#### Sample records for backbone dihedral angles

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

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

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

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

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

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

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?

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

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

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

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

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

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.

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

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

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

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

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.

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

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

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.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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.

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.

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

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

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

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

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.

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

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

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

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

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

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.

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

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

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

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

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

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

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

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)

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

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

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

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

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

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

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

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

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

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

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

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

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

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.

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

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

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

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

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.

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.

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

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

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

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

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...

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

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

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

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

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

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

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

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

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

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

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

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

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.

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

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

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

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

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

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

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

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

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

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

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

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+ÃŽÂ”opt size, where ÃŽÂ” 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.

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

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

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

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

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

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

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.

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

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

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

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.

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

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

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.

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

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

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

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

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.

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

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

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

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

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 todays 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

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

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

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

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

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

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.

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

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

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.

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

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

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

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

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

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

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"?

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…

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

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

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

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

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

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?

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

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

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.

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.

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

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.

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

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

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

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.

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

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

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

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

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

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

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

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

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

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

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

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

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.

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

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.

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

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

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

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

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

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.

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

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

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

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

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

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

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.

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

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

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

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

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

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

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.

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

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

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

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

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

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

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

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

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.

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.

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.

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

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

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.

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

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

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

Cazon, L

2013-01-01

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

Cazon L.

2013-06-01

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

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

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

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.

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

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.

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

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

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

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

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

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

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

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

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.

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

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

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.

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

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

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

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

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

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

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

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

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

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

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

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.

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

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

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

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 ...