

  19. Small Angle Neutron Scattering experiments on “side-on fixed"" liquid crystal polyacrylates

    OpenAIRE

    Leroux, N.; Keller, P.; Achard, M.; Noirez, L.; Hardouin, F.

    1993-01-01

    Small Angle Neutron Scattering experiments were carried out on liquid crystalline “side-on fixed” polyacrylates : we observe that the polymer backbone adopts a prolate conformation in the nematic phase. Such anisotropy of the global backbone is larger for smaller spacer length. In every case we measure at low temperatures a large chain extension as previously described in polysiloxanes.

  20. An Analytic Method for the Kinematics and Dynamics of a Multiple-Backbone Continuum Robot

    Directory of Open Access Journals (Sweden)

    Bin He

    2013-01-01

    Full Text Available Continuum robots have been the subject of extensive research due to their potential use in a wide range of applications. In this paper, we propose a new continuum robot with three backbones, and provide a unified analytic method for the kinematics and dynamics of a multiple‐backbone continuum robot. The robot achieves actuation by independently pulling three backbones to carry out a bending motion of two‐degrees‐of‐freedom (DoF. A three‐dimensional CAD model of the robot is built and the kinematical equation is established on the basis of the Euler‐Bernoulli beam. The dynamical model of the continuum robot is constructed by using the Lagrange method. The simulation and the experiment’s validation results show the continuum robot can exactly bend into pre‐set angles in the two‐dimensional space (the maximum error is less than 5% of the robot length and can make a circular motion in three‐dimensional space. The results demonstrate that the proposed analytic method for the kinematics and dynamics of a continuum robot is feasible.

  1. Security in Packet-Switched Land Mobile Radio Backbone Networks

    OpenAIRE

    Thomschutz, Hans Olaf Rutger

    2005-01-01

    Spurred by change in government regulations and to leverage lower-cost technology and services, many land mobile radio (LMR) operators have begun transitioning from circuit-switched to packet-switched backbone networks to handle their future communication needs. Due to the unique demands of packet-switched backbone networks for LMR, it may not be wise to carry over the previously implemented security methods used with circuit-switch systems or to treat an LMR backbone as a regular packet-swit...

  2. LOAD AWARE ADAPTIVE BACKBONE SYNTHESIS IN WIRELESS MESH NETWORKS

    Institute of Scientific and Technical Information of China (English)

    Yuan Yuan; Zheng Baoyu

    2009-01-01

    Wireless Mesh Networks (WMNs) are envisioned to support the wired backbone with a wireless Backbone Networks (BNet) for providing internet connectivity to large-scale areas.With a wide range of internet-oriented applications with different Quality of Service (QoS) requirement,the large-scale WMNs should have good scalability and large bandwidth.In this paper,a Load Aware Adaptive Backbone Synthesis (LAABS) algorithm is proposed to automatically balance the traffic flow in the WMNs.The BNet will dynamically split into smaller size or merge into bigger one according to statistic load information of Backbone Nodes (BNs).Simulation results show LAABS generates moderate BNet size and converges quickly,thus providing scalable and stable BNet to facilitate traffic flow.

  3. 使用Backbone JS搭建SPA

    Institute of Scientific and Technical Information of China (English)

    吕婷

    2012-01-01

    Backbone JSR从2010年发布以来,受到了业界的广泛关注。“豆瓣说”和“豆瓣阅读(阅读器)”是两款以它为基础框架搭建的SPA,本文将结合这两款产品,向读者介绍BackboneJS的方方面面。

  4. Side chain and backbone ordering in a polypeptide

    CERN Document Server

    Wei, Y; Hansmann, U H E

    2006-01-01

    We report results from multicanonical simulations of polyglutamic acid chains of length of ten residues. For this simple polypeptide we observe a decoupling of backbone and side-chain ordering in the folding process. While the details of the two transitions vary between the peptide in gas phase and in an implicit solvent, our results indicate that, independent of the specific surroundings, upon continuously lowering the temperature side-chain ordering occurs only after the backbone topology is completely formed.

  5. Large-scale measurement and modeling of backbone Internet traffic

    Science.gov (United States)

    Roughan, Matthew; Gottlieb, Joel

    2002-07-01

    There is a brewing controversy in the traffic modeling community concerning how to model backbone traffic. The fundamental work on self-similarity in data traffic appears to be contradicted by recent findings that suggest that backbone traffic is smooth. The traffic analysis work to date has focused on high-quality but limited-scope packet trace measurements; this limits its applicability to high-speed backbone traffic. This paper uses more than one year's worth of SNMP traffic data covering an entire Tier 1 ISP backbone to address the question of how backbone network traffic should be modeled. Although the limitations of SNMP measurements do not permit us to comment on the fine timescale behavior of the traffic, careful analysis of the data suggests that irrespective of the variation at fine timescales, we can construct a simple traffic model that captures key features of the observed traffic. Furthermore, the model's parameters are measurable using existing network infrastructure, making this model practical in a present-day operational network. In addition to its practicality, the model verifies basic statistical multiplexing results, and thus sheds deep insight into how smooth backbone traffic really is.

  6. A Consistent Phylogenetic Backbone for the Fungi

    Science.gov (United States)

    Ebersberger, Ingo; de Matos Simoes, Ricardo; Kupczok, Anne; Gube, Matthias; Kothe, Erika; Voigt, Kerstin; von Haeseler, Arndt

    2012-01-01

    The kingdom of fungi provides model organisms for biotechnology, cell biology, genetics, and life sciences in general. Only when their phylogenetic relationships are stably resolved, can individual results from fungal research be integrated into a holistic picture of biology. However, and despite recent progress, many deep relationships within the fungi remain unclear. Here, we present the first phylogenomic study of an entire eukaryotic kingdom that uses a consistency criterion to strengthen phylogenetic conclusions. We reason that branches (splits) recovered with independent data and different tree reconstruction methods are likely to reflect true evolutionary relationships. Two complementary phylogenomic data sets based on 99 fungal genomes and 109 fungal expressed sequence tag (EST) sets analyzed with four different tree reconstruction methods shed light from different angles on the fungal tree of life. Eleven additional data sets address specifically the phylogenetic position of Blastocladiomycota, Ustilaginomycotina, and Dothideomycetes, respectively. The combined evidence from the resulting trees supports the deep-level stability of the fungal groups toward a comprehensive natural system of the fungi. In addition, our analysis reveals methodologically interesting aspects. Enrichment for EST encoded data—a common practice in phylogenomic analyses—introduces a strong bias toward slowly evolving and functionally correlated genes. Consequently, the generalization of phylogenomic data sets as collections of randomly selected genes cannot be taken for granted. A thorough characterization of the data to assess possible influences on the tree reconstruction should therefore become a standard in phylogenomic analyses. PMID:22114356

  7. The nonabelian tensor square of Bieberbach group of dimension five with dihedral point group of order eight

    Science.gov (United States)

    Fauzi, Wan Nor Farhana Wan Mohd; Idrus, Nor'ashiqin Mohd; Masri, Rohaidah; Sarmin, Nor Haniza

    2014-07-01

    The nonabelian tensor product was originated in homotopy theory as well as in algebraic K-theory. The nonabelian tensor square is a special case of the nonabelian tensor product where the product is defined if the two groups act on each other in a compatible way and their action are taken to be conjugation. In this paper, the computation of nonabelian tensor square of a Bieberbach group, which is a torsion free crystallographic group, of dimension five with dihedral point group of order eight is determined. Groups, Algorithms and Programming (GAP) software has been used to assist and verify the results.

  8. Automated protein backbone assignment using the projection-decomposition approach

    International Nuclear Information System (INIS)

    Spectral projection experiments by NMR in conjunction with decomposition analysis have been previously introduced for the backbone assignment of proteins; various pulse sequences as well as the behaviour with low signal-to-noise or chemical shift degeneracy have been illustrated. As a guide for routine applications of this combined tool, we provide here a systematic analysis on different types of proteins using welldefined run-time parameters. As a second result of this study, the backbone assignment module SHABBA was extensively rewritten and improved. Calculations on ubiquitin yielded again fully correct and nearly complete backbone and CHβ assignments. For the 128 residue long azurin, missing assignments mostly affect Hα and Hβ. Among the remaining backbone (plus Cβ) nuclei 97.5% could be assigned with 1.0% differences to a reference. Finally, the new SHABBA algorithm was applied to projections recorded for a yeast histone protein domain at room temperature, where the protein is subject to partial unfolding: this leads to unobservable resonances (about a dozen missing signals in a normal 15N-HSQC) and extensive degeneracy among the resonances. From the clearly observable residues, 97.5% of the backbone and CHβresonances could be assigned, of which only 0.8 % showed differences to published shifts. An additional study on the protein MMP20, which exhibits spectral difficulties to an even larger extent, explores the limitations of the approach.

  9. Backbone Fragility and the Local Search Cost Peak

    CERN Document Server

    Gent, I P; Smaill, A; 10.1613/jair.711

    2011-01-01

    The local search algorithm WSat is one of the most successful algorithms for solving the satisfiability (SAT) problem. It is notably effective at solving hard Random 3-SAT instances near the so-called `satisfiability threshold', but still shows a peak in search cost near the threshold and large variations in cost over different instances. We make a number of significant contributions to the analysis of WSat on high-cost random instances, using the recently-introduced concept of the backbone of a SAT instance. The backbone is the set of literals which are entailed by an instance. We find that the number of solutions predicts the cost well for small-backbone instances but is much less relevant for the large-backbone instances which appear near the threshold and dominate in the overconstrained region. We show a very strong correlation between search cost and the Hamming distance to the nearest solution early in WSat's search. This pattern leads us to introduce a measure of the backbone fragility of an instance, ...

  10. High Performance Infiltrated Backbones for Cathode-Supported SOFC's

    DEFF Research Database (Denmark)

    Gil, Vanesa; Kammer Hansen, Kent

    2014-01-01

    The concept of using highly ionic conducting backbones with subsequent infiltration of electronically conducting particles has widely been used to develop alternative anode-supported SOFC's. In this work, the idea was to develop infiltrated backbones as an alternative design based on cathode-supported...... printed symmetrical cells. Samples with LSM/YSZ composite and YSZ backbones made with graphite+PMMA as pore formers exhibited comparable Rp values to the screen printed LSM/YSZ cathode. This route was chosen as the best to fabricate the cathode supported cells. SEM micrograph of a cathode supported cell...... with infiltrated LSM nanoparticles is shown in Fig. 1. Figure 1. Cross section of LSM infiltrated cathode supported cell. [Formula]...

  11. APPECT: An Approximate Backbone-Based Clustering Algorithm for Tags

    DEFF Research Database (Denmark)

    Zong, Yu; Xu, Guandong; Jin, Pin;

    2011-01-01

    resulting from the severe difficulty of ambiguity, redundancy and less semantic nature of tags. Clustering method is a useful tool to address the aforementioned difficulties. Most of the researches on tag clustering are directly using traditional clustering algorithms such as K-means or Hierarchical...... algorithm for Tags (APPECT). The main steps of APPECT are: (1) we execute the K-means algorithm on a tag similarity matrix for M times and collect a set of tag clustering results Z={C1,C2,…,Cm}; (2) we form the approximate backbone of Z by executing a greedy search; (3) we fix the approximate backbone as...

  12. 基于二面角的三角网格简化算法%An algorithm of triangle mesh simplication based on dihedral angle

    Institute of Scientific and Technical Information of China (English)

    陈志秋; 史立新

    2011-01-01

    逆向工程建模自动化技术的发展,提高了对网格简化质量的要求.为了在大规模简化时保持模型的重要几何特征,在Garland二次误差测度算法基础上,提出二面角的三角网格简化算法,编写了实现算法的Matlab程序.通过实例与Garland算法进行比较,结果表明基于二面角的三角网格简化算法很好地保留了模型的几何特征,提高了网格简化质量,能满足自动化建模的要求.%The development of automatic surface reconstruction technique in reverse engineering requires higher quality of mesh simplication. In order to remain more significant geometry fetures and information, an improved quadric error metric that can keep the shape features around edges based on Garland's quadric error metric is presented and complied by the program written in Matlab. Compare with Garland's algorithm through examples ,this algorithm can keep geometry fetures more perfectly and improves the quality of mesh simplication,and could meet the requirement of automatic surface reconstruction technique.

  13. The Graphical Representation of the Digital Astronaut Physiology Backbone

    Science.gov (United States)

    Briers, Demarcus

    2010-01-01

    This report summarizes my internship project with the NASA Digital Astronaut Project to analyze the Digital Astronaut (DA) physiology backbone model. The Digital Astronaut Project (DAP) applies integrated physiology models to support space biomedical operations, and to assist NASA researchers in closing knowledge gaps related to human physiologic responses to space flight. The DA physiology backbone is a set of integrated physiological equations and functions that model the interacting systems of the human body. The current release of the model is HumMod (Human Model) version 1.5 and was developed over forty years at the University of Mississippi Medical Center (UMMC). The physiology equations and functions are scripted in an XML schema specifically designed for physiology modeling by Dr. Thomas G. Coleman at UMMC. Currently it is difficult to examine the physiology backbone without being knowledgeable of the XML schema. While investigating and documenting the tags and algorithms used in the XML schema, I proposed a standard methodology for a graphical representation. This standard methodology may be used to transcribe graphical representations from the DA physiology backbone. In turn, the graphical representations can allow examination of the physiological functions and equations without the need to be familiar with the computer programming languages or markup languages used by DA modeling software.

  14. Determination of backbone chain direction of PDA using FFM

    Science.gov (United States)

    Jo, Sadaharu; Okamoto, Kentaro; Takenaga, Mitsuru

    2010-01-01

    The effect of backbone chains on friction force was investigated on both Langmuir-Blodgett (LB) films of 10,12-heptacosadiynoic acid and the (0 1 0) surfaces of single crystals of 2,4-hexadiene-1,6-diol using friction force microscopy (FFM). It was observed that friction force decreased when the scanning direction was parallel to the [0 0 1] direction in both samples. Moreover, friction force decreased when the scanning direction was parallel to the crystallographic [1 0 2], [1 0 1], [1 0 0] and [1 0 1¯] directions in only the single crystals. For the LB films, the [0 0 1] direction corresponds to the backbone chain direction of 10,12-heptacosadiynoic acid. For the single crystals, both the [0 0 1] and [1 0 1] directions correspond to the backbone chain direction, and the [1 0 2], [1 0 0] and [1 0 1¯] directions correspond to the low-index crystallographic direction. In both the LB films and single crystals, the friction force was minimized when the directions of scanning and the backbone chain were parallel.

  15. Protein-Backbone Thermodynamics across the Membrane Interface.

    Science.gov (United States)

    Bereau, Tristan; Kremer, Kurt

    2016-07-01

    The thermodynamics of insertion of a protein in a membrane depends on the fine interplay between backbone and side-chain contributions interacting with the lipid environment. Using computer simulations, we probe how different descriptions of the backbone glycyl unit affect the thermodynamics of insertion of individual residues, dipeptides, and entire transmembrane helices. Due to the lack of reference data, we first introduce an efficient methodology to estimate atomistic potential of mean force (PMF) curves from a series of representative and uncorrelated coarse-grained (CG) snapshots. We find strong discrepancies between two CG models, Martini and PLUM, against reference atomistic PMFs and experiments. Atomistic simulations suggest a weak free energy of insertion between water and a POPC membrane for the glycyl unit, in overall agreement with experimental results despite severe assumptions in our calculations. We show that refining the backbone contribution in PLUM significantly improves the PMF of insertion of the WALP16 transmembrane peptide. An improper balance between the glycyl backbone and the attached side chain will lead to energetic artifacts, rationalizing Martini's overstabilization of WALP's adsorbed interfacial state. It illustrates difficulties associated with free-energy-based parametrizations of single-residue models, as the relevant free energy of partitioning used for force-field parametrization does not arise from the entire residue but rather the solvent-accessible chemical groups. PMID:27138459

  16. Constructing Battery-Aware Virtual Backbones in Wireless Sensor Networks

    OpenAIRE

    Chi Ma; Yuanyuan Yang; Zhenghao Zhang

    2007-01-01

    A critical issue in battery-powered sensor networks is to construct energy efficient virtual backbones for network routing. Recent study in battery technology reveals that batteries tend to discharge more power than needed and reimburse the over-discharged power if they are recovered. In this paper we first provide a mathematical battery model suitable for implementation in sensor networks. We then introduce the concept of battery-aware connected dominating set (BACDS) and show that in gener...

  17. Primerjava JavaScript ogrodij Angular, Backbone in Ember

    OpenAIRE

    Simin, Matija

    2016-01-01

    Diplomsko delo primerja tri JavaScript ogrodja za razvoj spletnih aplikacij, in sicer AngularJS, Ember.js in Backbone.js. V okviru dela smo primerjali njihovo implementacijo MVC arhitekturnega modela ali različice le-tega. Poleg implementacije MVC arhitekturnega modela smo primerjali njihove funkcionalnosti in lastnosti, kot so sistem predlog, implementacija usmerjevalnika, komunikacija s strežnikom, podatkovne povezave, prilagodljivosti, velikost in aktivnost skupnosti, kvaliteta obstoje...

  18. Comparison of JavaScript frameworks, Angular, Backbone, and Ember

    OpenAIRE

    Simin, Matija

    2016-01-01

    The thesis compares three JavaScript frameworks for developing web applications: AngularJS, Ember.js and Backbone.js. In the thesis we compared their implementation of the MVC design pattern and their subversions. Besides their implementation of MVC design pattern we compared their functionalities and features, such as templating system, routing implementation, communications with a server, data binding, adjustability, size and activity of the community, quality of existing documentation, pos...

  19. Backbone decomposition for continuous-state branching processes with immigration

    CERN Document Server

    Ren, A E Kyprianou Y-X

    2011-01-01

    In the spirit of Duqesne and Winkel (2007) and Berestycki et al. (2011) we show that supercritical continuous-state branching process with a general branching mechanism and general immigration mechanism is equal in law to a continuous-time Galton Watson process with immigration with Poissonian dressing. The result also characterises the limiting backbone decomposition which is predictable from the work on consistent growth of Galton-Watson trees with immigration in Cao and Winkel (2010).

  20. Variation of protein backbone amide resonance by electrostatic field

    OpenAIRE

    Sharley, John N.

    2015-01-01

    Amide resonance is found to be sensitive to electrostatic field with component parallel or antiparallel the amide C-N bond. This effect is linear and without threshold in the biologically plausible electrostatic field range -0.005 to 0.005 au. Variation of amide resonance varies Resonance-Assisted Hydrogen Bonding such as occurs in the hydrogen bonded chains of backbone amides of protein secondary structures such as beta sheet and alpha helix, varying the stability of the secondary structure....

  1. Increasing protein production by directed vector backbone evolution

    OpenAIRE

    Jakob, Felix; Lehmann, Christian; Martinez, Ronny; Schwaneberg, Ulrich

    2013-01-01

    Recombinant protein production in prokaryotic and eukaryotic organisms was a key enabling technology for the rapid development of industrial and molecular biotechnology. However, despite all progress the improvement of protein production is an ongoing challenge and of high importance for cost-effective enzyme production. With the epMEGAWHOP mutagenesis protocol for vector backbone optimization we report a novel directed evolution based approach to increase protein production levels by randoml...

  2. Design of an IPTV Multicast System for Internet Backbone Networks

    OpenAIRE

    Gilbert, D.; Szymanski, T. H.

    2010-01-01

    The design of an IPTV multicast system for the Internet backbone network is presented and explored through extensive simulations. In the proposed system, a resource reservation algorithm such as RSVP, IntServ, or DiffServ is used to reserve resources (i.e., bandwidth and buffer space) in each router in an IP multicast tree. Each router uses an Input-Queued, Output-Queued, or Crosspoint-Queued switch architecture with unity speedup. A recently proposed Recursive Fair Stochastic Matrix Decompos...

  3. Performance of Flow-Aware Networking in LTE backbone

    DEFF Research Database (Denmark)

    Sniady, Aleksander; Soler, José

    2012-01-01

    According to traffic predictions, the growth in data networks usage will be increasing in the coming years, what will be especially visible in the mobile access networks. This brings new challenges in terms of traffic differentiation and network resource sharing, which need to be faced by wireless...... technologies, such as Long Term Evolution (LTE). This paper proposes usage of a modified Flow Aware Networking (FAN) technique for enhancing Quality of Service (QoS) in the all-IP transport networks underlying LTE backbone. The results obtained with OPNET Modeler show that FAN, in spite of being relatively...

  4. Synthesis of Polynucleotide Analogs Containing a Polyvinyl Alcohol Backbone

    Directory of Open Access Journals (Sweden)

    Per Carlsen

    2008-03-01

    Full Text Available Water soluble homo-base polynucleotide analogues were synthesized in whichpolyvinyl alcohol and partially phosphonated polyvinyl alcohol constituted the backbones,onto which were grafted uracil or adenine via 1,3-dioxane spacers formed by acetalformation with the 1,3-diol moieties in PVA. The resulting adenine-PVA polynucleotideanalogs exhibited hyperchromic effects, which was not the case for the correspondinguracil compounds. Mixtures of the adenine- and aracil PVA-phosphate polynucleotideanalogs in solutions exhibited characteristic S-shaped UV-absorbance vs temperature andmelting curves with melting points at approximately 40 oC.

  5. Application of Multicast-based Video Conference on CERNET Backbone

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Multicast-based video conference is a representative application in advanced network. In multi-point video conference using multicast can get better efficiency facilitated by inner-group broadcast mechanism. In the application, the multicast-based network resources assignment, management and security should be considered together. This paper presents a framework model of multicast-based video conferencing application with three layers. And a practical multicast-based video conferencing is implemented in CERNET(China Education and Research Network) backbone. The practice is valuable for the development of multicast-based video conferencing application in China.

  6. Constructing Battery-Aware Virtual Backbones in Wireless Sensor Networks

    Directory of Open Access Journals (Sweden)

    Chi Ma

    2007-05-01

    Full Text Available A critical issue in battery-powered sensor networks is to construct energy efficient virtual backbones for network routing. Recent study in battery technology reveals that batteries tend to discharge more power than needed and reimburse the over-discharged power if they are recovered. In this paper we first provide a mathematical battery model suitable for implementation in sensor networks. We then introduce the concept of battery-aware connected dominating set (BACDS and show that in general the minimum BACDS (MBACDS can achieve longer lifetime than the previous backbone structures. Then we show that finding a MBACDS is NP-hard and give a distributed approximation algorithm to construct the BACDS. The resulting BACDS constructed by our algorithm is at most (8+Δopt size, where Δ is the maximum node degree and opt is the size of an optimal BACDS. Simulation results show that the BACDS can save a significant amount of energy and achieve up to 30% longer network lifetime than previous schemes.

  7. Long-term forecasting of internet backbone traffic.

    Science.gov (United States)

    Papagiannaki, Konstantina; Taft, Nina; Zhang, Zhi-Li; Diot, Christophe

    2005-09-01

    We introduce a methodology to predict when and where link additions/upgrades have to take place in an Internet protocol (IP) backbone network. Using simple network management protocol (SNMP) statistics, collected continuously since 1999, we compute aggregate demand between any two adjacent points of presence (PoPs) and look at its evolution at time scales larger than 1 h. We show that IP backbone traffic exhibits visible long term trends, strong periodicities, and variability at multiple time scales. Our methodology relies on the wavelet multiresolution analysis (MRA) and linear time series models. Using wavelet MRA, we smooth the collected measurements until we identify the overall long-term trend. The fluctuations around the obtained trend are further analyzed at multiple time scales. We show that the largest amount of variability in the original signal is due to its fluctuations at the 12-h time scale. We model inter-PoP aggregate demand as a multiple linear regression model, consisting of the two identified components. We show that this model accounts for 98% of the total energy in the original signal, while explaining 90% of its variance. Weekly approximations of those components can be accurately modeled with low-order autoregressive integrated moving average (ARIMA) models. We show that forecasting the long term trend and the fluctuations of the traffic at the 12-h time scale yields accurate estimates for at least 6 months in the future. PMID:16252820

  8. Reconstruction of the Sunspot Group Number: the Backbone Method

    CERN Document Server

    Svalgaard, Leif

    2015-01-01

    We have reconstructed the sunspot group count, not by comparisons with other reconstructions and correcting those where they were deemed to be deficient, but by a re-assessment of original sources. The resulting series is a pure solar index and does not rely on input from other proxies, e.g. radionuclides, auroral sightings, or geomagnetic records. 'Backboning' the data sets, our chosen method, provides substance and rigidity by using long-time observers as a stiffness character. Solar activity, as defined by the Group Number, appears to reach and sustain for extended intervals of time the same level in each of the last three centuries since 1700 and the past several decades do not seem to have been exceptionally active, contrary to what is often claimed.

  9. Variation of protein backbone amide resonance by electrostatic field

    CERN Document Server

    Sharley, John N

    2015-01-01

    Amide resonance is found to be sensitive to electrostatic field with component parallel or antiparallel the amide C-N bond. This effect is linear and without threshold in the biologically plausible electrostatic field range -0.005 to 0.005 au. Variation of amide resonance varies Resonance Assisted Hydrogen Bonding such as occurs in the hydrogen bonded chains of backbone amides of protein secondary structures such as beta sheet and non-polyproline helix such as alpha helix, varying the stability of the secondary structure. The electrostatic properties including permittivity of amino acid residue sidegroups influence the electrostatic field component parallel or antiparallel the C-N bond of each amide. The significance of this factor relative to other factors in protein folding depends on the magnitude of electrostatic field component parallel or antiparallel the C-N bond of each amide, and preliminary protein-scale calculations of the magnitude of these components suggest this factor warrants investigation in ...

  10. Design of an IPTV Multicast System for Internet Backbone Networks

    Directory of Open Access Journals (Sweden)

    D. Gilbert

    2010-01-01

    Full Text Available The design of an IPTV multicast system for the Internet backbone network is presented and explored through extensive simulations. In the proposed system, a resource reservation algorithm such as RSVP, IntServ, or DiffServ is used to reserve resources (i.e., bandwidth and buffer space in each router in an IP multicast tree. Each router uses an Input-Queued, Output-Queued, or Crosspoint-Queued switch architecture with unity speedup. A recently proposed Recursive Fair Stochastic Matrix Decomposition algorithm used to compute near-perfect transmission schedules for each IP router. The IPTV traffic is shaped at the sources using Application-Specific Token Bucker Traffic Shapers, to limit the burstiness of incoming network traffic. The IPTV traffic is shaped at the destinations using Application-Specific Playback Queues, to remove residual network jitter and reconstruct the original bursty IPTV video streams at each destination. All IPTV traffic flows are regenerated at the destinations with essentially zero delay jitter and essentially-perfect QoS. The destination nodes deliver the IPTV streams to the ultimate end users using the same IPTV multicast system over a regional Metropolitan Area Network. It is shown that all IPTV traffic is delivered with essentially-perfect end-to-end QoS, with deterministic bounds on the maximum delay and jitter on each video frame. Detailed simulations of an IPTV distribution system, multicasting several hundred high-definition IPTV video streams over several essentially saturated IP backbone networks are presented.

  11. Backbone dynamics of the human CC-chemokine eotaxin

    International Nuclear Information System (INIS)

    Eotaxin is a CC chemokine with potent chemoattractant activity towards eosinophils. 15N NMR relaxation data have been used to characterize the backbone dynamics of recombinant human eotaxin. 15N longitudinal (R1) and transverse (R2) auto relaxation rates, heteronuclear 1H-15N steady-state NOEs, and transverse cross-relaxation rates (ηxy) were obtained at 30 deg. C for all resolved backbone secondary amide groups using 1 H-detected two-dimensional NMR experiments. Ratios of transverse auto and cross relaxation rates were used to identify NH groups influenced by slow conformational rearrangement. Relaxation data were fit to the extended model free dynamics formalism, yielding parameters describing axially symmetric molecular rotational diffusion and the internal dynamics of each NH group. The molecular rotational correlation time (τm) is 5.09±0.02 ns, indicating that eotaxin exists predominantly as a monomer under the conditions of the NMR study. The ratio of diffusion rates about unique and perpendicular axes (Dparallel/Dperpendicular) is 0.81±0.02. Residues with large amplitudes of subnanosecond motion are clustered in the N-terminal region (residues 1-19), the C-terminus (residues 68-73) and the loop connecting the first two β-strands (residues 30-37). N-terminal flexibility appears to be conserved throughout the chemokine family and may have implications for the mechanism of chemokine receptor activation. Residues exhibiting significant dynamics on the microsecond-millisecond time scale are located close to the two conserved disulfide bonds, suggesting that these motions may be coupled to disulfide bond isomerization

  12. Small angle neutron scattering experiments on ''side-on fixed'' liquid crystal polyacrylates

    Energy Technology Data Exchange (ETDEWEB)

    Leroux, N. (Centre de Recherche Paul Pascal, Bordeaux-1 Univ., 33 - Pessac (France)); Keller, P. (Lab. Leon Brillouin, CEA-CNRS/CE Saclay, 91 - Gif-sur-Yvette (France)); Achard, M.F. (Centre de Recherche Paul Pascal, Bordeaux-1 Univ., 33 -Pessac (France)); Noirez, L. (Lab. Leon Brillouin, CEA-CNRS/CE Saclay, 91 -Gif-sur-Yvette (France)); Hardouin, F. (Centre de Recherche Paul Pascal, Bordeaux-1 Univ., 33 - Pessac (France))

    1993-08-01

    Small Angle Neutron Scattering experiments were carried out on liquid crystalline ''side-on fixed'' polyacrylates: we observe that the polymer backbone adopts a prolate conformation in the nematic phase. Such anisotropy of the global backbone is larger for smaller spacer lenght. In every case we measure at low temperatures a large chain extension as previously described in polysiloxanes. (orig.).

  13. Perception of perspective angles

    NARCIS (Netherlands)

    Erkelens, C.J.

    2015-01-01

    We perceive perspective angles, that is, angles that have an orientation in depth, differently from what they are in physical space. Extreme examples are angles between rails of a railway line or between lane dividers of a long and straight road. In this study, subjects judged perspective angles bet

  14. A New Secondary Structure Assignment Algorithm Using Cα Backbone Fragments.

    Science.gov (United States)

    Cao, Chen; Wang, Guishen; Liu, An; Xu, Shutan; Wang, Lincong; Zou, Shuxue

    2016-01-01

    The assignment of secondary structure elements in proteins is a key step in the analysis of their structures and functions. We have developed an algorithm, SACF (secondary structure assignment based on Cα fragments), for secondary structure element (SSE) assignment based on the alignment of Cα backbone fragments with central poses derived by clustering known SSE fragments. The assignment algorithm consists of three steps: First, the outlier fragments on known SSEs are detected. Next, the remaining fragments are clustered to obtain the central fragments for each cluster. Finally, the central fragments are used as a template to make assignments. Following a large-scale comparison of 11 secondary structure assignment methods, SACF, KAKSI and PROSS are found to have similar agreement with DSSP, while PCASSO agrees with DSSP best. SACF and PCASSO show preference to reducing residues in N and C cap regions, whereas KAKSI, P-SEA and SEGNO tend to add residues to the terminals when DSSP assignment is taken as standard. Moreover, our algorithm is able to assign subtle helices (310-helix, π-helix and left-handed helix) and make uniform assignments, as well as to detect rare SSEs in β-sheets or long helices as outlier fragments from other programs. The structural uniformity should be useful for protein structure classification and prediction, while outlier fragments underlie the structure-function relationship. PMID:26978354

  15. Solid state radiation chemistry of the DNA backbone

    International Nuclear Information System (INIS)

    The long term goal of this program is to determine the fundamental rules needed to predict the type and yield of damage produced in DNA due to direct effects of ionizing radiation. The focus is on damage to the sugar-phosphate backbone, damage that would lead to strand breaks. Model systems have been chosen that permit various aspects of this problem to be investigated. The emphasis will be on single crystals of monosaccharides, nucleosides, and nucleotides but will also include some powder work on polynucleotides. In these model systems, free radical products and reactions are observed by electron spin resonance (ESR) and electron nuclear double resonance (ENDOR) techniques. The information thus gained is used in constructing rules that predict what primary free radicals are formed in single crystals of model compounds and the reactions stemming from the primary radicals. The formulation of a set of rules that work in model systems will represent a major advance toward formulating a set of rules that predict the direct damage in DNA itself. In a broader context this program is part of the effort to understand and predict the effects of exposure to ionizing radiation received at low dose rates over long periods of time. Assessment of low dose effects requires a basic understanding of the action of radiation at the molecular level. By contributing to that basic understanding, this program will help solve the problems of risk assessment under low dose conditions. 5 refs., 3 figs

  16. Backbone of complex networks of corporations: The flow of control

    Science.gov (United States)

    Glattfelder, J. B.; Battiston, S.

    2009-09-01

    We present a methodology to extract the backbone of complex networks based on the weight and direction of links, as well as on nontopological properties of nodes. We show how the methodology can be applied in general to networks in which mass or energy is flowing along the links. In particular, the procedure enables us to address important questions in economics, namely, how control and wealth are structured and concentrated across national markets. We report on the first cross-country investigation of ownership networks, focusing on the stock markets of 48 countries around the world. On the one hand, our analysis confirms results expected on the basis of the literature on corporate control, namely, that in Anglo-Saxon countries control tends to be dispersed among numerous shareholders. On the other hand, it also reveals that in the same countries, control is found to be highly concentrated at the global level, namely, lying in the hands of very few important shareholders. Interestingly, the exact opposite is observed for European countries. These results have previously not been reported as they are not observable without the kind of network analysis developed here.

  17. Data acquisition backbone core DABC release v1.0

    International Nuclear Information System (INIS)

    The new experiments at FAIR require new concepts of data acquisition systems for the distribution of self-triggered, time stamped data streams over high performance networks for event building. The Data Acquisition Backbone Core (DABC) is a general purpose software framework developed for the implementation of such data acquisition systems. A DABC application consists of functional components like data input, combiner, scheduler, event builder, filter, analysis and storage which can be configured at runtime. Application specific code including the support of all kinds of data channels (front-end systems) is implemented by C++ program plug-ins. DABC is also well suited as environment for various detector and readout components test beds. A set of DABC plug-ins has been developed for the FAIR experiment CBM (Compressed Baryonic Matter) at GSI. This DABC application is used as DAQ system for test beamtimes. Front-end boards equipped with n-XYTER ASICs and ADCs are connected to read-out controller boards (ROC). From there the data is sent over Ethernet (UDP), or over optics and PCIe interface cards into Linux PCs. DABC does the controlling, event building, archiving and data serving. The first release of DABC was published in 2009 and is available under GPL license.

  18. Resistance issues with new nucleoside/nucleotide backbone options.

    Science.gov (United States)

    Wainberg, Mark A; Turner, Dan

    2004-09-01

    The nucleoside and nucleotide reverse transcriptase inhibitors (NRTIs/NtRTIs) remain an enduring feature of combination therapy. As NRTI/NtRTI options continue to expand, questions arise about how best to combine these agents to create effective dual NRTI/NtRTI backbones in antiretroviral regimens while avoiding treatment-emergent drug resistance. Clinicians must consider how NRTIs/NtRTIs such as tenofovir DF (TDF), abacavir (ABC), and emtricitabine (FTC), as well as new once-daily and coformulated NRTIs/NtRTIs, interact with older agents when combined in novel regimens and how sequencing the new NRTIs can preserve future treatment options. Resistance data from clinical trials have revealed important information on the patterns, prevalence, and effects of resistance seen among patients experiencing virologic failure. In recent years, the prevalence of some mutations such as M184V and Q151M has remained relatively constant, while the L74V mutation, the 69 insertions, and thymidine analogue mutations have decreased in prevalence. Other mutations such as K65R and Y115F, while still relatively uncommon, are increasing in prevalence. This increase may be due to the use of new treatment combinations that select for these mutations at a higher rate. Clinical trials suggest that new regimens containing TDF or ABC select for K65R and that this mutation is observed more frequently with TDF; in contrast, L74V is observed more frequently in ABC-containing regimens but is not commonly selected by TDF-containing regimens. Several lines of evidence are converging to suggest that the presence of zidovudine may decrease the risk of L74V and K65R in ABC- or TDF-containing regimens. This review summarizes the clinical implications of resistance profiles associated with new NRTI/NtRTI regimens in current use and in advanced clinical studies. PMID:15319668

  19. Pseudo 5D HN(C)N Experiment to Facilitate the Assignment of Backbone Resonances in Proteins Exhibiting High Backbone Shift Degeneracy

    CERN Document Server

    Kumar, Dinesh; Shukla, Vaibhav Kumar; Pandey, Himanshu; Arora, Ashish; Guleria, Anupam

    2014-01-01

    Assignment of protein backbone resonances is most routinely carried out using triple resonance three dimensional NMR experiments involving amide 1H and 15N resonances. However for intrinsically unstructured proteins, alpha-helical proteins or proteins containing several disordered fragments, the assignment becomes problematic because of high degree of backbone shift degeneracy. In this backdrop, a novel reduced dimensionality (RD) experiment -(5,3)D-hNCO-CANH- is presented to facilitate (and/or to validate) the sequential backbone resonance assignment in such proteins. The proposed 3D NMR experiment makes use of the modulated amide 15N chemical shifts (resulting from the joint sampling along both its indirect dimensions) to resolve the ambiguity involved in connecting the neighboring amide resonances (i.e. HiNi and Hi-1Ni-1) for overlapping amide NH peaks. The experiment -encoding 5D spectral information- leads to a conventional 3D spectrum with significantly reduced spectral crowding and complexity. The impr...

  20. A transfer matrix for the backbone exponent of two-dimensional percolation

    International Nuclear Information System (INIS)

    Rephrasing the backbone of two-dimensional percolation as a monochromatic path crossing problem, we investigate the latter by a transfer matrix approach. Conformal invariance links the backbone dimension Db to the highest eigenvalue of the transfer matrix T, and we obtain the result Db=1.6431±0.0006. For a strip of width L, T is roughly of size 23L, but we manage to reduce it to ∼L!. We find that the value of Db is stable with respect to inclusion of additional 'blobs' tangent to the backbone in a finite number of points. (author)

  1. A synthetic HIV-1 subtype C backbone generates comparable PR and RT resistance profiles to a subtype B backbone in a recombinant virus assay.

    Directory of Open Access Journals (Sweden)

    David Nauwelaers

    Full Text Available In order to determine phenotypic protease and reverse transcriptase inhibitor-associated resistance in HIV subtype C virus, we have synthetically constructed an HIV-1 subtype C (HIV-1-C viral backbone for use in a recombinant virus assay. The in silico designed viral genome was divided into 4 fragments, which were chemically synthesized and joined together by conventional subcloning. Subsequently, gag-protease-reverse-transcriptase (GPRT fragments from 8 HIV-1 subtype C-infected patient samples were RT-PCR-amplified and cloned into the HIV-1-C backbone (deleted for GPRT using In-Fusion reagents. Recombinant viruses (1 to 5 per patient sample were produced in MT4-eGFP cells where cyto-pathogenic effect (CPE, p24 and Viral Load (VL were monitored. The resulting HIV-1-C recombinant virus stocks (RVS were added to MT4-eGFP cells in the presence of serial dilutions of antiretroviral drugs (PI, NNRTI, NRTI to determine the fold-change in IC50 compared to the IC50 of wild-type HIV-1 virus. Additionally, viral RNA was extracted from the HIV-1-C RVS and the amplified GPRT products were used to generate recombinant virus in a subtype B backbone. Phenotypic resistance profiles in a subtype B and subtype C backbone were compared. The following observations were made: i functional, infectious HIV-1 subtype C viruses were generated, confirmed by VL and p24 measurements; ii their rate of infection was slower than viruses generated in the subtype B backbone; iii they did not produce clear CPE in MT4 cells; and iv drug resistance profiles generated in both backbones were very similar, including re-sensitizing effects like M184V on AZT.

  2. Increasing Sequence Diversity with Flexible Backbone Protein Design: The Complete Redesign of a Protein Hydrophobic Core

    Energy Technology Data Exchange (ETDEWEB)

    Murphy, Grant S.; Mills, Jeffrey L.; Miley, Michael J.; Machius, Mischa; Szyperski, Thomas; Kuhlman, Brian (UNC); (Buffalo)

    2015-10-15

    Protein design tests our understanding of protein stability and structure. Successful design methods should allow the exploration of sequence space not found in nature. However, when redesigning naturally occurring protein structures, most fixed backbone design algorithms return amino acid sequences that share strong sequence identity with wild-type sequences, especially in the protein core. This behavior places a restriction on functional space that can be explored and is not consistent with observations from nature, where sequences of low identity have similar structures. Here, we allow backbone flexibility during design to mutate every position in the core (38 residues) of a four-helix bundle protein. Only small perturbations to the backbone, 12 {angstrom}, were needed to entirely mutate the core. The redesigned protein, DRNN, is exceptionally stable (melting point >140C). An NMR and X-ray crystal structure show that the side chains and backbone were accurately modeled (all-atom RMSD = 1.3 {angstrom}).

  3. Polyolefin Backbone Substitution in Binders for Low Temperature Powder Injection Moulding Feedstocks

    OpenAIRE

    Berenika Hausnerova; Ivo Kuritka; Davit Bleyan

    2014-01-01

    This paper reports the substitution of polyolefin backbone binder components with low melting temperature carnauba wax for powder injection moulding applications. The effect of various binder compositions of Al2O3 feedstock on thermal degradation parameters is investigated by thermogravimetric analysis. Within the experimental framework 29 original feedstock compositions were prepared and the superiority of carnauba wax over the polyethylene binder backbone was demonstrated in compositions co...

  4. Elucidating the backbone conformation of photoswitchable foldamers using vibrational circular dichroism

    OpenAIRE

    Domingos, S.R.; Roeters, S.J.; Amirjalayer, S.; Yu, Z.L.; Hecht, S; Woutersen, S.

    2013-01-01

    The backbone conformation of amphiphilic oligo(azobenzene) foldamers is investigated using vibrational circular dichroism (VCD) spectroscopy on a mode involving the stretching of the N=N bonds in the backbone. From denaturation experiments, we find that the VCD response in the helical conformation arises mainly from through-space interaction between the N=N-stretch transition-dipole moments, so that the coupled-oscillator model can be used to predict the VCD spectrum associated with a particu...

  5. Pseudo 5D HN(C)N experiment to facilitate the assignment of backbone resonances in proteins exhibiting high backbone shift degeneracy

    Energy Technology Data Exchange (ETDEWEB)

    Kumar, Dinesh, E-mail: dineshcbmr@gmail.com [Centre of Biomedical Research (CBMR), SGPGIMS Campus, Raibareli Road, Lucknow 226014 (India); Raikwal, Nisha [Centre of Biomedical Research (CBMR), SGPGIMS Campus, Raibareli Road, Lucknow 226014 (India); Shukla, Vaibhav Kumar; Pandey, Himanshu; Arora, Ashish [Molecular and Structural Biology Division, CSIR, Central Drug Research Institute, Lucknow 226031 (India); Guleria, Anupam, E-mail: anuguleriaphy@gmail.com [Centre of Biomedical Research (CBMR), SGPGIMS Campus, Raibareli Road, Lucknow 226014 (India)

    2014-09-30

    Graphical abstract: - Highlights: • A reduced dimensionality experiment – referred as pseudo 5D HN(C)N- is presented. • Encodes highly resolved 5D spectral information in a 3D spectrum. • Superior in terms of peak dispersion. • Facilitates assignment of crowded HSQC spectra of moderately sized proteins. • Modulated {sup 15}N chemical shifts are used to break the amide shift degeneracy. - Abstract: Assignment of protein backbone resonances is most routinely carried out using triple resonance three-dimensional NMR experiments involving amide {sup 1}H/{sup 15}N resonances. However for intrinsically unstructured proteins, alpha-helical proteins or proteins containing several disordered fragments, the assignment becomes problematic because of high-degree of backbone shift degeneracy. In this backdrop, a novel reduced-dimensionality (RD) experiment –(5, 3)D-hNCO-CANH- is presented to facilitate/validate the sequential backbone resonance assignment in such proteins. The proposed 3D NMR experiment makes use of the modulated amide {sup 15}N chemical shifts (resulting from the joint sampling along both its indirect dimensions) to resolve the ambiguity involved in connecting the neighboring amide resonances (i.e. H{sub i}N{sub i} and H{sub i−1}N{sub i−1}) for overlapping amide-NH peaks. The experiment -in combination with routine triple resonance 3D-NMR experiments involving backbone amide ({sup 1}H/{sup 15}N) and carbon ({sup 13}C{sup α}/{sup 13}C′) chemical shifts- will serve as a powerful complementary tool to achieve the nearly complete assignment of protein backbone resonances in a time efficient manner.

  6. Reading Angles in Maps

    Science.gov (United States)

    Izard, Véronique; O'Donnell, Evan; Spelke, Elizabeth S.

    2014-01-01

    Preschool children can navigate by simple geometric maps of the environment, but the nature of the geometric relations they use in map reading remains unclear. Here, children were tested specifically on their sensitivity to angle. Forty-eight children (age 47:15-53:30 months) were presented with fragments of geometric maps, in which angle sections…

  7. Optimal reconstruction angles

    International Nuclear Information System (INIS)

    The question of optimal projection angles has recently become of interest in the field of reconstruction from projections. Here, studies are concentrated on the n x n pixel space, where literative algorithms such as ART and direct matrix techniques due to Katz are considered. The best angles are determined in a Gauss--Markov statistical sense as well as with respect to a function-theoretical error bound. The possibility of making photon intensity a function of angle is also examined. Finally, the best angles to use in an ART-like algorithm are studied. A certain set of unequally spaced angles was found to be preferred in several contexts. 15 figures, 6 tables

  8. Photoelectric angle converter

    Science.gov (United States)

    Podzharenko, Volodymyr A.; Kulakov, Pavlo I.

    2001-06-01

    The photo-electric angle transmitter of rotation is offered, at which the output voltage is linear function of entering magnitude. In a transmitter the linear phototransducer is used on the basis of pair photo diode -- operating amplifier, which output voltage is linear function of the area of an illuminated photosensitive stratum, and modulator of a light stream of the special shape, which ensures a linear dependence of this area from an angle of rotation. The transmitter has good frequent properties and can be used for dynamic measurements of an angular velocity and angle of rotation, in systems of exact drives and systems of autocontrol.

  9. Quantification of protein backbone hydrogen-deuterium exchange rates by solid state NMR spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Lopez del Amo, Juan-Miguel; Fink, Uwe; Reif, Bernd, E-mail: reif@tum.d [Leibniz-Institut fuer Molekulare Pharmakologie (FMP) (Germany)

    2010-12-15

    We present the quantification of backbone amide hydrogen-deuterium exchange rates (HDX) for immobilized proteins. The experiments make use of the deuterium isotope effect on the amide nitrogen chemical shift, as well as on proton dilution by deuteration. We find that backbone amides in the microcrystalline {alpha}-spectrin SH3 domain exchange rather slowly with the solvent (with exchange rates negligible within the individual {sup 15}N-T{sub 1} timescales). We observed chemical exchange for 6 residues with HDX exchange rates in the range from 0.2 to 5 s{sup -1}. Backbone amide {sup 15}N longitudinal relaxation times that we determined previously are not significantly affected for most residues, yielding no systematic artifacts upon quantification of backbone dynamics (Chevelkov et al. 2008b). Significant exchange was observed for the backbone amides of R21, S36 and K60, as well as for the sidechain amides of N38, N35 and for W41{epsilon}. These residues could not be fit in our previous motional analysis, demonstrating that amide proton chemical exchange needs to be considered in the analysis of protein dynamics in the solid-state, in case D{sub 2}O is employed as a solvent for sample preparation. Due to the intrinsically long {sup 15}N relaxation times in the solid-state, the approach proposed here can expand the range of accessible HDX rates in the intermediate regime that is not accessible so far with exchange quench and MEXICO type experiments.

  10. Phase angle measurement techniques

    Energy Technology Data Exchange (ETDEWEB)

    Madge, R.; Fischer, D.

    1996-01-01

    Real-time measure of the power transfer across a transmission line was discussed. Phase angle measurement techniques, algorithms and applications relevant to power utilities were assessed. Phase-based applications compute the voltage angle difference between two stations, thereby allowing for power transfer calculations and power system control applications. A list of phase angle measurement applications was provided. It includes frequency measurement, state estimation, adaptive relaying, power system control, system restoration, real power flow monitoring and stability assessment, reactive power requirements monitoring, HVDC modulation, subsynchronous resonance, sequence of event recording, and loss reduction and fault location. The optimum timing requirement was determined for each application. Among the timing systems available today, the Global Positioning System (GPS), supported by powerful computers and other custom hardware, is the only tool that can provide the accuracy and coverage needed by today`s power system applications. Commercially available equipment for phase angle measurements was also reviewed. 30 refs., 32 tabs., 5 figs.

  11. 13C direct detected COCO-TOCSY: A tool for sequence specific assignment and structure determination in protonless NMR experiments

    Science.gov (United States)

    Balayssac, Stéphane; Jiménez, Beatriz; Piccioli, Mario

    2006-10-01

    A novel experiment is proposed to provide inter-residue sequential correlations among carbonyl spins in 13C detected, protonless NMR experiments. The COCO-TOCSY experiment connects, in proteins, two carbonyls separated from each other by three, four or even five bonds. The quantitative analysis provides structural information on backbone dihedral angles ϕ as well as on the side chain dihedral angles of Asx and Glx residues. This is the first dihedral angle constraint that can be obtained via a protonless approach. About 75% of backbone carbonyls in Calbindin D 9K, a 75 aminoacid dicalcium protein, could be sequentially connected via a COCO-TOCSY spectrum. 49 3J values were measured and related to backbone ϕ angles. Structural information can be extended to the side chain orientation of aminoacids containing carbonyl groups. Additionally, long range homonuclear coupling constants, 4JCC and 5JCC, could be measured. This constitutes an unprecedented case for proteins of medium and small size.

  12. Impact of Backbone Fluorination on π-Conjugated Polymers in Organic Photovoltaic Devices: A Review

    Directory of Open Access Journals (Sweden)

    Nicolas Leclerc

    2016-01-01

    Full Text Available Solution-processed bulk heterojunction solar cells have experienced a remarkable acceleration in performances in the last two decades, reaching power conversion efficiencies above 10%. This impressive progress is the outcome of a simultaneous development of more advanced device architectures and of optimized semiconducting polymers. Several chemical approaches have been developed to fine-tune the optoelectronics and structural polymer parameters required to reach high efficiencies. Fluorination of the conjugated polymer backbone has appeared recently to be an especially promising approach for the development of efficient semiconducting polymers. As a matter of fact, most currently best-performing semiconducting polymers are using fluorine atoms in their conjugated backbone. In this review, we attempt to give an up-to-date overview of the latest results achieved on fluorinated polymers for solar cells and to highlight general polymer properties’ evolution trends related to the fluorination of their conjugated backbone.

  13. A transfer matrix for the backbone exponent of two-dimensional percolation

    Energy Technology Data Exchange (ETDEWEB)

    Jacobsen, Jesper Lykke; Zinn-Justin, Paul [Laboratoire de Physique Theorique et Modeles Statistiques, Universite Paris-Sud, Orsay (France)

    2002-03-08

    Rephrasing the backbone of two-dimensional percolation as a monochromatic path crossing problem, we investigate the latter by a transfer matrix approach. Conformal invariance links the backbone dimension D{sub b} to the highest eigenvalue of the transfer matrix T, and we obtain the result D{sub b}=1.6431{+-}0.0006. For a strip of width L, T is roughly of size 2{sup 3L}, but we manage to reduce it to {approx}L{exclamation_point}. We find that the value of D{sub b} is stable with respect to inclusion of additional 'blobs' tangent to the backbone in a finite number of points. (author)

  14. Polyolefin Backbone Substitution in Binders for Low Temperature Powder Injection Moulding Feedstocks

    Directory of Open Access Journals (Sweden)

    Berenika Hausnerova

    2014-02-01

    Full Text Available This paper reports the substitution of polyolefin backbone binder components with low melting temperature carnauba wax for powder injection moulding applications. The effect of various binder compositions of Al2O3 feedstock on thermal degradation parameters is investigated by thermogravimetric analysis. Within the experimental framework 29 original feedstock compositions were prepared and the superiority of carnauba wax over the polyethylene binder backbone was demonstrated in compositions containing polyethylene glycol as the initial opening agent and governing the proper mechanism of the degradation process. Moreover, the replacement of synthetic polymer by the natural wax contributes to an increase of environmental sustainability of modern industrial technologies.

  15. Electric field induced localization phenomena in a ladder network with superlattice configuration: Effect of backbone environment

    Directory of Open Access Journals (Sweden)

    Paramita Dutta

    2014-09-01

    Full Text Available Electric field induced localization properties of a tight-binding ladder network in presence of backbone sites are investigated. Based on Green's function formalism we numerically calculate two-terminal transport together with density of states for different arrangements of atomic sites in the ladder and its backbone. Our results lead to a possibility of getting multiple mobility edges which essentially plays a switching action between a completely opaque to fully or partly conducting region upon the variation of system Fermi energy, and thus, support in fabricating mesoscopic or DNA-based switching devices.

  16. A Transfer Matrix for the Backbone Exponent of Two-Dimensional Percolation

    OpenAIRE

    Jacobsen, J. L.; Zinn-Justin, P.

    2001-01-01

    Rephrasing the backbone of two-dimensional percolation as a monochromatic path crossing problem, we investigate the latter by a transfer matrix approach. Conformal invariance links the backbone dimension D_b to the highest eigenvalue of the transfer matrix T, and we obtain the result D_b=1.6431 \\pm 0.0006. For a strip of width L, T is roughly of size 2^{3^L}, but we manage to reduce it to \\sim L!. We find that the value of D_b is stable with respect to inclusion of additional ``blobs'' tangen...

  17. Convenient and scalable synthesis of fmoc-protected Peptide nucleic Acid backbone.

    Science.gov (United States)

    Feagin, Trevor A; Shah, Nirmal I; Heemstra, Jennifer M

    2012-01-01

    The peptide nucleic acid backbone Fmoc-AEG-OBn has been synthesized via a scalable and cost-effective route. Ethylenediamine is mono-Boc protected, then alkylated with benzyl bromoacetate. The Boc group is removed and replaced with an Fmoc group. The synthesis was performed starting with 50 g of Boc anhydride to give 31 g of product in 32% overall yield. The Fmoc-protected PNA backbone is a key intermediate in the synthesis of nucleobase-modified PNA monomers. Thus, improved access to this molecule is anticipated to facilitate future investigations into the chemical properties and applications of nucleobase-modified PNA. PMID:22848796

  18. Convenient and Scalable Synthesis of Fmoc-Protected Peptide Nucleic Acid Backbone

    OpenAIRE

    Feagin, Trevor A.; Shah, Nirmal I.; Heemstra, Jennifer M.

    2012-01-01

    The peptide nucleic acid backbone Fmoc-AEG-OBn has been synthesized via a scalable and cost-effective route. Ethylenediamine is mono-Boc protected, then alkylated with benzyl bromoacetate. The Boc group is removed and replaced with an Fmoc group. The synthesis was performed starting with 50 g of Boc anhydride to give 31 g of product in 32% overall yield. The Fmoc-protected PNA backbone is a key intermediate in the synthesis of nucleobase-modified PNA monomers. Thus, improved access to this mo...

  19. Study of Sweep and Induced Dihedral Effects in Subsonic Axial Flow Compressor Passages—Part I: Design Considerations—Changes in Incidence, Deflection, and Streamline Curvature

    Directory of Open Access Journals (Sweden)

    P. V. Ramakrishna

    2009-01-01

    Full Text Available This article presents the study of Tip Chordline Sweeping (TCS and Axial Sweeping (AXS of low-speed axial compressor rotor blades against the performance of baseline unswept rotor (UNS for different tip clearance levels. The first part of the paper discusses the changes in design parameters when the blades are swept, while the second part throws light on the effect of sweep on tip leakage flow-related phenomena. 15 domains are studied with 5 sweep configurations (0∘, 20∘ TCS, 30∘ TCS, 20∘ AXS, and 30∘ AXS and for 3 tip clearances (0.0%, 0.7%, and 2.7% of the blade chord. A commercial CFD package is employed for the flow simulations and analysis. Results are well validated with experimental data. Forward sweep reduced the flow incidences. This is true all over the span with axial sweeping while little higher incidences below the mid span are observed with tip chordline sweeping. Sweeping is observed to lessen the flow turning. AXS rotors demonstrated more efficient energy transfer among the rotors. Tip chordline sweep deflected the flow towards the hub while effective positive dihedral induced with axial sweeping resulted in outward deflection of flow streamlines. These deflections are more at lower mass flow rates.

  20. Animals without Backbones: The Invertebrate Story. Grade Level 5-9.

    Science.gov (United States)

    Jerome, Brian; Fuqua, Paul

    This guide, when used in tandem with the videotape "Animals Without Backbones," helps students learn about invertebrates. These materials promote hands-on discovery and learning. The guide is composed of six curriculum-based teaching units: (1) "Getting Started"; (2) "Porifera"; (3) "Cnidarians"; (4) "Worms"; (5) "Mollusks"; (6) "Arthropods"; and…

  1. Quantum Chemical Benchmark Study on 46 RNA Backbone Families Using a Dinucleotide Unit

    Czech Academy of Sciences Publication Activity Database

    Kruse, H.; Mládek, Arnošt; Gkionis, Konstantinos; Hansen, A.; Grimme, S.; Šponer, Jiří

    2015-01-01

    Roč. 11, č. 10 (2015), s. 4972-4991. ISSN 1549-9618 R&D Projects: GA ČR(CZ) GBP305/12/G034 Institutional support: RVO:68081707 Keywords : MOLECULAR-DYNAMICS SIMULATIONS * DENSITY-FUNCTIONAL THEORY * SUGAR-PHOSPHATE BACKBONE Subject RIV: BO - Biophysics Impact factor: 5.498, year: 2014

  2. Purification, crystallization and halide phasing of a Streptococcus agalactiae backbone pilin GBS80 fragment

    OpenAIRE

    Vengadesan, Krishnan; Ma, Xin; Dwivedi, Prabhat; Ton-That, Hung; Narayana, Sthanam V. L

    2010-01-01

    The C-terminal fragment of Streptococcus agalactiae (group B streptococcus) major (backbone) pilin GBS80 was purified and crystallized in two different space groups. Single-wavelength anomalous dispersion (SAD) data collected to 2.0 Å resolution on a iodide (NaI) derivative crystal using the home source were used to obtain initial phases.

  3. Treatment Results of Injuries of Thoracic and Lumbar Backbone Departments at Osteoporosis Patients

    Directory of Open Access Journals (Sweden)

    D.Y. Sumin

    2009-06-01

    Full Text Available Information relates to radiologic (computer tomography manifestations providing the visualization of thoracic and lumbar backbone department injuries at osteoporotic patients. Contemporary methods of transcutaneous and trans-pedicle vertebroplasty with bone cement allows to obtain a stable positive healing effect against such pathologies.

  4. Relative specificities of water and ammonia losses from backbone fragments in collision-activated dissociation

    DEFF Research Database (Denmark)

    Savitski, Mikhail M; Kjeldsen, Frank; Nielsen, Michael L; Zubarev, Roman A

    2007-01-01

    Analysis of a database containing over 20,000 high-resolution collision-activation mass spectra of tryptic peptide dications was employed to study the relative specificity of neutral losses from backbone fragments. The high resolution of the FTMS instrument allowed for the first time the first is...

  5. High dimensional and high resolution pulse sequences for backbone resonance assignment of intrinsically disordered proteins

    Czech Academy of Sciences Publication Activity Database

    Zawadzka-Kazimierczuk, A.; Kozminski, W.; Šanderová, Hana; Krásný, Libor

    2012-01-01

    Roč. 52, č. 4 (2012), s. 329-337. ISSN 0925-2738 R&D Projects: GA ČR GA204/09/0583 Institutional research plan: CEZ:AV0Z50200510 Keywords : Intrinsically disordered proteins * Non-uniform sampling * Backbone assignment Subject RIV: EE - Microbiology, Virology Impact factor: 2.845, year: 2012

  6. Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field Parameters

    Czech Academy of Sciences Publication Activity Database

    Zgarbová, M.; Luque, F. J.; Šponer, Jiří; Cheatham III, Thomas E.; Otyepka, M.; Jurečka, P.

    2013-01-01

    Roč. 9, č. 5 (2013), s. 2339-2354. ISSN 1549-9618 Grant ostatní: GA ČR(CZ) GAP208/10/1742 Institutional support: RVO:68081707 Keywords : MOLECULAR- DYNAMICS SIMULATIONS * PHOSPHORUS CHEMICAL-SHIFTS * SUGAR-PHOSPHATE BACKBONE Subject RIV: BO - Biophysics Impact factor: 5.310, year: 2013

  7. Graduate Education in Kinesiology: Are We Part of "America's Backbone for Competitiveness and Innovation"?

    Science.gov (United States)

    DePauw, Karen P.

    2008-01-01

    Graduate education in the United States has been identified as being the backbone of American competitiveness and innovation in a recent report by the Council of Graduate Schools. The report provides a framework for examining the role of graduate education in partnership with business and government to advance an action agenda for achieving…

  8. The quadriceps angle

    DEFF Research Database (Denmark)

    Miles, James Edward; Frederiksen, Jane V.; Jensen, Bente Rona;

    2012-01-01

    : Pelvic limbs from red foxes (Vulpes vulpes). METHODS: Q angles were measured on hip dysplasia (HD) and whole limb (WL) view radiographs of each limb between the acetabular rim, mid-point (Q1: patellar center, Q2: femoral trochlea), and tibial tuberosity. Errors of 0.5-2.0 mm at measurement landmarks...

  9. Yaw Angle Demonstration

    Science.gov (United States)

    1994-01-01

    The Large Angle Magnetic Suspension Test Fixture (LAMSTF) is a 5 degree-of -freedom repulsive force magnetic suspension system designed to study the control of objects over large magnetic gaps. A digital control algorithm uses 6 sets of laser-sheet sensors and 5 control coils to position a cylinder 3' above the plane of electromagnetics

  10. The lateral angle revisited

    DEFF Research Database (Denmark)

    Morgan, Jeannie; Lynnerup, Niels; Hoppa, R.D.

    2013-01-01

    measurements taken from computed tomography (CT) scans. Previous reports have observed that the lateral angle size in females is significantly larger than in males. The method was applied to an independent series of 77 postmortem CT scans (42 males, 35 females) to validate its accuracy and reliability. The...

  11. Lactobacillus plantarum possesses the capability for wall teichoic acid backbone alditol switching

    Directory of Open Access Journals (Sweden)

    Bron Peter A

    2012-09-01

    Full Text Available Abstract Background Specific strains of Lactobacillus plantarum are marketed as health-promoting probiotics. The role and interplay of cell-wall compounds like wall- and lipo-teichoic acids (WTA and LTA in bacterial physiology and probiotic-host interactions remain obscure. L. plantarum WCFS1 harbors the genetic potential to switch WTA backbone alditol, providing an opportunity to study the impact of WTA backbone modifications in an isogenic background. Results Through genome mining and mutagenesis we constructed derivatives that synthesize alternative WTA variants. The mutants were shown to completely lack WTA, or produce WTA and LTA that lack D-Ala substitution, or ribitol-backbone WTA instead of the wild-type glycerol-containing backbone. DNA micro-array experiments established that the tarIJKL gene cluster is required for the biosynthesis of this alternative WTA backbone, and suggest ribose and arabinose are precursors thereof. Increased tarIJKL expression was not observed in any of our previously performed DNA microarray experiments, nor in qRT-PCR analyses of L. plantarum grown on various carbon sources, leaving the natural conditions leading to WTA backbone alditol switching, if any, to be identified. Human embryonic kidney NF-κB reporter cells expressing Toll like receptor (TLR-2/6 were exposed to purified WTAs and/or the TA mutants, indicating that WTA is not directly involved in TLR-2/6 signaling, but attenuates this signaling in a backbone independent manner, likely by affecting the release and exposure of immunomodulatory compounds such as LTA. Moreover, human dendritic cells did not secrete any cytokines when purified WTAs were applied, whereas they secreted drastically decreased levels of the pro-inflammatory cytokines IL-12p70 and TNF-α after stimulation with the WTA mutants as compared to the wild-type. Conclusions The study presented here correlates structural differences in WTA to their functional characteristics, thereby

  12. Phase behaviour of two-component bottle-brush polymers with flexible backbones under poor solvent conditions

    International Nuclear Information System (INIS)

    The phase behaviour of two-component bottle-brush polymers with fully flexible backbones under poor solvent conditions is studied via molecular-dynamics simulations, using a coarse-grained bead-spring model and side chains of up to N = 40 effective monomers. We consider a symmetric model where side chains of type A and B are grafted alternately onto a flexible backbone. The aim of this study is to explore the phase behaviour of two-component bottle-brushes depending on parameters, such as as the grafting density σ, the backbone length Nb, the side-chain length N, and the temperature T. Based on a cluster analysis, we identify for our range of parameters the regimes of fully phase separated systems, i.e., A-type side chains form one cluster and B-type chains another, while the interface that separates these two clusters contains the backbone monomers. We find that pearl-necklace or Janus-like structures, which normally occur for bottle-brush polymers with rigid backbones under poor solvent conditions, are fully attributed to the backbone rigidity, and, therefore, such structures are unlikely in the case of bottle brushes with fully flexible backbones. Also, a comparative discussion with earlier work on the phase behaviour of single-component bottle-brush polymers with flexible backbones is performed. (paper)

  13. Large Piwinski angle

    CERN Document Server

    Abelleira, J L; Bhat, C; Cornelis, K; De Maria, R; Fartoukh, S; Giachino, R; Holzer, E B; Lamont, M; Mastoridis, T; Macpherson, A; Papotti, G; Pieloni, T; Roncarolo, F; Roy, G; Salvachua, B; Valuch, D; Zimmermann, F; Ohmi, K

    2012-01-01

    Two high brightness bunches per beam were collided at injection energy with varying spectrometer strength in IP8 so that the corresponding Piwinski angle changed from about 1.2–1.3 to 0.2. One of the two bunches colliding in IP8 also collided in IPs 1 and 5, increasing its tune spread. A Piwinski angle of 1.2 is the biggest value ever achieved in a hadron collider. The goal of this experiemnt had been to investigate the influence of this parameter on the luminosity lifetime, beam lifetime and emittance growth rate. Due to technical problems and unavailability of luminosity signals from CMS this goal was only partially accomplished.

  14. Why are angles misperceived?

    OpenAIRE

    Nundy, Surajit; Lotto, Beau; Coppola, David; Shimpi, Amita; Purves, Dale

    2000-01-01

    Although it has long been apparent that observers tend to overestimate the magnitude of acute angles and underestimate obtuse ones, there is no consensus about why such distortions are seen. Geometrical modeling combined with psychophysical testing of human subjects indicates that these misperceptions are the result of an empirical strategy that resolves the inherent ambiguity of angular stimuli by generating percepts of the past significance of the stimulus rather than the geometry of its re...

  15. Angle states in quantum mechanics

    Science.gov (United States)

    de la Torre, A. C.; Iguain, J. L.

    1998-12-01

    Angle states and angle operators are defined for a system with arbitrary angular momentum. They provide a reasonable formalization of the concept of angle provided that we accept that the angular orientation is quantized. The angle operator is the generator of boosts in angular momentum and is, almost everywhere, linearly related to the logarithm of the shift operator. Angle states for fermions and bosons behave differently under parity transformation.

  16. Self-assembly of diphenylalanine backbone homologues and their combination with functionalized carbon nanotubes

    Science.gov (United States)

    Dinesh, Bhimareddy; Squillaci, Marco A.; Ménard-Moyon, Cécilia; Samorì, Paolo; Bianco, Alberto

    2015-09-01

    The integration of carbon nanotubes (CNTs) into organized nanostructures is of great interest for applications in materials science and biomedicine. In this work we studied the self-assembly of β and γ homologues of diphenylalanine peptides under different solvent and pH conditions. We aimed to investigate the role of peptide backbone in tuning the formation of different types of nanostructures alone or in combination with carbon nanotubes. In spite of having the same side chain, β and γ peptides formed distinctively different nanofibers, a clear indication of the role played by the backbone homologation on the self-assembly. The variation of the pH allowed to transform the nanofibers into spherical structures. Moreover, the co-assembly of β and γ peptides with carbon nanotubes covalently functionalized with the same peptide generated unique dendritic assemblies. This comparative study on self-assembly using diphenylalanine backbone homologues and of the co-assembly with CNT covalent conjugates is the first example exploring the capacity of β and γ peptides to adopt precise nanostructures, particularly in combination with carbon nanotubes. The dendritic organization obtained by mixing carbon nanotubes and peptides might find interesting applications in tissue engineering and neuronal interfacing.The integration of carbon nanotubes (CNTs) into organized nanostructures is of great interest for applications in materials science and biomedicine. In this work we studied the self-assembly of β and γ homologues of diphenylalanine peptides under different solvent and pH conditions. We aimed to investigate the role of peptide backbone in tuning the formation of different types of nanostructures alone or in combination with carbon nanotubes. In spite of having the same side chain, β and γ peptides formed distinctively different nanofibers, a clear indication of the role played by the backbone homologation on the self-assembly. The variation of the pH allowed to

  17. Smart-Grid Backbone Network Real-Time Delay Reduction via Integer Programming.

    Science.gov (United States)

    Pagadrai, Sasikanth; Yilmaz, Muhittin; Valluri, Pratyush

    2016-08-01

    This research investigates an optimal delay-based virtual topology design using integer linear programming (ILP), which is applied to the current backbone networks such as smart-grid real-time communication systems. A network traffic matrix is applied and the corresponding virtual topology problem is solved using the ILP formulations that include a network delay-dependent objective function and lightpath routing, wavelength assignment, wavelength continuity, flow routing, and traffic loss constraints. The proposed optimization approach provides an efficient deterministic integration of intelligent sensing and decision making, and network learning features for superior smart grid operations by adaptively responding the time-varying network traffic data as well as operational constraints to maintain optimal virtual topologies. A representative optical backbone network has been utilized to demonstrate the proposed optimization framework whose simulation results indicate that superior smart-grid network performance can be achieved using commercial networks and integer programming. PMID:25935050

  18. Elucidating the backbone conformation of photoswitchable foldamers using vibrational circular dichroism.

    Science.gov (United States)

    Domingos, Sérgio R; Roeters, Steven J; Amirjalayer, Saeed; Yu, Zhilin; Hecht, Stefan; Woutersen, Sander

    2013-10-28

    The backbone conformation of amphiphilic oligo(azobenzene) foldamers is investigated using vibrational circular dichroism (VCD) spectroscopy on a mode involving the stretching of the N=N bonds in the backbone. From denaturation experiments, we find that the VCD response in the helical conformation arises mainly from through-space interaction between the N=N-stretch transition-dipole moments, so that the coupled-oscillator model can be used to predict the VCD spectrum associated with a particular conformation. Using this approach, we elucidate the origin of the VCD signals in the folded conformation, and can assign the observed partial loss of VCD signals upon photo-induced unfolding to specific conformational changes. Our results show that the N=N-stretch VCD response provides an excellent probe of the helical conformation of the N=N bonds in this type of switchable molecular system. PMID:24018416

  19. Efficient identification of amino acid types for fast protein backbone assignments

    International Nuclear Information System (INIS)

    We describe a procedure that allows for very efficient identification of amino acid types in proteins by selective 15N-labeling. The usefulness of selective incorporation of 15N-labeled amino acids into proteins for the backbone assignment has been recognized for several years. However, widespread use of this method has been hindered by the need to purify each selectively labeled sample and by the relatively high cost of labeling with 15N-labeled amino acids. Here we demonstrate that purification of the selectively 15N-labeled samples is not necessary and that background-free HSQC spectra containing only the peaks of the overexpressed heterologous protein can be obtained in crude lysates from as little as 100 ml cultures, thus saving time and money. This method can be used for fast and automated backbone assignment of proteins

  20. New nucleoside/nucleotide backbone options: a review of recent studies.

    Science.gov (United States)

    Ruane, Peter J; DeJesus, Edwin

    2004-09-01

    The nucleoside/nucleotide reverse transcriptase inhibitor (NRTI/NtRTI) class continues to serve as an important component of the standard of care for HIV infection. Combinations of dual NRTIs/NtRTIs with protease inhibitors (PIs) or nonnucleoside reverse transcriptase inhibitors (NNRTIs) remain the most commonly used regimens in clinical practice. In recent years, clinical outcomes data on previously novel NRTI/NtRTI backbone combinations have provided clinicians with new options to address potency, tolerability, and convenience of antiretroviral therapy. However, the tolerability, drug-drug interactions, and resistance profiles of specific regimens using new NRTI/NtRTI combinations must be weighed against the needs and preferences of individual patients. This review summarizes recent efficacy and safety data on emerging NRTI/NtRTI combination backbones, including tenofovir DF (TDF) with lamivudine (3TC), abacavir with 3TC, didanosine (ddI) with 3TC, ddI with emtricitabine (FTC), and TDF with FTC. PMID:15319666

  1. Structure and dynamics of the RNA backbone resolved with NMR spin-spin couplings

    Czech Academy of Sciences Publication Activity Database

    Vokáčová, Zuzana; Buděšínský, Miloš; Rosenberg, Ivan; Schneider, Bohdan; Šponer, Jiří; Sychrovský, Vladimír

    Helsinki : University of Helsinki, 2009 - (J. Polvi and H. Ristolainen). s. 320-320 ISBN 978-952-10-5618-5. [International Congress of Quantum Chemistry ICQC /13./. 22.06.2009-27-06.2009, Helsinki] R&D Projects: GA AV ČR IAA400550701 Institutional research plan: CEZ:AV0Z40550506; CEZ:AV0Z50040507 Keywords : NMR * nucleic acid backbone * ab initio calculations Subject RIV: CF - Physical ; Theoretical Chemistry

  2. Extensive Air Showers: from the muonic smoking guns to the hadronic backbone

    OpenAIRE

    Cazon L.

    2013-01-01

    Extensive Air Showers are complex macroscopic objects initiated by single ultra-high energy particles. They are the result of millions of high energy reactions in the atmosphere and can be described as the superposition of hadronic and electromagnetic cascades. The hadronic cascade is the air shower backbone, and it is mainly made of pions. Decays of neutral pions initiate electromagnetic cascades, while the decays of charged pions produce muons which leave the hadronic core and travel many k...

  3. Backbone resonance assignments of the outer membrane lipoprotein FrpD from Neisseria meningitidis

    Czech Academy of Sciences Publication Activity Database

    Bumba, Ladislav; Sviridova, E.; Kutá-Smatanová, Ivana; Řezáčová, Pavlína; Veverka, Václav

    2014-01-01

    Roč. 8, č. 1 (2014), s. 53-55. ISSN 1874-2718 R&D Projects: GA ČR(CZ) GAP207/11/0717; GA MŠk(CZ) LK11205 Institutional support: RVO:61388963 ; RVO:61388971 ; RVO:67179843 Keywords : Neisseria meningitidis * FrpC * FrpD * backbone assignments * NMR * iron-regulated protein Subject RIV: CE - Biochemistry Impact factor: 0.760, year: 2014

  4. Integrating the university medical center. Phase one: providing an information backbone.

    OpenAIRE

    Berry, S J; Reber, E.; Offeman, W. E.

    1991-01-01

    UCLA School of Medicine represents a diverse computing community where the creation of each individual network has been driven by applications, price/performance and functionality. Indeed, the ability to connect to other computers has had no bearing on selection. Yet, there exists a need to seamlessly connect the individual networks to other minicomputers, mainframes and remote computers. We have created a school wide backbone network that will enable an individual from a single workstation t...

  5. Inferential protein structure determination and refinement using fast, electronic structure based backbone amide chemical shift predictions

    CERN Document Server

    Christensen, Anders S

    2015-01-01

    This report covers the development of a new, fast method for calculating the backbone amide proton chemical shifts in proteins. Through quantum chemical calculations, structure-based forudsiglese the chemical shift for amidprotonen in protein has been parameterized. The parameters are then implemented in a computer program called Padawan. The program has since been implemented in protein folding program Phaistos, wherein the method andvendes to de novo folding of the protein structures and to refine the existing protein structures.

  6. Tritium containing polymers having a polymer backbone substantially void of tritium

    Science.gov (United States)

    Jensen, George A.; Nelson, David A.; Molton, Peter M.

    1992-01-01

    A radioluminescent light source comprises a solid mixture of a phosphorescent substance and a tritiated polymer. The solid mixture forms a solid mass having length, width, and thickness dimensions, and is capable of self-support. In one aspect of the invention, the phosphorescent substance comprises solid phosphor particles supported or surrounded within a solid matrix by a tritium containing polymer. The tritium containing polymer comprises a polymer backbone which is essentially void of tritium.

  7. Effect of Backbone Structure on Membrane Properties for Poly(arylene ether) Random and Multiblock Copolymers

    OpenAIRE

    Rowlett, Jarrett Robert

    2014-01-01

    Poly(arylene ether)s are a well-established class of thermoplastics that are known for their mechanical toughness, thermal stability, and fabrication into membranes. These materials can undergo a myriad of modifications including backbone structure variability, sulfonation, and crosslinking. In this dissertation, structure-property relationships are considered for poly(arylene ether)s with regard to membrane applications for proton exchange and gas separation membranes. All of the proton...

  8. Synthesis, Characterization and Structure of Chiral Amino Acids and Their Corresponding Amino Alcohols with Camphoric Backbone

    Institute of Scientific and Technical Information of China (English)

    QIAN Hui-Fen; HUANG Wei; LI Hui-Hui; YAO Cheng

    2006-01-01

    Chiral amino acids and their corresponding amino alcohols bearing camphoric backbone were prepared from D-(+)-camphoric imide and characterized by infrared, elemental analysis, ESI-MS, and NMR measurements. Among them, one intermediate (lS,3R)-3-amino-2,2,3-trimethyl cyclopentane-1-carboxylic acid hydrochloride 3 was structurally elucidated by X-ray diffraction techniques. Versatile intermolecular hydrogen bonding interactions observed in its packing structure result in a two-dimensional framework.

  9. Backbone resonance assignments of human cytosolic dNT-1 nucleotidase

    Czech Academy of Sciences Publication Activity Database

    Hnízda, Aleš; Skleničková, Radka; Pachl, Petr; Fábry, Milan; Tošner, Z.; Brynda, Jiří; Veverka, Václav

    2014-01-01

    Roč. 8, č. 2 (2014), s. 425-428. ISSN 1874-2718 R&D Projects: GA MŠk(CZ) LK11205; GA ČR GA203/09/0820 Institutional support: RVO:61388963 ; RVO:68378050 Keywords : 5 '-nucleotidase * haloacid dehalogenase superfamily * backbone assignments * NMR * perdeuterated protein * dimer * pyrimidine nucleotides Subject RIV: CE - Biochemistry; EB - Genetics ; Molecular Biology (UMG-J) Impact factor: 0.760, year: 2014

  10. Hash: a program to accurately predict protein H{sup {alpha}} shifts from neighboring backbone shifts

    Energy Technology Data Exchange (ETDEWEB)

    Zeng Jianyang, E-mail: zengjy@gmail.com [Tsinghua University, Institute for Interdisciplinary Information Sciences (China); Zhou Pei [Duke University Medical Center, Department of Biochemistry (United States); Donald, Bruce Randall [Duke University, Department of Computer Science (United States)

    2013-01-15

    Chemical shifts provide not only peak identities for analyzing nuclear magnetic resonance (NMR) data, but also an important source of conformational information for studying protein structures. Current structural studies requiring H{sup {alpha}} chemical shifts suffer from the following limitations. (1) For large proteins, the H{sup {alpha}} chemical shifts can be difficult to assign using conventional NMR triple-resonance experiments, mainly due to the fast transverse relaxation rate of C{sup {alpha}} that restricts the signal sensitivity. (2) Previous chemical shift prediction approaches either require homologous models with high sequence similarity or rely heavily on accurate backbone and side-chain structural coordinates. When neither sequence homologues nor structural coordinates are available, we must resort to other information to predict H{sup {alpha}} chemical shifts. Predicting accurate H{sup {alpha}} chemical shifts using other obtainable information, such as the chemical shifts of nearby backbone atoms (i.e., adjacent atoms in the sequence), can remedy the above dilemmas, and hence advance NMR-based structural studies of proteins. By specifically exploiting the dependencies on chemical shifts of nearby backbone atoms, we propose a novel machine learning algorithm, called Hash, to predict H{sup {alpha}} chemical shifts. Hash combines a new fragment-based chemical shift search approach with a non-parametric regression model, called the generalized additive model, to effectively solve the prediction problem. We demonstrate that the chemical shifts of nearby backbone atoms provide a reliable source of information for predicting accurate H{sup {alpha}} chemical shifts. Our testing results on different possible combinations of input data indicate that Hash has a wide rage of potential NMR applications in structural and biological studies of proteins.

  11. Release management as the backbone of service delivery for business critical enterprise applications

    OpenAIRE

    Ojasalo, Hannu

    2013-01-01

    Application management services are initiated to take care of enterprise applications in the use phase of their lifecycle. Most important of the application management processes are incident, problem, change, knowledge and release management. The aim of this thesis of mine is to validate the position of release management. Release management can be the backbone for enterprise application management. It makes sure that the risk of negatively affecting the operation of the application is m...

  12. Navigating the massive world of reddit: Using backbone networks to map user interests in social media

    OpenAIRE

    Olson, Randal S.; Neal, Zachary P.

    2013-01-01

    In the massive online worlds of social media, users frequently rely on organizing themselves around specific topics of interest to find and engage with like-minded people. However, navigating these massive worlds and finding topics of specific interest often proves difficult because the worlds are mostly organized haphazardly, leaving users to find relevant interests by word of mouth or using a basic search feature. Here, we report on a method using the backbone of a network to create a map o...

  13. Power consumption evaluation of circuit-switched versus packet-switched optical backbone networks

    OpenAIRE

    Van Heddeghem W.; Lannoo B.; Colle D.; Pickavet M.; Musumeci F.; Pattavina A.; Idzikowski F.

    2013-01-01

    While telecommunication networks have historically been dominated by a circuit-switched paradigm, the last decades have seen a clear trend towards packet-switched networks. In this paper we evaluate how both paradigms perform in optical backbone networks from a power consumption point of view, and whether the general agreement of circuit switching being more power-efficient holds. We consider artificially generated topologies of various sizes, mesh degrees and not yet previously explored in t...

  14. Cerebellopontine angle Hodgkin's disease

    International Nuclear Information System (INIS)

    Intracranial Hodgkin's disease is a rare site of involvement, and even more rare is its presentation as a cerebellopontine angle mass. It can be difficult to diagnose especially when recurrent tumors occur because both CT and lumbar puncture have been shown to have a relatively low yield. Gadolinium-enhanced MRI is more sensitive. It is concluded that while the imaging findings can be non-specific, the rapid response to therapy (steroids) may provide a clue to diagnosis. Copyright (1999) Blackwell Science Pty Ltd

  15. Critical angle laser refractometer

    International Nuclear Information System (INIS)

    A simple laser refractometer based on the detection of the critical angle for liquids is presented. The calibrated refractometer presents up to 0.000 11 of uncertainty when the refractive index is in the range between 1.300 00 and 1.340 00. The experimental setup is easy to construct and the material needed is available at most optics laboratories. The calibration method is simple and can be used in other devices. The refractive index measurements in aqueous solutions of sodium chloride were carried out to test the device and a linear dependence between the refractive index and the salt concentration was found

  16. From lattice BF gauge theory to area-angle Regge calculus

    International Nuclear Information System (INIS)

    We consider Riemannian 4D BF lattice gauge theory, on a triangulation of spacetime. Introducing the simplicity constraints which turn BF theory into simplicial gravity, some geometric quantities of Regge calculus, areas, and 3D and 4D dihedral angles, are identified. The parallel transport conditions are taken care of to ensure a consistent gluing of simplices. We show that these gluing relations, together with the simplicity constraints, contain the constraints of area-angle Regge calculus in a simple way, via the group structure of the underlying BF gauge theory. This provides a precise road from constrained BF theory to area-angle Regge calculus. Doing so, a framework combining variables of lattice BF theory and Regge calculus is built. The action takes a form a la Regge and includes the contribution of the Immirzi parameter. In the absence of simplicity constraints, the standard spin foam model for BF theory is recovered. Insertions of local observables are investigated, leading to Casimir insertions for areas and reproducing for 3D angles known results obtained through angle operators on spin networks. The present formulation is argued to be suitable for deriving spin foam models from discrete path integrals and to unravel their geometric content.

  17. Monitoring Backbone Hydrogen-Bond Formation in β-Barrel Membrane Protein Folding.

    Science.gov (United States)

    Raschle, Thomas; Rios Flores, Perla; Opitz, Christian; Müller, Daniel J; Hiller, Sebastian

    2016-05-10

    β-barrel membrane proteins are key components of the outer membrane of bacteria, mitochondria and chloroplasts. Their three-dimensional structure is defined by a network of backbone hydrogen bonds between adjacent β-strands. Here, we employ hydrogen-deuterium (H/D) exchange in combination with NMR spectroscopy and mass spectrometry to monitor backbone hydrogen bond formation during folding of the outer membrane protein X (OmpX) from E. coli in detergent micelles. Residue-specific kinetics of interstrand hydrogen-bond formation were found to be uniform in the entire β-barrel and synchronized to formation of the tertiary structure. OmpX folding thus propagates via a long-lived conformational ensemble state in which all backbone amide protons exchange with the solvent and engage in hydrogen bonds only transiently. Stable formation of the entire OmpX hydrogen bond network occurs downhill of the rate-limiting transition state and thus appears cooperative on the overall folding time scale. PMID:27062600

  18. East vergent structure of Backbone Range: Insights from A-Lan-Yi area and sandbox modeling

    Science.gov (United States)

    Lee, C. A.; Lu, C. Y.

    2015-12-01

    Southern Taiwan, including Pingtung peninsula and Taitung, is the incipient oblique collision zone of Eurasian plate and Philippine Sea plate. The Luzon volcanic arc converged toward Taiwan Island and formed Hengchun Ridge south offshore Taiwan. Thus, Taiwan mountain belt developed from north to south as the Backbone Range, so that we can infer the incipient feature structure from the topography and outcrop study of southern Taiwan. Our field survey of this study concentrated at the southeast coastline of Taiwan, also known as A-Lan-Yi Trail. According to previous study, the deformational structures such as faults and folds are consistent with regional kinematic processes, and the preserved transpression structure is the most important evidence of incipient collision. In this study, we use the sedimentary sequences of study area to trace the regional tectonics from north to south. Discovered structures in this area show the similar kinematic history as the eastern flank of Backbone Range, so that we suggest they are at the same series of a tectonic event. To complete the regional structure mapping in this accessible area, besides the field geological data, we also applied the LiDAR-derived DTM which is a 3D visualization technology to improve our topography information. In addition, we use the sandbox modeling to demonstrate the development of structures in the eastern flank of Backbone Range. After combining the results of field observation and regional structure mapping, this study provides a strong evidence of backthrusting and backfolding deformation during the incipient oblique collision stage.

  19. Reconstruction of protein backbones from the BriX collection of canonical protein fragments.

    Science.gov (United States)

    Baeten, Lies; Reumers, Joke; Tur, Vicente; Stricher, François; Lenaerts, Tom; Serrano, Luis; Rousseau, Frederic; Schymkowitz, Joost

    2008-05-01

    As modeling of changes in backbone conformation still lacks a computationally efficient solution, we developed a discretisation of the conformational states accessible to the protein backbone similar to the successful rotamer approach in side chains. The BriX fragment database, consisting of fragments from 4 to 14 residues long, was realized through identification of recurrent backbone fragments from a non-redundant set of high-resolution protein structures. BriX contains an alphabet of more than 1,000 frequently observed conformations per peptide length for 6 different variation levels. Analysis of the performance of BriX revealed an average structural coverage of protein structures of more than 99% within a root mean square distance (RMSD) of 1 Angstrom. Globally, we are able to reconstruct protein structures with an average accuracy of 0.48 Angstrom RMSD. As expected, regular structures are well covered, but, interestingly, many loop regions that appear irregular at first glance are also found to form a recurrent structural motif, albeit with lower frequency of occurrence than regular secondary structures. Larger loop regions could be completely reconstructed from smaller recurrent elements, between 4 and 8 residues long. Finally, we observed that a significant amount of short sequences tend to display strong structural ambiguity between alpha helix and extended conformations. When the sequence length increases, this so-called sequence plasticity is no longer observed, illustrating the context dependency of polypeptide structures. PMID:18483555

  20. Variable angle correlation spectroscopy

    International Nuclear Information System (INIS)

    In this dissertation, a novel nuclear magnetic resonance (NMR) technique, variable angle correlation spectroscopy (VACSY) is described and demonstrated with 13C nuclei in rapidly rotating samples. These experiments focus on one of the basic problems in solid state NMR: how to extract the wealth of information contained in the anisotropic component of the NMR signal while still maintaining spectral resolution. Analysis of the anisotropic spectral patterns from poly-crystalline systems reveal information concerning molecular structure and dynamics, yet in all but the simplest of systems, the overlap of spectral patterns from chemically distinct sites renders the spectral analysis difficult if not impossible. One solution to this problem is to perform multi-dimensional experiments where the high-resolution, isotropic spectrum in one dimension is correlated with the anisotropic spectral patterns in the other dimensions. The VACSY technique incorporates the angle between the spinner axis and the static magnetic field as an experimental parameter that may be incremented during the course of the experiment to help correlate the isotropic and anisotropic components of the spectrum. The two-dimensional version of the VACSY experiments is used to extract the chemical shift anisotropy tensor values from multi-site organic molecules, study molecular dynamics in the intermediate time regime, and to examine the ordering properties of partially oriented samples. The VACSY technique is then extended to three-dimensional experiments to study slow molecular reorientations in a multi-site polymer system

  1. Variable angle correlation spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Y K [Univ. of California, Berkeley, CA (United States)

    1994-05-01

    In this dissertation, a novel nuclear magnetic resonance (NMR) technique, variable angle correlation spectroscopy (VACSY) is described and demonstrated with {sup 13}C nuclei in rapidly rotating samples. These experiments focus on one of the basic problems in solid state NMR: how to extract the wealth of information contained in the anisotropic component of the NMR signal while still maintaining spectral resolution. Analysis of the anisotropic spectral patterns from poly-crystalline systems reveal information concerning molecular structure and dynamics, yet in all but the simplest of systems, the overlap of spectral patterns from chemically distinct sites renders the spectral analysis difficult if not impossible. One solution to this problem is to perform multi-dimensional experiments where the high-resolution, isotropic spectrum in one dimension is correlated with the anisotropic spectral patterns in the other dimensions. The VACSY technique incorporates the angle between the spinner axis and the static magnetic field as an experimental parameter that may be incremented during the course of the experiment to help correlate the isotropic and anisotropic components of the spectrum. The two-dimensional version of the VACSY experiments is used to extract the chemical shift anisotropy tensor values from multi-site organic molecules, study molecular dynamics in the intermediate time regime, and to examine the ordering properties of partially oriented samples. The VACSY technique is then extended to three-dimensional experiments to study slow molecular reorientations in a multi-site polymer system.

  2. Angle performance on optima MDxt

    International Nuclear Information System (INIS)

    Angle control on medium current implanters is important due to the high angle-sensitivity of typical medium current implants, such as halo implants. On the Optima MDxt, beam-to-wafer angles are controlled in both the horizontal and vertical directions. In the horizontal direction, the beam angle is measured through six narrow slits, and any angle adjustment is made by electrostatically steering the beam, while cross-wafer beam parallelism is adjusted by changing the focus of the electrostatic parallelizing lens (P-lens). In the vertical direction, the beam angle is measured through a high aspect ratio mask, and any angle adjustment is made by slightly tilting the wafer platen prior to implant. A variety of tests were run to measure the accuracy and repeatability of Optima MDxt’s angle control. SIMS profiles of a high energy, channeling sensitive condition show both the cross-wafer angle uniformity, along with the small-angle resolution of the system. Angle repeatability was quantified by running a channeling sensitive implant as a regular monitor over a seven month period and measuring the sheet resistance-to-angle sensitivity. Even though crystal cut error was not controlled for in this case, when attributing all Rs variation to angle changes, the overall angle repeatability was measured as 0.16° (1σ). A separate angle repeatability test involved running a series of V-curves tests over a four month period using low crystal cut wafers selected from the same boule. The results of this test showed the angle repeatability to be <0.1° (1σ).

  3. Heterodyne Interferometer Angle Metrology

    Science.gov (United States)

    Hahn, Inseob; Weilert, Mark A.; Wang, Xu; Goullioud, Renaud

    2010-01-01

    A compact, high-resolution angle measurement instrument has been developed that is based on a heterodyne interferometer. The common-path heterodyne interferometer metrology is used to measure displacements of a reflective target surface. In the interferometer setup, an optical mask is used to sample the measurement laser beam reflecting back from a target surface. Angular rotations, around two orthogonal axes in a plane perpendicular to the measurement- beam propagation direction, are determined simultaneously from the relative displacement measurement of the target surface. The device is used in a tracking telescope system where pitch and yaw measurements of a flat mirror were simultaneously performed with a sensitivity of 0.1 nrad, per second, and a measuring range of 0.15 mrad at a working distance of an order of a meter. The nonlinearity of the device is also measured less than one percent over the measurement range.

  4. Synthesis of novel cationic lipids with fully or partially non-scissile linkages between the hydrocarbon chains and pseudoglyceryl backbone

    Indian Academy of Sciences (India)

    Santanu Bhattacharya; Saubhik Haldar

    2002-06-01

    Five novel cationic lipids with fully or partially non-scissile linkage regions between the pseudoglyceryl backbone and the hydrocarbon chains have been synthesized. The membrane-forming properties of these new lipids are briefly presented.

  5. Development of a Backbone Cyclic Peptide Library as Potential Antiparasitic Therapeutics Using Microwave Irradiation.

    Science.gov (United States)

    Qvit, Nir; Kornfeld, Opher S

    2016-01-01

    Protein-protein interactions (PPIs) are intimately involved in almost all biological processes and are linked to many human diseases. Therefore, there is a major effort to target PPIs in basic research and in the pharmaceutical industry. Protein-protein interfaces are usually large, flat, and often lack pockets, complicating the discovery of small molecules that target such sites. Alternative targeting approaches using antibodies have limitations due to poor oral bioavailability, low cell-permeability, and production inefficiency. Using peptides to target PPI interfaces has several advantages. Peptides have higher conformational flexibility, increased selectivity, and are generally inexpensive. However, peptides have their own limitations including poor stability and inefficiency crossing cell membranes. To overcome such limitations, peptide cyclization can be performed. Cyclization has been demonstrated to improve peptide selectivity, metabolic stability, and bioavailability. However, predicting the bioactive conformation of a cyclic peptide is not trivial. To overcome this challenge, one attractive approach it to screen a focused library to screen in which all backbone cyclic peptides have the same primary sequence, but differ in parameters that influence their conformation, such as ring size and position. We describe a detailed protocol for synthesizing a library of backbone cyclic peptides targeting specific parasite PPIs. Using a rational design approach, we developed peptides derived from the scaffold protein Leishmania receptor for activated C-kinase (LACK). We hypothesized that sequences in LACK that are conserved in parasites, but not in the mammalian host homolog, may represent interaction sites for proteins that are critical for the parasites' viability. The cyclic peptides were synthesized using microwave irradiation to reduce reaction times and increase efficiency. Developing a library of backbone cyclic peptides with different ring sizes facilitates a

  6. Simultaneous NMR assignment of backbone and side chain amides in large proteins with IS-TROSY

    International Nuclear Information System (INIS)

    A new strategy for the simultaneous NMR assignment of both backbone and side chain amides in large proteins with isotopomer-selective transverse-relaxation-optimized spectroscopy (IS-TROSY) is reported. The method considers aspects of both the NMR sample preparation and the experimental design. First, the protein is dissolved in a buffer with 50%H2O/50%D2O in order to promote the population of semideuterated NHD isotopomers in side chain amides of Asn/Gln residues. Second, a 13C'-coupled 2D 15N-1H IS-TROSY spectrum provides a stereospecific distinction between the geminal protons in the E and Z configurations of the carboxyamide group. Third, a suite of IS-TROSY-based triple-resonance NMR experiments, e.g. 3D IS-TROSY-HNCA and 3D IS-TROSY-HNCACB, are designed to correlate aliphatic carbon atoms with backbone amides and, for Asn/Gln residues, at the same time with side chain amides. The NMR assignment procedure is similar to that for small proteins using conventional 3D HNCA/3D HNCACB spectra, in which, however, signals from NH2 groups are often very weak or even missing due to the use of broad-band proton decoupling schemes and NOE data have to be used as a remedy. For large proteins, the use of conventional TROSY experiments makes resonances of side chain amides not observable at all. The application of IS-TROSY experiments to the 35-kDa yeast cytosine deaminase has established a complete resonance assignment for the backbone and stereospecific assignment for side chain amides, which otherwise could not be achieved with existing NMR experiments. Thus, the development of IS-TROSY-based method provides new opportunities for the NMR study of important structural and biological roles of carboxyamides and side chain moieties of arginine and lysine residues in large proteins as well as amino moieties in nucleic acids

  7. CORBA and MPI-based 'backbone' for coupling advanced simulation tools

    International Nuclear Information System (INIS)

    There is a growing international interest in using coupled, multidisciplinary computer simulations for a variety of purposes, including nuclear reactor safety analysis. Reactor behaviour can be modeled using a suite of computer programs simulating phenomena or predicting parameters that can be categorized into disciplines such as Thermalhydraulics, Neutronics, Fuel, Fuel Channels, Fission Product Release and Transport, Containment and Atmospheric Dispersion, and Severe Accident Analysis. Traditionally, simulations used for safety analysis individually addressed only the behaviour within a single discipline, based upon static input data from other simulation programs. The limitation of using a suite of stand-alone simulations is that phenomenological interdependencies or temporal feedback between the parameters calculated within individual simulations cannot be adequately captured. To remove this shortcoming, multiple computer simulations for different disciplines must exchange data during runtime to address these interdependencies. This article describes the concept of a new framework, which we refer to as the 'Backbone', to provide the necessary runtime exchange of data. The Backbone, currently under development at AECL for a preliminary feasibility study, is a hybrid design using features taken from the Common Object Request Broker Architecture (CORBA), a standard defined by the Object Management Group, and the Message Passing Interface (MPI), a standard developed by a group of researchers from academia and industry. Both have well-tested and efficient implementations, including some that are freely available under the GNU public licenses. The CORBA component enables individual programs written in different languages and running on different platforms within a network to exchange data with each other, thus behaving like a single application. MPI provides the process-to-process intercommunication between these programs. This paper outlines the different CORBA and

  8. Backbone tuning in indenylidene–ruthenium complexes bearing an unsaturated N-heterocyclic carbene

    Directory of Open Access Journals (Sweden)

    César A. Urbina-Blanco

    2010-11-01

    Full Text Available The steric and electronic influence of backbone substitution in IMes-based (IMes = 1,3-bis(2,4,6-trimethylphenylimidazol-2-ylidene N-heterocyclic carbenes (NHC was probed by synthesizing the [RhCl(CO2(NHC] series of complexes to quantify experimentally the Tolman electronic parameter (electronic and the percent buried volume (%Vbur, steric parameters. The corresponding ruthenium–indenylidene complexes were also synthesized and tested in benchmark metathesis transformations to establish possible correlations between reactivity and NHC electronic and steric parameters.

  9. Silence is Golden with High Probability: Maintaining a Connected Backbone in Wireless Sensor Networks

    OpenAIRE

    Santi, Paolo; Simon, J?nos

    2003-01-01

    Reducing node energy consumption to extend network life- time is a vital requirement in wireless sensor networks. In this paper, we present and analyze the energy consumption of a class of cell-based energy conservation protocols. The goal of our protocols is to alternately turn off/on the transceivers of the nodes, while maintaining a connected backbone of active nodes. The protocols presented in this paper are shown to be optimal, in the sense that they extend the network lifetime by a fact...

  10. Dynamic Resource Allocation and QoS Control Capabilities of the Japanese Academic Backbone Network

    Directory of Open Access Journals (Sweden)

    Michihiro Aoki

    2010-08-01

    Full Text Available Dynamic resource control capabilities have become increasingly important for academic networks that must support big scientific research projects at the same time as less data intensive research and educational activities. This paper describes the dynamic resource allocation and QoS control capabilities of the Japanese academic backbone network, called SINET3, which supports a variety of academic applications with a wide range of network services. The article describes the network architecture, networking technologies, resource allocation, QoS control, and layer-1 bandwidth on-demand services. It also details typical services developed for scientific research, including the user interface, resource control, and management functions, and includes performance evaluations.

  11. On the photostability of peptides after selective photoexcitation of the backbone: Prompt versus slow dissociation

    DEFF Research Database (Denmark)

    Byskov, Camilla Skinnerup; Jensen, Frank; Jørgensen, Thomas J D;

    2014-01-01

    , which is remote from the initial site of excitation. Hence loss of CE serves as direct proof that energy has reached the charge-site end, leaving the backbone intact. Our work demonstrates that excitation of tertiary amide moieties (proline linkages) results in both prompt dissociation and statistical...... present a protocol to disentangle slow and non-hazardous statistical dissociation from prompt cleavage of peptide bonds by 210 nm light based on experiments on protonated peptides isolated in vacuo and tagged by 18-crown-6 ether (CE). The weakest link in the system is between the charged site and CE...

  12. RosettaRemodel: a generalized framework for flexible backbone protein design.

    Directory of Open Access Journals (Sweden)

    Po-Ssu Huang

    Full Text Available We describe RosettaRemodel, a generalized framework for flexible protein design that provides a versatile and convenient interface to the Rosetta modeling suite. RosettaRemodel employs a unified interface, called a blueprint, which allows detailed control over many aspects of flexible backbone protein design calculations. RosettaRemodel allows the construction and elaboration of customized protocols for a wide range of design problems ranging from loop insertion and deletion, disulfide engineering, domain assembly, loop remodeling, motif grafting, symmetrical units, to de novo structure modeling.

  13. Small angle neutron scattering

    Directory of Open Access Journals (Sweden)

    Cousin Fabrice

    2015-01-01

    Full Text Available Small Angle Neutron Scattering (SANS is a technique that enables to probe the 3-D structure of materials on a typical size range lying from ∼ 1 nm up to ∼ a few 100 nm, the obtained information being statistically averaged on a sample whose volume is ∼ 1 cm3. This very rich technique enables to make a full structural characterization of a given object of nanometric dimensions (radius of gyration, shape, volume or mass, fractal dimension, specific area… through the determination of the form factor as well as the determination of the way objects are organized within in a continuous media, and therefore to describe interactions between them, through the determination of the structure factor. The specific properties of neutrons (possibility of tuning the scattering intensity by using the isotopic substitution, sensitivity to magnetism, negligible absorption, low energy of the incident neutrons make it particularly interesting in the fields of soft matter, biophysics, magnetic materials and metallurgy. In particular, the contrast variation methods allow to extract some informations that cannot be obtained by any other experimental techniques. This course is divided in two parts. The first one is devoted to the description of the principle of SANS: basics (formalism, coherent scattering/incoherent scattering, notion of elementary scatterer, form factor analysis (I(q→0, Guinier regime, intermediate regime, Porod regime, polydisperse system, structure factor analysis (2nd Virial coefficient, integral equations, characterization of aggregates, and contrast variation methods (how to create contrast in an homogeneous system, matching in ternary systems, extrapolation to zero concentration, Zero Averaged Contrast. It is illustrated by some representative examples. The second one describes the experimental aspects of SANS to guide user in its future experiments: description of SANS spectrometer, resolution of the spectrometer, optimization of

  14. Small angle neutron scattering

    International Nuclear Information System (INIS)

    Small Angle Neutron Scattering (SANS) is a technique that enables to probe the 3-D structure of materials on a typical size range lying from about 1 nm up to a few 100 nm, the obtained information being statistically averaged on a sample whose volume is ∼ 1 cm3. This very rich technique enables to make a full structural characterization of a given object of nano-metric dimensions (radius of gyration, shape, volume or mass, fractal dimension, specific area... ) through the determination of the form factor as well as the determination of the way objects are organized within in a continuous media, and therefore to describe interactions between them, through the determination of the structure factor. The specific properties of neutrons (possibility of tuning the scattering intensity by using the isotopic substitution, sensitivity to magnetism, negligible absorption, low energy of the incident neutrons) make it particularly interesting in the fields of soft matter, biophysics, magnetic materials and metallurgy. In particular, the contrast variation methods allow to extract some information that cannot be obtained by any other experimental techniques. This course is divided in two parts. The first one is devoted to the description of the principle of SANS: basics (formalism, coherent scattering/incoherent scattering, notion of elementary scatterer), form factor analysis (I(q→0), Guinier regime, intermediate regime, Porod regime, polydisperse system), structure factor analysis (2. Virial coefficient, integral equations, characterization of aggregates), and contrast variation methods (how to create contrast in an homogeneous system, matching in ternary systems, extrapolation to zero concentration, Zero Averaged Contrast). It is illustrated by some representative examples. The second one describes the experimental aspects of SANS to guide user in its future experiments: description of SANS spectrometer, resolution of the spectrometer, optimization of spectrometer

  15. Colloidal quantum dot lasers built on a passive two-dimensional photonic crystal backbone

    Science.gov (United States)

    Chang, Hojun; Min, Kyungtaek; Lee, Myungjae; Kang, Minsu; Park, Yeonsang; Cho, Kyung-Sang; Roh, Young-Geun; Woo Hwang, Sung; Jeon, Heonsu

    2016-03-01

    We report the room-temperature lasing action from two-dimensional photonic crystal (PC) structures composed of a passive Si3N4 backbone with an over-coat of CdSe/CdS/ZnS colloidal quantum dots (CQDs) for optical gain. When optically excited, devices lased in dual PC band-edge modes, with the modal dominance governed by the thickness of the CQD over-layer. The demonstrated laser platform should have an impact on future photonic integrated circuits as the on-chip coupling between active and passive components is readily achievable.We report the room-temperature lasing action from two-dimensional photonic crystal (PC) structures composed of a passive Si3N4 backbone with an over-coat of CdSe/CdS/ZnS colloidal quantum dots (CQDs) for optical gain. When optically excited, devices lased in dual PC band-edge modes, with the modal dominance governed by the thickness of the CQD over-layer. The demonstrated laser platform should have an impact on future photonic integrated circuits as the on-chip coupling between active and passive components is readily achievable. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr08544f

  16. On the role of thermal backbone fluctuations in myoglobin ligand gate dynamics

    CERN Document Server

    Krokhotin, Andrey; Peng, Xubiao

    2012-01-01

    We construct an energy function that describes the crystallographic structure of spermwhale myoglobin backbone. As a model in our construction, we use the Protein Data Bank entry 1ABS that has been measured at liquid helium temperature. Consequently the thermal B-factor fluctuations are very small, which is an advantage in our construction. The energy function that we utilize resembles that of the discrete non-linear Schrodinger equation. Likewise, ours supports solitons as local minimum energy configurations. We describe the 1ABS backbone in terms of solitons with a precision that deviates from 1ABS by an average root-mean-square distance, which is less than the experimentally observed Debye-Waller B-factor fluctuation distance. We then subject the multisoliton solution to extensive numerical heating and cooling experiments, over a very wide range of temperatures. We concentrate in particular to temperatures above 300K and below the theta-point unfolding temperature, which is around 348K. We confirm that the...

  17. Investigating the Tradeoffs between Power Consumption and Quality of Service in a Backbone Network

    Directory of Open Access Journals (Sweden)

    Erol Gelenbe

    2013-05-01

    Full Text Available Energy saving in networks has traditionally focussed on reducing battery consumption through smart wireless network design. Recently, researchers have turned their attention to the energy cost and carbon emissions of the backbone network that both fixed and mobile communications depend on, proposing primarily mechanisms that turn equipments OFF or put them into deep sleep. This is an effective way of saving energy, provided that the nodes can return to working condition quickly, but it introduces increased delays and packet losses that directly affect the quality of communication experienced by the users. Here we investigate the associated tradeoffs between power consumption and quality of service in backbone networks that employ deep sleep energy savings. We examine these tradeoffs by conducting experiments on a real PC-based network topology, where nodes are put into deep sleep at random times and intervals, resulting in a continuously changing network with reduced total power consumption. The average power consumption, the packet loss and the average delay of this network are examined with respect to the average value of the ON rate and the ON/OFF cycle of the nodes.

  18. An Optimized microRNA Backbone for Effective Single-Copy RNAi

    Directory of Open Access Journals (Sweden)

    Christof Fellmann

    2013-12-01

    Full Text Available Short hairpin RNA (shRNA technology enables stable and regulated gene repression. For establishing experimentally versatile RNAi tools and minimizing toxicities, synthetic shRNAs can be embedded into endogenous microRNA contexts. However, due to our incomplete understanding of microRNA biogenesis, such “shRNAmirs” often fail to trigger potent knockdown, especially when expressed from a single genomic copy. Following recent advances in design of synthetic shRNAmir stems, here we take a systematic approach to optimize the experimental miR-30 backbone. Among several favorable features, we identify a conserved element 3′ of the basal stem as critically required for optimal shRNAmir processing and implement it in an optimized backbone termed “miR-E”, which strongly increases mature shRNA levels and knockdown efficacy. Existing miR-30 reagents can be easily converted to miR-E, and its combination with up-to-date design rules establishes a validated and accessible platform for generating effective single-copy shRNA libraries that will facilitate the functional annotation of the genome.

  19. An optimized microRNA backbone for effective single-copy RNAi.

    Science.gov (United States)

    Fellmann, Christof; Hoffmann, Thomas; Sridhar, Vaishali; Hopfgartner, Barbara; Muhar, Matthias; Roth, Mareike; Lai, Dan Yu; Barbosa, Inês A M; Kwon, Jung Shick; Guan, Yuanzhe; Sinha, Nishi; Zuber, Johannes

    2013-12-26

    Short hairpin RNA (shRNA) technology enables stable and regulated gene repression. For establishing experimentally versatile RNAi tools and minimizing toxicities, synthetic shRNAs can be embedded into endogenous microRNA contexts. However, due to our incomplete understanding of microRNA biogenesis, such "shRNAmirs" often fail to trigger potent knockdown, especially when expressed from a single genomic copy. Following recent advances in design of synthetic shRNAmir stems, here we take a systematic approach to optimize the experimental miR-30 backbone. Among several favorable features, we identify a conserved element 3' of the basal stem as critically required for optimal shRNAmir processing and implement it in an optimized backbone termed "miR-E", which strongly increases mature shRNA levels and knockdown efficacy. Existing miR-30 reagents can be easily converted to miR-E, and its combination with up-to-date design rules establishes a validated and accessible platform for generating effective single-copy shRNA libraries that will facilitate the functional annotation of the genome. PMID:24332856

  20. Protein backbone motions viewed by intraresidue and sequential HN-Hα residual dipolar couplings

    International Nuclear Information System (INIS)

    Triple resonance E.COSY-based techniques were used to measure intra-residue and sequential HN-Hα residual dipolar couplings (RDCs) for the third IgG-binding domain of protein G (GB3), aligned in Pf1 medium. Measurements closely correlate with values predicted on the basis of an NMR structure, previously determined on the basis of a large number of one-bond backbone RDCs measured in five alignment media. However, in particular the sequential HN-Hα RDCs are smaller than predicted for a static structure, suggesting a degree of motion for these internuclear vectors that exceeds that of the backbone amide N-H vectors. Of all experimentally determined GB3 structures available, the best correlation between experimental 1H-1H couplings is observed for a GB3 ensemble, previously derived to generate a realistic picture of the conformational space sampled by GB3 (Clore and Schwieters, J Mol Biol 355:879-886, 2006). However, for both NMR and X-ray-derived structures the 1H-1H couplings are found to be systematically smaller than expected on the basis of alignment tensors derived from 15N-1H amide RDCs, assuming librationally corrected N-H bond lengths of 1.041 A

  1. A fusion networking model for smart grid power distribution backbone communication network based on PTN

    Directory of Open Access Journals (Sweden)

    Wang Hao

    2016-01-01

    Full Text Available In current communication network for distribution in Chinese power grid systems, the fiber communication backbone network for distribution and TD-LTE power private wireless backhaul network of power grid are both bearing by the SDH optical transmission network, which also carries the communication network of transformer substation and main electric. As the data traffic of the distribution communication and TD-LTE power private wireless network grow rapidly in recent years, it will have a big impact with the SDH network’s bearing capacity which is mainly used for main electric communication in high security level. This paper presents a fusion networking model which use a multiple-layer PTN network as the unified bearing of the TD-LTE power private wireless backhaul network and fiber communication backbone network for distribution. Network dataflow analysis shows that this model can greatly reduce the capacity pressure of the traditional SDH network as well as ensure the reliability of the transmission of the communication network for distribution and TD-LTE power private wireless network.

  2. Control of polymer-packing orientation in thin films through synthetic tailoring of backbone coplanarity

    KAUST Repository

    Chen, Mark S.

    2013-10-22

    Controlling solid-state order of π-conjugated polymers through macromolecular design is essential for achieving high electronic device performance; yet, it remains a challenge, especially with respect to polymer-packing orientation. Our work investigates the influence of backbone coplanarity on a polymer\\'s preference to pack face-on or edge-on relative to the substrate. Isoindigo-based polymers were synthesized with increasing planarity by systematically substituting thiophenes for phenyl rings in the acceptor comonomer. This increasing backbone coplanarity, supported by density functional theory (DFT) calculations of representative trimers, leads to the narrowing of polymer band gaps as characterized by ultraviolet-visible-near infrared (UV-vis-NIR) spectroscopy and cyclic voltammetry. Among the polymers studied, regiosymmetric II and TII polymers exhibited the highest hole mobilities in organic field-effect transistors (OFETs), while in organic photovoltaics (OPVs), TBII polymers that display intermediate levels of planarity provided the highest power conversion efficiencies. Upon thin-film analysis by atomic force microscropy (AFM) and grazing-incidence X-ray diffraction (GIXD), we discovered that polymer-packing orientation could be controlled by tuning polymer planarity and solubility. Highly soluble, planar polymers favor face-on orientation in thin films while the less soluble, nonplanar polymers favor an edge-on orientation. This study advances our fundamental understanding of how polymer structure influences nanostructural order and reveals a new synthetic strategy for the design of semiconducting materials with rationally engineered solid-state properties. © 2013 American Chemical Society.

  3. Influence of Backbone Fluorination in Regioregular Poly(3-alkyl-4-fluoro)thiophenes

    KAUST Repository

    Fei, Zhuping

    2015-06-03

    © 2015 American Chemical Society. We report two strategies toward the synthesis of 3-alkyl-4-fluorothiophenes containing straight (hexyl and octyl) and branched (2-ethylhexyl) alkyl groups. We demonstrate that treatment of the dibrominated monomer with 1 equiv of alkyl Grignard reagent leads to the formation of a single regioisomer as a result of the pronounced directing effect of the fluorine group. Polymerization of the resulting species affords highly regioregular poly(3-alkyl-4-fluoro)thiophenes. Comparison of their properties to those of the analogous non-fluorinated polymers shows that backbone fluorination leads to an increase in the polymer ionization potential without a significant change in optical band gap. Fluorination also results in an enhanced tendency to aggregate in solution, which is ascribed to a more co-planar backbone on the basis of Raman and DFT calculations. Average charge carrier mobilities in field-effect transistors are found to increase by up to a factor of 5 for the fluorinated polymers.

  4. Di-Isocyanate Crosslinked Aerogels with 1, 6-Bis (Trimethoxysilyl) Hexane Incorporated in Silica Backbone

    Science.gov (United States)

    Vivod, Stephanie L.; Meador, Mary Ann B.; Nguyen, Baochau N.; Quade, Derek; Randall, Jason; Perry, Renee

    2008-01-01

    Silica aerogels are desirable materials for many applications that take advantage of their light weight and low thermal conductivity. Addition of a conformal polymer coating which bonds with the amine decorated surface of the silica network improves the strength of the aerogels by as much as 200 times. Even with vast improvement in strength they still tend to undergo brittle failure due to the rigid silica backbone. We hope to increase the flexibility and elastic recovery of the silica based aerogel by altering the silica back-bone by incorporation of more flexible hexane links. To this end, we investigated the use of 1,6-bis(trimethoxysilyl)hexane (BTMSH), a polysilsesquioxane precursor3, as an additional co-reactant to prepare silica gels which were subsequently cross-linked with di-isocyanate. Previously, this approach of adding flexibility by BTMSH incorporation was demonstrated with styrene cross-linked aerogels. In our study, we varied silane concentration, mol % of silicon from BTMSH and di-isocyanate concentration by weight percent to attempt to optimize both the flexibility and the strength of the aerogels.

  5. Improving VANETs Connectivity with a Totally Ad Hoc Living Mobile Backbone

    Directory of Open Access Journals (Sweden)

    Joilson Alves Junior

    2015-01-01

    Full Text Available The vehicular ad hoc network (VANET for intelligent transportation systems is an emerging concept to improve transportation security, reliability, and management. The network behavior can be totally different in topological aspects because of the mobility of vehicular nodes. The topology can be fully connected when the flow of vehicles is high and may have low connectivity or be invalid when the flow of vehicles is low or unbalanced. In big cities, the metropolitan buses that travel on exclusive lanes may be used to set up a metropolitan vehicular data network (backbone, raising the connectivity among the vehicles. Therefore, this paper proposes the implementation of a living mobile backbone, totally ad hoc (MOB-NET, which will provide infrastructure and raise the network connectivity. In order to show the viability of MOB-NET, statistical analyses were made with real data of express buses that travel through exclusive lanes, besides evaluations through simulations and analytic models. The statistic, analytic, and simulation results prove that the buses that travel through exclusive lanes can be used to build a communication network totally ad hoc and provide connectivity in more than 99% of the time, besides raising the delivery rate up to 95%.

  6. Spinning angle optical calibration apparatus

    Science.gov (United States)

    Beer, Stephen K.; Pratt, II, Harold R.

    1991-01-01

    An optical calibration apparatus is provided for calibrating and reproducing spinning angles in cross-polarization, nuclear magnetic resonance spectroscopy. An illuminated magnifying apparatus enables optical setting an accurate reproducing of spinning "magic angles" in cross-polarization, nuclear magnetic resonance spectroscopy experiments. A reference mark scribed on an edge of a spinning angle test sample holder is illuminated by a light source and viewed through a magnifying scope. When the "magic angle" of a sample material used as a standard is attained by varying the angular position of the sample holder, the coordinate position of the reference mark relative to a graduation or graduations on a reticle in the magnifying scope is noted. Thereafter, the spinning "magic angle" of a test material having similar nuclear properties to the standard is attained by returning the sample holder back to the originally noted coordinate position.

  7. A renormalization approach to describe charge transport in quasiperiodic dangling backbone ladder (DBL)-DNA molecules

    International Nuclear Information System (INIS)

    Highlights: → One-step renormalization approach to describe the DBL-DNA molecule. → Electronic tight-binding Hamiltonian model. → A quasiperiodic sequence to mimic the DNA nucleotides arrangement. → Electronic transmission spectra. → I-V characteristics. -- Abstract: We study the charge transport properties of a dangling backbone ladder (DBL)-DNA molecule focusing on a quasiperiodic arrangement of its constituent nucleotides forming a Rudin-Shapiro (RS) and Fibonacci (FB) Poly (CG) sequences, as well as a natural DNA sequence (Ch22) for the sake of comparison. Making use of a one-step renormalization process, the DBL-DNA molecule is modeled in terms of a one-dimensional tight-binding Hamiltonian to investigate its transmissivity and current-voltage (I-V) profiles. Beyond the semiconductor I-V characteristics, a striking similarity between the electronic transport properties of the RS quasiperiodic structure and the natural DNA sequence was found.

  8. A recombinant, chimeric tetravalent dengue vaccine candidate based on a dengue virus serotype 2 backbone.

    Science.gov (United States)

    Osorio, Jorge E; Wallace, Derek; Stinchcomb, Dan T

    2016-04-01

    Dengue fever is caused by infection with one of four dengue virus (DENV) serotypes (DENV-1-4), necessitating tetravalent dengue vaccines that can induce protection against all four DENV. Takeda's live attenuated tetravalent dengue vaccine candidate (TDV) comprises an attenuated DENV-2 strain plus chimeric viruses containing the prM and E genes of DENV-1, -3 and -4 cloned into the attenuated DENV-2 'backbone'. In Phase 1 and 2 studies, TDV was well tolerated by children and adults aged 1.5-45 years, irrespective of prior dengue exposure; mild injection-site symptoms were the most common adverse events. TDV induced neutralizing antibody responses and seroconversion to all four DENV as well as cross-reactive T cell-mediated responses that may be necessary for broad protection against dengue fever. PMID:26635182

  9. Modulation of Backbone Flexibility for Effective Dissociation of Antibacterial and Hemolytic Activity in Cyclic Peptides.

    Science.gov (United States)

    Oddo, Alberto; Thomsen, Thomas T; Britt, Hannah M; Løbner-Olesen, Anders; Thulstrup, Peter W; Sanderson, John M; Hansen, Paul R

    2016-08-11

    Bacterial resistance to antibiotic therapy is on the rise and threatens to evolve into a worldwide emergency: alternative solutions to current therapies are urgently needed. Cationic amphipathic peptides are potent membrane-active agents that hold promise as the next-generation therapy for multidrug-resistant infections. The peptides' behavior upon encountering the bacterial cell wall is crucial, and much effort has been dedicated to the investigation and optimization of this amphipathicity-driven interaction. In this study we examined the interaction of a novel series of nine-membered flexible cyclic AMPs with liposomes mimicking the characteristics of bacterial membranes. Employed techniques included circular dichroism and marker release assays, as well as microbiological experiments. Our analysis was aimed at correlating ring flexibility with their antimicrobial, hemolytic, and membrane activity. By doing so, we obtained useful insights to guide the optimization of cyclic antimicrobial peptides via modulation of their backbone flexibility without loss of activity. PMID:27563396

  10. Increased Diels-Alderase activity through backbone remodeling guided by Foldit players.

    Science.gov (United States)

    Eiben, Christopher B; Siegel, Justin B; Bale, Jacob B; Cooper, Seth; Khatib, Firas; Shen, Betty W; Players, Foldit; Stoddard, Barry L; Popovic, Zoran; Baker, David

    2012-02-01

    Computational enzyme design holds promise for the production of renewable fuels, drugs and chemicals. De novo enzyme design has generated catalysts for several reactions, but with lower catalytic efficiencies than naturally occurring enzymes. Here we report the use of game-driven crowdsourcing to enhance the activity of a computationally designed enzyme through the functional remodeling of its structure. Players of the online game Foldit were challenged to remodel the backbone of a computationally designed bimolecular Diels-Alderase to enable additional interactions with substrates. Several iterations of design and characterization generated a 24-residue helix-turn-helix motif, including a 13-residue insertion, that increased enzyme activity >18-fold. X-ray crystallography showed that the large insertion adopts a helix-turn-helix structure positioned as in the Foldit model. These results demonstrate that human creativity can extend beyond the macroscopic challenges encountered in everyday life to molecular-scale design problems. PMID:22267011

  11. Extensive Air Showers: From the muonic smoking guns to the hadronic backbone

    International Nuclear Information System (INIS)

    Extensive Air Showers are complex macroscopic objects initiated by single ultra-high energy particles. They are the result of millions of high energy reactions in the atmosphere and can be described as the superposition of hadronic and electromagnetic cascades. The hadronic cascade is the air shower backbone, and it is mainly made of pions. Decays of neutral pions initiate electromagnetic cascades, while the decays of charged pions produce muons which leave the hadronic core and travel many kilometers almost unaffected. Muons are smoking guns of the hadronic cascade: the energy, transverse momentum, spatial distribution and depth of production are key to reconstruct the history of the air shower. In this work, we overview the phenomenology of muons on the air shower and its relation to the hadronic cascade. We briefly review the experimental efforts to analyze muons within air showers and discuss possible paths to use this information. (authors)

  12. Polystyrene Backbone Polymers Consisting of Alkyl-Substituted Triazine Side Groups for Phosphorescent OLEDs

    Directory of Open Access Journals (Sweden)

    Beatrice Ch. D. Salert

    2012-01-01

    Full Text Available This paper describes the synthesis of new electron-transporting styrene monomers and their corresponding polystyrenes all with a 2,4,6-triphenyl-1,3,5-triazine basic structure in the side group. The monomers differ in the alkyl substitution and in the meta-/paralinkage of the triazine to the polymer backbone. The thermal and spectroscopic properties of the new electron-transporting polymers are discussed in regard to their chemical structures. Phosphorescent OLEDs were prepared using the obtained electron-transporting polymers as the emissive layer material in blend systems together with a green iridium-based emitter 13 and a small molecule as an additional cohost with wideband gap characteristics (CoH-001. The performance of the OLEDs was characterized and discussed in regard to the chemical structure of the new electron-transporting polymers.

  13. Sequential backbone resonance assignments of the E. coli dihydrofolate reductase Gly67Val mutant: folate complex.

    Science.gov (United States)

    Puthenpurackal Narayanan, Sunilkumar; Maeno, Akihiro; Wada, Yuji; Tate, Shin-Ichi; Akasaka, Kazuyuki

    2016-04-01

    Occasionally, a mutation in an exposed loop region causes a significant change in protein function and/or stability. A single mutation Gly67Val of E. coli dihydrofolate reductase (DHFR) in the exposed CD loop is such an example. We have carried out the chemical shift assignments for H(N), N(H), C(α) and C(β) atoms of the Gly67Val mutant of E. coli DHFR complexed with folate at pH 7.0, 35 °C, and then evaluated the H(N), N(H), C(α) and C(β) chemical shift changes caused by the mutation. The result indicates that, while the overall secondary structure remains the same, the single mutation Gly67Val causes site-specific conformational changes of the polypeptide backbone restricted around the adenosine-binding subdomain (residues 38-88) and not in the distant catalytic domain. PMID:26482924

  14. Side chain and backbone contributions of Phe508 to CFTR folding

    Energy Technology Data Exchange (ETDEWEB)

    Thibodeau, Patrick H.; Brautigam, Chad A.; Machius, Mischa; Thomas, Philip J. (U. of Texas-SMED)

    2010-12-07

    Mutations in the cystic fibrosis transmembrane conductance regulator (CFTR), an integral membrane protein, cause cystic fibrosis (CF). The most common CF-causing mutant, deletion of Phe508, fails to properly fold. To elucidate the role Phe508 plays in the folding of CFTR, missense mutations at this position were generated. Only one missense mutation had a pronounced effect on the stability and folding of the isolated domain in vitro. In contrast, many substitutions, including those of charged and bulky residues, disrupted folding of full-length CFTR in cells. Structures of two mutant nucleotide-binding domains (NBDs) reveal only local alterations of the surface near position 508. These results suggest that the peptide backbone plays a role in the proper folding of the domain, whereas the side chain plays a role in defining a surface of NBD1 that potentially interacts with other domains during the maturation of intact CFTR.

  15. A renormalization approach to describe charge transport in quasiperiodic dangling backbone ladder (DBL)-DNA molecules

    Energy Technology Data Exchange (ETDEWEB)

    Sarmento, R.G. [Departamento de Fisica, Universidade Federal do Rio Grande do Norte, 59072-970 Natal, RN (Brazil); Fulco, U.L. [Departamento de Biofisica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970 Natal, RN (Brazil); Albuquerque, E.L., E-mail: eudenilson@gmail.com [Departamento de Biofisica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970 Natal, RN (Brazil); Caetano, E.W.S. [Instituto Federal de Educacao, Ciencia e Tecnologia do Ceara, 60040-531 Fortaleza, CE (Brazil); Freire, V.N. [Departamento de Fisica, Universidade Federal do Ceara, 60455-760 Fortaleza, CE (Brazil)

    2011-10-31

    Highlights: → One-step renormalization approach to describe the DBL-DNA molecule. → Electronic tight-binding Hamiltonian model. → A quasiperiodic sequence to mimic the DNA nucleotides arrangement. → Electronic transmission spectra. → I-V characteristics. -- Abstract: We study the charge transport properties of a dangling backbone ladder (DBL)-DNA molecule focusing on a quasiperiodic arrangement of its constituent nucleotides forming a Rudin-Shapiro (RS) and Fibonacci (FB) Poly (CG) sequences, as well as a natural DNA sequence (Ch22) for the sake of comparison. Making use of a one-step renormalization process, the DBL-DNA molecule is modeled in terms of a one-dimensional tight-binding Hamiltonian to investigate its transmissivity and current-voltage (I-V) profiles. Beyond the semiconductor I-V characteristics, a striking similarity between the electronic transport properties of the RS quasiperiodic structure and the natural DNA sequence was found.

  16. Extensive Air Showers: from the muonic smoking guns to the hadronic backbone

    CERN Document Server

    Cazon, L

    2013-01-01

    Extensive Air Showers are complex macroscopic objects initiated by single ultra-high energy particles. They are the result of millions of high energy reactions in the atmosphere and can be described as the superposition of hadronic and electromagnetic cascades. The hadronic cascade is the air shower backbone, and it is mainly made of pions. Decays of neutral pions initiate electromagnetic cascades, while the decays of charged pions produce muons which leave the hadronic core and travel many kilometers almost unaffected. Muons are smoking guns of the hadronic cascade: the energy, transverse momentum, spatial distribution and depth of production are key to reconstruct the history of the air shower. In this work, we overview the phenomenology of muons on the air shower and its relation to the hadronic cascade. We briefly review the experimental efforts to analyze muons within air showers and discuss possible paths to use this information.

  17. Extensive Air Showers: from the muonic smoking guns to the hadronic backbone

    Directory of Open Access Journals (Sweden)

    Cazon L.

    2013-06-01

    Full Text Available Extensive Air Showers are complex macroscopic objects initiated by single ultra-high energy particles. They are the result of millions of high energy reactions in the atmosphere and can be described as the superposition of hadronic and electromagnetic cascades. The hadronic cascade is the air shower backbone, and it is mainly made of pions. Decays of neutral pions initiate electromagnetic cascades, while the decays of charged pions produce muons which leave the hadronic core and travel many kilometers almost unaffected. Muons are smoking guns of the hadronic cascade: the energy, transverse momentum, spatial distribution and depth of production are key to reconstruct the history of the air shower. In this work, we overview the phenomenology of muons on the air shower and its relation to the hadronic cascade. We briefly review the experimental efforts to analyze muons within air showers and discuss possible paths to use this information.

  18. Constructing Path Efficient and Energy Aware Virtual Multicast Backbones in Static Ad Hoc Wireless Networks

    Directory of Open Access Journals (Sweden)

    Tamaghna Acharya

    2010-05-01

    Full Text Available For stationary wireless ad hoc networks, one of the key challenging issues in routing and multicasting isto conserve as much energy as possible without compromising path efficiency measured as end-to-enddelay. In this paper, we address the problem of path efficient and energy aware multicasting in staticwireless ad hoc networks. We propose a novel distributed scalable algorithm for finding a virtualmulticast backbone (VMB. Based on this VMB, we have further developed a multicasting scheme thatjointly improves path efficiency and energy conservation. By exploiting inherent broadcast advantage ofwireless communication and employing a more realistic energy consumption model for wirelesscommunication which not only depends on radio propagation losses but also on energy losses intransceiver circuitry, our simulation results show that the proposed VMB-based multicasting schemeoutperforms existing prominent tree based energy conserving, path efficient multicasting schemes.

  19. Computational Study of Environmental Effects on Torsional Free Energy Surface of N-Acetyl-N'-methyl-L-alanylamide Dipeptide

    Science.gov (United States)

    Carlotto, Silvia; Zerbetto, Mirco

    2014-01-01

    We propose an articulated computational experiment in which both quantum mechanics (QM) and molecular mechanics (MM) methods are employed to investigate environment effects on the free energy surface for the backbone dihedral angles rotation of the small dipeptide N-Acetyl-N'-methyl-L-alanylamide. This computation exercise is appropriate for an…

  20. Effects of Tryptophan Content and Backbone Spacing on the Uptake Efficiency of Cell-Penetrating Peptides

    KAUST Repository

    Rydberg, Hanna A.

    2012-07-10

    Cell-penetrating peptides (CPPs) are able to traverse cellular membranes and deliver macromolecular cargo. Uptake occurs through both endocytotic and nonendocytotic pathways, but the molecular requirements for efficient internalization are not fully understood. Here we investigate how the presence of tryptophans and their position within an oligoarginine influence uptake mechanism and efficiency. Flow cytometry and confocal fluorescence imaging are used to estimate uptake efficiency, intracellular distribution and toxicity in Chinese hamster ovarian cells. Further, membrane leakage and lipid membrane affinity are investigated. The peptides contain eight arginine residues and one to four tryptophans, the tryptophans positioned either at the N-terminus, in the middle, or evenly distributed along the amino acid sequence. Our data show that the intracellular distribution varies among peptides with different tryptophan content and backbone spacing. Uptake efficiency is higher for the peptides with four tryptophans in the middle, or evenly distributed along the peptide sequence, than for the peptide with four tryptophans at the N-terminus. All peptides display low cytotoxicity except for the one with four tryptophans at the N-terminus, which was moderately toxic. This finding is consistent with their inability to induce efficient leakage of dye from lipid vesicles. All peptides have comparable affinities for lipid vesicles, showing that lipid binding is not a decisive parameter for uptake. Our results indicate that tryptophan content and backbone spacing can affect both the CPP uptake efficiency and the CPP uptake mechanism. The low cytotoxicity of these peptides and the possibilities of tuning their uptake mechanism are interesting from a therapeutic point of view. © 2012 American Chemical Society.

  1. Antigenic characterization of influenza viruses produced using synthetic DNA and novel backbones.

    Science.gov (United States)

    Suphaphiphat, Pirada; Whittaker, Lynne; De Souza, Ivna; Daniels, Rodney S; Dormitzer, Philip R; McCauley, John W; Settembre, Ethan C

    2016-07-12

    The global system for manufacturing seasonal influenza vaccines has been developed to respond to the natural evolution of influenza viruses, but the problem of antigenic mismatch continues to be a challenge in certain years. In some years, mismatches arise naturally due to the antigenic drift of circulating viruses after vaccine strain selection has already been made. In other years, antigenic differences between the vaccine virus and circulating viruses are introduced as part of the current system, which relies on the use of egg-adapted isolates as a starting material for candidate vaccine viruses (CVVs). Improving the current process for making vaccine viruses can provide great value. We have previously established a synthetic approach for rapidly generating influenza viruses in a vaccine-approved Madin Darby canine kidney (MDCK) cell line using novel, high-growth backbones that increase virus rescue efficiency and antigen yield. This technology also has the potential to produce viruses that maintain antigenic similarity to the intended reference viruses, depending on the hemagglutinin (HA) and neuraminidase (NA) sequences used for gene synthesis. To demonstrate this utility, we generated a panel of synthetic viruses using HA and NA sequences from recent isolates and showed by hemagglutination inhibition (HI) tests that all synthetic viruses were antigenically-like their conventional egg- or cell-propagated reference strains and there was no impact of the novel backbones on antigenicity. This synthetic approach can be used for the efficient production of CVVs that may be more representative of circulating viruses and may be used for both egg- and cell-based vaccine manufacturing platforms. When combined with mammalian cell culture technology for antigen production, synthetic viruses generated using HA and NA sequences from a non-egg-adapted prototype can help to reduce the potential impact of antigenic differences between vaccine virus and circulating viruses on

  2. 40-Gbps optical backbone network deep packet inspection based on FPGA

    Science.gov (United States)

    Zuo, Yuan; Huang, Zhiping; Su, Shaojing

    2014-11-01

    In the era of information, the big data, which contains huge information, brings about some problems, such as high speed transmission, storage and real-time analysis and process. As the important media for data transmission, the Internet is the significant part for big data processing research. With the large-scale usage of the Internet, the data streaming of network is increasing rapidly. The speed level in the main fiber optic communication of the present has reached 40Gbps, even 100Gbps, therefore data on the optical backbone network shows some features of massive data. Generally, data services are provided via IP packets on the optical backbone network, which is constituted with SDH (Synchronous Digital Hierarchy). Hence this method that IP packets are directly mapped into SDH payload is named POS (Packet over SDH) technology. Aiming at the problems of real time process of high speed massive data, this paper designs a process system platform based on ATCA for 40Gbps POS signal data stream recognition and packet content capture, which employs the FPGA as the CPU. This platform offers pre-processing of clustering algorithms, service traffic identification and data mining for the following big data storage and analysis with high efficiency. Also, the operational procedure is proposed in this paper. Four channels of 10Gbps POS signal decomposed by the analysis module, which chooses FPGA as the kernel, are inputted to the flow classification module and the pattern matching component based on TCAM. Based on the properties of the length of payload and net flows, buffer management is added to the platform to keep the key flow information. According to data stream analysis, DPI (deep packet inspection) and flow balance distribute, the signal is transmitted to the backend machine through the giga Ethernet ports on back board. Practice shows that the proposed platform is superior to the traditional applications based on ASIC and NP.

  3. Quantum chemical benchmark study on 46 RNA backbone families using a dinucleotide unit.

    Science.gov (United States)

    Kruse, Holger; Mladek, Arnost; Gkionis, Konstantinos; Hansen, Andreas; Grimme, Stefan; Sponer, Jiri

    2015-10-13

    We have created a benchmark set of quantum chemical structure-energy data denoted as UpU46, which consists of 46 uracil dinucleotides (UpU), representing all known 46 RNA backbone conformational families. Penalty-function-based restrained optimizations with COSMO TPSS-D3/def2-TZVP ensure a balance between keeping the target conformation and geometry relaxation. The backbone geometries are close to the clustering-means of their respective RNA bioinformatics family classification. High-level wave function methods (DLPNO-CCSD(T) as reference) and a wide-range of dispersion-corrected or inclusive DFT methods (DFT-D3, VV10, LC-BOP-LRD, M06-2X, M11, and more) are used to evaluate the conformational energies. The results are compared to the Amber RNA bsc0χOL3 force field. Most dispersion-corrected DFT methods surpass the Amber force field significantly in accuracy and yield mean absolute deviations (MADs) for relative conformational energies of ∼0.4-0.6 kcal/mol. Double-hybrid density functionals represent the most accurate class of density functionals. Low-cost quantum chemical methods such as PM6-D3H+, HF-3c, DFTB3-D3, as well as small basis set calculations corrected for basis set superposition errors (BSSEs) by the gCP procedure are also tested. Unfortunately, the presently available low-cost methods are struggling to describe the UpU conformational energies with satisfactory accuracy. The UpU46 benchmark is an ideal test for benchmarking and development of fast methods to describe nucleic acids, including force fields. PMID:26574283

  4. Calculations of the Wigner angle

    International Nuclear Information System (INIS)

    Two new methods to determine Wigner's angle in special relativity are presented. The first one consists in calculating the angle between the compositions u-bar x ν-bar and ν-bar x u-bar of the two non-collinear velocities u-bar and ν-bar. In another method we introduce a generalization in the complex plane of Einstein's addition law of parallel velocities. (author)

  5. In the Near Future Backbone Aluminum Enterprises will Close Down About 2.4 million Tonnes of Capacity

    Institute of Scientific and Technical Information of China (English)

    2015-01-01

    On August 21,China Nonferrous Metals Industry Association Aluminum Industry Branch assembled some backbone aluminum enterprises and Henan Nonferrous Metal Industry Association to hold a discussion meeting in Beijing over the current operation trend of aluminum industry,dilemma and opportunity ahead and measures to diffuse surplus capacity,the meeting also discussed the

  6. VPLS: alternativa de interconexión a través del backbone IP/MPLS de ETECSA

    Directory of Open Access Journals (Sweden)

    Osmel Barreto Prieto

    2013-03-01

    Full Text Available La Empresa de Telecomunicaciones de Cuba (ETECSA maneja en condiciones de exclusividad la infraestructura de telecomunicaciones del país, por lo que el resto de los proveedores necesitan utilizar dicha infraestructura como soporte para la interconexión de los nodos que componen sus redes. Teniendo en cuenta el desarrollo de las tecnologías de las telecomunicaciones, ETECSA ha apostado por la implementación de un backbone IP/MPLS (Internet Protocol over  MultiProtocol Label Switching: Protocolo de Internet sobre Conmutación Multiprotocolo basada en Etiquetas en su red, el cual se espera absorba todos los servicios actualmente soportados por el backbone ATM (Asynchronous Transfer Mode/Frame Relay. Sin embargo, en estos momentos, la red IP/MPLS solamente oferta servicios VPN (Virtual Private Network: Red Privada Virtual a nivel de red (nivel tres del modelo OSI, cuestión que, para los otros proveedores, resulta inadmisible. El presente artículo describe una propuesta de implementación de una entidad VPLS (Virtual Private LAN Service: Servicio de LAN Privada Virtual como alternativa para la migración de los servicios de VPN de nivel dos que actualmente se soportan sobre el backbone ATM/Frame Relay, hacia el backbone IP/MPLS, variante que garantiza la independencia por parte de los proveedores que son clientes de ETECSA en la operación y enrutamiento de su red.

  7. Adsorption of molecular brushes with polyelectrolyte backbones onto oppositely charged surfaces: A self-consistent field theory

    NARCIS (Netherlands)

    Feuz, L.; Leermakers, F.A.M.; Textor, M.; Borisov, O.V.

    2008-01-01

    The two-gradient version of the Scheutjens¿Fleer self-consistent field (SF-SCF) theory is employed to model the interaction between a molecular bottle brush with a polyelectrolyte backbone and neutral hydrophilic side chains and an oppositely charged surface. Our system mimics graft-copolymers with

  8. Interaction of Al-induced peptide backbone ring structure with the sidechains of His, Phe, Trp and Tyr

    Institute of Scientific and Technical Information of China (English)

    吴清雷; 宋波

    2015-01-01

    Aluminium is widely used as an antimicrobial coagulant, food additive, and cookware. However, many reports indicate that aluminium may be a critical factor in many amyloid diseases, such as Alzheimer’s disease and Parkinson’s disease. Unfortunately, the underlying mechanism is still poorly understood, which limits efforts to prevent and treat these diseases. In this paper, using an ab initio method, we studied the interaction of Al-backbone ring structure with theπ-electron-rich sidechains of His, Phe, Trp, and Tyr. We found that in the absence of water, the Al-backbone ring can stably bind with those sidechains. In the presence of water, the Al-backbone ring can bind to the His sidechain and cannot bind to the other sidechains. As revealed by further investigations, this could be attributed to the fact that there was a coordinate bond of the Al-backbone ring with the His sidechain, while there were theπ-πstacking and cation-π-like interactions with the other sidechains. These findings potentially provide a molecular understanding of Al-related toxicity, and may be helpful in designing drugs for those aforementioned aluminum-linked diseases and encourage treatment of Al-polluted water.

  9. Frequency scaling for angle gathers

    KAUST Repository

    Zuberi, M. A H

    2014-01-01

    Angle gathers provide an extra dimension to analyze the velocity after migration. Space-shift and time shift-imaging conditions are two methods used to obtain angle gathers, but both are reasonably expensive. By scaling the time-lag axis of the time-shifted images, the computational cost of the time shift imaging condition can be considerably reduced. In imaging and more so Full waveform inversion, frequencydomain Helmholtz solvers are used more often to solve for the wavefields than conventional time domain extrapolators. In such cases, we do not need to extend the image, instead we scale the frequency axis of the frequency domain image to obtain the angle gathers more efficiently. Application on synthetic data demonstrate such features.

  10. Systematic variations in divergence angle

    CERN Document Server

    Okabe, Takuya

    2012-01-01

    Practical methods for quantitative analysis of radial and angular coordinates of leafy organs of vascular plants are presented and applied to published phyllotactic patterns of various real systems from young leaves on a shoot tip to florets on a flower head. The constancy of divergence angle is borne out with accuracy of less than a degree. It is shown that apparent fluctuations in divergence angle are in large part systematic variations caused by the invalid assumption of a fixed center and/or by secondary deformations, while random fluctuations are of minor importance.

  11. An Enhanced Backbone-Assisted Reliable Framework for Wireless Sensor Networks

    Directory of Open Access Journals (Sweden)

    Amna Ali

    2010-03-01

    Full Text Available An extremely reliable source to sink communication is required for most of the contemporary WSN applications especially pertaining to military, healthcare and disaster-recovery. However, due to their intrinsic energy, bandwidth and computational constraints, Wireless Sensor Networks (WSNs encounter several challenges in reliable source to sink communication. In this paper, we present a novel reliable topology that uses reliable hotlines between sensor gateways to boost the reliability of end-to-end transmissions. This reliable and efficient routing alternative reduces the number of average hops from source to the sink. We prove, with the help of analytical evaluation, that communication using hotlines is considerably more reliable than traditional WSN routing. We use reliability theory to analyze the cost and benefit of adding gateway nodes to a backbone-assisted WSN. However, in hotline assisted routing some scenarios where source and the sink are just a couple of hops away might bring more latency, therefore, we present a Signature Based Routing (SBR scheme. SBR enables the gateways to make intelligent routing decisions, based upon the derived signature, hence providing lesser end-to-end delay between source to the sink communication. Finally, we evaluate our proposed hotline based topology with the help of a simulation tool and show that the proposed topology provides manifold increase in end-to-end reliability.

  12. Aggregation tendencies in the p53 family are modulated by backbone hydrogen bonds.

    Science.gov (United States)

    Cino, Elio A; Soares, Iaci N; Pedrote, Murilo M; de Oliveira, Guilherme A P; Silva, Jerson L

    2016-01-01

    The p53 family of proteins is comprised of p53, p63 and p73. Because the p53 DNA binding domain (DBD) is naturally unstable and possesses an amyloidogenic sequence, it is prone to form amyloid fibrils, causing loss of functions. To develop p53 therapies, it is necessary to understand the molecular basis of p53 instability and aggregation. Light scattering, thioflavin T (ThT) and high hydrostatic pressure (HHP) assays showed that p53 DBD aggregates faster and to a greater extent than p63 and p73 DBDs, and was more susceptible to denaturation. The aggregation tendencies of p53, p63, and p73 DBDs were strongly correlated with their thermal stabilities. Molecular Dynamics (MD) simulations indicated specific regions of structural heterogeneity unique to p53, which may be promoted by elevated incidence of exposed backbone hydrogen bonds (BHBs). The results indicate regions of structural vulnerability in the p53 DBD, suggesting new targetable sites for modulating p53 stability and aggregation, a potential approach to cancer therapy. PMID:27600721

  13. 4D experiments measured with APSY for automated backbone resonance assignments of large proteins

    International Nuclear Information System (INIS)

    Detailed structural and functional characterization of proteins by solution NMR requires sequence-specific resonance assignment. We present a set of transverse relaxation optimization (TROSY) based four-dimensional automated projection spectroscopy (APSY) experiments which are designed for resonance assignments of proteins with a size up to 40 kDa, namely HNCACO, HNCOCA, HNCACB and HN(CO)CACB. These higher-dimensional experiments include several sensitivity-optimizing features such as multiple quantum parallel evolution in a ‘just-in-time’ manner, aliased off-resonance evolution, evolution-time optimized APSY acquisition, selective water-handling and TROSY. The experiments were acquired within the concept of APSY, but they can also be used within the framework of sparsely sampled experiments. The multidimensional peak lists derived with APSY provided chemical shifts with an approximately 20 times higher precision than conventional methods usually do, and allowed the assignment of 90 % of the backbone resonances of the perdeuterated primase-polymerase ORF904, which contains 331 amino acid residues and has a molecular weight of 38.4 kDa.

  14. Suitability assessment of OPC UA as the backbone of ground-based observatory control systems

    International Nuclear Information System (INIS)

    A common requirement of modern observatory control systems is to allow interaction between various heterogeneous subsystems in a transparent way. However, the integration of off-the-shelf (OTS) industrial products - such as Programmable Logic Controllers (PLCs) and Supervisory Control And Data Acquisition (SCADA) software - has long been hampered by the lack of an adequate interfacing method. With the advent of the Unified Architecture (UA) version of OPC (Object Linking and Embedding for Process Control), the limitations of the original industry accepted interface are now lifted, and also much more functionality has been defined. In this paper the most important features of OPC UA are matched against the requirements of ground-based observatory control systems in general and in particular of the 1.2 m Mercator Telescope. We investigate the opportunities of the 'information modelling' idea behind OPC UA, which could allow an extensive standardization in the field of astronomical instrumentation, similar to the efforts emerging in several industry domains. Because OPC UA is designed for both horizontal and vertical integration of heterogeneous subsystems, we explore its capabilities to serve as the backbone of a dependable and scalable observatory control system, treating industrial components like PLCs no differently than custom software components. Performance measurements and tests with a sample of OTS OPC UA products are presented. (authors)

  15. Toward High Performance n-Type Thermoelectric Materials by Rational Modification of BDPPV Backbones.

    Science.gov (United States)

    Shi, Ke; Zhang, Fengjiao; Di, Chong-An; Yan, Tian-Wei; Zou, Ye; Zhou, Xu; Zhu, Daoben; Wang, Jie-Yu; Pei, Jian

    2015-06-10

    Three n-type polymers BDPPV, ClBDPPV, and FBDPPV which exhibit outstanding electrical conductivities when mixed with an n-type dopant, N-DMBI ((4-(1,3-dimethyl-2,3-dihydro-1H-benzoimidazol-2-yl)phenyl)dimethylamine), in solution. High electron mobility and an efficient doping process endow FBDPPV with the highest electrical conductivities of 14 S cm(-1) and power factors up to 28 μW m(-1) K(-2), which is the highest thermoelectric (TE) power factor that has been reported for solution processable n-type conjugated polymers. Our investigations reveal that introduction of halogen atoms to the polymer backbones has a dramatic influence on not only the electron mobilities but also the doping levels, both of which are critical to the electrical conductivities. This work suggests the significance of rational modification of polymer structures and opens the gate for applying the rapidly developed organic semiconductors with high carrier mobilities to thermoelectric field. PMID:25997085

  16. Highly automated protein backbone resonance assignment within a few hours: the strategy and software package

    International Nuclear Information System (INIS)

    Sequential resonance assignment represents an essential step towards the investigation of protein structure, dynamics, and interaction surfaces. Although the experimental sensitivity has significantly increased in recent years, with the availability of high field magnets and cryogenically cooled probes, resonance assignment, even of small globular proteins, still generally requires several days of data collection and analysis using standard protocols. Here we introduce the BATCH strategy for fast and highly automated backbone resonance assignment of 13C, 15N-labelled proteins. BATCH makes use of the fast data acquisition and analysis tools BEST, ASCOM, COBRA, and HADAMAC, recently developed in our laboratory. An improved Hadamard encoding scheme, presented here, further increases the performance of the HADAMAC experiment. A new software platform, interfaced to the NMRView software package, has been developed that enables highly automated NMR data processing and analysis, sequential resonance assignment, and 13C chemical shift extraction. We demonstrate for four small globular proteins that sequential resonance assignment can be routinely obtained within a few hours, or less, in a highly automated and robust way

  17. STARD6 on steroids: solution structure, multiple timescale backbone dynamics and ligand binding mechanism

    Science.gov (United States)

    Létourneau, Danny; Bédard, Mikaël; Cabana, Jérôme; Lefebvre, Andrée; LeHoux, Jean-Guy; Lavigne, Pierre

    2016-01-01

    START domain proteins are conserved α/β helix-grip fold that play a role in the non-vesicular and intracellular transport of lipids and sterols. The mechanism and conformational changes permitting the entry of the ligand into their buried binding sites is not well understood. Moreover, their functions and the identification of cognate ligands is still an active area of research. Here, we report the solution structure of STARD6 and the characterization of its backbone dynamics on multiple time-scales through 15N spin-relaxation and amide exchange studies. We reveal for the first time the presence of concerted fluctuations in the Ω1 loop and the C-terminal helix on the microsecond-millisecond time-scale that allows for the opening of the binding site and ligand entry. We also report that STARD6 binds specifically testosterone. Our work represents a milestone for the study of ligand binding mechanism by other START domains and the elucidation of the biological function of STARD6. PMID:27340016

  18. Reversible Self-Assembly of Backbone-Thermoresponsive Long Chain Hyperbranched Poly(N-Isopropyl Acrylamide

    Directory of Open Access Journals (Sweden)

    Ting-Ting Liu

    2016-01-01

    Full Text Available In this paper, we mainly described the reversible self-assembly of a backbone-thermoresponsive, long-chain, hyperbranched poly(N-isopropyl acrylamide (LCHBPNIPAM in aqueous solution. Here, we revealed a reversible self-assembly behavior of LCHBPNIPAM aqueous solution derived from temperature. By controlling the temperature of LCHBPNIPAM aqueous solution, we tune the morphology of the LCHBPNIPAM self-assemblies. When the solution temperature increased from the room temperature to the lower critical solution temperature of PNIPAM segments, LCHBPNIPAM self-assembled from multi-compartment vesicles into solid micelles. The morphology of LCHBPNIPAM self-assemblies changed from solid micelles to multi-compartment vesicles again when the temperature decreased back to the room temperature. The size presented, at first, an increase, and then a decrease, tendency in the heating-cooling process. The above thermally-triggered self-assembly behavior of LCHBPNIPAM aqueous solution was investigated by dynamic/static light scattering, transmission electron microscopy, atomic force microscopy, fluorescence spectroscopy, 1H nuclear magnetic resonance in D2O, and attenuated total reflectance Fourier transform infrared spectroscopy. These results indicated that LCHBPNIPAM aqueous solution presents a reversible self-assembly process. The controlled release behaviors of doxorubicin from the vesicles and micelles formed by LCHBPNIPAM further proved the feasibility of these self-assemblies as the stimulus-responsive drug delivery system.

  19. Aggregation tendencies in the p53 family are modulated by backbone hydrogen bonds

    Science.gov (United States)

    Cino, Elio A.; Soares, Iaci N.; Pedrote, Murilo M.; de Oliveira, Guilherme A. P.; Silva, Jerson L.

    2016-01-01

    The p53 family of proteins is comprised of p53, p63 and p73. Because the p53 DNA binding domain (DBD) is naturally unstable and possesses an amyloidogenic sequence, it is prone to form amyloid fibrils, causing loss of functions. To develop p53 therapies, it is necessary to understand the molecular basis of p53 instability and aggregation. Light scattering, thioflavin T (ThT) and high hydrostatic pressure (HHP) assays showed that p53 DBD aggregates faster and to a greater extent than p63 and p73 DBDs, and was more susceptible to denaturation. The aggregation tendencies of p53, p63, and p73 DBDs were strongly correlated with their thermal stabilities. Molecular Dynamics (MD) simulations indicated specific regions of structural heterogeneity unique to p53, which may be promoted by elevated incidence of exposed backbone hydrogen bonds (BHBs). The results indicate regions of structural vulnerability in the p53 DBD, suggesting new targetable sites for modulating p53 stability and aggregation, a potential approach to cancer therapy. PMID:27600721

  20. APSY-NMR for protein backbone assignment in high-throughput structural biology

    Energy Technology Data Exchange (ETDEWEB)

    Dutta, Samit Kumar; Serrano, Pedro; Proudfoot, Andrew; Geralt, Michael [The Scripps Research Institute, Department of Integrative Structural and Computational Biology (United States); Pedrini, Bill [Paul Scherrer Institute (PSI), SwissFEL Project (Switzerland); Herrmann, Torsten [Université de Lyon, Institut des Sciences Analytiques, Centre de RMN à Très Hauts Champs, UMR 5280 CNRS, ENS Lyon, UCB Lyon 1 (France); Wüthrich, Kurt, E-mail: wuthrich@scripps.edu [The Scripps Research Institute, Department of Integrative Structural and Computational Biology (United States)

    2015-01-15

    A standard set of three APSY-NMR experiments has been used in daily practice to obtain polypeptide backbone NMR assignments in globular proteins with sizes up to about 150 residues, which had been identified as targets for structure determination by the Joint Center for Structural Genomics (JCSG) under the auspices of the Protein Structure Initiative (PSI). In a representative sample of 30 proteins, initial fully automated data analysis with the software UNIO-MATCH-2014 yielded complete or partial assignments for over 90 % of the residues. For most proteins the APSY data acquisition was completed in less than 30 h. The results of the automated procedure provided a basis for efficient interactive validation and extension to near-completion of the assignments by reference to the same 3D heteronuclear-resolved [{sup 1}H,{sup 1}H]-NOESY spectra that were subsequently used for the collection of conformational constraints. High-quality structures were obtained for all 30 proteins, using the J-UNIO protocol, which includes extensive automation of NMR structure determination.

  1. Noise assisted excitation energy transfer in a linear model of a selectivity filter backbone strand

    Science.gov (United States)

    Bassereh, Hassan; Salari, Vahid; Shahbazi, Farhad

    2015-07-01

    In this paper, we investigate the effect of noise and disorder on the efficiency of excitation energy transfer (EET) in a N=5 sites linear chain with ‘static’ dipole-dipole couplings. In fact, here, the disordered chain is a toy model for one strand of the selectivity filter backbone in ion channels. It has recently been discussed that the presence of quantum coherence in the selectivity filter is possible and can play a role in mediating ion-conduction and ion-selectivity in the selectivity filter. The question is ‘how a quantum coherence can be effective in such structures while the environment of the channel is dephasing (i.e. noisy)?’ Basically, we expect that the presence of the noise should have a destructive effect in the quantum transport. In fact, we show that such expectation is valid for ordered chains. However, our results indicate that introducing the dephasing in the disordered chains leads to the weakening of the localization effects, arising from the multiple back-scatterings due to the randomness, and then increases the efficiency of quantum energy transfer. Thus, the presence of noise is crucial for the enhancement of EET efficiency in disordered chains. We also show that the contribution of both classical and quantum mechanical effects are required to improve the speed of energy transfer along the chain. Our analysis may help for better understanding of fast and efficient functioning of the selectivity filters in ion channels.

  2. Dependence of crystallite formation and preferential backbone orientations on the side chain pattern in PBDTTPD polymers

    KAUST Repository

    El Labban, Abdulrahman

    2014-11-26

    (Figure Presented) Alkyl substituents appended to the π-conjugated main chain account for the solution-processability and film-forming properties of most π-conjugated polymers for organic electronic device applications, including field-effect transistors (FETs) and bulk-heterojunction (BHJ) solar cells. Beyond film-forming properties, recent work has emphasized the determining role that side-chain substituents play on polymer self-assembly and thin-film nanostructural order, and, in turn, on device performance. However, the factors that determine polymer crystallite orientation in thin-films, implying preferential backbone orientation relative to the device substrate, are a matter of some debate, and these structural changes remain difficult to anticipate. In this report, we show how systematic changes in the side-chain pattern of poly(benzo[1,2-b:4,5-b′]dithiophene-alt-thieno[3,4-c]pyrrole-4,6-dione) (PBDTTPD) polymers can (i) influence the propensity of the polymer to order in the π-stacking direction, and (ii) direct the preferential orientation of the polymer crystallites in thin films (e.g., "face-on" vs "edge-on"). Oriented crystallites, specifically crystallites that are well-ordered in the π-stacking direction, are believed to be a key contributor to improved thin-film device performance in both FETs and BHJ solar cells.

  3. APSY-NMR for protein backbone assignment in high-throughput structural biology

    International Nuclear Information System (INIS)

    A standard set of three APSY-NMR experiments has been used in daily practice to obtain polypeptide backbone NMR assignments in globular proteins with sizes up to about 150 residues, which had been identified as targets for structure determination by the Joint Center for Structural Genomics (JCSG) under the auspices of the Protein Structure Initiative (PSI). In a representative sample of 30 proteins, initial fully automated data analysis with the software UNIO-MATCH-2014 yielded complete or partial assignments for over 90 % of the residues. For most proteins the APSY data acquisition was completed in less than 30 h. The results of the automated procedure provided a basis for efficient interactive validation and extension to near-completion of the assignments by reference to the same 3D heteronuclear-resolved [1H,1H]-NOESY spectra that were subsequently used for the collection of conformational constraints. High-quality structures were obtained for all 30 proteins, using the J-UNIO protocol, which includes extensive automation of NMR structure determination

  4. Discovering the Inscribed Angle Theorem

    Science.gov (United States)

    Roscoe, Matt B.

    2012-01-01

    Learning to play tennis is difficult. It takes practice, but it also helps to have a coach--someone who gives tips and pointers but allows the freedom to play the game on one's own. Learning to act like a mathematician is a similar process. Students report that the process of proving the inscribed angle theorem is challenging and, at times,…

  5. Contactless angle detection using permalloy

    NARCIS (Netherlands)

    Eijkel, Kees J.; Rijk, Rolf

    1988-01-01

    An overview is given of measurements on angle detectors. The detectors consist of a pair of planar-Hall elements opposite to a rotatable magnet. The measurements are performed on a number of planar-Hall elements of different shape and size, and show good agreement with a previously described theoret

  6. Dolutegravir treatment response by baseline viral load and NRTI backbone in treatment-naïve HIV-infected individuals

    Directory of Open Access Journals (Sweden)

    C Small

    2012-11-01

    Full Text Available Background: In two 48-week studies in naïve subjects, dolutegravir with NRTI of choice has shown non-inferiority to raltegravir and, with ABC/3TC, superiority to Atripla. Factors that influenced choice of NRTIs included viral load, resistance and safety. Methods: We analysed response rates and time to virologic failure by NRTI backbone and baseline viral load in the pivotal DTG-naïve studies. SPRING-2 randomized participants to DTG 50 mg QD or RAL 400 mg BID, each in combination with investigator-selected NRTIs (TDF/FTC or ABC/3TC. SINGLE randomised participants to DTG 50 mg+ABC/3TC QD or TDF/FTC/EFV (Atripla QD. In SPRING-2, changes in serum creatinine were examined by INI and NRTI backbone. Results: The two studies randomized and treated 1655 subjects, of whom 249 (15% were female, 388 (23% non-white, 495 (30% had HIV-1 RNA >100,000 c/ml, and 224 (14% had CD4+ count <200 cells/mm3. Primary analyses demonstrated non-inferiority of DTG to RAL in SPRING-2 (Δ=2.5%; 95% CI:−2.2% to +7.1%, excluding −10%, and superiority of the DTG regimen in SINGLE (7.4%; +2.5% to +12.3%. In SPRING-2, response rates by NRTI backbone were comparable in each viral load stratum. In SINGLE, a 7% difference in response (favoring DTG+ABC/3TC was observed in each viral load stratum. Exploratory analyses examining time-to-virologic failure showed no difference in response rates between the NRTIs irrespective of baseline viral load or study. Resistance to INIs or NRTIs was not demonstrated in any subject on DTG-based therapy through 48 weeks. Withdrawals due to AEs on DTG-based regimen were few (2% in both studies. In SPRING-2, no significant differences were observed in serum creatinine change from baseline to Week 48 by NRTI backbones. Conclusions: In SPRING-2 and SINGLE, DTG was effective with both ABC/3TC and TDF/FTC, and in subjects with high and low viral load. DTG was well tolerated in both studies. Renal safety also was similar by NRTI backbone. DTG is a once

  7. Catalytic mechanism of RNA backbone cleavage by ribonuclease H from quantum mechanics/molecular mechanics simulations.

    Science.gov (United States)

    Rosta, Edina; Nowotny, Marcin; Yang, Wei; Hummer, Gerhard

    2011-06-15

    We use quantum mechanics/molecular mechanics simulations to study the cleavage of the ribonucleic acid (RNA) backbone catalyzed by ribonuclease H. This protein is a prototypical member of a large family of enzymes that use two-metal catalysis to process nucleic acids. By combining Hamiltonian replica exchange with a finite-temperature string method, we calculate the free energy surface underlying the RNA-cleavage reaction and characterize its mechanism. We find that the reaction proceeds in two steps. In a first step, catalyzed primarily by magnesium ion A and its ligands, a water molecule attacks the scissile phosphate. Consistent with thiol-substitution experiments, a water proton is transferred to the downstream phosphate group. The transient phosphorane formed as a result of this nucleophilic attack decays by breaking the bond between the phosphate and the ribose oxygen. In the resulting intermediate, the dissociated but unprotonated leaving group forms an alkoxide coordinated to magnesium ion B. In a second step, the reaction is completed by protonation of the leaving group, with a neutral Asp132 as a likely proton donor. The overall reaction barrier of ∼15 kcal mol(-1), encountered in the first step, together with the cost of protonating Asp132, is consistent with the slow measured rate of ∼1-100/min. The two-step mechanism is also consistent with the bell-shaped pH dependence of the reaction rate. The nonmonotonic relative motion of the magnesium ions along the reaction pathway agrees with X-ray crystal structures. Proton-transfer reactions and changes in the metal ion coordination emerge as central factors in the RNA-cleavage reaction. PMID:21539371

  8. Catalytic Mechanism of RNA Backbone Cleavage by Ribonuclease H from QM/MM Simulations

    Science.gov (United States)

    Rosta, Edina; Nowotny, Marcin; Yang, Wei; Hummer, Gerhard

    2011-01-01

    We use quantum mechanics/molecular mechanics (QM/MM) simulations to study the cleavage of the ribonucleic acid (RNA) backbone catalyzed by ribonuclease H. This protein is a prototypical member of a large family of enzymes that use two-metal catalysis to process nucleic acids. By combining Hamiltonian replica exchange with a finite-temperature string method, we calculate the free energy surface underlying the RNA cleavage reaction and characterize its mechanism. We find that the reaction proceeds in two steps. In a first step, catalyzed primarily by magnesium ion A and its ligands, a water molecule attacks the scissile phosphate. Consistent with thiol-substitution experiments, a water proton is transferred to the downstream phosphate group. The transient phosphorane formed as a result of this nucleophilic attack decays by breaking the bond between the phosphate and the ribose oxygen. In the resulting intermediate, the dissociated but unprotonated leaving group forms an alkoxide coordinated to magnesium ion B. In a second step, the reaction is completed by protonation of the leaving group, with a neutral Asp132 as a likely proton donor. The overall reaction barrier of ~15 kcal mol−1, encountered in the first step, together with the cost of protonating Asp132, is consistent with the slow measured rate of ~1–100/min. The two-step mechanism is also consistent with the bell-shaped pH dependence of the reaction rate. The non-monotonic relative motion of the magnesium ions along the reaction pathway agrees with X-ray crystal structures. Proton transfer reactions and changes in the metal ion coordination emerge as central factors in the RNA cleavage reaction. PMID:21539371

  9. On Ramachandran angles, closed strings and knots in protein structure

    Science.gov (United States)

    Chen, Si; Niemi, Antti J.

    2016-08-01

    The Ramachandran angles (φ,\\psi ) of a protein backbone form the vertices of a piecewise geodesic curve on the surface of a torus. When the ends of the curve are connected to each other similarly, by a geodesic, the result is a closed string that in general wraps around the torus a number of times both in the meridional and the longitudinal directions. The two wrapping numbers are global characteristics of the protein structure. A statistical analysis of the wrapping numbers in terms of crystallographic x-ray structures in the protein data bank (PDB) reveals that proteins have no net chirality in the ϕ direction but in the ψ direction, proteins prefer to display chirality. A comparison between the wrapping numbers and the concept of folding index discloses a non-linearity in their relationship. Thus these three integer valued invariants can be used in tandem, to scrutinize and classify the global loop structure of individual PDB proteins, in terms of the overall fold topology.

  10. Reduced Dimensionality (4,3)D-hnCOCANH Experiment: An Efficient Backbone Assignment tool for NMR studies of Proteins

    CERN Document Server

    Kumar, Dinesh

    2013-01-01

    Sequence specific resonance assignment and secondary structure determination of proteins form the basis for variety of structural and functional proteomics studies by NMR. In this context, an efficient standalone method for rapid assignment of backbone (1H, 15N, 13Ca and 13C') resonances and secondary structure determination of proteins has been presented here. Compared to currently available strategies used for the purpose, the method employs only a single reduced dimensionality (RD) experiment -(4,3)D-hnCOCANH and exploits the linear combinations of backbone (13Ca and 13C') chemical shifts to achieve a dispersion relatively better compared to those of individual chemical shifts (see the text) for efficient and rapid data analysis. Further, the experiment leads to the spectrum with direct distinction of self (intra-residue) and sequential (inter-residue) carbon correlation peaks; these appear opposite in signs and therefore can easily be discriminated without using an additional complementary experiment. On ...

  11. Free vibration analysis of a robotic fish based on a continuous and non-uniform flexible backbone with distributed masses

    Science.gov (United States)

    Coral, W.; Rossi, C.; Curet, O. M.

    2015-12-01

    This paper presents a Differential Quadrature Element Method for free transverse vibration of a robotic fish based on a continuous and non-uniform flexible backbone with distributed masses (fish ribs). The proposed method is based on the theory of a Timoshenko cantilever beam. The effects of the masses (number, magnitude and position) on the value of natural frequencies are investigated. Governing equations, compatibility and boundary conditions are formulated according to the Differential Quadrature rules. The convergence, efficiency and accuracy are compared to other analytical solution proposed in the literature. Moreover, the proposed method has been validate against the physical prototype of a flexible fish backbone. The main advantages of this method, compared to the exact solutions available in the literature are twofold: first, smaller computational cost and second, it allows analysing the free vibration in beams whose section is an arbitrary function, which is normally difficult or even impossible with other analytical methods.

  12. Fluorous Peptide Nucleic Acids: PNA Analogues with Fluorine in Backbone (γ-CF2-apg-PNA) Enhance Cellular Uptake.

    Science.gov (United States)

    Ellipilli, Satheesh; Ganesh, Krishna N

    2015-09-18

    Fluorous PNA analogues possessing fluorine as inherent part of aminopropylglycine (apg) backbone (γ-CF2-apg PNA) have been synthesized and evaluated for biophysical and cell penetrating properties. These form duplexes of higher thermal stability with cRNA than cDNA, although destabilized compared to duplexes of standard aeg-PNA. Cellular uptake of the fluorinated γ-CF2-apg PNAs in NIH 3T3 and HeLa cells was 2-3-fold higher compared to that of nonfluorinated apg PNA, with NIH 3T3 cells showing better permeability compared to HeLa cells. The backbone fluorinated PNAs, which are first in this class, when combined with other chemical modifications may have potential for future PNA-based antisense agents. PMID:26322827

  13. A new default restraint library for the protein backbone in Phenix: a conformation-dependent geometry goes mainstream

    Science.gov (United States)

    Moriarty, Nigel W.; Tronrud, Dale E.; Adams, Paul D.; Karplus, P. Andrew

    2016-01-01

    Chemical restraints are a fundamental part of crystallographic protein structure refinement. In response to mounting evidence that conventional restraints have shortcomings, it has previously been documented that using backbone restraints that depend on the protein backbone conformation helps to address these shortcomings and improves the performance of refinements [Moriarty et al. (2014 ▸), FEBS J. 281, 4061–4071]. It is important that these improvements be made available to all in the protein crystallography community. Toward this end, a change in the default geometry library used by Phenix is described here. Tests are presented showing that this change will not generate increased numbers of outliers during validation, or deposition in the Protein Data Bank, during the transition period in which some validation tools still use the conventional restraint libraries. PMID:26894545

  14. Direct measurement of the correlated dynamics of the protein-backbone and proximal waters of hydration in mechanically strained elastin

    CERN Document Server

    Sun, Cheng; Huang, Jiaxin; Boutis, Gregory S

    2011-01-01

    We report on the direct measurement of the correlation times of the protein backbone carbons and proximal waters of hydration in mechanically strained elastin by nuclear magnetic resonance methods. The experimental data indicate a decrease in the correlation times of the carbonyl carbons as the strain on the biopolymer is increased. These observations are in good agreement with short 4ns molecular dynamics simulations of (VPGVG)3, a well studied mimetic peptide of elastin. The experimental results also indicate a reduction in the correlation time of proximal waters of hydration with increasing strain applied to the elastomer. A simple model is suggested that correlates the increase in the motion of proximal waters of hydration to the increase in frequency of libration of the protein backbone that develops with increasing strain. Together, the reduction in the protein entropy accompanied with the increase in entropy of the proximal waters of hydration with increasing strain, support the notion that the source ...

  15. Backbone dynamics of reduced plastocyanin from the cyanobacterium Anabaena variabilis: Regions involved in electron transfer have enhanced mobility

    DEFF Research Database (Denmark)

    Ma, L.X.; Hass, M.A.S.; Vierick, N.; Kristensen, S.M.; Ulstrup, Jens; Led, J.J.

    2003-01-01

    -free approach. The C-13 relaxation studies were performed using C-13 in natural abundance. Overall, it is found that the protein backbone is rigid. However, the regions that are important for the function of the protein show moderate mobility primarily on the microsecond to millisecond time scale. These regions...... are the "northern" hydrophobic site close to the metal site, the metal site itself, and the "eastern" face of the molecule. In particular, the mobility of the latter region is interesting in light of recent findings indicating that residues also on the eastern face of plastocyanins from prokaryotes...... are important for the function of the protein. The study also demonstrates that relaxation rates and NOEs of the C-13(alpha) nuclei of proteins are valuable supplements to the conventional N-15 relaxation measurements in studies of protein backbone dynamics....

  16. TRX-LOGOS - a graphical tool to demonstrate DNA information content dependent upon backbone dynamics in addition to base sequence

    OpenAIRE

    Fortin, Connor H.; Schulze, Katharina V.; Babbitt, Gregory A.

    2015-01-01

    Background It is now widely-accepted that DNA sequences defining DNA-protein interactions functionally depend upon local biophysical features of DNA backbone that are important in defining sites of binding interaction in the genome (e.g. DNA shape, charge and intrinsic dynamics). However, these physical features of DNA polymer are not directly apparent when analyzing and viewing Shannon information content calculated at single nucleobases in a traditional sequence logo plot. Thus, sequence lo...

  17. De novo backbone and sequence design of an idealized alpha/beta-barrel protein: Evidence of stable tertiary structure

    OpenAIRE

    Offredi, Fabrice; Dubail, Fabien; Kischel, Philippe; Sarinski, K.; Stern, A S; Van de Weerdt, Cécile; Hoch, J. C.; Prosperi, Christelle; François, Jean-Marie; Mayo, S. L.; Martial, Joseph

    2003-01-01

    We have designed, synthesized, and characterized a 216 amino acid residue sequence encoding a putative idealized alpha/beta-barrel protein. The design was elaborated in two steps. First, the idealized backbone was defined with geometric parameters representing our target fold: a central eight parallel-stranded beta-sheet surrounded by eight parallel alpha-helices, connected together with short structural turns on both sides of the barrel. An automated sequence selection algorithm, based on th...

  18. The topology and the emerging urban geographies of the Internet backbone and aviation networks in Europe: a comparative study

    OpenAIRE

    Emmanouil Tranos

    2011-01-01

    The objective of this paper is to compare the topology and the emerging urban geographies of two infrastructural networks across European cities: the international intercity Internet backbone and aviation networks. Both of them are facilitators of the knowledge economy and contribute to what was identified by Castells as the first layer of the space of flows, supporting the world city process. In order to compare them, network analysis methods and complex networks theory are employed. The res...

  19. Disorders of the cerebellopontine angle

    International Nuclear Information System (INIS)

    Disorders of the cerebellopontine angle may present by symptoms like vertigo, hearing problems, affection of the trigeminal or facial nerve. Ipsilateral ataxia and contralateral hemiparesis develop in case of a rather large tumor in this region and display an involvement of the cerebellum and/or brainstem. However, some of these typical symptoms are not recognized by the patient. Thus, in case of a suspicion of a disorder of the cerebellopontine angle the relevant functions have to be tested clinically. In addition, electrophysiology can confirm dysfunction of these cranial nerves. Mainstay of the therapy should be the treatment of the underlying cause. Nevertheless, not seldom it is necessary to treat symptoms like vertigo or facial pain. (orig.)

  20. Multi-angle compound imaging

    DEFF Research Database (Denmark)

    Jespersen, Søren Kragh; Wilhjelm, Jens Erik; Sillesen, Henrik

    1998-01-01

    This paper reports on a scanning technique, denoted multi-angle compound imaging (MACI), using spatial compounding. The MACI method also contains elements of frequency compounding, as the transmit frequency is lowered for the highest beam angles in order to reduce grating lobes. Compared to...... conventional B-mode imaging MACI offers better defined tissue boundaries and lower variance of the speckle pattern, resulting in an image with reduced random variations. Design and implementation of a compound imaging system is described, images of rubber tubes and porcine aorta are shown and effects on...... visualization are discussed. The speckle reduction is analyzed numerically and the results are found to be in excellent agreement with existing theory. An investigation of detectability of low-contrast lesions shows significant improvements compared to conventional imaging. Finally, possibilities for improving...

  1. Wide-angle electron detector

    International Nuclear Information System (INIS)

    The design, functioning, and main calibration, characteristics of a wide-angle detector, capable of recording electrons with energies >= 8 keV and insensitive to u.v. solar radiation are described. A description of the sensor (electron trap) and its electronics in the analog (DEGAFOC) and counting (DEGAFOI) modes is given. Examples of telemetry recordings, illustrating the operation of the detector are included. (Auth.)

  2. C alpha-C backbone fragmentation dominates in electron detachment dissociation of gas-phase polypeptide polyanions

    DEFF Research Database (Denmark)

    Silivra, Oleg A; Ivonin, Igor A; Haselmann, Kim F;

    2005-01-01

    Fragmentation of peptide polyanions by electron detachment dissociation (EDD) has been induced by electron irradiation of deprotonated polypeptides [M-nH](n-) with >10 eV electrons. EDD has been found to lead preferentially to a* and x fragment ions (C(alpha)-C backbone cleavage) arising from the...... dissociation of oxidized radical anions [M-nH]((n-1)-*. We demonstrate that C(alpha)-C cleavages, which are otherwise rarely observed in tandem mass spectrometry, can account for most of the backbone fragmentation, with even-electron x fragments dominating over radical a* ions. Ab initio calculations at the B3...... LYP level of theory with the 6-311+G(2 p,2 d)//6-31+G(d,p) basis set suggested a unidirectional mechanism for EDD (cleavage always N-terminal to the radical site), with a*, x formation being favored over a, x* fragmentation by 74.2 kJ mol(-1). Thus, backbone C(alpha)-C bonds N-terminal to proline...

  3. The Role of Backbone Hydrogen Bonds in the Transition State for Protein Folding of a PDZ Domain.

    Directory of Open Access Journals (Sweden)

    Søren W. Pedersen

    Full Text Available Backbone hydrogen bonds are important for the structure and stability of proteins. However, since conventional site-directed mutagenesis cannot be applied to perturb the backbone, the contribution of these hydrogen bonds in protein folding and stability has been assessed only for a very limited set of small proteins. We have here investigated effects of five amide-to-ester mutations in the backbone of a PDZ domain, a 90-residue globular protein domain, to probe the influence of hydrogen bonds in a β-sheet for folding and stability. The amide-to-ester mutation removes NH-mediated hydrogen bonds and destabilizes hydrogen bonds formed by the carbonyl oxygen. The overall stability of the PDZ domain generally decreased for all amide-to-ester mutants due to an increase in the unfolding rate constant. For this particular region of the PDZ domain, it is therefore clear that native hydrogen bonds are formed after crossing of the rate-limiting barrier for folding. Moreover, three of the five amide-to-ester mutants displayed an increase in the folding rate constant suggesting that the hydrogen bonds are involved in non-native interactions in the transition state for folding.

  4. Backbone Dynamics of Alamethicin Bound to Lipid Membranes: Spin-Echo Electron Paramagnetic Resonance of TOAC-Spin Labels

    Science.gov (United States)

    Bartucci, Rosa; Guzzi, Rita; De Zotti, Marta; Toniolo, Claudio; Sportelli, Luigi; Marsh, Derek

    2008-01-01

    Alamethicin F50/5 is a hydrophobic peptide that is devoid of charged residues and that induces voltage-dependent ion channels in lipid membranes. The peptide backbone is likely to be involved in the ion conduction pathway. Electron spin-echo spectroscopy of alamethicin F50/5 analogs in which a selected Aib residue (at position n = 1, 8, or 16) is replaced by the TOAC amino-acid spin label was used to study torsional dynamics of the peptide backbone in association with phosphatidylcholine bilayer membranes. Rapid librational motions of limited angular amplitude were observed at each of the three TOAC sites by recording echo-detected spectra as a function of echo delay time, 2τ. Simulation of the time-resolved spectra, combined with conventional EPR measurements of the librational amplitude, shows that torsional fluctuations of the peptide backbone take place on the subnanosecond to nanosecond timescale, with little temperature dependence. Associated fluctuations in polar fields from the peptide could facilitate ion permeation. PMID:18096632

  5. NAA-modified DNA oligonucleotides with zwitterionic backbones: stereoselective synthesis of A-T phosphoramidite building blocks.

    Science.gov (United States)

    Schmidtgall, Boris; Höbartner, Claudia; Ducho, Christian

    2015-01-01

    Modifications of the nucleic acid backbone are essential for the development of oligonucleotide-derived bioactive agents. The NAA-modification represents a novel artificial internucleotide linkage which enables the site-specific introduction of positive charges into the otherwise polyanionic backbone of DNA oligonucleotides. Following initial studies with the introduction of the NAA-linkage at T-T sites, it is now envisioned to prepare NAA-modified oligonucleotides bearing the modification at X-T motifs (X = A, C, G). We have therefore developed the efficient and stereoselective synthesis of NAA-linked 'dimeric' A-T phosphoramidite building blocks for automated DNA synthesis. Both the (S)- and the (R)-configured NAA-motifs were constructed with high diastereoselectivities to furnish two different phosphoramidite reagents, which were employed for the solid phase-supported automated synthesis of two NAA-modified DNA oligonucleotides. This represents a significant step to further establish the NAA-linkage as a useful addition to the existing 'toolbox' of backbone modifications for the design of bioactive oligonucleotide analogues. PMID:25670992

  6. Coupling Protein Side-Chain and Backbone Flexibility Improves the Re-design of Protein-Ligand Specificity.

    Directory of Open Access Journals (Sweden)

    Noah Ollikainen

    Full Text Available Interactions between small molecules and proteins play critical roles in regulating and facilitating diverse biological functions, yet our ability to accurately re-engineer the specificity of these interactions using computational approaches has been limited. One main difficulty, in addition to inaccuracies in energy functions, is the exquisite sensitivity of protein-ligand interactions to subtle conformational changes, coupled with the computational problem of sampling the large conformational search space of degrees of freedom of ligands, amino acid side chains, and the protein backbone. Here, we describe two benchmarks for evaluating the accuracy of computational approaches for re-engineering protein-ligand interactions: (i prediction of enzyme specificity altering mutations and (ii prediction of sequence tolerance in ligand binding sites. After finding that current state-of-the-art "fixed backbone" design methods perform poorly on these tests, we develop a new "coupled moves" design method in the program Rosetta that couples changes to protein sequence with alterations in both protein side-chain and protein backbone conformations, and allows for changes in ligand rigid-body and torsion degrees of freedom. We show significantly increased accuracy in both predicting ligand specificity altering mutations and binding site sequences. These methodological improvements should be useful for many applications of protein-ligand design. The approach also provides insights into the role of subtle conformational adjustments that enable functional changes not only in engineering applications but also in natural protein evolution.

  7. Generalised dihedral subalgebras from the Monster

    OpenAIRE

    Rehren, Felix

    2015-01-01

    The conjugacy classes of the Monster which occur in the McKay observation correspond to the isomorphism types of certain 2-generated subalgebras of the Griess algebra. Sakuma, Ivanov and others showed that these subalgebras match the classification of vertex algebras generated by two Ising conformal vectors, or of Majorana algebras generated by two axes. In both cases, the eigenvalues parametrising the theory are fixed to $\\alpha=\\frac14,\\beta=\\frac1{32}$. We generalise these parameters and t...

  8. Ocular Biometry in Angle Closure

    Directory of Open Access Journals (Sweden)

    Mohammad Reza Razeghinejad

    2013-01-01

    Full Text Available Purpose: To compare ocular biometric parameters in primary angle closure suspects (PACS, primary angle closure glaucoma (PACG and acute primary angle closure (APAC. Methods: This cross-sectional study was performed on 113 patients including 33 cases of PACS, 45 patients with PACG and 35 subjects with APAC. Central corneal thickness (CCT, axial length (AL, anterior chamber depth (ACD and lens thickness (LT were measured with an ultrasonic biometer. Lens-axial length factor (LAF, relative lens position, corrected ACD (CACD and corrected lens position were calculated. The parameters were measured bilaterally but only data from the right eyes were compared. In the APAC group, biometric parameters were also compared between affected and unaffected fellow eyes. Logistic regression analysis was performed to identify risk factors. Results: No statistically significant difference was observed in biometric parameters between PACS and PACG eyes, or between affected and fellow eyes in the APAC group (P>0.05 for all comparisons. However, eyes with APAC had thicker cornea (P=0.001, thicker lens (P<0.0001, shallower ACD (P=0.009, shallower CACD (P=0.003 and larger LAF (P<0.0001. Based on ROC curve analysis, lower ACD, and larger LT, LAF and CCT values were associated with APAC. In the APAC group, LAF (P<0.0001 and CCT (P=0.001 were significant risk factors. Conclusion: This study revealed no significant difference in biometric characteristics in eyes with PACS and PACG. However, larger LAF and CCT were predictive of APAC.

  9. Small angle scattering and polymers

    International Nuclear Information System (INIS)

    The determination of polymer structure is a problem of interest for both statistical physics and industrial applications. The average polymer structure is defined. Then, it is shown why small angle scattering, associated with isotopic substitution, is very well suited to the measurement of the chain conformation. The corresponding example is the old, but pedagogic, measurement of the chain form factor in the polymer melt. The powerful contrast variation method is illustrated by a recent determination of the concentration profile of a polymer interface. (author) 12 figs., 48 refs

  10. Opening Angles of Collapsar Jets

    OpenAIRE

    Mizuta, Akira; Ioka, Kunihito

    2013-01-01

    We investigate the jet propagation and breakout from the stellar progenitor for gamma-ray burst (GRB) collapsars by performing two-dimensional relativistic hydrodynamic simulations and analytical modeling. We find that the jet opening angle is given by $\\theta_j \\sim 1/5 \\Gamma_{0}$, and infer the initial Lorentz factor of the jet at the central engine, $\\Gamma_0$, is a few for existing observations of $\\theta_j$. The jet keeps the Lorentz factor low inside the star by converging cylindricall...

  11. Small angle scattering and polymers

    Energy Technology Data Exchange (ETDEWEB)

    Cotton, J.P. [Laboratoire Leon Brillouin (LLB) - Centre d`Etudes de Saclay, 91 - Gif-sur-Yvette (France)

    1996-12-31

    The determination of polymer structure is a problem of interest for both statistical physics and industrial applications. The average polymer structure is defined. Then, it is shown why small angle scattering, associated with isotopic substitution, is very well suited to the measurement of the chain conformation. The corresponding example is the old, but pedagogic, measurement of the chain form factor in the polymer melt. The powerful contrast variation method is illustrated by a recent determination of the concentration profile of a polymer interface. (author) 12 figs., 48 refs.

  12. (Z-N-{(E-10-[(2,6-Diisopropylphenylimino]-9,10-dihydrophenanthren-9-ylidene}-2,6-dimethylaniline

    Directory of Open Access Journals (Sweden)

    Haiying Liang

    2012-03-01

    Full Text Available The title compound, C34H34N2, adopts a Z,E configuration with respect to the N=C—C=N backbone, with an N—C—C—N torsion angle of 41.1 (4° The dihedral angle between the benzene rings in the 9,10-dihydrophenanthrene moiety is 18.0 (1°.

  13. SYNTHESIS OF BIMODAL POLYETHYLENE WITH UNSYMMETRICAL α-DIIMINE NICKEL COMPLEXES: INFLUENCE OF LIGAND BACKBONE AND UNSYM-SUBSTITUTED ANILINE MOIETY

    Institute of Scientific and Technical Information of China (English)

    Hai-yang Gao; Feng-shou Liu; Hai-bin Hu; Fang-ming Zhu; Qing Wu

    2013-01-01

    A series of unsymmetrical α-diimine nickel complexes with various backbones and substituted aniline moieties were synthesized and characterized.The crystallographic analysis of the nickel complexes confirmed the existence of mesoand rac-configuration in solid structure.Nickel complexes after activation by MAO were screened for ethylene polymerization to evaluate backbone substituent effect on synthesis of bimodal PE.Acenaphthyl nickel complex with planar backbone afforded a bimodal PE with a broad polydispersity,whereas camphyl nickel complex with rigid and bulky backbone afforded a monomodal PE with a narrow polydispersity.Steric effect of aniline moiety for acenaphthyl nickel complex was also examined,and bimodal PE with dominant high-molecular-weight fraction was obtained by modifying substituents on aniline moiety.

  14. Small-angle neutron-scattering experiments

    International Nuclear Information System (INIS)

    A brief introduction to small-angle scattering (SAS) is given. Initial results obtained using the AERE small-angle diffractometer are presented for four materials of interest: doped uranium dioxide, nitrided steel, graphite and alumina. (U.K.)

  15. The Complex Angle in Normed Spaces

    International Nuclear Information System (INIS)

    We consider a generalized angle in complex normed vector spaces. Its definition corresponds to the definition of the well known Euclidean angle in real inner product spaces. Not surprisingly it yields complex values as 'angles'. This 'angle' has some simple properties, which are known from the usual angle in real inner product spaces. But to do ordinary Euclidean geometry real angles are necessary. We show that even in a complex normed space there are many pure real valued 'angles'. The situation improves yet in inner product spaces. There we can use the known theory of orthogonal systems to find many pairs of vectors with real angles, and to do geometry which is based on the Greeks 2000 years ago

  16. An Angle Criterion for Riesz Bases

    DEFF Research Database (Denmark)

    Lindner, Alexander M; Bittner, B.

    We present a characterization of Riesz bases in terms ofthe angles between certain finite dimensional subspaces. Correlationsbetween the bounds of the Riesz basis and the size of the angles arederived....

  17. The qualitative criterion of transient angle stability

    OpenAIRE

    Lyu, R; Xue, Y.; Xue, F; Wu, Qiuwei; Yang, Guangya; Zhou, H; Ju, P.

    2015-01-01

    In almost all the literatures, the qualitative assessment of transient angle stability extracts the angle information of generators based on the swing curve. As the angle (or angle difference) of concern and the threshold value rely strongly on the engineering experience, the validity and robust of these criterions are weak. Based on the stability mechanism from the extended equal area criterion (EEAC) theory and combining with abundant simulations of real system, this paper analyzes the crit...

  18. Explicit angle structures for veering triangulations

    CERN Document Server

    Futer, David

    2010-01-01

    Agol recently introduced the notion of a veering triangulation, and showed that such triangulations naturally arise as layered triangulations of fibered hyperbolic 3-manifolds. We prove, by a constructive argument, that every veering triangulation admits positive angle structures, recovering a result of Hodgson, Rubinstein, Segerman, and Tillmann. Our construction leads to explicit lower bounds on the smallest angle in this positive angle structure, and to information about angled holonomy of the boundary tori.

  19. 30 CFR 56.19037 - Fleet angles.

    Science.gov (United States)

    2010-07-01

    ... 30 Mineral Resources 1 2010-07-01 2010-07-01 false Fleet angles. 56.19037 Section 56.19037 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF LABOR METAL AND NONMETAL MINE SAFETY AND... Sheaves § 56.19037 Fleet angles. Fleet angles on hoists installed after November 15, 1979, shall not...

  20. 30 CFR 57.19037 - Fleet angles.

    Science.gov (United States)

    2010-07-01

    ... 30 Mineral Resources 1 2010-07-01 2010-07-01 false Fleet angles. 57.19037 Section 57.19037 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF LABOR METAL AND NONMETAL MINE SAFETY AND... Sheaves § 57.19037 Fleet angles. Fleet angles on hoists installed after November 15, 1979, shall not...

  1. Protein side-chain resonance assignment and NOE assignment using RDC-defined backbones without TOCSY data

    Energy Technology Data Exchange (ETDEWEB)

    Zeng Jianyang [Duke University, Department of Computer Science (United States); Zhou Pei [Duke University Medical Center, Department of Biochemistry (United States); Donald, Bruce Randall [Duke University, Department of Computer Science (United States)

    2011-08-15

    One bottleneck in NMR structure determination lies in the laborious and time-consuming process of side-chain resonance and NOE assignments. Compared to the well-studied backbone resonance assignment problem, automated side-chain resonance and NOE assignments are relatively less explored. Most NOE assignment algorithms require nearly complete side-chain resonance assignments from a series of through-bond experiments such as HCCH-TOCSY or HCCCONH. Unfortunately, these TOCSY experiments perform poorly on large proteins. To overcome this deficiency, we present a novel algorithm, called Nasca (NOE Assignment and Side-Chain Assignment), to automate both side-chain resonance and NOE assignments and to perform high-resolution protein structure determination in the absence of any explicit through-bond experiment to facilitate side-chain resonance assignment, such as HCCH-TOCSY. After casting the assignment problem into a Markov Random Field (MRF), Nasca extends and applies combinatorial protein design algorithms to compute optimal assignments that best interpret the NMR data. The MRF captures the contact map information of the protein derived from NOESY spectra, exploits the backbone structural information determined by RDCs, and considers all possible side-chain rotamers. The complexity of the combinatorial search is reduced by using a dead-end elimination (DEE) algorithm, which prunes side-chain resonance assignments that are provably not part of the optimal solution. Then an A* search algorithm is employed to find a set of optimal side-chain resonance assignments that best fit the NMR data. These side-chain resonance assignments are then used to resolve the NOE assignment ambiguity and compute high-resolution protein structures. Tests on five proteins show that Nasca assigns resonances for more than 90% of side-chain protons, and achieves about 80% correct assignments. The final structures computed using the NOE distance restraints assigned by Nasca have backbone RMSD 0

  2. Synthesis of graft copolymers with 1,4-polybutadiene backbone and polar grafts by combination of ROP and ROMP

    OpenAIRE

    Leroux, Flavien

    2014-01-01

    The objective of this work was the preparation of graft copolymers with a poly(1,4-butadiene) backbone and a high density of polar grafts. We used a consecutive Ring-Opening Metathesis Polymerization (ROMP)/Ring-Opening Polymerization (ROP) route to prepare poly(1,4-butadiene)-g-polyesters from cyclobutenyl macromonomers bearing one or two polyester segment(s) derived from L-lactide (L-LA) or Ɛ-caprolactone (Ɛ-CL). Poly(L-lactide)s (PLLA) or poly(Ɛ-caprolactone)s (PCL) are important polymers ...

  3. Synthesis of graft polyrotaxane by simultaneous capping of backbone and grafting from rings of pseudo-polyrotaxane

    OpenAIRE

    Kazuaki Kato; Katsunari Inoue; Masabumi Kudo; Kohzo Ito

    2014-01-01

    Graft polyrotaxanes, with poly(ε-caprolactone) (PCL) graft chains on the ring components were synthesized by the simultaneous ring-opening polymerization of ε-caprolactone from both ends of the backbone polymer, an end-functionalized polyethylene glycol (PEG) and the formation of inclusion complexes with α-cyclodextrin (α-CD). PEG with multiple functional groups at each end was prepared by the condensation of PEG-amine and D-gluconic acid; the PEG derivative formed an inclusion complex with α...

  4. IMMUNOMODULATION OF SYNTHESIZED POLYMERS CONTAINING PHOSPHORUS IN THE BACKBONE —EFFECT ON THE PROLIFERATION OF LYMPHOCYTES

    Institute of Scientific and Technical Information of China (English)

    ZhuoRenxi; WangJun; 等

    1997-01-01

    The immunomodulation of several Charged synthetic polymers containing phosphorus in the backbone was studied in vitro through examining their inhibition or promotion effect on the proliferatioin of both T and B lymphocytes,It is found that polymers based on long chain alkyl ester of tyrosine exhibit immunomodulative activity.Negatively charged polymers show stimulative activity on LPS-induced B lymphocytes proliferation.Positively charged polymers exhibit inhibitory activity on both Con A-induced T lymphocytes and LPS-induced B lymplhyocytes proliferation.

  5. An Unusual Conformational Isomer of Verrucosidin Backbone from a Hydrothermal Vent Fungus, Penicillium sp. Y-50-10.

    Science.gov (United States)

    Pan, Chengqian; Shi, Yutong; Auckloo, Bibi Nazia; Chen, Xuegang; Chen, Chen-Tung Arthur; Tao, Xinyi; Wu, Bin

    2016-01-01

    A new verrucosidin derivative, methyl isoverrucosidinol (1), was isolated from the marine fungus Penicillium sp. Y-50-10, dwelling in sulfur rich sediment in the Kueishantao hydrothermal vents off Taiwan. The structure was established by spectroscopic means including HRMS and 2D-NMR spectroscopic analysis. The absolute configuration was defined mainly by comparison of quantum chemical TDDFT calculated and experimental ECD spectra. Among hitherto known compounds with a verrucosidine backbone isolated from natural resource, compound 1 represents the first example of a new conformational isomer of its skeleton, exhibiting antibiotic activity against Bacillus subtilis with MIC value 32 μg/mL. PMID:27548192

  6. An Unusual Conformational Isomer of Verrucosidin Backbone from a Hydrothermal Vent Fungus, Penicillium sp. Y-50-10

    Directory of Open Access Journals (Sweden)

    Chengqian Pan

    2016-08-01

    Full Text Available A new verrucosidin derivative, methyl isoverrucosidinol (1, was isolated from the marine fungus Penicillium sp. Y-50-10, dwelling in sulfur rich sediment in the Kueishantao hydrothermal vents off Taiwan. The structure was established by spectroscopic means including HRMS and 2D-NMR spectroscopic analysis. The absolute configuration was defined mainly by comparison of quantum chemical TDDFT calculated and experimental ECD spectra. Among hitherto known compounds with a verrucosidine backbone isolated from natural resource, compound 1 represents the first example of a new conformational isomer of its skeleton, exhibiting antibiotic activity against Bacillus subtilis with MIC value 32 μg/mL.

  7. The "Legislative Backbone" keeping the Institution upright? The Role of European Parliament Committees in the EU Policy-Making Process

    OpenAIRE

    Christine Neuhold

    2001-01-01

    Over the past five decades the European Parliament (EP) has moved from being a largely consultative assembly to being a genuine co-legislature. The growth in the EPs powers was accompanied by a revaluation of its Standing Committees. It is in these committees, the legislative backbone of the EP, that scrutiny of European Union (EU) legislation takes place. As in the US Congress the real work of the Parliament is done in its committees. They have become a key element in the EU policy-making pr...

  8. The Q-angle and sport

    DEFF Research Database (Denmark)

    Hahn, Thomas; Foldspang, Anders

    1997-01-01

    Quadriceps muscle contraction tends to straighten the Q angle. We expected that sports comprising a high amount of quadriceps training could be associated with low Q angles. The aim of the present study was to estimate the Q angle in athletes and to investigate its potential associations with par......Quadriceps muscle contraction tends to straighten the Q angle. We expected that sports comprising a high amount of quadriceps training could be associated with low Q angles. The aim of the present study was to estimate the Q angle in athletes and to investigate its potential associations...... with participation in sport. Three hundred and thirty-nine athletes had their Q angle measured. The mean of right-side Q angles was higher than left side, and the mean Q angle was higher in women than in men. The Q angle was positively associated with years of jogging, and negatively with years of soccer, swimming...... and sports participation at all. It is concluded that the use of Q angle measurements is questionable....

  9. Phi (Φ) and psi (Ψ) angles involved in malarial peptide bonds determine sterile protective immunity

    International Nuclear Information System (INIS)

    Highlights: ► Phi (Φ) and psi (Ψ) angles determine sterile protective immunity. ► Modified peptide’s tendency to assume a regular conformation related to a PPIIL. ► Structural modifications in mHABPs induce Ab and protective immunity. ► mHABP backbone atom’s interaction with HLA-DRβ1∗ is stabilised by H-bonds. -- Abstract: Modified HABP (mHABP) regions interacting with HLA-DRβ1∗ molecules have a more restricted conformation and/or sequence than other mHABPs which do not fit perfectly into their peptide binding regions (PBR) and do not induce an acceptable immune response due to the critical role of their Φ and Ψ torsion angles. These angle’s critical role was determined in such highly immunogenic, protection-inducing response against experimental malaria using the conformers (mHABPs) obtained by 1H-NMR and superimposed into HLA-DRβ1∗-like Aotus monkey molecules; their phi (Φ) and psi (Ψ) angles were measured and the H-bond formation between these molecules was evaluated. The aforementioned mHABP propensity to assume a regular conformation similar to a left-handed polyproline type II helix (PPIIL) led to suggesting that favouring these conformations according to their amino acid sequence would lead to high antibody titre production and sterile protective immunity induction against malaria, thereby adding new principles or rules for vaccine development, malaria being one of them.

  10. Evaluation of blotchy pigments in the anterior chamber angle as a sign of angle closure

    Directory of Open Access Journals (Sweden)

    Harsha L Rao

    2012-01-01

    Full Text Available Background: Blotchy pigments in the anterior chamber (AC angle are considered diagnostic of primary angle closure (PAC. But there are no reports either on the prevalence of blotchy pigments in AC angles or the validity of this sign. Aims: To determine the prevalence of blotchy pigments in AC angles and to evaluate their relationship with glaucomatous optic neuropathy (GON in eyes with occludable angles. Setting and Design: Cross-sectional, comparative study. Materials and Methods: Gonioscopy was performed in 1001 eyes of 526 subjects (245 eyes of 148 consecutive, occludable angle subjects and 756 eyes of 378 non-consecutive, open angle subjects, above 35 years of age. Quadrant-wise location of blotchy pigments was documented. Statistical Analysis: Odds of blotchy pigments in occludable angles against that in open angles were evaluated. Relationship of GON with blotchy pigments in occludable angle eyes was evaluated using a multivariate model. Results: Prevalence of blotchy pigments in occludable angles was 28.6% (95% CI, 22.9-34.3 and in open angles was 4.7% (95% CI, 3.2-6.3. Blotchy pigments were more frequently seen in inferior (16% and superior quadrants (15% of occludable angles, and inferior quadrant of open angles (4%. Odds of superior quadrant blotchy pigments in occludable angles were 33 times that in open angles. GON was seen in 107 occludable angle eyes. Blotchy pigments were not significantly associated with GON (odds ratio = 0.5; P = 0.1. Conclusions: Blotchy pigments were seen in 28.6% of occludable angle eyes and 4.7% of open angles eyes. Presence of blotchy pigments in the superior quadrant is more common in occludable angles. Presence of GON in occludable angle eyes was not associated with blotchy pigments.

  11. Synthesis of graft polyrotaxane by simultaneous capping of backbone and grafting from rings of pseudo-polyrotaxane

    Directory of Open Access Journals (Sweden)

    Kazuaki Kato

    2014-11-01

    Full Text Available Graft polyrotaxanes, with poly(ε-caprolactone (PCL graft chains on the ring components were synthesized by the simultaneous ring-opening polymerization of ε-caprolactone from both ends of the backbone polymer, an end-functionalized polyethylene glycol (PEG and the formation of inclusion complexes with α-cyclodextrin (α-CD. PEG with multiple functional groups at each end was prepared by the condensation of PEG-amine and D-gluconic acid; the PEG derivative formed an inclusion complex with α-CD. The polymerization of multiple hydroxy groups at the backbone ends resulted in a star-shaped end group, which served as a bulky capping group to prevent dethreading. In contrast, PEG with only one hydroxy group at each end did not produce polyrotaxanes, indicating that single PCL chains were too thin to confine α-CDs to the complex. In addition, the grafting polymerization proceeded properly only when robust hydrogen bonds formed between α-CDs were dissociated using a basic catalyst. Since the dissociation also induced dethreading, kinetic control of the polymerization and dissociation were crucial for producing graft polyrotaxanes. Consequently, this three-step reaction yielded graft polyrotaxanes in a good yield, demonstrating a significant simplification of the synthesis of graft polyrotaxanes.

  12. Vanishing amplitude of backbone dynamics causes a true protein dynamical transition: H2 NMR studies on perdeuterated C-phycocyanin

    Science.gov (United States)

    Kämpf, Kerstin; Kremmling, Beke; Vogel, Michael

    2014-03-01

    Using a combination of H2 nuclear magnetic resonance (NMR) methods, we study internal rotational dynamics of the perdeuterated protein C-phycocyanin (CPC) in dry and hydrated states over broad temperature and dynamic ranges with high angular resolution. Separating H2 NMR signals from methyl deuterons, we show that basically all backbone deuterons exhibit highly restricted motion occurring on time scales faster than microseconds. The amplitude of this motion increases when a hydration shell exists, while it decreases upon cooling and vanishes near 175 K. We conclude that the vanishing of the highly restricted motion marks a dynamical transition, which is independent of the time window and of a fundamental importance. This conclusion is supported by results from experimental and computational studies of the proteins myoglobin and elastin. In particular, we argue based on findings in molecular dynamics simulations that the behavior of the highly restricted motion of proteins at the dynamical transition resembles that of a characteristic secondary relaxation of liquids at the glass transition, namely the nearly constant loss. Furthermore, H2 NMR studies on perdeuterated CPC reveal that, in addition to highly restricted motion, small fractions of backbone segments exhibit weakly restricted dynamics when temperature and hydration are sufficiently high.

  13. Dynamics of ultraviolet-induced DNA lesions: Dewar formation guided by pre-tension induced by the backbone

    International Nuclear Information System (INIS)

    The photophysical and photochemical processes driving the formation of the ultraviolet (UV)-induced DNA Dewar lesion from the T(6-4)T dimer are investigated by time-resolved spectroscopy and quantum chemical modelling. Time-resolved absorption and emission spectroscopy in the UV revealed a biexponential decay of the electronically excited state (S1) with time constants in the 100 ps and 1 ns range. From the S1 state the system forms the Dewar lesion (proven by time-resolved infrared spectroscopy), the triplet state of the T(6-4)T dimer and the ground state of the original T(6-4)T dimer. The decay process from the excited singlet is activated and thus temperature dependent. Quantum chemical modelling is used to describe the reaction path via a minimum on the excited electronic potential energy surface in close proximity to a triplet state. The transition to the Dewar isomer competes with internal conversion and with triplet formation. Only if the backbone between the two thymines is closed, is the Dewar isomer formed with a significant yield. The simulations reveal that the tension built up by the backbone is required for guiding the reaction to the conical intersection leading to the Dewar isomer. (paper)

  14. Improved site-specific recombinase-based method to produce selectable marker- and vector-backbone-free transgenic cells

    Science.gov (United States)

    Yu, Yuan; Tong, Qi; Li, Zhongxia; Tian, Jinhai; Wang, Yizhi; Su, Feng; Wang, Yongsheng; Liu, Jun; Zhang, Yong

    2014-02-01

    PhiC31 integrase-mediated gene delivery has been extensively used in gene therapy and animal transgenesis. However, random integration events are observed in phiC31-mediated integration in different types of mammalian cells; as a result, the efficiencies of pseudo attP site integration and evaluation of site-specific integration are compromised. To improve this system, we used an attB-TK fusion gene as a negative selection marker, thereby eliminating random integration during phiC31-mediated transfection. We also excised the selection system and plasmid bacterial backbone by using two other site-specific recombinases, Cre and Dre. Thus, we generated clean transgenic bovine fetal fibroblast cells free of selectable marker and plasmid bacterial backbone. These clean cells were used as donor nuclei for somatic cell nuclear transfer (SCNT), indicating a similar developmental competence of SCNT embryos to that of non-transgenic cells. Therefore, the present gene delivery system facilitated the development of gene therapy and agricultural biotechnology.

  15. Quantitative analysis of backbone motion in proteins using MAS solid-state NMR spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Chevelkov, Veniamin; Fink, Uwe; Reif, Bernd [Leibniz-Forschungsinstitut fuer Molekulare Pharmakologie (FMP) (Germany)], E-mail: reif@fmp-berlin.de

    2009-09-15

    We present a comprehensive analysis of protein dynamics for a micro-crystallin protein in the solid-state. Experimental data include {sup 15}N T{sub 1} relaxation times measured at two different magnetic fields as well as {sup 1}H-{sup 15}N dipole, {sup 15}N CSA cross correlated relaxation rates which are sensitive to the spectral density function J(0) and are thus a measure of T{sub 2} in the solid-state. In addition, global order parameters are included from a {sup 1}H,{sup 15}N dipolar recoupling experiment. The data are analyzed within the framework of the extended model-free Clore-Lipari-Szabo theory. We find slow motional correlation times in the range of 5 and 150 ns. Assuming a wobbling in a cone motion, the amplitude of motion of the respective amide moiety is on the order of 10 deg. for the half-opening angle of the cone in most of the cases. The experiments are demonstrated using a perdeuterated sample of the chicken {alpha}-spectrin SH3 domain.

  16. Caustic graphene plasmons with Kelvin angle

    CERN Document Server

    Shi, Xihang; Gao, Fei; Xu, Hongyi; Yang, Zhaoju; Zhang, Baile

    2015-01-01

    A century-long argument made by Lord Kelvin that all swimming objects have an effective Mach number of 3, corresponding to the Kelvin angle of 19.5 degree for ship waves, has been recently challenged with the conclusion that the Kelvin angle should gradually transit to the Mach angle as the ship velocity increases. Here we show that a similar phenomenon can happen for graphene plasmons. By analyzing the caustic wave pattern of graphene plasmons stimulated by a swift charged particle moving uniformly above graphene, we show that at low velocities of the charged particle, the caustics of graphene plasmons form the Kelvin angle. At large velocities of the particle, the caustics disappear and the effective semi-angle of the wave pattern approaches the Mach angle. Our study introduces caustic wave theory to the field of graphene plasmonics, and reveals a novel physical picture of graphene plasmon excitation during electron energy-loss spectroscopy measurement.

  17. Treatment of Gram-negative pneumonia in the critical care setting: is the beta-lactam antibiotic backbone broken beyond repair?

    Science.gov (United States)

    Bassetti, Matteo; Welte, Tobias; Wunderink, Richard G

    2016-01-01

    Beta-lactam antibiotics form the backbone of treatment for Gram-negative pneumonia in mechanically ventilated patients in the intensive care unit. However, this beta-lactam antibiotic backbone is increasingly under pressure from emerging resistance across all geographical regions, and health-care professionals in many countries are rapidly running out of effective treatment options. Even in regions that currently have only low levels of resistance, the effects of globalization are likely to increase local pressures on the beta-lactam antibiotic backbone in the near future. Therefore, clinicians are increasingly faced with a difficult balancing act: the need to prescribe adequate and appropriate antibiotic therapy while reducing the emergence of resistance and the overuse of antibiotics. In this review, we explore the burden of Gram-negative pneumonia in the critical care setting and the pressure that antibiotic resistance places on current empiric therapy regimens (and the beta-lactam antibiotic backbone) in this patient population. New treatment approaches, such as systemic and inhaled antibiotic alternatives, are on the horizon and are likely to help tackle the rising levels of beta-lactam antibiotic resistance. In the meantime, it is imperative that the beta-lactam antibiotic backbone of currently available antibiotics be supported through stringent antibiotic stewardship programs. PMID:26821535

  18. OPTIMIZATION OF TILT ANGLE FOR PHOTOVOLTAIC ARRAY

    OpenAIRE

    Ashok Kumar; N.S.Thakur,; Rahul Makade,; Maneesh Kumar Shivhar

    2011-01-01

    The performance of a solar radiation conversion system is affected by its tilt angle with the horizontal plane, thus photovoltaic array need to be tilted at the correct angle to maximize the performance of the System, This paper deals with the determination of optimum tilt angle for solar PV array in order to maximize incident solar irradiance. The model starts by calculating the monthly averaged daily solar irradiation components (direct, diffuse, ground- eflected) absorbed by the solar PV a...

  19. Backbone dynamics of free barnase and its complex with barstar determined by 15N NMR relaxation study.

    Science.gov (United States)

    Sahu, S C; Bhuyan, A K; Udgaonkar, J B; Hosur, R V

    2000-10-01

    Backbone dynamics of uniformly 15N-labeled free barnase and its complex with unlabelled barstar have been studied at 40 degrees C, pH 6.6, using 15N relaxation data obtained from proton-detected 2D [1H]-15N NMR spectroscopy. 15N spin-lattice relaxation rate constants (R1), spin-spin relaxation rate constants (R2), and steady-state heteronuclear [1H]-15N NOEs have been measured at a magnetic field strength of 14.1 Tesla for 91 residues of free barnase and for 90 residues out of a total of 106 in the complex (excluding three prolines and the N-terminal residue) backbone amide 15N sites of barnase. The primary relaxation data for both the cases have been analyzed in the framework of the model-free formalism using both isotropic and axially symmetric models of the rotational diffusion tensor. As per the latter, the overall rotational correlation times (tau(m)) are 5.0 and 9.5 ns for the free and complexed barnase, respectively. The average order parameter is found to be 0.80 for free barnase and 0.86 for the complex. However, the changes are not uniform along the backbone and for about 5 residues near the binding interface there is actually a significant decrease in the order parameters on complex formation. These residues are not involved in the actual binding. For the residues where the order parameter increases, the magnitudes vary significantly. It is observed that the complex has much less internal mobility, compared to free barnase. From the changes in the order parameters, the entropic contribution of NH bond vector motion to the free energy of complex formation has been calculated. It is apparent that these motion's cause significant unfavorable contributions and therefore must be compensated by many other favorable contributions to effect tight complex formation. The observed variations in the motion and their different locations with regard to the binding interface may have important implications for remote effects and regulation of the enzyme action. PMID

  20. Backbone dynamics of free barnase and its complex with barstar determined by 15N NMR relaxation study

    International Nuclear Information System (INIS)

    Backbone dynamics of uniformly 15N-labeled free barnase and its complex with unlabelled barstar have been studied at 40 deg. C, pH 6.6, using 15N relaxation data obtained from proton-detected 2D {1H}-15N NMR spectroscopy. 15N spin-lattice relaxation rate constants (R1), spin-spin relaxation rate constants (R2), and steady-state heteronuclear {1H}-15N NOEs have been measured at a magnetic field strength of 14.1 Tesla for 91 residues of free barnase and for 90 residues out of a total of 106 in the complex (excluding three prolines and the N-terminal residue) backbone amide 15N sites of barnase. The primary relaxation data for both the cases have been analyzed in the framework of the model-free formalism using both isotropic and axially symmetric models of the rotational diffusion tensor. As per the latter, the overall rotational correlation times (τm) are 5.0 and 9.5 ns for the free and complexed barnase, respectively. The average order parameter is found to be 0.80 for free barnase and 0.86 for the complex. However, the changes are not uniform along the backbone and for about 5 residues near the binding interface there is actually a significant decrease in the order parameters on complex formation. These residues are not involved in the actual binding. For the residues where the order parameter increases, the magnitudes vary significantly. It is observed that the complex has much less internal mobility, compared to free barnase. From the changes in the order parameters, the entropic contribution of NH bond vector motion to the free energy of complex formation has been calculated. It is apparent that these motions cause significant unfavorable contributions and therefore must be compensated by many other favorable contributions to effect tight complex formation. The observed variations in the motion and their different locations with regard to the binding interface may have important implications for remote effects and regulation of the enzyme action

  1. Backbone dynamics of free barnase and its complex with barstar determined by 15N NMR relaxation study

    Energy Technology Data Exchange (ETDEWEB)

    Sahu, Sarata C. [Tata Institute of Fundamental Research, Department of Chemical Sciences (India); Bhuyan, Abani K.; Udgaonkar, Jayant B. [University of Agricultural Sciences (UAS), National Centre for Biological Sciences, Tata Institute of Fundamental Research (India); Hosur, R.V. [Tata Institute of Fundamental Research, Department of Chemical Sciences (India)

    2000-10-15

    Backbone dynamics of uniformly {sup 15}N-labeled free barnase and its complex with unlabelled barstar have been studied at 40 deg. C, pH 6.6, using {sup 15}N relaxation data obtained from proton-detected 2D {l_brace}{sup 1}H{r_brace}-{sup 15}N NMR spectroscopy. {sup 15}N spin-lattice relaxation rate constants (R{sub 1}), spin-spin relaxation rate constants (R{sub 2}), and steady-state heteronuclear {l_brace}{sup 1}H{r_brace}-{sup 15}N NOEs have been measured at a magnetic field strength of 14.1 Tesla for 91 residues of free barnase and for 90 residues out of a total of 106 in the complex (excluding three prolines and the N-terminal residue) backbone amide {sup 15}N sites of barnase. The primary relaxation data for both the cases have been analyzed in the framework of the model-free formalism using both isotropic and axially symmetric models of the rotational diffusion tensor. As per the latter, the overall rotational correlation times ({tau}{sub m}) are 5.0 and 9.5 ns for the free and complexed barnase, respectively. The average order parameter is found to be 0.80 for free barnase and 0.86 for the complex. However, the changes are not uniform along the backbone and for about 5 residues near the binding interface there is actually a significant decrease in the order parameters on complex formation. These residues are not involved in the actual binding. For the residues where the order parameter increases, the magnitudes vary significantly. It is observed that the complex has much less internal mobility, compared to free barnase. From the changes in the order parameters, the entropic contribution of NH bond vector motion to the free energy of complex formation has been calculated. It is apparent that these motions cause significant unfavorable contributions and therefore must be compensated by many other favorable contributions to effect tight complex formation. The observed variations in the motion and their different locations with regard to the binding interface

  2. Behavior of Tilted Angle Shear Connectors.

    Directory of Open Access Journals (Sweden)

    Koosha Khorramian

    Full Text Available According to recent researches, angle shear connectors are appropriate to transfer longitudinal shear forces across the steel-concrete interface. Angle steel profile has been used in different positions as L-shaped or C-shaped shear connectors. The application of angle shear connectors in tilted positions is of interest in this study. This study investigates the behaviour of tilted-shaped angle shear connectors under monotonic loading using experimental push out tests. Eight push-out specimens are tested to investigate the effects of different angle parameters on the ultimate load capacity of connectors. Two different tilted angles of 112.5 and 135 degrees between the angle leg and steel beam are considered. In addition, angle sizes and lengths are varied. Two different failure modes were observed consisting of concrete crushing-splitting and connector fracture. By increasing the size of connector, the maximum load increased for most cases. In general, the 135 degrees tilted angle shear connectors have a higher strength and stiffness than the 112.5 degrees type.

  3. Pitch angle of galactic spiral arms

    International Nuclear Information System (INIS)

    One of the key parameters that characterizes spiral arms in disk galaxies is a pitch angle that measures the inclination of a spiral arm to the direction of galactic rotation. The pitch angle differs from galaxy to galaxy, which suggests that the rotation law of galactic disks determines it. In order to investigate the relation between the pitch angle of spiral arms and the shear rate of galactic differential rotation, we perform local N-body simulations of pure stellar disks. We find that the pitch angle increases with the epicycle frequency and decreases with the shear rate and obtain the fitting formula. This dependence is explained by the swing amplification mechanism.

  4. Best Angle to Orient Two Intersecting Lines

    Energy Technology Data Exchange (ETDEWEB)

    Awwal, A S; Ferguson, S W; Shull, P B

    2006-07-25

    Fiducials in the form of intersecting straight lines are used to align the target in the final target chamber of the National Ignition Facility of Lawrence Livermore National Laboratory. One of the techniques used to locate these lines is the Hough transform. When two lines intersect at a 90 degree angle, it is tempting to orient the lines to horizontal and vertical directions. There are other possible angles at which the lines may be oriented. One question that arises while designing the fiducials is whether there is a preferred angle or range of angles that leads to higher accuracy. This work attempts to answer this question through detailed computer simulation.

  5. Lateral angle and cranial base sexual dimorphism

    DEFF Research Database (Denmark)

    Duquesnel Mana, Mathilde; Adalian, Pascal; Lynnerup, Niels

    2016-01-01

    , to examine sexual dimorphism in the relationship between the lateral angle and cranial base shape. The lateral angle method was tested using a forensic sample of 102 CT scans of the head with known sex. We measured the angle using two methods: measurements directly on the CT slide, the method usually...... major overlap between the female and male shapes. In the light of the observed results, we confirm the lack of accuracy reported when using the lateral angle method to determine sex and we hypothesise that it may be explained by a lack of sexual dimorphism of the cranial base in terms of shape....

  6. The qualitative criterion of transient angle stability

    DEFF Research Database (Denmark)

    Lyu, R.; Xue, Y.; Xue, F.;

    2015-01-01

    In almost all the literatures, the qualitative assessment of transient angle stability extracts the angle information of generators based on the swing curve. As the angle (or angle difference) of concern and the threshold value rely strongly on the engineering experience, the validity and robust of...... these criterions are weak. Based on the stability mechanism from the extended equal area criterion (EEAC) theory and combining with abundant simulations of real system, this paper analyzes the criterions in most literatures and finds that the results could be too conservative or too optimistic. It is...

  7. Thermoresponsive Poly(2-oxazoline) Molecular Brushes by Living Ionic Polymerization: Kinetic Investigations of Pendant Chain Grafting and Cloud Point Modulation by Backbone and Side Chain Length Variation

    KAUST Repository

    Zhang, Ning

    2012-04-17

    Molecular brushes of poly(2-oxazoline)s were prepared by living anionic polymerization of 2-iso-propenyl-2-oxazoline to form the backbone and subsequent living cationic ring-opening polymerization of 2-n- or 2-iso-propyl-2-oxazoline for pendant chain grafting. In situ kinetic studies indicate that the initiation efficiency and polymerization rates are independent from the number of initiator functions per initiator molecule. This was attributed to the high efficiency of oxazolinium salt and the stretched conformation of the backbone, which is caused by the electrostatic repulsion of the oxazolinium moieties along the macroinitiator. The resulting molecular brushes showed thermoresponsive properties, that is, having a defined cloud point (CP). The dependence of the CP as a function of backbone and side chain length as well as concentration was studied. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. Synthesis and Characterization of New Polyimide Containing Calix[4]arenes in the Polymer Backbone with Transport Ability

    Institute of Scientific and Technical Information of China (English)

    LI Lei; XIAN Chun-ying; ZHENG Li-min

    2008-01-01

    New polyimide containing cvalix[4]arene moieties on the polymer backbone was successfully synthesized in N-methyl-2-pyrrolidone(NMP) by polycondensations of 3,3', 4, 4'- oxydiphthalic anhydride (ODPA) with the diaminocalix[4]arene monomer using 3,3'-dimethyl-4, 4'-diaminodiphenylmethane(DADPM) as a third comononmer.The polyimide prepared is soluble in common solvents, such as NMP, DMAc, DMF and chloroform. The polyimide films obtained have excellent thermal stability and mechanical property. At the same time, the liquid membrane transport of potassimn ions by the new polyimide was investigated, which testified that compared to ODPA-DADPM polyimide, the polyimide containing calix[4] arenes has the transport ability to metal ions in regard to bulky, cone-like calix [4] arene moieties.

  9. Backbone structure of Yersinia pestis Ail determined in micelles by NMR-restrained simulated annealing with implicit membrane solvation

    Energy Technology Data Exchange (ETDEWEB)

    Marassi, Francesca M., E-mail: fmarassi@sbmri.org; Ding, Yi [Sanford-Burnham Medical Research Institute (United States); Schwieters, Charles D. [National Institutes of Health, Division of Computational Bioscience, Center for Information Technology (United States); Tian, Ye; Yao, Yong [Sanford-Burnham Medical Research Institute (United States)

    2015-09-15

    The outer membrane protein Ail (attachment invasion locus) is a virulence factor of Yersinia pestis that mediates cell invasion, cell attachment and complement resistance. Here we describe its three-dimensional backbone structure determined in decyl-phosphocholine (DePC) micelles by NMR spectroscopy. The NMR structure was calculated using the membrane function of the implicit solvation potential, eefxPot, which we have developed to facilitate NMR structure calculations in a physically realistic environment. We show that the eefxPot force field guides the protein towards its native fold. The resulting structures provide information about the membrane-embedded global position of Ail, and have higher accuracy, higher precision and improved conformational properties, compared to the structures calculated with the standard repulsive potential.

  10. Backbone and stereospecific (13)C methyl Ile (δ1), Leu and Val side-chain chemical shift assignments of Crc.

    Science.gov (United States)

    Sharma, Rakhi; Sahu, Bhubanananda; Ray, Malay K; Deshmukh, Mandar V

    2015-04-01

    Carbon catabolite repression (CCR) allows bacteria to selectively assimilate a preferred compound among a mixture of several potential carbon sources, thus boosting growth and economizing the cost of adaptability to variable nutrients in the environment. The RNA-binding catabolite repression control (Crc) protein acts as a global post-transcriptional regulator of CCR in Pseudomonas species. Crc triggers repression by inhibiting the expression of genes involved in transport and catabolism of non-preferred substrates, thus indirectly favoring assimilation of preferred one. We report here a nearly complete backbone and stereospecific (13)C methyl side-chain chemical shift assignments of Ile (δ1), Leu and Val of Crc (~ 31 kDa) from Pseudomonas syringae Lz4W. PMID:24496608

  11. Poly(meta-phenylene) Derivative with Rigid Twisted Biphenyl Units in Backbone: Synthesis, Structural Characterization,Photophysical Properties and Electroluminescence

    Institute of Scientific and Technical Information of China (English)

    ZHENG Yan; YANG Bing; ZHANG Hai-quan; LU Ping; SHEN Fang-zhong; LIU Lin-lin; XU Hai; YANG Guang-di; MA Yu-guang

    2007-01-01

    A soluble poly(meta-phenylene) derivative with rigid twisted biphenyl unit was synthesized by the Yamamoto coupling reaction. The polymer is soluble in common organic solvents, and the number-average molecular weight is about 6500. The UV-Vis and quantum chemical calculation indicate that the different conformation segments named "conformers" exist in the polymer backbones; it was also further confirmed by the single crystal X-ray diffraction study of the dimeric model compound. The π-π* transition of biphenyl segments of twisted and planar conformations made the polymer exhibit a strong absorption around 256 nm and a weak absorption at about 300 nm. Furthermore,the polymer exhibits a strong UV photoluminescence at 372 nm when the excitation wavelengths are longer than 300 nm. The ultraviolet-emitting electroluminescence(EL) device with the single layer structure shows EL λmax of the derivative at 370 nm.

  12. Backbone structure of Yersinia pestis Ail determined in micelles by NMR-restrained simulated annealing with implicit membrane solvation

    International Nuclear Information System (INIS)

    The outer membrane protein Ail (attachment invasion locus) is a virulence factor of Yersinia pestis that mediates cell invasion, cell attachment and complement resistance. Here we describe its three-dimensional backbone structure determined in decyl-phosphocholine (DePC) micelles by NMR spectroscopy. The NMR structure was calculated using the membrane function of the implicit solvation potential, eefxPot, which we have developed to facilitate NMR structure calculations in a physically realistic environment. We show that the eefxPot force field guides the protein towards its native fold. The resulting structures provide information about the membrane-embedded global position of Ail, and have higher accuracy, higher precision and improved conformational properties, compared to the structures calculated with the standard repulsive potential

  13. Binary Assembly of Au Nanoparticles with Controllable Two-dimensional Architecture Directed by Phosphate Backbone Modified Oligonucleotide

    Institute of Scientific and Technical Information of China (English)

    MA,Yu-Dan; GUO,Yi; LI,Jun; YANG,Wen-Sheng

    2008-01-01

    A three complementary strand oligonucleotide system was employed to assemble two different-sized,15 and 25 nm,Au nanoparticles into binary two-dimensional (2D) structures.First,two non-complementary strands of phosphate backbone modified oligonucleotides (PM oligo-DNA) were loaded on the surface of the 15 and 25 nm Au nanoparticles,respectively.Upon the addition of the third linker DNA,which was half complementary to each of the modified DNA,the An nanoparticles would be assembled to binary 2D aggregates.The number of the 15 nm Au nanoparticles around a 25 nm Au naoparticle can be readily controlled by the length of the DNA helix used.

  14. Ultrafast vibrational dynamics of the DNA backbone at different hydration levels mapped by two-dimensional infrared spectroscopy.

    Science.gov (United States)

    Guchhait, Biswajit; Liu, Yingliang; Siebert, Torsten; Elsaesser, Thomas

    2016-07-01

    DNA oligomers are studied at 0% and 92% relative humidity, corresponding to N  20 water molecules per base pair. Two-dimensional (2D) infrared spectroscopy of DNA backbone modes between 920 and 1120 cm(-1) maps fluctuating interactions at the DNA surface. At both hydration levels, a frequency fluctuation correlation function with a 300 fs decay and a slow decay beyond 10 ps is derived from the 2D lineshapes. The fast component reflects motions of DNA helix, counterions, and water shell. Its higher amplitude at high hydration level reveals a significant contribution of water to the fluctuating forces. The slow component reflects disorder-induced inhomogeneous broadening. PMID:26798841

  15. Photoleucine Survives Backbone Cleavage by Electron Transfer Dissociation. A Near-UV Photodissociation and Infrared Multiphoton Dissociation Action Spectroscopy Study

    Science.gov (United States)

    Shaffer, Christopher J.; Martens, Jonathan; Marek, Aleš; Oomens, Jos; Tureček, František

    2016-07-01

    We report a combined experimental and computational study aimed at elucidating the structure of N-terminal fragment ions of the c type produced by electron transfer dissociation of photo-leucine (L*) peptide ions GL*GGKX. The c 4 ion from GL*GGK is found to retain an intact diazirine ring that undergoes selective photodissociation at 355 nm, followed by backbone cleavage. Infrared multiphoton dissociation action spectra point to the absence in the c 4 ion of a diazoalkane group that could be produced by thermal isomerization of vibrationally hot ions. The c 4 ion from ETD of GL*GGK is assigned an amide structure by a close match of the IRMPD action spectrum and calculated IR absorption. The energetics and kinetics of c 4 ion dissociations are discussed.

  16. Electric myographic control of electric therapeutic apparatus -ceragem master cgm 3500 influence on backbone of patients with scoliosis

    Directory of Open Access Journals (Sweden)

    Kupreenko M. V.

    2015-09-01

    Full Text Available Purpose: determination of effectiveness of electric therapeutic apparatus Ceragem master CGM 3500 in its influence on backbone of patients with scoliosis. Material: in examination 11 female patients with scoliosis of age from 21 to 35 years and 12 practically healthy persons participated. The research of para-vertebral muscles of back was fulfilled with method of electric myography. Results: we determined positive effect in nervous-muscular functioning of back. The proof was increase of integrated amplitude of back muscles’ electric activity on convex and concave sides of scolytinae arc; increase of maximal amplitude of H-reflex and M-response. Conclusions: standard electric myography permits to receive objective information about functional state of muscles of patients with scoliosis and assess effectiveness of rehabilitation process with application of electric therapeutic apparatus - - Ceragem Master CGM 3500.

  17. Backbone cyclised peptides from plants show molluscicidal activity against the rice pest Pomacea canaliculata (golden apple snail).

    Science.gov (United States)

    Plan, Manuel Rey R; Saska, Ivana; Cagauan, Arsenia G; Craik, David J

    2008-07-01

    Golden apple snails ( Pomacea canaliculata) are serious pests of rice in South East Asia. Cyclotides are backbone cyclized peptides produced by plants from Rubiaceae and Violaceae. In this study, we investigated the molluscicidal activity of cyclotides against golden apple snails. Crude cyclotide extracts from both Oldenlandia affinis and Viola odorata plants showed molluscicidal activity comparable to the synthetic molluscicide metaldehyde. Individual cyclotides from each extract demonstrated a range of molluscicidal activities. The cyclotides cycloviolacin O1, kalata B1, and kalata B2 were more toxic to golden apple snails than metaldehyde, while kalata B7 and kalata B8 did not cause significant mortality. The toxicity of the cyclotide kalata B2 on a nontarget species, the Nile tilapia ( Oreochromis niloticus), was three times lower than the common piscicide rotenone. Our findings suggest that the existing diversity of cyclotides in plants could be used to develop natural molluscicides. PMID:18557620

  18. General order parameter based correlation analysis of protein backbone motions between experimental NMR relaxation measurements and molecular dynamics simulations

    International Nuclear Information System (INIS)

    Internal backbone dynamic motions are essential for different protein functions and occur on a wide range of time scales, from femtoseconds to seconds. Molecular dynamic (MD) simulations and nuclear magnetic resonance (NMR) spin relaxation measurements are valuable tools to gain access to fast (nanosecond) internal motions. However, there exist few reports on correlation analysis between MD and NMR relaxation data. Here, backbone relaxation measurements of 15N-labeled SH3 (Src homology 3) domain proteins in aqueous buffer were used to generate general order parameters (S2) using a model-free approach. Simultaneously, 80 ns MD simulations of SH3 domain proteins in a defined hydrated box at neutral pH were conducted and the general order parameters (S2) were derived from the MD trajectory. Correlation analysis using the Gromos force field indicated that S2 values from NMR relaxation measurements and MD simulations were significantly different. MD simulations were performed on models with different charge states for three histidine residues, and with different water models, which were SPC (simple point charge) water model and SPC/E (extended simple point charge) water model. S2 parameters from MD simulations with charges for all three histidines and with the SPC/E water model correlated well with S2 calculated from the experimental NMR relaxation measurements, in a site-specific manner. - Highlights: • Correlation analysis between NMR relaxation measurements and MD simulations. • General order parameter (S2) as common reference between the two methods. • Different protein dynamics with different Histidine charge states in neutral pH. • Different protein dynamics with different water models

  19. Lactobacillus rhamnosus accelerates zebrafish backbone calcification and gonadal differentiation through effects on the GnRH and IGF systems.

    Directory of Open Access Journals (Sweden)

    Matteo A Avella

    Full Text Available Endogenous microbiota play essential roles in the host's immune system, physiology, reproduction and nutrient metabolism. We hypothesized that a continuous administration of an exogenous probiotic might also influence the host's development. Thus, we treated zebrafish from birth to sexual maturation (2-months treatment with Lactobacillus rhamnosus, a probiotic species intended for human use. We monitored for the presence of L. rhamnosus during the entire treatment. Zebrafish at 6 days post fertilization (dpf exhibited elevated gene expression levels for Insulin-like growth factors -I and -II, Peroxisome proliferator activated receptors -α and -β, VDR-α and RAR-γ when compared to untreated-10 days old zebrafish. Using a gonadotropin-releasing hormone 3 GFP transgenic zebrafish (GnRH3-GFP, higher GnRH3 expression was found at 6, 8 and 10 dpf upon L. rhamnosus treatment. The same larvae exhibited earlier backbone calcification and gonad maturation. Noteworthy in the gonad development was the presence of first testes differentiation at 3 weeks post fertilization in the treated zebrafish population -which normally occurs at 8 weeks- and a dramatic sex ratio modulation (93% females, 7% males in control vs. 55% females, 45% males in the treated group. We infer that administration of L. rhamnosus stimulated the IGF system, leading to a faster backbone calcification. Moreover we hypothesize a role for administration of L. rhamnosus on GnRH3 modulation during early larval development, which in turn affects gonadal development and sex differentiation. These findings suggest a significant role of the microbiota composition on the host organism development profile and open new perspectives in the study of probiotics usage and application.

  20. The backbone of the post-synaptic density originated in a unicellular ancestor of choanoflagellates and metazoans

    Directory of Open Access Journals (Sweden)

    Manuel Michaël

    2010-02-01

    Full Text Available Abstract Background Comparative genomics of the early diverging metazoan lineages and of their unicellular sister-groups opens new window to reconstructing the genetic changes which preceded or accompanied the evolution of multicellular body plans. A recent analysis found that the genome of the nerve-less sponges encodes the homologues of most vertebrate post-synaptic proteins. In vertebrate excitatory synapses, these proteins assemble to form the post-synaptic density, a complex molecular platform linking membrane receptors, components of their signalling pathways, and the cytoskeleton. Newly available genomes from Monosiga brevicollis (a member of Choanoflagellata, the closest unicellular relatives of animals and Trichoplax adhaerens (a member of Placozoa: besides sponges, the only nerve-less metazoans offer an opportunity to refine our understanding of post-synaptic protein evolution. Results Searches for orthologous proteins and reconstruction of gene gains/losses based on the taxon phylogeny indicate that post-synaptic proteins originated in two main steps. The backbone scaffold proteins (Shank, Homer, DLG and some of their partners were acquired in a unicellular ancestor of choanoflagellates and metazoans. A substantial additional set appeared in an exclusive ancestor of the Metazoa. The placozoan genome contains most post-synaptic genes but lacks some of them. Notably, the master-scaffold protein Shank might have been lost secondarily in the placozoan lineage. Conclusions The time of origination of most post-synaptic proteins was not concomitant with the acquisition of synapses or neural-like cells. The backbone of the scaffold emerged in a unicellular context and was probably not involved in cell-cell communication. Based on the reconstructed protein composition and potential interactions, its ancestral function could have been to link calcium signalling and cytoskeleton regulation. The complex later became integrated into the evolving

  1. General order parameter based correlation analysis of protein backbone motions between experimental NMR relaxation measurements and molecular dynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Qing; Shi, Chaowei [Hefei National Laboratory for Physical Sciences at The Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026 (China); Yu, Lu [Hefei National Laboratory for Physical Sciences at The Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026 (China); High Magnetic Field Laboratory, Chinese Academy of Science, Hefei, Anhui, 230031 (China); Zhang, Longhua [Hefei National Laboratory for Physical Sciences at The Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026 (China); Xiong, Ying, E-mail: yxiong73@ustc.edu.cn [Hefei National Laboratory for Physical Sciences at The Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026 (China); Tian, Changlin, E-mail: cltian@ustc.edu.cn [Hefei National Laboratory for Physical Sciences at The Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026 (China); High Magnetic Field Laboratory, Chinese Academy of Science, Hefei, Anhui, 230031 (China)

    2015-02-13

    Internal backbone dynamic motions are essential for different protein functions and occur on a wide range of time scales, from femtoseconds to seconds. Molecular dynamic (MD) simulations and nuclear magnetic resonance (NMR) spin relaxation measurements are valuable tools to gain access to fast (nanosecond) internal motions. However, there exist few reports on correlation analysis between MD and NMR relaxation data. Here, backbone relaxation measurements of {sup 15}N-labeled SH3 (Src homology 3) domain proteins in aqueous buffer were used to generate general order parameters (S{sup 2}) using a model-free approach. Simultaneously, 80 ns MD simulations of SH3 domain proteins in a defined hydrated box at neutral pH were conducted and the general order parameters (S{sup 2}) were derived from the MD trajectory. Correlation analysis using the Gromos force field indicated that S{sup 2} values from NMR relaxation measurements and MD simulations were significantly different. MD simulations were performed on models with different charge states for three histidine residues, and with different water models, which were SPC (simple point charge) water model and SPC/E (extended simple point charge) water model. S{sup 2} parameters from MD simulations with charges for all three histidines and with the SPC/E water model correlated well with S{sup 2} calculated from the experimental NMR relaxation measurements, in a site-specific manner. - Highlights: • Correlation analysis between NMR relaxation measurements and MD simulations. • General order parameter (S{sup 2}) as common reference between the two methods. • Different protein dynamics with different Histidine charge states in neutral pH. • Different protein dynamics with different water models.

  2. Marburg virus VP35 can both fully coat the backbone and cap the ends of dsRNA for interferon antagonism.

    Directory of Open Access Journals (Sweden)

    Shridhar Bale

    2012-09-01

    Full Text Available Filoviruses, including Marburg virus (MARV and Ebola virus (EBOV, cause fatal hemorrhagic fever in humans and non-human primates. All filoviruses encode a unique multi-functional protein termed VP35. The C-terminal double-stranded (dsRNA-binding domain (RBD of VP35 has been implicated in interferon antagonism and immune evasion. Crystal structures of the VP35 RBD from two ebolaviruses have previously demonstrated that the viral protein caps the ends of dsRNA. However, it is not yet understood how the expanses of dsRNA backbone, between the ends, are masked from immune surveillance during filovirus infection. Here, we report the crystal structure of MARV VP35 RBD bound to dsRNA. In the crystal structure, molecules of dsRNA stack end-to-end to form a pseudo-continuous oligonucleotide. This oligonucleotide is continuously and completely coated along its sugar-phosphate backbone by the MARV VP35 RBD. Analysis of dsRNA binding by dot-blot and isothermal titration calorimetry reveals that multiple copies of MARV VP35 RBD can indeed bind the dsRNA sugar-phosphate backbone in a cooperative manner in solution. Further, MARV VP35 RBD can also cap the ends of the dsRNA in solution, although this arrangement was not captured in crystals. Together, these studies suggest that MARV VP35 can both coat the backbone and cap the ends, and that for MARV, coating of the dsRNA backbone may be an essential mechanism by which dsRNA is masked from backbone-sensing immune surveillance molecules.

  3. Controlled Conjugated Backbone Twisting for an Increased Open-Circuit Voltage while Having a High Short-Circuit Current in Poly(hexylthiophene) Derivatives

    KAUST Repository

    Ko, Sangwon

    2012-03-21

    Conjugated polymers with nearly planar backbones have been the most commonly investigated materials for organic-based electronic devices. More twisted polymer backbones have been shown to achieve larger open-circuit voltages in solar cells, though with decreased short-circuit current densities. We systematically impose twists within a family of poly(hexylthiophene)s and examine their influence on the performance of polymer:fullerene bulk heterojunction (BHJ) solar cells. A simple chemical modification concerning the number and placement of alkyl side chains along the conjugated backbone is used to control the degree of backbone twisting. Density functional theory calculations were carried out on a series of oligothiophene structures to provide insights on how the sterically induced twisting influences the geometric, electronic, and optical properties. Grazing incidence X-ray scattering measurements were performed to investigate how the thin-film packing structure was affected. The open-circuit voltage and charge-transfer state energy of the polymer:fullerene BHJ solar cells increased substantially with the degree of twist induced within the conjugated backbone-due to an increase in the polymer ionization potential-while the short-circuit current decreased as a result of a larger optical gap and lower hole mobility. A controlled, moderate degree of twist along the poly(3,4-dihexyl-2,2′:5′,2′′- terthiophene) (PDHTT) conjugated backbone led to a 19% enhancement in the open-circuit voltage (0.735 V) vs poly(3-hexylthiophene)-based devices, while similar short-circuit current densities, fill factors, and hole-carrier mobilities were maintained. These factors resulted in a power conversion efficiency of 4.2% for a PDHTT:[6,6]-phenyl-C 71-butyric acid methyl ester (PC 71BM) blend solar cell without thermal annealing. This simple approach reveals a molecular design avenue to increase open-circuit voltage while retaining the short-circuit current. © 2012 American

  4. Small solid angle device setup and application

    International Nuclear Information System (INIS)

    To quantize the weight of Uranium-plate accurately, the small solid angle device was redesigned. To fit the requirement of homogeneity check, the sliding base was introduced in the design. This paper presents the detailed application of small solid angle device setup and quantization of Uranium-plate and homogeneity check. (authors)

  5. Distribution of angles in hyperbolic lattices

    DEFF Research Database (Denmark)

    Risager, Morten Skarsholm; Truelsen, Jimi Lee

    2010-01-01

    We prove an effective equidistribution result about angles in a hyperbolic lattice. We use this to generalize a result from the study by Boca.......We prove an effective equidistribution result about angles in a hyperbolic lattice. We use this to generalize a result from the study by Boca....

  6. Distribution of Angles in Hyperbolic Lattices

    DEFF Research Database (Denmark)

    S. Risager, Morten; L. Truelsen, Jimi

    2008-01-01

    We prove an effective equidistribution result about angles in a hyperbolic lattice. We use this to generalize a result due to F. P. Boca.......We prove an effective equidistribution result about angles in a hyperbolic lattice. We use this to generalize a result due to F. P. Boca....

  7. Backbone dynamics of a biologically active human FGF-1 monomer, complexed to a hexasaccharide heparin-analogue, by {sup 15}N NMR relaxation methods

    Energy Technology Data Exchange (ETDEWEB)

    Canales-Mayordomo, Angeles; Fayos, Rosa [Centro de Investigaciones Biologicas, CSIC, Departamento de Estructura y Funcion de Proteinas (Spain); Angulo, Jesus; Ojeda, Rafael [Instituto de Investigaciones Quimicas, CSIC, Grupo de Carbohidratos (Spain); Martin-Pastor, Manuel [Unidad de RM y Unidad de RMN de Biomoleculas Asociada al CSIC, Laboratorio de Estructura e Estructura de Biomoleculas Jose Carracido (Spain); Nieto, Pedro M.; Martin-Lomas, Manuel [Instituto de Investigaciones Quimicas, CSIC, Grupo de Carbohidratos (Spain); Lozano, Rosa; Gimenez-Gallego, Guillermo; Jimenez-Barbero, Jesus [Centro de Investigaciones Biologicas, CSIC, Departamento de Estructura y Funcion de Proteinas (Spain)], E-mail: jjbarbero@cib.csic.es

    2006-08-15

    The binding site and backbone dynamics of a bioactive complex formed by the acidic fibroblast growth factor (FGF-1) and a specifically designed heparin hexasaccharide has been investigated by HSQC and relaxation NMR methods. The comparison of the relaxation data for the free and bound states has allowed showing that the complex is monomeric, and still induces mutagenesis, and that the protein backbone presents reduced motion in different timescale in its bound state, except in certain points that are involved in the interaction with the fibroblast growth factor receptor (FGFR)

  8. Differentiable, multi-dimensional, knowledge-based energy terms for torsion angle probabilities and propensities.

    Science.gov (United States)

    Amir, El-Ad David; Kalisman, Nir; Keasar, Chen

    2008-07-01

    Rotatable torsion angles are the major degrees of freedom in proteins. Adjacent angles are highly correlated and energy terms that rely on these correlations are intensively used in molecular modeling. However, the utility of torsion based terms is not yet fully exploited. Many of these terms do not capture the full scale of the correlations. Other terms, which rely on lookup tables, cannot be used in the context of force-driven algorithms because they are not fully differentiable. This study aims to extend the usability of torsion terms by presenting a set of high-dimensional and fully-differentiable energy terms that are derived from high-resolution structures. The set includes terms that describe backbone conformational probabilities and propensities, side-chain rotamer probabilities, and an elaborate term that couples all the torsion angles within the same residue. The terms are constructed by cubic spline interpolation with periodic boundary conditions that enable full differentiability and high computational efficiency. We show that the spline implementation does not compromise the accuracy of the original database statistics. We further show that the side-chain relevant terms are compatible with established rotamer probabilities. Despite their very local characteristics, the new terms are often able to identify native and native-like structures within decoy sets. Finally, force-based minimization of NMR structures with the new terms improves their torsion angle statistics with minor structural distortion (0.5 A RMSD on average). The new terms are freely available in the MESHI molecular modeling package. The spline coefficients are also available as a documented MATLAB file. PMID:18186478

  9. Phi ({Phi}) and psi ({Psi}) angles involved in malarial peptide bonds determine sterile protective immunity

    Energy Technology Data Exchange (ETDEWEB)

    Patarroyo, Manuel E., E-mail: mepatarr@gmail.com [Fundacion Instituto de Inmunologia de Colombia (FIDIC), Bogota (Colombia); Universidad Nacional de Colombia, Bogota (Colombia); Moreno-Vranich, Armando; Bermudez, Adriana [Fundacion Instituto de Inmunologia de Colombia (FIDIC), Bogota (Colombia)

    2012-12-07

    Highlights: Black-Right-Pointing-Pointer Phi ({Phi}) and psi ({Psi}) angles determine sterile protective immunity. Black-Right-Pointing-Pointer Modified peptide's tendency to assume a regular conformation related to a PPII{sub L}. Black-Right-Pointing-Pointer Structural modifications in mHABPs induce Ab and protective immunity. Black-Right-Pointing-Pointer mHABP backbone atom's interaction with HLA-DR{beta}1{sup Asterisk-Operator} is stabilised by H-bonds. -- Abstract: Modified HABP (mHABP) regions interacting with HLA-DR{beta}1{sup Asterisk-Operator} molecules have a more restricted conformation and/or sequence than other mHABPs which do not fit perfectly into their peptide binding regions (PBR) and do not induce an acceptable immune response due to the critical role of their {Phi} and {Psi} torsion angles. These angle's critical role was determined in such highly immunogenic, protection-inducing response against experimental malaria using the conformers (mHABPs) obtained by {sup 1}H-NMR and superimposed into HLA-DR{beta}1{sup Asterisk-Operator }-like Aotus monkey molecules; their phi ({Phi}) and psi ({Psi}) angles were measured and the H-bond formation between these molecules was evaluated. The aforementioned mHABP propensity to assume a regular conformation similar to a left-handed polyproline type II helix (PPII{sub L}) led to suggesting that favouring these conformations according to their amino acid sequence would lead to high antibody titre production and sterile protective immunity induction against malaria, thereby adding new principles or rules for vaccine development, malaria being one of them.

  10. A lattice determination of gA and left angle x right angle from overlap fermions

    International Nuclear Information System (INIS)

    We present results for the nucleon's axial charge gA and the first moment left angle x right angle of the unpolarized parton distribution function from a simulation of quenched overlap fermions. (orig.)

  11. Apparent Contact Angle and Contact Angle Hysteresis on Liquid Infused Surfaces

    OpenAIRE

    Semprebon, Ciro; McHale, Glen; Kusumaatmaja, Halim

    2016-01-01

    We theoretically investigate the apparent contact angle and contact angle hysteresis of a droplet placed on a liquid infused surface. We show that the apparent contact angle is not uniquely defined by material parameters, but also has a strong dependence on the relative size between the droplet and its surrounding wetting ridge formed by the infusing liquid. We derive a closed form expression for the contact angle in the limit of vanishing wetting ridge, and compute the correction for small b...

  12. Nonadiabatic Hannay's Angle of Spin One Half in Grassmannian Version and Invariant Angle Coherent States

    OpenAIRE

    Cherbal, Omar; Maamache, Mustapha; Drir, Mahrez

    2003-01-01

    We propose to determinate the nonadiabatic Hannay’s angle of spin one half in a varying external magnetic field, by using an averaged version of the variational principal. We also show how the evolution and this nonadiabatic Hannay’s angle is associated with the evolution of Grassmannian invariant-angle coherent states.

  13. Analysis of factors affecting angle ANB.

    Science.gov (United States)

    Hussels, W; Nanda, R S

    1984-05-01

    Cephalometric analyses based on angular and linear measurements have obvious fallacies, which have been discussed in detail by Moyers and Bookstein. However, the clinical application of such an analysis by the orthodontic profession in treatment planning is widely accepted. Variations of angle ANB are commonly used to determine relative jaw relationships in most of the cephalometric evaluations. Several authors, including points A and B influences angle ANB, as does rotational growth of the upper and lower jaws. In addition, the authors point out that growth in a vertical direction (distance N to B) and an increase of the dental height (distance A to B) may contribute to changes in angle ANB. For a Class I relation (Wits = 0 mm), a mathematical formula has been developed which enables the authors to study the geometric influence of angle ANB caused by the following four effects: (1) rotation of the jaws and/or occlusal plane relative to the anterior cranial base; (2) anteroposterior position of N relative to point B, (3) vertical growth (distance N to B); (4) increase in dental height (distance A to B). It was observed that, contrary to the common belief that an ANB angle of 2 +/- 3.0 degrees is considered normal for a skeletal Class I relation, the calculated values of angle ANB will vary widely with changes in these four controlling factors under the same skeletal Class I conditions (Wits = 0 mm). Therefore, in a case under consideration, angle ANB must be corrected for these geometric effects in order to get a proper perspective of the skeletal discrepancy. This is facilitated by comparing the measured ANB angle with the corresponding ANB angle calculated by a formula for a Class I relationship. The corresponding calculated angle ANB can be taken from the tables which are based upon the formula using the same values for SNB, omega (angle between occlusal plane and anterior cranial base), b (which is distance N to B) and a (dental height measured as perpendicular

  14. A molecular mechanical model to predict the helix twist angles of B-DNA.

    Science.gov (United States)

    Tung, C S; Harvey, S C

    1984-04-11

    We present here a model for the prediction of helix twist angles in B-DNA, a model composed of a collection of torsional springs. Statistically averaged conformational energy calculations show that, for a specified basepair step, the basepair-basepair conformational energy is quadratically dependent on the helix twist angle, so the calculations provide the spring parameters for the basepair-basepair interactions. Torsional springs can also be used to model the effects of the backbone on the helix twist, and the parameters for those springs are derived by fitting the model to experimental data. The model predicts a macroscopic torsional stiffness and a longitudinal compressibility (Young's modulus) which are both in good agreement with experiment. One biological consequence of the model is examined, the sequence specificity of the Eco RI restriction endonuclease, and it is shown that the discriminatory power of the enzyme receives a substantial contribution from the energetic cost of torsional deformations of the DNA when wrong sequences are forced into the enzyme binding site. PMID:6326059

  15. Qualitative criterion for atom sputtering angle distributions

    International Nuclear Information System (INIS)

    A model is introduced to explain the shape of atom polar emission angle distributions for monocomponent targets sputtered by normally incident keV - energy ions. Analytical expressions are obtained from the model which make it possible to identify three known kinds of the angle distributions - subcosinus, isotropic and supracosinus, for given ion energies and target-ion pairs. Furthermore the fourth, hybrid false-isotropic distribution is found, which is superposition of supracosinus and subcosinus distributions. The theoretical predictions of the angle distributions shape agree with the numerical modeling for sputtering of carbon and platinum by 0.1-10 keV Ar+ ions

  16. The Driven Pendulum at Any Drive Angle

    CERN Document Server

    VanDalen, G J

    2002-01-01

    The driven inverted pendulum undergoes stable oscillations if the drive amplitude and frequency are large enough. This classroom demonstration is best used in junior or graduate level Classical Mechanics courses. This paper reintroduces the equation of motion of the driven pendulum, generalizing to arbitrary driving angle. The pendulum will oscillate about a stable angle, other than straight down, if the drive amplitude and frequency are large enough for a given drive angle. We will explore what is meant by ``large enough.'' Emphasis is given to parameters associated with a simply made demonstration apparatus.

  17. Compression failure of angle-ply laminates

    OpenAIRE

    Peel, Larry D

    1991-01-01

    The present work deals with modes and mechanisms of failure in compression of angleply laminates. Experimental results were obtained from 42 angle-ply IM7/8551-7a specimens with a lay-up of [ (±9) / (=F9)] 6s where 9, the off-axis angle, ranged from 0° to 90°. The results showed four failure modes, these modes being a function of off-axis angle. Failure modes include fiber compression, inplane transverse tension, inplane shear, and inplane transverse compression. Excessive inte...

  18. A statistically derived parameterization for the collagen triple-helix

    OpenAIRE

    Rainey, Jan K.; Goh, M. Cynthia

    2002-01-01

    The triple-helix is a unique secondary structural motif found primarily within the collagens. In collagen, it is a homo- or hetero-tripeptide with a repeating primary sequence of (Gly-X-Y)n, displaying characteristic peptide backbone dihedral angles. Studies of bulk collagen fibrils indicate that the triple-helix must be a highly repetitive secondary structure, with very specific constraints. Primary sequence analysis shows that most collagen molecules are primarily triple-helical; however, n...

  19. Live virus vaccines based on a yellow fever vaccine backbone: Standardized template with key considerations for a risk/benefit assessment

    OpenAIRE

    Monath, Thomas P.; Seligman, Stephen J.; Robertson, James S; Guy, Bruno; Hayes, Edward B.; Condit, Richard C.; Excler, Jean Louis; Mac, Lisa Marie; Carbery, Baevin; Chen, Robert T.

    2014-01-01

    The Brighton Collaboration Viral Vector Vaccines Safety Working Group (V3SWG) was formed to evaluate the safety of live, recombinant viral vaccines incorporating genes from heterologous viruses inserted into the backbone of another virus (so-called "chimeric virus vaccines"). Many viral vector vaccines are in advanced clinical trials. The first such vaccine to be approved for mark...

  20. Backbone and sidechain 1H, 15N and 13C assignments of Tyrosine Phosphatase related to Biofilm formation A (TpbA) of Pseudomonas aeruginosa

    OpenAIRE

    Koveal, Dorothy; Jayasundera, Thusitha B.; Wood, Thomas K.; Peti, Wolfgang; Page, Rebecca

    2012-01-01

    The backbone and side chain resonance assignments of the Tyrosine Phosphatase related to Biofilm formation A (TpbA) of Pseudomonas aeruginosa have been determined based on triple-resonance experiments using uniformly [13C,15N]-labeled protein. This assignment is the first step towards the determination of the 3-dimensional structure of TpbA.

  1. Organocatalytic and enantioselective Michael reaction between α-nitroesters and nitroalkenes. Syn/anti-selectivity control using catalysts with the same absolute backbone chirality.

    Science.gov (United States)

    Martínez, Jose I; Uria, Uxue; Muñiz, Maria; Reyes, Efraím; Carrillo, Luisa; Vicario, Jose L

    2015-01-01

    The asymmetric and catalytic Michael reaction between α-nitroesters and nitroalkenes has been studied in the presence of two bifunctional catalysts both containing the same absolute chirality at the carbon backbone. The reaction performed in similar conditions allows us to control the syn or anti selectivity of the Michael adduct obtaining good yields and high enantiocontrol in all cases. PMID:26734103

  2. Peptide backbone orientation and dynamics in spider dragline silk and two-photon excitation in nuclear magnetic and quadrupole resonance

    International Nuclear Information System (INIS)

    In the first part of the dissertation, spider dragline silk is studied by solid state NMR techniques. The dependence of NMR frequency on molecular orientation is exploited using the DECODER experiment to determine the orientation of the protein backbone within the silk fibre. Practical experimental considerations require that the silk fibres be wound about a cylindrical axis perpendicular to the external magnetic field, complicating the reconstruction of the underlying orientation distribution and necessitating the development of numerical techniques for this purpose. A two-component model of silk incorporating static b-sheets and polyglycine II helices adequately fits the NMR data and suggests that the b-sheets are well aligned along the silk axis (20 FWHM) while the helices are poorly aligned (68 FWHM). The effects of fibre strain, draw rate and hydration on orientation are measured. Measurements of the time-scale for peptide backbone motion indicate that when wet, a strain-dependent fraction of the poorly aligned component becomes mobile. This suggests a mechanism for the supercontraction of silk involving latent entropic springs that undergo a local strain-dependent phase transition, driving supercontraction. In the second part of this dissertation a novel method is developed for exciting NMR and nuclear quadrupole resonance (NQR) by rf irradiation at multiple frequencies that sum to (or differ by) the resonance frequency. This is fundamentally different than traditional NMR experiments where irradiation is applied on-resonance. With excitation outside the detection bandwidth, two-photon excitation allows for detection of free induction signals during excitation, completely eliminating receiver dead-time. A theoretical approach to describing two-photon excitation is developed based on average Hamiltonian theory. An intuition for two-photon excitation is gained by analogy to the coherent absorption of multiple photons requiring conservation of total energy and

  3. Effects of ion binding on the backbone dynamics of calbindin D9k determined by 15N NMR relaxation.

    Science.gov (United States)

    Akke, M; Skelton, N J; Kördel, J; Palmer, A G; Chazin, W J

    1993-09-21

    The backbone dynamics of apo- and (Cd2+)1-calbindin D9k have been characterized by 15N nuclear magnetic resonance spectroscopy. Spin-lattice and spin-spin relaxation rate constants and steady-state [1H]-15N nuclear Overhauser effects were measured at a magnetic field strength of 11.74 T by two-dimensional, proton-detected heteronuclear NMR experiments using 15N-enriched samples. The relaxation parameters were analyzed using a model-free formalism that characterizes the dynamics of the N-H bond vectors in terms of generalized order parameters and effective correlation times. The data for the apo and (Cd2+)1 states were compared to those for the (Ca2+)2 state [Kördel, J., Skelton, N. J., Akke, M., Palmer, A. G., & Chazin, W. J. (1992) Biochemistry 31, 4856-4866] to ascertain the effects on ion ligation on the backbone dynamics of calbindin D9k. The two binding loops respond differently to ligation by metal ions: high-frequency (10(9)-10(12) s-1) fluctuations of the N-terminal ion-binding loop are not affected by ion binding, whereas residues G57, D58, G59, and E60 in the C-terminal ion-binding loop have significantly lower order parameters in the apo state than in the metal-bound states. The dynamical responses of the four helices to binding of ions are much smaller than that for the C-terminal binding loop, with the strongest effect on helix III, which is located between the linker loop and binding site II. Significant fluctuations on slower time scales also were detected in the unoccupied N-terminal ion-binding loop of the apo and (Cd2+)1 states; the apparent rates were greater for the (Cd2+)1 state. These results on the dynamical response to ion binding in calbindin D9k provide insights into the molecular details of the binding process and qualitative evidence for entropic contributions to the cooperative phenomenon of calcium binding for the pathway in which the ion binds first in the C-terminal site. PMID:8373781

  4. Ducted turbine theory with right angled ducts

    International Nuclear Information System (INIS)

    This paper describes the use of an inviscid approach to model a ducted turbine – also known as a diffuser augmented turbine – and a comparison of results with a particular one-dimensional theory. The aim of the investigation was to gain a better understanding of the relationship between a real duct and the ideal diffuser, which is a concept that is developed in the theory. A range of right angled ducts, which have a rim for a 90° exit angle, were modelled. As a result, the performance of right angled ducts has been characterised in inviscid flow. It was concluded that right angled ducts cannot match the performance of their associated ideal diffuser and that the optimum rotor loading for these turbines varies with the duct dimensions

  5. The solid angle through the vertical rectangle

    Science.gov (United States)

    Schröer, H.

    We want to determine the solid angle through the vertical rectangle. We use the cosine law for sides and the spherical law of sines. The relation to luminous flux (radiant flux or radiant power) is shown.

  6. The solid angle through the isosceles triangle

    Science.gov (United States)

    Schröer, H.

    We want to determine the solid angle through the isosceles triangle. We use the cosine law for sides and the spherical law of sines. The relation to luminous flux(radiant flux or radiant power) is shown.

  7. The solid angle through the inclined rectangle

    Science.gov (United States)

    Schröer, H.

    We want to determine the solid angle through the inclined rectangle. We use the cosine law for sides and the spherical law of sines. The relation to luminous flux(radiant flux or radiant power) is shown.

  8. Optical fibre angle sensor used in MEMS

    International Nuclear Information System (INIS)

    There is a need for displacement and angle measurements in many movable MEMS structures. The use of fibre optical sensors helps to measure micrometre displacements and small rotation angles. Advantages of this type of transducers are their simple design, high precision of processing, low costs and ability of a non-contact measurement. The study shows an analysis of a fibre-optic intensity sensor used for MEMS movable structure rotation angle measurement. An intensity of the light in the photodetector is basically dependent on a distance between a reflecting surface and a head surface of the fibre transmitting arm, and the deflection angle. Experimental tests were made for PMMA 980/1000 plastic fibres, ΘNA=33°. The study shows both analytical and practical results. It proves that calculated and experimental characteristics for the analysed transducers are similar.

  9. EMERGENCE ANGLE OF FLOW OVER AN AERATOR

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Aerator is an important device for release works of hydraulic structures with high-speed flow in order to protect them from cavitation damage. This kind of protecting effect is related closely to cavity length below the aerator, while the cavity length is dominated by the emergence angle over the aerator. Therefore it is crucial to determine this angle accurately. In the present paper the affecting intensities of flow depth and the fluctuating velocity on this angle were analyzed through two introduced parameters. Furthermore, the improved expressions of emergence angle estimation, for both ramp-type and step-type aerators, were presented by means of 68 sets of experimental data from 6 projects based on error theory. The results showed that the present method has higher accuracy than the previously reported methods.

  10. Low angle X-ray scattering

    International Nuclear Information System (INIS)

    The theoretical and experimental problems appearing in diffraction experiments at very low angles by several kinds of materials are discussed. The importance of synchrotron radiation in such problems is shown. (L.C.)

  11. Angles between subspaces and their tangents

    OpenAIRE

    Zhu, Peizhen; Knyazev, Andrew V.

    2012-01-01

    Principal angles between subspaces (PABS) (also called canonical angles) serve as a classical tool in mathematics, statistics, and applications, e.g., data mining. Traditionally, PABS are introduced via their cosines. The cosines and sines of PABS are commonly defined using the singular value decomposition. We utilize the same idea for the tangents, i.e., explicitly construct matrices, such that their singular values are equal to the tangents of PABS, using several approaches: orthonormal and...

  12. Flipped Angles and Phases: A Systematic Study

    OpenAIRE

    Ellis, J.; Lopez, J; Nanopoulos, D.; Olive, K.

    1993-01-01

    We discuss systematically the fermion mass and mixing matrices in a generic \\linebreak field-theoretical flipped $SU(5)$ model, with particular applications to neutrino and baryon number-changing physics. We demonstrate that the different quark flavour branching ratios in proton decay are related to the Cabibbo-Kobayashi-Maskawa angles, whereas the lepton flavour branching ratios are undetermined. The light neutrino mixing angles observable via oscillation effects are related to the heavy con...

  13. Primary angle-closure glaucoma: an update.

    Science.gov (United States)

    Wright, Carrie; Tawfik, Mohammed A; Waisbourd, Michael; Katz, Leslie J

    2016-05-01

    Primary angle-closure glaucoma is potentially a devastating disease, responsible for half of glaucoma-related blindness worldwide. Angle closure is characterized by appositional approximation or contact between the iris and trabecular meshwork. It tends to develop in eyes with shallow anterior chambers, anteriorly positioned or pushed lenses, and angle crowding. Risk of primary angle-closure glaucoma is high among women, the elderly and the hyperopic, and it is most prevalent in Asia. Investigation into genetic mechanisms of glaucoma inheritance is underway. Diagnosis relies on gonioscopy and may be aided by anterior segment optical coherence tomography and ultrasound biomicroscopy. Treatment is designed to control intraocular pressure while monitoring changes to the angle and optic nerve head. Treatment typically begins with medical management through pressure-reducing topical medications. Peripheral iridotomy is often performed to alleviate pupillary block, while laser iridoplasty has been found effective for mechanisms of closure other than pupillary block, such as plateau iris syndrome. Phacoemulsification, with or without goniosynechialysis, both in eyes with existing cataracts and in those with clear lenses, is thus far a viable treatment alternative. Long-term research currently underway will examine its efficacy in cases of angle closure in early stages of the disease. Endoscopic cyclophotocoagulation is another treatment option, which can be combined with cataract surgery. Trabeculectomy remains effective therapy for more advanced cases. PMID:26119516

  14. Viewing angle analysis of integral imaging

    Science.gov (United States)

    Wang, Hong-Xia; Wu, Chun-Hong; Yang, Yang; Zhang, Lan

    2007-12-01

    Integral imaging (II) is a technique capable of displaying 3D images with continuous parallax in full natural color. It is becoming the most perspective technique in developing next generation three-dimensional TV (3DTV) and visualization field due to its outstanding advantages. However, most of conventional integral images are restricted by its narrow viewing angle. One reason is that the range in which a reconstructed integral image can be displayed with consistent parallax is limited. The other is that the aperture of system is finite. By far many methods , an integral imaging method to enhance the viewing angle of integral images has been proposed. Nevertheless, except Ren's MVW (Maximum Viewing Width) most of these methods involve complex hardware and modifications of optical system, which usually bring other disadvantages and make operation more difficult. At the same time the cost of these systems should be higher. In order to simplify optical systems, this paper systematically analyzes the viewing angle of traditional integral images instead of modified ones. Simultaneously for the sake of cost the research was based on computer generated integral images (CGII). With the analysis result we can know clearly how the viewing angle can be enhanced and how the image overlap or image flipping can be avoided. The result also promotes the development of optical instruments. Based on theoretical analysis, preliminary calculation was done to demonstrate how the other viewing properties which are closely related with the viewing angle, such as viewing distance, viewing zone, lens pitch, and etc. affect the viewing angle.

  15. NMR characterization of structure, backbone dynamics, and glutathione binding of the human macrophage migration inhibitory factor (MIF).

    Science.gov (United States)

    Mühlhahn, P; Bernhagen, J; Czisch, M; Georgescu, J; Renner, C; Ross, A; Bucala, R; Holak, T A

    1996-10-01

    Human macrophage migration inhibitory factor is a 114 amino acid protein that belongs to the family of immunologic cytokines. Assignments of 1H, 15N, and 13C resonances have enabled the determination of the secondary structure of the protein, which consists of two alpha-helices (residues 18-31 and 89-72) and a central four-stranded beta-sheet. In the beta-sheet, two parallel beta-sheets are connected in an antiparallel sense. From the total of three cysteines present in the primary structure of MIF, none was found to form disulfide bridges. 1H-15N heteronuclear T1, T2, and steady-state NOE measurements indicate that the backbone of MIF exists in a rigid structure of limited conformational flexibility (on the nanosecond to picosecond time scale). Several residues located in the loop regions and at the N termini of two helices exhibit internal motions on the 1-3 ns time scale. The capacity to bind glutathione was investigated by titration of a uniform 15N-labeled sample and led us to conclude that MIF has, at best, very low affinity for glutathione. PMID:8897610

  16. High resolution 4D HPCH experiment for sequential assignment of 13C-labeled RNAs via phosphodiester backbone

    International Nuclear Information System (INIS)

    The three-dimensional structure determination of RNAs by NMR spectroscopy requires sequential resonance assignment, often hampered by assignment ambiguities and limited dispersion of 1H and 13C chemical shifts, especially of C4′/H4′. Here we present a novel through-bond 4D HPCH NMR experiment involving phosphate backbone where C4′–H4′ correlations are resolved along the 1H3′–31P spectral planes. The experiment provides high peak resolution and effectively removes ambiguities encountered during assignments. Enhanced peak dispersion is provided by the inclusion of additional 31P and 1H3′ dimensions and constant-time evolution of chemical shifts. High spectral resolution is obtained by using non-uniform sampling in three indirect dimensions. The experiment fully utilizes the isotopic 13C-labeling with evolution of C4′ carbons. Band selective 13C inversion pulses are used to achieve selectivity and prevent signal dephasing due to the C4′–C3′ and C4′–C5′ homonuclear couplings. Multiple quantum line narrowing is employed to minimize sensitivity loses. The 4D HPCH experiment is verified and successfully applied to a non-coding 34-nt RNA consisting typical structure elements and a 14-nt RNA hairpin capped by cUUCGg tetraloop

  17. Dialkylaluminium-, -gallium-, and -indium-based poly-Lewis acids with a 1,8-diethynylanthracene backbone.

    Science.gov (United States)

    Chmiel, Jasmin; Neumann, Beate; Stammler, Hans-Georg; Mitzel, Norbert W

    2010-10-18

    Potential host systems based on a rigid 1,8-diethynylanthracendiyl backbone were synthesised by treatment of 1,8-diethynylanthracene with the Group 13 trialkyls AlMe(3), GaMe(3), InMe(3), AlEt(3) and GaEt(3). The resulting products were characterised by IR and multinuclear NMR spectroscopy, elemental analyses and determination of their crystal structures by X-ray diffraction. The compounds are dimeric in the solid state and comprise two M(2)C(2) heterocycles. Depending on the steric demand of the alkyl substituents at the metal atom, different types of binding modes were observed, which can be classified to lie between the ideals of side-on coordination with almost linear primary M-C≡C units and the 3c-2e coordination with symmetrically bridging alkynyl units in M-C-M bonds. As a solution in THF the dimers are broken into monomers and some are found to undergo ligand scrambling reactions. PMID:20827789

  18. Synthesis and in vitro antioxidant functions of protein hydrolysate from backbones of Rastrelliger kanagurta by proteolytic enzymes.

    Science.gov (United States)

    Sheriff, Sheik Abdulazeez; Sundaram, Balasubramanian; Ramamoorthy, Baranitharan; Ponnusamy, Ponmurugan

    2014-01-01

    Every year, a huge quantity of fishery wastes and by-products are generated by fish processing industries. These wastes are either underutilized to produce low market value products or dumped leading to environmental issues. Complete utilization of fishery wastes for recovering value added products would be beneficial to the society and individual. The fish protein hydrolysates and derived peptides of fishery resources are widely used as nutritional supplements, functional ingredients, and flavor enhancers in food, beverage and pharmaceutical industries. Antioxidants from fishery resources have attracted the attention of researchers as they are cheaper in cost, easy to derive, and do not have side effects. Thus the present investigation was designed to produce protein hydrolysate by pepsin and papain digestion from the backbones of Rastrelliger kanagurta (Indian mackerel) and evaluate its antioxidant properties through various in vitro assays. The results reveal that both hydrolysates are potent antioxidants, capable of scavenging 46% and 36% of DPPH (1,1-diphenyl-2 picrylhydrazyl) and 58.5% and 37.54% of superoxide radicals respectively. The hydrolysates exhibit significant (p hydrolysates produced, pepsin derived fraction is superior than papain derived fraction in terms of yield, DH (Degree of hydrolysis), and antioxidant activity. PMID:24596496

  19. Pressure dependence of backbone chemical shifts in the model peptides Ac-Gly-Gly-Xxx-Ala-NH2.

    Science.gov (United States)

    Erlach, Markus Beck; Koehler, Joerg; Crusca, Edson; Kremer, Werner; Munte, Claudia E; Kalbitzer, Hans Robert

    2016-06-01

    For a better understanding of nuclear magnetic resonance (NMR) detected pressure responses of folded as well as unstructured proteins the availability of data from well-defined model systems are indispensable. In this work we report the pressure dependence of chemical shifts of the backbone atoms (1)H(α), (13)C(α) and (13)C' in the protected tetrapeptides Ac-Gly-Gly-Xxx-Ala-NH2 (Xxx one of the 20 canonical amino acids). Contrary to expectation the chemical shifts of these nuclei have a nonlinear dependence on pressure in the range from 0.1 to 200 MPa. The polynomial pressure coefficients B 1 and B 2 are dependent on the type of amino acid studied. The coefficients of a given nucleus show significant linear correlations suggesting that the NMR observable pressure effects in the different amino acids have at least partly the same physical cause. In line with this observation the magnitude of the second order coefficients of nuclei being direct neighbors in the chemical structure are also weakly correlated. PMID:27335085

  20. Three-Dimensional Protein Fold Determination from Backbone Amide Pseudocontact Shifts Generated by Lanthanide Tags at Multiple Sites

    KAUST Repository

    Yagi, Hiromasa

    2013-06-01

    Site-specific attachment of paramagnetic lanthanide ions to a protein generates pseudocontact shifts (PCS) in the nuclear magnetic resonance (NMR) spectra of the protein that are easily measured as changes in chemical shifts. By labeling the protein with lanthanide tags at four different sites, PCSs are observed for most amide protons and accurate information is obtained about their coordinates in three-dimensional space. The approach is demonstrated with the chaperone ERp29, for which large differences have been reported between X-ray and NMR structures of the C-terminal domain, ERp29-C. The results unambiguously show that the structure of rat ERp29-C in solution is similar to the crystal structure of human ERp29-C. PCSs of backbone amides were the only structural restraints required. Because these can be measured for more dilute protein solutions than other NMR restraints, the approach greatly widens the range of proteins amenable to structural studies in solution. © 2013 Elsevier Ltd. All rights reserved.

  1. Insight into a molecular interaction force supporting peptide backbones and its implication to protein loops and folding.

    Science.gov (United States)

    Du, Qi-Shi; Chen, Dong; Xie, Neng-Zhong; Huang, Ri-Bo; Chou, Kuo-Chen

    2015-09-01

    Although not being classified as the most fundamental protein structural elements like α-helices and β-strands, the loop segment may play considerable roles for protein stability, flexibility, and dynamic activity. Meanwhile, the protein loop is also quite elusive; i.e. its interactions with the other parts of protein as well as its own shape-maintaining forces have still remained as a puzzle or at least not quite clear yet. Here, we report a molecular force, the so-called polar hydrogen-π interaction (Hp-π), which may play an important role in supporting the backbones of protein loops. By conducting the potential energy surface scanning calculations on the quasi π-plane of peptide bond unit, we have observed the following intriguing phenomena: (1) when the polar hydrogen atom of a peptide unit is perpendicularly pointing to the π-plane of other peptide bond units, a remarkable Hp-π interaction occurs; (2) the interaction is distance and orientation dependent, acting in a broad space, and belonging to the 'point-to-plane' one. The molecular force reported here may provide useful interaction concepts and insights into better understanding the loop's unique stability and flexibility feature, as well as the driving force of the protein global folding. PMID:25375237

  2. High resolution 4D HPCH experiment for sequential assignment of {sup 13}C-labeled RNAs via phosphodiester backbone

    Energy Technology Data Exchange (ETDEWEB)

    Saxena, Saurabh; Stanek, Jan [University of Warsaw, Faculty of Chemistry, Biological and Chemical Research Centre (Poland); Cevec, Mirko; Plavec, Janez [National Institute of Chemistry, Slovenian NMR Centre (Slovenia); Koźmiński, Wiktor, E-mail: kozmin@chem.uw.edu.pl [University of Warsaw, Faculty of Chemistry, Biological and Chemical Research Centre (Poland)

    2015-11-15

    The three-dimensional structure determination of RNAs by NMR spectroscopy requires sequential resonance assignment, often hampered by assignment ambiguities and limited dispersion of {sup 1}H and {sup 13}C chemical shifts, especially of C4′/H4′. Here we present a novel through-bond 4D HPCH NMR experiment involving phosphate backbone where C4′–H4′ correlations are resolved along the {sup 1}H3′–{sup 31}P spectral planes. The experiment provides high peak resolution and effectively removes ambiguities encountered during assignments. Enhanced peak dispersion is provided by the inclusion of additional {sup 31}P and {sup 1}H3′ dimensions and constant-time evolution of chemical shifts. High spectral resolution is obtained by using non-uniform sampling in three indirect dimensions. The experiment fully utilizes the isotopic {sup 13}C-labeling with evolution of C4′ carbons. Band selective {sup 13}C inversion pulses are used to achieve selectivity and prevent signal dephasing due to the C4′–C3′ and C4′–C5′ homonuclear couplings. Multiple quantum line narrowing is employed to minimize sensitivity loses. The 4D HPCH experiment is verified and successfully applied to a non-coding 34-nt RNA consisting typical structure elements and a 14-nt RNA hairpin capped by cUUCGg tetraloop.

  3. The "Legislative Backbone" keeping the Institution upright? The Role of European Parliament Committees in the EU Policy-Making Process

    Directory of Open Access Journals (Sweden)

    Christine Neuhold

    2001-08-01

    Full Text Available Over the past five decades the European Parliament (EP has moved from being a largely consultative assembly to being a genuine co-legislature. The growth in the EPs powers was accompanied by a revaluation of its Standing Committees. It is in these committees, the legislative backbone of the EP, that scrutiny of European Union (EU legislation takes place. As in the US Congress the real work of the Parliament is done in its committees. They have become a key element in the EU policy-making process and make vital contributions to the shaping of legislation. Although these committees play such a major role in the EP, they have rarely been the subject of empirical inquiries. This paper, which is part of a wider project studying the role of committees, intends to fill this gap. In an examination of how legislative acts have been processed by such committees on the basis of interviews and documentary analysis, this paper focuses on the following main questions: 1. How do EP committees operate? 2. How do they interact with other institutions within the EU system of governance? 3. How do they affect the "link" to the EU citizen? From an analytical perspective answers to these questions are important as they help us to understand some characteristics of the EU decision-making process. From a normative perspective our research also tries to answer the question of whether EP committees help increase the EPs accountability to EU citizens.

  4. Impairment assessment of orthogonal frequency division multiplexing over dispersion-managed links in backbone and backhaul networks

    Science.gov (United States)

    Tamilarasan, Ilavarasan; Saminathan, Brindha; Murugappan, Meenakshi

    2016-04-01

    The past decade has seen the phenomenal usage of orthogonal frequency division multiplexing (OFDM) in the wired as well as wireless communication domains, and it is also proposed in the literature as a future proof technique for the implementation of flexible resource allocation in cognitive optical networks. Fiber impairment assessment and adaptive compensation becomes critical in such implementations. A comprehensive analytical model for impairments in OFDM-based fiber links is developed. The proposed model includes the combined impact of laser phase fluctuations, fiber dispersion, self phase modulation, cross phase modulation, four-wave mixing, the nonlinear phase noise due to the interaction of amplified spontaneous emission with fiber nonlinearities, and the photodetector noises. The bit error rate expression for the proposed model is derived based on error vector magnitude estimation. The performance analysis of the proposed model is presented and compared for dispersion compensated and uncompensated backbone/backhaul links. The results suggest that OFDM would perform better for uncompensated links than the compensated links due to the negligible FWM effects and there is a need for flexible compensation. The proposed model can be employed in cognitive optical networks for accurate assessment of fiber-related impairments.

  5. Longitudinal Changes of Angle Configuration in Primary Angle-Closure Suspects

    Science.gov (United States)

    Jiang, Yuzhen; Chang, Dolly S.; Zhu, Haogang; Khawaja, Anthony P.; Aung, Tin; Huang, Shengsong; Chen, Qianyun; Munoz, Beatriz; Grossi, Carlota M.

    2015-01-01

    Objective To determine longitudinal changes in angle configuration in the eyes of primary angle-closure suspects (PACS) treated by laser peripheral iridotomy (LPI) and in untreated fellow eyes. Design Longitudinal cohort study. Participants Primary angle-closure suspects aged 50 to 70 years were enrolled in a randomized, controlled clinical trial. Methods Each participant was treated by LPI in 1 randomly selected eye, with the fellow eye serving as a control. Angle width was assessed in a masked fashion using gonioscopy and anterior segment optical coherence tomography (AS-OCT) before and at 2 weeks, 6 months, and 18 months after LPI. Main Outcome Measures Angle width in degrees was calculated from Shaffer grades assessed under static gonioscopy. Angle configuration was also evaluated using angle opening distance (AOD250, AOD500, AOD750), trabecular-iris space area (TISA500, TISA750), and angle recess area (ARA) measured in AS-OCT images. Results No significant difference was found in baseline measures of angle configuration between treated and untreated eyes. At 2 weeks after LPI, the drainage angle on gonioscopy widened from a mean of 13.5° at baseline to a mean of 25.7° in treated eyes, which was also confirmed by significant increases in all AS-OCT angle width measures (P<0.001 for all variables). Between 2 weeks and 18 months after LPI, a significant decrease in angle width was observed over time in treated eyes (P<0.001 for all variables), although the change over the first 5.5 months was not statistically significant for angle width measured under gonioscopy (P = 0.18), AOD250 (P = 0.167) and ARA (P = 0.83). In untreated eyes, angle width consistently decreased across all follow-up visits after LPI, with a more rapid longitudinal decrease compared with treated eyes (P values for all variables ≤0.003). The annual rate of change in angle width was equivalent to 1.2°/year (95% confidence interval [CI], 0.8–1.6) in treated eyes and 1.6°/year (95% CI, 1

  6. Bioelectric impedance phase angle in breast carcinoma

    Directory of Open Access Journals (Sweden)

    Ruchi Tyagi

    2014-01-01

    Full Text Available Context: Worldwide breast cancer is the most frequently diagnosed life threatening cancer and the leading cause of death in women. Bioelectric impedance analysis (BIA affords an emerging opportunity to assess prognosis because of its ability to non invasively assess cell and plasma membrane structure and function by means of phase angle. Aims: To compare the phase angle between patients of breast cancer and their matched control with the help of BIA. Settings and Design: After taking clearance from ethical committee, a total of 34 female cases of histologically proven infiltrating ductal breast carcinoma were included from the surgery IPD, department of surgery. Equal numbers of the matched controls were recruited from the friends and relatives of cases. Materials and Methods: Bio Electrical Impedance Analyzer (BIA BODY STAT QUAD SCAN 4000 was used to measure resistance (R and reactance (Xc by recording a voltage drop in applied current. Phase angle is the ratio of reactance to resistance and is a measure of cell vitality. Statistical analysis used: Unpaired "t" test was applied. Results: In control group, the phase angle showed a mean of 5.479 whereas in test group, it showed a mean value of 4.726. The P value showed a significant difference (P < 0.0001. The smaller the phase angle values were higher was the tumor, nodes, metastases (TNM staging. The phase angles differed significantly from the healthy age matched control values. Conclusions: This study demonstrated that phase angle is a strong predictor of severity of breast cancer and differed significantly between the two groups.

  7. On the NMR structure determination of a 44n RNA pseudoknot: Assignment strategies and derivation of torsion angle restraints

    Energy Technology Data Exchange (ETDEWEB)

    Kolk, Michael H. [University of Nijmegen, Toernooiveld, NSR Center for Molecular Structure, Design and Synthesis, Laboratory of Biophysical Chemistry (Netherlands); Wijmenga, Sybren S. [University of Umea, Department of Medical Biochemistry and Biophysics (Sweden); Heus, Hans A.; Hilbers, Cornelis W. [University of Nijmegen, Toernooiveld, NSR Center for Molecular Structure, Design and Synthesis, Laboratory of Biophysical Chemistry (Netherlands)

    1998-10-15

    The complete T- and pseudoknotted acceptor arm of the tRNA-like structure of turnip yellow mosaic virus (TYMV) genomic RNA has been studied by NMR spectroscopy. Resonance assignment and the gathering of restraints of the 44-mer are impeded by spectral complexity as well as by line broadening. The latter is caused by local dynamical effects in the pseudoknot domain in the molecule. These specific problems could be solved by using different field strengths and selectively {sup 13}C/{sup 15} labeled samples. Experiments for assigning the sugar spin systems were adjusted to satisfy the requirements of this system. Furthermore, the quality of the structure could be improved by determining the backbone torsion angles {beta}, {gamma} and {epsilon}, using new approaches that were tailored for use in large RNA molecules.

  8. Geometric structures on moment-angle manifolds

    International Nuclear Information System (INIS)

    A moment-angle complex ZK is a cell complex with a torus action constructed from a finite simplicial complex K. When this construction is applied to a triangulated sphere K or, in particular, to the boundary of a simplicial polytope, the result is a manifold. Moment-angle manifolds and complexes are central objects in toric topology, and currently are gaining much interest in homotopy theory and complex and symplectic geometry. The geometric aspects of the theory of moment-angle complexes are the main theme of this survey. Constructions of non-Kähler complex-analytic structures on moment-angle manifolds corresponding to polytopes and complete simplicial fans are reviewed, and invariants of these structures such as the Hodge numbers and Dolbeault cohomology rings are described. Symplectic and Lagrangian aspects of the theory are also of considerable interest. Moment-angle manifolds appear as level sets for quadratic Hamiltonians of torus actions, and can be used to construct new families of Hamiltonian-minimal Lagrangian submanifolds in a complex space, complex projective space, or toric varieties. Bibliography: 59 titles

  9. Backbone.js cookbook

    CERN Document Server

    Mirgorod, Vadim

    2013-01-01

    Written in a friendly, example driven Beginner's Guide format, there are plenty of step-by-step instructions to get you started fast!Pentaho 4.0 By Example: Beginner's Guide is the ideal companion for a wide-variety of developers. Whether you are new to the world of Business Intelligence reporting, or an experienced BI analyst, this book will guide you through the creation of your first reports in Pentaho. We assume some knowledge of the SQL language and database systems.

  10. Backbone.js essentials

    CERN Document Server

    Walker, Jeremy

    2015-01-01

    If you are a developer with baseline JavaScript proficiency and are familiar with the jQuery library, then this book is ideal for you. Whether you've tried building complex web applications before and been frustrated by the challenge of doing so without the proper tools, or whether you've only built simple websites and are now looking to create full-featured web applications, this book has everything you need to get ahead of the curve.

  11. High brightness angled cavity quantum cascade lasers

    International Nuclear Information System (INIS)

    A quantum cascade laser (QCL) with an output power of 203 W is demonstrated in pulsed mode at 283 K with an angled cavity. The device has a ridge width of 300 μm, a cavity length of 5.8 mm, and a tilt angle of 12°. The back facet is high reflection coated, and the front facet is anti-reflection coated. The emitting wavelength is around 4.8 μm. In distinct contrast to a straight cavity broad area QCL, the lateral far field is single lobed with a divergence angle of only 3°. An ultrahigh brightness value of 156 MW cm−2 sr−1 is obtained, which marks the brightest QCL to date

  12. High brightness angled cavity quantum cascade lasers

    Energy Technology Data Exchange (ETDEWEB)

    Heydari, D.; Bai, Y.; Bandyopadhyay, N.; Slivken, S.; Razeghi, M., E-mail: razeghi@eecs.northwestern.edu [Center for Quantum Devices, Department of Electrical Engineering and Computer Science, Northwestern University, Evanston, Illinois 60208 (United States)

    2015-03-02

    A quantum cascade laser (QCL) with an output power of 203 W is demonstrated in pulsed mode at 283 K with an angled cavity. The device has a ridge width of 300 μm, a cavity length of 5.8 mm, and a tilt angle of 12°. The back facet is high reflection coated, and the front facet is anti-reflection coated. The emitting wavelength is around 4.8 μm. In distinct contrast to a straight cavity broad area QCL, the lateral far field is single lobed with a divergence angle of only 3°. An ultrahigh brightness value of 156 MW cm{sup −2 }sr{sup −1} is obtained, which marks the brightest QCL to date.

  13. A heterodyne interferometer for angle metrology

    International Nuclear Information System (INIS)

    We have developed a compact, high-resolution, angle measurement instrument based on a heterodyne interferometer. Common-path heterodyne interferometer metrology is used to measure displacements of a reflective target surface. In the interferometer set up, an optical mask is used to sample the laser beam reflecting back from four areas on a target surface. From the relative displacement measurements of the target surface areas, we can simultaneously determine angular rotations around two orthogonal axes in a plane perpendicular to the measurement beam propagation direction. The device is used in a testbed for a tracking telescope system where pitch and yaw angle measurements of a flat mirror are performed. Angle noise measurement of the device shows 0.1 nrad/√(Hz) at 1 Hz, at a working distance of 1 m. The operation range and nonlinearity of the device when used with a flat mirror is approximately ±0.15 mrad, and 3 μrad rms, respectively.

  14. Notes on large angle crossing graphs

    CERN Document Server

    Dujmovic, Vida; Morin, Pat; Wolle, Thomas

    2009-01-01

    A graph G is an a-angle crossing (aAC) graph if every pair of crossing edges in G intersect at an angle of at least a. The concept of right angle crossing (RAC) graphs (a=Pi/2) was recently introduced by Didimo et. al. It was shown that any RAC graph with n vertices has at most 4n-10 edges and that there are infinitely many values of n for which there exists a RAC graph with n vertices and 4n-10 edges. In this paper, we give upper and lower bounds for the number of edges in aAC graphs for all 0 < a < Pi/2.

  15. Precision measurements of the CKM angle gamma

    CERN Document Server

    CERN. Geneva

    2016-01-01

    The level of CP-violation permitted within the Standard Model cannot account for the matter dominated universe in which we live. Within the Standard Model the CKM matrix, which describes the quark couplings, is expected to be unitary. By making precise measurements of the CKM matrix parameters new physics models can be constrained, or with sufficient precision the effects of physics beyond the standard model might become apparent. The CKM angle gamma is the least well known angle of the unitarity triangle. It is the only angle easily accessible at tree-level, and furthermore has almost no theoretical uncertainties. Therefore it provides an invaluable Standard Model benchmark against which other new physics sensitive tests of the CP-violation can be made. I will discuss recent measurements of gamma using the the Run 1 LHCb dataset, which improve our knowledge of this key parameter.

  16. The wave vane - A device to measure the breaker angle

    Digital Repository Service at National Institute of Oceanography (India)

    Chandramohan, P.; Nayak, B.U.; Anand, N.M.

    , ,~ ~ O BEACH c /~ ' ! , THEODOLITE Fig. 4. Definition sketch. 178 P. CHANDRAMOHAN ET AL. angle AOC can be calculated, which would be the wave breaker angle with respect to the coastline. It is assumed that the angle made by the crestline...

  17. Positron Emission Mammography with Multiple Angle Acquisition

    International Nuclear Information System (INIS)

    Positron emission mammography (PEM) of F-18 fluorodeoxyglucose (FDG) uptake in breast tumors with dedicated detectors typically has been accomplished with two planar detectors in a fixed position with the breast under compression. The potential use of PEM imaging at two detector positions to guide stereotactic breast biopsy has motivated us to use PEM coincidence data acquired at two or more detector positions together in a single image reconstruction. Multiple angle PEM acquisition and iterative image reconstruction were investigated using point source and compressed breast phantom acquisitions with 5, 9, 12 and 15 mm diameter spheres and a simulated tumor:background activity concentration ratio of 6:1. Image reconstruction was performed with an iterative MLEM algorithm that used coincidence events between any two detector pixels on opposed detector heads at each detector position. This present study compared two acquisition protocols: 2 angle acquisition with detector angular positions of -15 and +15 degrees and 11 angle acquisition with detector positions spaced at 3 degree increments over the range -15 to +15 degrees. Three- dimensional image resolution was assessed for the point source acquisitions, and contrast and signal-to-noise metrics were evaluated for the compressed breast phantom with different simulated tumor sizes. Radial and tangential resolutions were similar for the two protocols, while normal resolution was better for the 2 angle acquisition. Analysis is complicated by the asymmetric point spread functions. Signal- to-noise vs. contrast tradeoffs were better for 11 angle acquisition for the smallest visible 9 mm sphere, while tradeoff results were mixed for the larger and more easily visible 12 mm and 15 mm diameter spheres. Additional study is needed to better understand the performance of limited angle tomography for PEM. PEM tomography experiments with complete angular sampling are planned

  18. Ship wakes: Kelvin or Mach angle?

    Science.gov (United States)

    Rabaud, Marc; Moisy, Frédéric

    2013-05-24

    From the analysis of a set of airborne images of ship wakes, we show that the wake angles decrease as U(-1) at large velocities, in a way similar to the Mach cone for supersonic airplanes. This previously unnoticed Mach-like regime is in contradiction with the celebrated Kelvin prediction of a constant angle of 19.47° independent of the ship's speed. We propose here a model, confirmed by numerical simulations, in which the finite size of the disturbance explains this transition between the Kelvin and Mach regimes at a Froude number Fr=U/√[gL]~/=0.5, where L is the hull ship length. PMID:23745883

  19. Angle-Resolved Spectroscopy of Parametric Fluorescence

    CERN Document Server

    Hsu, Feng-kuo

    2013-01-01

    The parametric fluorescence from a nonlinear crystal forms a conical radiation pattern. We measure the angular and spectral distributions of parametric fluorescence in a beta-barium borate crystal pumped by a 405-nm diode laser employing angle-resolved imaging spectroscopy. The experimental angle-resolved spectra and the generation efficiency of parametric down conversion are compared with a plane-wave theoretical analysis. The parametric fluorescence is used as a broadband light source for the calibration of the instrument spectral response function in the wavelength range from 450 to 1000 nm.

  20. Ship wakes: Kelvin or Mach angle?

    CERN Document Server

    Rabaud, Marc

    2013-01-01

    From the analysis of a set of airborne images of ship wakes, we show that the wake angles decrease as $U^{-1}$ at large velocities, in a way similar to the Mach cone for supersonic airplanes. This previously unnoticed Mach-like regime is in contradiction with the celebrated Kelvin prediction of a constant angle of $19.47\\degree$ independent of the ship's speed. We propose here a model, confirmed by numerical simulations, in which the finite size of the disturbance explains this transition between the Kelvin and Mach regimes at a Froude number $Fr = U/\\sqrt{gL} \\simeq 0.5$, where $L$ is the hull ship length.

  1. Clinical tibiofemoral angle in south Indian children

    OpenAIRE

    Mathew, S. E.; V. Madhuri

    2013-01-01

    Objectives The development of tibiofemoral angle in children has shown ethnic variations. However this data is unavailable for our population. Methods We measured the tibiofemoral angle (TFA) and intercondylar and intermalleolar distances in 360 children aged between two and 18 years, dividing them into six interrupted age group intervals: two to three years; five to six years; eight to nine years; 11 to 12 years; 14 to 15 years; and 17 to 18 years. Each age group comprised 30 boys and 30 gir...

  2. Characterization of the Burkholderia mallei tonB Mutant and Its Potential as a Backbone Strain for Vaccine Development.

    Directory of Open Access Journals (Sweden)

    Tiffany M Mott

    Full Text Available In this study, a Burkholderia mallei tonB mutant (TMM001 deficient in iron acquisition was constructed, characterized, and evaluated for its protective properties in acute inhalational infection models of murine glanders and melioidosis.Compared to the wild-type, TMM001 exhibits slower growth kinetics, siderophore hyper-secretion and the inability to utilize heme-containing proteins as iron sources. A series of animal challenge studies showed an inverse correlation between the percentage of survival in BALB/c mice and iron-dependent TMM001 growth. Upon evaluation of TMM001 as a potential protective strain against infection, we found 100% survival following B. mallei CSM001 challenge of mice previously receiving 1.5 x 10(4 CFU of TMM001. At 21 days post-immunization, TMM001-treated animals showed significantly higher levels of B. mallei-specific IgG1, IgG2a and IgM when compared to PBS-treated controls. At 48 h post-challenge, PBS-treated controls exhibited higher levels of serum inflammatory cytokines and more severe pathological damage to target organs compared to animals receiving TMM001. In a cross-protection study of acute inhalational melioidosis with B. pseudomallei, TMM001-treated mice were significantly protected. While wild type was cleared in all B. mallei challenge studies, mice failed to clear TMM001.Although further work is needed to prevent chronic infection by TMM001 while maintaining immunogenicity, our attenuated strain demonstrates great potential as a backbone strain for future vaccine development against both glanders and melioidosis.

  3. Comparison of backbone dynamics of the type III antifreeze protein and antifreeze-like domain of human sialic acid synthase

    International Nuclear Information System (INIS)

    Antifreeze proteins (AFPs) are found in a variety of cold-adapted (psychrophilic) organisms to promote survival at subzero temperatures by binding to ice crystals and decreasing the freezing temperature of body fluids. The type III AFPs are small globular proteins that consist of one α-helix, three 310-helices, and two β-strands. Sialic acids play important roles in a variety of biological functions, such as development, recognition, and cell adhesion and are synthesized by conserved enzymatic pathways that include sialic acid synthase (SAS). SAS consists of an N-terminal catalytic domain and a C-terminal antifreeze-like (AFL) domain, which is similar to the type III AFPs. Despite having very similar structures, AFL and the type III AFPs exhibit very different temperature-dependent stability and activity. In this study, we have performed backbone dynamics analyses of a type III AFP (HPLC12 isoform) and the AFL domain of human SAS (hAFL) at various temperatures. We also characterized the structural/dynamic properties of the ice-binding surfaces by analyzing the temperature gradient of the amide proton chemical shift and its correlation with chemical shift deviation from random coil. The dynamic properties of the two proteins were very different from each other. While HPLC12 was mostly rigid with a few residues exhibiting slow motions, hAFL showed fast internal motions at low temperature. Our results provide insight into the molecular basis of thermostability and structural flexibility in homologous psychrophilic HPLC12 and mesophilic hAFL proteins

  4. Complete resonance assignment for the polypeptide backbone of interleukin 1β using three-dimensional heteronuclear NMR spectroscopy

    International Nuclear Information System (INIS)

    The complete sequence-specific assignment of the 15N and 1H backbone resonances of the NMR spectrum of recombinant human interleukin 1β has been obtained by using primarily 15N-1H heteronuclear three-dimensional (3D) NMR techniques in combination with 15N-1H heteronuclear and 1H homonuclear two-dimensional NMR. The fingerprint region of the spectrum was analyzed by using a combination of 3D heteronuclear 1H Hartmann-Hahn 15N-1H multiple quantum coherence (3D HOHAHA-HMQC) and 3D heteronuclear 1H nuclear Overhauser 15N-1H multiple quantum coherence (3D NOESY-HMQC) spectroscopies. The authors show that the problems of amide NH and CαH chemical shift degeneracy that are prevalent for proteins of the size are readily overcome by using the 3D heteronuclear NMR technique. A doubling of some peaks in the spectrum was found to be due to N-terminal heterogeneity of the 15N-labeled protein, corresponding to a mixture of wild-type and des-Ala-1-interleukin 1β. The complete list of 15N and 1H assignments is given for all the amide NH and CαH resonances of all non-proline residues, as well as the 1H assignments for some of the amino acid side chains. This first example of the sequence-specific assignment of a protein using heteronuclear 3D NMR provides a basis for further conformational and dynamic studies of interleukin 1β

  5. Combining automated peak tracking in SAR by NMR with structure-based backbone assignment from 15N-NOESY

    KAUST Repository

    Jang, Richard

    2012-03-21

    Background: Chemical shift mapping is an important technique in NMR-based drug screening for identifying the atoms of a target protein that potentially bind to a drug molecule upon the molecule\\'s introduction in increasing concentrations. The goal is to obtain a mapping of peaks with known residue assignment from the reference spectrum of the unbound protein to peaks with unknown assignment in the target spectrum of the bound protein. Although a series of perturbed spectra help to trace a path from reference peaks to target peaks, a one-to-one mapping generally is not possible, especially for large proteins, due to errors, such as noise peaks, missing peaks, missing but then reappearing, overlapped, and new peaks not associated with any peaks in the reference. Due to these difficulties, the mapping is typically done manually or semi-automatically, which is not efficient for high-throughput drug screening.Results: We present PeakWalker, a novel peak walking algorithm for fast-exchange systems that models the errors explicitly and performs many-to-one mapping. On the proteins: hBclXL, UbcH5B, and histone H1, it achieves an average accuracy of over 95% with less than 1.5 residues predicted per target peak. Given these mappings as input, we present PeakAssigner, a novel combined structure-based backbone resonance and NOE assignment algorithm that uses just 15N-NOESY, while avoiding TOCSY experiments and 13C-labeling, to resolve the ambiguities for a one-to-one mapping. On the three proteins, it achieves an average accuracy of 94% or better.Conclusions: Our mathematical programming approach for modeling chemical shift mapping as a graph problem, while modeling the errors directly, is potentially a time- and cost-effective first step for high-throughput drug screening based on limited NMR data and homologous 3D structures. 2012 Jang et al.; licensee BioMed Central Ltd.

  6. Comparison of backbone dynamics of the type III antifreeze protein and antifreeze-like domain of human sialic acid synthase

    Energy Technology Data Exchange (ETDEWEB)

    Choi, Yong-Geun [Gyeongsang National University, Department of Chemistry and Research Institute of Natural Science (Korea, Republic of); Park, Chin-Ju [Gwangju Institute of Science and Technology, Division of Liberal Arts and Sciences and Department of Chemistry (Korea, Republic of); Kim, Hee-Eun; Seo, Yeo-Jin; Lee, Ae-Ree; Choi, Seo-Ree; Lee, Shim Sung; Lee, Joon-Hwa, E-mail: joonhwa@gnu.ac.kr [Gyeongsang National University, Department of Chemistry and Research Institute of Natural Science (Korea, Republic of)

    2015-02-15

    Antifreeze proteins (AFPs) are found in a variety of cold-adapted (psychrophilic) organisms to promote survival at subzero temperatures by binding to ice crystals and decreasing the freezing temperature of body fluids. The type III AFPs are small globular proteins that consist of one α-helix, three 3{sub 10}-helices, and two β-strands. Sialic acids play important roles in a variety of biological functions, such as development, recognition, and cell adhesion and are synthesized by conserved enzymatic pathways that include sialic acid synthase (SAS). SAS consists of an N-terminal catalytic domain and a C-terminal antifreeze-like (AFL) domain, which is similar to the type III AFPs. Despite having very similar structures, AFL and the type III AFPs exhibit very different temperature-dependent stability and activity. In this study, we have performed backbone dynamics analyses of a type III AFP (HPLC12 isoform) and the AFL domain of human SAS (hAFL) at various temperatures. We also characterized the structural/dynamic properties of the ice-binding surfaces by analyzing the temperature gradient of the amide proton chemical shift and its correlation with chemical shift deviation from random coil. The dynamic properties of the two proteins were very different from each other. While HPLC12 was mostly rigid with a few residues exhibiting slow motions, hAFL showed fast internal motions at low temperature. Our results provide insight into the molecular basis of thermostability and structural flexibility in homologous psychrophilic HPLC12 and mesophilic hAFL proteins.

  7. The influence of DNA binding on the backbone dynamics of the yeast cell-cycle protein Mbp1

    International Nuclear Information System (INIS)

    Mbp1 is a transcription factor involved in the regulation of the cell cycle in yeast. The N-terminus of this protein contains a DNA binding domain that includes a winged helix-turn-helix motif. The C-terminal 24 residues of this domain (the 'tail') are disordered in the crystal state, but are important for DNA binding. We have measured 15N NMR relaxation rates at 11.75 and 14.1 T to determine the dynamics of the free protein and in its complex with a specific DNA duplex. The dynamics data were quantitatively analysed using both spectral density mapping and the Lipari-Szabo formalism including the effects of chemical exchange and rotational anisotropy. A detailed analysis has been made of the effect of anisotropy, exchange and experimental precision on the recovered motional parameters. The backbone NH relaxation is affected by motions on a variety of time scales from millisecond to tens of picoseconds. The relaxation data show a structured core of 100 residues corresponding to that observed in the crystal state. Within the core of the protein, two regions on either side of the putative recognition helix (helix B) show slow (ca. 0.2 ms) conformational exchange dynamics that are quenched upon DNA binding. The C-terminal 24 residues are generally more dynamic than in the core. However, in the free protein, a stretch of ∼8 residues in the middle of the tail show relaxation behaviour similar to that in the core, indicating a structured region. NOEs between Ala 114 in this structured part of the tail and residues in the N-terminal beta strand of the core of the protein demonstrate that the tail folds back onto the core of the protein. In the complex with DNA, the structured part of the tail extends by ca. 3 residues. These data provide a framework for understanding the biochemical data on the mechanism and specificity of DNA binding

  8. Combining ambiguous chemical shift mapping with structure-based backbone and NOE assignment from 15N-NOESY

    KAUST Repository

    Jang, Richard

    2011-01-01

    Chemical shift mapping is an important technique in NMRbased drug screening for identifying the atoms of a target protein that potentially bind to a drug molecule upon the molecule\\'s introduction in increasing concentrations. The goal is to obtain a mapping of peaks with known residue assignment from the reference spectrum of the unbound protein to peaks with unknown assignment in the target spectrum of the bound protein. Although a series of perturbed spectra help to trace a path from reference peaks to target peaks, a one-to-one mapping generally is not possible, especially for large proteins, due to errors, such as noise peaks, missing peaks, missing but then reappearing, overlapped, and new peaks not associated with any peaks in the reference. Due to these difficulties, the mapping is typically done manually or semi-automatically. However, automated methods are necessary for high-throughput drug screening. We present PeakWalker, a novel peak walking algorithm for fast-exchange systems that models the errors explicitly and performs many-to-one mapping. On the proteins: hBclXL, UbcH5B, and histone H1, it achieves an average accuracy of over 95% with less than 1.5 residues predicted per target peak. Given these mappings as input, we present PeakAssigner, a novel combined structure-based backbone resonance and NOE assignment algorithm that uses just 15N-NOESY, while avoiding TOCSY experiments and 13C- labeling, to resolve the ambiguities for a one-toone mapping. On the three proteins, it achieves an average accuracy of 94% or better. Copyright © 2011 ACM.

  9. The "Legislative Backbone" keeping the Institution upright? The Role of European Parliament Committees in the EU Policy-Making Process

    Directory of Open Access Journals (Sweden)

    Christine Neuhold

    2001-08-01

    Full Text Available Over the past five decades the European Parliament (EP has moved from being a largely consultative assembly to being a genuine co-legislature. The growth in the EP’s powers was accompanied by a revaluation of its Standing Committees. It is in these committees, the “legislative backbone” of the EP, that scrutiny of European Union (EU legislation takes place. As in the US Congress the “real” work of the Parliament is done in its committees. They have become a key element in the EU policy-making process and make vital contributions to the shaping of legislation. Although these committees play such a major role in the EP, they have rarely been the subject of empirical inquiries. This paper, which is part of a wider project studying the role of committees, intends to fill this gap. In an examination of how legislative acts have been processed by such committees on the basis of interviews and documentary analysis, this paper focuses on the following main questions: 1. How do EP committees operate? 2. How do they interact with other institutions within the EU system of governance? 3. How do they affect the "link" to the EU citizen? From an analytical perspective answers to these questions are important as they help us to understand some characteristics of the EU decision-making process. From a normative perspective our research also tries to answer the question of whether EP committees help increase the EP’s accountability to EU citizens.

  10. A fringe shadow method for measuring flapping angle and torsional angle of a dragonfly wing

    Science.gov (United States)

    Zeng, Lijiang; Matsumoto, Hirokazu; Kawachi, Keiji

    1996-05-01

    A fringe shadow (FS) method was developed for measuring the flapping angle and torsional angle of a dragonfly wing during beating motion. This new method involves two sets of fringe patterns projected onto the wing from orthogonal directions. The torsional angle is determined using the length of the shadow of the wing chord that is cast by the two sets of fringe patterns. The flapping angle is determined using the shadowgraph of the wing projected by a laser. The advantages of the FS method are its capability (i) to measure the flapping angle and torsional angle of a dragonfly wing simultaneously using only one high-speed camera and (ii) to recognize the spanwise position of a section from the number of fringes, without having to use diffuse marks that are common in current methods. The resolution of the FS method can be changed easily by adjusting the fringe spacing. The measurement results for the torsional angle and flapping angle of a dragonfly wing prove the effectiveness of the FS method in studying the flight performance of dragonflies.

  11. Sulfur-infiltrated graphene-backboned mesoporous carbon nanosheets with a conductive polymer coating for long-life lithium-sulfur batteries

    Science.gov (United States)

    Dong, Yanfeng; Liu, Shaohong; Wang, Zhiyu; Liu, Yang; Zhao, Zongbin; Qiu, Jieshan

    2015-04-01

    Sandwich-type, two-dimensional hybrid nanosheets were fabricated by the infiltration of nanosized sulfur into graphene-backboned mesoporous carbon with a PPy nanocoating. They exhibit a high reversible capacity for as long as 400 cycles with an ultra slow decay rate of 0.05% per cycle at the high rate of 1-3 C due to the efficient immobilization of polysulfides.Sandwich-type, two-dimensional hybrid nanosheets were fabricated by the infiltration of nanosized sulfur into graphene-backboned mesoporous carbon with a PPy nanocoating. They exhibit a high reversible capacity for as long as 400 cycles with an ultra slow decay rate of 0.05% per cycle at the high rate of 1-3 C due to the efficient immobilization of polysulfides. Electronic supplementary information (ESI) available: Experimental details, BET, SEM, XPS and more electrochemical data. See DOI: 10.1039/c5nr01015b

  12. Beta-scission of alkoxyl radicals on peptides and proteins can give rise to backbone cleavage and loss of side-chains

    International Nuclear Information System (INIS)

    Full text: Exposure of proteins to radicals in the presence of O2 brings about multiple changes including side-chain oxidation, backbone fragmentation, cross-linking, unfolding, changes in hydrophobicity and conformation, altered susceptibility to proteolytic enzymes and formation of new reactive groups (e.g. hydroperoxides and 3,4-dihydroxyphenylalanine). All of these processes can result in loss of structural or enzymatic activity. The mechanisms that give rise to backbone cleavage are only partly understood. Whilst it is known that direct hydrogen atom abstraction at a-carbon sites gives backbone cleavages it has also been proposed that initial attack at side-chain sites might also give rise to backbone cleavage. In this study we have examined whether initial attack at the β- (C-3) position can give rise to α-carbon radicals (and hence backbone cleavage) via the formation, and subsequent β- scission, of C-3 alkoxyl radicals. This process has been observed previously with protected amino acids in organic solvents (J. Chem. Soc. Perkin Trans. 2, 1997, 503-507) but the occurrence of such reactions with proteins in aqueous solution has not been explored. Alkoxyl radicals were generated at the C-3 position of a variety of protected amino acids and small peptides by two methods: metal-ion catalysed decomposition of hydroperoxides formed as a result of γ-radiolysis in the presence of O2, and UV photolysis of nitrate esters. In most cases radicals have been detected by EPR spectroscopy using nitroso and nitrone spin traps, which can be assigned by comparison with literature data to α-carbon radicals; in some case assignments were confirmed by the generation of the putative species by other routes. With Ala peptide hydroperoxides and nitrate esters, and MNP as the spin trap, the major radical detected in each case has been assigned to the adduct of an α-carbon radical with partial structure - NH-.CH-C(O) - consistent with the rapid occurrence of the above reaction

  13. Mnn10 Maintains Pathogenicity in Candida albicans by Extending α-1,6-Mannose Backbone to Evade Host Dectin-1 Mediated Antifungal Immunity.

    Science.gov (United States)

    Zhang, Shi Qun; Zou, Zui; Shen, Hui; Shen, Shuai Shuai; Miao, Qi; Huang, Xin; Liu, Wei; Li, Li Ping; Chen, Si Min; Yan, Lan; Zhang, Jun Dong; Zhao, Jing Jun; Xu, Guo Tong; An, Mao Mao; Jiang, Yuan Ying

    2016-05-01

    The cell wall is a dynamic structure that is important for the pathogenicity of Candida albicans. Mannan, which is located in the outermost layer of the cell wall, has been shown to contribute to the pathogenesis of C. albicans, however, the molecular mechanism by which this occurs remains unclear. Here we identified a novel α-1,6-mannosyltransferase encoded by MNN10 in C. albicans. We found that Mnn10 is required for cell wall α-1,6-mannose backbone biosynthesis and polysaccharides organization. Deletion of MNN10 resulted in significant attenuation of the pathogenesis of C. albicans in a murine systemic candidiasis model. Inhibition of α-1,6-mannose backbone extension did not, however, impact the invasive ability of C. albicans in vitro. Notably, mnn10 mutant restored the invasive capacity in athymic nude mice, which further supports the notion of an enhanced host antifungal defense related to this backbone change. Mnn10 mutant induced enhanced Th1 and Th17 cell mediated antifungal immunity, and resulted in enhanced recruitment of neutrophils and monocytes for pathogen clearance in vivo. We also demonstrated that MNN10 could unmask the surface β-(1,3)-glucan, a crucial pathogen-associated molecular pattern (PAMP) of C. albicans recognized by host Dectin-1. Our results demonstrate that mnn10 mutant could stimulate an enhanced Dectin-1 dependent immune response of macrophages in vitro, including the activation of nuclear factor-κB, mitogen-activated protein kinase pathways, and secretion of specific cytokines such as TNF-α, IL-6, IL-1β and IL-12p40. In summary, our study indicated that α-1,6-mannose backbone is critical for the pathogenesis of C. albicans via shielding β-glucan from recognition by host Dectin-1 mediated immune recognition. Moreover, our work suggests that inhibition of α-1,6-mannose extension by Mnn10 may represent a novel modality to reduce the pathogenicity of C. albicans. PMID:27144456

  14. Selective Acid Hydrolysis Condition for the Composition and Linkage with a Fructofuranosyl Backbone of a Polysaccharide from Angelica sinensis (Oliv) Diels

    Institute of Scientific and Technical Information of China (English)

    Gui Yun XU; Yang CHEN; Ru Xian CHEN

    2006-01-01

    A new polysaccharide was extracted and purified from the roots of Angelica sinensis (Oliv) Diels (ASD). Its composition and linkage was elucidated by selective hydrolysis and GC/MS analysis of its derivatives. The polysaccharide was made of→1) Fruf(2→and→6) GlCp (1→as its backbone with highly branched structure. To our best knowledge, this is the first report of the fructose residue in polysaccharides from the roots of the ASD.

  15. Mnn10 Maintains Pathogenicity in Candida albicans by Extending α-1,6-Mannose Backbone to Evade Host Dectin-1 Mediated Antifungal Immunity.

    Directory of Open Access Journals (Sweden)

    Shi Qun Zhang

    2016-05-01

    Full Text Available The cell wall is a dynamic structure that is important for the pathogenicity of Candida albicans. Mannan, which is located in the outermost layer of the cell wall, has been shown to contribute to the pathogenesis of C. albicans, however, the molecular mechanism by which this occurs remains unclear. Here we identified a novel α-1,6-mannosyltransferase encoded by MNN10 in C. albicans. We found that Mnn10 is required for cell wall α-1,6-mannose backbone biosynthesis and polysaccharides organization. Deletion of MNN10 resulted in significant attenuation of the pathogenesis of C. albicans in a murine systemic candidiasis model. Inhibition of α-1,6-mannose backbone extension did not, however, impact the invasive ability of C. albicans in vitro. Notably, mnn10 mutant restored the invasive capacity in athymic nude mice, which further supports the notion of an enhanced host antifungal defense related to this backbone change. Mnn10 mutant induced enhanced Th1 and Th17 cell mediated antifungal immunity, and resulted in enhanced recruitment of neutrophils and monocytes for pathogen clearance in vivo. We also demonstrated that MNN10 could unmask the surface β-(1,3-glucan, a crucial pathogen-associated molecular pattern (PAMP of C. albicans recognized by host Dectin-1. Our results demonstrate that mnn10 mutant could stimulate an enhanced Dectin-1 dependent immune response of macrophages in vitro, including the activation of nuclear factor-κB, mitogen-activated protein kinase pathways, and secretion of specific cytokines such as TNF-α, IL-6, IL-1β and IL-12p40. In summary, our study indicated that α-1,6-mannose backbone is critical for the pathogenesis of C. albicans via shielding β-glucan from recognition by host Dectin-1 mediated immune recognition. Moreover, our work suggests that inhibition of α-1,6-mannose extension by Mnn10 may represent a novel modality to reduce the pathogenicity of C. albicans.

  16. Sulfur-infiltrated graphene-backboned mesoporous carbon nanosheets with a conductive polymer coating for long-life lithium-sulfur batteries.

    Science.gov (United States)

    Dong, Yanfeng; Liu, Shaohong; Wang, Zhiyu; Liu, Yang; Zhao, Zongbin; Qiu, Jieshan

    2015-05-01

    Sandwich-type, two-dimensional hybrid nanosheets were fabricated by the infiltration of nanosized sulfur into graphene-backboned mesoporous carbon with a PPy nanocoating. They exhibit a high reversible capacity for as long as 400 cycles with an ultra slow decay rate of 0.05% per cycle at the high rate of 1-3 C due to the efficient immobilization of polysulfides. PMID:25832361

  17. Mnn10 Maintains Pathogenicity in Candida albicans by Extending α-1,6-Mannose Backbone to Evade Host Dectin-1 Mediated Antifungal Immunity

    Science.gov (United States)

    Zhang, Shi Qun; Zou, Zui; Shen, Hui; Shen, Shuai Shuai; Miao, Qi; Huang, Xin; Liu, Wei; Li, Li Ping; Chen, Si Min; Yan, Lan; Zhang, Jun Dong; Zhao, Jing Jun; Xu, Guo Tong; An, Mao Mao; Jiang, Yuan Ying

    2016-01-01

    The cell wall is a dynamic structure that is important for the pathogenicity of Candida albicans. Mannan, which is located in the outermost layer of the cell wall, has been shown to contribute to the pathogenesis of C. albicans, however, the molecular mechanism by which this occurs remains unclear. Here we identified a novel α-1,6-mannosyltransferase encoded by MNN10 in C. albicans. We found that Mnn10 is required for cell wall α-1,6-mannose backbone biosynthesis and polysaccharides organization. Deletion of MNN10 resulted in significant attenuation of the pathogenesis of C. albicans in a murine systemic candidiasis model. Inhibition of α-1,6-mannose backbone extension did not, however, impact the invasive ability of C. albicans in vitro. Notably, mnn10 mutant restored the invasive capacity in athymic nude mice, which further supports the notion of an enhanced host antifungal defense related to this backbone change. Mnn10 mutant induced enhanced Th1 and Th17 cell mediated antifungal immunity, and resulted in enhanced recruitment of neutrophils and monocytes for pathogen clearance in vivo. We also demonstrated that MNN10 could unmask the surface β-(1,3)-glucan, a crucial pathogen-associated molecular pattern (PAMP) of C. albicans recognized by host Dectin-1. Our results demonstrate that mnn10 mutant could stimulate an enhanced Dectin-1 dependent immune response of macrophages in vitro, including the activation of nuclear factor-κB, mitogen-activated protein kinase pathways, and secretion of specific cytokines such as TNF-α, IL-6, IL-1β and IL-12p40. In summary, our study indicated that α-1,6-mannose backbone is critical for the pathogenesis of C. albicans via shielding β-glucan from recognition by host Dectin-1 mediated immune recognition. Moreover, our work suggests that inhibition of α-1,6-mannose extension by Mnn10 may represent a novel modality to reduce the pathogenicity of C. albicans. PMID:27144456

  18. Energies and 2 '-Hydroxyl Group Orientations of RNA Backbone Conformations. Benchmark CCSD(T)/CBS Database, Electronic Analysis, and Assessment of DFT Methods and MD Simulations

    Czech Academy of Sciences Publication Activity Database

    Mládek, Arnošt; Banáš, P.; Jurečka, P.; Otyepka, M.; Zgarbová, M.; Šponer, Jiří

    2014-01-01

    Roč. 10, č. 1 (2014), s. 463-480. ISSN 1549-9618 R&D Projects: GA ČR(CZ) GAP208/12/1878; GA MŠk(CZ) ED1.1.00/02.0068 Institutional support: RVO:68081707 Keywords : DENSITY-FUNCTIONAL THEORY * SUGAR-PHOSPHATE BACKBONE * QUANTUM-CHEMICAL CALCULATIONS Subject RIV: BO - Biophysics Impact factor: 5.498, year: 2014

  19. Investigation of novel solid oxide fuel cell cathodes based on impregnation of SrTixFe1-xO3-δ into ceria-based backbones

    DEFF Research Database (Denmark)

    Brinch-Larsen, Mathias; Søgaard, Martin; Hjelm, Johan;

    2013-01-01

    performance is believed to originate from poor electronic conduction in the electrodes and possibly also reactions between Sr-containing compounds and CGO. To circumvent the low electronic conductivity, backbones of a composite cathode containing LaCo0.4Ni0.6O 3-δ (LCN60) and CGO were also tried infiltrated......Solid oxide fuel cell (SOFC) cathodes were prepared by impregnating the nitrates corresponding to SrTixFe1-xO3-δ (STF), x= 0; 0.1; 0.2; 0.3; 0.4 and 0.5, into a porous backbone of Ce 0.9Gd0.1O2-δ (CGO). STF was chosen as very high oxygen surface exchange rate, high ionic conductivity and...... backbone. All prepared electrodes were characterized as symmetric cells using impedance spectroscopy. Within the investigated series the infiltrate with x = 0.1 (STF10) showed the best performance with an area specific resistance (ASR) of ASR ≈ 6.4 Ω cm2 (STF10) at 600°C in air. The relatively poor...

  20. Transgene sequences free of CG dinucleotides lead to high level, long-term expression in the lung independent of plasmid backbone design.

    Science.gov (United States)

    Bazzani, Reto P; Pringle, Ian A; Connolly, Mary M; Davies, Lee A; Sumner-Jones, Stephanie G; Schleef, Martin; Hyde, Stephen C; Gill, Deborah R

    2016-07-01

    Non-viral aerosol gene therapy offers great potential for treating chronic lung diseases of the airways such as cystic fibrosis (CF). Early clinical trials showed that transgene expression in the airways was transient whereas maximal duration of transgene expression is essential in order to minimise the frequency of aerosol treatments. Improved vector design, such as careful selection of the promoter/enhancer, can lead to more persistent levels of transgene expression, but multiple factors affect expression in vivo. Following aerosol delivery to the lungs of mice, we measured reporter gene expression from a CpG-free luciferase transgene cassette in the context of both a plasmid and minicircle vector configuration and showed that the vector backbone had no effect on expression. Transgene activity was affected by the vector backbone however, when a similar, but sub-optimal CpG-containing transgene was used, suggesting that aspects of the plasmid backbone had a negative impact on transgene expression. Similar studies were performed in Toll-like receptor-9 (TLR9) knockout mice to investigate a potential role for the TLR9 signalling pathway in detecting CpGs in the vector sequence. Even in the absence of TLR9, persistent expression could only be achieved with a CpG-free transgene. Together, these data indicate that in order to achieve high levels of persistent expression in vivo, a CpG-free transgene cassette is required. PMID:27061267

  1. In Sup35p filaments (the [PSI+] prion), the globular C-terminal domains are widely offset from the amyloid fibril backbone

    Energy Technology Data Exchange (ETDEWEB)

    Baxa, U.; Wall, J.; Keller, P. W.; Cheng, N.; Steven, A. C.

    2011-01-01

    In yeast cells infected with the [PSI+] prion, Sup35p forms aggregates and its activity in translation termination is downregulated. Transfection experiments have shown that Sup35p filaments assembled in vitro are infectious, suggesting that they reproduce or closely resemble the prion. We have used several EM techniques to study the molecular architecture of filaments, seeking clues as to the mechanism of downregulation. Sup35p has an N-terminal 'prion' domain; a highly charged middle (M-)domain; and a C-terminal domain with the translation termination activity. By negative staining, cryo-EM and scanning transmission EM (STEM), filaments of full-length Sup35p show a thin backbone fibril surrounded by a diffuse 65-nm-wide cloud of globular C-domains. In diameter ({approx}8 nm) and appearance, the backbones resemble amyloid fibrils of N-domains alone. STEM mass-per-unit-length data yield -1 subunit per 0.47 nm for N-fibrils, NM-filaments and Sup35p filaments, further supporting the fibril backbone model. The 30 nm radial span of decorating C-domains indicates that the M-domains assume highly extended conformations, offering an explanation for the residual Sup35p activity in infected cells, whereby the C-domains remain free enough to interact with ribosomes.

  2. Ischemia detection from morphological QRS angle changes.

    Science.gov (United States)

    Romero, Daniel; Martínez, Juan Pablo; Laguna, Pablo; Pueyo, Esther

    2016-07-01

    In this paper, an ischemia detector is presented based on the analysis of QRS-derived angles. The detector has been developed by modeling ischemic effects on the QRS angles as a gradual change with a certain transition time and assuming a Laplacian additive modeling error contaminating the angle series. Both standard and non-standard leads were used for analysis. Non-standard leads were obtained by applying the PCA technique over specific lead subsets to represent different potential locations of the ischemic zone. The performance of the proposed detector was tested over a population of 79 patients undergoing percutaneous coronary intervention in one of the major coronary arteries (LAD (n  =  25), RCA (n  =  16) and LCX (n  =  38)). The best detection performance, obtained for standard ECG leads, was achieved in the LAD group with values of sensitivity and specificity of [Formula: see text], [Formula: see text], followed by the RCA group with [Formula: see text], Sp  =  94.4 and the LCX group with [Formula: see text], [Formula: see text], notably outperforming detection based on the ST series in all cases, with the same detector structure. The timing of the detected ischemic events ranged from 30 s up to 150 s (mean  =  66.8 s) following the start of occlusion. We conclude that changes in the QRS angles can be used to detect acute myocardial ischemia. PMID:27243441

  3. Small Angle Light Scattering by Biological Objects

    International Nuclear Information System (INIS)

    In this paper the small angle laser radiation scattering by the particles of different shape and size is analyzed. Experimental results and theoretical calculations show that after ejection from bacteriophage DNA forms the scattering medium consisted of quasi-spherical elements with radius of R⁓10λ0. (author)

  4. Association between Bolton discrepancy and Angle malocclusions

    Directory of Open Access Journals (Sweden)

    Rodrigo Hermont CANÇADO

    2015-01-01

    Full Text Available This study aimed to assess and compare the overall and anterior ratios of tooth size discrepancies in all Angle malocclusion groups. The following null hypothesis (H0 was tested: no difference between tooth size discrepancies (overall and anterior would be observed among Angle malocclusion groups. The sample comprised of 711 pre-orthodontic treatment study casts of Brazilian patients with a mean age of 17.42 years selected from private practices in Brazil. The casts were divided into 3 groups according to the type of malocclusion: Class I (n = 321, Class II (n = 324, and Class III patients (n = 66. The measurement of the greatest mesiodistal width of the teeth was performed using a centesimal precision digital caliper directly on the study casts, from the distal surface of the left first molar to the distal surface of the right first molar. The overall and anterior ratios between the maxillary and mandibular teeth were evaluated using Bolton’s method. The following statistical tests were applied: chi-square, independent t-test, and one-way ANOVA. Results showed that all Angle malocclusions groups exhibited a ratio compatible with those recommended by Bolton. With respect to the overall and anterior ratios among the malocclusion groups, no statistically significant differences were found. The null hypothesis was accepted because the results showed no differences in the overall and anterior ratios of tooth size discrepancies among different Angle malocclusion groups.

  5. Testing CMB polarization data using position angles

    CERN Document Server

    Preece, Michael

    2014-01-01

    We consider a novel null test for contamination which can be applied to CMB polarization data that involves analysis of the statistics of the polarization position angles. Specifically, we will concentrate on using histograms of the measured position angles to illustrate the idea. Such a test has been used to identify systematics in the NVSS point source catalogue with an amplitude well below the noise level. We explore the statistical properties of polarization angles in CMB maps. If the polarization angle is not correlated between pixels, then the errors follow a simple $\\sqrt{N_{pix}}$ law. However this is typically not the case for CMB maps since these have correlations which result in an increase in the variance since the effective number of independent pixels is reduced. Then we illustrate how certain classes of systematic errors can result in very obvious patterns in these histograms, and thus that these errors could possibly be identified using this method. We discuss how this idea might be applied in...

  6. Status of the CDF small angle spectrometer

    International Nuclear Information System (INIS)

    During the 1987 Tevatron collider period the CDF small angle spectrometer system was partially installed and elastic scattering events were recorded in a special high-β run. The design and physics goals of this system are described and results from an analysis of the elastic scattering data are discussed

  7. Improved Beam Angle Control with SPV Metrology

    International Nuclear Information System (INIS)

    A method of real-time monitoring of implant angle for state-of-the-art ion implant doping in integrated circuit manufacturing has been developed using Surface Photo Voltage measurements on conventional monitor wafers. Measurement results are analyzed and compared to other techniques.

  8. Veering triangulations admit strict angle structures

    CERN Document Server

    Hodgson, Craig D; Segerman, Henry; Tillmann, Stephan

    2010-01-01

    Agol recently introduced the concept of a veering taut triangulation, which is a taut triangulation with some extra combinatorial structure. We define the weaker notion of a "veering triangulation" and use it to show that all veering triangulations admit strict angle structures. We also answer a question of Agol, giving an example of a veering taut triangulation that is not layered.

  9. Experimental technique of small angle neutron scattering

    International Nuclear Information System (INIS)

    The main parts of Small Angle Neutron Scattering (SANS) spectrometer, and their function and different parameters are introduced from experimental aspect. Detailed information is also introduced for SANS spectrometer 'Membrana-2'. Based on practical experiments, the fundamental requirements and working condition for SANS experiments, including sample preparation, detector calibration, standard sample selection and data preliminary process are described. (authors)

  10. Mie scattering near the critical angle

    International Nuclear Information System (INIS)

    Complex angular momentum theory is applied to the problem of high-frequency critical light scattering by a spherical cavity near the critical angle. The main contributions to the scattering arise from a critical domain close to critical incidence. The results are in good agreement with the exact Mie solution. (author)

  11. SANS-1: Small angle neutron scattering

    OpenAIRE

    Heinemann, André; Mühlbauer, Sebastian

    2015-01-01

    The new small angle scattering instrument SANS-1, jointly operated by the Technische Universität München and GEMS, Helmholtz-Zentrum Geesthacht, has completed commissioning and is in regular user service (Gilles et al., 2006). SANS-1 is located at the end of neutron guide NL4a in the Neutron Guide Hall West.

  12. Small angle neutron scattering in invar alloys

    International Nuclear Information System (INIS)

    Some results of low angle neutron scattering on 70-30 and 65-35 FeNi alloys are presented showing the existence of chemical small clusters associated with a magnetization inhomogeneity. A noticeable result is the appearance of a pseudo-periodical magnetization static fluctuation in a 65-35 FeNi alloy after irradiation with 2 MeV electrons

  13. 聚酰亚胺主链结构对液晶取向膜性能的影响%Properties of polyimide liquid crystal alignment layer with different backbone structure

    Institute of Scientific and Technical Information of China (English)

    刘露露; 刘明; 龚世铭; 汪映寒

    2015-01-01

    A series polyimides (PIs)were prepared by one-step method.These PIs were comprised of a functional diamine N,N-bis (4-aminophenyl )-4-(dodecylo-xy-biphenyl )-4′-amino-phenylether (C1 2 -BAAPE),one of two commercially available diamines 2,2′-Bis(trifluoromethy-l)-4,4′-diaminobiphe-nyl (TFDB),4,4′-Oxydianiline (ODA)and one of two dianhydride 4,4′-(hexafluoroisopropylidene) diphthalic anhydride (6FDA)and 4,4′-Oxydiphthalic anhydride (ODPA)in order to get different backbone structures.The structures and thermo properties of these PIs were characterized by NMR, FT-IR,DSC and TGA.Pretilt angles and alignment abilities were carried out by pretilt angle tester and polarization microscope.Solubility of PIs was tested by dissolving PIs in various organic solvents. DSC and TGA curves showed that PI-2 had higher glass transition temperature (T g )and decomposi-tion temperature (T d )than PI-1 and PI-3.Three PI films presented vertical alignment before mechan-ical rubbing and only PI-2 maintained it after rubbing process.Conformations of these PIs were simu-lated by Material Studio (MS).The vertical conformation existed in PI-2 ’s backbones improved rubbing resistance and showed vertical alignment ability after rubbing.%采用一步法,以 N,N-二(4-氨基苯基)-4-(十二烷氧基联苯基)-4’-氨基苯醚(C12-BAAPE)为控制预倾角的功能性二胺,2,2’-双三氟甲基-4,4’-联苯二胺(TFDB)或4,4’-二氨基二苯醚(ODA)为辅助二胺,分别与2,2’-双(3,4-二羧苯基)六氟丙烷四羧酸二酐(6FDA)和4,4’-联苯醚二酐(ODPA)聚合,得到三种主链结构不同的聚酰亚胺(PI-1、PI-2和PI-3)。利用 NMR、FT-IR、DSC、TGA、偏光显微镜和预倾角测试仪对聚合物的结构、热性能以及制备的液晶盒的取向性进行了表征,同时测试了3种 PI 的溶解性能。结果表明,PI-2液晶取向膜的耐摩擦性能明显优于 PI-1和 PI-3,且具有更高的玻璃化转变温度(T g )和分解温度(T d ),更好

  14. Correlating the P-31 NMR Chemical Shielding Tensor and the (2)J(P,C) Spin-Spin Coupling Constants with Torsion Angles zeta and alpha in the Backbone of Nucleic Acids

    Czech Academy of Sciences Publication Activity Database

    Benda, Ladislav; Sochorová Vokáčová, Zuzana; Straka, Michal; Sychrovský, Vladimír

    2012-01-01

    Roč. 116, č. 12 (2012), s. 3823-3833. ISSN 1520-6106 R&D Projects: GA ČR GAP205/10/0228; GA ČR GPP208/10/P398; GA ČR GA203/09/2037 Institutional research plan: CEZ:AV0Z40550506 Keywords : nucleic acids * phosphorus NMR * NMR calculations * cross-correlated relaxation * spin–spin coupling constants Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.607, year: 2012

  15. n Silico Analysis of Envelope Dengue Virus-2 and Envelope Dengue Virus-3 Protein as the Backbone of Dengue Virus Tetravalent Vaccine by Using Homology Modeling Method

    Directory of Open Access Journals (Sweden)

    Rizky I. Taufik

    2009-01-01

    Full Text Available Problem statement: Dengue fever, which was caused by Dengue virus infection, had became a major public health problem in the tropic and subtropical countries. Dengue virus (DENV had four serotypes (DENV-1, DENV-2, DENV-3 and DENV-4, based on their immunogenic in the human body. Preventive measure will be necessary to decrease the prevalence of dengue fever, by developing modern vaccine. Approach: This research was focused on in silico study of dengue virus vaccines, by using envelope (E protein of DENV-2 and DENV-3 as their backbones. T cell epitope prediction was determined by using MULTIPRED server and B cell epitope prediction was determined by using Conformational Epitope Prediction server (CEP. Homology modeling study of E DENV-3 protein as the vaccine backbone had produced six dengue vaccine peptides (HMM Vaccine 1-6. Moreover, homology modeling study of E DENV-2 protein as vaccine backbone had produced six dengue vaccine peptides (ANN vaccine 1-6. Results: The BLAST analysis of HMM and ANN vaccines had produced 93% and 91% identity, respectively. The Ramachandran Plot of both vaccines had shown less than 15% non glycine residue in the disallowed region, therefore it showed the solid stability of the proteins. The VAST analysis of E DENV-3 backbone vaccines had determined, that HMM4 and HMM6 had the highest structure similarity with native E DENV-3. HMM4 and HMM6 had the highest VAST score of 64.5. Moreover, the VAST analysis of E DENV-2 backbone vaccines had determined, that ANN1, ANN3, ANN4, ANN5 and ANN6 had the highest structure similarity with native E DENV-2. ANN1, ANN3, ANN4, ANN5 and ANN6 have the highest VAST score of 64.7. Conclusion/Recommendation: It could be inferred from this research that HMM4; HMM6; ANN1; ANN3; ANN4; ANN5; and ANN6 were the best in silico vaccine design, based on their similarity with native E DENV Proteins. This research could be applied for the wet

  16. Selectively dispersed isotope labeling for protein structure determination by magic angle spinning NMR

    Energy Technology Data Exchange (ETDEWEB)

    Eddy, Matthew T. [Massachusetts Institute of Technology, Department of Chemistry (United States); Belenky, Marina [Brandeis University, Department of Chemistry (United States); Sivertsen, Astrid C. [Massachusetts Institute of Technology, Francis Bitter Magnet Laboratory (United States); Griffin, Robert G. [Massachusetts Institute of Technology, Department of Chemistry (United States); Herzfeld, Judith, E-mail: herzfeld@brandeis.edu [Brandeis University, Department of Chemistry (United States)

    2013-10-15

    The power of nuclear magnetic resonance spectroscopy derives from its site-specific access to chemical, structural and dynamic information. However, the corresponding multiplicity of interactions can be difficult to tease apart. Complimentary approaches involve spectral editing on the one hand and selective isotope substitution on the other. Here we present a new 'redox' approach to the latter: acetate is chosen as the sole carbon source for the extreme oxidation numbers of its two carbons. Consistent with conventional anabolic pathways for the amino acids, [1-{sup 13}C] acetate does not label {alpha} carbons, labels other aliphatic carbons and the aromatic carbons very selectively, and labels the carboxyl carbons heavily. The benefits of this labeling scheme are exemplified by magic angle spinning spectra of microcrystalline immunoglobulin binding protein G (GB1): the elimination of most J-couplings and one- and two-bond dipolar couplings provides narrow signals and long-range, intra- and inter-residue, recoupling essential for distance constraints. Inverse redox labeling, from [2-{sup 13}C] acetate, is also expected to be useful: although it retains one-bond couplings in the sidechains, the removal of CA-CO coupling in the backbone should improve the resolution of NCACX spectra.

  17. Small-angle neutron scattering investigation of polyurethane aged in dry and wet air

    Directory of Open Access Journals (Sweden)

    Q. Tian

    2014-05-01

    Full Text Available The microstructures of Estane 5703 aged at 70°C in dry and wet air have been studied by small-angle neutron scattering. The samples were swollen in deuterated toluene for enhancing the contrast. The scattering data show the characteristic domain structure of polyurethanes consisting of soft and hard segments. Debye-Anderson-Brumberger function used with hard sphere structure factor, and the Teubner-Strey model are used to analyze the two-phase domain structure of the polymer. The combined effects of temperature and humidity have a strong disruption effect on the microstructures of Estane. For the sample aged at 70°C in wet air for 1 month, the domain size, described by the correlation length, increases from 2.3 to 3.8 nm and their distance, expressed by hard-sphere interaction radius, increases from 8.4 to 10.6 nm. The structure development is attributed to degradation of polymer chains as revealed by gel permeation chromatography. The hydrolysis of ester links on polymer backbone at 70°C in the presence of water humidity is the main reason for the changes of the microstructure. These findings can contribute to developing predictive models for the safety, performance, and lifetime of polyurethanes.

  18. Gaia: focus, straylight and basic angle

    CERN Document Server

    Mora, A; Bombrun, A; Boyadian, J; Chassat, F; Corberand, P; Davidson, M; Doyle, D; Escolar, D; Gielesen, W L M; Guilpain, T; Hernandez, J; Kirschner, V; Klioner, S A; Koeck, C; Laine, B; Lindegren, L; Serpell, E; Tatry, P; Thoral, P

    2016-01-01

    The Gaia all-sky astrometric survey is challenged by several issues affecting the spacecraft stability. Amongst them, we find the focus evolution, straylight and basic angle variations Contrary to pre-launch expectations, the image quality is continuously evolving, during commissioning and the nominal mission. Payload decontaminations and wavefront sensor assisted refocuses have been carried out to recover optimum performance. An ESA-Airbus DS working group analysed the straylight and basic angle issues and worked on a detailed root cause analysis. In parallel, the Gaia scientists have also analysed the data, most notably comparing the BAM signal to global astrometric solutions, with remarkable agreement. In this contribution, a status review of these issues will be provided, with emphasis on the mitigation schemes and the lessons learned for future space missions where extreme stability is a key requirement.

  19. Choroidal physiology and primary angle closure disease.

    Science.gov (United States)

    Zhang, Xiulan; Wang, Wei; Aung, Tin; Jonas, Jost B; Wang, Ningli

    2015-01-01

    Primary angle closure disease (PACD), prevalent in Asian countries, is generally associated with a shallower anterior chamber, a shorter axial length, thicker lens, hyperopia, and female sex. Other physiologic factors, however, may be important, especially with regard to triggering acute primary angle closure. Thickening of the choroid has been demonstrated in untreated and treated, acute and chronic PACD eyes. Recently, there has been growing interest in studying the role of the choroid in the pathophysiology of PACD. The emergence of new imaging technology such as the enhanced depth imaging mode of spectral-domain optical coherence tomography and swept-source optical coherence tomography has contributed to understanding PACD pathologies. We summarize the functions of the choroid and choroidal changes in the pathogenesis of PACD, and discuss potential future developments. PMID:26164737

  20. Weak mixing angle measurements at hadron colliders

    CERN Document Server

    Di Simone, Andrea; The ATLAS collaboration

    2015-01-01

    The Talk will cover weak mixing angle measurements at hadron colliders ATLAS and CMS in particular. ATLAS has measured the forward-backward asymmetry for the neutral current Drell Yan process in a wide mass range around the Z resonance region using dielectron and dimuon final states with $\\sqrt{s}$ =7 TeV data. For the dielectron channel, the measurement includes electrons detected in the forward calorimeter which extends the covered phase space. The result is then used to extract a measurement of the effective weak mixing angle. Uncertainties from the limited knowledge on the parton distribution functions in the proton constitute a significant part of the uncertainty and a dedicated study is performed to obtain a PDF set describing W and Z data measured previously by ATLAS. Similar studies from CMS will be reported.

  1. The Contact Angle in Inviscid Fluid Mechanics

    Indian Academy of Sciences (India)

    P N Shankar; R Kidambi

    2005-05-01

    We show that in general, the specification of a contact angle condition at the contact line in inviscid fluid motions is incompatible with the classical field equations and boundary conditions generally applicable to them. The limited conditions under which such a specification is permissible are derived;however, these include cases where the static meniscus is not flat. In view of this situation, the status of the many `solutions’ in the literature which prescribe a contact angle in potential flows comes into question. We suggest that these solutions which attempt to incorporate a phenomenological, but incompatible, condition are in some, imprecise sense `weak-type solutions’;they satisfy or are likely to satisfy, at least in the limit, the governing equations and boundary conditions everywhere except in the neighbourhood of the contact line. We discuss the implications of the result for the analysis of inviscid flows with free surfaces.

  2. Sparse regularization in limited angle tomography

    CERN Document Server

    Frikel, Jürgen

    2011-01-01

    We investigate the reconstruction problem of limited angle tomography. Such problems arise naturally in applications like digital breast tomosynthesis, dental tomography, electron microscopy etc. Since the acquired tomographic data is highly incomplete, the reconstruction problem is severely ill-posed and the traditional reconstruction methods, such as filtered backprojection (FBP), do not perform well in such situations. To stabilize the reconstruction procedure additional prior knowledge about the unknown object has to be integrated into the reconstruction process. In this work, we propose the use of the sparse regularization technique in combination with curvelets. We argue that this technique gives rise to an edge-preserving reconstruction. Moreover, we show that the dimension of the problem can be significantly reduced in the curvelet domain. To this end, we give a characterization of the kernel of limited angle Radon transform in terms of curvelets and derive a characterization of solutions obtained thr...

  3. Modeling small angle scattering data using FISH

    International Nuclear Information System (INIS)

    Full text: Small angle neutron scattering (SANS) and small angle x-ray scattering (SAXS) are important techniques for the characterisation of samples on the nanometer scale. From the scattered intensity pattern information about the sample such as particle size distribution, concentration and particle interaction can be determined. Since the experimental data is in reciprocal space and information is needed about real space, modeling of the scattering data to obtain parameters is extremely important and several paradigms are available. The use of computer programs to analyze the data is imperative for a robust description of the sample to be obtained. This presentation gives an overview of the SAS process and describes the data-modeling program FISH, written by R. Heenan 1983-2000. The results of using FISH to obtain the particle size distribution of bubbles in the aluminum hydrogen system and other systems of interest are described. Copyright (2002) Australian X-ray Analytical Association Inc

  4. Dancing droplets: Contact angle, drag, and confinement

    Science.gov (United States)

    Benusiglio, Adrien; Cira, Nate; Prakash, Manu

    2015-11-01

    When deposited on a clean glass slide, a mixture of water and propylene glycol forms a droplet of given contact angle, when both pure liquids spread. (Cira, Benusiglio, Prakash: Nature, 2015). The droplet is stabilized by a gradient of surface tension due to evaporation that induces a Marangoni flow from the border to the apex of the droplets. The apparent contact angle of the droplets depends on both their composition and the external humidity as captured by simple models. These droplets present remarkable properties such as lack of a large pinning force. We discuss the drag on these droplets as a function of various parameters. We show theoretical and experimental results of how various confinement geometries change the vapor gradient and the dynamics of droplet attraction.

  5. The small angle diffractometer SANS at PSI

    Energy Technology Data Exchange (ETDEWEB)

    Wagner, W. [Paul Scherrer Inst. (PSI), Villigen (Switzerland)

    1996-11-01

    With the start-up of SINQ an instrument for small angle neutron scattering will be operational which compares well with the world`s largest and most powerful facilities of this kind. Following the classical principle of the D11-instrument of ILL, it is equipped with state-of-the-art components as are nowadays available, including options for further upgrading. Great emphasis was laid upon providing a flexible, universal multi-user facility which guarantees a comfortable and reliable operation. In the present paper, the principle layout of the instrument is presented, and the individual components are described in detail. The paper concludes with model application of small angle scattering to a system of dilute CuCo alloys which undergo a phase separation under thermal treatment, forming spherical Co-precipitates dispersed in a Cu-rich matrix. (author) 3 figs., 1 tab., 14 refs.

  6. Foreign Body Embedded in Anterior Chamber Angle

    OpenAIRE

    Shmuel Graffi; Beatrice Tiosano; Ran Ben Cnaan; Jonathan Bahir; Modi Naftali

    2012-01-01

    Introduction. We present a case of a metallic foreign body embedded in the anterior chamber angle. After standing in close proximity to a construction worker breaking a tile, a 26-year-old woman using soft contact lens for the correction of mild myopia presented to emergency department for evaluation of a foreign body sensation of her right eye. Methods and Results. Diagnosis was confirmed by gonioscopic examination and a noncontrast CT scan of head and orbits. The foreign body was removed by...

  7. Cognitive models for the concept of angle

    OpenAIRE

    Matos, José Manuel Leonardo de

    1999-01-01

    The instructional models taught in class were similar to the students' models. The teachers addressed angle as a basic-level category, discussed its submodels, clarified the boundaries, and established cognitive reference points. They gradually increased the use of complex metaphors and of several models. The study enriched the characterization of the first two levels of van Hiele theory and demonstrated the value of categorization theory in understanding how our comprehension ...

  8. Lorentz angle measurements in silicon detectors

    Energy Technology Data Exchange (ETDEWEB)

    Bartsch, V.; Boer, W. de E-mail: wim.de.boer@cern.ch; Bol, J.; Dierlamm, A.; Grigoriev, E.; Hauler, F.; Heising, S.; Herz, O.; Jungermann, L.; Keraenen, R.; Koppenhoefer, M.; Roederer, F.; Schneider, T

    2002-02-01

    In this paper we study the Lorentz angles of both electrons and holes in magnetic fields up to 8 T and temperatures between 77 and 300 K. This is done before and after irradiating a detector with 21 MeV protons up to a fluence of 10{sup 13}/cm{sup 2}, which is equivalent to {approx}2.8x10{sup 13}/cm{sup 2} 1 MeV neutrons.

  9. Low angle resistivity anomaly in layered superconductors

    International Nuclear Information System (INIS)

    The pinning effect of vortex lines by the layered structure (intrinsic pinning) on resistivity of high-Tc, superconductors in the mixed state is investigated by means of perturbation theory. A sharp drop in the resistivity at small angles for which vortex lines are almost aligned with the ab-planes is shown to occur even in a high-temperature region where the pinning potential is reduced by thermal fluctuations

  10. Angles between subspaces computed in Clifford Algebra

    OpenAIRE

    Hitzer, Eckhard

    2013-01-01

    We first review the definition of the angle between subspaces and how it is computed using matrix algebra. Then we introduce the Grassmann and Clifford algebra description of subspaces. The geometric product of two subspaces yields the full relative angular information in an explicit manner. We explain and interpret the result of the geometric product of subspaces gaining thus full practical access to the relative orientation information.

  11. Studies in small angle scattering techniques

    International Nuclear Information System (INIS)

    Small angle scattering of neutrons, X-rays and γ-rays are found among the spectroscopic methods developed in the recent years. Although these techniques differ from each other in many respects, e.g. radiation sources and technical equipment needed, their power to resolve physical phenomena and areas of application can be discussed in a general scheme. Selected examples are given illustrating the use of specific technical methods. Jahn-Teller driven structural phase transitions in Rare Earth zircons were studied with neutron scattering as well as small angle γ-ray diffraction. The study of neutron scattering from formations of magnetic domains in the Ising ferromagnet LiTbF4 is a second example. Both these examples represent more than experimental test cases since the theoretical interpretations of the data obtained are discussed as well. As a last example the use of small angle scattering methods for the study of molecular biological samples is discussed. In particular the experimental procedures used in connection with scattering from aqueous solutions of proteins and protein complexes are given. (Auth.)

  12. Moment-angle complexes from simplicial posets

    CERN Document Server

    Lu, Zhi

    2009-01-01

    We extend the construction of moment-angle complexes to simplicial posets by associating a certain T^m-space Z_S to an arbitrary simplicial poset S on m vertices. Face rings Z[S] of simplicial posets generalise those of simplicial complexes, but have much more complicated algebraic structure. Our primary motivation is to study the face rings Z[S] by topological methods. The space Z_S has many important topological properties of the original moment-angle complex Z_K associated to a simplicial complex K. In particular, we prove that the integral cohomology algebra of Z_S is isomorphic to the Tor-algebra of the face ring Z[S]. This leads directly to a generalisation of Hochster's theorem, expressing the algebraic Betti numbers of the ring Z[S] in terms of the homology of full subposets in S. Finally, we estimate the total amount of homology of Z_S from below by proving the toral rank conjecture for the moment-angle complexes Z_S.

  13. Off-Angle Iris Correction Methods

    Energy Technology Data Exchange (ETDEWEB)

    Santos-Villalobos, Hector J [ORNL; Thompson, Joseph T [ORNL; Karakaya, Mahmut [ORNL; Boehnen, Chris Bensing [ORNL

    2016-01-01

    In many real world iris recognition systems obtaining consistent frontal images is problematic do to inexperienced or uncooperative users, untrained operators, or distracting environments. As a result many collected images are unusable by modern iris matchers. In this chapter we present four methods for correcting off-angle iris images to appear frontal which makes them compatible with existing iris matchers. The methods include an affine correction, a retraced model of the human eye, measured displacements, and a genetic algorithm optimized correction. The affine correction represents a simple way to create an iris image that appears frontal but it does not account for refractive distortions of the cornea. The other method account for refraction. The retraced model simulates the optical properties of the cornea. The other two methods are data driven. The first uses optical flow to measure the displacements of the iris texture when compared to frontal images of the same subject. The second uses a genetic algorithm to learn a mapping that optimizes the Hamming Distance scores between off-angle and frontal images. In this paper we hypothesize that the biological model presented in our earlier work does not adequately account for all variations in eye anatomy and therefore the two data-driven approaches should yield better performance. Results are presented using the commercial VeriEye matcher that show that the genetic algorithm method clearly improves over prior work and makes iris recognition possible up to 50 degrees off-angle.

  14. Orientation Preferences of Backbone Secondary Amide Functional Groups in Peptide Nucleic Acid Complexes: Quantum Chemical Calculations Reveal an Intrinsic Preference of Cationic D-Amino Acid-Based Chiral PNA Analogues for the P-form

    OpenAIRE

    Topham, Christopher M.; Smith, Jeremy C.

    2006-01-01

    Geometric descriptions of nonideal interresidue hydrogen bonding and backbone-base water bridging in the minor groove are established in terms of polyamide backbone carbonyl group orientation from analyses of residue junction conformers in experimentally determined peptide nucleic acid (PNA) complexes. Two types of interresidue hydrogen bonding are identified in PNA conformers in heteroduplexes with nucleic acids that adopt A-like basepair stacking. Quantum chemical calculations on the bindin...

  15. Perceptions of tilt angles of an agricultural tractor.

    Science.gov (United States)

    Görücü, Serap; Cavallo, Eugenio; Murphy, Dennis

    2014-01-01

    A tractor stability simulator has been developed to help study tractor operators' perceptions of angles when the simulator is tilted to the side. The simulator is a trailer-mounted tractor cab equipped with hydraulic lift that can tilt the tractor cabin up to 30 degrees. This paper summarizes data from 82 participants who sat in the simulator while it was tilted. Demographic variables, estimates of tilt angles, and measured tilt angles were collected. The effects of age, gender, tractor driving experience, and frequency of operation on the estimated and measured tilt angles were analyzed. The results showed that about 50% of the participants reported estimations of side tilt angles within ±5 degrees of the actual angles, and nearly the same percentage overestimated the actual side tilt angles. Only a small percentage underestimated the angles. Older, more experienced, and male participants set higher limits on the actual angle at which they felt uncomfortable and would not drive. PMID:24417527

  16. Exopolysaccharide Biosynthesis in Lactococcus lactis NIZO B40: Functional Analysis of the Glycosyltransferase Genes Involved in Synthesis of the Polysaccharide Backbone

    OpenAIRE

    Kranenburg, Richard van; van Swam, Iris I.; Marugg, Joey D.; Kleerebezem, Michiel; de Vos, Willem M.

    1999-01-01

    We used homologous and heterologous expression of the glycosyltransferase genes of the Lactococcus lactis NIZO B40 eps gene cluster to determine the activity and substrate specificities of the encoded enzymes and established the order of assembly of the trisaccharide backbone of the exopolysaccharide repeating unit. EpsD links glucose-1-phosphate from UDP-glucose to a lipid carrier, EpsE and EpsF link glucose from UDP-glucose to lipid-linked glucose, and EpsG links galactose from UDP-galactos...

  17. Effects of a vanadium post-metallocene catalyst-induced polymer backbone inhomogeneity on UV oxidative degradation of the resulting polyethylene film

    KAUST Repository

    Atiqullah, M.

    2012-07-01

    A Group 5 post-metallocene precatalyst, (ONO)VCl(THF) 2 (ONO = a bis(phenolate)pyridine LX 2 pincer ligand), activated with modified methylaluminoxane (MMAO-3A) produced a linear ethylene homopolymer (nm-HomoPE)and an unusual inhomogeneous copolymer (nm-CopolyPE) with 1-hexene having very low backbone unsaturation. The nm-CopolyPE inhomogeneity was reflected in the distributions of short chain branches, 1-hexene composition, and methylene sequence length. The 1-hexene incorporation into the polyethylene backbone strongly depended on the molecular weight of the growing polymer chain. (ONO)VCl(THF) 2, because of site diversity and easier removal of a tertiary (vs. a secondary) hydrogen, produced a skewed short chain branching (SCB) profile, incorporating 1-hexene more efficiently in the low molecular weight region than in the high molecular weight region. The significant decrease in molecular weight by 1-hexene showed that the (ONO)VCl(THF) 2 catalytic sites were also highly responsive to chain-transfer directly to 1-hexene itself, producing vinyl and trans-vinylene termini. Subsequently, the effect of backbone inhomogeneity on the UV oxidative degradation of films made from both polyethylenes was investigated. The major functional group accumulated in the branched nm-CopolyPE film was carbonyl followed by carboxyl, then vinyl/ester, whereas that in the linear nm-HomoPE film was carboxyl. However, (carbonyl, carboxyl, vinyl, and ester) nm-CopolyPE film >> (carboxyl) nm-HomoPE film). The distributions of the tertiary C-H sites and methylene sequence length in the branched nm-CopolyPE film enhanced abstraction of H, decomposition of hydroperoxide group ROOH, and generation of carbonyl compounds as compared with those in the linear nm-HomoPE film. This clearly establishes the role played by the backbone inhomogeneity. The effect of short chain branches and sequence length distributions on peak melting temperature T pm, and most probably lamellar thickness L o, was

  18. The DNA and RNA sugar-phosphate backbone emerges as the key player. An overview of quantum-chemical, structural biology and simulation studies

    Czech Academy of Sciences Publication Activity Database

    Šponer, Jiří; Mládek, Arnošt; Šponer, Judit E.; Svozil, Daniel; Zgarbová, M.; Banáš, Pavel; Jurečka, P.; Otyepka, M.

    2012-01-01

    Roč. 14, č. 44 (2012), s. 15257-15277. ISSN 1463-9076 R&D Projects: GA ČR(CZ) GD203/09/H046; GA ČR(CZ) GAP208/10/2302; GA ČR(CZ) GAP208/11/1822; GA ČR(CZ) GAP208/12/1878; GA ČR(CZ) GA203/09/1476; GA ČR(CZ) GBP305/12/G034 Institutional research plan: CEZ:AV0Z50040702 Keywords : DNA * RNA * sugar -phosphate backbone Subject RIV: BO - Biophysics Impact factor: 3.829, year: 2012

  19. Analyzing biomolecular interactions by variable angle ellipsometry

    Science.gov (United States)

    Wu, Jiun-Yan; Lee, Chih-Kung; Lee, J. H.; Shiue, Shuen-Chen; Lee, Shu-Sheng; Lin, Shiming

    2001-10-01

    In this paper, an innovative ellipsometer is developed and applied to metrology of the biomolecular interaction on a protein biochip. Both the theory, optical and opto-mechanical configurations of this newly developed ellipsometer and methodologies adopted in system design to improve the system performance are presented. It will be shown that by measuring the ellipsometric parameters, the corresponding concentration variation in biochemical reaction can be calculated according to stoichiometry analysis. By applying the variable angle ellipsometry to analysis of a multi-layered sample, the thickness and concentration are resolved. It is believed that the newly developed ellipsometer biosensor is able to undertake an accurate measurement on biomedical interaction.

  20. CDF status report on small angle physics

    International Nuclear Information System (INIS)

    The 1988-1989 Tevatron Collider run at Fermilab was very fruitfull for CDF. More than 4.5 inverse pbarn were written to tape with a trigger emphasizing hard, short distance interactions. A minor part of the run was devoted to special high - beta runs for the measurement of σtot, σel, dσel/dt and of diffraction dissociation. These measurements are performed in CDF with a double-arm magnetic spectrometer at extremely small angles around the beam pipe and a tracking detector surrounding completely the interaction region. The design and the performance of these systems are described and the quality of data is discussed. (orig.)

  1. Small angles Bhabha scattering: two loop approximation

    International Nuclear Information System (INIS)

    The elastic and inelastic cross sections for small angles e+e- scattering at high energies are considered. We prove that all the diagrams with two or more virtual photons in scattering channel may be omitted when calculating the radiative corrections with accuracy of the order 0.1%. It is the consequence of the generalized eikonal representation for elastic and inelastic amplitudes. We take into account the processes of single and double bremsstrahlung in the same and opposite directions and the pair production processes. Basing on this calculations we construct the combined formula for the inclusive scattering electron and positron cross section in terms of the structure functions. 15 refs.; 10 figs

  2. Optimum Staging with Varying Thrust Attitude Angle

    Directory of Open Access Journals (Sweden)

    T. N. Srivastava

    1966-07-01

    Full Text Available Optimum staging programme for step rockets of arbitrary number of stages having different specific impulses and mass fractions with stages is derived, the optimization criterion being minimum take-off weight for a desired burntout velocity at an assigned altitude. Variation of thrust attitude angle from stage to stage and effects of gravity factor are taken into account. Analysis is performed for a degenerate problem obtained by relaxing the altitude constraint and it has been shown that problems of Weisbord, Subotowicz, Hall & Zambelli and Malina & Summerfield are the particular cases of the degenerate problem.

  3. Euler angles as torsional flat spaces

    Science.gov (United States)

    Trejo-Mandujano, Hector A.

    In this work we use general tensor calculus to compare the geodesic equation of motion and Newton's first law for force-free classical systems that are described by an arbitrary number of generalized coordinates in spaces with and without torsion. We choose as objects of study the flat torsional Euler angle metric spaces for rigid rotators. We tested the equivalence of the two motion equations using computational software that allowed algebraic manipulation. The main result is that the equivalence only holds for torsion-free spaces, and for isotropic force-free rotators. We present analytical calculations for the isotropic case and computational results for the general case.

  4. Embedability between right-angled Artin groups

    CERN Document Server

    Kim, Sang-hyun

    2011-01-01

    In this article we study the right-angled Artin subgroups of a given right-angled Artin group. Starting with a graph $\\gam$, we produce a new graph through a purely combinatorial procedure, and call it the extension graph $\\gam^e$ of $\\gam$. We produce a second graph $\\gam^e_k$, the clique graph of $\\gam^e$, by adding extra vertices for each complete subgraph of $\\gam^e$. We prove that each finite induced subgraph $\\Lambda$ of $\\gam^e$ gives rise to an inclusion $A(\\Lambda)\\to A(\\gam)$. Conversely, we show that if there is an inclusion $A(\\Lambda)\\to A(\\gam)$ then $\\Lambda$ is an induced subgraph of $\\gam^e_k$. These results have a number of corollaries. Let $P_4$ denote the path on four vertices and let $C_n$ denote a cycle of length $n$. We prove that $A(P_4)$ embeds in $A(\\gam)$ if and only if $P_4$ is an induced subgraph of $\\gam$. We prove that if $F$ is any finite forest then $A(F)$ embeds in $A(P_4)$. We recover the first author's result on co--contraction of graphs and prove that if $\\gam$ has no tria...

  5. Diphotons, New Vacuum Angles, and Strong CP

    CERN Document Server

    Draper, Patrick

    2016-01-01

    The Standard Model contains a well-understood, natural, spin-0 diphoton resonance: the $\\pi^0$. Numerous studies have pointed out that the hint of a new diphoton resonance at 750 GeV could be a pion analog, identified with the pseudo-Nambu-Goldstone boson of a chiral symmetry spontaneously broken by new strong dynamics at the TeV scale. These "hypercolor" models are generically expected to violate parity through a topological angle $\\tilde\\theta$. We discuss the physics of $\\tilde\\theta$ and its impact on the phenomenology of the new sector. We also describe some of the theoretical implications of a nonzero $\\tilde\\theta$. In particular, $\\tilde\\theta$ can generate an ${\\cal O}(1)$ threshold correction to the QCD vacuum angle $\\theta$ near the TeV scale, sharply constraining ultraviolet solutions to the strong CP problem. Alternatively, finding that $\\tilde\\theta$ is small may be interpreted as evidence in favor of UV solutions to strong CP, particularly those based on spontaneously broken P or CP symmetries.

  6. Active limited-angle tomographic phase microscope

    Science.gov (United States)

    Kuś, Arkadiusz; Krauze, Wojciech; Kujawińska, Małgorzata

    2015-11-01

    We demonstrate an active, holographic tomography system, working with limited angle of projections, realized by optical-only, diffraction-based beam steering. The system created for this purpose is a Mach-Zehnder interferometer modified to serve as a digital holographic microscope with a high numerical aperture illumination module and a spatial light modulator (SLM). Such a solution is fast and robust. Apart from providing an elegant solution to viewing angle shifting, it also adds new capabilities of the holographic microscope system. SLM, being an active optical element, allows wavefront correction in order to improve measurement accuracy. Integrated phase data captured with different illumination scenarios within a highly limited angular range are processed by a new tomographic reconstruction algorithm based on the compressed sensing technique: total variation minimization, which is applied here to reconstruct nonpiecewise constant samples. Finally, the accuracy of full measurement and the proposed processing path is tested for a calibrated three-dimensional micro-object as well as a biological object-C2C12 myoblast cell.

  7. Hidden topological angles and Lefschetz thimbles

    CERN Document Server

    Behtash, Alireza; Schaefer, Thomas; Unsal, Mithat

    2015-01-01

    We demonstrate the existence of hidden topological angles (HTAs) in a large class of quantum field theories and quantum mechanical systems. HTAs are distinct from theta-parameters in the lagrangian. They arise as invariant angle associated with saddle points of the complexified path integral and their descent manifolds (Lefschetz thimbles). Physical effects of HTAs become most transparent upon analytic continuation in $n_f$ to non-integer number of flavors, reducing in the integer $n_f$ limit to a $\\mathbb Z_2$ valued phase difference between dominant saddles. In ${\\cal N}=1$ super Yang-Mills theory we demonstrate the microscopic mechanism for the vanishing of the gluon condensate. The same effect leads to an anomalously small condensate in a QCD-like $SU(N)$ gauge theory with fermions in the two-index representation. The basic phenomenon is that, contrary to folklore, the gluon condensate can receive both positive and negative contributions in a semi-classical expansion. In quantum mechanics, a HTA leads to ...

  8. Cluster headache or narrow angle glaucoma?

    Directory of Open Access Journals (Sweden)

    Prasad Palimar

    1991-01-01

    Full Text Available A 47 year old man with episodes of attacks of pain, redness and mild blurring of vision was investigated for narrow angle glaucoma in view of shallow anterior chambers and a cupped optic disc. The history was reviewed following a spontaneous attack in hospital, which had features other than acute glaucoma. A diagnosis of cluster headache was made on the basis of tests. Cluster headache has been defined as unilateral intense pain, involving the eye and head on one side, usually associated with flushing, nasal congestion and lacrimation; the attacks recurring one or more times daily and lasting 20 - 120 minutes. Such attacks commonly continue for weeks or months and are separated by an asymptomatic period of months to years. This episodic nature, together with unilaterality and tendency to occur at night, closely mimics narrow angle glaucoma. Further, if patients have shallow anterior chambers and disc cupping, the differentiation becomes more difficult yet critical. Resource to provocative tests is often the only answer as the following case report demonstrates.

  9. Contact angles of liquid metals on quasicrystals

    International Nuclear Information System (INIS)

    Wetting with μm-sized Pb droplets on thin polycrystalline films of decagonal Al13Co4 is reported. The films were prepared under high vacuum conditions in order to have Pb droplets lying on a clean surface. The method used is sequential deposition and annealing of specific stackings of Al and Co layers of nanometric thicknesses. A 300 nm thick Pb slab was then deposited on top of the films and dewetting experiments were followed in situ in a scanning Auger microprobe. The contact angle between the Pb droplet and the surface of the film is measured to be 49 deg. ± 7 deg. Further investigation performed by cross section transmission electron microscopy allows us to better characterize the interface. Taking into account the rugosity of the film, it is concluded that there is partial wetting of the film, which corresponds to a smaller contact angle. The comparison with other results obtained either with pure metals or with a cubic AlCo compound leads to the conclusion that the wetting behaviour of Pb on the surface of a decagonal compound is close to that of a metal with a high melting point and not significantly different from that of a crystalline compound with a small unit cell

  10. Diphotons, new vacuum angles, and strong CP

    Science.gov (United States)

    Draper, Patrick; McKeen, David

    2016-04-01

    The Standard Model contains a well-understood, natural, spin-0 diphoton resonance: the π 0. Numerous studies have pointed out that the hint of a new diphoton resonance at 750 GeV could be a pion analog, identified with the pseudo-Nambu-Goldstone boson of a chiral symmetry spontaneously broken by new strong dynamics at the TeV scale. These "hypercolor" models are generically expected to violate parity through a topological angle tilde{θ} . We discuss the physics of tilde{θ} and its impact on the phenomenology of the new sector. We also describe some of the theoretical implications of a nonzero tilde{θ} . In particular, tilde{θ} can generate an O(1) threshold correction to the QCD vacuum angle θ near the TeV scale, sharply constraining ultraviolet solutions to the strong CP problem. Alternatively, finding that tilde{θ} is small may be interpreted as evidence in favor of UV solutions to strong CP, particularly those based on spontaneously broken P or CP symmetries.

  11. Alternative IR geometries for TESLA with a small crossing angle

    OpenAIRE

    Appleby, R.; Angal-Kalinin, D; Bambade, P.; Mouton, B.; Napoly, O.; Payet, J.; Collaboration, the TESLA

    2004-01-01

    The formulation of hybrid crossing angle schemes has been a recent development of the TESLA collision geometry debate. Here we report on two such schemes, characterised by either a small vertical or horizontal beam crossing angle.

  12. Lateral angle: a method for sexing using the petrous bone

    DEFF Research Database (Denmark)

    Norén, Anna; Lynnerup, Niels; Czarnetzki, Alfred;

    2005-01-01

    very fragmented skeletal remains or cremated bones, where the petrous bone may still be readily recognizable. The method was tested using a forensic sample of 113 petrous bones with known sex. Intra- and interobserver testing was also performed. We found a statistically significant difference in angle......We report on the results of applying the so-called lateral angle method for sex determination on skeletal remains. The lateral angle denotes the angle of the internal auditory canal in relation to the medial surface of the petrous part of the temporal bone. The method involves making a small cast...... size between males and females (mean angle size of males, 39.3 degrees ; mean angle size of females, 48.2 degrees ; P < 0.001). There was no bilateral difference in angle size. In blind trials, 83.2% of petrous bones were assigned to the correct sex. We also tested the lateral angle method against an...

  13. Note on Four Dp-Branes at Angles

    CERN Document Server

    Vancea, I V

    2001-01-01

    In this note we analyse the potential of a system of four Dp-branes at arbitrary angles. The equilibrium configurations for various values of the relative angles and distances among branes are discussed.

  14. Backbone conformational flexibility of the lipid modified membrane anchor of the human N-Ras protein investigated by solid-state NMR and molecular dynamics simulation.

    Science.gov (United States)

    Vogel, Alexander; Reuther, Guido; Roark, Matthew B; Tan, Kui-Thong; Waldmann, Herbert; Feller, Scott E; Huster, Daniel

    2010-02-01

    The lipid modified human N-Ras protein, implicated in human cancer development, is of particular interest due to its membrane anchor that determines the activity and subcellular location of the protein. Previous solid-state NMR investigations indicated that this membrane anchor is highly dynamic, which may be indicative of backbone conformational flexibility. This article aims to address if a dynamic exchange between three structural models exist that had been determined previously. We applied a combination of solid-state nuclear magnetic resonance (NMR) methods and replica exchange molecular dynamics (MD) simulations using a Ras peptide that represents the terminal seven amino acids of the human N-Ras protein. Analysis of correlations between the conformations of individual amino acids revealed that Cys 181 and Met 182 undergo collective conformational exchange. Two major structures constituting about 60% of all conformations could be identified. The two conformations found in the simulation are in rapid exchange, which gives rise to low backbone order parameters and nuclear spin relaxation as measured by experimental NMR methods. These parameters were also determined from two 300 ns conventional MD simulations, providing very good agreement with the experimental data. PMID:19819220

  15. Significant Role of DNA Backbone in Mediating the Transition Origin of Electronic Excitations of B-DNA - Implication from Long Range Corrected TDDFT and Quantified NTO Analysis

    CERN Document Server

    Li, Jian-Hao; Guo, Guang-Yu; Hayashi, Michitoshi

    2011-01-01

    We systematically investigate the possible complex transition origin of electronic excitations of giant molecular systems by using the recently proposed QNTO analysis [J.-H. Li, J.-D. Chai, G. Y. Guo and M. Hayashi, Chem. Phys. Lett., 2011, 514, 362.] combined with long-range corrected TDDFT calculations. Thymine (Thy) related excitations of biomolecule B-DNA are then studied as examples, where the model systems have been constructed extracting from the perfect or a X-ray crystal (PDB code 3BSE) B-DNA structure with at least one Thy included. In the first part, we consider the systems composed of a core molecular segment (e.g. Thy, di-Thy) and a surrounding physical/chemical environment of interest (e.g. backbone, adjacent stacking nucleobases) and examine how the excitation properties of the core vary in response to the environment. We find that the orbitals contributed from DNA backbone and surrounding nucleobases often participate in a transition of Thy-related excitations affecting their composition, abso...

  16. Molecular Data for a Biochemical Model of DNA Radiation Damage: Electron Impact Ionization and Dissociative Ionization of DNA Bases and Sugar-Phosphate Backbone

    Science.gov (United States)

    Dateo, Christopher E.; Fletcher, Graham D.

    2004-01-01

    As part of the database for building up a biochemical model of DNA radiation damage, electron impact ionization cross sections of sugar-phosphate backbone and DNA bases have been calculated using the improved binary-encounter dipole (iBED) model. It is found that the total ionization cross sections of C3'- and C5'-deoxyribose-phospate, two conformers of the sugar-phosphate backbone, are close to each other. Furthermore, the sum of the ionization cross sections of the separate deoxyribose and phosphate fragments is in close agreement with the C3'- and C5'-deoxyribose-phospate cross sections, differing by less than 10%. Of the four DNA bases, the ionization cross section of guanine is the largest, then in decreasing order, adenine, thymine, and cytosine. The order is in accordance with the known propensity of oxidation of the bases by ionizing radiation. Dissociative ionization (DI), a process that both ionizes and dissociates a molecule, is investigated for cytosine. The DI cross section for the formation of H and (cytosine-Hl)(+), with the cytosine ion losing H at the 1 position, is also reported. The threshold of this process is calculated to be 17.1 eV. Detailed analysis of ionization products such as in DI is important to trace the sequential steps in the biochemical process of DNA damage.

  17. Nuclear magnetic resonance secondary shifts of a light-harvesting 2 complex reveal local backbone perturbations induced by its higher-order interactions.

    Science.gov (United States)

    Pandit, Anjali; Wawrzyniak, Piotr K; van Gammeren, Adriaan J; Buda, Francesco; Ganapathy, Swapna; de Groot, Huub J M

    2010-01-26

    Protein nuclear magnetic resonance (NMR) secondary chemical shifts are widely used to predict the secondary structure, and in solid-state NMR, they are often the only unambiguous structural parameters available. However, the employed prediction methods are empirical in nature, relying on the assumption that secondary shifts are only affected by shielding effects of neighboring atoms. We analyzed the secondary shifts of a photosynthetic membrane protein with a high density of chromophores and very tight packing, the light-harvesting 2 (LH2) complex of Rhodopseudomonas acidophila. A relation was found between secondary shift anomalies and protein-protein or pigment-protein tertiary and quaternary contacts. For several residues, including the bacteriochlorophyll-coordinating histidines (alphaH31 and betaH30) and the phenylalanine alphaF41 that has strongly twisted C(b)-C(a)-C and C(a)-C-N conformations in the LH2 crystal structure, the perturbing effects on the backbone chemical shifts were tested by density functional theory (DFT) calculations. We propose that higher-order interactions in the tightly packed complex can induce localized perturbations of the backbone conformation and electronic structure, related to functional pigment-protein or protein-protein interactions. PMID:19954238

  18. Legionella pneumophila strain associated with the first evidence of person-to-person transmission of Legionnaires’ disease: a unique mosaic genetic backbone

    Science.gov (United States)

    Borges, Vítor; Nunes, Alexandra; Sampaio, Daniel A.; Vieira, Luís; Machado, Jorge; Simões, Maria J.; Gonçalves, Paulo; Gomes, João P.

    2016-01-01

    A first strong evidence of person-to-person transmission of Legionnaires’ Disease (LD) was recently reported. Here, we characterize the genetic backbone of this case-related Legionella pneumophila strain (“PtVFX/2014”), which also caused a large outbreak of LD. PtVFX/2014 is phylogenetically divergent from the most worldwide studied outbreak-associated L. pneumophila subspecies pneumophila serogroup 1 strains. In fact, this strain is also from serogroup 1, but belongs to the L. pneumophila subspecies fraseri. Its genomic mosaic backbone reveals eight horizontally transferred regions encompassing genes, for instance, involved in lipopolysaccharide biosynthesis or encoding virulence-associated Dot/Icm type IVB secretion system (T4BSS) substrates. PtVFX/2014 also inherited a rare ~65 kb pathogenicity island carrying virulence factors and detoxifying enzymes believed to contribute to the emergence of best-fitted strains in water reservoirs and in human macrophages, as well as a inter-species transferred (from L. oakridgensis) ~37.5 kb genomic island (harboring a lvh/lvr T4ASS cluster) that had never been found intact within L. pneumophila species. PtVFX/2014 encodes another lvh/lvr cluster near to CRISPR-associated genes, which may boost L. pneumophila transition from an environmental bacterium to a human pathogen. Overall, this unique genomic make-up may impact PtVFX/2014 ability to adapt to diverse environments, and, ultimately, to be transmitted and cause human disease. PMID:27196677

  19. Legionella pneumophila strain associated with the first evidence of person-to-person transmission of Legionnaires' disease: a unique mosaic genetic backbone.

    Science.gov (United States)

    Borges, Vítor; Nunes, Alexandra; Sampaio, Daniel A; Vieira, Luís; Machado, Jorge; Simões, Maria J; Gonçalves, Paulo; Gomes, João P

    2016-01-01

    A first strong evidence of person-to-person transmission of Legionnaires' Disease (LD) was recently reported. Here, we characterize the genetic backbone of this case-related Legionella pneumophila strain ("PtVFX/2014"), which also caused a large outbreak of LD. PtVFX/2014 is phylogenetically divergent from the most worldwide studied outbreak-associated L. pneumophila subspecies pneumophila serogroup 1 strains. In fact, this strain is also from serogroup 1, but belongs to the L. pneumophila subspecies fraseri. Its genomic mosaic backbone reveals eight horizontally transferred regions encompassing genes, for instance, involved in lipopolysaccharide biosynthesis or encoding virulence-associated Dot/Icm type IVB secretion system (T4BSS) substrates. PtVFX/2014 also inherited a rare ~65 kb pathogenicity island carrying virulence factors and detoxifying enzymes believed to contribute to the emergence of best-fitted strains in water reservoirs and in human macrophages, as well as a inter-species transferred (from L. oakridgensis) ~37.5 kb genomic island (harboring a lvh/lvr T4ASS cluster) that had never been found intact within L. pneumophila species. PtVFX/2014 encodes another lvh/lvr cluster near to CRISPR-associated genes, which may boost L. pneumophila transition from an environmental bacterium to a human pathogen. Overall, this unique genomic make-up may impact PtVFX/2014 ability to adapt to diverse environments, and, ultimately, to be transmitted and cause human disease. PMID:27196677

  20. Modified Wide-angle Beam Propagation Method Using Douglas Operators①

    Institute of Scientific and Technical Information of China (English)

    1997-01-01

    A modified wide-angle beam propagation based on the Douglas operators is presented .The truncation error in the modified wide-angle beam propagation is reduced to o(△x)4in the transverse direction nearly without any increase of the computation time,whereas the error in the ordinary wide-angle beam propagation method is typically o(△x)2.With trivial programming changes,the accuracy is higher,especially in wide-angle propagation.

  1. Range-Angle-Dependent Beamforming by Frequency Diverse Array Antenna

    OpenAIRE

    Wen-Qin Wang; Huaizong Shao; Jingye Cai

    2012-01-01

    This paper proposes a range-angle-dependent beamforming for frequency diverse array (FDA) antenna systems. Unlike conventional phased-array antenna, the FDA antenna employs a small amount of frequency increment compared to the carrier frequency across the array elements. The use of frequency increment generates an antenna pattern that is a function of range, time and angle. The range-angle-dependent beamforming allows the FDA antenna to transmit energy over a desired range or angle. This prov...

  2. Hybrid algorithm for rotor angle security assessment in power systems

    OpenAIRE

    D. Prasad Wadduwage; Udaya D. Annakkage; Christine Qiong Wu

    2015-01-01

    Transient rotor angle stability assessment and oscillatory rotor angle stability assessment subsequent to a contingency are integral components of dynamic security assessment (DSA) in power systems. This study proposes a hybrid algorithm to determine whether the post-fault power system is secure due to both transient rotor angle stability and oscillatory rotor angle stability subsequent to a set of known contingencies. The hybrid algorithm first uses a new security measure developed based on ...

  3. Optimal Angle Reduction - A Behavioral Approach to Linear System Approximation

    NARCIS (Netherlands)

    Roorda, B.; Weiland, S.

    2000-01-01

    We investigate the problem of optimal state reduction under minimization of the angle between system behaviors. The angle is defined in a worst-case sense, as the largest angle that can occur between a system trajectory and its optimal approximation in the reduced order model. This problem is analys

  4. Surgery for an "Acute Erection Angle," When Counseling Fails

    NARCIS (Netherlands)

    Nugteren, Helena M.; Pascal, Astrid L.; Schultz, Willibrord C. M. Weijmar; van Driel, Mels F.

    2010-01-01

    Introduction. During erection, the penis increases in volume, rigidity, and angle. Textbooks of urology and sexology provide only very limited information about erection angle dysfunction. In some men, this angle is too tight toward their belly, causing problems with intercourse. Aim. We reported tw

  5. Strike a Balance: Optimization of Backbone Torsion Parameters of AMBER Polarizable Force Field for Simulations of Proteins and Peptides

    Science.gov (United States)

    WANG, ZHI-XIANG; ZHANG, WEI; WU, CHUN; LEI, HONGXING; CIEPLAK, PIOTR; DUAN, YONG

    2014-01-01

    Based on the AMBER polarizable model (ff02), we have reoptimized the parameters related to the main-chain (Φ, Ψ) torsion angles by fitting to the Boltzmann-weighted average quantum mechanical (QM) energies of the important regions (i.e., β, PII, αR, and αL regions). Following the naming convention of the AMBER force field series, this release will be called ff02pol.rl The force field has been assessed both by energetic comparison against the QM data and by the replica exchange molecular dynamics simulations of short alanine peptides in water. For Ace-Ala-Nme, the simulated populations in the β, PII and αR regions were approximately 30, 43, and 26%, respectively. For Ace-(Ala)7-Nme, the populations in these three regions were approximately 24, 49, and 26%. Both were in qualitative agreement with the NMR and CD experimental conclusions. In comparison with the previous force field, ff02pol.rl demonstrated good balance among these three important regions. The optimized torsion parameters, together with those in ff02, allow us to carry out simulations on proteins and peptides with the consideration of polarization. PMID:16526038

  6. Superwide-angle acoustic propagations above the critical angles of the Snell law in liquid—solid superlattice

    International Nuclear Information System (INIS)

    In this paper, superwide-angle acoustic propagations above the critical angles of the Snell law in liquid—solid superlattice are investigated. Incident waves above the critical angles of the Snell law usually inevitably induce total reflection. However, incident waves with big oblique angles through the liquid—solid superlattice will produce a superwide angle transmission in a certain frequency range so that total reflection does not occur. Together with the simulation by finite element analysis, theoretical analysis by using transfer matrix method suggests the Bragg scattering of the Lamb waves as the physical mechanism of acoustic wave super-propagation far beyond the critical angle. Incident angle, filling fraction, and material thickness have significant influences on propagation. Superwide-angle propagation phenomenon may have potential applications in nondestructive evaluation of layered structures and controlling of energy flux. (electromagnetism, optics, acoustics, heat transfer, classical mechanics, and fluid dynamics)

  7. On large angle multiple gluon radiation

    CERN Document Server

    Dokshitzer, Y L; Dokshitzer, Yu.L.

    2003-01-01

    Jet shape observables which involve measurements restricted to a part of phase space are sensitive to multiplication of soft gluon with large relative angles and give rise to specific single logarithmically enhanced (SL) terms (non-global logs). We consider associated distributions in two variables which combine measurement of a jet shape V in the whole phase space (global) and that of the transverse energy flow away from the jet direction, Eout (non-global). We show that associated distributions factorize into the global distribution in V and a factor that takes into account SL contributions from multi-gluon ``hedgehog'' configurations in all orders. The latter is the same that describes the single-variable Eout distribution, but evaluated at a rescaled energy VQ.

  8. Angle-resolved cathodoluminescence imaging polarimetry

    CERN Document Server

    Osorio, Clara I; Brenny, Benjamin; Polman, Albert; Koenderink, A Femius

    2015-01-01

    Cathodoluminescence spectroscopy (CL) allows characterizing light emission in bulk and nanostructured materials and is a key tool in fields ranging from materials science to nanophotonics. Previously, CL measurements focused on the spectral content and angular distribution of emission, while the polarization was not fully determined. Here we demonstrate a technique to access the full polarization state of the cathodoluminescence emission, that is the Stokes parameters as a function of the emission angle. Using this technique, we measure the emission of metallic bullseye nanostructures and show that the handedness of the structure as well as nanoscale changes in excitation position induce large changes in polarization ellipticity and helicity. Furthermore, by exploiting the ability of polarimetry to distinguish polarized from unpolarized light, we quantify the contributions of different types of coherent and incoherent radiation to the emission of a gold surface, silicon and gallium arsenide bulk semiconductor...

  9. Small angle electron diffraction and deflection

    Directory of Open Access Journals (Sweden)

    T. Koyama

    2012-03-01

    Full Text Available Electron optical system is constructed in order to obtain small angle diffraction and Lorentz deflection of electrons at the order of down to 10-6 radian in the reciprocal space. Long-distance camera length up to 3000 m is achieved in a conventional transmission electron microscope with LaB6 thermal emission type. The diffraction pattern at 5 × 10-6 radian is presented in a carbon replica grating with 500 nm lattice spacing while the magnetic deflection pattern at 2 × 10-5 radian is exhibited in Permalloy elements. A simultaneous recording of electron diffraction and Lorentz deflection is also demonstrated in 180 degree striped magnetic domains of La0.825Sr0.175MnO3.

  10. Wide-angle energy-momentum spectroscopy

    CERN Document Server

    Dodson, Christopher M; Li, Dongfang; Zia, Rashid

    2014-01-01

    Light emission is defined by its distribution in energy, momentum, and polarization. Here, we demonstrate a method that resolves these distributions by means of wide-angle energy-momentum spectroscopy. Specifically, we image the back focal plane of a microscope objective through a Wollaston prism to obtain polarized Fourier-space momentum distributions, and disperse these two-dimensional radiation patterns through an imaging spectrograph without an entrance slit. The resulting measurements represent a convolution of individual radiation patterns at adjacent wavelengths, which can be readily deconvolved using any well-defined basis for light emission. As an illustrative example, we use this technique with the multipole basis to quantify the intrinsic emission rates for electric and magnetic dipole transitions in europium-doped yttrium oxide (Eu$^{3+}$:Y$_{2}$O$_{3}$) and chromium-doped magnesium oxide (Cr$^{3+}$:MgO). Once extracted, these rates allow us to reconstruct the full, polarized, two-dimensional radi...

  11. Foreign Body Embedded in Anterior Chamber Angle

    Directory of Open Access Journals (Sweden)

    Shmuel Graffi

    2012-01-01

    Full Text Available Introduction. We present a case of a metallic foreign body embedded in the anterior chamber angle. After standing in close proximity to a construction worker breaking a tile, a 26-year-old woman using soft contact lens for the correction of mild myopia presented to emergency department for evaluation of a foreign body sensation of her right eye. Methods and Results. Diagnosis was confirmed by gonioscopic examination and a noncontrast CT scan of head and orbits. The foreign body was removed by an external approach without utilizing a magnet. The patient's final outcome was favorable. Discussion. The above is a rare clinical situation, which is impossible to detect on slit-lamp examination without a gonioscopic view. Proper imaging and a specific management are mandatory in order to achieve favorable outcome.

  12. Small-angle scattering in materials science

    International Nuclear Information System (INIS)

    Small-angle scattering (SAS) of X-rays (SAXS) or neutrons (SANS) are a powerful tools to investigate inhomogeneities in the size range from ∼ 1 nm to ∼ 100 nm. Typical examples in materials science are pores, precipitates in metal alloys or nano-particles in composites. Frequently, these inhomogeneities are not spherical and their alignment is not random, quite in contrast to many other applications of SAS. This requires the use of pinhole geometry and area detectors for the experimental set-up. The present paper focuses on evaluation techniques of two-dimensional (2D) SAS-patterns from some materials investigated by the authors, i.e. metal alloys, carbon composites, wood and bone. Although the examples shown are derived exclusively from SAXS measurements, most of them could stem from SANS measurements as well. (author)

  13. Angle-independent structural colors of silicon

    DEFF Research Database (Denmark)

    Højlund-Nielsen, Emil; Weirich, Johannes; Nørregaard, Jesper;

    2014-01-01

    Structural colors are optical phenomena of physical origin, where microscale and nanoscale structures determine the reflected spectrum of light. Artificial structural colors have been realized within recent years. However, multilayer structures require substantial fabrication. Instead we considered...... one-layer surface textures of silicon.We explored four patterns of square structures in a square lattice with periods of 500, 400, 300, and 200 nm. The reflectivity and daylight-colors were measured and compared with simulations based on rigorously coupledwave analysis with excellent agreement. Based...... on the 200-nm periodic pattern, it was found that angle-independent specular colors up to 60 deg of incidence may be provided. The underlying mechanisms include (1) the suppression of diffraction and (2) a strong coupling of light to localized surface states. The strong coupling yields absorption...

  14. Angle-resolved photoemission extended fine structure

    International Nuclear Information System (INIS)

    Measurements of the Angle-Resolved Photoemission Extended Fine Structure (ARPEFS) from the S(1s) core level of a c(2 x 2)S/Ni(001) are analyzed to determine the spacing between the S overlayer and the first and second Ni layers. ARPEFS is a type of photoelectron diffraction measurement in which the photoelectron kinetic energy is swept typically from 100 to 600 eV. By using this wide range of intermediate energies we add high precision and theoretical simplification to the advantages of the photoelectron diffraction technique for determining surface structures. We report developments in the theory of photoelectron scattering in the intermediate energy range, measurement of the experimental photoemission spectra, their reduction to ARPEFS, and the surface structure determination from the ARPEFS by combined Fourier and multiple-scattering analyses. 202 refs., 67 figs., 2 tabs

  15. Narrow-angle astrometry with PRIMA

    CERN Document Server

    Sahlmann, J; Mérand, A; Zimmerman, N; Abuter, R; Chazelas, B; Delplancke, F; Henning, T; Kaminski, A; Köhler, R; Launhardt, R; Mohler, M; Pepe, F; Queloz, D; Quirrenbach, A; Reffert, S; Schmid, C; Schuhler, N; Schulze-Hartung, T

    2012-01-01

    The Extrasolar Planet Search with PRIMA project (ESPRI) aims at characterising and detecting extrasolar planets by measuring the host star's reflex motion using the narrow-angle astrometry capability of the PRIMA facility at the Very Large Telescope Interferometer. A first functional demonstration of the astrometric mode was achieved in early 2011. This marked the start of the astrometric commissioning phase with the purpose of characterising the instrument's performance, which ultimately has to be sufficient for exoplanet detection. We show results obtained from the observation of bright visual binary stars, which serve as test objects to determine the instrument's astrometric precision, its accuracy, and the plate scale. Finally, we report on the current status of the ESPRI project, in view of starting its scientific programme.

  16. Guanosine Quadruplexes in Solution: A Small-Angle X-Ray Scattering Analysis of Temperature Effects on Self-Assembling of Deoxyguanosine Monophosphate

    Directory of Open Access Journals (Sweden)

    P. Mariani

    2010-01-01

    Full Text Available We investigated quadruplex formation in aqueous solutions of 2′-deoxyriboguanosine 5′-monophosphate, d(pG, which takes place in the absence of the covalent axial backbone. A series of in-solution small angle X-ray scattering experiments on d(pG have been performed as a function of temperature in the absence of excess salt, at a concentration just above the critical one at which self-assembling occurs. A global fit approach has been used to derive composition and size distribution of the scattering particles as a function of temperature. The obtained results give thermodynamical justification for the observed phase-behavior, indicating that octamer formation is essential for quadruplex elongation. Our investigation shows that d(pG quadruplexes are very suitable to assess the potential of G-quadruplex formation and to study the self-assembling thermodynamics.

  17. Spondylolysis and the sacro-horizontal angle in athletes

    International Nuclear Information System (INIS)

    The frequency of spondylolysis and the relationship between spondylolysis and the sacro-horizontal angle in 143 athletes and 30 non-athletes is reported. Athletes had a larger sacro-horizontal angle than non-athletes. The sacro-horizontal angle was larger in athletes with spondylolysis as compared with those without. An increased incidence of spondylolysis with an increased angle was demonstrated. It is suggested that an increased sacro-horizontal angle may predispose to spondylolysis, especially in combination with the high mechanical loads sustained in certain sports. (orig.)

  18. Temperature Influence on Divergence Angles of Quartz Crystal Wollaston Prism

    International Nuclear Information System (INIS)

    We propose a structural angle and main refractive indices as two key factors to understand the temperature influence on the divergence angles of the Wollaston prism. The temperature influence on the divergence angles of quartz crystal Wollaston prism is studied theoretically The results show that divergence angles decrease with increasing temperature, while the divergence angle of e-light decrease more quickly than that of o-light. The testing system is established to verify the above results, and the experimental results are in agreement well with the theoretical analysis. (fundamental areas of phenomenology (including applications))

  19. Absolute small-angle measurement based on optical feedback interferometry

    Institute of Scientific and Technical Information of China (English)

    Jingang Zhong; Xianhua Zhang; Zhixiang Ju

    2008-01-01

    We present a simple but effective method for small-angle measurement based on optical feedback inter-ferometry (or laser self-mixing interferometry). The absolute zero angle can be defined at the biggest fringe amplitude point, so this method can also achieve absolute angle measurement. In order to verify the method, we construct an angle measurement system. The Fourier-transform method is used to analysis the interference signal. Rotation angles are experimentally measured with a resolution of 10-6 rad and a measurement range of approximately from -0.0007 to +0.0007 rad.

  20. Preferred conformation and dynamics of the glycerol backbone in phospholipids. An NMR and X-ray single-crystal analysis

    International Nuclear Information System (INIS)

    The conformation of the glycerol group of a number of diacyl and monoacyl (lyso) phospholipids differing in the chemical nature of the head group was studied by 1H high-resolution NMR and X-ray crystallography. The NMR measurements were carried out with solutions or micellar dispersions of the lipids in deuteriated organic solvents or 2H2O. Both solutions, in which the lipid is present as monomers, and lipid micelles give rise to good high-resolution NMR spectra exhibiting spin coupling hyperfine interactions. From 1H spin coupling it is concluded that there are two stable conformations about the glycerol C(2)-C(3) bond of phospholipids. By comparison of NMR and single-crystal X-ray data it is obvious that both conformations are minimum free energy conformations. Rotamer A is the conformation prevailing in phospholipid single-crystal structures. The conformation of rotamer B is also found in phospholipid single-crystal structures though to a lesser extent. NMR measurements indicate that in liquid crystals the diacylglycerol part of phospholipids fluctuates between the two stable staggered conformations of rotamers A and B. The transition between rotamers A and B is fast on the NMR time scale and must be accompanied by appropriate changes in the torsion angles β1 to β4 and γ1 to γ4 of the two fatty acyl chains. It is clear from the data presented that the parallel alignment of the hydrocarbon chains or chain stacking in phospholipid aggregates such as bilayers or micelles is the fundamental principle governing the conformation of the C(2)-C(3) glycerol bond

  1. Impacts of tropical cyclone inflow angle on ocean surface waves

    Institute of Scientific and Technical Information of China (English)

    ZHAO Wei; HONG Xin

    2011-01-01

    The inflow angle of tropical cyclones (TC) is generally neglected in numerical studies of ocean surface waves induced by TC. In this study, the impacts of TC inflow angle on ocean surface waves were investigated using a high-resolution wave model. Six numerical experiments were conducted to examine, in detail, the effects of inflow angle on mean wave parameters and the spectrum of wave directions. A comparison of the waves simulated in these experiments shows that inflow angle significantly modifies TC-induced ocean surface waves. As the inflow angle increases, the asymmetric axis of the significant wave height (SWH) field shifts 30° clockwise, and the maximum SWH moves from the front-right to the rear-right quadrant. Inflow angle also affects other mean wave parameters, especially in the rear-left quadrant, such as the mean wave direction, the mean wavelength, and the peak direction. Inflow angle is a key factor in wave models for the reproduction of double-peak or multi-peak patterns in the spectrum of wave directions. Sensitivity experiments also show that the simulation with a 40° inflow angle is the closest to that of the NOAA statistical SLOSH inflow angle. This suggests that 40° can be used as the inflow angle in future TC-induced ocean surface wave simulations when SLOSH or observed inflow angles are not available.

  2. Angle Kappa and its importance in refractive surgery

    Directory of Open Access Journals (Sweden)

    Majid Moshirfar

    2013-01-01

    Full Text Available Angle kappa is the difference between the pupillary and visual axis. This measurement is of paramount consideration in refractive surgery, as proper centration is required for optimal results. Angle kappa may contribute to MFIOL decentration and its resultant photic phenomena. Adjusting placement of MFIOLs for angle kappa is not supported by the literature but is likely to help reduce glare and haloes. Centering LASIK in angle kappa patients over the corneal light reflex is safe, efficacious, and recommended. Centering in-between the corneal reflex and the entrance pupil is also safe and efficacious. The literature regarding PRK in patients with an angle kappa is sparse but centering on the corneal reflex is assumed to be similar to centering LASIK on the corneal reflex. Thus, centration of MFIOLs, LASIK, and PRK should be focused on the corneal reflex for patients with a large angle kappa. More research is needed to guide surgeons′ approach to angle kappa.

  3. Predicting 15N chemical shifts in proteins using the preceding residue-specific individual shielding surfaces from φ, ψi-1, and χ1torsion angles

    International Nuclear Information System (INIS)

    Empirical shielding surfaces are most commonly used to predict chemical shifts in proteins from known backbone torsion angles, φ and ψ. However, the prediction of 15N chemical shifts using this technique is significantly poorer, compared to that for the other nuclei such as 1Hα, 13Cα, and 13Cβ. In this study, we investigated the effects from the preceding residue and the side-chain geometry, χ1, on 15N chemical shifts by statistical methods. For an amino acid sequence XY, the 15N chemical shift of Y is expressed as a function of the amino acid types of X and Y, as well as the backbone torsion angles, φ and ψi-1. Accordingly, 380 empirical 'Preceding Residue Specific Individual (PRSI)' 15N chemical shift shielding surfaces, representing all the combinations of X and Y (except for Y=Pro), were built and used to predict 15N chemical shift from φ and ψi-1. We further investigated the χ1 effects, which were found to account for differences in 15N chemical shifts by ∼5 ppm for amino acids Val, Ile, Thr, Phe, His, Tyr, and Trp. Taking the χ1 effects into account, the χ1-calibrated PRSI shielding surfaces (XPRSI) were built and used to predict 15N chemical shifts for these amino acids. We demonstrated that 15N chemical shift predictions are significantly improved by incorporating the preceding residue and χ1 effects. The present PRSI and XPRSI shielding surfaces were extensively compared with three recently published programs, SHIFTX (Neal et al., 2003), SHIFTS (Xu and Case, 2001 and 2002), and PROSHIFT (Meiler, 2003) on a set of ten randomly selected proteins. A set of Java programs using XPRSI shielding surfaces to predict 15N chemical shifts in proteins were developed and are freely available for academic users at http://www.pronmr.com or by sending email to one of the authors Yunjun Wang

  4. Reduced dimensionality tailored HN(C)N experiments for facile backbone resonance assignment of proteins through unambiguous identification of sequential HSQC peaks

    Science.gov (United States)

    Kumar, Dinesh

    2013-12-01

    Two novel reduced dimensionality (RD) tailored HN(C)N [S.C. Panchal, N.S. Bhavesh, R.V. Hosur, Improved 3D triple resonance experiments, HNN and HN(C)N, for HN and 15N sequential correlations in (13C, 15N) labeled proteins: application to unfolded proteins, J. Biomol. NMR 20 (2001) 135-147] experiments are proposed to facilitate the backbone resonance assignment of proteins both in terms of its accuracy and speed. These experiments - referred here as (4,3)D-hNCOcaNH and (4,3)D-hNcoCANH - exploit the linear combination of backbone 15N and 13C‧/13Cα chemical shifts simultaneously to achieve higher peak dispersion and randomness along their respective F1 dimensions. Simply, this has been achieved by modulating the backbone 15N(i) chemical shifts with that of 13C‧ (i - 1)/13Cα (i - 1) spins following the established reduced dimensionality NMR approach [T. Szyperski, D.C. Yeh, D.K. Sukumaran, H.N. Moseley, G.T. Montelione, Reduced-dimensionality NMR spectroscopy for high-throughput protein resonance assignment, Proc. Natl. Acad. Sci. USA 99 (2002) 8009-8014]. Though the modification is simple it has resulted an ingenious improvement of HN(C)N both in terms of peak dispersion and easiness of establishing the sequential connectivities. The increased dispersion along F1 dimension solves two purposes here: (i) resolves the ambiguities arising because of degenerate 15N chemical shifts and (ii) reduces the signal overlap in F2(15N)-F3(1H) planes (an important requisite in HN(C)N based assignment protocol for facile and unambiguous identification of sequentially connected HSQC peaks). The performance of both these experiments and the assignment protocol has been demonstrated using bovine apo Calbindin-d9k (75 aa) and urea denatured UNC60B (a 152 amino acid ADF/cofilin family protein of Caenorhabditis elegans), as representatives of folded and unfolded protein systems, respectively.

  5. Multi-angle Imaging SpectroRadiometer

    Science.gov (United States)

    Diner, David J. (Principal Investigator)

    MISR views the sunlit Earth simultaneously at nine widely spaced angles and provides ongoing global coverage with high spatial detail. Its imagery is carefully calibrated to provide accurate measures of the brightness, contrast, and color of reflected sunlight. MISR provides new types of information for scientists studying Earth's climate, such as the regional and global distribution of different types of atmospheric particles and aerosols. The change in reflection at different view angles provides the means to distinguish aerosol types, cloud forms, and land surface cover. Combined with stereoscopic techniques, this enables construction of 3-D cloud models and estimation of the total amount of sunlight reflected by Earth's diverse environments. MISR was built for NASA by the Jet Propulsion Laboratory (JPL) in Pasadena, California. It is part of NASA's first Earth Observing System (EOS) spacecraft, the Terra spacecraft, which was launched into polar orbit from Vandenberg Air Force Base on December 18, 1999. MISR has been continuously providing data since February 24, 2000. [Mission Objectives] The MISR instrument acquires systematic multi-angle measurements for global monitoring of top-of-atmosphere and surface albedos and for measuring the shortwave radiative properties of aerosols, clouds, and surface scenes in order to characterize their impact on the Earth's climate. The Earth's climate is constantly changing -- as a consequence of both natural processes and human activities. Scientists care a great deal about even small changes in Earth's climate, since they can affect our comfort and well-being, and possibly our survival. A few years of below-average rainfall, an unusually cold winter, or a change in emissions from a coal-burning power plant, can influence the quality of life of people, plants, and animals in the region involved. The goal of NASA's Earth Observing System (EOS) is to increase our understanding of the climate changes that are occurring on our

  6. Mechanical reliability of porous low-k dielectrics for advanced interconnect: Study of the instability mechanisms in porous low-k dielectrics and their mediation through inert plasma induced re-polymerization of the backbone structure

    Science.gov (United States)

    Sa, Yoonki

    dielectric constant, shows striking difference with small change in the chemical bond structure. Comparison of peak extracted by using FTIR (Fourier transform infrared spectroscopy) reveals that viscoplastic deformation and dielectric constant change correctly reflect the evolution in morphological structure of Si-O-Si peak. It is also found that hydrophilic nature of PLK matrix induced by silanol group is more involved with viscoplastic deformation rate and cage-like crosslinking in Si-O-Si peak is responsible for dielectric constant change. However, the level of instability driven by plasma exposure in PLK matrix is found to recover and desired mechanical and electrical properties are obtained by modifying the chemical bond configuration. Silylation process by HMDS (hexamethyldisilazane) works on recovery of hydrophobicity because it replenishes -C while removing -OH bonds. Contact angle is restored by controlling process temperature, however, the silylating agent cannot penetrate deep into PLK matrix without an adequate medium such as supercritical CO2, making it difficult to implement. As a way of overcoming the limitation of UV cure, soft x-ray cure with Al Kalpha target is applied to induce gentle reconfiguration of chemical bond. It is possible to break bond links selectively by controlling x-ray energy level and also reduce thermal curing temperature due to the increased penetration depth. As a result of soft x-ray cure, film thickness loss almost not occurred. However, influence of x-ray radiation on the moisture removal is limited. Basically, oxidative plasma damage appears in two extensive areas. The first is the loss of -C from PLK matrix, and the second is the increase in hydrophilic nature involved with the formation of Si-OH terminal bonds and H2O. Both alternations cause the dielectric constant to degrade because of increased density and/or loss of free volume, but the second causes PLK to lose thermal and mechanical stability because Si-OH and H2O act as

  7. Moderate positive spin Hall angle in uranium

    Science.gov (United States)

    Singh, Simranjeet; Anguera, Marta; del Barco, Enrique; Springell, Ross; Miller, Casey W.

    2015-12-01

    We report measurements of spin pumping and the inverse spin Hall effect in Ni80Fe20/uranium bilayers designed to study the efficiency of spin-charge interconversion in a super-heavy element. We employ broad-band ferromagnetic resonance on extended films to inject a spin current from the Ni80Fe20 (permalloy) into the uranium layer, which is then converted into an electric field by the inverse spin Hall effect. Surprisingly, our results suggest a spin mixing conductance of order 2 × 1019 m-2 and a positive spin Hall angle of 0.004, which are both merely comparable with those of several transition metals. These results thus support the idea that the electronic configuration may be at least as important as the atomic number in governing spin pumping across interfaces and subsequent spin Hall effects. In fact, given that both the magnitude and the sign are unexpected based on trends in d-electron systems, materials with unfilled f-electron orbitals may hold additional exploration avenues for spin physics.

  8. Wide-angle tail galaxies in ATLAS

    CERN Document Server

    Mao, Minnie Y; Saikia, D J; Norris, Ray P; Johnston-Hollitt, Melanie; Middelberg, Enno; Lovell, Jim E J

    2010-01-01

    We present radio images of a sample of six Wide-Angle Tail (WAT) radio sources identified in the ATLAS 1.4 GHz radio survey, and new spectroscopic redshifts for four of these sources. These WATs are in the redshift range of 0.1469 - 0.3762, and we find evidence of galaxy overdensities in the vicinity of four of the WATs from either spectroscopic or photometric redshifts. We also present follow-up spectroscopic observations of the area surrounding the largest WAT, S1189, which is at a redshift of ~0.22. The spectroscopic observations, taken using the AAOmega spectrograph on the AAT, show an overdensity of galaxies at this redshift. The galaxies are spread over an unusually large area of ~12 Mpc with a velocity spread of ~4500 km/s. This large-scale structure includes a highly asymmetric FRI radio galaxy and also appears to host a radio relic. It may represent an unrelaxed system with different sub-structures interacting or merging with one another. We discuss the implications of these observations for future l...

  9. LDEF yaw and pitch angle estimates

    Science.gov (United States)

    Banks, Bruce A.; Gebauer, Linda

    1992-01-01

    Quantification of the LDEF yaw and pitch misorientations is crucial to the knowledge of atomic oxygen exposure of samples placed on LDEF. Video camera documentation of the LDEF spacecraft prior to grapple attachment, atomic oxygen shadows on experiment trays and longerons, and a pinhole atomic oxygen camera placed on LDEF provided sources of documentation of the yaw and pitch misorientation. Based on uncertainty-weighted averaging of data, the LDEF yaw offset was found to be 8.1 plus or minus 0.6 degrees, allowing higher atomic oxygen exposure of row 12 than initially anticipated. The LDEF pitch angle offset was found to be 0.8 plus or minus 0.4 degrees, such that the space end was tipped forward toward the direction of travel. The resulting consequences of the yaw and pitch misorientation of LDEF on the atomic oxygen fluence is a factor of 2.16 increase for samples located on row 12, and a factor of 1.18 increase for samples located on the space end compared to that which would be expected for perfect orientation.

  10. Moderate positive spin Hall angle in uranium

    Energy Technology Data Exchange (ETDEWEB)

    Singh, Simranjeet; Anguera, Marta; Barco, Enrique del, E-mail: delbarco@ucf.edu, E-mail: cwmsch@rit.edu [Department of Physics, University of Central Florida, Orlando, Florida 32816 (United States); Springell, Ross [H. H. Will Laboratory, University of Bristol, Bristol BS2 8BS (United Kingdom); Miller, Casey W., E-mail: delbarco@ucf.edu, E-mail: cwmsch@rit.edu [School of Chemistry and Materials Science, Rochester Institute of Technology, Rochester, New York 14623 (United States)

    2015-12-07

    We report measurements of spin pumping and the inverse spin Hall effect in Ni{sub 80}Fe{sub 20}/uranium bilayers designed to study the efficiency of spin-charge interconversion in a super-heavy element. We employ broad-band ferromagnetic resonance on extended films to inject a spin current from the Ni{sub 80}Fe{sub 20} (permalloy) into the uranium layer, which is then converted into an electric field by the inverse spin Hall effect. Surprisingly, our results suggest a spin mixing conductance of order 2 × 10{sup 19} m{sup −2} and a positive spin Hall angle of 0.004, which are both merely comparable with those of several transition metals. These results thus support the idea that the electronic configuration may be at least as important as the atomic number in governing spin pumping across interfaces and subsequent spin Hall effects. In fact, given that both the magnitude and the sign are unexpected based on trends in d-electron systems, materials with unfilled f-electron orbitals may hold additional exploration avenues for spin physics.

  11. Malocclusion Pattern (Angle's) in Mauritian Orthodontic Patients

    Science.gov (United States)

    Durgesh, B. H.; Prakash, Prashanth; Ramakrishnaiah, Ravikumar; Subashchandra Phulari, Basavaraj; Al Kheraif, Abdul Aziz A.

    2012-01-01

    The aim of the study was to assess the pattern of malocclusion in different ethnic group of Mauritian population visiting the Orthodontic Department at Mauras College of Dentistry and Hospital, Republic of Mauritius. The study population comprised of 624 patients who visited the orthodontic department during 2010. The clinical examination was conducted by a well-calibrated orthodontist. The data were recorded in the case sheets and was analyzed for presence of angles class I, class II, and class III malocclusion in both male and female patients of Asian, African, Caucasian, and Chinese ethnicity aged 5–55 years. Malocclusion was found to be high in females compared to males. 414 patients (150 male + 264 female) presented with class I, 182 patients (52 male + 130 female) presented with class II, and 28 patients (12 male + 16 female) presented with class III. Asian ethnic group were more affected and patient seeking orthodontic treatment was high in 11–15 years age group. PMID:22655203

  12. Impact Angle Control of Interplanetary Shock Geoeffectiveness

    CERN Document Server

    Oliveira, D M

    2015-01-01

    We use OpenGGCM global MHD simulations to study the nightside magnetospheric, magnetotail, and ionospheric responses to interplanetary (IP) fa st forward shocks. Three cases are presented in this study: two inclined oblique shocks, here after IOS-1 and IOS-2, where the latter has a Mach number twice stronger than the former. Both shocks have impact angles of 30$^o$ in relation to the Sun-Earth line. Lastly, we choose a frontal perpendicular shock, FPS, whose shock normal is along the Sun-Earth line, with the same Mach number as IOS-1. We find that, in the IOS-1 case, due to the north-south asymmetry, the magnetotail is deflected southward, leading to a mild compression. The geomagnetic activity observed in the nightside ionosphere is then weak. On the other hand, in the head-on case, the FPS compresses the magnetotail from both sides symmetrically. This compression triggers a substorm allowing a larger amount of stored energy in the magnetotail to be released to the nightside ionosphere, resulting in stronger...

  13. Moderate positive spin Hall angle in uranium

    International Nuclear Information System (INIS)

    We report measurements of spin pumping and the inverse spin Hall effect in Ni80Fe20/uranium bilayers designed to study the efficiency of spin-charge interconversion in a super-heavy element. We employ broad-band ferromagnetic resonance on extended films to inject a spin current from the Ni80Fe20 (permalloy) into the uranium layer, which is then converted into an electric field by the inverse spin Hall effect. Surprisingly, our results suggest a spin mixing conductance of order 2 × 1019 m−2 and a positive spin Hall angle of 0.004, which are both merely comparable with those of several transition metals. These results thus support the idea that the electronic configuration may be at least as important as the atomic number in governing spin pumping across interfaces and subsequent spin Hall effects. In fact, given that both the magnitude and the sign are unexpected based on trends in d-electron systems, materials with unfilled f-electron orbitals may hold additional exploration avenues for spin physics

  14. Rubber hand illusion affects joint angle perception.

    Directory of Open Access Journals (Sweden)

    Martin V Butz

    Full Text Available The Rubber Hand Illusion (RHI is a well-established experimental paradigm. It has been shown that the RHI can affect hand location estimates, arm and hand motion towards goals, the subjective visual appearance of the own hand, and the feeling of body ownership. Several studies also indicate that the peri-hand space is partially remapped around the rubber hand. Nonetheless, the question remains if and to what extent the RHI can affect the perception of other body parts. In this study we ask if the RHI can alter the perception of the elbow joint. Participants had to adjust an angular representation on a screen according to their proprioceptive perception of their own elbow joint angle. The results show that the RHI does indeed alter the elbow joint estimation, increasing the agreement with the position and orientation of the artificial hand. Thus, the results show that the brain does not only adjust the perception of the hand in body-relative space, but it also modifies the perception of other body parts. In conclusion, we propose that the brain continuously strives to maintain a consistent internal body image and that this image can be influenced by the available sensory information sources, which are mediated and mapped onto each other by means of a postural, kinematic body model.

  15. To-Do with JavaScript MV* : A study into the differences between Backbone.js and AngularJS

    OpenAIRE

    Runeberg, Joakim

    2013-01-01

    Arbetet undersöker skillnader mellan de två mest populära JavaScript ramverken: An-gularJS och Backbone.js. Målet med undersökningen är att se ifall det ena gränssnittet är att föredra over det andra, och vilka arkitektoniska skillnader det finns emellan de två gränssnitten. Det här sker genom att använda det öppna projektet TodoMVC, med HTML5s localStorage för att lagra information. I samband med undersökningen utveck-lades automatiserade test med hjälp av PhantomJS, ett JavaScript gränssnit...

  16. Mapping of low flip angles in magnetic resonance

    Energy Technology Data Exchange (ETDEWEB)

    Balezeau, Fabien; Saint-Jalmes, Herve [LTSI, INSERM U642, Universite Rennes 1 (France); Eliat, Pierre-Antoine [PRISM, IFR 140, Universite Rennes 1 (France); Cayamo, Alejandro Bordelois, E-mail: fabien.balezeau@gmail.com [Centro De BiofIsika Medica, Universidad de Oriente, Santiago de Cuba (Cuba)

    2011-10-21

    Errors in the flip angle have to be corrected in many magnetic resonance imaging applications, especially for T1 quantification. However, the existing methods of B1 mapping fail to measure lower values of the flip angle despite the fact that these are extensively used in dynamic acquisition and 3D imaging. In this study, the nonlinearity of the radiofrequency (RF) transmit chain, especially for very low flip angles, is investigated and a simple method is proposed to accurately determine both the gain of the RF transmitter and the B1 field map for low flip angles. The method makes use of the spoiled gradient echo sequence with long repetition time (TR), such as applied in the double-angle method. It uses an image acquired with a flip angle of 90{sup 0} as a reference image that is robust to B1 inhomogeneity. The ratio of the image at flip angle alpha to the image at a flip angle of 90{sup 0} enables us to calculate the actual value of alpha. This study was carried out at 1.5 and 4.7 T, showing that the linearity of the RF supply system is highly dependent on the hardware. The method proposed here allows us to measure the flip angle from 1{sup 0} to 60{sup 0} with a maximal uncertainty of 10% and to correct T1 maps based on the variable flip angle method.

  17. Study of the advancing and receding contact angles: liquid sorption as a cause of contact angle hysteresis.

    Science.gov (United States)

    Lam, C N C; Wu, R; Li, D; Hair, M L; Neumann, A W

    2002-02-25

    Two types of experiments were used to study the behavior of both advancing and receding contact angles, namely the dynamic one-cycle contact angle (DOCA) and the dynamic cycling contact angle (DCCA) experiments. For the preliminary study, DOCA measurements of different liquids on different solids were performed using an automated axisymmetric drop shape analysis-profile (ADSA-P). From these experimental results, four patterns of receding contact angle were observed: (1) time-dependent receding contact angle; (2) constant receding contact angle; (3) 'stick/slip'; (4) no receding contact angle. For the purpose of illustration, results from four different solid surfaces are shown. These solids are: FC-732-coated surface; poly(methyl methacrylate/n-butyl methacrylate) [P(MMA/nBMA)]; poly(lactic acid) (DL-PLA); and poly(lactic/glycolic acid) 50/50 (DL-PLGA 50/50). Since most of the surfaces in our studies exhibit time dependence in the receding contact angle, a more extended study was conducted using only FC-732-coated surfaces to better understand the possible causes of decreasing receding contact angle and contact angle hysteresis. Contact angle measurements of 21 liquids from two homologous series (i.e. n-alkanes and 1-alcohols) and octamethylcyclotetrasiloxane (OCMTS) on FC-732-coated surfaces were performed. It is apparent that the contact angle hysteresis decreases with the chain length of the liquid. It was found that the receding contact angle equals the advancing angle when the alkane molecules are infinitely large. These results strongly suggest that the chain length and size of the liquid molecule could contribute to contact angle hysteresis phenomena. Furthermore, DCCA measurements of six liquids from the two homologous series on FC-732-coated surfaces were performed. With these experimental results, one can construe that the time dependence of contact angle hysteresis on relatively smooth and homogeneous surfaces is mainly caused by liquid retention

  18. Numerical aperture characteristics of angle-ended plastic optical fiber

    Science.gov (United States)

    Gao, Cheng; Farrell, Gerard

    2003-03-01

    With the increasing information rates demanded in consumer, automotive and aeronautical applications, a low cost and high performance physical transmission medium is required. Compared with Silica Optical Fiber, Plastic Optical Fiber (POF) offers an economic solution for a range of high-capacity, short-haul applications in industrial and military environments. Recently, a new type of POF, the perfluorinated graded-index plastic optical fiber (PF GI-POF), has been introduced that has low losses and high bandwidth at the communication wavelengths 850 nm and 1300nm. POF is normally terminated perpendicular to the fiber axis. We propose an angle-ended POF, which is terminated at non-perpendicular angles to the fiber axis. The aim of the research is to investigate the numerical aperture (NA) characteristics of angle-ended POF along the major axis of the elliptical endface. A theoretical model indicates that the NA of the angle-ended POF will increase nonlinearly with tilt-angle and the acceptance cone will be deflected with the angle of the deflection increasing nonlinearly with tilt-angle. We present results for the measured NA and the measured deflection angle using the far-field radiation method. Results are presented for 13 angle-ended SI-POF tilt-angles. We also present results for theoretical value of NA and deflection angle as a function of tilt-angle. The agreement between the measured and theoretical value is good up to tilt-angles of about 15 degrees, beyond which deviation occurs.

  19. Optimization of the Redundant Route in Enterprise Backbone Network%企业骨干网链路冗余后路由的优化

    Institute of Scientific and Technical Information of China (English)

    金海峰

    2013-01-01

    In the network age, along with the development of the QQ, micro message, WEB browsing, online shopping, of ice network ,etc., people depend on network more and more, and the requirements of the network performance is also much higher than before. The traditional network,using a single point of access,is prone to a single point of failure. That an equipment or a port fails directly af ects the work of its lower device and host. After discussing the redundancy of enterprise backbone network in detail,this paper optimizes redundant route by using OSPF route, Cost, floating route, policy route, NAPT technology, and thus achieves the data load balancing of enterprise backbone network.%  在当代网络中,伴随着QQ、微信、WEB浏览、网络购物、网络办公等网络业务的不断发展,人们越来越依赖网络,对网络的性能要求也是越来越高,传统企业网络采用单点接入,容易出现单点故障,某台设备或某个端口出现故障,会直接影响其下联设备和主机的工作。文章重点讨论了企业骨干网链路冗余后,运用OSPF路由、接口Cost值、浮动路由、策略路由、NAPT等技术对冗余路由进行优化,实现骨干网链路上数据的负载均衡。

  20. Contact pressure distribution and support angle optimization of kiln tyre

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    According to the shearing force character and the deformation coordination condition of shell at the station of supports, the mathematical models to calculate contact angle and contact pressure distribution between tyre and shell were set up, the formulae of bending moment and bending stress of tyre were obtained. Taking the maximum of tyre fatigue life as the optimal objective, the optimization model of tyre support angle was built. The computational results show that when tyre support angle is 30°, tyre life is far less than that when tyre support angle is optimal, which is 35.6°, and it is unsuitable to stipulate tyre support angle to be 30° in traditional design. The larger the load, the less the nominal stress amplitude increment of tyre, the more favorable the tyre fatigue life when tyre support angle is optimal.